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|15646185|ref|NP_208369.1| LPS biosynthesis protein
[Helicobacter pylori 26695]
(372 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_223749.1| putative lipopolysaccharide biosynthesis p... 218 2e-58
ref|NP_223748.1| putative lipopolysaccharide biosynthesis p... 209 9e-56
ref|NP_224029.1| lipopolysaccharide biosynthesis protein [H... 96 2e-21
ref|NP_222915.1| putative lipopolysaccharide biosynthesis p... 82 2e-17
ref|NP_223538.1| putative lipopolysaccharide biosynthesis p... 79 2e-16
ref|NP_222868.1| putative lipopolysaccharide biosynthesis p... 75 2e-15
ref|NP_223466.1| putative [Helicobacter pylori J99] 27 0.65
ref|NP_223973.1| putative [Helicobacter pylori J99] 26 1.9
ref|NP_223733.1| RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BET... 24 5.5
ref|NP_224124.1| L-SERYL-TRNA(SER) SELENIUM TRANSFERASE [He... 24 7.2
ref|NP_223778.1| ATP synthase F1, subunit gamma [Helicobact... 24 7.2
ref|NP_223294.1| Hydrogenase, cytochrome subunit [Helicobac... 24 7.2
ref|NP_223123.1| putative [Helicobacter pylori J99] 23 9.4
ref|NP_223101.1| putative [Helicobacter pylori J99] 23 9.4
>ref|NP_223749.1| putative lipopolysaccharide biosynthesis protein [Helicobacter
pylori J99]
Length = 398
Score = 218 bits (555), Expect = 2e-58
Identities = 127/351 (36%), Positives = 186/351 (52%), Gaps = 32/351 (9%)
Query: 5 IPIAFAFDKNYLKTGAVALYSLLHA-HRAVEGVFFSIYIFYSGLNEDDLNRLQETIKPFK 63
IPIAFAFDKNYL +YSLL + +A + + ++++ GLNE+D +L + +PFK
Sbjct: 16 IPIAFAFDKNYLIPAGACIYSLLESIAKANKKIRYTLHALVVGLNEEDKTKLNQITEPFK 75
Query: 64 HFAALKCQDISATLDSLPTITDSAWVNRYSRMILVKYLLPSLFPQYSKMIWSDVDVVFCR 123
FA L+ +DI LD++P D + R+S+M+LVKY L LFP+YSKM+WSDVDV+FC
Sbjct: 76 EFAVLEVKDIEPFLDTIPNPFDEDFTKRFSKMVLVKYFLADLFPKYSKMVWSDVDVIFCN 135
Query: 124 AFADDFIALDTSESFHLSGVISLVSQSVTEGFWFCNLDYMRKHSFTQQVLEKFKIQVMRP 183
F+ DF+ + ++ + GV+ + + EGF FCNLDY RK +FT ++ E K +
Sbjct: 136 EFSADFLNIKENDENYFYGVLEVEKHHMMEGFLFCNLDYQRKKNFTLRMHELLKGNEAKG 195
Query: 184 YFKEPTLIHHLHAYIKELPLHYCVLPYYYQEELDDLRHKASLPIRFEIIHQDKPNEFIHR 243
E +K L + YCV PYYY + D N +++
Sbjct: 196 ---ELDFTKWCWPNMKALGIEYCVFPYYYTIK-------------------DFSNAYLNE 233
Query: 244 QQIPYEISQIQNILSNPIIMHYESDKDALGIYNGKPWEFPLGNQYHLWLEMLAHTPFWKD 303
Y+ I NP I+HY++ A+ KPW++P G + LWL LA TPF D
Sbjct: 234 N---YK-KTILEARENPTIIHYDAWWGAV-----KPWDYPFGLKADLWLNALAKTPFMSD 284
Query: 304 FTLEMQKKRIEYRDIAQKIHYFSQDKRLYEVSIRSIKVFASHYYNLVVKER 354
+T +M Y + HYFS K E+ ++ +F Y +V KER
Sbjct: 285 YTKKMHTNESFYTTKMAEQHYFSSVKSSKEIVFKAPYLFFKSYLFVVFKER 335
>ref|NP_223748.1| putative lipopolysaccharide biosynthesis protein [Helicobacter
pylori J99]
Length = 393
Score = 209 bits (532), Expect = 9e-56
Identities = 122/351 (34%), Positives = 185/351 (51%), Gaps = 39/351 (11%)
Query: 5 IPIAFAFDKNYLKTGAVALYSLLHA-HRAVEGVFFSIYIFYSGLNEDDLNRLQETIKPFK 63
IPIAFAFDKNYL +YSLL + +A + + ++++ GLNE+D +L + +PFK
Sbjct: 16 IPIAFAFDKNYLIPAGACIYSLLESIAKANKKIRYTLHALVVGLNEEDKTKLNQITEPFK 75
Query: 64 HFAALKCQDISATLDSLPTITDSAWVNRYSRMILVKYLLPSLFPQYSKMIWSDVDVVFCR 123
FA L+ +DI LD++P D + R+S+M+LVKY L LFP+YSKM+WSDVDV+FC
Sbjct: 76 EFAVLEVKDIEPFLDTIPNPFDEDFTKRFSKMVLVKYFLADLFPKYSKMVWSDVDVIFCN 135
Query: 124 AFADDFIALDTSESFHLSGVISLVSQSVTEGFWFCNLDYMRKHSFTQQVLEKFKIQVMRP 183
F+ DF+ + + + GV + EGF++CNL Y RK+ F +++LE + Q +
Sbjct: 136 EFSADFLNIKEDDENYFYGVYDKIYP--YEGFFYCNLTYQRKNQFCKKILEIIRAQKID- 192
Query: 184 YFKEPTLIHHLHAYIKELPLHYCVLPYYYQEELDDLRHKASLPIRFEIIHQDKPNEFIHR 243
KEP L + I L + YC+ P+YY + L+ A N H
Sbjct: 193 --KEPQLTEFCRSKIAPLKIEYCIFPHYYSLSEEHLKGVA--------------NAIYH- 235
Query: 244 QQIPYEISQIQNILSNPIIMHYESDKDALGIYNGKPWEFPLGNQYHLWLEMLAHTPFWKD 303
+ I+ L PI++ Y+S + KPW +P G + LWL LA TPF D
Sbjct: 236 -------NTIKQALREPIVIQYDSHP----YFQIKPWTYPFGLKADLWLNALAKTPFMSD 284
Query: 304 FTLEMQ-------KKRIEYRDIAQKIHYFSQDKRLYEVSIRSIKVFASHYY 347
++ + +K Y IA +YF K +++ ++K F HY+
Sbjct: 285 WSYLITGGGGIGGEKWHYYHGIAAYHYYFPLWKAEEQIAHDALKTFLKHYF 335
>ref|NP_224029.1| lipopolysaccharide biosynthesis protein [Helicobacter pylori J99]
Length = 367
Score = 95.5 bits (236), Expect = 2e-21
Identities = 79/263 (30%), Positives = 118/263 (44%), Gaps = 53/263 (20%)
Query: 5 IPIAFAFDKNYLKTGAVALYSLL-HAHRAVEGVFFS----------------IYIFYSGL 47
IPI +FDKNY V+LYSLL HA R + FS I+ G+
Sbjct: 11 IPIFMSFDKNYALGAGVSLYSLLSHASRHTSMIDFSPLNQSNKLLGANIVYKIHCLVKGV 70
Query: 48 NEDDLNRLQETIKPFKHFAALKCQDISATLDSLPTITDSAWVNRYSRM-ILVKYLLPSLF 106
+ N+L +TI+PFK FA+L+ DI++ S+ + + + RY + +L + LL SLF
Sbjct: 71 TLEQQNKLLKTIEPFKKFASLEFIDINSLDHSIESYLNESCSKRYGGLLVLCRLLLASLF 130
Query: 107 PQYSKMIWSDVDVVFCRAFADDFIALD----------------------------TSESF 138
P YSK+I DVD VF A + ALD T ++F
Sbjct: 131 PNYSKIISIDVDTVFLGDVASAYFALDNEPTKLLGMVRDTFSHLPFEAFCDFCERTCKNF 190
Query: 139 HL------SGVISLVSQSVTEGFWFCNLDYMRKHSFTQQVLEKFKIQVMRPYFKEPTLIH 192
+ + + Q GF NLD R++ F + LE K + ++ E LI+
Sbjct: 191 KIDLLRFSQNELKRIHQGFNMGFLVANLDLWRENGFEKIALEFLKTRGKDLFYPEQCLIN 250
Query: 193 HLH-AYIKELPLHYCVLPYYYQE 214
+ I ELP+HY +++E
Sbjct: 251 MVFLERILELPIHYNCYSDFFKE 273
>ref|NP_222915.1| putative lipopolysaccharide biosynthesis protein [Helicobacter
pylori J99]
Length = 394
Score = 82.0 bits (201), Expect = 2e-17
Identities = 73/270 (27%), Positives = 115/270 (42%), Gaps = 59/270 (21%)
Query: 1 MQHEIPIAFAFDKNYLKTGAVALYSLL-HAHRAVEGV--FFSIYIFYSGLNEDDLNRLQE 57
MQ IPI AFD NY V+LYS+L HA R E V F+ I+ L+ +++ +L+E
Sbjct: 1 MQEIIPIVVAFDNNYCIPAGVSLYSMLVHAKRERERVKLFYQIHCLVEDLSLENIAKLEE 60
Query: 58 TIKPFKHFAALKCQDIS------------------ATLDSLPTITDSAWVNRYSRMILVK 99
TI PF F++++ DI+ + L ++ R+S+MI+ +
Sbjct: 61 TIAPFSAFSSIEFLDITDKELEPRHNYYKLDPLIAGEIKKLYLKLNAFSQKRFSKMIMCR 120
Query: 100 YLLPSLFPQYSKMIWSDVDVVFCRAFAD-----------------DFIALDTSESFHLSG 142
+ SLFPQY KMI DVD +F ++ D IA+D + + L
Sbjct: 121 FFFASLFPQYDKMIMFDVDTLFVGDISESFFIPLGTHYFGAVREKDLIAMDRNSAKDLYE 180
Query: 143 VISLVSQSV--------------------TEGFWFCNLDYMRKHSFTQQVLEKFKIQVMR 182
+ + ++S+ GF NL RK + Q++E F ++ +
Sbjct: 181 LRQMHAKSIGIADAFPNLEETQILFDNYFNAGFLALNLKSWRKENLENQLIEFFLLKNEK 240
Query: 183 PYFK-EPTLIHHLHAYIKELPLHYCVLPYY 211
F + L I ELP Y P +
Sbjct: 241 LLFNDQDALCFVCRGRILELPYSYNAHPSF 270
>ref|NP_223538.1| putative lipopolysaccharide biosynthesis protein [Helicobacter
pylori J99]
Length = 373
Score = 79.0 bits (193), Expect = 2e-16
Identities = 52/144 (36%), Positives = 75/144 (51%), Gaps = 10/144 (6%)
Query: 5 IPIAFAFDKNYLKTGAVALYS-LLHAHRAVEGV--FFSIYIFYSGLNEDDLNRLQETIKP 61
IPI AFD NY V+LYS LL+A R +GV F+ I+ L+ ++ +L+ TI P
Sbjct: 17 IPIVVAFDNNYCIPAGVSLYSMLLNAKRERDGVKLFYQIHCLVDSLSAENAEKLKRTISP 76
Query: 62 FKHFAALKCQDISAT-------LDSLPTITDSAWVNRYSRMILVKYLLPSLFPQYSKMIW 114
F F+ ++ DIS + L + R+S+MIL + LL S+FPQY K+I
Sbjct: 77 FSAFSGIEFCDISKNGAYPFKLVSQLFLRLNPFAKKRFSKMILCRLLLASIFPQYEKIIM 136
Query: 115 SDVDVVFCRAFADDFIALDTSESF 138
DVD +F ++ F E F
Sbjct: 137 FDVDTLFVGDISEGFFTPMDGEYF 160
>ref|NP_222868.1| putative lipopolysaccharide biosynthesis protein [Helicobacter
pylori J99]
Length = 377
Score = 75.5 bits (184), Expect = 2e-15
Identities = 83/354 (23%), Positives = 150/354 (41%), Gaps = 48/354 (13%)
Query: 1 MQHEIPIAFAFDKNYLKTGAVALYSLLHAHRAV-------------EGVFFSIYIFYSGL 47
M IPI AFD +Y V+LYS+L ++ + +F+ I+ L
Sbjct: 1 MSITIPIVIAFDNHYAIPAGVSLYSMLACAKSENPKSQNPQLQSDNKKLFYKIHCLVDNL 60
Query: 48 NEDDLNRLQETIKPFKHFAALKCQDISA----TLDSLPTITDSAWV----------NRYS 93
+ ++ +L+ET+ PF FA++ DIS T P++ D R+S
Sbjct: 61 SLENQQKLKETLVPFSAFASVDFLDISTPNLYTTSVEPSVIDKIHEAFLQLNIYAKTRFS 120
Query: 94 RMILVKYLLPSLFPQYSKMIWSDVDVVFCRAFADD-FIALDTSESFHLSGVISLVSQSVT 152
+M++ + L SLFPQY K+I D D +F ++ FI LD S++ S
Sbjct: 121 KMVMCRLFLASLFPQYDKIIMFDADTLFLNDVSESFFIPLD---SYYFGAAKDFSSPKSL 177
Query: 153 EGFWF-CNLDYMRKHSFTQQVLEKFKIQVM-RPYFKEPTLIHHLHAYIKELPLHYCVLPY 210
+ F + +K S + L++ +Q++ ++ LI +L + +
Sbjct: 178 KHFQTEREREPRQKFSLYEHYLKEKDMQIICENHYNVGFLIVNLKLWRAD---------- 227
Query: 211 YYQEELDDLRHKASLPIRFEIIHQDKPNEFIHRQ--QIPYEISQIQNILSNPIIMHYESD 268
+E L +L H+ + QD +++ Q+PY + + + + + +
Sbjct: 228 KLEEHLLNLTHQKGQCVFCP--EQDLLTLACYQKVLQLPYIYNAHPFMANQKRFIPNQQE 285
Query: 269 KDALGIY-NGKPWEFPLGNQYHLWLEMLAHTPFWKDFTLEMQKKRIEYRDIAQK 321
L Y GKPW P W E+L TPF+ +++++ K+ E + K
Sbjct: 286 IIMLHFYFVGKPWILPTALYSKEWHEILLKTPFYAEYSVKFLKQMTECLSLQDK 339
>ref|NP_223466.1| putative [Helicobacter pylori J99]
Length = 336
Score = 27.3 bits (59), Expect = 0.65
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 39 SIYIFYSGLNEDDLNRLQETIKPFKHFAALKCQDISATLDSLPTITDSAWVNRYSRMILV 98
S ++F S D+L R ++ FK+ AL +DI L SL +D + +S LV
Sbjct: 207 SSWVFLSFDYGDELERKDMHLRAFKNHQALDFKDILNHLASLYQQSDLTYDVNFS---LV 263
Query: 99 KYLLPSLFPQYS 110
++L Q+S
Sbjct: 264 RFLFEKHHAQFS 275
>ref|NP_223973.1| putative [Helicobacter pylori J99]
Length = 253
Score = 25.8 bits (55), Expect = 1.9
Identities = 26/117 (22%), Positives = 54/117 (45%), Gaps = 18/117 (15%)
Query: 160 LDYMRKHSFTQQVLEKFKIQVMRPY--FKEPTLIHHLH-----AYIKELPLHYCVLPYYY 212
L+Y +KH F+Q + + ++ FK+ L++ ++ A+ K++ +H
Sbjct: 26 LNYAKKH-FSQCHMLSSSLLILNDTECFKKNYLLNWVYHALECAHEKDISMH-------- 76
Query: 213 QEELDDLRHKASLPIRFEIIHQDKPNEFIHRQQIPYEISQIQNILSNPIIMHYESDK 269
L+++ K+ LPIR +I+ Q+ E I + + + I +PI + K
Sbjct: 77 --SLEEILQKSHLPIRIKIMAQNTLLEKIEVKVLTFGAEYALFITKHPIAKRFLRQK 131
>ref|NP_223733.1| RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN [Helicobacter
pylori J99]
Length = 341
Score = 24.3 bits (51), Expect = 5.5
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 289 HLWLEMLAHTPFWKDFTLEMQKKRIEYRDIAQKIHY 324
HLW MLA+T F ++ ++ K+ +KI Y
Sbjct: 43 HLWKTMLANTWFAEEVSMNDDKRDYLKLSAEEKIGY 78
>ref|NP_224124.1| L-SERYL-TRNA(SER) SELENIUM TRANSFERASE [Helicobacter pylori J99]
Length = 390
Score = 23.9 bits (50), Expect = 7.2
Identities = 17/65 (26%), Positives = 26/65 (39%), Gaps = 4/65 (6%)
Query: 159 NLDYMRKHSFTQQVLEKFKIQVMRPYFKEPTLIHHLHAYIKELPLHYCVLPYYYQEELDD 218
N Y+R + K + P FK+ T L A KE + ++ YY ++D
Sbjct: 147 NRAYLRDYRLALNENSKMLFKTHNPTFKKDTSFKDLQALAKE----HGLIDYYNLGDVDL 202
Query: 219 LRHKA 223
L A
Sbjct: 203 LNRTA 207
>ref|NP_223778.1| ATP synthase F1, subunit gamma [Helicobacter pylori J99]
Length = 301
Score = 23.9 bits (50), Expect = 7.2
Identities = 11/23 (47%), Positives = 18/23 (77%), Gaps = 1/23 (4%)
Query: 218 DLRHKASLPIRFEIIHQD-KPNE 239
++R K LPI ++IIHQ+ +P+E
Sbjct: 190 EIRVKTILPIGYKIIHQNPQPSE 212
>ref|NP_223294.1| Hydrogenase, cytochrome subunit [Helicobacter pylori J99]
Length = 224
Score = 23.9 bits (50), Expect = 7.2
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 137 SFHLSGVISLVSQSVTEGF-WFCNLDYMRKHSFTQQVLEKFKIQVMRPYF 185
SFH+ L+S + + +F M + SF+Q + K I M+ YF
Sbjct: 62 SFHVMFGFLLISALIFRTYLFFTKESLMERRSFSQLLSPKAWIDQMKAYF 111
>ref|NP_223123.1| putative [Helicobacter pylori J99]
Length = 409
Score = 23.5 bits (49), Expect = 9.4
Identities = 10/22 (45%), Positives = 11/22 (49%), Gaps = 8/22 (36%)
Query: 204 HYCVLPY--------YYQEELD 217
HYC+ PY YY E LD
Sbjct: 156 HYCIAPYLPCYDTAIYYNEALD 177
>ref|NP_223101.1| putative [Helicobacter pylori J99]
Length = 347
Score = 23.5 bits (49), Expect = 9.4
Identities = 11/60 (18%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 302 KDFTLEMQKKRIEYRDIAQKIHYFSQDKRLYEVSIRSIKVFASHYYNLVVKER--WSKPI 359
KD +++ I +++A+ H++ D + + + F YY ++ + W +P+
Sbjct: 86 KDIQIQLLDHHISGKEVAESFHWYFLDTN--RCATKIVYEFLKKYYAILESKNTLWLEPL 143
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
0.326 0.140 0.436
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 401,102
Number of Sequences: 1491
Number of extensions: 18131
Number of successful extensions: 94
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 67
Number of HSP's gapped (non-prelim): 16
length of query: 372
length of database: 494,079
effective HSP length: 79
effective length of query: 293
effective length of database: 376,290
effective search space: 110252970
effective search space used: 110252970
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)