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|15645255|ref|NP_207425.1| quinone-reactive Ni/Fe
hydrogenase, small subunit (hydA) [Helicobacter pylori 26695]
(384 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1H2A|S Chain S, Single Crystals Of Hydrogenase From Des... 293 3e-80
pdb|1FRF|S Chain S, Crystal Structure Of The Ni-Fe Hydrogen... 274 1e-74
pdb|1H2R|S Chain S, Three-Dimensional Structure Of Ni-Fe Hy... 271 9e-74
pdb|1E3D|A Chain A, [nife] Hydrogenase From Desulfovibrio D... 262 5e-71
pdb|1FRV|A Chain A, Crystal Structure Of The Oxidized Form ... 261 9e-71
pdb|2FRV|A Chain A, Crystal Structure Of The Oxidized Form ... 260 2e-70
pdb|1CC1|S Chain S, Crystal Structure Of A Reduced, Active ... 169 6e-43
pdb|1ZPD|A Chain A, Pyruvate Decarboxylase From Zymomonas M... 29 0.78
pdb|1KK7|A Chain A, Scallop Myosin In The Near Rigor Confor... 26 8.6
pdb|1L2O|A Chain A, Scallop Myosin S1-Adp-P-Pdm In The Acti... 26 8.6
pdb|1WDC|A Chain A, Scallop Myosin Regulatory Domain 26 8.6
pdb|1DFL|A Chain A, Scallop Myosin S1 Complexed With Mgadp:... 26 8.6
pdb|1DFK|A Chain A, Nucleotide-Free Scallop Myosin S1-Near ... 26 8.6
>pdb|1H2A|S Chain S, Single Crystals Of Hydrogenase From Desulfovibrio Vulgaris
Length = 317
Score = 293 bits (749), Expect = 3e-80
Identities = 140/308 (45%), Positives = 202/308 (65%), Gaps = 6/308 (1%)
Query: 29 KNLQDEFKGAGISRRDLLKWAGMMSTALALPASFAPLTLKAVEVANRLPVIWLHMAECTG 88
+ +++ G+SRRD LK+ ++ + + +FAP +A+ R V++LH AECTG
Sbjct: 10 EGVEERLAERGVSRRDFLKFCTAIAVTMGMGPAFAPEVARALMGPRRPSVVYLHNAECTG 69
Query: 89 CSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLHDAIEKHKNNYILMVEGGI 148
CSES+LR+ +P ID++I D ++L+YHETIM A+G AE +L A+ + +I +VEGGI
Sbjct: 70 CSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNS-PHGFIAVVEGGI 128
Query: 149 PQGTEYFLTQGPNAETGAEECRKAAQYAAAIFAIGTCSSFGGVQAAYPNPSNAQPLH--- 205
P + N T + C + A A+ A GTC++FGGVQAA PNP+ A+ ++
Sbjct: 129 PTAANGIYGKVAN-HTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDAL 187
Query: 206 KIIDKPVINVPGCPPSEKNIVGNVLYYLMFGALPKLDAYNRPSWAYGNRIHDLCERRGHF 265
K + IN+ GCPP+ N+VG ++YYL A P+LD+ NRP+ +G +H+ C R HF
Sbjct: 188 KHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHF 247
Query: 266 DAGEFVEHFGDENAKRGFCLYKMGCKGPYTFNNCSKLRFNSHTSWPIGAGHGCIGCSEPN 325
DAGEF F E A++G+CLY++GCKGP T NNC K++FN T+WP+ AGH CIGCSEP+
Sbjct: 248 DAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFN-QTNWPVDAGHPCIGCSEPD 306
Query: 326 FWDTMSPF 333
FWD M+PF
Sbjct: 307 FWDAMTPF 314
>pdb|1FRF|S Chain S, Crystal Structure Of The Ni-Fe Hydrogenase From
Desulfovibrio Fructosovorans
Length = 264
Score = 274 bits (700), Expect = 1e-74
Identities = 135/265 (50%), Positives = 179/265 (66%), Gaps = 10/265 (3%)
Query: 74 NRLPVIWLHMAECTGCSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLHDAI 133
+R V+WLH AECTGC+E+ +R+ P ID++I D I+L+Y ETIM A+G +E +LH+A+
Sbjct: 5 HRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGETSEAALHEAL 64
Query: 134 EKHKNNYILMVEGGIP--QGTEYFLTQG-PNAETGAEECRKAAQYAAAIFAIGTCSSFGG 190
E K+ Y L+VEGG+P G ++ + G P ET C+KAA A I IGTCS +GG
Sbjct: 65 EG-KDGYYLVVEGGLPTIDGGQWGMVAGHPMIET----CKKAAAKAKGIICIGTCSPYGG 119
Query: 191 VQAAYPNPSNAQPLHKIIDKPVINVPGCPPSEKNIVGNVLYYLMFGALPKLDAYNRPSWA 250
VQ A PNPS A+ + + + IN+PGCPP+ N VG V++ L G +P LD RP
Sbjct: 120 VQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKG-IPDLDENGRPKLF 178
Query: 251 YGNRIHDLCERRGHFDAGEFVEHFGDENAKRGFCLYKMGCKGPYTFNNCSKLRFNSHTSW 310
YG +HD C R HF+A EF F E AK+GFCLY++GCKGP T+NNC K+ FN +W
Sbjct: 179 YGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFN-QVNW 237
Query: 311 PIGAGHGCIGCSEPNFWDTMSPFEE 335
P+ AGH C+GCSEP+FWDTM+PF E
Sbjct: 238 PVQAGHPCLGCSEPDFWDTMTPFYE 262
>pdb|1H2R|S Chain S, Three-Dimensional Structure Of Ni-Fe Hydrogenase From
Desulfivibrio Vulgaris Miyazaki F In The Reduced Form At
1.4 A Resolution
Length = 267
Score = 271 bits (693), Expect = 9e-74
Identities = 129/262 (49%), Positives = 178/262 (67%), Gaps = 6/262 (2%)
Query: 75 RLPVIWLHMAECTGCSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLHDAIE 134
R V++LH AECTGCSES+LR+ +P ID++I D ++L+YHETIM A+G AE +L A+
Sbjct: 6 RPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVN 65
Query: 135 KHKNNYILMVEGGIPQGTEYFLTQGPNAETGAEECRKAAQYAAAIFAIGTCSSFGGVQAA 194
+ +I +VEGGIP + N T + C + A A+ A GTC++FGGVQAA
Sbjct: 66 S-PHGFIAVVEGGIPTAANGIYGKVAN-HTMLDICSRILPKAQAVIAYGTCATFGGVQAA 123
Query: 195 YPNPSNAQPLH---KIIDKPVINVPGCPPSEKNIVGNVLYYLMFGALPKLDAYNRPSWAY 251
PNP+ A+ ++ K + IN+ GCPP+ N+VG ++YYL A P+LD+ NRP+ +
Sbjct: 124 KPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFF 183
Query: 252 GNRIHDLCERRGHFDAGEFVEHFGDENAKRGFCLYKMGCKGPYTFNNCSKLRFNSHTSWP 311
G +H+ C R HFDAGEF F E A++G+CLY++GCKGP T NNC K++FN T+WP
Sbjct: 184 GQTVHEQCPRLPHFDAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFN-QTNWP 242
Query: 312 IGAGHGCIGCSEPNFWDTMSPF 333
+ AGH CIGCSEP+FWD M+PF
Sbjct: 243 VDAGHPCIGCSEPDFWDAMTPF 264
>pdb|1E3D|A Chain A, [nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc
27774
pdb|1E3D|C Chain C, [nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc
27774
Length = 266
Score = 262 bits (669), Expect = 5e-71
Identities = 131/265 (49%), Positives = 177/265 (66%), Gaps = 11/265 (4%)
Query: 74 NRLPVIWLHMAECTGCSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLHDAI 133
+R V++LH AECTGCSE+LLR+ P ID++I D I+L+YHETIM A+G AE++L A+
Sbjct: 5 SRPSVVYLHAAECTGCSEALLRTYQPFIDTLILDTISLDYHETIMAAAGEAAEEALQAAV 64
Query: 134 EKHKNNYILMVEGGIPQGTE--YFLTQGPNAETGAEECRKAAQYAAAIFAIGTCSSFGGV 191
+ +I +VEG IP G + Y G T + C+ A A+ +IGTC+ +GG+
Sbjct: 65 NG-PDGFICLVEGAIPTGMDNKYGYIAG---HTMYDICKNILPKAKAVVSIGTCACYGGI 120
Query: 192 QAAYPNPSNAQPLHKI---IDKPVINVPGCPPSEKNIVGNVLYYLMFGALPKLDAYNRPS 248
QAA PNP+ A+ ++ + INVPGCPP+ N+VG ++ +L G +LD RP
Sbjct: 121 QAAKPNPTAAKGINDCYADLGVKAINVPGCPPNPLNMVGTLVAFLK-GQKIELDEVGRPV 179
Query: 249 WAYGNRIHDLCERRGHFDAGEFVEHFGDENAKRGFCLYKMGCKGPYTFNNCSKLRFNSHT 308
+G +HDLCERR HFDAGEF F E A++G+CLY +GCKGP T+NNC K+ FN T
Sbjct: 180 MFFGQSVHDLCERRKHFDAGEFAPSFNSEEARKGWCLYDVGCKGPETYNNCPKVLFN-ET 238
Query: 309 SWPIGAGHGCIGCSEPNFWDTMSPF 333
+WP+ AGH CIGCSEPNFWD M+PF
Sbjct: 239 NWPVAAGHPCIGCSEPNFWDDMTPF 263
>pdb|1FRV|A Chain A, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|1FRV|C Chain C, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
Length = 264
Score = 261 bits (667), Expect = 9e-71
Identities = 125/262 (47%), Positives = 172/262 (64%), Gaps = 9/262 (3%)
Query: 75 RLPVIWLHMAECTGCSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLHDAIE 134
R V++LH AECTGCSESLLR+ DP +D +I D I+++YHET+M +G E++LH+AI
Sbjct: 6 RPSVVYLHNAECTGCSESLLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAI- 64
Query: 135 KHKNNYILMVEGGIPQGTEYFLTQGPNAETGAEECRKAAQYAAAIFAIGTCSSFGGVQAA 194
K +++ ++EGGIP G + + + C + A A A+ AIGTC+++GGVQAA
Sbjct: 65 --KGDFVCVIEGGIPMGDGGYWGK-VGRRNMYDICAEVAPKAKAVIAIGTCATYGGVQAA 121
Query: 195 YPNPSNAQPLHKIIDK---PVINVPGCPPSEKNIVGNVLYYLMFGALPKLDAYNRPSWAY 251
PNP+ +++ + K IN+ GCPP+ N VG V++ L G +P+LD RP +
Sbjct: 122 KPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKG-MPELDKQGRPVMFF 180
Query: 252 GNRIHDLCERRGHFDAGEFVEHFGDENAKRGFCLYKMGCKGPYTFNNCSKLRFNSHTSWP 311
G +HD C R HF+AGEF FG AK+G+CLY++GCKGP T+NNC K FN +WP
Sbjct: 181 GETVHDNCPRLKHFEAGEFATSFGSPEAKKGYCLYELGCKGPDTYNNCPKQLFN-QVNWP 239
Query: 312 IGAGHGCIGCSEPNFWDTMSPF 333
+ AGH CI CSEPNFWD SPF
Sbjct: 240 VQAGHPCIACSEPNFWDLYSPF 261
>pdb|2FRV|A Chain A, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|C Chain C, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|E Chain E, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|G Chain G, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|I Chain I, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|S Chain S, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
Length = 264
Score = 260 bits (665), Expect = 2e-70
Identities = 124/262 (47%), Positives = 172/262 (65%), Gaps = 9/262 (3%)
Query: 75 RLPVIWLHMAECTGCSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLHDAIE 134
R V++LH AECTGCSES+LR+ DP +D +I D I+++YHET+M +G E++LH+AI
Sbjct: 6 RPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAI- 64
Query: 135 KHKNNYILMVEGGIPQGTEYFLTQGPNAETGAEECRKAAQYAAAIFAIGTCSSFGGVQAA 194
K +++ ++EGGIP G + + + C + A A A+ AIGTC+++GGVQAA
Sbjct: 65 --KGDFVCVIEGGIPMGDGGYWGK-VGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAA 121
Query: 195 YPNPSNAQPLHKIIDK---PVINVPGCPPSEKNIVGNVLYYLMFGALPKLDAYNRPSWAY 251
PNP+ +++ + K IN+ GCPP+ N VG V++ L G +P+LD RP +
Sbjct: 122 KPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKG-MPELDKQGRPVMFF 180
Query: 252 GNRIHDLCERRGHFDAGEFVEHFGDENAKRGFCLYKMGCKGPYTFNNCSKLRFNSHTSWP 311
G +HD C R HF+AGEF FG AK+G+CLY++GCKGP T+NNC K FN +WP
Sbjct: 181 GETVHDNCPRLKHFEAGEFATSFGSPEAKKGYCLYELGCKGPDTYNNCPKQLFN-QVNWP 239
Query: 312 IGAGHGCIGCSEPNFWDTMSPF 333
+ AGH CI CSEPNFWD SPF
Sbjct: 240 VQAGHPCIACSEPNFWDLYSPF 261
>pdb|1CC1|S Chain S, Crystal Structure Of A Reduced, Active Form Of The
Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum
Length = 283
Score = 169 bits (427), Expect = 6e-43
Identities = 103/283 (36%), Positives = 148/283 (51%), Gaps = 26/283 (9%)
Query: 71 EVANRLPVIWLHMAECTGCSESLLRSADPTIDSIIFDYINLEYHETIMVASGFQAEKSLH 130
E A + PVIW+ CTGCS SLL + P I I+ D I+LE+H T+M + G A ++
Sbjct: 3 EGAKKAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMY 62
Query: 131 DAIEKHKNNYILMVEGGIPQGTE-YFLTQGPNAETGA--------EECRKAAQYAAAIFA 181
+ EK N+ L+VEG IP E + G + A E R A + A A
Sbjct: 63 EIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKAHHHEVTMMELIRDLAPKSLATVA 122
Query: 182 IGTCSSFGGVQAAYPNPSNAQPLHKI-----IDKPVINVPGCPPSEKNIVGNVLYYLMF- 235
+GTCS++GG+ AA N + ++ + I+K ++NVPGCPP +VG ++
Sbjct: 123 VGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHV 182
Query: 236 -----GALPKLDAYNRPSWAYGNRIHDLCERRGHFDAGEFVEHFGDENAKRGFCLYKMGC 290
LP+LD RP +G+ IH+ C +D EF E F K G C ++GC
Sbjct: 183 LNPTEHPLPELDDDGRPLLFFGDNIHENCPYLDKYDNSEFAETF----TKPG-CKAELGC 237
Query: 291 KGPYTFNNCSKLRFNSHTSWPIGAGHGCIGCSEPNFWDTMSPF 333
KGP T+ +C+K R+N+ +W + CIGC EP+F D SPF
Sbjct: 238 KGPSTYADCAKRRWNNGINWCV-ENAVCIGCVEPDFPDGKSPF 279
>pdb|1ZPD|A Chain A, Pyruvate Decarboxylase From Zymomonas Mobilis
pdb|1ZPD|B Chain B, Pyruvate Decarboxylase From Zymomonas Mobilis
pdb|1ZPD|E Chain E, Pyruvate Decarboxylase From Zymomonas Mobilis
pdb|1ZPD|F Chain F, Pyruvate Decarboxylase From Zymomonas Mobilis
Length = 568
Score = 29.3 bits (64), Expect = 0.78
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 11/64 (17%)
Query: 171 KAAQYAAAIFAIGTCSSFGGVQAAYPNPSNAQPLHKIIDKPVINVPGCPPSEKNIVGNVL 230
K A A +++G S+F + AY + PVI + G P + + G+VL
Sbjct: 64 KGAAAAVVTYSVGALSAFDAIGGAYAE-----------NLPVILISGAPNNNDHAAGHVL 112
Query: 231 YYLM 234
++ +
Sbjct: 113 HHAL 116
>pdb|1KK7|A Chain A, Scallop Myosin In The Near Rigor Conformation
pdb|1KK8|A Chain A, Scallop Myosin (S1-Adp-Befx) In The Actin-Detached
Conformation
Length = 837
Score = 25.8 bits (55), Expect = 8.6
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 13 EERLD-IVRSFNAH-------NEHKNLQDEFKGAGISRRDLLKW 48
+ERL I+ F AH +K LQD+ G + +R++ KW
Sbjct: 775 DERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKW 818
>pdb|1L2O|A Chain A, Scallop Myosin S1-Adp-P-Pdm In The Actin-Detached
Conformation
pdb|1B7T|A Chain A, Myosin Digested By Papain
Length = 835
Score = 25.8 bits (55), Expect = 8.6
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 13 EERLD-IVRSFNAH-------NEHKNLQDEFKGAGISRRDLLKW 48
+ERL I+ F AH +K LQD+ G + +R++ KW
Sbjct: 775 DERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKW 818
>pdb|1WDC|A Chain A, Scallop Myosin Regulatory Domain
Length = 64
Score = 25.8 bits (55), Expect = 8.6
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 13 EERLD-IVRSFNAH-------NEHKNLQDEFKGAGISRRDLLKW 48
+ERL I+ F AH +K LQD+ G + +R++ KW
Sbjct: 2 DERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKW 45
>pdb|1DFL|A Chain A, Scallop Myosin S1 Complexed With Mgadp:vanadate-Transition
State
pdb|1DFL|B Chain B, Scallop Myosin S1 Complexed With Mgadp:vanadate-Transition
State
Length = 831
Score = 25.8 bits (55), Expect = 8.6
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 13 EERLD-IVRSFNAH-------NEHKNLQDEFKGAGISRRDLLKW 48
+ERL I+ F AH +K LQD+ G + +R++ KW
Sbjct: 771 DERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKW 814
>pdb|1DFK|A Chain A, Nucleotide-Free Scallop Myosin S1-Near Rigor State
Length = 830
Score = 25.8 bits (55), Expect = 8.6
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 13 EERLD-IVRSFNAH-------NEHKNLQDEFKGAGISRRDLLKW 48
+ERL I+ F AH +K LQD+ G + +R++ KW
Sbjct: 770 DERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKW 813
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.319 0.136 0.420
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,368,118
Number of Sequences: 13198
Number of extensions: 99822
Number of successful extensions: 269
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 229
Number of HSP's gapped (non-prelim): 13
length of query: 384
length of database: 2,899,336
effective HSP length: 90
effective length of query: 294
effective length of database: 1,711,516
effective search space: 503185704
effective search space used: 503185704
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: 55 (25.8 bits)