BLASTP 2.2.1 [Apr-13-2001]
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= gi|15644721|ref|NP_206891.1| type II restriction enzyme
R protein (hsdR) [Helicobacter pylori 26695]
(277 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_223536.1| CYSTEINYL-TRNA SYNTHETASE [Helicobacter py... 30 0.070
ref|NP_224135.1| CHROMOSOMAL REPLICATION INITIATOR PROTEIN ... 29 0.12
ref|NP_223838.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT ... 26 1.0
ref|NP_224148.1| putative [Helicobacter pylori J99] 25 1.7
ref|NP_223344.1| IRON(III) DICITRATE TRANSPORT PROTEIN [Hel... 25 1.7
ref|NP_224199.1| putative [Helicobacter pylori J99] 25 2.9
ref|NP_222991.1| putative [Helicobacter pylori J99] 25 2.9
ref|NP_222797.1| methyl-accepting chemotaxis protein (MCP) ... 25 2.9
ref|NP_223213.1| cag island protein, CYTOTOXICITY ASSOCIATE... 24 3.8
ref|NP_222890.1| putative [Helicobacter pylori J99] 24 3.8
ref|NP_224015.1| putative TYPE III RESTRICTION ENZYME [Heli... 24 5.0
ref|NP_224011.1| ATP-DEPENDENT PROTEASE LA [Helicobacter py... 24 5.0
ref|NP_223433.1| putative [Helicobacter pylori J99] 24 5.0
ref|NP_223194.1| cag island protein [Helicobacter pylori J99] 24 5.0
ref|NP_223140.1| OLIGOPEPTIDASE [Helicobacter pylori J99] 24 5.0
ref|NP_222904.1| S-adenosylmethionine synthetase [Helicobac... 24 5.0
ref|NP_224089.1| putative ATP-DEPENDENT DNA HELICASE [Helic... 23 8.5
ref|NP_224002.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 23 8.5
ref|NP_223811.1| putative Outer membrane protein [Helicobac... 23 8.5
ref|NP_223203.1| cag island protein [Helicobacter pylori J99] 23 8.5
ref|NP_223061.1| putative Outer membrane protein [Helicobac... 23 8.5
>ref|NP_223536.1| CYSTEINYL-TRNA SYNTHETASE [Helicobacter pylori J99]
Length = 465
Score = 30.0 bits (66), Expect = 0.070
Identities = 33/144 (22%), Positives = 61/144 (41%), Gaps = 22/144 (15%)
Query: 141 NARKNRSGKVMENHLSGLFTNAQLNFKEQVEIREFEDLCQAF-------------GDDIK 187
+A KN G+++ N+L G+ + LNF E+ + + L + + + K
Sbjct: 282 DALKNYDGEILRNYLLGVHYRSVLNFNEEDLLMSKKRLDKIYRLKQRVLGTLGGINPNFK 341
Query: 188 KFDFVVCGKD-----KTYFIEANFYTISGSKLNEVARSYQDLALKFEAFPNYEFIWITDG 242
K + + C +D K + + + + KL++ + ++ ALK E N +FI G
Sbjct: 342 K-EILECMQDDLNVSKALSVLESMLSSTNEKLDQ---NPKNKALKGEILANLKFIEELLG 397
Query: 243 IGWLDAKNKLQEAYKSVEIYNLSN 266
IG+ D Q E + N
Sbjct: 398 IGFKDPSAYFQLGVSESEKQEIEN 421
>ref|NP_224135.1| CHROMOSOMAL REPLICATION INITIATOR PROTEIN [Helicobacter pylori J99]
Length = 457
Score = 29.3 bits (64), Expect = 0.12
Identities = 26/72 (36%), Positives = 36/72 (49%), Gaps = 9/72 (12%)
Query: 22 DFFTDWQKCLKNKNKISI--ALNHLNFLLGKDTKELKNCIKSLFKEYPKAFNVLN----- 74
DF TD+ K L NKN S H +F L D + L+ K L +E+ FN L+
Sbjct: 181 DFLTDFLKHLDNKNMDSFKKKYRHCDFFLLDDAQFLQGKPK-LEEEFFHTFNELHANSKQ 239
Query: 75 -ILIAVRDKKDI 85
+LI+ R K+I
Sbjct: 240 IVLISDRSPKNI 251
>ref|NP_223838.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT [Helicobacter pylori J99]
Length = 2890
Score = 26.2 bits (56), Expect = 1.0
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 18/65 (27%)
Query: 55 LKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEFIRQTG 114
LKN +++ F + P V N+L+ RD Y + Y +DG +++G
Sbjct: 7 LKNRLRADFTKTPTDLEVPNLLLLQRDS-----------YDSFLYSKDG-------KESG 48
Query: 115 LERIF 119
+E++F
Sbjct: 49 IEKVF 53
>ref|NP_224148.1| putative [Helicobacter pylori J99]
Length = 282
Score = 25.4 bits (54), Expect = 1.7
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 9/56 (16%)
Query: 123 NIKDLNDFVFGIEVGLDSNARKNRSGKVMENHLSGLFTNAQLNFKEQVEIREFEDL 178
N KD DFV+ +E DS A KN++ K N+L + K+ ++ +E +D+
Sbjct: 138 NAKD--DFVYALEHFNDSQASKNKNNK--NNYLKN-----AICLKDYLKEKEIKDI 184
>ref|NP_223344.1| IRON(III) DICITRATE TRANSPORT PROTEIN [Helicobacter pylori J99]
Length = 767
Score = 25.4 bits (54), Expect = 1.7
Identities = 9/21 (42%), Positives = 14/21 (65%)
Query: 229 EAFPNYEFIWITDGIGWLDAK 249
E F NY +W++D I + D+K
Sbjct: 440 EMFNNYTAVWLSDKIEFFDSK 460
>ref|NP_224199.1| putative [Helicobacter pylori J99]
Length = 254
Score = 24.6 bits (52), Expect = 2.9
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 61 SLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFY 94
+L K YPKAF VL+ A ++L+ + FY
Sbjct: 141 NLLKSYPKAFGVLHCFNA----DSMLLELSDRFY 170
>ref|NP_222991.1| putative [Helicobacter pylori J99]
Length = 418
Score = 24.6 bits (52), Expect = 2.9
Identities = 15/51 (29%), Positives = 23/51 (44%)
Query: 50 KDTKELKNCIKSLFKEYPKAFNVLNILIAVRDKKDIVLDANGNFYPLYSYF 100
+D+K+ N IK L KAF L + + K + +G F L +F
Sbjct: 336 EDSKKRLNAIKDLIFHKNKAFRQLQLKLNTPLKALVEAQKDGEFKALDQFF 386
>ref|NP_222797.1| methyl-accepting chemotaxis protein (MCP) [Helicobacter pylori J99]
Length = 673
Score = 24.6 bits (52), Expect = 2.9
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 40 ALNHLNFLLGKDTKELKNCIKSLFKEYPKAFNVL-NILIAVRDKKDIVLDANGNFYPLYS 98
ALNH ++K+LK C+ +L K K L N ++ + +I+ + + S
Sbjct: 488 ALNH-------ESKDLKTCVDNLTKTAHKQERSLKNTTQSLEEITNIITMIDSKSQEMIS 540
Query: 99 YFEDGEKVYEFIR 111
ED + V + IR
Sbjct: 541 QGEDIKSVVDMIR 553
>ref|NP_223213.1| cag island protein, CYTOTOXICITY ASSOCIATED IMMUNODOMINANT ANTIGEN
[Helicobacter pylori J99]
Length = 1167
Score = 24.3 bits (51), Expect = 3.8
Identities = 32/174 (18%), Positives = 70/174 (39%), Gaps = 13/174 (7%)
Query: 106 VYEFIRQTGLERIFCNRNIKDLNDFVFGIEVGLDSNARKNRSGKVMENHLSGLFTNAQLN 165
+Y+ + TG +R I++ DF+ E +NA+ + K + + Q +
Sbjct: 379 LYKEDQLTGSQRALSQEEIQNKVDFM---EFLAQNNAKLDNLSKKEKEKFQNEIEDFQKD 435
Query: 166 FKEQVEIREFEDLCQAFGDDIKKFDFVV-CGKDKTYFIEANFYTISGSKLNEVARSYQDL 224
K ++ + + D K V G + + ++ + L+ A++
Sbjct: 436 SKAYLDALGNDHIAFVSKKDKKHLALVAEFGNGELSYTLKDYGKKADKALDREAKTTLQG 495
Query: 225 ALKFEA--FPNYEFIWITD-------GIGWLDAKNKLQEAYKSVEIYNLSNVND 269
+LK + F +Y T+ G+G + + L+ + V ++NL N+N+
Sbjct: 496 SLKHDGVMFVDYSNFKYTNASKSPDKGVGATNGVSHLEAGFSKVAVFNLPNLNN 549
>ref|NP_222890.1| putative [Helicobacter pylori J99]
Length = 236
Score = 24.3 bits (51), Expect = 3.8
Identities = 16/60 (26%), Positives = 30/60 (49%), Gaps = 3/60 (5%)
Query: 68 KAFNVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKV-YEFIRQTGLERIFCNRNIKD 126
K F VL+ ++ K D++ DAN + F + V + +R G++ + +N+KD
Sbjct: 112 KTFLVLSFILYALSKMDLMKDANAYLQEKSAIFPTMKSVASKIMRLDGVKHV--EKNLKD 169
>ref|NP_224015.1| putative TYPE III RESTRICTION ENZYME [Helicobacter pylori J99]
Length = 779
Score = 23.9 bits (50), Expect = 5.0
Identities = 37/162 (22%), Positives = 64/162 (38%), Gaps = 30/162 (18%)
Query: 12 KSLKTSNRTLDFFTDWQKCLKNKNKISIALNHLNFLLGKDTKELKNCIKSLFKEY-PKAF 70
++LK TL F++ + C KN S++ + +T+ L C+ SL+KE +
Sbjct: 178 ENLKVVTYTLKQFSEDKFC---KNIYSLSYENKEL----ETRFLGACVSSLYKELLAQHH 230
Query: 71 NVLNILIAVRDKKDIVLDANGNFYPLYSYFEDGEKVYEFIRQTGLERIFCNRNIKDLNDF 130
N+ N + K + + ++ N ++ E N + DL +F
Sbjct: 231 NIENFKPCILFKSERIEESKKNQERFNAFLE-------------------NLSFLDLENF 271
Query: 131 VFGIEVGLDSNARKNRSGKVMENHLSGLFTNAQLNFKEQVEI 172
F A K+ + +NH L Q FKE V+I
Sbjct: 272 -FNHSRNAFFKAAKSFFDE--QNHTPNLVALLQNKFKESVQI 310
>ref|NP_224011.1| ATP-DEPENDENT PROTEASE LA [Helicobacter pylori J99]
Length = 831
Score = 23.9 bits (50), Expect = 5.0
Identities = 13/38 (34%), Positives = 19/38 (49%), Gaps = 2/38 (5%)
Query: 181 AFGDDIKKFDFVVCGKDKTYFIEANFYTIS--GSKLNE 216
A+ + K F+ C KDK EA +Y + GS + E
Sbjct: 39 AYAKNNKSLVFIACQKDKLNDNEAPYYDVGVIGSVMRE 76
>ref|NP_223433.1| putative [Helicobacter pylori J99]
Length = 227
Score = 23.9 bits (50), Expect = 5.0
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 3 NHLPFDIFLKSLKT 16
N LPFD+F+KS T
Sbjct: 10 NMLPFDVFIKSYPT 23
>ref|NP_223194.1| cag island protein [Helicobacter pylori J99]
Length = 1819
Score = 23.9 bits (50), Expect = 5.0
Identities = 14/29 (48%), Positives = 18/29 (61%), Gaps = 5/29 (17%)
Query: 247 DAKNKLQEAYKSVEIYNLSNVNDFISKAQ 275
+AK KL+EA KSV Y D +SKA+
Sbjct: 640 EAKKKLEEAKKSVRAY-----LDCVSKAK 663
>ref|NP_223140.1| OLIGOPEPTIDASE [Helicobacter pylori J99]
Length = 578
Score = 23.9 bits (50), Expect = 5.0
Identities = 20/63 (31%), Positives = 28/63 (43%), Gaps = 18/63 (28%)
Query: 10 FLKSLKTSNRTLDFFTDWQKCLKN----------------KNKISIALNHLNFLLGKDTK 53
FLK+L+T + +F +Q LKN KIS A+ + L K+TK
Sbjct: 21 FLKTLQTEVQ--EFENAYQNNLKNLDAAKFANTLKHYENLSEKISRAMAYAQLLFAKNTK 78
Query: 54 ELK 56
E K
Sbjct: 79 EAK 81
>ref|NP_222904.1| S-adenosylmethionine synthetase [Helicobacter pylori J99]
Length = 385
Score = 23.9 bits (50), Expect = 5.0
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 54 ELKNCIKSLFKEYPK 68
EL+ C+KS+FK PK
Sbjct: 325 ELEKCVKSVFKLTPK 339
>ref|NP_224089.1| putative ATP-DEPENDENT DNA HELICASE [Helicobacter pylori J99]
Length = 681
Score = 23.1 bits (48), Expect = 8.5
Identities = 23/89 (25%), Positives = 38/89 (41%), Gaps = 8/89 (8%)
Query: 148 GKVMENHLSGLFTNAQLNFKEQVEIREFEDLCQAFGD-DIKKFDFVVCGKDKTYFIEANF 206
GK+ + + L LN +E ++I F+D + +KKF ++ G+ + F
Sbjct: 403 GKITQEWIFSLLDEEGLNLEEALKIGAFKDKLNPKNEYALKKFTAMI-GRLREAF----- 456
Query: 207 YTISGSKLNEVARSYQDLALKFEAFPNYE 235
IS K E +L +E NYE
Sbjct: 457 -EISVEKFCERFLEETNLLKSYEKEDNYE 484
>ref|NP_224002.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 649
Score = 23.1 bits (48), Expect = 8.5
Identities = 15/51 (29%), Positives = 22/51 (42%)
Query: 7 FDIFLKSLKTSNRTLDFFTDWQKCLKNKNKISIALNHLNFLLGKDTKELKN 57
FD L K N +D D + +K+K+ + LN L K T+ N
Sbjct: 21 FDTSLLESKKYNEKVDLIFDLKSIVKDKDTKTNTLNFSVTLSSKGTQTKTN 71
>ref|NP_223811.1| putative Outer membrane protein [Helicobacter pylori J99]
Length = 471
Score = 23.1 bits (48), Expect = 8.5
Identities = 19/86 (22%), Positives = 37/86 (42%), Gaps = 13/86 (15%)
Query: 94 YPLYSYFEDGEKVYEFIRQTGLERIFCNRNIKDLNDFVFG-------------IEVGLDS 140
Y L+ Y++ VY I QT ++ K++ ++VF I+ G
Sbjct: 103 YNLFGYYDGFMGVYTNILQTDSLETQNMKHNKNVRNYVFSDAYLEYAYKNYFEIKAGRYL 162
Query: 141 NARKNRSGKVMENHLSGLFTNAQLNF 166
+ +SG+ +SG + +A+L +
Sbjct: 163 STMPYKSGQTQGFQVSGQYKHARLTW 188
>ref|NP_223203.1| cag island protein [Helicobacter pylori J99]
Length = 376
Score = 23.1 bits (48), Expect = 8.5
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 116 ERIFCNRNIKDLND-FVFGIEVGLDSNARKNRSGKVMENHLSGLFTNAQLNFKEQVEI 172
ER+ + I +N+ ++ G E SN KN V N L+ FTN +L+F ++ ++
Sbjct: 251 ERLAFSMAIDKINEKYLRGYEAF--SNLLKNVKDDVELNTLTKNFTNQKLSFAQKQKL 306
>ref|NP_223061.1| putative Outer membrane protein [Helicobacter pylori J99]
Length = 479
Score = 23.1 bits (48), Expect = 8.5
Identities = 24/93 (25%), Positives = 41/93 (43%), Gaps = 8/93 (8%)
Query: 119 FCNRNIKD----LNDFVFGIEVGLDSNARK-NRSGKVMENHLSGLFTNAQLNFKEQVEIR 173
F ++++KD L V G G+ ++ K N+ G V+ N++ + + L K +
Sbjct: 73 FLSKSLKDQGHVLEGKVGGTIGGIAYDSTKFNQGGSVIYNYIG--YWDGYLGGKRALLDG 130
Query: 174 EFEDLCQAFGDDIKKFDFVVCGKDKTYFIEANF 206
C A G D K D + CG + I N+
Sbjct: 131 TSIHEC-ALGSDGKVIDSIACGNARANKIRRNY 162
Database: NC_000921.faa
Posted date: Dec 10, 2001 4:36 PM
Number of letters in database: 494,079
Number of sequences in database: 1491
Lambda K H
0.322 0.140 0.416
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 327,078
Number of Sequences: 1491
Number of extensions: 16821
Number of successful extensions: 62
Number of sequences better than 10.0: 21
Number of HSP's better than 10.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 49
Number of HSP's gapped (non-prelim): 21
length of query: 277
length of database: 494,079
effective HSP length: 76
effective length of query: 201
effective length of database: 380,763
effective search space: 76533363
effective search space used: 76533363
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)