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|15645993|ref|NP_208174.1| restriction modification
system S subunit [Helicobacter pylori 26695]
(160 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_224140.1| putative TYPE I RESTRICTION ENZYME (SPECIF... 143 3e-36
ref|NP_223133.1| TYPE I RESTRICTION ENZYME (SPECIFICITY SUB... 60 4e-11
ref|NP_223444.1| putative TYPE I RESTRICTION ENZYME (SPECIF... 34 0.002
ref|NP_223711.1| PRIMOSOMAL PROTEIN N' (REPLICATION FACTOR ... 32 0.008
ref|NP_223503.1| TYPE I RESTRICTIONENZYME (SPECIFICITY SUBU... 30 0.031
ref|NP_223155.1| putative [Helicobacter pylori J99] 28 0.12
ref|NP_223657.1| putative [Helicobacter pylori J99] 25 0.78
ref|NP_223787.1| putative [Helicobacter pylori J99] 25 1.3
ref|NP_223824.1| putative transporter [Helicobacter pylori ... 24 2.3
ref|NP_223497.1| PANTOTHENATE METABOLISM FLAVOPROTEIN [Heli... 24 2.3
ref|NP_223195.1| cag island protein [Helicobacter pylori J99] 23 2.9
ref|NP_223622.1| putative cation efflux system protein [Hel... 22 6.6
ref|NP_222972.1| DIHYDROOROTASE [Helicobacter pylori J99] 22 8.6
>ref|NP_224140.1| putative TYPE I RESTRICTION ENZYME (SPECIFICITY SUBUNIT)
[Helicobacter pylori J99]
Length = 624
Score = 143 bits (360), Expect = 3e-36
Identities = 75/103 (72%), Positives = 84/103 (80%)
Query: 32 NNEFLYYLILTLKNKLLKLASGSTFLEVSPNKIKNLLIPLPPLNEQIAIANILSDLDRYL 91
NN F++ I + L A+GS ++ N IKNLLIPLPPLNEQIAIANILSD+DRYL
Sbjct: 126 NNLFIFKQIANYERVLKTFANGSATKTITKNVIKNLLIPLPPLNEQIAIANILSDVDRYL 185
Query: 92 YNLDALILKKESVKKALSFELLSQRKRLKGFNQAWQRVRLGDI 134
+LDALILKKESVKKALSFELLSQRKRLKGFNQ WQ+VRLGDI
Sbjct: 186 CSLDALILKKESVKKALSFELLSQRKRLKGFNQNWQKVRLGDI 228
Score = 104 bits (260), Expect = 1e-24
Identities = 60/106 (56%), Positives = 75/106 (70%), Gaps = 2/106 (1%)
Query: 31 INNEFLYYLILTL--KNKLLKLASGSTFLEVSPNKIKNLLIPLPPLNEQIAIANILSDLD 88
+++ FL YLI + + LA GST +S + N+ + LPPLNEQIAIANILSD+D
Sbjct: 327 VDSLFLSYLINSEIGRKAFENLAQGSTRYNLSKSGFNNVCLILPPLNEQIAIANILSDVD 386
Query: 89 RYLYNLDALILKKESVKKALSFELLSQRKRLKGFNQAWQRVRLGDI 134
+ +L + E+VKKALSFELLSQRKRLKGFNQ WQ+VRLGDI
Sbjct: 387 SEIISLKNKKRQFENVKKALSFELLSQRKRLKGFNQNWQKVRLGDI 432
Score = 63.2 bits (152), Expect = 3e-12
Identities = 39/91 (42%), Positives = 58/91 (62%), Gaps = 2/91 (2%)
Query: 31 INNEFLYYLILTL--KNKLLKLASGSTFLEVSPNKIKNLLIPLPPLNEQIAIANILSDLD 88
+++ FL YLI + + LA GST +S + N+ + LPPLNEQIAIANILSD+D
Sbjct: 531 VDSLFLSYLINSEIGRKAFENLAQGSTRYNLSKSGFNNVCLILPPLNEQIAIANILSDVD 590
Query: 89 RYLYNLDALILKKESVKKALSFELLSQRKRL 119
+ +L + E+VKKAL+ +L+S + R+
Sbjct: 591 SEIISLKNKKRQFENVKKALNHDLMSAKIRV 621
Score = 23.5 bits (49), Expect = 2.9
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 126 WQRVRLGDIANYL 138
WQ+VRLGDI L
Sbjct: 14 WQKVRLGDILELL 26
>ref|NP_223133.1| TYPE I RESTRICTION ENZYME (SPECIFICITY SUBUNIT) [Helicobacter
pylori J99]
Length = 409
Score = 59.7 bits (143), Expect = 4e-11
Identities = 35/86 (40%), Positives = 52/86 (59%), Gaps = 1/86 (1%)
Query: 9 LVILKEIATTNQGFQSLIPLEKINNEFLYYLILTLKNKLLKLASGSTFLEVSPNKIKNLL 68
+ I ++ TNQGF+S+IP +KI EFLYYL+ K+ + + G+TF EVS +
Sbjct: 85 VAIAEKRLCTNQGFKSIIPNKKIYFEFLYYLLKYYKDNISNIGGGTTFKEVSGATLGLFQ 144
Query: 69 IPLPP-LNEQIAIANILSDLDRYLYN 93
+ +PP EQ IA+ LS LD+ + N
Sbjct: 145 VKIPPTYYEQQKIAHTLSILDQKIEN 170
Score = 32.0 bits (71), Expect = 0.008
Identities = 26/108 (24%), Positives = 43/108 (39%), Gaps = 15/108 (13%)
Query: 2 FLASGVILVILKEIATTNQGFQSLIPLEKINNEFLYYLILTLKNKLLKLASGSTFLEVSP 61
F G V L +I+ NQ Q I Y +K L ST ++
Sbjct: 299 FGLQGAYNVALSKISVLNQSMQEYIRS--------YLNSKPIKKYLSNACMASTRASLNE 350
Query: 62 NKIKNLLIPLPPLNEQIAIANILSDLDRYLYNLDALILKKESVKKALS 109
N I +L++P+PP+ N+L ++ N+ I+K + L+
Sbjct: 351 NHIYSLMLPIPPI-------NLLQKYEKIAKNIITAIIKNNQSTQTLT 391
>ref|NP_223444.1| putative TYPE I RESTRICTION ENZYME (SPECIFICITY SUBUNIT)
[Helicobacter pylori J99]
Length = 454
Score = 34.3 bits (77), Expect = 0.002
Identities = 27/100 (27%), Positives = 46/100 (46%), Gaps = 11/100 (11%)
Query: 32 NNEFLYYLILT--LKNKLLKLASGSTFLEVSPNKIKNLLIPLPPLNEQIAIANILSDLDR 89
N +F+ Y T + + K +G+ + + N +K + IP+PPL Q I IL
Sbjct: 354 NPKFIIYYFQTYFFQKEKEKKITGTKVMRIHENDLKQITIPIPPLEIQQEIVTILDQFSA 413
Query: 90 YLYNLDALI-----LKKESV----KKALSFELLSQRKRLK 120
+L A I +K+ +K L+F+ L+ K +K
Sbjct: 414 LTTDLQAGIPAEIKARKKQYEYYREKLLTFKPLTLNKEVK 453
Score = 30.8 bits (68), Expect = 0.018
Identities = 18/55 (32%), Positives = 27/55 (48%), Gaps = 2/55 (3%)
Query: 32 NNEFLYYLI--LTLKNKLLKLASGSTFLEVSPNKIKNLLIPLPPLNEQIAIANIL 84
N FL + + + + K+A+G T VS + + IP+PPL Q I IL
Sbjct: 126 NPSFLKHFLRDYNFRKNISKVANGVTRFNVSKQLLLKITIPIPPLEIQQEIVTIL 180
>ref|NP_223711.1| PRIMOSOMAL PROTEIN N' (REPLICATION FACTOR Y) [Helicobacter pylori
J99]
Length = 619
Score = 32.0 bits (71), Expect = 0.008
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 3 LASGVILVILKEIATTNQGFQSLIPLEKINNEFLYYLILTLKNKLLKLASGSTFLEVSPN 62
L + L + E T F++ P+EKI + + Y ++L KN L + S FL+ +PN
Sbjct: 549 LEASQTLSLCLEKGVTLSNFKA--PIEKIASSYRYLILLRSKNPLSLIKSVHAFLKTAPN 606
>ref|NP_223503.1| TYPE I RESTRICTIONENZYME (SPECIFICITY SUBUNIT) [Helicobacter pylori
J99]
Length = 207
Score = 30.0 bits (66), Expect = 0.031
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 34 EFLYYLILTLKNKLLK-LASGSTFLEVSPNKIKNLLIPLPPLNEQIAIANILSDLDRYLY 92
+FLY+ + T + ++++ L + ++ I+ L IP+PPL Q I IL
Sbjct: 109 KFLYFYLKTNETQIMENLVFRGSIPALNKADIETLTIPIPPLEIQQEIVTILDQFSALTT 168
Query: 93 NLDALILKKESVKK 106
+L A I + +K
Sbjct: 169 DLQAGIPAEIKARK 182
>ref|NP_223155.1| putative [Helicobacter pylori J99]
Length = 314
Score = 28.1 bits (61), Expect = 0.12
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 16/88 (18%)
Query: 60 SPNKIKNLLIPLPPLNEQIAIANILSDLDRYLYNLDALILKKESVKKALSFELLSQRKRL 119
+P ++L +PL LNE+ A++ Y+L + + +S + ++ +L +Q
Sbjct: 58 NPQAREDLEVPL--LNEKEIPASVR-------YSLGGVAMDDKSKVRGMALKLENQ---- 104
Query: 120 KGFNQAWQRVRLGDIANYLMNPSKIARF 147
N +W V L N+ NP + A+F
Sbjct: 105 ---NASWTMVMLNTEINFAKNPEEFAQF 129
>ref|NP_223657.1| putative [Helicobacter pylori J99]
Length = 325
Score = 25.4 bits (54), Expect = 0.78
Identities = 14/48 (29%), Positives = 25/48 (51%), Gaps = 3/48 (6%)
Query: 71 LPPLNEQIAIANILSDLDRY---LYNLDALILKKESVKKALSFELLSQ 115
L P + + +LS++D +YN ILK ++ KK ++ L+Q
Sbjct: 184 LYPQADDVVCQKVLSNIDELNARIYNFPQSILKDDNDKKINYYDFLTQ 231
>ref|NP_223787.1| putative [Helicobacter pylori J99]
Length = 759
Score = 24.6 bits (52), Expect = 1.3
Identities = 40/178 (22%), Positives = 75/178 (41%), Gaps = 35/178 (19%)
Query: 3 LASGVILVILKEIATTNQGFQSLIPLEKINNEFLYYL----ILTLKNKLLKLASGSTFLE 58
++SG+ + LK++AT ++ S L+ IN F+Y T + L LA +
Sbjct: 16 VSSGISQISLKKVATFDENGASFENLKSIN--FIYGANGSGKTTTSSFLKNLAENGIEDK 73
Query: 59 VSPNKI---KNLLIPLPPLNEQIAIANILSDLDRYLY--------NLDALILKKES---- 103
+ +KI N + + N+Q + + + ++ NL+ + KKES
Sbjct: 74 FANSKIAWYNNESLKIEVYNKQFKEEQLRNSQVKGIFTLGKKTNENLEKIESKKESINKE 133
Query: 104 ----VKKALSFELLSQRKRL--KGF-NQAWQRVRLGDIANYLMNPSKIARFLGGCKKR 154
+K S ++L+Q+K K F + W+ + Y N + L G K++
Sbjct: 134 NEKKIKNEASLQVLTQKKEKEEKDFTDSCWKNL-------YKKNEEEFKEILEGFKRK 184
>ref|NP_223824.1| putative transporter [Helicobacter pylori J99]
Length = 443
Score = 23.9 bits (50), Expect = 2.3
Identities = 11/24 (45%), Positives = 15/24 (61%)
Query: 54 STFLEVSPNKIKNLLIPLPPLNEQ 77
S FL +P+K KN+ PL NE+
Sbjct: 376 SLFLLHNPSKQKNVYFPLDAYNEE 399
>ref|NP_223497.1| PANTOTHENATE METABOLISM FLAVOPROTEIN [Helicobacter pylori J99]
Length = 425
Score = 23.9 bits (50), Expect = 2.3
Identities = 17/46 (36%), Positives = 24/46 (51%), Gaps = 5/46 (10%)
Query: 86 DLDRYLYNLDA---LILKKESVK--KALSFELLSQRKRLKGFNQAW 126
+L R L+ A +++ K + K K LSFE LS K L N+ W
Sbjct: 34 ELVRLLFKSGASIQVVMSKGAQKFIKPLSFEALSHHKVLHDRNEKW 79
>ref|NP_223195.1| cag island protein [Helicobacter pylori J99]
Length = 522
Score = 23.5 bits (49), Expect = 2.9
Identities = 29/137 (21%), Positives = 55/137 (39%), Gaps = 22/137 (16%)
Query: 24 SLIPLEKINNEFLYYLILTLKNKLLKLASGSTFLEVSPNKIK-NLLIPLPPLNEQIAIAN 82
++I LEK +E + Y I T NK + S + + P +K NL+ E + A
Sbjct: 65 TVIQLEK--DETISY-ITTGFNKGWSIVPNSNHIFIQPKSVKSNLMFE----KEAVNFAL 117
Query: 83 ILSDLDRYLYNLDALI--------------LKKESVKKALSFELLSQRKRLKGFNQAWQR 128
+ D +L ++ L+KE K + + ++ + +A R
Sbjct: 118 MTRDYQEFLKTKKLIVDAPDPKELEEQKKALEKEKEAKEQAQKAQKDKREKRKEERAKNR 177
Query: 129 VRLGDIANYLMNPSKIA 145
L ++ N + NP ++
Sbjct: 178 ANLENLTNAMSNPQNLS 194
>ref|NP_223622.1| putative cation efflux system protein [Helicobacter pylori J99]
Length = 359
Score = 22.3 bits (46), Expect = 6.6
Identities = 22/100 (22%), Positives = 43/100 (43%), Gaps = 6/100 (6%)
Query: 8 ILVILKEIATTNQGFQSLIPLEKINN-----EFLYYLILTLKNKLLKLASGSTFLEVSPN 62
++ + KEI + F + I + ++ F ++ K + ++ +G EVS
Sbjct: 42 VIKLDKEIFSKGLPFNAYIDFDSKSSVVQSLSFDASVVAVYKREGEQVKAGDAICEVSSI 101
Query: 63 KIKNLLIPLPPLNEQIAIANILSDLDRYLYNLDALILKKE 102
+ NL L ++ IA ++ D LY +I K+E
Sbjct: 102 DLSNLYFELQNNQNKLKIAKDITKKDLELYRA-GVIPKRE 140
>ref|NP_222972.1| DIHYDROOROTASE [Helicobacter pylori J99]
Length = 378
Score = 21.9 bits (45), Expect = 8.6
Identities = 21/64 (32%), Positives = 33/64 (50%), Gaps = 9/64 (14%)
Query: 12 LKEIATT-NQGFQSLIP-----LEKINNEFLYY---LILTLKNKLLKLASGSTFLEVSPN 62
L +IAT N+G + LI LE I++ Y L+++L+N L SG+ E+ N
Sbjct: 100 LADIATLKNKGGEILIAPSDAFLELISHYAKSYNLPLLISLENSFEALNSGALAYELGQN 159
Query: 63 KIKN 66
+ N
Sbjct: 160 FVDN 163
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
0.323 0.140 0.388
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 164,492
Number of Sequences: 1491
Number of extensions: 7126
Number of successful extensions: 33
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 18
Number of HSP's gapped (non-prelim): 18
length of query: 160
length of database: 494,079
effective HSP length: 71
effective length of query: 89
effective length of database: 388,218
effective search space: 34551402
effective search space used: 34551402
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: 45 (21.9 bits)