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= psy3876
(477 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 140 bits (354), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 115/409 (28%), Positives = 182/409 (44%), Gaps = 39/409 (9%)
Query: 70 TDCLACSGCITSAESVLITQQSHEEVMKVIRENNAHKASSNENTKTIVLSLAIQPVLSLG 129
T+CL C CI + ++++SH + +K NA A K +++++A S+G
Sbjct: 188 TNCLLCGQCIIACPVAALSEKSHMDRVK-----NALNAPE----KHVIVAMAPSVRASIG 238
Query: 130 AKFALSHE-QVVAKLCGFFKRLGVDLVLDVGIAHCFSLVELENEFLDRFLSGGG-PLFTS 187
F + V K+ ++LG D + D+ +++E E + R + G P+FTS
Sbjct: 239 ELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTS 298
Query: 188 ECPGWVCYAEKSHGEFILPYISRVKSPQQVMGSLIKTHLAEKLGVHPSHIYHVTLMPCYD 247
CPGWV AE + E +L +S KSPQQ+ G+ KT+ G+ P +++ VT+MPC
Sbjct: 299 CCPGWVRQAENYYPE-LLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTS 357
Query: 248 KKLEASRADFYNEELGYRDVDCVIXXXXXXXXXXXXXXXXXXXXXKDGILDWPWDEHNPH 307
KK EA R E+ G RD+D VI KD + + E +
Sbjct: 358 KKFEADRPQM--EKDGLRDIDAVI------------TTRELAKMIKDAKIPFAKLEDSEA 403
Query: 308 RMLLVNGTGSG---GYAHNVLSHAIRQLCP----GESPVVEFKPLRNPD-IREATFTCGD 359
+ +G+G G V+ A+R E +E+K +R + I+EA +
Sbjct: 404 DPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINN 463
Query: 360 VTLRFCIANGFRNIQNLIQKLKRKRLPYDFIEIMACPSGCLNGGAQIRN-----EKVASP 414
+ NG N+ ++ Y FIE+MAC GC+NGG Q EKV
Sbjct: 464 NKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIK 523
Query: 415 KETALELETILCDLAKSEPRENATLEHLYKAWLGGKSTDKGKHMLNTSY 463
K A L L+K + EN L +Y+ + G + +L+ Y
Sbjct: 524 KVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKY 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 = 101 bits (252), Expect = 9e-22, Method: Compositional matrix adjust.
Identities = 92/337 (27%), Positives = 144/337 (42%), Gaps = 39/337 (11%)
Query: 72 CLACSGCITSA-ESVLITQQSH-EEVMKVIRENNAHKASSNENTKTIVLSLAIQPVLSLG 129
C+ C C+T E+ + QS EV K +++ K I + A +LG
Sbjct: 66 CINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGK---------VKCIAMP-APAVRYALG 115
Query: 130 AKFALSHEQVV-AKLCGFFKRLGVDLVLDVGIAHCFSLVELENEFLDRFLSGGG---PLF 185
F + V K+ ++LG D ++ E +EF++R P F
Sbjct: 116 DAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQF 175
Query: 186 TSECPGWVCYAEKSHGEFILPYISRVKSPQQVMGSLIKTHLAEKLGVHPSHIYHVTLMPC 245
TS CPGW YAE + E +LP+ S KSP + G+L KT+ AE++ P +Y V++MPC
Sbjct: 176 TSCCPGWQKYAETYYPE-LLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPC 234
Query: 246 YDKKLEASRADFYNEELGYRDVDCVIXXXXXXXXXXXXXXXXXXXXXKDGILDWPWDEHN 305
KK E R + + G RD+D + K +D+
Sbjct: 235 IAKKYEGLRPELKSS--GMRDIDATL------------TTRELAYMIKKAGIDFAKLPDG 280
Query: 306 PHRMLLVNGTGSG---GYAHNVLSHAIR---QLCPGESP-VVEFKPLRNPD-IREATFTC 357
L+ TG G V+ A+R + G+ P +FK +R D I+EAT
Sbjct: 281 KRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNV 340
Query: 358 GDVTLRFCIANGFRNIQNLIQKLKRKRLPYDFIEIMA 394
G ++ + +G + + + +K + PY FIE MA
Sbjct: 341 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 = 101 bits (251), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 92/337 (27%), Positives = 144/337 (42%), Gaps = 39/337 (11%)
Query: 72 CLACSGCITSA-ESVLITQQSH-EEVMKVIRENNAHKASSNENTKTIVLSLAIQPVLSLG 129
C+ C C+T E+ + QS EV K +++ K I + A +LG
Sbjct: 40 CINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGK---------VKCIAMP-APAVRYALG 89
Query: 130 AKFALSHEQVV-AKLCGFFKRLGVDLVLDVGIAHCFSLVELENEFLDRFLSGGG---PLF 185
F + V K+ ++LG D ++ E +EF++R P F
Sbjct: 90 DAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQF 149
Query: 186 TSECPGWVCYAEKSHGEFILPYISRVKSPQQVMGSLIKTHLAEKLGVHPSHIYHVTLMPC 245
TS CPGW YAE + E +LP+ S KSP + G+L KT+ AE++ P +Y V++MPC
Sbjct: 150 TSCCPGWQKYAETYYPE-LLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPC 208
Query: 246 YDKKLEASRADFYNEELGYRDVDCVIXXXXXXXXXXXXXXXXXXXXXKDGILDWPWDEHN 305
KK E R + + G RD+D + K +D+
Sbjct: 209 IAKKYEGLRPELKSS--GMRDIDATL------------TTRELAYMIKKAGIDFAKLPDG 254
Query: 306 PHRMLLVNGTGSG---GYAHNVLSHAIR---QLCPGESP-VVEFKPLRNPD-IREATFTC 357
L+ TG G V+ A+R + G+ P +FK +R D I+EAT
Sbjct: 255 KRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNV 314
Query: 358 GDVTLRFCIANGFRNIQNLIQKLKRKRLPYDFIEIMA 394
G ++ + +G + + + +K + PY FIE MA
Sbjct: 315 GGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMA 351
>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 = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 50/140 (35%), Positives = 76/140 (54%), Gaps = 11/140 (7%)
Query: 142 KLCGFFKRLGVDLVLDVGIAHCFSLVELENEFLDRFL---------SGGGPLFTSECPGW 192
+L +RLG D V D +++E +E L R P+FTS CPGW
Sbjct: 74 QLAEGLRRLGFDEVFDTLFGADLTIMEEGSELLHRLTEHLEAHPHSDEPLPMFTSCCPGW 133
Query: 193 VCYAEKSHGEFILPYISRVKSPQQVMGSLIKTHLAEKLGVHPSHIYHVTLMPCYDKKLEA 252
+ EKS+ + I PY+S KSPQ ++ +++K++LAEK G+ P + V++MPC K+ EA
Sbjct: 134 IAMLEKSYPDLI-PYVSSCKSPQMMLAAMVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEA 192
Query: 253 SRADF-YNEELGYRDVDCVI 271
R F + + R +D VI
Sbjct: 193 DRDWFCVDADPTLRQLDHVI 212
Score = 75.1 bits (183), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 38/106 (35%), Positives = 55/106 (51%)
Query: 358 GDVTLRFCIANGFRNIQNLIQKLKRKRLPYDFIEIMACPSGCLNGGAQIRNEKVASPKET 417
G +TLR +ANG N + LI K++ YDF+EIMACP+GC+ GG Q R+ A ++
Sbjct: 340 GGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGGQPRSTDKAITQKR 399
Query: 418 ALELETILCDLAKSEPRENATLEHLYKAWLGGKSTDKGKHMLNTSY 463
L + EN ++ LY +LG K +L+T Y
Sbjct: 400 QAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLHTHY 445
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
0.319 0.136 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,889,926
Number of Sequences: 62578
Number of extensions: 561470
Number of successful extensions: 1231
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1215
Number of HSP's gapped (non-prelim): 11
length of query: 477
length of database: 14,973,337
effective HSP length: 102
effective length of query: 375
effective length of database: 8,590,381
effective search space: 3221392875
effective search space used: 3221392875
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)