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= 015642
(403 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 = 173 bits (439), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 122/423 (28%), Positives = 194/423 (45%), Gaps = 73/423 (17%)
Query: 18 KAVIISLSPQSRASLAEHFGISP-LQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNE 76
K V + ++P R ++AE G++P K+L L+ LG +FDT DLT++E +E
Sbjct: 45 KHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADLTIMEEGSE 104
Query: 77 FIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSY--ILPYISSVKSPQQTIGA 134
+ R + E+ S+ LPM +S CPGWI EK SY ++PY+SS KSPQ + A
Sbjct: 105 LLHRLTEHLEAH-PHSDEPLPMFTSCCPGWIAMLEK---SYPDLIPYVSSCKSPQMMLAA 160
Query: 135 TIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDS 194
+K ++ +K G P ++ V++MPC K+ EA R+ F D T R ++D
Sbjct: 161 MVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEADRDWFCVDADP---TLR-------QLDH 210
Query: 195 VLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKT 254
V+TT E+ ++ + + +N L E D + G L+ G++GG E R A +
Sbjct: 211 VITTVELGNIFKERGINLAELPEGEWDNPMGVGSGAGVLF---GTTGGVMEAALRTAYEL 267
Query: 255 LFGKVIEGHLEFKTIRNSD----------------FREV--------------------- 277
G + L +R D F E+
Sbjct: 268 FTGTPLP-RLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAAARAEAAAHGTPGPLA 326
Query: 278 --------ALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGG 329
+ + G L+ A+ G N + ++ K++ + Y FVE+MACP+GC+ GGG
Sbjct: 327 WDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGG 386
Query: 330 QIKPKPGQSPKELIKTLETIYL---ENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVH 386
Q P + K + + + E L +NP +R LYD +L +P KA + +H
Sbjct: 387 Q----PRSTDKAITQKRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLH 442
Query: 387 TEY 389
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 = 164 bits (414), Expect = 1e-40, Method: Compositional matrix adjust.
Identities = 117/394 (29%), Positives = 186/394 (47%), Gaps = 35/394 (8%)
Query: 3 EKQSLDEFLSNINKG-KAVIISLSPQSRASLAEHFGIS-PLQVFKKLTTFLKSLGVKSIF 60
EK +D + +N K VI++++P RAS+ E F + + V K+ T L+ LG IF
Sbjct: 207 EKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIF 266
Query: 61 DTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILP 120
D + D+T++E E + R + +N PM +S CPGW+ AE +L
Sbjct: 267 DINFGADMTIMEEATELVQRIE---------NNGPFPMFTSCCPGWVRQAENYYPE-LLN 316
Query: 121 YISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEE 180
+SS KSPQQ G K + G P ++ VTVMPC KK EA R +++
Sbjct: 317 NLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQM------EKD 370
Query: 181 TYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSS 240
RD +D+V+TT E+ +I+ + F LE+S D + G ++G ++
Sbjct: 371 GLRD-------IDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFG---AT 420
Query: 241 GGYAETVFRHAAKTLFGKVIEGHLEFKTIRN-SDFREVALEVEGKTLLKFALCYGFQNLQ 299
GG E R A +E +E+K +R + +E +E+ A+ G NL
Sbjct: 421 GGVMEAALRSAKDFAENAELE-DIEYKQVRGLNGIKEAEVEINNNKY-NVAVINGASNLF 478
Query: 300 NIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELIKTLETIYL----ENVM 355
++ + + Y F+EVMAC GC+NGGGQ P K IK + L E++
Sbjct: 479 KFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLS 538
Query: 356 LADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEY 389
+N + +Y + +PG +A + +H +Y
Sbjct: 539 KRKSHENTALVKMYQNYFGKPGEGRAHEILHFKY 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 = 129 bits (325), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 93/323 (28%), Positives = 157/323 (48%), Gaps = 30/323 (9%)
Query: 1 MLEKQS-LDEFLSNINKGKAVIISL-SPQSRASLAEHFGISPLQVFK-KLTTFLKSLGVK 57
+ E QS + E + GK I++ +P R +L + FG+ V K+ L+ LG
Sbjct: 81 IYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFA 140
Query: 58 SIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSY 117
+DT + D+T+ E +EF+ R + +S+ LP +S CPGW YAE
Sbjct: 141 HCWDTEFTADVTIWEEGSEFVERLTK-------KSDMPLPQFTSCCPGWQKYAETYYPE- 192
Query: 118 ILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDS 177
+LP+ S+ KSP GA K + +++ + P ++Y V++MPC KK E R +
Sbjct: 193 LLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPEL------ 246
Query: 178 QEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVA 237
+ G+ ++D+ LTT E+ +I+ ++F L + D ++ ++GV
Sbjct: 247 -----KSSGMR--DIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGV- 298
Query: 238 GSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSD-FREVALEVEGKTLLKFALCYGFQ 296
+GG E R A + + GK + +FK +R D +E + V G T +K A+ +G +
Sbjct: 299 --TGGVMEAALRFAYEAVTGKKPD-SWDFKAVRGLDGIKEATVNV-GGTDVKVAVVHGAK 354
Query: 297 NLQNIVRKVKMRKCDYQFVEVMA 319
+ + VK K Y F+E MA
Sbjct: 355 RFKQVCDDVKAGKSPYHFIEYMA 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 = 129 bits (324), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 93/323 (28%), Positives = 157/323 (48%), Gaps = 30/323 (9%)
Query: 1 MLEKQS-LDEFLSNINKGKAVIISL-SPQSRASLAEHFGISPLQVFK-KLTTFLKSLGVK 57
+ E QS + E + GK I++ +P R +L + FG+ V K+ L+ LG
Sbjct: 55 IYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFA 114
Query: 58 SIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSY 117
+DT + D+T+ E +EF+ R + +S+ LP +S CPGW YAE
Sbjct: 115 HCWDTEFTADVTIWEEGSEFVERLTK-------KSDMPLPQFTSCCPGWQKYAETYYPE- 166
Query: 118 ILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDS 177
+LP+ S+ KSP GA K + +++ + P ++Y V++MPC KK E R +
Sbjct: 167 LLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPEL------ 220
Query: 178 QEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVA 237
+ G+ ++D+ LTT E+ +I+ ++F L + D ++ ++GV
Sbjct: 221 -----KSSGMR--DIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGV- 272
Query: 238 GSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSD-FREVALEVEGKTLLKFALCYGFQ 296
+GG E R A + + GK + +FK +R D +E + V G T +K A+ +G +
Sbjct: 273 --TGGVMEAALRFAYEAVTGKKPD-SWDFKAVRGLDGIKEATVNV-GGTDVKVAVVHGAK 328
Query: 297 NLQNIVRKVKMRKCDYQFVEVMA 319
+ + VK K Y F+E MA
Sbjct: 329 RFKQVCDDVKAGKSPYHFIEYMA 351
>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 = 3.3, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 212 FEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFG 257
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 = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 212 FEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFG 257
F+ L++ L ++T + LY +AG S G ++ F T FG
Sbjct: 1158 FQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFG 1203
>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 = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 223 MLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLF 256
+LT VD G+L GVA GG + RH AK L+
Sbjct: 368 ILTFVDTPGYLPGVAQEHGG----IIRHGAKLLY 397
>pdb|1GSL|A Chain A, Lectin (Fourth Isolated From (Griffonia Simplicifolia))
Complex With Y Human Blood Group Determinant
pdb|1LEC|A Chain A, Structures Of The Lectin Iv Of Griffonia Simplicifolia And
Its Complex With The Lewis B Human Blood Group
Determinant At 2.0 Angstroms Resolution
pdb|1LED|A Chain A, Structures Of The Lectin Iv Of Griffonia Simplicifolia And
Its Complex With The Lewis B Human Blood Group
Determinant At 2.0 Angstroms Resolution
Length = 243
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 357 ADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKSITAQLHN 402
ADP KN +V +D W+ + ++ H+ + + +V T + N
Sbjct: 118 ADPSKNQVVAVEFDTWINKDWNDPPYPHIGIDVNSIVSVATTRWEN 163
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 0.134 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,845,596
Number of Sequences: 62578
Number of extensions: 483775
Number of successful extensions: 1451
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1426
Number of HSP's gapped (non-prelim): 10
length of query: 403
length of database: 14,973,337
effective HSP length: 101
effective length of query: 302
effective length of database: 8,652,959
effective search space: 2613193618
effective search space used: 2613193618
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)