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|15644820|ref|NP_206990.1| fumarate reductase,
iron-sulfur subunit (frdB) [Helicobacter pylori 26695]
(245 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|1QLA|B Chain B, Respiratory Complex Ii-Like Fumarate Re... 377 e-106
pdb|1KF6|B Chain B, E. Coli Quinol-Fumarate Reductase With ... 109 3e-25
pdb|1KQF|B Chain B, Formate Dehydrogenase N From E. Coli >g... 28 0.74
pdb|1FEH|A Chain A, Fe-Only Hydrogenase From Clostridium Pa... 28 1.3
pdb|2FDN| 2[4fe-4s] Ferredoxin From Clostridium Acidi-Uri... 27 1.7
pdb|1HLR|A Chain A, Structure Refinement Of The Aldehyde Ox... 27 2.2
pdb|1FCA| Ferredoxin 27 2.8
pdb|1BC6| 7-Fe Ferredoxin From Bacillus Schlegelii, Nmr, ... 26 3.7
pdb|1BQX|A Chain A, Artificial Fe8s8 Ferredoxin: The D13c V... 26 3.7
pdb|1H98|A Chain A, New Insights Into Thermostability Of Ba... 26 3.7
pdb|1ROE| Nmr Study Of 2fe-2s Ferredoxin Of Synechococcus... 26 3.7
pdb|1BD6| 7-Fe Ferredoxin From Bacillus Schlegelii, Nmr, ... 26 3.7
pdb|1AWD| Ferredoxin [2fe-2s] Oxidized Form From Chlorell... 26 4.8
pdb|1QOB|A Chain A, Ferredoxin Mutation D62k >gi|2914608|pd... 25 6.3
pdb|1CZP|A Chain A, Anabaena Pcc7119 [2fe-2s] Ferredoxin In... 25 6.3
pdb|1DOI| 2fe-2s Ferredoxin From Haloarcula Marismortui 25 6.3
pdb|1J7A|A Chain A, Structure Of The Anabaena Ferredoxin D6... 25 6.3
pdb|1QOF|A Chain A, Ferredoxin Mutation Q70k >gi|2914613|pd... 25 6.3
pdb|1E0Z|A Chain A, [2fe-2s]-Ferredoxin From Halobacterium ... 25 6.3
pdb|1J7B|A Chain A, Structure Of The Anabaena Ferredoxin Mu... 25 6.3
pdb|1QOG|A Chain A, Ferredoxin Mutation S47a >gi|2914615|pd... 25 6.3
pdb|1J7C|A Chain A, Structure Of The Anabaena Ferredoxin Mu... 25 6.3
pdb|1GAQ|B Chain B, Crystal Structure Of The Complex Betwee... 25 6.3
pdb|1H2A|S Chain S, Single Crystals Of Hydrogenase From Des... 25 8.2
pdb|1PFD| The Solution Structure Of High Plant Parsley [2... 25 8.2
pdb|1H2R|S Chain S, Three-Dimensional Structure Of Ni-Fe Hy... 25 8.2
>pdb|1QLA|B Chain B, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
pdb|1QLA|E Chain E, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
pdb|1QLB|B Chain B, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
pdb|1QLB|E Chain E, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
pdb|1E7P|B Chain B, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|E Chain E, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|H Chain H, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|K Chain K, Quinol:fumarate Reductase From Wolinella Succinogenes
Length = 239
Score = 377 bits (969), Expect = e-106
Identities = 167/236 (70%), Positives = 207/236 (86%)
Query: 6 RTIVVRVLKFDPQSAVSKPHFKEYQLKETPSMTLFIALNLIREHQDPDLSFDFVCRAGIC 65
R + +RV K+DPQSAVSKPHF+EY+++E PSMT+FI LN+IRE DPDL+FDFVCRAGIC
Sbjct: 3 RMLTIRVFKYDPQSAVSKPHFQEYKIEEAPSMTIFIVLNMIRETYDPDLNFDFVCRAGIC 62
Query: 66 GSCAMMVNGRPRLACKTLTSSFESGVITLMPMPSFTLIKDLSVNTGDWFLDMTKRVESWA 125
GSC MM+NGRP LAC+TLT FE GVITL+P+P+F LIKDLSV+TG+WF M++RVESW
Sbjct: 63 GSCGMMINGRPSLACRTLTKDFEDGVITLLPLPAFKLIKDLSVDTGNWFNGMSQRVESWI 122
Query: 126 HSKEEVDITRPEKRVEPDEAQEVFELDRCIECGCCIASCGTKLMRPNFIGAAGMNRAMRF 185
H+++E DI++ E+R+EP+ AQEVFELDRCIECGCCIA+CGTK+MR +F+GAAG+NR +RF
Sbjct: 123 HAQKEHDISKLEERIEPEVAQEVFELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRF 182
Query: 186 MIDSHDERNDDDFYELVGDDDGVFGCMSLIACHDTCPKELPLQSSIATLRNRMLKV 241
MID HDER D+D+YEL+GDDDGVFGCM+L+ACHD CPK LPLQS IA LR +M+ V
Sbjct: 183 MIDPHDERTDEDYYELIGDDDGVFGCMTLLACHDVCPKNLPLQSKIAYLRRKMVSV 238
>pdb|1KF6|B Chain B, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
Hqno
pdb|1KF6|N Chain N, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
Hqno
pdb|1L0V|B Chain B, Quinol-Fumarate Reductase With Menaquinol Molecules
pdb|1L0V|N Chain N, Quinol-Fumarate Reductase With Menaquinol Molecules
pdb|1KFY|B Chain B, Quinol-Fumarate Reductase With Quinol Inhibitor 2-[1-(4-
Chloro-Phenyl)-Ethyl]-4,6-Dinitro-Phenol
pdb|1KFY|N Chain N, Quinol-Fumarate Reductase With Quinol Inhibitor 2-[1-(4-
Chloro-Phenyl)-Ethyl]-4,6-Dinitro-Phenol
Length = 243
Score = 109 bits (272), Expect = 3e-25
Identities = 68/231 (29%), Positives = 113/231 (48%), Gaps = 15/231 (6%)
Query: 6 RTIVVRVLKFDPQSAVSKPHFKEYQLKETPSMTLFIALNLIREHQDPDLSFDFVCRAGIC 65
+ + + V++++P+ + PH Y++ + +L AL I+++ PDLS+ + CR IC
Sbjct: 4 KNLKIEVVRYNPEVDTA-PHSAFYEVPYDATTSLLDALGYIKDNLAPDLSYRWSCRMAIC 62
Query: 66 GSCAMMVNGRPRLACKTLTSSFESGVITLMPMPSFTLIKDLSVNTGDWFLDMTKRVESWA 125
GSC MMVN P+LACKT + G + + + +F + +DL V DMT +ES
Sbjct: 63 GSCGMMVNNVPKLACKTFLRDYTDG-MKVEALANFPIERDLVV-------DMTHFIESLE 114
Query: 126 HSKEEV-----DITRPEKRVEPDEAQEVFELDRCIECGCCIASCGTKLMRPNFIGAAGMN 180
K + + P + + + CI CG C A+C + P FIG A +
Sbjct: 115 AIKPYIIGNSRTADQGTNIQTPAQMAKYHQFSGCINCGLCYAACPQFGLNPEFIGPAAIT 174
Query: 181 RAMRFMIDSHDERNDDDFYELVGDDDGVFGCMSLIACHDTCPKELPLQSSI 231
A R+ DS D + +L +GV+ C + C + CPK + ++I
Sbjct: 175 LAHRYNEDSRDHGKKERMAQL-NSQNGVWSCTFVGYCSEVCPKHVDPAAAI 224
>pdb|1KQF|B Chain B, Formate Dehydrogenase N From E. Coli
pdb|1KQG|B Chain B, Formate Dehydrogenase N From E. Coli
Length = 294
Score = 28.5 bits (62), Expect = 0.74
Identities = 11/24 (45%), Positives = 14/24 (57%)
Query: 149 FELDRCIECGCCIASCGTKLMRPN 172
F+ + CI CG CIA C + R N
Sbjct: 128 FQSENCIGCGYCIAGCPFNIPRLN 151
>pdb|1FEH|A Chain A, Fe-Only Hydrogenase From Clostridium Pasteurianum
pdb|1C4A|A Chain A, Binding Of Exogenously Added Carbon Monoxide At The Active
Site Of The Fe-Only Hydrogenase (Cpi) From Clostridium
Pasteurianum
pdb|1C4C|A Chain A, Binding Of Exogenously Added Carbon Monoxide At The Active
Site Of The Fe-Only Hydrogenase (Cpi) From Clostridium
Pasteurianum
Length = 574
Score = 27.7 bits (60), Expect = 1.3
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 143 DEAQEVFELDR--CIECGCCIASCG--TKLMRPNFIGAAGMNRAMRFMIDSHDERNDDD 197
DE + +DR C+ CG C+ +CG T+ F +N+ + +I + DE+ DD
Sbjct: 134 DERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKF-----LNKNGKTIIGAEDEKCFDD 187
>pdb|2FDN| 2[4fe-4s] Ferredoxin From Clostridium Acidi-Urici
pdb|1FDN| Ferredoxin
Length = 55
Score = 27.3 bits (59), Expect = 1.7
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 136 PEKRVEPDEAQEVFELDRCIECGCCIASC 164
P + + + V + D CI+CG C C
Sbjct: 19 PVNAISSGDDRYVIDADTCIDCGACAGVC 47
>pdb|1HLR|A Chain A, Structure Refinement Of The Aldehyde Oxidoreductase From
Desulfovibrio Gigas At 1.28 A
Length = 907
Score = 26.9 bits (58), Expect = 2.2
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 60 CRAGICGSCAMMVNGRPRLACKT 82
C G CG+C+++++G+ AC T
Sbjct: 40 CEQGQCGACSVILDGKVVRACVT 62
>pdb|1FCA| Ferredoxin
Length = 55
Score = 26.6 bits (57), Expect = 2.8
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 136 PEKRVEPDEAQEVFELDRCIECGCCIASC 164
P + ++ V + D CI+CG C C
Sbjct: 19 PVDAISQGGSRYVIDADTCIDCGACAGVC 47
>pdb|1BC6| 7-Fe Ferredoxin From Bacillus Schlegelii, Nmr, 20 Structures
Length = 77
Score = 26.2 bits (56), Expect = 3.7
Identities = 11/29 (37%), Positives = 14/29 (47%)
Query: 136 PEKRVEPDEAQEVFELDRCIECGCCIASC 164
P + E Q + D CI+CG C A C
Sbjct: 21 PVDCIHEGEDQYYIDPDVCIDCGACEAVC 49
>pdb|1BQX|A Chain A, Artificial Fe8s8 Ferredoxin: The D13c Variant Of Bacillus
Schlegelii Fe7s8 Ferredoxin
pdb|1BWE|A Chain A, Artificial Fe8s8 Ferredoxin: The D13c Variant Of Bacillus
Schlegelii Fe7s8 Ferredoxin
Length = 77
Score = 26.2 bits (56), Expect = 3.7
Identities = 11/29 (37%), Positives = 14/29 (47%)
Query: 136 PEKRVEPDEAQEVFELDRCIECGCCIASC 164
P + E Q + D CI+CG C A C
Sbjct: 21 PVDCIHEGEDQYYIDPDVCIDCGACEAVC 49
>pdb|1H98|A Chain A, New Insights Into Thermostability Of Bacterial
Ferredoxins: High Resolution Crystal Structure Of The
Seven-Iron Ferredoxin From Thermus Thermophilus
Length = 78
Score = 26.2 bits (56), Expect = 3.7
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 152 DRCIECGCCIASCGTKLMRP 171
+ CI+CG C+ +C + P
Sbjct: 37 EECIDCGACVPACPVNAIYP 56
>pdb|1ROE| Nmr Study Of 2fe-2s Ferredoxin Of Synechococcus Elongatus
pdb|2CJN| Structure Of Ferredoxin, Nmr, Minimized Average Structure
pdb|2CJO| Structure Of Ferredoxin, Nmr, 10 Structures
Length = 97
Score = 26.2 bits (56), Expect = 3.7
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 46 IREHQDPDLSFDFVCRAGICGSCA 69
+ E Q DL F CRAG C +CA
Sbjct: 28 VAEEQGLDLPFS--CRAGACSTCA 49
>pdb|1BD6| 7-Fe Ferredoxin From Bacillus Schlegelii, Nmr, Minimized Average
Structure
Length = 77
Score = 26.2 bits (56), Expect = 3.7
Identities = 11/29 (37%), Positives = 14/29 (47%)
Query: 136 PEKRVEPDEAQEVFELDRCIECGCCIASC 164
P + E Q + D CI+CG C A C
Sbjct: 21 PVDCIHEGEDQYYIDPDVCIDCGACEAVC 49
>pdb|1AWD| Ferredoxin [2fe-2s] Oxidized Form From Chlorella Fusca
Length = 94
Score = 25.8 bits (55), Expect = 4.8
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 50 QDPDLSFDFVCRAGICGSCA 69
++ L + CRAG C SCA
Sbjct: 27 EEAGLDLPYSCRAGACSSCA 46
>pdb|1QOB|A Chain A, Ferredoxin Mutation D62k
pdb|1QOB|B Chain B, Ferredoxin Mutation D62k
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 12/22 (54%), Positives = 13/22 (58%), Gaps = 2/22 (9%)
Query: 48 EHQDPDLSFDFVCRAGICGSCA 69
E Q DL F CRAG C +CA
Sbjct: 31 EEQGYDLPFS--CRAGACSTCA 50
>pdb|1CZP|A Chain A, Anabaena Pcc7119 [2fe-2s] Ferredoxin In The Reduced And
Oxixized State At 1.17 A
pdb|1CZP|B Chain B, Anabaena Pcc7119 [2fe-2s] Ferredoxin In The Reduced And
Oxixized State At 1.17 A
pdb|1QT9|A Chain A, Oxidized [2fe-2s] Ferredoxin From Anabaena Pcc7119
pdb|1EWY|C Chain C, Anabaena Pcc7119 Ferredoxin:ferredoxin-Nadp+-Reductase
Complex
pdb|1FXA|A Chain A, [2Fe-2S] Ferredoxin
pdb|1FXA|B Chain B, [2Fe-2S] Ferredoxin
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 12/22 (54%), Positives = 13/22 (58%), Gaps = 2/22 (9%)
Query: 48 EHQDPDLSFDFVCRAGICGSCA 69
E Q DL F CRAG C +CA
Sbjct: 31 EEQGYDLPFS--CRAGACSTCA 50
>pdb|1DOI| 2fe-2s Ferredoxin From Haloarcula Marismortui
Length = 128
Score = 25.4 bits (54), Expect = 6.3
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 58 FVCRAGICGSCAMMV 72
F CRAG C +CA +V
Sbjct: 61 FSCRAGACANCAAIV 75
>pdb|1J7A|A Chain A, Structure Of The Anabaena Ferredoxin D68k Mutant
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 12/22 (54%), Positives = 13/22 (58%), Gaps = 2/22 (9%)
Query: 48 EHQDPDLSFDFVCRAGICGSCA 69
E Q DL F CRAG C +CA
Sbjct: 31 EEQGYDLPFS--CRAGACSTCA 50
>pdb|1QOF|A Chain A, Ferredoxin Mutation Q70k
pdb|1QOF|B Chain B, Ferredoxin Mutation Q70k
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 12/22 (54%), Positives = 13/22 (58%), Gaps = 2/22 (9%)
Query: 48 EHQDPDLSFDFVCRAGICGSCA 69
E Q DL F CRAG C +CA
Sbjct: 31 EEQGYDLPFS--CRAGACSTCA 50
>pdb|1E0Z|A Chain A, [2fe-2s]-Ferredoxin From Halobacterium Salinarum
pdb|1E10|A Chain A, [2fe-2s]-Ferredoxin From Halobacterium Salinarum
Length = 128
Score = 25.4 bits (54), Expect = 6.3
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 58 FVCRAGICGSCAMMV 72
F CRAG C +CA +V
Sbjct: 61 FSCRAGACANCASIV 75
>pdb|1J7B|A Chain A, Structure Of The Anabaena Ferredoxin Mutant E94k
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 12/22 (54%), Positives = 13/22 (58%), Gaps = 2/22 (9%)
Query: 48 EHQDPDLSFDFVCRAGICGSCA 69
E Q DL F CRAG C +CA
Sbjct: 31 EEQGYDLPFS--CRAGACSTCA 50
>pdb|1QOG|A Chain A, Ferredoxin Mutation S47a
pdb|1QOG|B Chain B, Ferredoxin Mutation S47a
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 12/22 (54%), Positives = 13/22 (58%), Gaps = 2/22 (9%)
Query: 48 EHQDPDLSFDFVCRAGICGSCA 69
E Q DL F CRAG C +CA
Sbjct: 31 EEQGYDLPFS--CRAGACATCA 50
>pdb|1J7C|A Chain A, Structure Of The Anabaena Ferredoxin Mutant E95k
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 12/22 (54%), Positives = 13/22 (58%), Gaps = 2/22 (9%)
Query: 48 EHQDPDLSFDFVCRAGICGSCA 69
E Q DL F CRAG C +CA
Sbjct: 31 EEQGYDLPFS--CRAGACSTCA 50
>pdb|1GAQ|B Chain B, Crystal Structure Of The Complex Between Ferredoxin And
Ferredoxin-Nadp+ Reductase
Length = 98
Score = 25.4 bits (54), Expect = 6.3
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 45 LIREHQDPDLSFDFVCRAGICGSCA 69
++ + ++ + + CRAG C SCA
Sbjct: 24 ILDQAEEDGIDLPYSCRAGSCSSCA 48
>pdb|1H2A|S Chain S, Single Crystals Of Hydrogenase From Desulfovibrio Vulgaris
Length = 317
Score = 25.0 bits (53), Expect = 8.2
Identities = 11/32 (34%), Positives = 17/32 (52%)
Query: 155 IECGCCIASCGTKLMRPNFIGAAGMNRAMRFM 186
I G C G + +PN GA G+N A++ +
Sbjct: 159 IAYGTCATFGGVQAAKPNPTGAKGVNDALKHL 190
>pdb|1PFD| The Solution Structure Of High Plant Parsley [2fe-2s]
Ferredoxin, Nmr, 18 Structures
Length = 96
Score = 25.0 bits (53), Expect = 8.2
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 45 LIREHQDPDLSFDFVCRAGICGSCA 69
++ + ++ + + CRAG C SCA
Sbjct: 24 VLDQAEEEGIDIPYSCRAGSCSSCA 48
>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 = 25.0 bits (53), Expect = 8.2
Identities = 11/32 (34%), Positives = 17/32 (52%)
Query: 155 IECGCCIASCGTKLMRPNFIGAAGMNRAMRFM 186
I G C G + +PN GA G+N A++ +
Sbjct: 109 IAYGTCATFGGVQAAKPNPTGAKGVNDALKHL 140
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
0.323 0.137 0.422
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,410,306
Number of Sequences: 13198
Number of extensions: 55306
Number of successful extensions: 148
Number of sequences better than 10.0: 26
Number of HSP's better than 10.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 124
Number of HSP's gapped (non-prelim): 29
length of query: 245
length of database: 2,899,336
effective HSP length: 86
effective length of query: 159
effective length of database: 1,764,308
effective search space: 280524972
effective search space used: 280524972
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)