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|15646147|ref|NP_208331.1| ubiquinol cytochrome c
oxidoreductase, Rieske 2Fe-2S subunit (fbcF) [Helicobacter pylori
26695]
(167 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|1KB9|E Chain E, Yeast Cytochrome Bc1 Complex >gi|142777... 64 9e-12
pdb|1BCC|E Chain E, Cytochrome Bc1 Complex From Chicken >gi... 64 1e-11
pdb|1BE3|E Chain E, Cytochrome Bc1 Complex From Bovine >gi|... 64 1e-11
pdb|1RIE| Structure Of A Water Soluble Fragment Of The Ri... 62 3e-11
pdb|1RFS| Rieske Soluble Fragment From Spinach 49 2e-07
pdb|1G8K|B Chain B, Crystal Structure Analysis Of Arsenite ... 39 4e-04
pdb|1G8J|D Chain D, Crystal Structure Analysis Of Arsenite ... 39 4e-04
pdb|1EG9|A Chain A, Naphthalene 1,2-Dioxygenase With Indole... 27 0.93
pdb|1C8B|A Chain A, Crystal Structure Of A Novel Germinatio... 27 1.6
pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agal... 26 2.1
pdb|1OPG|H Chain H, Opg2 Fab Fragment >gi|4930277|pdb|1BM3|... 26 2.1
pdb|1TFA|A Chain A, Ovotransferrin, N-Terminal Lobe, Apo Fo... 26 2.7
pdb|1IEJ|A Chain A, Ovotransferrin, N-Terminal Lobe, Holo F... 26 2.7
pdb|1NNT| Ovotransferrin (Monoferric N-Terminal Half-Mole... 25 3.5
pdb|1AY0|A Chain A, Identification Of Catalytically Importa... 25 3.5
pdb|1AIV| Apo Ovotransferrin >gi|1127086|pdb|1OVT| Mol_i... 25 3.5
pdb|2CGR|H Chain H, Igg2b (Kappa) Fab Fragment Complexed Wi... 25 3.5
pdb|1HRU|A Chain A, The Structure Of The Yrdc Gene Product ... 25 4.6
>pdb|1KB9|E Chain E, Yeast Cytochrome Bc1 Complex
pdb|1EZV|E Chain E, Structure Of The Yeast Cytochrome Bc1 Complex Co-
Crystallized With An Antibody Fv-Fragment
pdb|1KYO|E Chain E, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
pdb|1KYO|P Chain P, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
Length = 185
Score = 63.9 bits (154), Expect = 9e-12
Identities = 40/159 (25%), Positives = 77/159 (48%), Gaps = 14/159 (8%)
Query: 9 FLGMSLASVTAIGAIASLVAMKKTWDPLPSVVSAGFTTIDVANMQEGQFSTVEWRGKPVY 68
F+ ++ +++ GA +++ + V++ +++A + G+ V+W+GKPV+
Sbjct: 28 FMVGAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVF 87
Query: 69 ILKRSKKE-------GFNEKRD-----FKVGESVFTTAIQICTHLGCIPTYQ-DEEKGFL 115
I R+ E + +D +V + + + ICTHLGC+P + + G+
Sbjct: 88 IRHRTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWF 147
Query: 116 CPCHGGRFTSDGVNIAGTPPPRPFDIPPFKIEGTKITFG 154
CPCHG + G I P P +IP ++ +G K+ G
Sbjct: 148 CPCHGSHYDISG-RIRKGPAPLNLEIPAYEFDGDKVIVG 185
>pdb|1BCC|E Chain E, Cytochrome Bc1 Complex From Chicken
pdb|2BCC|E Chain E, Stigmatellin-Bound Cytochrome Bc1 Complex From Chicken
pdb|3BCC|E Chain E, Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex
From Chicken
Length = 196
Score = 63.5 bits (153), Expect = 1e-11
Identities = 40/142 (28%), Positives = 70/142 (49%), Gaps = 27/142 (19%)
Query: 17 VTAIGAIASLVAMKKTWDPLPSVVSAGFTTIDVANMQEGQFSTVEWRGKPVYILKRSKKE 76
V+++ A A ++AM K I ++++ EG+ +WRGKP+++ R+KKE
Sbjct: 59 VSSMSASADVLAMSKI-------------EIKLSDIPEGKNMAFKWRGKPLFVRHRTKKE 105
Query: 77 -------GFNEKRD-----FKVGESVFTTAIQICTHLGCIP-TYQDEEKGFLCPCHGGRF 123
++ RD +V + + I +CTHLGC+P + G+ CPCHG +
Sbjct: 106 IDQEAAVEVSQLRDPQHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHY 165
Query: 124 TSDGVNIAGTPPPRPFDIPPFK 145
+ G I P P ++P ++
Sbjct: 166 DASG-RIRKGPAPLNLEVPSYE 186
>pdb|1BE3|E Chain E, Cytochrome Bc1 Complex From Bovine
pdb|1BGY|Q Chain Q, Cytochrome Bc1 Complex From Bovine
pdb|1BGY|E Chain E, Cytochrome Bc1 Complex From Bovine
pdb|1QCR|E Chain E, Crystal Structure Of Bovine Mitochondrial Cytochrome Bc1
Complex, Alpha Carbon Atoms Only
Length = 196
Score = 63.5 bits (153), Expect = 1e-11
Identities = 40/142 (28%), Positives = 70/142 (49%), Gaps = 27/142 (19%)
Query: 17 VTAIGAIASLVAMKKTWDPLPSVVSAGFTTIDVANMQEGQFSTVEWRGKPVYILKRSKKE 76
V+++ A A ++AM K I ++++ EG+ +WRGKP+++ R+KKE
Sbjct: 59 VSSMSASADVLAMSKI-------------EIKLSDIPEGKNMAFKWRGKPLFVRHRTKKE 105
Query: 77 -------GFNEKRD-----FKVGESVFTTAIQICTHLGCIP-TYQDEEKGFLCPCHGGRF 123
++ RD +V + + I +CTHLGC+P + G+ CPCHG +
Sbjct: 106 IDQEAAVEVSQLRDPQHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHY 165
Query: 124 TSDGVNIAGTPPPRPFDIPPFK 145
+ G I P P ++P ++
Sbjct: 166 DASG-RIRKGPAPLNLEVPSYE 186
>pdb|1RIE| Structure Of A Water Soluble Fragment Of The Rieske Iron-Sulfur
Protein Of The Bovine Heart Mitochondrial Cytochrome
Bc1-Complex
Length = 129
Score = 62.4 bits (150), Expect = 3e-11
Identities = 34/112 (30%), Positives = 59/112 (52%), Gaps = 14/112 (12%)
Query: 47 IDVANMQEGQFSTVEWRGKPVYILKRSKKE-------GFNEKRD-----FKVGESVFTTA 94
I ++++ EG+ +WRGKP+++ R+KKE ++ RD +V + +
Sbjct: 9 IKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKKPEWVIL 68
Query: 95 IQICTHLGCIP-TYQDEEKGFLCPCHGGRFTSDGVNIAGTPPPRPFDIPPFK 145
I +CTHLGC+P + G+ CPCHG + + G I P P ++P ++
Sbjct: 69 IGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASG-RIRKGPAPLNLEVPSYE 119
>pdb|1RFS| Rieske Soluble Fragment From Spinach
Length = 139
Score = 49.3 bits (116), Expect = 2e-07
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 72 RSKKEGFNEKRDFKVGESVFTTAI----QICTHLGCIPTYQDEEKGFLCPCHGGRFTSDG 127
R+ +G + V ES T A +CTHLGC+ + E F+CPCHG ++ + G
Sbjct: 37 RTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAENKFICPCHGSQYNNQG 96
Query: 128 VNIAGTPPPRPFDIPPFKIEGTKITF 153
+ G P P + ++ K+ F
Sbjct: 97 RVVRG-PAPLSLALAHCDVDDGKVVF 121
>pdb|1G8K|B Chain B, Crystal Structure Analysis Of Arsenite Oxidase From
Alcaligenes Faecalis
pdb|1G8K|D Chain D, Crystal Structure Analysis Of Arsenite Oxidase From
Alcaligenes Faecalis
pdb|1G8K|F Chain F, Crystal Structure Analysis Of Arsenite Oxidase From
Alcaligenes Faecalis
pdb|1G8K|H Chain H, Crystal Structure Analysis Of Arsenite Oxidase From
Alcaligenes Faecalis
Length = 133
Score = 38.5 bits (88), Expect = 4e-04
Identities = 13/30 (43%), Positives = 18/30 (59%)
Query: 97 ICTHLGCIPTYQDEEKGFLCPCHGGRFTSD 126
+CTH+GC +Y K F CPCH F ++
Sbjct: 59 LCTHMGCPTSYDSSSKTFSCPCHFTEFDAE 88
>pdb|1G8J|D Chain D, Crystal Structure Analysis Of Arsenite Oxidase From
Alcaligenes Faecalis
pdb|1G8J|B Chain B, Crystal Structure Analysis Of Arsenite Oxidase From
Alcaligenes Faecalis
Length = 133
Score = 38.5 bits (88), Expect = 4e-04
Identities = 13/30 (43%), Positives = 18/30 (59%)
Query: 97 ICTHLGCIPTYQDEEKGFLCPCHGGRFTSD 126
+CTH+GC +Y K F CPCH F ++
Sbjct: 59 LCTHMGCPTSYDSSSKTFSCPCHFTEFDAE 88
>pdb|1EG9|A Chain A, Naphthalene 1,2-Dioxygenase With Indole Bound In The
Active Site.
pdb|1NDO|A Chain A, Napthalene 1,2-Dioxygenase
pdb|1NDO|C Chain C, Napthalene 1,2-Dioxygenase
pdb|1NDO|E Chain E, Napthalene 1,2-Dioxygenase
Length = 449
Score = 27.3 bits (59), Expect = 0.93
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 75 KEGFNEKRDFKVGESVFTTAIQICTHLG--CIPTYQDEEKGFLCPCHGGRFTSDG 127
K G +E + + + +C H G + KGF+C HG F S+G
Sbjct: 58 KMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNG 112
>pdb|1C8B|A Chain A, Crystal Structure Of A Novel Germination Protease From
Spores Of Bacillus Megaterium: Structural Rearrangements
And Zymogen Activation
pdb|1C8B|B Chain B, Crystal Structure Of A Novel Germination Protease From
Spores Of Bacillus Megaterium: Structural Rearrangements
And Zymogen Activation
Length = 371
Score = 26.6 bits (57), Expect = 1.6
Identities = 27/78 (34%), Positives = 36/78 (45%), Gaps = 4/78 (5%)
Query: 36 LPSVVSAGFTTIDVANMQEGQFST-VEWRGKPVYILKRSKKEGFNEKRDFKVGESVFTTA 94
+P+VV A T D + F ++ +GKP L S F EK+ K+ E
Sbjct: 242 IPTVVDAVSITSDTIDFILKHFGREMKEQGKPSKSLLPSGMT-FGEKK--KLTEDDLPNE 298
Query: 95 IQICTHLGCIPTYQDEEK 112
Q T+LG I T DEEK
Sbjct: 299 EQRQTYLGMIGTLPDEEK 316
>pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Hexasaccharide Unit Of Hyaluronan
pdb|1I8Q|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Enzyme Product, Unsaturated
Disaccharide Hyaluronan
pdb|1F1S|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase At 2.1 Angstrom Resolution
Length = 814
Score = 26.2 bits (56), Expect = 2.1
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 9 FLGMSLASVTAIGAIASLVAMKKTWDPLPSVVSAGFTTIDVANMQEGQFSTVEWRGKPVY 68
FLG ++ + IG +++ + +K P TID+ QF+ K V+
Sbjct: 604 FLGSNIKNTNGIGNVSTTIDQRKDDSKTPYTTYVNGKTIDLKQASSQQFTDT----KSVF 659
Query: 69 ILKRSKKEGFN 79
+ SK+ G N
Sbjct: 660 L--ESKEPGRN 668
>pdb|1OPG|H Chain H, Opg2 Fab Fragment
pdb|1BM3|H Chain H, Immunoglobulin Opg2 Fab-Peptide Complex
Length = 227
Score = 26.2 bits (56), Expect = 2.1
Identities = 16/51 (31%), Positives = 24/51 (46%), Gaps = 3/51 (5%)
Query: 93 TAIQICTHLGCIPTYQDEEKGFLCPCHGGRFTSDGVNIAGTPPPRPFDIPP 143
TA+ CT P Y+ + + H G+ TS V+ A T PP + + P
Sbjct: 91 TALYYCTRH---PFYRYDGGNYYAMDHWGQGTSVTVSAAKTTPPSVYPLAP 138
>pdb|1TFA|A Chain A, Ovotransferrin, N-Terminal Lobe, Apo Form
pdb|1NFT|A Chain A, Ovotransferrin, N-Terminal Lobe, Iron Loaded Open Form
Length = 329
Score = 25.8 bits (55), Expect = 2.7
Identities = 21/88 (23%), Positives = 33/88 (36%), Gaps = 9/88 (10%)
Query: 79 NEKRDFKVGESVFTTAIQICTHLGCIPTYQDEEKGFLCPCHGGRFTSDGVNIAGTPPPRP 138
N RD E + T +Q T+L CI + E + GG+ G+ P
Sbjct: 18 NNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAI-SLDGGQVFEAGL--------AP 68
Query: 139 FDIPPFKIEGTKITFGEAGAEYKKMMAK 166
+ + P E + T G + Y + K
Sbjct: 69 YKLKPIAAEVYEHTEGSTTSYYAVAVVK 96
>pdb|1IEJ|A Chain A, Ovotransferrin, N-Terminal Lobe, Holo Form, At 1.65 A
Resolution
Length = 332
Score = 25.8 bits (55), Expect = 2.7
Identities = 21/88 (23%), Positives = 33/88 (36%), Gaps = 9/88 (10%)
Query: 79 NEKRDFKVGESVFTTAIQICTHLGCIPTYQDEEKGFLCPCHGGRFTSDGVNIAGTPPPRP 138
N RD E + T +Q T+L CI + E + GG+ G+ P
Sbjct: 21 NNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAI-TLDGGQVFEAGL--------AP 71
Query: 139 FDIPPFKIEGTKITFGEAGAEYKKMMAK 166
+ + P E + T G + Y + K
Sbjct: 72 YKLKPIAAEVYEHTEGSTTSYYAVAVVK 99
>pdb|1NNT| Ovotransferrin (Monoferric N-Terminal Half-Molecule)
Length = 328
Score = 25.4 bits (54), Expect = 3.5
Identities = 21/88 (23%), Positives = 33/88 (36%), Gaps = 9/88 (10%)
Query: 79 NEKRDFKVGESVFTTAIQICTHLGCIPTYQDEEKGFLCPCHGGRFTSDGVNIAGTPPPRP 138
N RD E + T +Q T+L CI + E + GG+ G+ P
Sbjct: 17 NNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAI-SLDGGQAFEAGL--------AP 67
Query: 139 FDIPPFKIEGTKITFGEAGAEYKKMMAK 166
+ + P E + T G + Y + K
Sbjct: 68 YKLKPIAAEVYEHTEGSTTSYYAVAVVK 95
>pdb|1AY0|A Chain A, Identification Of Catalytically Important Residues In
Yeast Transketolase
pdb|1AY0|B Chain B, Identification Of Catalytically Important Residues In
Yeast Transketolase
Length = 680
Score = 25.4 bits (54), Expect = 3.5
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 1/72 (1%)
Query: 20 IGAIASLVAMKKTWDPLPSVVSAGFTTIDVANMQEGQFSTVEWRGKPVYILKRSKKEGFN 79
+ IA +A K P+++ TTI ++ G S K + + K GFN
Sbjct: 224 LAGIAKAIAQAKLSKDKPTLIKMT-TTIGYGSLHAGSHSVAGAPLKADDVKQLKSKFGFN 282
Query: 80 EKRDFKVGESVF 91
+ F V + V+
Sbjct: 283 PDKSFVVPQEVY 294
>pdb|1AIV| Apo Ovotransferrin
pdb|1OVT| Mol_id: 1; Molecule: Ovotransferrin; Chain: Null; Synonym:
Conalbumin; Heterogen: Iron (Fe); Heterogen: Bicarbonate
(Co3); Other_details: Diferric Form
Length = 686
Score = 25.4 bits (54), Expect = 3.5
Identities = 21/88 (23%), Positives = 33/88 (36%), Gaps = 9/88 (10%)
Query: 79 NEKRDFKVGESVFTTAIQICTHLGCIPTYQDEEKGFLCPCHGGRFTSDGVNIAGTPPPRP 138
N RD E + T +Q T+L CI + E + GG+ G+ P
Sbjct: 21 NNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAI-SLDGGQAFEAGL--------AP 71
Query: 139 FDIPPFKIEGTKITFGEAGAEYKKMMAK 166
+ + P E + T G + Y + K
Sbjct: 72 YKLKPIAAEVYEHTEGSTTSYYAVAVVK 99
>pdb|2CGR|H Chain H, Igg2b (Kappa) Fab Fragment Complexed With Antigen
N-(P-Cyanophenyl)-N'-(Diphenylemethyl) Guanidineacetic
Acid
pdb|1CGS|H Chain H, Igg2b (Kappa) Fab Fragment Against Antigen
N-(P-Cyanophenyl)-N'-(Diphenylemethyl) Guanidineacetic
Acid
Length = 214
Score = 25.4 bits (54), Expect = 3.5
Identities = 28/104 (26%), Positives = 46/104 (43%), Gaps = 15/104 (14%)
Query: 60 VEWRGKPVYILKRSKKEGFNEKRDFKVGESVFTTAIQICTHLGCIPTYQDEE-------K 112
+EW G+ IL S + + EK FK G++ FT T + + E+ +
Sbjct: 45 LEWIGE---ILPGSGRTNYREK--FK-GKATFTADTSSNTAYMQLSSLTSEDSAVYYCTR 98
Query: 113 GFLCPCHGGRFTSDGVNIAGTPPPRPFDIPP--FKIEGTKITFG 154
G+ + G+ TS V+ A T PP + + P G+ +T G
Sbjct: 99 GYSSMDYWGQGTSVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLG 142
>pdb|1HRU|A Chain A, The Structure Of The Yrdc Gene Product From E.Coli
pdb|1HRU|B Chain B, The Structure Of The Yrdc Gene Product From E.Coli
Length = 188
Score = 25.0 bits (53), Expect = 4.6
Identities = 10/26 (38%), Positives = 13/26 (49%)
Query: 115 LCPCHGGRFTSDGVNIAGTPPPRPFD 140
LC +G S N++G PP R D
Sbjct: 127 LCQAYGKPLVSTSANLSGLPPCRTVD 152
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
0.320 0.137 0.418
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 996,805
Number of Sequences: 13198
Number of extensions: 42350
Number of successful extensions: 94
Number of sequences better than 10.0: 18
Number of HSP's better than 10.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 74
Number of HSP's gapped (non-prelim): 20
length of query: 167
length of database: 2,899,336
effective HSP length: 81
effective length of query: 86
effective length of database: 1,830,298
effective search space: 157405628
effective search space used: 157405628
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: 51 (24.3 bits)