BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 011877
(475 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3LX4|A Chain A, Stepwise [fefe]-Hydrogenase H-Cluster Assembly Revealed In
The Structure Of Hyda(Deltaefg)
pdb|3LX4|B Chain B, Stepwise [fefe]-Hydrogenase H-Cluster Assembly Revealed In
The Structure Of Hyda(Deltaefg)
Length = 457
Score = 174 bits (441), Expect = 9e-44, Method: Compositional matrix adjust.
Identities = 122/423 (28%), Positives = 194/423 (45%), Gaps = 73/423 (17%)
Query: 90 KAVIISLSPQSRASLAEHFGISP-LQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNE 148
K V + ++P R ++AE G++P K+L L+ LG +FDT DLT++E +E
Sbjct: 45 KHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADLTIMEEGSE 104
Query: 149 FIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSY--ILPYISSVKSPQQTIGA 206
+ R + E+ S+ LPM +S CPGWI EK SY ++PY+SS KSPQ + A
Sbjct: 105 LLHRLTEHLEAH-PHSDEPLPMFTSCCPGWIAMLEK---SYPDLIPYVSSCKSPQMMLAA 160
Query: 207 TIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDS 266
+K ++ +K G P ++ V++MPC K+ EA R+ F D T R ++D
Sbjct: 161 MVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEADRDWFCVDADP---TLR-------QLDH 210
Query: 267 VLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKT 326
V+TT E+ ++ + + +N L E D + G L+ G++GG E R A +
Sbjct: 211 VITTVELGNIFKERGINLAELPEGEWDNPMGVGSGAGVLF---GTTGGVMEAALRTAYEL 267
Query: 327 LFGKVIEGHLEFKTIRNSD----------------FREV--------------------- 349
G + L +R D F E+
Sbjct: 268 FTGTPLP-RLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAAARAEAAAHGTPGPLA 326
Query: 350 --------ALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGG 401
+ + G L+ A+ G N + ++ K++ + Y FVE+MACP+GC+ GGG
Sbjct: 327 WDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGG 386
Query: 402 QIKPKPGQSPKELIKTLETIYL---ENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVH 458
Q P + K + + + E L +NP +R LYD +L +P KA + +H
Sbjct: 387 Q----PRSTDKAITQKRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLH 442
Query: 459 TEY 461
T Y
Sbjct: 443 THY 445
>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
pdb|3C8Y|A Chain A, 1.39 Angstrom Crystal Structure Of Fe-Only Hydrogenase
Length = 574
Score = 174 bits (440), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 123/412 (29%), Positives = 194/412 (47%), Gaps = 36/412 (8%)
Query: 58 DCLACSGCITSAETVML-EKQSLDEFLSNINK-GKAVIISLSPQSRASLAEHFGIS-PLQ 114
+CL C CI + L EK +D + +N K VI++++P RAS+ E F + +
Sbjct: 189 NCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVD 248
Query: 115 VFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSA 174
V K+ T L+ LG IFD + D+T++E E + R + +N PM +S
Sbjct: 249 VTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIE---------NNGPFPMFTSC 299
Query: 175 CPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDK 234
CPGW+ AE +L +SS KSPQQ G K + G P ++ VTVMPC K
Sbjct: 300 CPGWVRQAENYYPE-LLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSK 358
Query: 235 KLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDK 294
K EA R +++ RD +D+V+TT E+ +I+ + F LE+S D
Sbjct: 359 KFEADRPQM------EKDGLRD-------IDAVITTRELAKMIKDAKIPFAKLEDSEADP 405
Query: 295 MLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRN-SDFREVALEV 353
+ G ++G ++GG E R A +E +E+K +R + +E +E+
Sbjct: 406 AMGEYSGAGAIFG---ATGGVMEAALRSAKDFAENAELE-DIEYKQVRGLNGIKEAEVEI 461
Query: 354 EGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKE 413
A+ G NL ++ + + Y F+EVMAC GC+NGGGQ P K
Sbjct: 462 NNNKY-NVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKV 520
Query: 414 LIKTLETIYL----ENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEY 461
IK + L E++ +N + +Y + +PG +A + +H +Y
Sbjct: 521 DIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKY 572
>pdb|1HFE|L Chain L, 1.6 A Resolution Structure Of The Fe-Only Hydrogenase From
Desulfovibrio Desulfuricans
pdb|1HFE|M Chain M, 1.6 A Resolution Structure Of The Fe-Only Hydrogenase From
Desulfovibrio Desulfuricans
Length = 421
Score = 139 bits (349), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 101/351 (28%), Positives = 170/351 (48%), Gaps = 32/351 (9%)
Query: 47 QQAEPVKIS-LKDCLACSGCITSA-ETVMLEKQS-LDEFLSNINKGKAVIISL-SPQSRA 102
+ EP I ++ C+ C C+T E + E QS + E + GK I++ +P R
Sbjct: 53 EMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRY 112
Query: 103 SLAEHFGISPLQVFK-KLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDD 161
+L + FG+ V K+ L+ LG +DT + D+T+ E +EF+ R +
Sbjct: 113 ALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTK------ 166
Query: 162 ERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPD 221
+S+ LP +S CPGW YAE +LP+ S+ KSP GA K + +++ + P
Sbjct: 167 -KSDMPLPQFTSCCPGWQKYAETYYPE-LLPHFSTCKSPIGMNGALAKTYGAERMKYDPK 224
Query: 222 EIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKA 281
++Y V++MPC KK E R + + G+ ++D+ LTT E+ +I+
Sbjct: 225 QVYTVSIMPCIAKKYEGLRPEL-----------KSSGMR--DIDATLTTRELAYMIKKAG 271
Query: 282 VNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTI 341
++F L + D ++ ++GV +GG E R A + + GK + +FK +
Sbjct: 272 IDFAKLPDGKRDSLMGESTGGATIFGV---TGGVMEAALRFAYEAVTGKKPD-SWDFKAV 327
Query: 342 RNSD-FREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMA 391
R D +E + V G T +K A+ +G + + + VK K Y F+E MA
Sbjct: 328 RGLDGIKEATVNV-GGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMA 377
>pdb|1E08|A Chain A, Structural Model Of The [fe]-HydrogenaseCYTOCHROME C553
Complex Combining Nmr And Soft-Docking
pdb|1GX7|A Chain A, Best Model Of The Electron Transfer Complex Between
Cytochrome C3 And [fe]-Hydrogenase
Length = 371
Score = 139 bits (349), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 101/351 (28%), Positives = 170/351 (48%), Gaps = 32/351 (9%)
Query: 47 QQAEPVKIS-LKDCLACSGCITSA-ETVMLEKQS-LDEFLSNINKGKAVIISL-SPQSRA 102
+ EP I ++ C+ C C+T E + E QS + E + GK I++ +P R
Sbjct: 27 EMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRY 86
Query: 103 SLAEHFGISPLQVFK-KLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDD 161
+L + FG+ V K+ L+ LG +DT + D+T+ E +EF+ R +
Sbjct: 87 ALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTK------ 140
Query: 162 ERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPD 221
+S+ LP +S CPGW YAE +LP+ S+ KSP GA K + +++ + P
Sbjct: 141 -KSDMPLPQFTSCCPGWQKYAETYYPE-LLPHFSTCKSPIGMNGALAKTYGAERMKYDPK 198
Query: 222 EIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKA 281
++Y V++MPC KK E R + + G+ ++D+ LTT E+ +I+
Sbjct: 199 QVYTVSIMPCIAKKYEGLRPEL-----------KSSGMR--DIDATLTTRELAYMIKKAG 245
Query: 282 VNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTI 341
++F L + D ++ ++GV +GG E R A + + GK + +FK +
Sbjct: 246 IDFAKLPDGKRDSLMGESTGGATIFGV---TGGVMEAALRFAYEAVTGKKPD-SWDFKAV 301
Query: 342 RNSD-FREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMA 391
R D +E + V G T +K A+ +G + + + VK K Y F+E MA
Sbjct: 302 RGLDGIKEATVNV-GGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMA 351
>pdb|1VRG|A Chain A, Crystal Structure Of Propionyl-coa Carboxylase, Beta
Subunit (tm0716) From Thermotoga Maritima At 2.30 A
Resolution
pdb|1VRG|B Chain B, Crystal Structure Of Propionyl-coa Carboxylase, Beta
Subunit (tm0716) From Thermotoga Maritima At 2.30 A
Resolution
pdb|1VRG|C Chain C, Crystal Structure Of Propionyl-coa Carboxylase, Beta
Subunit (tm0716) From Thermotoga Maritima At 2.30 A
Resolution
pdb|1VRG|D Chain D, Crystal Structure Of Propionyl-coa Carboxylase, Beta
Subunit (tm0716) From Thermotoga Maritima At 2.30 A
Resolution
pdb|1VRG|E Chain E, Crystal Structure Of Propionyl-coa Carboxylase, Beta
Subunit (tm0716) From Thermotoga Maritima At 2.30 A
Resolution
pdb|1VRG|F Chain F, Crystal Structure Of Propionyl-coa Carboxylase, Beta
Subunit (tm0716) From Thermotoga Maritima At 2.30 A
Resolution
Length = 527
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 295 MLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLF 328
+LT VD G+L GVA GG + RH AK L+
Sbjct: 368 ILTFVDTPGYLPGVAQEHGG----IIRHGAKLLY 397
>pdb|3QMZ|A Chain A, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
pdb|3QMZ|B Chain B, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
Length = 2486
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 284 FEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFG 329
F+ L++ L ++T + LY +AG S G ++ F T FG
Sbjct: 939 FQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFG 984
>pdb|4AI6|A Chain A, Dynein Motor Domain - Adp Complex
pdb|4AI6|B Chain B, Dynein Motor Domain - Adp Complex
pdb|4AKG|A Chain A, Dynein Motor Domain - Atp Complex
pdb|4AKG|B Chain B, Dynein Motor Domain - Atp Complex
pdb|4AKH|A Chain A, Dynein Motor Domain - Amppnp Complex
pdb|4AKH|B Chain B, Dynein Motor Domain - Amppnp Complex
pdb|4AKI|A Chain A, Dynein Motor Domain - Luac Derivative
pdb|4AKI|B Chain B, Dynein Motor Domain - Luac Derivative
Length = 2695
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 284 FEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFG 329
F+ L++ L ++T + LY +AG S G ++ F T FG
Sbjct: 1158 FQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFG 1203
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,634,669
Number of Sequences: 62578
Number of extensions: 544715
Number of successful extensions: 1663
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1637
Number of HSP's gapped (non-prelim): 9
length of query: 475
length of database: 14,973,337
effective HSP length: 102
effective length of query: 373
effective length of database: 8,590,381
effective search space: 3204212113
effective search space used: 3204212113
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)