National Center for Biotechnology Information (NCBI)
welcome to the blast network service.
PEPTIDE SEQUENCE DATABASES
nr Non-redundant GenBank CDS translations+PDB+SwissProt+PIR
month All new or revised GenBank CDS translation+PDB+SwissProt+PIR
sequences released in the last 30 days
pdb PDB protein sequences
yeast Yeast (Saccharomyces cerevisiae) protein sequences.
kabat Kabat Sequences of Proteins of Immunological Interest
alu * Translations of Select Alu Repeats from REPBASE
swissprot SwissProt sequences
NUCLEOTIDE SEQUENCE DATABASES
nr Non-redundant GenBank+EMBL+DDBJ+PDB sequences
(but no EST, STS, GSS, or HTGS sequences)
month All new or revised GenBank+EMBL+DDBJ+PDB sequences released in
the last 30 days
yeast Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences.
est + Non-redundant Database of GenBank+EMBL+DDBJ EST Division
sts + Non-redundant Database of GenBank+EMBL+DDBJ STS Division
htgs High Throughput Genomic Sequences
pdb PDB nucleotide sequences
vector Vector subset of GenBank
mito * Database of mitochondrial sequences, Rel. 1.0, July 1995
gss Genome Survey Sequences (includes single-pass genomic data, exon-
trapped sequences, and Alu PCR primers.
kabat Kabat Sequences of Nucleic Acid of Immunological Interest
epd Eukaryotic Promotor Database
alu *+ Select Alu Repeats from REPBASE
BLASTP 2.2.3 [Apr-24-2002]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= orf1 [1-14]
(13 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.403 0.181 0.000
Gapped
Lambda K H
0.267 0.0410 0.000
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,809,448
Number of Sequences: 930587
Number of extensions: 3025
Number of successful extensions: 25
Number of sequences better than 5.0e-02: 0
Number of HSP's better than 0.1 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 25
Number of HSP's gapped (non-prelim): 0
length of query: 13
length of database: 291,933,107
effective HSP length: 0
effective length of query: 24
effective length of database: 291,933,107
effective search space: 7006394568
effective search space used: 7006394568
T: 11
A: 40
X1: 13 ( 7.6 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 33 (21.7 bits)
S2: 85 (37.4 bits)
Query= orf2 [25-183]
(157 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049890.1| (NC_000867) gp a [Alteromonas phage PM2] >... 323 5e-088
>ref|NP_049890.1| (NC_000867) gp a [Alteromonas phage PM2]
gb|AAD43538.1|AF155037_1 (AF155037) gp a [Alteromonas phage PM2]
Length = 157
Score = 323 bits (827), Expect = 5e-088
Identities = 157/157 (100%), Positives = 157/157 (100%)
Query: 1 MTDFKQLLFRAGFMNFGKLDRRAAMEFLFINSERTLERWIAENKPCPRAVAMLKQRINGG 60
MTDFKQLLFRAGFMNFGKLDRRAAMEFLFINSERTLERWIAENKPCPRAVAMLKQRINGG
Sbjct: 1 MTDFKQLLFRAGFMNFGKLDRRAAMEFLFINSERTLERWIAENKPCPRAVAMLKQRINGG 60
Query: 61 MALHKDWGGFYICRGGYLWTPRGKKYDASYINKLDFLQSSVRYNESHVNALQNQIDHLHD 120
MALHKDWGGFYICRGGYLWTPRGKKYDASYINKLDFLQSSVRYNESHVNALQNQIDHLHD
Sbjct: 61 MALHKDWGGFYICRGGYLWTPRGKKYDASYINKLDFLQSSVRYNESHVNALQNQIDHLHD 120
Query: 121 LVAASETLKTIGNDLIKMSDSLALKEIVMKYGDKQRA 157
LVAASETLKTIGNDLIKMSDSLALKEIVMKYGDKQRA
Sbjct: 121 LVAASETLKTIGNDLIKMSDSLALKEIVMKYGDKQRA 157
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.323 0.138 0.000
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 86,159,035
Number of Sequences: 930587
Number of extensions: 3210812
Number of successful extensions: 7451
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 7450
Number of HSP's gapped (non-prelim): 1
length of query: 157
length of database: 291,933,107
effective HSP length: 110
effective length of query: 47
effective length of database: 189,568,537
effective search space: 8909721239
effective search space used: 8909721239
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 86 (37.7 bits)
Query= orf3 [283-376]
(92 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049893.1| (NC_000867) gp c [Alteromonas phage PM2] >... 184 2e-046
>ref|NP_049893.1| (NC_000867) gp c [Alteromonas phage PM2]
gb|AAD43540.1|AF155037_3 (AF155037) gp c [Alteromonas phage PM2]
Length = 92
Score = 184 bits (467), Expect = 2e-046
Identities = 92/92 (100%), Positives = 92/92 (100%)
Query: 1 MKITTSIELLDWFKSVVDIDSDYMVSKLTGIPKQTLSTVRTGNSEFSDYTALKLLLVGEH 60
MKITTSIELLDWFKSVVDIDSDYMVSKLTGIPKQTLSTVRTGNSEFSDYTALKLLLVGEH
Sbjct: 1 MKITTSIELLDWFKSVVDIDSDYMVSKLTGIPKQTLSTVRTGNSEFSDYTALKLLLVGEH 60
Query: 61 PEPLKGMALLEAHKAERNGNEEQAKLWRKSVA 92
PEPLKGMALLEAHKAERNGNEEQAKLWRKSVA
Sbjct: 61 PEPLKGMALLEAHKAERNGNEEQAKLWRKSVA 92
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.313 0.130 0.000
Gapped
Lambda K H
0.267 0.0410 0.000
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 49,340,492
Number of Sequences: 930587
Number of extensions: 1540096
Number of successful extensions: 2696
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2695
Number of HSP's gapped (non-prelim): 1
length of query: 92
length of database: 291,933,107
effective HSP length: 68
effective length of query: 24
effective length of database: 228,653,191
effective search space: 5487676584
effective search space used: 5487676584
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 84 (37.0 bits)
Query= orf4 [453-528]
(74 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049894.1| (NC_000867) gp d [Alteromonas phage PM2] >... 142 6e-034
>ref|NP_049894.1| (NC_000867) gp d [Alteromonas phage PM2]
gb|AAD43541.1|AF155037_4 (AF155037) gp d [Alteromonas phage PM2]
Length = 74
Score = 142 bits (359), Expect = 6e-034
Identities = 74/74 (100%), Positives = 74/74 (100%)
Query: 1 MYIDATQYRNDDEFTQYAKGKVAQLRLMLNSKKSALQKDKELQQQAKAQESALAGEELRR 60
MYIDATQYRNDDEFTQYAKGKVAQLRLMLNSKKSALQKDKELQQQAKAQESALAGEELRR
Sbjct: 1 MYIDATQYRNDDEFTQYAKGKVAQLRLMLNSKKSALQKDKELQQQAKAQESALAGEELRR 60
Query: 61 RALSLATQNRMVTL 74
RALSLATQNRMVTL
Sbjct: 61 RALSLATQNRMVTL 74
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.312 0.124 0.000
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,450,467
Number of Sequences: 930587
Number of extensions: 753978
Number of successful extensions: 3897
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 3896
Number of HSP's gapped (non-prelim): 1
length of query: 74
length of database: 291,933,107
effective HSP length: 50
effective length of query: 24
effective length of database: 245,403,757
effective search space: 5889690168
effective search space used: 5889690168
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 84 (37.0 bits)
Query= orf5 [526-607]
(80 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049895.1| (NC_000867) gp e [Alteromonas phage PM2] >... 167 3e-041
>ref|NP_049895.1| (NC_000867) gp e [Alteromonas phage PM2]
gb|AAD43542.1|AF155037_5 (AF155037) gp e [Alteromonas phage PM2]
Length = 80
Score = 167 bits (422), Expect = 3e-041
Identities = 80/80 (100%), Positives = 80/80 (100%)
Query: 1 MSQRGISKGLLVCHSVRLAKVWVDQIEISIPLGVEPEPKQIEGISDLIDSLHSYDCSVCS 60
MSQRGISKGLLVCHSVRLAKVWVDQIEISIPLGVEPEPKQIEGISDLIDSLHSYDCSVCS
Sbjct: 1 MSQRGISKGLLVCHSVRLAKVWVDQIEISIPLGVEPEPKQIEGISDLIDSLHSYDCSVCS 60
Query: 61 VVAHKLDDAMCRWCELLLDA 80
VVAHKLDDAMCRWCELLLDA
Sbjct: 61 VVAHKLDDAMCRWCELLLDA 80
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.323 0.138 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 47,522,313
Number of Sequences: 930587
Number of extensions: 1642023
Number of successful extensions: 3142
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 3141
Number of HSP's gapped (non-prelim): 1
length of query: 80
length of database: 291,933,107
effective HSP length: 56
effective length of query: 24
effective length of database: 239,820,235
effective search space: 5755685640
effective search space used: 5755685640
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 84 (37.0 bits)
Query= orf6 [605-1240]
(634 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049896.1| (NC_000867) putative replication initiatio... 1204 0.0
ref|NP_052289.1| (NC_001317) A protein [Enterobacteria phag... 300 4e-080
pir||S10632 replication initiation gene A protein [similari... 300 4e-080
ref|NP_536816.1| (NC_003315) rep [Haemophilus phage HP2] >g... 285 1e-075
ref|NP_043478.1| (NC_001697) Rep [Haemophilus phage HP1] >g... 285 1e-075
ref|NP_046795.1| (NC_001895) gpA [Enterobacteria phage P2] ... 258 2e-067
ref|NP_310660.1| (NC_002695) putative phage replication pro... 242 1e-062
ref|NP_536641.1| (NC_003313) rep [Bacteriophage K139] >gi|1... 227 3e-058
gb|AAB66811.1| (AF008938) putative replication protein [Vib... 226 8e-058
ref|NP_457859.1| (NC_003198) possible endonuclease [Salmone... 215 1e-054
ref|NP_461656.1| (NC_003197) Fels-2 prophage: similar to re... 214 2e-054
>ref|NP_049896.1| (NC_000867) putative replication initiation protein P12
[Alteromonas phage PM2]
gb|AAD43543.1|AF155037_6 (AF155037) putative replication initiation protein P12 [Alteromonas
phage PM2]
Length = 634
Score = 1204 bits (3114), Expect = 0.0
Identities = 606/634 (95%), Positives = 606/634 (95%)
Query: 1 MRSIAIGHEPIKGGLKPIELIRPVPFCSPAFGFDKAAEYAKEQLKKIPTTYLRRHAAKLY 60
MRSIAIGHEPIKGGLKPIELIRPVPFCSPAFGFDKAAEYAKEQLKKIPTTYLRRHAAKLY
Sbjct: 1 MRSIAIGHEPIKGGLKPIELIRPVPFCSPAFGFDKAAEYAKEQLKKIPTTYLRRHAAKLY 60
Query: 61 AARFNSTTAKNPEKSANIFMRELVKRVDQIVTRSPLNITEXXXXXXXXXXXXXXXXICQQ 120
AARFNSTTAKNPEKSANIFMRELVKRVDQIVTRSPLNITE ICQQ
Sbjct: 61 AARFNSTTAKNPEKSANIFMRELVKRVDQIVTRSPLNITELQRDKRRKDKAKQLALICQQ 120
Query: 121 MGIVDFDKSMTLEQATALVISKYQKLAEFTINQIDTAPAYSTYEAFMKKGGNPEILADKL 180
MGIVDFDKSMTLEQATALVISKYQKLAEFTINQIDTAPAYSTYEAFMKKGGNPEILADKL
Sbjct: 121 MGIVDFDKSMTLEQATALVISKYQKLAEFTINQIDTAPAYSTYEAFMKKGGNPEILADKL 180
Query: 181 EIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKSQQK 240
EIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKSQQK
Sbjct: 181 EIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKSQQK 240
Query: 241 WLDSMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFYTIT 300
WLDSMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFYTIT
Sbjct: 241 WLDSMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFYTIT 300
Query: 301 APSKYHANSKKYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATPHWHM 360
APSKYHANSKKYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATPHWHM
Sbjct: 301 APSKYHANSKKYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATPHWHM 360
Query: 361 LLFMLPEHEQVTTKALRGYAMQIDGDEKGAEQARFTAENIDPSKGSAVGYIAKYISKNIN 420
LLFMLPEHEQVTTKALRGYAMQIDGDEKGAEQARFTAENIDPSKGSAVGYIAKYISKNIN
Sbjct: 361 LLFMLPEHEQVTTKALRGYAMQIDGDEKGAEQARFTAENIDPSKGSAVGYIAKYISKNIN 420
Query: 421 ANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQFQFVGGASVGVWREIRRAKPEML 480
ANHIEGEKD LVLNVGAWASRWRIRQFQFVGGASVGVWREIRRAKPEML
Sbjct: 421 ANHIEGEKDNETGGEFNNENGLVLNVGAWASRWRIRQFQFVGGASVGVWREIRRAKPEML 480
Query: 481 DKSTDVLREIFSAADNSQFAQFINLMGGAFAKRSERPIQISRVADGLNEYGEEKKRVVGL 540
DKSTDVLREIFSAADNSQFAQFINLMGGAFAKRSERPIQISRVADGLNEYGEEKKRVVGL
Sbjct: 481 DKSTDVLREIFSAADNSQFAQFINLMGGAFAKRSERPIQISRVADGLNEYGEEKKRVVGL 540
Query: 541 ESCSNVLKTRLMRFALKKRSDSDAPWSTENNCNHPANDWQIGAGDRLNPIAFIPKEIRNN 600
ESCSNVLKTRLMRFALKKRSDSDAPWSTENNCNHPANDWQIGAGDRLNPIAFIPKEIRNN
Sbjct: 541 ESCSNVLKTRLMRFALKKRSDSDAPWSTENNCNHPANDWQIGAGDRLNPIAFIPKEIRNN 600
Query: 601 VLRGATYYEVDEQLKTITEFKVKNNQLTQESIGL 634
VLRGATYYEVDEQLKTITEFKVKNNQLTQESIGL
Sbjct: 601 VLRGATYYEVDEQLKTITEFKVKNNQLTQESIGL 634
>ref|NP_052289.1| (NC_001317) A protein [Enterobacteria phage 186]
sp|P41064|VPA_BP186 REPLICATION GENE A PROTEIN (GPA)
gb|AAC34186.1| (U32222) A protein [Enterobacteria phage 186]
Length = 694
Score = 300 bits (767), Expect = 4e-080
Identities = 168/426 (39%), Positives = 241/426 (56%), Gaps = 29/426 (6%)
Query: 178 DKLEIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKS 237
D++ A+ RM + WW+ +L R EHL I +G V+KK+ YAS V +++ K+
Sbjct: 202 DEIAPAVMRMFNEVWWRGRLRRIAAAWREHLQIAVGNVSKKRHAYASKNCVTDWREQKRR 261
Query: 238 QQKWLDSMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFY 297
+++L + LE ++G + L E + GSV+NP IRR ELM RIRG+E E G FY
Sbjct: 262 TREFLKGLDLEDEEGNR-ISLIEKYDGSVANPAIRRCELMARIRGFENICNELGYVGEFY 320
Query: 298 TITAPSKYHANSK------KYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPH 351
T+TAPSKYHA +K K+N A+P +TQ++L WA+ RA+L++ ++ +FG+RV EPH
Sbjct: 321 TLTAPSKYHATTKAGYRNSKWNGASPSDTQSYLTGLWARIRAKLHREEIRIFGIRVAEPH 380
Query: 352 HDATPHWHMLLFMLPEHEQVTTKALRGYAMQIDGDE---KGAEQARFTAENIDPSKGSAV 408
HD TPHWHML+FMLPE + +R YA + D E A++ARF AE IDP KGSA
Sbjct: 381 HDGTPHWHMLMFMLPEDVERVRLIIRDYAWEEDHYELRSDKAKKARFHAEAIDPEKGSAT 440
Query: 409 GYIAKYISKNINANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQFQFVGGASVGV 468
GY+AKYISKNI+ ++GE D V AWA+RW IRQFQF+GGA V V
Sbjct: 441 GYVAKYISKNIDGYALDGETDDESGELLKETAPA---VSAWAARWHIRQFQFIGGAPVTV 497
Query: 469 WREIRR-AKPEMLDKSTDVLREIFSAADNSQFAQFINLMGGAFAKRSERPIQ-ISRVADG 526
+RE+RR A PE + + AA ++A ++N GG F +R + ++ +
Sbjct: 498 YRELRRMADPETARALSVEFAAVHDAAHYGRWADYVNAQGGPFVRRDDLQVRTLYEPRTE 557
Query: 527 LNEYGEEKKRVVGLESCS--------------NVLKTRLMRFALKKRSDSDAPWSTENNC 572
N+YGEE + G+ S ++ R + A+ + S S+ NNC
Sbjct: 558 FNQYGEETVCIKGVYDASIGAGSPILTRLTQWKIVPKRAVDLAVDVKGASAPSRSSVNNC 617
Query: 573 NHPAND 578
+D
Sbjct: 618 TGSESD 623
>pir||S10632 replication initiation gene A protein [similarity] - phage 186
Length = 694
Score = 300 bits (767), Expect = 4e-080
Identities = 168/426 (39%), Positives = 241/426 (56%), Gaps = 29/426 (6%)
Query: 178 DKLEIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKS 237
D++ A+ RM + WW+ +L R EHL I +G V+KK+ YAS V +++ K+
Sbjct: 202 DEIAPAVMRMFNEVWWRGRLRRIAAAWREHLQIAVGNVSKKRHAYASKNCVTDWREQKRR 261
Query: 238 QQKWLDSMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFY 297
+++L + LE ++G + L E + GSV+NP IRR ELM RIRG+E E G FY
Sbjct: 262 TREFLKGLDLEDEEGNR-ISLIEKYDGSVANPAIRRCELMARIRGFENICNELGYVGEFY 320
Query: 298 TITAPSKYHANSK------KYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPH 351
T+TAPSKYHA +K K+N A+P +TQ++L WA+ RA+L++ ++ +FG+RV EPH
Sbjct: 321 TLTAPSKYHATTKAGYRNSKWNGASPSDTQSYLTGLWARIRAKLHREEIRIFGIRVAEPH 380
Query: 352 HDATPHWHMLLFMLPEHEQVTTKALRGYAMQIDGDE---KGAEQARFTAENIDPSKGSAV 408
HD TPHWHML+FMLPE + +R YA + D E A++ARF AE IDP KGSA
Sbjct: 381 HDGTPHWHMLMFMLPEDVERVRLIIRDYAWEEDHYELRSDKAKKARFHAEAIDPEKGSAT 440
Query: 409 GYIAKYISKNINANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQFQFVGGASVGV 468
GY+AKYISKNI+ ++GE D V AWA+RW IRQFQF+GGA V V
Sbjct: 441 GYVAKYISKNIDGYALDGETDDESGELLKETAPA---VSAWAARWHIRQFQFIGGAPVTV 497
Query: 469 WREIRR-AKPEMLDKSTDVLREIFSAADNSQFAQFINLMGGAFAKRSERPIQ-ISRVADG 526
+RE+RR A PE + + AA ++A ++N GG F +R + ++ +
Sbjct: 498 YRELRRMADPETARALSVEFAAVHDAAHYGRWADYVNAQGGPFVRRDDLQVRTLYEPRTE 557
Query: 527 LNEYGEEKKRVVGLESCS--------------NVLKTRLMRFALKKRSDSDAPWSTENNC 572
N+YGEE + G+ S ++ R + A+ + S S+ NNC
Sbjct: 558 FNQYGEETVCIKGVYDASIGAGSPILTRLTQWKIVPKRAVDLAVDVKGASAPSRSSVNNC 617
Query: 573 NHPAND 578
+D
Sbjct: 618 TGSESD 623
>ref|NP_536816.1| (NC_003315) rep [Haemophilus phage HP2]
gb|AAK37793.1| (AY027935) rep [Haemophilus influenzae phage HP2] [Haemophilus
phage HP2]
Length = 775
Score = 285 bits (728), Expect = 1e-075
Identities = 155/425 (36%), Positives = 248/425 (57%), Gaps = 30/425 (7%)
Query: 175 ILADKLEIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYA 234
I A+ ++ + R+TC+KWW +++ + +EH+ I G V + Y S Q+ E++
Sbjct: 274 IKAEHIDSTLIRLTCEKWWFKQMRDIQKRMVEHIAIACGEVRANAASYISNQSFQEWQLQ 333
Query: 235 KKSQQKWLDSMQLES-DDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMK 293
++ +L +M +E+ D+ E ++L ++F S SNP +RR E+MVR+RG EE+A+E +
Sbjct: 334 QRKNHDYLRAMIIENIDNPEEQVELFDMFLKSSSNPALRRNEMMVRLRGLEEWAEENNNE 393
Query: 294 AVFYTITAPSKYHANS--KKYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPH 351
A+F T+TAPS +HA + KK+ P+ETQ +L W + RA L+K ++ +G+RV EPH
Sbjct: 394 ALFLTLTAPSSFHAGNGNKKWLGVNPRETQNYLNKVWQQFRALLSKRNIKFYGMRVAEPH 453
Query: 352 HDATPHWHMLLFMLPEHEQVTTKALRGYAMQIDGDEKGAEQARFTAENIDPSKGSAVGYI 411
D TPHWH L ++ EH++ + + A+++DG+EKGA + R E D +KGSA YI
Sbjct: 454 KDGTPHWHALAYVPAEHKEEVIRLFKQKALELDGNEKGAAEHRCKVEKCDKTKGSATAYI 513
Query: 412 AKYISKNINANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQFQFVGGASVGVWRE 471
AKYI+KNI+ + GE L V AWASRW IRQFQF GGAS+ VWRE
Sbjct: 514 AKYIAKNIDGFALAGEVSDEDPTLSLHDN--ALRVRAWASRWGIRQFQFYGGASICVWRE 571
Query: 472 IRRAKPEMLDKSTDVLREIFSAAD-NSQFAQFINLMGGAFAKRSERPIQISRVADGLNEY 530
+RR D +++ + +AA + +A ++ + GGA AKR+++PI++ N+Y
Sbjct: 572 LRRLISGQAD--DEIINKAQAAAGIANDYAAYMEIQGGALAKRADQPIKLDYETKPANKY 629
Query: 531 GEEKKRVVGLESCSNVLK--TRLMRFALKKR--------------------SDSDAPWST 568
GE++K ++GL + ++ + +R ++ +KKR S APW+
Sbjct: 630 GEQRKAIIGLANRFSLKQVISRTKKWQIKKRPQDFAQRTESMVERSSTANNSARSAPWTC 689
Query: 569 ENNCN 573
+NCN
Sbjct: 690 VSNCN 694
>ref|NP_043478.1| (NC_001697) Rep [Haemophilus phage HP1]
sp|P51711|REP_BPHP1 REPLICATION PROTEIN
pir||S69515 replication initiation gene A protein [similarity] - phage HP1
gb|AAB09194.1| (U24159) Rep [Haemophilus phage HP1]
Length = 775
Score = 285 bits (728), Expect = 1e-075
Identities = 155/425 (36%), Positives = 248/425 (57%), Gaps = 30/425 (7%)
Query: 175 ILADKLEIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYA 234
I A+ ++ + R+TC+KWW +++ + +EH+ I G V + Y S Q+ E++
Sbjct: 274 IKAEHIDSTLIRLTCEKWWFKQMRDIQKRMVEHIAIACGEVRANAASYISNQSFQEWQLQ 333
Query: 235 KKSQQKWLDSMQLES-DDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMK 293
++ +L +M +E+ D+ E ++L ++F S SNP +RR E+MVR+RG EE+A+E +
Sbjct: 334 QRKNHDYLRAMIIENIDNPEEQVELFDMFLKSSSNPALRRNEMMVRLRGLEEWAEENNNE 393
Query: 294 AVFYTITAPSKYHANS--KKYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPH 351
A+F T+TAPS +HA + KK+ P+ETQ +L W + RA L+K ++ +G+RV EPH
Sbjct: 394 ALFLTLTAPSSFHAGNGNKKWLGVNPRETQNYLNKVWQQFRALLSKRNIKFYGMRVAEPH 453
Query: 352 HDATPHWHMLLFMLPEHEQVTTKALRGYAMQIDGDEKGAEQARFTAENIDPSKGSAVGYI 411
D TPHWH L ++ EH++ + + A+++DG+EKGA + R E D +KGSA YI
Sbjct: 454 KDGTPHWHALAYVPAEHKEEVIRLFKQKALELDGNEKGAAEHRCKVEKCDKTKGSATAYI 513
Query: 412 AKYISKNINANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQFQFVGGASVGVWRE 471
AKYI+KNI+ + GE L V AWASRW IRQFQF GGAS+ VWRE
Sbjct: 514 AKYIAKNIDGFALAGEVSDEDPTLSLHDN--ALRVRAWASRWGIRQFQFYGGASICVWRE 571
Query: 472 IRRAKPEMLDKSTDVLREIFSAAD-NSQFAQFINLMGGAFAKRSERPIQISRVADGLNEY 530
+RR D +++ + +AA + +A ++ + GGA AKR+++PI++ N+Y
Sbjct: 572 LRRLISGQAD--DEIINKAQAAAGIANDYAAYMEIQGGALAKRADQPIKLDYETKPANKY 629
Query: 531 GEEKKRVVGLESCSNVLK--TRLMRFALKKR--------------------SDSDAPWST 568
GE++K ++GL + ++ + +R ++ +KKR S APW+
Sbjct: 630 GEQRKAIIGLANRFSLKQVISRTKKWQIKKRPQDFAQRTESMVERSSTANNSARSAPWTC 689
Query: 569 ENNCN 573
+NCN
Sbjct: 690 VSNCN 694
>ref|NP_046795.1| (NC_001895) gpA [Enterobacteria phage P2]
sp|Q06419|VPA_BPP2 REPLICATION GENE A PROTEIN (GPA)
gb|AAD03306.1| (AF063097) gpA [Enterobacteria phage P2]
Length = 761
Score = 258 bits (658), Expect = 2e-067
Identities = 151/405 (37%), Positives = 226/405 (55%), Gaps = 29/405 (7%)
Query: 157 APAYSTYEAFMKKGGNPEILADKLEIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVN 216
A A++ + KK ++ + AI R+ D+WW +L R E L I +G VN
Sbjct: 184 ARAFNISPLYWKKYRKGQMTTRQAYSAIARLFNDEWWTHQLKGQRMRWHETLLIAVGEVN 243
Query: 217 KKKSPYASLQAVNEFKYAKKSQQKWLDSMQLESDDGETTLDLAEVFKGSVSNPEIRRVEL 276
K +SPYAS A+ + + +++ ++L S LE+ + +DL GS+SNPEIRR+EL
Sbjct: 244 KDRSPYASKHAIRDVRARRQANLEFLKSCDLENRETGERIDLISKVMGSISNPEIRRMEL 303
Query: 277 MVRIRGYEEYAQEQGMKAVFYTITAPSKYHA------------------NSKKYNNATPK 318
M I G E YA +G +F T+TAPSKYH N + +N PK
Sbjct: 304 MNTIAGIERYAAAEGDVGMFITLTAPSKYHPTRQVGKGESKTVQLNHGWNDEAFN---PK 360
Query: 319 ETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATPHWHMLLFMLPEHEQVTTKALRG 378
+ Q +L + W+ R D+ V+G+RVVEPHHD TPHWHM+LF P + +R
Sbjct: 361 DAQRYLCHIWSLMRTAFKDNDLQVYGLRVVEPHHDGTPHWHMMLFCNPRQRNQIIEIMRR 420
Query: 379 YAMQIDGDEKGAEQARFTAENIDPSKGSAVGYIAKYISKNINANHIEGEKDXXXXXXXXX 438
YA++ DGDE+GA + RF A+++ ++G A GYIAKYISKNI+ ++G+ D
Sbjct: 421 YALKEDGDERGAARNRFQAKHL--NQGGAAGYIAKYISKNIDGYALDGQLDNDTGRPLKD 478
Query: 439 XXXLVLNVGAWASRWRIRQFQFVGGASVGVWREIRRAK--PEMLDKSTDVLREIFSAADN 496
V AWAS WRI QF+ VG ++G +RE+R+ + D+ + + +AAD+
Sbjct: 479 TAAAVT---AWASTWRIPQFKTVGLPTMGAYRELRKLPRGVSIADEFDERVEAARAAADS 535
Query: 497 SQFAQFINLMGGAFAKRSERPIQISR-VADGLNEYGEEKKRVVGL 540
FA +I+ GGA R + ++++R +D +NEY EE +RVVG+
Sbjct: 536 GDFALYISAQGGANVPRDCQTVRVARSPSDEVNEYEEEVERVVGI 580
>ref|NP_310660.1| (NC_002695) putative phage replication protein [Escherichia coli
O157:H7]
dbj|BAB36056.1| (AP002559) putative phage replication protein [Escherichia coli
O157:H7]
Length = 894
Score = 242 bits (617), Expect = 1e-062
Identities = 163/497 (32%), Positives = 242/497 (47%), Gaps = 50/497 (10%)
Query: 117 ICQQMGIVDFDKSMTLEQATALVISKYQKLAEFTINQIDTAPAYSTYEAFMKKGGNPEIL 176
+C G D + +M + + YQ LA ++ P Y + P+
Sbjct: 153 LCDGFGATDGELTMDV------TLKAYQMLARMALHLHAMPPHYDALTTDKDRRNEPD-- 204
Query: 177 ADKLEIAIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKK 236
+ L AI R+TC +WW+RKL R E LV++K SPY S A++EF+ ++
Sbjct: 205 TELLPGAILRLTCAEWWKRKLWLLRCEWREEQLRAACLVSRKTSPYLSQDALSEFRAQRE 264
Query: 237 SQQKWLDSMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVF 296
+ +L S LE++DG T+DL V+ VSNP R+ E+M ++G E A+ +G KAVF
Sbjct: 265 KTRDFLKSFMLENEDG-FTIDLETVYYAGVSNPVHRKAEMMATMKGLELLAEARGDKAVF 323
Query: 297 YTITAPSKYHANSK------KYNNATPKETQAFLVNQ-WAKARAELNKIDVPVFGVRVVE 349
T+T PSKYHA ++ K+N AT +++ +LVN +A R +LN+ + +G+R VE
Sbjct: 324 LTVTCPSKYHATTENGHPNPKWNGATMRDSSDYLVNTFFAAVRKKLNRDGLRWYGIRTVE 383
Query: 350 PHHDATPHWHMLLFMLPEHEQVTTKALRGYAMQIDGDEKGAE-QARFTAENIDPSKGSAV 408
PHHD T HWHM++F PE R A+Q D E G + RF AE +D SKG+
Sbjct: 384 PHHDGTVHWHMMVFAHPEEIDTIVSHTRDIAIQEDRHELGDDITPRFKAEYVDGSKGTPT 443
Query: 409 GYIAKYISKNINANHIEG-----EKDXXXXXXXXXXXXLVLNVGAWASRWRIRQFQFVGG 463
YIA YI KN+++ ++G K V WA R+RQFQF G
Sbjct: 444 SYIATYIGKNLDSRAVDGIDPKTGKPRVDHETGKSMTESVERAIGWARLHRVRQFQFFGI 503
Query: 464 ASVGVWREIRRAKPEMLDK-------STDVLREIFSAADNSQFAQFINLMGGAFAKRSER 516
S VWRE+RR +M D + + +AAD F +I GG R +
Sbjct: 504 PSRQVWRELRRLASQMARNPEGPQRLKDDAMDAVLAAADAGCFTTYIEKQGGVLVPRKDY 563
Query: 517 PIQIS-RVADGLNEYGEEKKRVVGLES---------CSNVLKTRLMR-----------FA 555
I+ + +AD LN+YGE+ ++ G+ S C++ +L+R
Sbjct: 564 LIRTAYDLADELNDYGEQSVQIYGIWSPLIGESSRVCTHPDNWKLVRRKPGVEDSARENG 623
Query: 556 LKKRSDSDAPWSTENNC 572
+ APW+ NNC
Sbjct: 624 FDLQGGPAAPWTRGNNC 640
>ref|NP_536641.1| (NC_003313) rep [Bacteriophage K139]
gb|AAL47508.1|AF125163_14 (AF125163) rep [Bacteriophage K139]
Length = 800
Score = 227 bits (578), Expect = 3e-058
Identities = 157/493 (31%), Positives = 227/493 (45%), Gaps = 106/493 (21%)
Query: 184 IRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKSQQKWLD 243
I RM D WW +L + R + EHL I +G V+ SPYAS V E + ++ + +
Sbjct: 193 IMRMISDSWWLGRLVKVRKIMREHLAIAMGQVSNNASPYASWDCVREHQEQQQRNYEAIK 252
Query: 244 SMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFYTITAPS 303
+M L ++ E DL ++ K SVSNP IRR ELMVR RG E+ E G++ +F T+T PS
Sbjct: 253 NMVLFDEETEEEHDLWDMVKKSVSNPAIRRHELMVRCRGCEDIGNELGLQGLFLTLTTPS 312
Query: 304 KYHANSKK------YNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATPH 357
KYH + KK +N A+P++ QA+L +W RA+LN+ ++ FGVRV EPHHD TPH
Sbjct: 313 KYHNSYKKGGFIDHWNGASPRDAQAYLNKKWQLIRAKLNRDEIRWFGVRVAEPHHDGTPH 372
Query: 358 WHMLLFMLPEHEQVTTKALRGYAMQIDGDEKGAE--------------------QARFTA 397
WH+L+++ E YA + D E E + R
Sbjct: 373 WHLLIWVRKEDISAVRDTFITYATEEDRGELHPEFEKEKQKPFRKGVYVGPLDYRPRCDF 432
Query: 398 ENIDPSKGSAVGYIAKYISKNINANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQ 457
IDP+KG+A GYIAKYISKNI+ ++G+ + NV AW SRW IRQ
Sbjct: 433 GYIDPTKGTATGYIAKYISKNIDGYAMDGD---ISDETGKPVKDMARNVSAWKSRWSIRQ 489
Query: 458 FQFVGGASVGVWREIRRA-----------------------------------KPEMLDK 482
FQF GGA V +RE+RR KP +
Sbjct: 490 FQFFGGAPVTTYRELRRLANQNKKAFMEYIFMQERADLISMYELLHYQLIGAFKPARVMT 549
Query: 483 STDVLREI------------------FSAADNSQFAQFINLMGGAFAKRSERPIQISRVA 524
+ +++ I +AD ++ +I GG F KR E + ++ V
Sbjct: 550 NQELVEVIAQSYEARAKTEIPHVAAVLRSADEGRWHGYIMNQGGPFVKRKE--LLVTNVY 607
Query: 525 DGL---NEYGEEKKRVVGLESCSNVLKTRLMRFALKKR-------------------SDS 562
L + Y E +++ G+ + V+KTR + +K++ S
Sbjct: 608 QELPFASPYAEAIRKLEGIATPEQVIKTREKVWTIKRKGKETTEGEAVGFGSEATAFGGS 667
Query: 563 DAPWSTENNCNHP 575
A S+ NNC P
Sbjct: 668 AASRSSVNNCTDP 680
>gb|AAB66811.1| (AF008938) putative replication protein [Vibrio cholerae V86 phage]
Length = 532
Score = 226 bits (575), Expect = 8e-058
Identities = 128/317 (40%), Positives = 174/317 (54%), Gaps = 29/317 (9%)
Query: 184 IRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKSQQKWLD 243
I RM D WW +L + R + EHL I +G V+ SPYAS V E + ++ + +
Sbjct: 153 IMRMISDSWWLGRLVKVRKIMREHLAIAMGQVSNNASPYASWDCVREHQEQQQRNYEAIK 212
Query: 244 SMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFYTITAPS 303
+M L ++ E DL ++ K SVSNP IRR ELMVR RG E+ E G++ +F T+T PS
Sbjct: 213 NMVLFDEETEEEHDLWDMVKKSVSNPAIRRHELMVRCRGCEDIGNELGLQGLFLTLTTPS 272
Query: 304 KYHANSKK------YNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATPH 357
KYH + KK +N A+P++ QA+L +W RA+LN+ ++ FGVRV EPHHD TPH
Sbjct: 273 KYHNSYKKGGFIDHWNGASPRDAQAYLNKKWQLIRAKLNRDEIRWFGVRVAEPHHDGTPH 332
Query: 358 WHMLLFMLPEHEQVTTKALRGYAMQIDGDEKGAE--------------------QARFTA 397
WH+L+++ E YA + D E E + R
Sbjct: 333 WHLLIWVRKEDISAVRDTFITYATEEDRGELHPEFEKEKQKPFRKGVYVGPLDYRPRCDF 392
Query: 398 ENIDPSKGSAVGYIAKYISKNINANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQ 457
IDP+KG+A GYIAKYISKNI+ ++G+ + NV AW SRW IRQ
Sbjct: 393 GYIDPTKGTATGYIAKYISKNIDGYAMDGD---ISDETGKPVKDMARNVSAWKSRWSIRQ 449
Query: 458 FQFVGGASVGVWREIRR 474
FQF GGA V +RE+RR
Sbjct: 450 FQFFGGAPVTTYRELRR 466
>ref|NP_457859.1| (NC_003198) possible endonuclease [Salmonella enterica subsp.
enterica serovar Typhi]
emb|CAD09429.1| (AL627279) possible endonuclease [Salmonella enterica subsp.
enterica serovar Typhi]
Length = 804
Score = 215 bits (548), Expect = 1e-054
Identities = 150/464 (32%), Positives = 232/464 (49%), Gaps = 43/464 (9%)
Query: 143 YQKLAEFTINQIDTAPAYSTYEAFMKKGGNPEILADKLEIAIRRMTCDKWWQRKLNRARD 202
++K+A T+ PA+ K+ + + + ++ RM C WW RKL + R
Sbjct: 227 WEKVAAETLRLDVIPPAFEQLRR--KRNRRKPVPYELIPGSLARMLCADWWYRKLWKMRC 284
Query: 203 MTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKSQQKWLDSMQLESDDGETTLDLAEVF 262
E + LV+KK SPY S +A+ + ++ ++ S +L ++DG+T LD+ +V
Sbjct: 285 EWREEQLRAVCLVSKKASPYVSYEAMMHKREQRRKSLEFFRSHELVNEDGDT-LDMEDVV 343
Query: 263 KGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFYTITAPSKYHAN------SKKYNNAT 316
S SNP RR E+M ++G E A+ +G AVFYTIT PS++H+ + + N T
Sbjct: 344 NASSSNPAHRRNEMMACVKGLELIAEMRGDCAVFYTITCPSRFHSTLNNGRPNPTWTNTT 403
Query: 317 PKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATPHWHMLLFMLPEHEQVTTKAL 376
+++ +LV +A R ++K + +GVRV EPHHD T HWH+L FM + + T L
Sbjct: 404 VRQSSDYLVGMFAAFRKAMHKAGLRWYGVRVAEPHHDGTVHWHLLCFMRKKDRRTITALL 463
Query: 377 RGYAMQIDGDEKGAEQA-RFTAENIDPSKGSAVGYIAKYISKNINANHIEGEKDXXXXXX 435
R +A++ D +E G RF +E I+P KG+ YIAKYISKNI+ + GE
Sbjct: 464 RKFAIREDREELGNNTGPRFKSELINPRKGTPTSYIAKYISKNIDGRGLAGEISKETGKS 523
Query: 436 XXXXXXLVLNVGAWASRWRIRQFQFVGGASVGVWREIR----RAKPEMLDKSTDV----- 486
V AWAS R++QF+F G +RE+R +A + DK
Sbjct: 524 LRDNAEY---VNAWASLHRVQQFRFFGIPGRQAYRELRLLAGQAARQQGDKKAGAPVLDN 580
Query: 487 --LREIFSAADNSQFAQFINLMGGAFAKRSERPIQISRVADGLNE----YGEEKKRVVGL 540
L I +AAD FA +I GG R + R A +NE YG+ R+ G+
Sbjct: 581 PRLDAILAAADAGCFATYIMKQGGVLVPRK---YHLIRTAYEINEEPTAYGDHGIRIYGI 637
Query: 541 ES-------CSNVLKTRLMRFALKKR-----SDSDAPWSTENNC 572
S C++ +K +++R A+ + + APW+ NNC
Sbjct: 638 WSPIAEGKICTHAVKWKMVRKAVDVQEAAADQGACAPWTRGNNC 681
>ref|NP_461656.1| (NC_003197) Fels-2 prophage: similar to retron in E coli
[Salmonella typhimurium LT2]
gb|AAL21615.1| (AE008824) Fels-2 prophage: similar to retron in E coli [Salmonella
typhimurium LT2]
Length = 809
Score = 214 bits (545), Expect = 2e-054
Identities = 149/456 (32%), Positives = 228/456 (49%), Gaps = 45/456 (9%)
Query: 183 AIRRMTCDKWWQRKLNRARDMTLEHLNITLGLVNKKKSPYASLQAVNEFKYAKKSQQKWL 242
++ RM C WW RKL + R E + LVNKK SPY S +AV + ++ ++
Sbjct: 270 SLARMLCADWWCRKLWQMRCEWREEQLRAVCLVNKKASPYVSYEAVIHKREQRRKSLEFF 329
Query: 243 DSMQLESDDGETTLDLAEVFKGSVSNPEIRRVELMVRIRGYEEYAQEQGMKAVFYTITAP 302
S +L ++DG+T LD+ +V S SNP RR E+M ++G E A+ +G AVFYTIT P
Sbjct: 330 RSHELINEDGDT-LDMEDVVNASNSNPAHRRNEMMACVKGLELIAEMRGDCAVFYTITCP 388
Query: 303 SKYHAN------SKKYNNATPKETQAFLVNQWAKARAELNKIDVPVFGVRVVEPHHDATP 356
S++HA + K+ +AT +++ +LV+ +A R ++K + +GVRV EPHHD T
Sbjct: 389 SRFHATLNNGRPNPKWTSATVRQSSDYLVDTFAAFRKAMHKTGLRWYGVRVAEPHHDGTV 448
Query: 357 HWHMLLFMLPEHEQVTTKALRGYAMQIDGDEKGAEQA-RFTAENIDPSKGSAVGYIAKYI 415
HWH+L FM + + T LR +A++ D +E G RF +E I+P KG+ YIAKYI
Sbjct: 449 HWHLLCFMRKKDRRSITALLRKFAIREDREELGTNTGPRFKSELINPRKGTPTSYIAKYI 508
Query: 416 SKNINANHIEGEKDXXXXXXXXXXXXLVLNVGAWASRWRIRQFQFVGGASVGVWREI--- 472
SKNI+ + E +V AWAS R++QF+F G +RE+
Sbjct: 509 SKNIDGRGLAKEISKETGRPLRDSAE---HVSAWASLHRVQQFRFFGIPGRQAYRELRLL 565
Query: 473 ----------RRAKPEMLDKSTDVLREIFSAADNSQFAQFINLMGGAFAKRSERPIQIS- 521
R+A +LD L + +AAD FA +I GG R ++ +
Sbjct: 566 AGQAARVQGERKAGAPVLDNPR--LDAVLAAADAGCFATYIMKQGGVLVPRKHHLVRTAY 623
Query: 522 RVADGLNEYGEEKKRVVGLES-------CSNVLKTRLMRFALKKR-----SDSDAPWSTE 569
+ D + YG+ R+ G+ S C++ +K + +R A+ + + APW+
Sbjct: 624 ELNDEPSAYGDHGIRIYGIWSPIAEGKICTHAMKWKKVRKAVDVQEAAADQGACAPWTRG 683
Query: 570 NNC------NHPANDWQIGAGDRLNPIAFIPKEIRN 599
NNC N D G R + KE+ +
Sbjct: 684 NNCPLAENLNQQEKDKSADGGTRTDITRMDDKELHD 719
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.317 0.132 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 333,699,595
Number of Sequences: 930587
Number of extensions: 13322567
Number of successful extensions: 30476
Number of sequences better than 5.0e-02: 17
Number of HSP's better than 0.1 without gapping: 17
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 30379
Number of HSP's gapped (non-prelim): 20
length of query: 634
length of database: 291,933,107
effective HSP length: 127
effective length of query: 507
effective length of database: 173,748,558
effective search space: 88090518906
effective search space used: 88090518906
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 94 (40.8 bits)
Query= orf7 [1238-1303]
(64 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049897.1| (NC_000867) gp f [Alteromonas phage PM2] >... 92 1e-018
>ref|NP_049897.1| (NC_000867) gp f [Alteromonas phage PM2]
gb|AAD43544.1|AF155037_7 (AF155037) gp f [Alteromonas phage PM2]
Length = 64
Score = 92.0 bits (227), Expect = 1e-018
Identities = 49/64 (76%), Positives = 49/64 (76%)
Query: 1 MNRDIYTQIETVGVLEKRVEKAGTFEXXXXXXXXXXXXXXXSVLLAKGMAELEDRLKIAE 60
MNRDIYTQIETVGVLEKRVEKAGTFE SVLLAKGMAELEDRLKIAE
Sbjct: 1 MNRDIYTQIETVGVLEKRVEKAGTFELKAAAMALAKAQRKLSVLLAKGMAELEDRLKIAE 60
Query: 61 LRTK 64
LRTK
Sbjct: 61 LRTK 64
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.315 0.133 3.81e+257
Gapped
Lambda K H
0.267 0.0410 2.11e+214
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,364,290
Number of Sequences: 930587
Number of extensions: 347784
Number of successful extensions: 323
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 322
Number of HSP's gapped (non-prelim): 1
length of query: 64
length of database: 291,933,107
effective HSP length: 40
effective length of query: 24
effective length of database: 254,709,627
effective search space: 6113031048
effective search space used: 6113031048
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 84 (37.0 bits)
Query= orf8 [1302-1404]
(101 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049898.1| (NC_000867) gp g [Alteromonas phage PM2] >... 178 1e-044
>ref|NP_049898.1| (NC_000867) gp g [Alteromonas phage PM2]
gb|AAD43545.1|AF155037_8 (AF155037) gp g [Alteromonas phage PM2]
Length = 101
Score = 178 bits (451), Expect = 1e-044
Identities = 85/101 (84%), Positives = 85/101 (84%)
Query: 1 MNPTIAKITCPLCGNDEATVHRQKDRKKKLYYRCTGATFADGCGTIQCTGASGQAFISKN 60
MNPTIAKITCPLCGNDEATVHRQKDRKKKLYYRCTGATFADGCGTIQCTGASGQAFISKN
Sbjct: 1 MNPTIAKITCPLCGNDEATVHRQKDRKKKLYYRCTGATFADGCGTIQCTGASGQAFISKN 60
Query: 61 MKPLNGVXXXXXXXXXXXXXXXXQVKPNKKRSFLDFLVDDE 101
MKPLNGV QVKPNKKRSFLDFLVDDE
Sbjct: 61 MKPLNGVESEDAAIEAAEDAKAEQVKPNKKRSFLDFLVDDE 101
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.320 0.136 2.11e+214
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 49,499,688
Number of Sequences: 930587
Number of extensions: 1511485
Number of successful extensions: 2446
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2445
Number of HSP's gapped (non-prelim): 1
length of query: 101
length of database: 291,933,107
effective HSP length: 77
effective length of query: 24
effective length of database: 220,277,908
effective search space: 5286669792
effective search space used: 5286669792
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 84 (37.0 bits)
Query= orf9 [1404-1548]
(143 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049899.1| (NC_000867) gp h [Alteromonas phage PM2] >... 246 3e-065
>ref|NP_049899.1| (NC_000867) gp h [Alteromonas phage PM2]
gb|AAD43546.1|AF155037_9 (AF155037) gp h [Alteromonas phage PM2]
Length = 143
Score = 246 bits (628), Expect = 3e-065
Identities = 127/143 (88%), Positives = 127/143 (88%)
Query: 1 MPAAKKQIEEKPEVEQDLGAPDFSDLLDDDEKTLIXXXXXXXXXXXXXXXXAIGMAVGEL 60
MPAAKKQIEEKPEVEQDLGAPDFSDLLDDDEKTLI AIGMAVGEL
Sbjct: 1 MPAAKKQIEEKPEVEQDLGAPDFSDLLDDDEKTLIDSVVNDDDESDELTDDAIGMAVGEL 60
Query: 61 VGMGVMFLTDYLAERRGEHWNVSTKELKQLAKAVDGSVPDTELSPAWALVAVSVGMFAPR 120
VGMGVMFLTDYLAERRGEHWNVSTKELKQLAKAVDGSVPDTELSPAWALVAVSVGMFAPR
Sbjct: 61 VGMGVMFLTDYLAERRGEHWNVSTKELKQLAKAVDGSVPDTELSPAWALVAVSVGMFAPR 120
Query: 121 VVVDIQLNKRKVIEVENDDKKAD 143
VVVDIQLNKRKVIEVENDDKKAD
Sbjct: 121 VVVDIQLNKRKVIEVENDDKKAD 143
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.314 0.133 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 71,049,255
Number of Sequences: 930587
Number of extensions: 2382113
Number of successful extensions: 4236
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 4235
Number of HSP's gapped (non-prelim): 1
length of query: 143
length of database: 291,933,107
effective HSP length: 119
effective length of query: 24
effective length of database: 181,193,254
effective search space: 4348638096
effective search space used: 4348638096
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 83 (36.6 bits)
Query= orf10 [1560-1757]
(196 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049900.1| (NC_000867) gp i* [Alteromonas phage PM2] ... 394 e-109
ref|NP_049901.1| (NC_000867) gp i [Alteromonas phage PM2] >... 227 6e-059
ref|NP_240918.1| (NC_002570) BH0052~unknown [Bacillus halod... 50 2e-005
ref|NP_355006.1| (NC_003062) AGR_C_3693p [Agrobacterium tum... 44 0.001
ref|NP_386221.1| (NC_003047) HYPOTHETICAL PROTEIN [Sinorhiz... 44 0.001
ref|NP_532714.1| (NC_003304) conserved hypothetical protein... 44 0.001
gb|AAG60902.1|AF322013_21 (AF322013) ID475 [Bradyrhizobium ... 42 0.004
ref|NP_560342.1| (NC_003364) conserved hypothetical protein... 41 0.006
>ref|NP_049900.1| (NC_000867) gp i* [Alteromonas phage PM2]
gb|AAD43560.3|AF155037_23 (AF155037) gp i* [Alteromonas phage PM2]
Length = 196
Score = 394 bits (1013), Expect = e-109
Identities = 195/196 (99%), Positives = 196/196 (99%)
Query: 1 VVGATGSGKSAFIRDQVDFKGARVLAWDVDEDYRLPRVRSIKQFEKLVKKSGFGAIRCAL 60
+VGATGSGKSAFIRDQVDFKGARVLAWDVDEDYRLPRVRSIKQFEKLVKKSGFGAIRCAL
Sbjct: 1 MVGATGSGKSAFIRDQVDFKGARVLAWDVDEDYRLPRVRSIKQFEKLVKKSGFGAIRCAL 60
Query: 61 TVEPTEENFERFCQLVFAISHAGAPMVVIVEELADVARIGKASPHWGQLSRKGRKYGVQL 120
TVEPTEENFERFCQLVFAISHAGAPMVVIVEELADVARIGKASPHWGQLSRKGRKYGVQL
Sbjct: 61 TVEPTEENFERFCQLVFAISHAGAPMVVIVEELADVARIGKASPHWGQLSRKGRKYGVQL 120
Query: 121 YVATQSPQEIDKTIVRQCNFKFCGALNSASAWRSMADNLDLSTREIKQLENIPKKQVQYW 180
YVATQSPQEIDKTIVRQCNFKFCGALNSASAWRSMADNLDLSTREIKQLENIPKKQVQYW
Sbjct: 121 YVATQSPQEIDKTIVRQCNFKFCGALNSASAWRSMADNLDLSTREIKQLENIPKKQVQYW 180
Query: 181 LKDGTRPTEKKTLTFK 196
LKDGTRPTEKKTLTFK
Sbjct: 181 LKDGTRPTEKKTLTFK 196
>ref|NP_049901.1| (NC_000867) gp i [Alteromonas phage PM2]
gb|AAD43547.1|AF155037_10 (AF155037) gp i [Alteromonas phage PM2]
Length = 111
Score = 227 bits (578), Expect = 6e-059
Identities = 111/111 (100%), Positives = 111/111 (100%)
Query: 86 MVVIVEELADVARIGKASPHWGQLSRKGRKYGVQLYVATQSPQEIDKTIVRQCNFKFCGA 145
MVVIVEELADVARIGKASPHWGQLSRKGRKYGVQLYVATQSPQEIDKTIVRQCNFKFCGA
Sbjct: 1 MVVIVEELADVARIGKASPHWGQLSRKGRKYGVQLYVATQSPQEIDKTIVRQCNFKFCGA 60
Query: 146 LNSASAWRSMADNLDLSTREIKQLENIPKKQVQYWLKDGTRPTEKKTLTFK 196
LNSASAWRSMADNLDLSTREIKQLENIPKKQVQYWLKDGTRPTEKKTLTFK
Sbjct: 61 LNSASAWRSMADNLDLSTREIKQLENIPKKQVQYWLKDGTRPTEKKTLTFK 111
>ref|NP_240918.1| (NC_002570) BH0052~unknown [Bacillus halodurans]
dbj|BAB03771.1| (AP001507) BH0052~unknown [Bacillus halodurans]
Length = 610
Score = 49.7 bits (117), Expect = 2e-005
Identities = 30/88 (34%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 85 PMVVIVEELADVARIG---KASPHWGQLSRKGRKYGVQLYVATQSPQEIDKTIVRQCNFK 141
P V++ +E + A G A P +++++GRKYGV L ATQ P +D+TI Q N K
Sbjct: 410 PFVIVTDEAHNFAPKGYEAPAKPVLKEIAQEGRKYGVFLIFATQRPTLLDETITAQLNSK 469
Query: 142 FCGALNSASAWRSMADNLDLSTREIKQL 169
F + +++ + DL+ E K+L
Sbjct: 470 FVFRTVRGTDIQTIKEETDLTNEEGKRL 497
>ref|NP_355006.1| (NC_003062) AGR_C_3693p [Agrobacterium tumefaciens] [Agrobacterium
tumefaciens str. C58 (Cereon)]
gb|AAK87791.1| (AE008120) AGR_C_3693p [Agrobacterium tumefaciens str. C58
(Cereon)]
Length = 657
Score = 43.9 bits (102), Expect = 0.001
Identities = 27/88 (30%), Positives = 46/88 (51%), Gaps = 15/88 (17%)
Query: 73 CQLVF---AISHAGAPMVVIVEELADVARIGKASPHWG---------QLSRKGRKYGVQL 120
C++ F ++ M+++ EE R A P G Q++++GRKYG+ L
Sbjct: 374 CRMSFELAVLARGSLHMLIVCEE---AHRYVPADPERGFFPTRQSIAQIAKEGRKYGISL 430
Query: 121 YVATQSPQEIDKTIVRQCNFKFCGALNS 148
V +Q P E+D+TI+ QC+ F L++
Sbjct: 431 GVISQRPSELDQTILSQCSTVFAMRLSN 458
>ref|NP_386221.1| (NC_003047) HYPOTHETICAL PROTEIN [Sinorhizobium meliloti]
emb|CAC46694.1| (AL591789) HYPOTHETICAL PROTEIN [Sinorhizobium meliloti]
Length = 678
Score = 43.9 bits (102), Expect = 0.001
Identities = 31/103 (30%), Positives = 47/103 (45%), Gaps = 12/103 (11%)
Query: 73 CQLVFAISHAGAPMVVIVEELADVARIGKASPHWG---------QLSRKGRKYGVQLYVA 123
C++ F I G + ++ + R A P G +++++GRKYGV L +
Sbjct: 385 CRMAFEIGLWGNGAIHMLVVCEEAHRYVPADPSLGFVPTRQAIARIAKEGRKYGVSLGII 444
Query: 124 TQSPQEIDKTIVRQCNFKFCGAL---NSASAWRSMADNLDLST 163
TQ P E+D TI+ QC+ F L RS N +ST
Sbjct: 445 TQRPGELDPTILSQCSTVFAMRLANDRDQEIIRSAIANSSIST 487
>ref|NP_532714.1| (NC_003304) conserved hypothetical protein [Agrobacterium
tumefaciens str. C58 (U. Washington)]
gb|AAL43030.1| (AE009155) conserved hypothetical protein [Agrobacterium
tumefaciens str. C58 (U. Washington)]
Length = 668
Score = 43.9 bits (102), Expect = 0.001
Identities = 27/88 (30%), Positives = 46/88 (51%), Gaps = 15/88 (17%)
Query: 73 CQLVF---AISHAGAPMVVIVEELADVARIGKASPHWG---------QLSRKGRKYGVQL 120
C++ F ++ M+++ EE R A P G Q++++GRKYG+ L
Sbjct: 385 CRMSFELAVLARGSLHMLIVCEE---AHRYVPADPERGFFPTRQSIAQIAKEGRKYGISL 441
Query: 121 YVATQSPQEIDKTIVRQCNFKFCGALNS 148
V +Q P E+D+TI+ QC+ F L++
Sbjct: 442 GVISQRPSELDQTILSQCSTVFAMRLSN 469
>gb|AAG60902.1|AF322013_21 (AF322013) ID475 [Bradyrhizobium japonicum]
Length = 702
Score = 42.0 bits (97), Expect = 0.004
Identities = 33/108 (30%), Positives = 56/108 (51%), Gaps = 19/108 (17%)
Query: 85 PMVVIVEELADVARIGK------ASPH------WGQLSRKGRKYGVQLYVATQSPQEIDK 132
P V+++EE R GK +SP + +++R+GRK+G+ L +++Q P E+
Sbjct: 534 PTVLVLEEAHTFVRRGKDDDGPASSPTQLCREVFERIAREGRKFGLGLVLSSQRPSELSP 593
Query: 133 TIVRQCN-FKFCGALNSAS---AWRSMADNLDLSTREIKQLENIPKKQ 176
T++ QCN F +N A R + DN+ RE L ++P +Q
Sbjct: 594 TVLAQCNTFVLHRIVNDADQNLVARLVPDNVGGLLRE---LPSLPSRQ 638
>ref|NP_560342.1| (NC_003364) conserved hypothetical protein [Pyrobaculum aerophilum]
gb|AAL64524.1| (AE009900) conserved hypothetical protein [Pyrobaculum aerophilum]
Length = 608
Score = 41.2 bits (95), Expect = 0.006
Identities = 26/94 (27%), Positives = 49/94 (51%), Gaps = 7/94 (7%)
Query: 85 PMVVIVEELADVA-----RIGKASPHWGQLSRKGRKYGVQLYVATQSPQEIDKTIVRQCN 139
P+V+ VEE A R K+ +++ +GRK+GV L + +Q P ++D I+ QC
Sbjct: 389 PVVLFVEEAHRFAPPKTLRKTKSYEALSRVASEGRKFGVYLVIISQRPSKVDPDIISQCQ 448
Query: 140 FKFCGALNSASAWRSMADNLDLSTREIKQLENIP 173
+ + + ++ ++ +L +E LEN+P
Sbjct: 449 SQVIMRIINPKDQEAVRESSELLAQEF--LENLP 480
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.320 0.135 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 109,647,731
Number of Sequences: 930587
Number of extensions: 4130474
Number of successful extensions: 11511
Number of sequences better than 5.0e-02: 17
Number of HSP's better than 0.1 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 11501
Number of HSP's gapped (non-prelim): 19
length of query: 196
length of database: 291,933,107
effective HSP length: 114
effective length of query: 82
effective length of database: 185,846,189
effective search space: 15239387498
effective search space used: 15239387498
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 88 (38.5 bits)
Query= orf11 [1841-2111]
(269 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049903.1| (NC_000867) major capsid protein P2 [Alter... 533 e-151
sp|P15794|COA2_BPPM2 COAT PROTEIN II >gi|76793|pir||A12629 ... 62 8e-009
>ref|NP_049903.1| (NC_000867) major capsid protein P2 [Alteromonas phage PM2]
gb|AAD43549.1|AF155037_12 (AF155037) major capsid protein P2 [Alteromonas phage PM2]
Length = 269
Score = 533 bits (1374), Expect = e-151
Identities = 269/269 (100%), Positives = 269/269 (100%)
Query: 1 MRSFLNLNSIPNVAAGNSCSIKLPIGQTYEVIDLRYSGVTPSQIKNVRVELDGRLLSTYK 60
MRSFLNLNSIPNVAAGNSCSIKLPIGQTYEVIDLRYSGVTPSQIKNVRVELDGRLLSTYK
Sbjct: 1 MRSFLNLNSIPNVAAGNSCSIKLPIGQTYEVIDLRYSGVTPSQIKNVRVELDGRLLSTYK 60
Query: 61 TLNDLILENTRHKRKIKAGVVSFHFVRPEMKGVNVTDLVQQRMFALGTVGLTTCEIKFDI 120
TLNDLILENTRHKRKIKAGVVSFHFVRPEMKGVNVTDLVQQRMFALGTVGLTTCEIKFDI
Sbjct: 61 TLNDLILENTRHKRKIKAGVVSFHFVRPEMKGVNVTDLVQQRMFALGTVGLTTCEIKFDI 120
Query: 121 DEAAAGPKLSAIAQKSVGTAPSWLTMRRNFFKQLNNGTTEIADLPRPVGYRIAAIHIKAA 180
DEAAAGPKLSAIAQKSVGTAPSWLTMRRNFFKQLNNGTTEIADLPRPVGYRIAAIHIKAA
Sbjct: 121 DEAAAGPKLSAIAQKSVGTAPSWLTMRRNFFKQLNNGTTEIADLPRPVGYRIAAIHIKAA 180
Query: 181 GVDAVEFQIDGTKWRDLLKKADNDYILEQYGKAVLDNTYTIDFMLEGDVYQSVLLDQMIQ 240
GVDAVEFQIDGTKWRDLLKKADNDYILEQYGKAVLDNTYTIDFMLEGDVYQSVLLDQMIQ
Sbjct: 181 GVDAVEFQIDGTKWRDLLKKADNDYILEQYGKAVLDNTYTIDFMLEGDVYQSVLLDQMIQ 240
Query: 241 DLRLKIDSTMDEQAEIIVEYMGVWSRNGF 269
DLRLKIDSTMDEQAEIIVEYMGVWSRNGF
Sbjct: 241 DLRLKIDSTMDEQAEIIVEYMGVWSRNGF 269
>sp|P15794|COA2_BPPM2 COAT PROTEIN II
pir||A12629 coat protein II - Alteromonas phage PM2 (fragment)
Length = 39
Score = 61.6 bits (148), Expect = 8e-009
Identities = 31/36 (86%), Positives = 31/36 (86%)
Query: 1 MRSFLNLNSIPNVAAGNSCSIKLPIGQTYEVIDLRY 36
MRSFLNLN IPNVAA N IKLPIGQTYEVIDLRY
Sbjct: 1 MRSFLNLNCIPNVAACNXEPIKLPIGQTYEVIDLRY 36
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.320 0.137 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 146,602,694
Number of Sequences: 930587
Number of extensions: 5696717
Number of successful extensions: 14625
Number of sequences better than 5.0e-02: 2
Number of HSP's better than 0.1 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 14623
Number of HSP's gapped (non-prelim): 2
length of query: 269
length of database: 291,933,107
effective HSP length: 118
effective length of query: 151
effective length of database: 182,123,841
effective search space: 27500699991
effective search space used: 27500699991
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 90 (39.3 bits)
Query= orf12 [2115-2220]
(104 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049904.1| (NC_000867) structural protein P3 [Alterom... 150 2e-036
>ref|NP_049904.1| (NC_000867) structural protein P3 [Alteromonas phage PM2]
gb|AAD43550.1|AF155037_13 (AF155037) structural protein P3 [Alteromonas phage PM2]
Length = 104
Score = 150 bits (379), Expect = 2e-036
Identities = 78/104 (75%), Positives = 78/104 (75%)
Query: 1 MNTSVPTSVPTNQSVWGNVSTGLDALISGWARVEQIKAAKASTGQGRVEQAMTPELDNGX 60
MNTSVPTSVPTNQSVWGNVSTGLDALISGWARVEQIKAAKASTGQGRVEQAMTPELDNG
Sbjct: 1 MNTSVPTSVPTNQSVWGNVSTGLDALISGWARVEQIKAAKASTGQGRVEQAMTPELDNGA 60
Query: 61 XXXXXXXXXXXQPSETLVFGVPQKTXXXXXXXXXXXXXXMRGNK 104
QPSETLVFGVPQKT MRGNK
Sbjct: 61 AVVVEAPKKAAQPSETLVFGVPQKTLLLGFGGLLVLGLVMRGNK 104
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.308 0.124 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 43,120,869
Number of Sequences: 930587
Number of extensions: 1157029
Number of successful extensions: 1617
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1616
Number of HSP's gapped (non-prelim): 1
length of query: 104
length of database: 291,933,107
effective HSP length: 80
effective length of query: 24
effective length of database: 217,486,147
effective search space: 5219667528
effective search space used: 5219667528
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 84 (37.0 bits)
Query= orf13 [2219-2260]
(40 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049905.1| (NC_000867) structural protein P4 [Alterom... 84 4e-016
>ref|NP_049905.1| (NC_000867) structural protein P4 [Alteromonas phage PM2]
gb|AAA32194.1| (M26134) structural protein [Alteromonas phage PM2]
gb|AAD43551.1|AF155037_14 (AF155037) structural protein P4 [Alteromonas phage PM2]
Length = 40
Score = 84.0 bits (206), Expect = 4e-016
Identities = 40/40 (100%), Positives = 40/40 (100%)
Query: 1 MQKPSGKGLKYFAYGVAISAAGAILAEYVRDWMRKPKAKS 40
MQKPSGKGLKYFAYGVAISAAGAILAEYVRDWMRKPKAKS
Sbjct: 1 MQKPSGKGLKYFAYGVAISAAGAILAEYVRDWMRKPKAKS 40
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.318 0.132 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,068,632
Number of Sequences: 930587
Number of extensions: 478424
Number of successful extensions: 1592
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1591
Number of HSP's gapped (non-prelim): 1
length of query: 40
length of database: 291,933,107
effective HSP length: 16
effective length of query: 24
effective length of database: 277,043,715
effective search space: 6649049160
effective search space used: 6649049160
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 84 (37.0 bits)
Query= orf14 [2260-2336]
(75 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049906.1| (NC_000867) structural protein P8 [Alterom... 57 4e-008
>ref|NP_049906.1| (NC_000867) structural protein P8 [Alteromonas phage PM2]
gb|AAD43552.1|AF155037_15 (AF155037) structural protein P8 [Alteromonas phage PM2]
Length = 75
Score = 57.0 bits (136), Expect = 4e-008
Identities = 33/50 (66%), Positives = 33/50 (66%)
Query: 26 IASSSSAETGQQTQXXXXXXXXXXXXXXXXXQLLIVGAVVIGLFLVIKRK 75
IASSSSAETGQQTQ QLLIVGAVVIGLFLVIKRK
Sbjct: 26 IASSSSAETGQQTQSGNFTGGGINFGSNNNNQLLIVGAVVIGLFLVIKRK 75
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.319 0.133 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,661,115
Number of Sequences: 930587
Number of extensions: 139377
Number of successful extensions: 197
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 196
Number of HSP's gapped (non-prelim): 1
length of query: 75
length of database: 291,933,107
effective HSP length: 51
effective length of query: 24
effective length of database: 244,473,170
effective search space: 5867356080
effective search space used: 5867356080
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 84 (37.0 bits)
Query= orf15 [2359-2639]
(279 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049907.1| (NC_000867) gp j [Alteromonas phage PM2] >... 499 e-140
pir||S61428 embryonic abundant protein group 3 precursor (c... 50 3e-005
pir||S52714 sericin1B - silkworm >gi|755700|emb|CAA88741.1|... 44 0.001
pir||S61426 late embryogenesis abundant protein group 3 (cl... 44 0.002
pir||S33520 Lea protein - soybean >gi|311698|emb|CAA80491.1... 43 0.003
gb|AAK77860.1|AF394927_2 (AF394927) RscA [Yersinia enteroco... 41 0.011
>ref|NP_049907.1| (NC_000867) gp j [Alteromonas phage PM2]
gb|AAD43553.1|AF155037_16 (AF155037) gp j [Alteromonas phage PM2]
Length = 279
Score = 499 bits (1284), Expect = e-140
Identities = 260/279 (93%), Positives = 260/279 (93%)
Query: 1 MGLFXXXXXXXXXXXXXXXXXXXIATQGDNLGAVINGNGNSVTMTDHGLVDALVDIGGYM 60
MGLF IATQGDNLGAVINGNGNSVTMTDHGLVDALVDIGGYM
Sbjct: 1 MGLFGGGNSKSTSNQTTNNENTNIATQGDNLGAVINGNGNSVTMTDHGLVDALVDIGGYM 60
Query: 61 SDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFGRDALS 120
SDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFGRDALS
Sbjct: 61 SDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFGRDALS 120
Query: 121 VTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFSGAMDSLNQS 180
VTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFSGAMDSLNQS
Sbjct: 121 VTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFSGAMDSLNQS 180
Query: 181 NNNMALLAEFTSNQSTDLARDSMAFGADLMAQYQDNISASNYDAREHMLDASKTAMQFAD 240
NNNMALLAEFTSNQSTDLARDSMAFGADLMAQYQDNISASNYDAREHMLDASKTAMQFAD
Sbjct: 181 NNNMALLAEFTSNQSTDLARDSMAFGADLMAQYQDNISASNYDAREHMLDASKTAMQFAD 240
Query: 241 NMSRSDGQQLAKDSNKTLMIGIVAVSAAVGLYAISKGVN 279
NMSRSDGQQLAKDSNKTLMIGIVAVSAAVGLYAISKGVN
Sbjct: 241 NMSRSDGQQLAKDSNKTLMIGIVAVSAAVGLYAISKGVN 279
>pir||S61428 embryonic abundant protein group 3 precursor (clone PM10) - soybean
gb|AAA91965.1| (U02966) 51 kDa seed maturation protein [Glycine max]
Length = 473
Score = 49.7 bits (117), Expect = 3e-005
Identities = 46/210 (21%), Positives = 87/210 (40%), Gaps = 24/210 (11%)
Query: 56 IGGYMSDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFG 115
+ Y +D+ Q + A+D A S ++AG A DYA + + D A + S ++
Sbjct: 94 VSDYATDTAQKSKDYATDTAQKSKDYAGDAAQKSKDYAGDAAQKTKDYASDTAQTSKDYA 153
Query: 116 RDAL----SVTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFS 171
DA GD +Y DA + + A + D +T T D S
Sbjct: 154 GDAAQKSKGYVGDAAQKTKEYVGDAAQKTKDYATDAAQKTKDYATQKT-------KDYAS 206
Query: 172 GAMDSLNQSNNNMALLAEFTSNQSTDLARDSMAFGADLMAQY--------QDNISASNYD 223
A D+ ++ + A + +++++D+A+++ + A Y +D S
Sbjct: 207 DATDAAKKTKDYAAQKTKDYASEASDVAQNTKDYAAQKTKDYASGGAQKTKDYASGGAQK 266
Query: 224 AREHMLDASKTAMQFADNMSRSDGQQLAKD 253
+++ DA++ +A SDG Q +K+
Sbjct: 267 TKDYASDAAQKTKDYA-----SDGAQKSKE 291
>pir||S52714 sericin1B - silkworm
emb|CAA88741.1| (Z48802) sericin1B [Bombyx mori]
Length = 1217
Score = 44.3 bits (103), Expect = 0.001
Identities = 56/215 (26%), Positives = 87/215 (40%), Gaps = 22/215 (10%)
Query: 58 GYMSDSTQAAFGA--ASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNF- 114
GY SDS + + +S +ST+ AG + T G G + DS D + S N
Sbjct: 879 GYSSDSRDGSVSSTGSSSNTDASTDLAGSS-TSGGSSTYGYSSDSRDGSVSSTGSSSNTD 937
Query: 115 -GRDALSVTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFSGA 173
D + + YSSD+ S+ + DAST +TG S + G T+ +
Sbjct: 938 ASTDLAGSSTSGGSSTYGYSSDSRDGSVSSTGSSSNT--DASTDLTGSSTSGGSSTYGYS 995
Query: 174 MDSLNQSNNNMALLAEFTSNQSTDLARDSMAFGADLMAQYQDNI--------SASNYDA- 224
DS + S ++ + ++ STDLA S + G+ N S+SN DA
Sbjct: 996 SDSRDGSVSSTG--SSSNTDASTDLAGSSTSGGSSTYGYSSSNRDGSVSATGSSSNTDAS 1053
Query: 225 --REHMLDASKTAMQFADNMSRSDGQQLAKDSNKT 257
E A + ++ S DG + D + T
Sbjct: 1054 TTEESTTSAGSSTEGYSS--SSHDGSVTSTDGSST 1086
>pir||S61426 late embryogenesis abundant protein group 3 (clone pGmPM8) -
soybean (fragment)
Length = 350
Score = 43.5 bits (101), Expect = 0.002
Identities = 48/213 (22%), Positives = 81/213 (37%), Gaps = 29/213 (13%)
Query: 59 YMSDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFGRDA 118
Y D+ Q + A D A + ++AG DYA + S D A + S + DA
Sbjct: 3 YAGDAAQKSKDYAGDTAQKTKDYAGDTAQKTKDYAGDTAQTSKDYAGDAAQKSKGYVGDA 62
Query: 119 LSVT----GDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFSGAM 174
T GD M Y++DA A + D +T T + D
Sbjct: 63 AQKTKEYVGDAAQKTMDYATDA-----------AQKTKDYATQKTKDYASDATDAAKKTK 111
Query: 175 DSLNQSNNNMALLAEFTSNQSTDLA----RDSMAFGADLMAQYQDNISASNYD------- 223
D Q + A A + ++ D A +D + GA Y D + D
Sbjct: 112 DYAAQKTKDYASDATDAAKKTKDYAAQKTKDYASGGAQKTKDYADGAAQKTKDYASDAAQ 171
Query: 224 -AREHMLDASKTAMQFADNMSRS--DGQQLAKD 253
++H D ++ + ++A +++++ D Q +KD
Sbjct: 172 RTKDHASDGAQKSKEYAGDVAQNAKDYAQKSKD 204
Score = 40.0 bits (92), Expect = 0.026
Identities = 44/195 (22%), Positives = 79/195 (39%), Gaps = 13/195 (6%)
Query: 59 YMSDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFGRDA 118
Y SD+ Q ASD A S E+AG + DYA+ S D A + ++ ++ DA
Sbjct: 165 YASDAAQRTKDHASDGAQKSKEYAGDVAQNAKDYAQ----KSKDYAGDVAQNIKDYANDA 220
Query: 119 LSVTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFSGAMDSLN 178
+ D DA S +A + E V DA+ Q + S A
Sbjct: 221 AHKSKDYAGDASHKSKEASDYASETAQKTKDYVGDAA-----QKSKEASEYASDAAQRTK 275
Query: 179 QSNNNMALLAEFTSNQSTDLARDSMAFGAD----LMAQYQDNISASNYDAREHMLDASKT 234
+ + ++ S+ + D+AR + + +D + QD S + + E +
Sbjct: 276 EYAGDATKRSKEASDHANDMARRTKDYASDTAQRTKEKLQDIASEAGQYSTEKAREMKDA 335
Query: 235 AMQFADNMSRSDGQQ 249
A + A +++++ Q+
Sbjct: 336 AAEKASDIAKAAKQK 350
Score = 39.3 bits (90), Expect = 0.044
Identities = 42/186 (22%), Positives = 75/186 (39%), Gaps = 23/186 (12%)
Query: 59 YMSDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFGRDA 118
Y SD+T AA D A T+ DYA G + + D A+G + + ++ DA
Sbjct: 121 YASDATDAA-KKTKDYAAQKTK----------DYASGGAQKTKDYADGAAQKTKDYASDA 169
Query: 119 LSVTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFSGAMDSLN 178
T D +D Q S + AG V + +S ++ D D N
Sbjct: 170 AQRTKDHASDGAQKSKE-----------YAGDVAQNAKDYAQKSKDYAGDVAQNIKDYAN 218
Query: 179 QSNNNMALLAEFTSNQSTDLARDSMAFGADLMAQYQDNISASNYDAREHMLDASKTAMQF 238
+ + A S++S + A D + A Y + + + +A E+ DA++ ++
Sbjct: 219 DAAHKSKDYAGDASHKSKE-ASDYASETAQKTKDYVGDAAQKSKEASEYASDAAQRTKEY 277
Query: 239 ADNMSR 244
A + ++
Sbjct: 278 AGDATK 283
>pir||S33520 Lea protein - soybean
emb|CAA80491.1| (Z22872) Lea protein [Glycine max]
Length = 458
Score = 43.1 bits (100), Expect = 0.003
Identities = 48/210 (22%), Positives = 81/210 (37%), Gaps = 35/210 (16%)
Query: 56 IGGYMSDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRDSLNFG 115
+ Y D+ Q + A D A + ++AG DYA + S D A + S +
Sbjct: 91 VSDYAGDAAQKSKDYAGDTAQKTKDYAGDTAQKTKDYAGDTAQTSKDYAGDAAQKSKGYV 150
Query: 116 RDALSVT----GDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTFS 171
DA T GD M Y++DA A + D +T T D S
Sbjct: 151 GDAAQKTKEYVGDAAQKTMDYATDA-----------AQKTKDYATQKT-------KDYAS 192
Query: 172 GAMDSLNQSNNNMALLAEFTSNQSTDLARDSMAFGADLMAQY--------QDNISASNYD 223
A D+ ++ + A + ++ +TD A+ + + A Y +D S +
Sbjct: 193 DATDAAKKTKDYAAQKTKDYASDATDAAKKTKDYAAQKTKDYASGGAQKTKDYASGAAQK 252
Query: 224 AREHMLDASKTAMQFADNMSRSDGQQLAKD 253
+++ DA++ A SDG Q +K+
Sbjct: 253 TKDYASDAAQRTKDHA-----SDGAQKSKE 277
Score = 42.0 bits (97), Expect = 0.007
Identities = 42/205 (20%), Positives = 83/205 (40%), Gaps = 8/205 (3%)
Query: 51 DALVDIGGYMSDSTQAAFGAASDMAYSSTEFAGQAITDGFDYAEGVNRDSLDMAEGINRD 110
DA Y D+ Q A D A + ++AG DYA + S +
Sbjct: 97 DAAQKSKDYAGDTAQKTKDYAGDTAQKTKDYAGDTAQTSKDYAGDAAQKSKGYVGDAAQK 156
Query: 111 SLNFGRDALSVTGDLMTDAMQYSSDAMLASIEGNAGLAGQVMDASTTMTGQSLNFGLDTF 170
+ + DA T D TDA Q + D + + A DA+ + D
Sbjct: 157 TKEYVGDAAQKTMDYATDAAQKTKD---YATQKTKDYASDATDAAKKTKDYAAQKTKDYA 213
Query: 171 SGAMDSLNQSNNNMALLAEFTSNQSTDLARDSMAFGADLMAQYQDNISASNYDAREHMLD 230
S A D+ ++ + A+ T + ++ A+ + + + + +D S + ++H D
Sbjct: 214 SDATDAAKKTKD---YAAQKTKDYASGGAQKTKDYASGAAQKTKDYASDAAQRTKDHASD 270
Query: 231 ASKTAMQFADNMSRS--DGQQLAKD 253
++ + ++A +++++ D Q +KD
Sbjct: 271 GAQKSKEYAGDVAQNAKDYAQKSKD 295
>gb|AAK77860.1|AF394927_2 (AF394927) RscA [Yersinia enterocolitica]
Length = 2065
Score = 41.2 bits (95), Expect = 0.011
Identities = 46/225 (20%), Positives = 90/225 (39%), Gaps = 31/225 (13%)
Query: 32 GAVINGNGNSVTMTDHGLVDALVDIGGYMSDSTQAAFGAASDMAYSSTEFAGQAITDGFD 91
G+ ++GN +V + G + G++ + A + A ++T G I+ D
Sbjct: 763 GSKVSGNNVNVEINTKG-------VDGFLLRDSHITATAGNISANATTTHKGLWISGDTD 815
Query: 92 YAEGVNRDSLDMAEGINRDSLNFGRDALSVTGDLMTDAMQYSSDAMLASIEGNAGL-AGQ 150
+N +G+ +S G DA+ ++G+ + + ++ ++ + N G G
Sbjct: 816 ----LNASKNIKLQGVTTNSTTVGADAIKISGNSSSVQVNMAAGGNISMVAVNKGTEVGS 871
Query: 151 VMDASTT---MTGQSLNFGLDTFSGA-MDSLNQSNNNMALLAEFTSNQSTDLARDSMAFG 206
+ A T G N + G+ ++N S +N+ L + N + + +A
Sbjct: 872 TISADYTNIKAQGGDFNLNISGVKGSPFSNVNISADNIILNGNISDNDAVVMTNTFLAAK 931
Query: 207 ADLMAQYQDNISASNYDAREHMLDASKTAMQFADNMSRSDGQQLA 251
D+ A N+S+ NY A+ F N S GQ L+
Sbjct: 932 GDIKA----NLSSPNY-----------KALYFKGNGGMSAGQNLS 961
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.312 0.127 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 124,644,049
Number of Sequences: 930587
Number of extensions: 4593655
Number of successful extensions: 10251
Number of sequences better than 5.0e-02: 9
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 10194
Number of HSP's gapped (non-prelim): 32
length of query: 279
length of database: 291,933,107
effective HSP length: 119
effective length of query: 160
effective length of database: 181,193,254
effective search space: 28990920640
effective search space used: 28990920640
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 90 (39.3 bits)
Query= orf16 [2639-2975]
(335 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049908.1| (NC_000867) spike protein P1 [Alteromonas ... 644 0.0
>ref|NP_049908.1| (NC_000867) spike protein P1 [Alteromonas phage PM2]
gb|AAD43554.1|AF155037_17 (AF155037) spike protein P1 [Alteromonas phage PM2]
Length = 335
Score = 644 bits (1660), Expect = 0.0
Identities = 322/335 (96%), Positives = 322/335 (96%)
Query: 1 MIVKKKLAAGEFAETFKNGNNITIIKAVGELVLRAYGADGGEGLRTIVRQGVSIKGMNYT 60
MIVKKKLAAGEFAETFKNGNNITIIKAVGELVLRAYGADGGEGLRTIVRQGVSIKGMNYT
Sbjct: 1 MIVKKKLAAGEFAETFKNGNNITIIKAVGELVLRAYGADGGEGLRTIVRQGVSIKGMNYT 60
Query: 61 SVMLHTEYAQEIEYWVGDLDYSFQEQTTKSRDVNSFQIPLRDGVRELLPEDASRNRASIK 120
SVMLHTEYAQEIEYWVGDLDYSFQEQTTKSRDVNSFQIPLRDGVRELLPEDASRNRASIK
Sbjct: 61 SVMLHTEYAQEIEYWVGDLDYSFQEQTTKSRDVNSFQIPLRDGVRELLPEDASRNRASIK 120
Query: 121 SPVDIWIGGENMTALNGIVDGGRKFEAGQEFQINTFGSVNYWVSDEEIRVFKEYSARAKY 180
SPVDIWIGGENMTALNGIVDGGRKFEAGQEFQINTFGSVNYWVSDEEIRVFKEYSARAKY
Sbjct: 121 SPVDIWIGGENMTALNGIVDGGRKFEAGQEFQINTFGSVNYWVSDEEIRVFKEYSARAKY 180
Query: 181 AQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYI 240
AQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYI
Sbjct: 181 AQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYI 240
Query: 241 TEGDETTDTLIKXXXXXXXXXXXXXDFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEV 300
TEGDETTDTLIK DFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEV
Sbjct: 241 TEGDETTDTLIKYTSYGSTGSHSGYDFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEV 300
Query: 301 QHDWYDESFTTFIEVYSDDPLLTVKGYAQILMERT 335
QHDWYDESFTTFIEVYSDDPLLTVKGYAQILMERT
Sbjct: 301 QHDWYDESFTTFIEVYSDDPLLTVKGYAQILMERT 335
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.316 0.136 0.000
Gapped
Lambda K H
0.267 0.0410 0.000
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 185,441,236
Number of Sequences: 930587
Number of extensions: 7557671
Number of successful extensions: 14991
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 14990
Number of HSP's gapped (non-prelim): 1
length of query: 335
length of database: 291,933,107
effective HSP length: 121
effective length of query: 214
effective length of database: 179,332,080
effective search space: 38377065120
effective search space used: 38377065120
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 91 (39.7 bits)
Query= orf17 [2975-3136]
(160 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049909.1| (NC_000867) structural protein P5 [Alterom... 332 6e-091
ref|NP_569521.1| (NC_003385) hypothetical protein [Salmonel... 76 1e-013
ref|NP_455539.1| (NC_003198) putative bacteriophage protein... 73 9e-013
>ref|NP_049909.1| (NC_000867) structural protein P5 [Alteromonas phage PM2]
gb|AAD43555.1|AF155037_18 (AF155037) structural protein P5 [Alteromonas phage PM2]
Length = 160
Score = 332 bits (852), Expect = 6e-091
Identities = 160/160 (100%), Positives = 160/160 (100%)
Query: 1 MKKAHMFLATAAALGVAMFPTQINEAARGLRNNNPLNIKEGSDGGAQWEGEHELDLDPTF 60
MKKAHMFLATAAALGVAMFPTQINEAARGLRNNNPLNIKEGSDGGAQWEGEHELDLDPTF
Sbjct: 1 MKKAHMFLATAAALGVAMFPTQINEAARGLRNNNPLNIKEGSDGGAQWEGEHELDLDPTF 60
Query: 61 EEFKTPVHGIRAGARILRTYAVKYGLESIEGIIARWAPEEENDTENYINFVANKTGIPRN 120
EEFKTPVHGIRAGARILRTYAVKYGLESIEGIIARWAPEEENDTENYINFVANKTGIPRN
Sbjct: 61 EEFKTPVHGIRAGARILRTYAVKYGLESIEGIIARWAPEEENDTENYINFVANKTGIPRN 120
Query: 121 QKLNDETYPAVISAMIDMENGSNPYTYDEIKKGFEWGFYG 160
QKLNDETYPAVISAMIDMENGSNPYTYDEIKKGFEWGFYG
Sbjct: 121 QKLNDETYPAVISAMIDMENGSNPYTYDEIKKGFEWGFYG 160
>ref|NP_569521.1| (NC_003385) hypothetical protein [Salmonella enterica subsp.
enterica serovar Typhi]
emb|CAD09916.1| (AL513384) hypothetical protein [Salmonella enterica subsp.
enterica serovar Typhi]
Length = 230
Score = 75.9 bits (185), Expect = 1e-013
Identities = 49/126 (38%), Positives = 69/126 (53%), Gaps = 13/126 (10%)
Query: 28 RGLRNNNPLNIKEGSDGGAQWEGEHELDLDPTFEEFKTPVHGIRAGARILRTYAVKY--- 84
RG+RNNNP N+ D G+ W+G + +P F FK PV GIRA A L TY K
Sbjct: 5 RGIRNNNPGNL----DKGSPWQGLIDNPAEPRFCTFKDPVWGIRALAVTLITYHDKRRAK 60
Query: 85 ---GLESIEGIIARWAPEEENDTENYINFVANKTGIPRNQ--KLND-ETYPAVISAMIDM 138
+++I +I RWAP EN+T Y+N V+ G+ + L+D +T ++ A+I
Sbjct: 61 DGSSIDTIREVIERWAPPHENNTVAYVNEVSKAVGVTPDMIIDLHDYDTLRPLVEAIIRH 120
Query: 139 ENGSNP 144
ENG P
Sbjct: 121 ENGRGP 126
>ref|NP_455539.1| (NC_003198) putative bacteriophage protein [Salmonella enterica
subsp. enterica serovar Typhi]
emb|CAD05454.1| (AL627268) putative bacteriophage protein [Salmonella enterica
subsp. enterica serovar Typhi]
Length = 662
Score = 73.2 bits (178), Expect = 9e-013
Identities = 51/137 (37%), Positives = 70/137 (50%), Gaps = 10/137 (7%)
Query: 28 RGLRNNNPLNIKEGSDGGAQWEGEHELDLDPTFEEFKTPVHGIRAGARILRTYAVKYGLE 87
RG RNNNP N+ GA E F F+T G+RA AR L YA + G+
Sbjct: 486 RGERNNNPGNLNFAGQAGASLERP-----GGRFARFETAFDGLRALARQLMLYAGR-GIN 539
Query: 88 SIEGIIARWAP-EEENDTENYINFVANKTGIPRNQKLN---DETYPAVISAMIDMENGSN 143
S+E II+ WAP + N+T YI V+ + G+ LN +T A++S++I ENG N
Sbjct: 540 SVEKIISTWAPASDNNNTTAYIRAVSQRLGVDPRAALNMSDPQTMSALMSSIIQHENGRN 599
Query: 144 PYTYDEIKKGFEWGFYG 160
Y+ + I K G G
Sbjct: 600 IYSRELINKAAVAGISG 616
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.315 0.135 0.000
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 99,792,364
Number of Sequences: 930587
Number of extensions: 4104777
Number of successful extensions: 8378
Number of sequences better than 5.0e-02: 3
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 8374
Number of HSP's gapped (non-prelim): 3
length of query: 160
length of database: 291,933,107
effective HSP length: 111
effective length of query: 49
effective length of database: 188,637,950
effective search space: 9243259550
effective search space used: 9243259550
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 86 (37.7 bits)
Query= orf18 [3133-3261]
(127 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049910.1| (NC_000867) structural protein P6 [Alterom... 258 6e-069
>ref|NP_049910.1| (NC_000867) structural protein P6 [Alteromonas phage PM2]
gb|AAD43556.1|AF155037_19 (AF155037) structural protein P6 [Alteromonas phage PM2]
Length = 127
Score = 258 bits (660), Expect = 6e-069
Identities = 127/127 (100%), Positives = 127/127 (100%)
Query: 1 MANFLTKNFVWILAAGVGVWFYQKADNAAKTATKPIADFLAELQFLVNGSNYVKFPNAGF 60
MANFLTKNFVWILAAGVGVWFYQKADNAAKTATKPIADFLAELQFLVNGSNYVKFPNAGF
Sbjct: 1 MANFLTKNFVWILAAGVGVWFYQKADNAAKTATKPIADFLAELQFLVNGSNYVKFPNAGF 60
Query: 61 VLTRDALQDDFIAYDDRIKAWLGTHDRHKDFLAEILDHERRVKPVYRKLIGNIIDASTIR 120
VLTRDALQDDFIAYDDRIKAWLGTHDRHKDFLAEILDHERRVKPVYRKLIGNIIDASTIR
Sbjct: 61 VLTRDALQDDFIAYDDRIKAWLGTHDRHKDFLAEILDHERRVKPVYRKLIGNIIDASTIR 120
Query: 121 AASGVEL 127
AASGVEL
Sbjct: 121 AASGVEL 127
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.324 0.139 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 69,991,997
Number of Sequences: 930587
Number of extensions: 2545059
Number of successful extensions: 7223
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 7222
Number of HSP's gapped (non-prelim): 1
length of query: 127
length of database: 291,933,107
effective HSP length: 103
effective length of query: 24
effective length of database: 196,082,646
effective search space: 4705983504
effective search space used: 4705983504
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 83 (36.6 bits)
Query= orf19 [3307-3359]
(51 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
930,587 sequences; 291,933,107 total letters
Searching done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_049912.1| (NC_000867) gp l [Alteromonas phage PM2] >... 100 3e-021
>ref|NP_049912.1| (NC_000867) gp l [Alteromonas phage PM2]
gb|AAD43558.1|AF155037_21 (AF155037) gp l [Alteromonas phage PM2]
Length = 51
Score = 100 bits (250), Expect = 3e-021
Identities = 51/51 (100%), Positives = 51/51 (100%)
Query: 1 MFSTLAKYLAVKLLTETFIKRVCLATAKHLANKSENTLDNELIDALEDALN 51
MFSTLAKYLAVKLLTETFIKRVCLATAKHLANKSENTLDNELIDALEDALN
Sbjct: 1 MFSTLAKYLAVKLLTETFIKRVCLATAKHLANKSENTLDNELIDALEDALN 51
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 3, 2002 6:15 AM
Number of letters in database: 291,933,107
Number of sequences in database: 930,587
Lambda K H
0.318 0.130 4.65e-269
Gapped
Lambda K H
0.267 0.0410 4.65e-269
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,705,893
Number of Sequences: 930587
Number of extensions: 470910
Number of successful extensions: 1099
Number of sequences better than 5.0e-02: 1
Number of HSP's better than 0.1 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1098
Number of HSP's gapped (non-prelim): 1
length of query: 51
length of database: 291,933,107
effective HSP length: 27
effective length of query: 24
effective length of database: 266,807,258
effective search space: 6403374192
effective search space used: 6403374192
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 84 (37.0 bits)