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|15646146|ref|NP_208330.1| ubiquinol cytochrome c
oxidoreductase, cytochrome b subunit (fbcH) [Helicobacter pylori
26695]
(412 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|1BCC|C Chain C, Cytochrome Bc1 Complex From Chicken >gi... 249 4e-67
pdb|1QCR|C Chain C, Crystal Structure Of Bovine Mitochondri... 241 1e-64
pdb|1BGY|C Chain C, Cytochrome Bc1 Complex From Bovine >gi|... 241 1e-64
pdb|1KB9|C Chain C, Yeast Cytochrome Bc1 Complex >gi|142777... 217 2e-57
pdb|1DHX| Adenovirus, Hexon Protein, Coat Protein Mol_id:... 27 5.6
pdb|1RUX|A Chain A, Maximum Likelihood Refinement Of Adenov... 27 5.6
pdb|1HH2|P Chain P, Crystal Structure Of Nusa From Thermoto... 26 9.5
pdb|1KQF|C Chain C, Formate Dehydrogenase N From E. Coli >g... 26 9.5
>pdb|1BCC|C Chain C, Cytochrome Bc1 Complex From Chicken
pdb|2BCC|C Chain C, Stigmatellin-Bound Cytochrome Bc1 Complex From Chicken
pdb|3BCC|C Chain C, Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex
From Chicken
Length = 380
Score = 249 bits (636), Expect = 4e-67
Identities = 145/385 (37%), Positives = 204/385 (52%), Gaps = 21/385 (5%)
Query: 22 KLVKVLMTEYWIPKNINFLWAMGVILLTLFGVLVVSGIFLLMYYKPDAKMAFDSVNFTIM 81
K++ + + P NI+ W G +L +++G+ L M+Y D +AF SV T
Sbjct: 13 KMINNSLIDLPAPSNISAWWNFGSLLAVCLMTQILTGLLLAMHYTADTSLAFSSVAHTC- 71
Query: 82 QEVAYGWLWRHMHATAASMIFVIIYIHMFVGIYYGSYKKGREMIWISGMILFVVFSAEAF 141
+ V YGWL R++HA AS F+ I++H+ G+YYGSY + W +G+IL + A AF
Sbjct: 72 RNVQYGWLIRNLHANGASFFFICIFLHIGRGLYYGSYLY--KETWNTGVILLLTLMATAF 129
Query: 142 SGYMLPWGQMSYWAAAVITNLFGGIPFIGADVVEWIRGNYVVADSTLTRFFMLHVFLLPI 201
GY+LPWGQMS+W A VITNLF IP+IG +VEW G + V + TLTRFF LH FLLP
Sbjct: 130 VGYVLPWGQMSFWGATVITNLFSAIPYIGHTLVEWAWGGFSVDNPTLTRFFALH-FLLPF 188
Query: 202 AIILLVGVHFYSLRIPHVNNQEGEEIDFELEEKKFIEGKKKESKVIPFWPVFLSKDIFVV 261
AI + +H L NN G D S IPF P + KDI +
Sbjct: 189 AIAGITIIHLTFLHESGSNNPLGISSD---------------SDKIPFHPYYSFKDILGL 233
Query: 262 CAFMVFFFYLVCYHYDFAMDPINFERANSLKTPPHIYPEWYFLWSYEVLRGFFFSADLGL 321
+ F L + + DP NF AN L TPPHI PEWYFL++Y +LR G+
Sbjct: 234 TLMLTPFLTLALFSPNLLGDPENFTPANPLVTPPHIKPEWYFLFAYAILRSIPNKLG-GV 292
Query: 322 MAFGVAQVIFFLLPFLDRSPVVAPAHKRPAFMVWFWLVIIDMIVLTIYGKLPPLGIGKYI 381
+A + +I FL+PFL +S RP FWL++ ++++LT G P I
Sbjct: 293 LALAASVLILFLIPFLHKSKQRTMTF-RPLSQTLFWLLVANLLILTWIGSQPVEHPFIII 351
Query: 382 GLAGSITFLALFFVVLPIITIAESK 406
G S+++ + ++ P I E+K
Sbjct: 352 GQMASLSYFTILLILFPTIGTLENK 376
>pdb|1QCR|C Chain C, Crystal Structure Of Bovine Mitochondrial Cytochrome Bc1
Complex, Alpha Carbon Atoms Only
Length = 378
Score = 241 bits (614), Expect = 1e-64
Identities = 144/385 (37%), Positives = 199/385 (51%), Gaps = 21/385 (5%)
Query: 22 KLVKVLMTEYWIPKNINFLWAMGVILLTLFGVLVVSGIFLLMYYKPDAKMAFDSVNFTIM 81
K+V + P NI+ W G +L + +++G+FL M+Y D AF SV I
Sbjct: 11 KIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTTAFSSVTH-IC 69
Query: 82 QEVAYGWLWRHMHATAASMIFVIIYIHMFVGIYYGSYKKGREMIWISGMILFVVFSAEAF 141
++V YGW+ R+MHA ASM F+ +Y+H+ G+YYGSY W G+IL + A AF
Sbjct: 70 RDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLET--WNIGVILLLTVMATAF 127
Query: 142 SGYMLPWGQMSYWAAAVITNLFGGIPFIGADVVEWIRGNYVVADSTLTRFFMLHVFLLPI 201
GY+LPWGQMS+W A VITNL IP+IG ++VEWI G + V +TLTRFF H F+LP
Sbjct: 128 MGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFH-FILPF 186
Query: 202 AIILLVGVHFYSLRIPHVNNQEGEEIDFELEEKKFIEGKKKESKVIPFWPVFLSKDIFVV 261
I+ + VH L NN G D + IPF P + KDI
Sbjct: 187 IIMAIAMVHLLFLHETGSNNPTGISSDVD---------------KIPFHPYYTIKDILGA 231
Query: 262 CAFMVFFFYLVCYHYDFAMDPINFERANSLKTPPHIYPEWYFLWSYEVLRGFFFSADLGL 321
++ LV + D DP N+ AN L TPPHI PEWYFL++Y +LR G+
Sbjct: 232 LLLILALMLLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLG-GV 290
Query: 322 MAFGVAQVIFFLLPFLDRSPVVAPAHKRPAFMVWFWLVIIDMIVLTIYGKLPPLGIGKYI 381
+A + +I L+P L S + RP FW ++ D++ LT G P I
Sbjct: 291 LALAFSILILALIPLLHTSKQRSMMF-RPLSQCLFWALVADLLTLTWIGGQPVEHPYITI 349
Query: 382 GLAGSITFLALFFVVLPIITIAESK 406
G S+ + L V++P E+K
Sbjct: 350 GQLASVLYFLLILVLMPTAGTIENK 374
>pdb|1BGY|C Chain C, Cytochrome Bc1 Complex From Bovine
pdb|1BGY|O Chain O, Cytochrome Bc1 Complex From Bovine
pdb|1BE3|C Chain C, Cytochrome Bc1 Complex From Bovine
Length = 379
Score = 241 bits (614), Expect = 1e-64
Identities = 144/385 (37%), Positives = 199/385 (51%), Gaps = 21/385 (5%)
Query: 22 KLVKVLMTEYWIPKNINFLWAMGVILLTLFGVLVVSGIFLLMYYKPDAKMAFDSVNFTIM 81
K+V + P NI+ W G +L + +++G+FL M+Y D AF SV I
Sbjct: 12 KIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTTAFSSVTH-IC 70
Query: 82 QEVAYGWLWRHMHATAASMIFVIIYIHMFVGIYYGSYKKGREMIWISGMILFVVFSAEAF 141
++V YGW+ R+MHA ASM F+ +Y+H+ G+YYGSY W G+IL + A AF
Sbjct: 71 RDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLET--WNIGVILLLTVMATAF 128
Query: 142 SGYMLPWGQMSYWAAAVITNLFGGIPFIGADVVEWIRGNYVVADSTLTRFFMLHVFLLPI 201
GY+LPWGQMS+W A VITNL IP+IG ++VEWI G + V +TLTRFF H F+LP
Sbjct: 129 MGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFH-FILPF 187
Query: 202 AIILLVGVHFYSLRIPHVNNQEGEEIDFELEEKKFIEGKKKESKVIPFWPVFLSKDIFVV 261
I+ + VH L NN G D + IPF P + KDI
Sbjct: 188 IIMAIAMVHLLFLHETGSNNPTGISSDVD---------------KIPFHPYYTIKDILGA 232
Query: 262 CAFMVFFFYLVCYHYDFAMDPINFERANSLKTPPHIYPEWYFLWSYEVLRGFFFSADLGL 321
++ LV + D DP N+ AN L TPPHI PEWYFL++Y +LR G+
Sbjct: 233 LLLILALMLLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLG-GV 291
Query: 322 MAFGVAQVIFFLLPFLDRSPVVAPAHKRPAFMVWFWLVIIDMIVLTIYGKLPPLGIGKYI 381
+A + +I L+P L S + RP FW ++ D++ LT G P I
Sbjct: 292 LALAFSILILALIPLLHTSKQRSMMF-RPLSQCLFWALVADLLTLTWIGGQPVEHPYITI 350
Query: 382 GLAGSITFLALFFVVLPIITIAESK 406
G S+ + L V++P E+K
Sbjct: 351 GQLASVLYFLLILVLMPTAGTIENK 375
>pdb|1KB9|C Chain C, Yeast Cytochrome Bc1 Complex
pdb|1EZV|C Chain C, Structure Of The Yeast Cytochrome Bc1 Complex Co-
Crystallized With An Antibody Fv-Fragment
pdb|1KYO|C Chain C, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
pdb|1KYO|N Chain N, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
Length = 385
Score = 217 bits (553), Expect = 2e-57
Identities = 128/372 (34%), Positives = 199/372 (53%), Gaps = 19/372 (5%)
Query: 34 PKNINFLWAMGVILLTLFGVLVVSGIFLLMYYKPDAKMAFDSVNFTIMQEVAYGWLWRHM 93
P +IN+ W MG +L + +V+GIF+ M+Y + ++AF SV IM++V G++ R++
Sbjct: 23 PSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIELAFSSVEH-IMRDVHNGYILRYL 81
Query: 94 HATAASMIFVIIYIHMFVGIYYGSYKKGREMIWISGMILFVVFSAEAFSGYMLPWGQMSY 153
HA AS F+++++HM G+YYGSY+ R +W G+I+F + A AF GY +GQMS+
Sbjct: 82 HANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVIIFTLTIATAFLGYCCVYGQMSH 141
Query: 154 WAAAVITNLFGGIPFIGADVVEWIRGNYVVADSTLTRFFMLHVFLLPIAIILLVGVHFYS 213
W A VITNLF IPF+G D+V W+ G + V++ T+ RFF LH +L+P I +V +H +
Sbjct: 142 WGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFFALH-YLVPFIIAAMVIMHLMA 200
Query: 214 LRIPHVNNQEGEEIDFELEEKKFIEGKKKESKVIPFWPVFLSKDIFVVCAFMVFFFYLVC 273
L I +N G I L+ IP F+ KD+ V FM+ V
Sbjct: 201 LHIHGSSNPLG--ITGNLDR-------------IPMHSYFIFKDLVTVFLFMLILALFVF 245
Query: 274 YHYDFAMDPINFERANSLKTPPHIYPEWYFLWSYEVLRGFFFSADLGLMAFGVAQVIFFL 333
Y + P N+ N L TP I PEWY L Y +LR LG++ A ++ +
Sbjct: 246 YSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKL-LGVITMFAAILVLLV 304
Query: 334 LPFLDRSPVVAPAHKRPAFMVWFWLVIIDMIVLTIYGKLPPLGIGKYIGLAGSITFLALF 393
LPF DRS V K +F++ + + ++L G +G + + A F
Sbjct: 305 LPFTDRSVVRGNTFK-VLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYFAYF 363
Query: 394 FVVLPIITIAES 405
+++P+I+ E+
Sbjct: 364 LIIVPVISTIEN 375
>pdb|1DHX| Adenovirus, Hexon Protein, Coat Protein Mol_id: 1; Molecule:
Adenovirus Type 2 Hexon; Chain: Null; Synonym:
Adenovirus Type 2 Polypeptide Ii
Length = 967
Score = 26.6 bits (57), Expect = 5.6
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 305 WSYEVLRGFFFSADL--GLMAFGVAQVIFFLLPFLDRSPVVAPAH 347
WSY + G S L GL+ F A +F L R+P VAP H
Sbjct: 9 WSYMHISGQDASEYLSPGLVQFARATETYFSLNNKFRNPTVAPTH 53
>pdb|1RUX|A Chain A, Maximum Likelihood Refinement Of Adenovirus Type 5 Hexon
With Tnt
Length = 951
Score = 26.6 bits (57), Expect = 5.6
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 305 WSYEVLRGFFFSADL--GLMAFGVAQVIFFLLPFLDRSPVVAPAH 347
WSY + G S L GL+ F A +F L R+P VAP H
Sbjct: 9 WSYMHISGQDASEYLSPGLVQFARATETYFSLNNKFRNPTVAPTH 53
>pdb|1HH2|P Chain P, Crystal Structure Of Nusa From Thermotoga Maritima
Length = 344
Score = 25.8 bits (55), Expect = 9.5
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 10 LGEWLDMRLGTNKLVKVLMTEYWIP 34
+GEW D+R+G KL L + WIP
Sbjct: 146 MGEWADIRIG--KLETRLPKKEWIP 168
>pdb|1KQF|C Chain C, Formate Dehydrogenase N From E. Coli
pdb|1KQG|C Chain C, Formate Dehydrogenase N From E. Coli
Length = 217
Score = 25.8 bits (55), Expect = 9.5
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 47 LLTLFGVLVVSGIFLLMYYKPDAKMAFDSVNFTIMQEVAYGWLWRHMHATAASMIFVIIY 106
++++ VL+V+G+ + Y + MQ V Y L +HA A ++ I
Sbjct: 120 IMSMIFVLLVTGVIIWRPY---------FAQYFPMQVVRYSLL---IHAAAGIILIHAIL 167
Query: 107 IHMFVGIYYGSYKKG 121
IHM++ + KG
Sbjct: 168 IHMYMAFWVKGSIKG 182
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
0.332 0.147 0.476
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,351,275
Number of Sequences: 13198
Number of extensions: 93904
Number of successful extensions: 232
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 207
Number of HSP's gapped (non-prelim): 8
length of query: 412
length of database: 2,899,336
effective HSP length: 90
effective length of query: 322
effective length of database: 1,711,516
effective search space: 551108152
effective search space used: 551108152
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 55 (25.8 bits)