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|15646080|ref|NP_208262.1| type IIS restriction enzyme
R protein (BCGIB) [Helicobacter pylori 26695]
(397 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_224082.1| putative TYPE II RESTRICTION ENZYME [Helic... 517 e-148
ref|NP_223066.1| putative [Helicobacter pylori J99] 28 0.41
ref|NP_223575.1| putative Outer membrane protein [Helicobac... 26 1.6
ref|NP_223497.1| PANTOTHENATE METABOLISM FLAVOPROTEIN [Heli... 26 1.6
ref|NP_223147.1| putative Outer membrane protein [Helicobac... 26 1.6
ref|NP_222794.1| PEPTIDE CHAIN RELEASE FACTOR 1 [Helicobact... 26 2.0
ref|NP_223289.1| putative [Helicobacter pylori J99] 25 4.5
ref|NP_223764.1| FLAGELLAR HOOK-ASSOCIATED PROTEIN 1 (HAP1)... 24 5.9
ref|NP_223671.1| putative [Helicobacter pylori J99] 24 5.9
ref|NP_223203.1| cag island protein [Helicobacter pylori J99] 24 5.9
ref|NP_224140.1| putative TYPE I RESTRICTION ENZYME (SPECIF... 24 7.8
ref|NP_223641.1| putative [Helicobacter pylori J99] 24 7.8
>ref|NP_224082.1| putative TYPE II RESTRICTION ENZYME [Helicobacter pylori J99]
Length = 406
Score = 517 bits (1332), Expect = e-148
Identities = 284/391 (72%), Positives = 306/391 (77%), Gaps = 24/391 (6%)
Query: 15 IHDTQIENSYPYVVRAA-TNNGIKGFIIDDPTFANKKNTLSFAQDTF-TVFYQKQPY--F 70
I I + +V+ A +NNG+ G D + +T++ D F FY+ Y
Sbjct: 32 IQKRHINHKGEFVITAGLSNNGVLGQS-DIKAKVFESHTITI--DMFGCAFYRSFAYKMV 88
Query: 71 TGNKVKILKPKFAFKSPKILHSISAILQFIL----KPLTWGLGSTTESIAEFKFSLPLKP 126
T +V LKPKF +I H I L + K + + I K LPLKP
Sbjct: 89 THARVFSLKPKF-----EINHKIGLFLSTLFFGYHKKFGYENMCSWAKIKNDKVILPLKP 143
Query: 127 TANAQTLEDIDFDFMEKFIAELEQCRLAELEQCRLAELQAYLKATGLENTTLSNDEENAL 186
TAN QTLE IDFDFMEKFIAELEQCRLAEL QAYLKATGLENTTLSNDEENAL
Sbjct: 144 TANTQTLEGIDFDFMEKFIAELEQCRLAEL--------QAYLKATGLENTTLSNDEENAL 195
Query: 187 NVFNNSGGGGGNTPCGLTWQSFRLGDLFEIEKTLSFNKDALTQGEDYDYITRTSQNQGVL 246
NVFNNSGGGGGNTPCGLTWQ F+LGDLFEIEKTLSFNKDALTQG+DYDYITRTSQNQGVL
Sbjct: 196 NVFNNSGGGGGNTPCGLTWQHFKLGDLFEIEKTLSFNKDALTQGQDYDYITRTSQNQGVL 255
Query: 247 QTTGFVNAENLNPPFTWSLGLLQMDFFYRKKSWYAGQFMRKITPKTEIENKIDLRIANYF 306
QTTGFVNAENLNPPFTWSLGLLQMDFFYRKKSWYAGQFMRKITPKTEI+NKI+ RIA+YF
Sbjct: 256 QTTGFVNAENLNPPFTWSLGLLQMDFFYRKKSWYAGQFMRKITPKTEIKNKINSRIAHYF 315
Query: 307 TTLLNALKRPLLSVLVRDIDKTFREQKIQLPLKPTAKTQTLDGIDFDFMHTLINALMKQT 366
TTLLNALKRPLLSVLVRDIDKTFREQKIQLPLKPTAKTQ+LDGIDFDFMHTLINALMKQT
Sbjct: 316 TTLLNALKRPLLSVLVRDIDKTFREQKIQLPLKPTAKTQSLDGIDFDFMHTLINALMKQT 375
Query: 367 IQGVAQYCDAKIQATKEVISQEAPVQKDSLF 397
IQGV QYCDAKIQATKEVISQE P+QKDSLF
Sbjct: 376 IQGVVQYCDAKIQATKEVISQETPIQKDSLF 406
Score = 55.1 bits (131), Expect = 3e-09
Identities = 53/176 (30%), Positives = 73/176 (41%), Gaps = 10/176 (5%)
Query: 203 LTWQSFRLGDLFEIEK-TLSFNKDALTQGEDYDYITRTSQNQGVLQTTGFVNAENLNPPF 261
+ W F+LGDLFE K + ++ IT N GVL + +
Sbjct: 12 IKWGEFKLGDLFEASNGDFDIQKRHINHKGEF-VITAGLSNNGVLGQSDIKAKVFESHTI 70
Query: 262 TWSL-GLLQMDFFYRKKSWYAGQFMRKITPKTEIENKIDLRIANYFTTLLNALKRPLLSV 320
T + G F K +A F K PK EI +KI L ++ F +
Sbjct: 71 TIDMFGCAFYRSFAYKMVTHARVFSLK--PKFEINHKIGLFLSTLFFGYHKKFGYENMCS 128
Query: 321 LVRDIDKTFREQKIQLPLKPTAKTQTLDGIDFDFMHTLINALMKQTIQGVAQYCDA 376
+ + K+ LPLKPTA TQTL+GIDFDFM I L + + + Y A
Sbjct: 129 WAK-----IKNDKVILPLKPTANTQTLEGIDFDFMEKFIAELEQCRLAELQAYLKA 179
>ref|NP_223066.1| putative [Helicobacter pylori J99]
Length = 167
Score = 28.1 bits (61), Expect = 0.41
Identities = 20/59 (33%), Positives = 32/59 (53%), Gaps = 9/59 (15%)
Query: 139 DFMEKFIAELEQCRLAE----LEQCRLAELQAYLKATGLENTTLSNDEENALNVFNNSG 193
+F++ F LE + E ++ R L AYL+A GLEN T +N ++VF++ G
Sbjct: 67 EFLKCFEGYLECIKSKEHYKPIKNIRKNMLYAYLEALGLENLTKTN-----IDVFDSKG 120
>ref|NP_223575.1| putative Outer membrane protein [Helicobacter pylori J99]
Length = 366
Score = 26.2 bits (56), Expect = 1.6
Identities = 11/32 (34%), Positives = 17/32 (52%)
Query: 3 SSKKIYHANTIKIHDTQIENSYPYVVRAATNN 34
+ KIY N +K T + N++ Y+ A NN
Sbjct: 57 AQNKIYKLNQVKNEITNMPNTFNYINNALKNN 88
>ref|NP_223497.1| PANTOTHENATE METABOLISM FLAVOPROTEIN [Helicobacter pylori J99]
Length = 425
Score = 26.2 bits (56), Expect = 1.6
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 16/81 (19%)
Query: 69 YFTGNKVKILKPKFAFKSPKILHSISA----------------ILQFILKPLTWGLGSTT 112
YF G KV ++ F PK + S+ + + LKPL + L + +
Sbjct: 241 YFKGAKVTLIASNFPTPLPKEIASVLVSDTASYENALNEAAKNLQKHALKPLLFNLAAIS 300
Query: 113 ESIAEFKFSLPLKPTANAQTL 133
+ + + F+ LK + +TL
Sbjct: 301 DYLPKTSFNHKLKKSELGETL 321
>ref|NP_223147.1| putative Outer membrane protein [Helicobacter pylori J99]
Length = 371
Score = 26.2 bits (56), Expect = 1.6
Identities = 11/32 (34%), Positives = 17/32 (52%)
Query: 3 SSKKIYHANTIKIHDTQIENSYPYVVRAATNN 34
+ KIY N +K T + N++ Y+ A NN
Sbjct: 62 AQNKIYKLNQVKNEITNMPNTFNYINNALKNN 93
>ref|NP_222794.1| PEPTIDE CHAIN RELEASE FACTOR 1 [Helicobacter pylori J99]
Length = 352
Score = 25.8 bits (55), Expect = 2.0
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 148 LEQCRLAEL--EQCRLAELQAYLKATGLENTTLSNDEENALNVFNNSGGGGGNTPCGLTW 205
LE L+EL E+ ++ E+Q T ++ + D + N++ G G G+
Sbjct: 68 LEDKELSELAKEELKILEIQKSELETAIKQLLIPKDPNDDKNIYLELRAGTGGDEAGIF- 126
Query: 206 QSFRLGDLFE 215
+GDLF+
Sbjct: 127 ----VGDLFK 132
>ref|NP_223289.1| putative [Helicobacter pylori J99]
Length = 352
Score = 24.6 bits (52), Expect = 4.5
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 179 SNDEENALNVFNNSGGGGGNTPCGLTWQSFRLGDLF--EIEKTLSFNKDALTQGED 232
SND+ENAL ++ + GG C F G + K +S+ K + G D
Sbjct: 153 SNDKENALQLYAVACQGGDMLACNNLGWMFANGSGVPKDYYKAMSYYKFSCENGND 208
>ref|NP_223764.1| FLAGELLAR HOOK-ASSOCIATED PROTEIN 1 (HAP1) [Helicobacter pylori
J99]
Length = 606
Score = 24.3 bits (51), Expect = 5.9
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 9 HANTIKIHDTQIENSYPYVVRAATNNGIKGFIIDDPTFANKKNTLSFAQD--TFTVFYQK 66
+ANT D EN + A+ NN K F+I P A++ +S + F +
Sbjct: 404 NANTDDNQDNNTENDFDDYFTASFNNETKKFVI-QPKNASQGLFVSMKDNGTNFMGALKL 462
Query: 67 QPYFTGN 73
P+F G+
Sbjct: 463 NPFFQGD 469
>ref|NP_223671.1| putative [Helicobacter pylori J99]
Length = 146
Score = 24.3 bits (51), Expect = 5.9
Identities = 12/29 (41%), Positives = 18/29 (61%)
Query: 160 RLAELQAYLKATGLENTTLSNDEENALNV 188
R AE+Q + A +++ T+ DEE AL V
Sbjct: 79 RGAEVQQSVFALKIDHDTIGTDEEGALKV 107
>ref|NP_223203.1| cag island protein [Helicobacter pylori J99]
Length = 376
Score = 24.3 bits (51), Expect = 5.9
Identities = 15/58 (25%), Positives = 23/58 (38%)
Query: 296 NKIDLRIANYFTTLLNALKRPLLSVLVRDIDKTFREQKIQLPLKPTAKTQTLDGIDFD 353
+KI+ + + N LK V + + K F QK+ K LD +FD
Sbjct: 260 DKINEKYLRGYEAFSNLLKNVKDDVELNTLTKNFTNQKLSFAQKQKLCLLVLDSFNFD 317
>ref|NP_224140.1| putative TYPE I RESTRICTION ENZYME (SPECIFICITY SUBUNIT)
[Helicobacter pylori J99]
Length = 624
Score = 23.9 bits (50), Expect = 7.8
Identities = 28/113 (24%), Positives = 41/113 (35%), Gaps = 25/113 (22%)
Query: 205 WQSFRLGDLFEIEKTLSFN------KDALTQGEDYDYITRTSQNQGVLQTTGFVNAENLN 258
WQ RLGD+ E+ N K+ +T ++ D+ +++TT F N + N
Sbjct: 14 WQKVRLGDILELLTDYHANGSYEILKNNVTLLKNVDFAI-------MIRTTNFENNDFKN 66
Query: 259 PPFTWSLGLLQMDFFYRKKSWYAGQFMRKITPKTEIENKIDLRIANYFTTLLN 311
D Y K Y K+ + NKI YF LN
Sbjct: 67 ------------DLIYIDKKAYEFLSKSKVFAGDILVNKIANAGTAYFMPKLN 107
>ref|NP_223641.1| putative [Helicobacter pylori J99]
Length = 268
Score = 23.9 bits (50), Expect = 7.8
Identities = 13/40 (32%), Positives = 20/40 (49%)
Query: 79 KPKFAFKSPKILHSISAILQFILKPLTWGLGSTTESIAEF 118
KP +F S +L S S+ F + L+ G+G E + F
Sbjct: 171 KPSVSFGSFSLLSSSSSFSSFEVSFLSRGIGLDCEKLKSF 210
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
0.319 0.135 0.390
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 416,329
Number of Sequences: 1491
Number of extensions: 19758
Number of successful extensions: 58
Number of sequences better than 10.0: 12
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 46
Number of HSP's gapped (non-prelim): 13
length of query: 397
length of database: 494,079
effective HSP length: 80
effective length of query: 317
effective length of database: 374,799
effective search space: 118811283
effective search space used: 118811283
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)