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= 013734
(437 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3F6R|A Chain A, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin
pdb|3F6R|B Chain B, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin
pdb|3F6R|C Chain C, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin
pdb|3F6R|D Chain D, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin
pdb|3F6S|A Chain A, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F6S|B Chain B, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F6S|D Chain D, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F6S|E Chain E, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F6S|F Chain F, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F6S|H Chain H, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F6S|I Chain I, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F6S|G Chain G, Desulfovibrio Desulfuricans (Atcc 29577) Oxidized
Flavodoxin Alternate Conformers
pdb|3F90|A Chain A, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
pdb|3F90|B Chain B, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
pdb|3F90|D Chain D, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
pdb|3F90|E Chain E, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
pdb|3F90|F Chain F, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
pdb|3F90|H Chain H, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
pdb|3F90|I Chain I, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
pdb|3F90|G Chain G, Desulfovibrio Desulfuricans (Atcc 29577) Semiquinone
Flavodoxin
Length = 148
Score = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 39/94 (41%), Gaps = 18/94 (19%)
Query: 194 DLMAKGMKNAQNAVLSGCSAGGLTSILHCDNFRALFP-------VGTKVKCFADAGYFIN 246
D A+ + + +AVL GCSA G+ + D+F +LF G KV FA
Sbjct: 40 DASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFDRIGLAGRKVAAFA------- 92
Query: 247 AKDVSGASHIEQFYAQVVATHGSAKHLPASCTSR 280
SG E F V A AK L A+ +
Sbjct: 93 ----SGDQEYEHFCGAVPAIEERAKELGATIIAE 122
>pdb|1AKQ|A Chain A, D95a Oxidized Flavodoxin Mutant From D. Vulgaris
pdb|1AKU|A Chain A, D95a Hydroquinone Flavodoxin Mutant From D. Vulgaris
pdb|1AKV|A Chain A, D95a Semiquinone Flavodoxin Mutant From D. Vulgaris
Length = 147
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 44/121 (36%), Gaps = 20/121 (16%)
Query: 165 ASFTGDVE--AVNPANNLHFRGARVFQAVMEDLMAKGMKNAQNAVLSGCSAGGLTSILHC 222
S TG+ E A A L G V + A G+ + VL GCS G SI
Sbjct: 8 GSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQ 67
Query: 223 DNFRALFPV-------GTKVKCFADAGYFINAKDVSGASHIEQFYAQVVATHGSAKHLPA 275
D+F LF G KV CF GAS E F V A K+L A
Sbjct: 68 DDFIPLFDSLEETGAQGRKVACFG-----------CGASSYEYFCGAVDAIEEKLKNLGA 116
Query: 276 S 276
Sbjct: 117 E 117
>pdb|3IZB|E Chain E, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|B Chain B, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|B Chain B, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 254
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 20/83 (24%)
Query: 293 ARQITT--PLFIINAAYDSWQIKNILAPGVADPHGTWHSCKLDINNCSPTQLQTMQSFRT 350
A +ITT +F+ + +QI + L PG+ D ++ N P Q QT RT
Sbjct: 47 AGKITTIEEIFLHSLPVKEFQIIDTLLPGLQD----------EVMNIKPVQKQTRAGQRT 96
Query: 351 QFL--------NALAGLGISSSR 365
+F N GLGI +++
Sbjct: 97 RFKAVVVVGDSNGHVGLGIKTAK 119
>pdb|1C7E|A Chain A, D95e Hydroquinone Flavodoxin Mutant From D. Vulgaris
pdb|1C7E|B Chain B, D95e Hydroquinone Flavodoxin Mutant From D. Vulgaris
pdb|1C7F|A Chain A, D95e Oxidized Flavodoxin Mutant From D. Vulgaris
pdb|1C7F|B Chain B, D95e Oxidized Flavodoxin Mutant From D. Vulgaris
Length = 147
Score = 28.9 bits (63), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 43/121 (35%), Gaps = 20/121 (16%)
Query: 165 ASFTGDVE--AVNPANNLHFRGARVFQAVMEDLMAKGMKNAQNAVLSGCSAGGLTSILHC 222
S TG+ E A A L G V + A G+ + VL GCS G SI
Sbjct: 8 GSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQ 67
Query: 223 DNFRALFPV-------GTKVKCFADAGYFINAKDVSGASHIEQFYAQVVATHGSAKHLPA 275
D+F LF G KV CF G S E F V A K+L A
Sbjct: 68 DDFIPLFDSLEETGAQGRKVACFG-----------CGESSYEYFCGAVDAIEEKLKNLGA 116
Query: 276 S 276
Sbjct: 117 E 117
>pdb|2HYX|A Chain A, Structure Of The C-Terminal Domain Of Dipz From
Mycobacterium Tuberculosis
pdb|2HYX|B Chain B, Structure Of The C-Terminal Domain Of Dipz From
Mycobacterium Tuberculosis
pdb|2HYX|C Chain C, Structure Of The C-Terminal Domain Of Dipz From
Mycobacterium Tuberculosis
pdb|2HYX|D Chain D, Structure Of The C-Terminal Domain Of Dipz From
Mycobacterium Tuberculosis
Length = 352
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 177 ANNLHFRGARVFQAVMEDLMAKGMKNAQNAVLSGCSAG 214
+ NL+F+ + + E L G+ NAQNA LS CS G
Sbjct: 12 SENLYFQSGAM--EIREQLNLGGIVNAQNAQLSNCSDG 47
>pdb|1BU5|A Chain A, X-Ray Crystal Structure Of The Desulfovibrio Vulgaris
(Hildenborough) Apoflavodoxin-Riboflavin Complex
pdb|1BU5|B Chain B, X-Ray Crystal Structure Of The Desulfovibrio Vulgaris
(Hildenborough) Apoflavodoxin-Riboflavin Complex
Length = 147
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 43/121 (35%), Gaps = 20/121 (16%)
Query: 165 ASFTGDVE--AVNPANNLHFRGARVFQAVMEDLMAKGMKNAQNAVLSGCSAGGLTSILHC 222
S TG+ E A A L G V + A G+ + VL GCS G SI
Sbjct: 8 GSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQ 67
Query: 223 DNFRALFPV-------GTKVKCFADAGYFINAKDVSGASHIEQFYAQVVATHGSAKHLPA 275
D+F LF G KV CF G S E F V A K+L A
Sbjct: 68 DDFIPLFDSLEETGAQGRKVACFG-----------CGDSSYEYFCGAVDAIEEKLKNLGA 116
Query: 276 S 276
Sbjct: 117 E 117
>pdb|1J8Q|A Chain A, Low Temperature (100k) Crystal Structure Of Flavodoxin D.
Vulgaris Wild-Type At 1.35 Angstrom Resolution
pdb|2FX2|A Chain A, Comparison Of The Crystal Structures Of A Flavodoxin In
Its Three Oxidation States At Cryogenic Temperatures
pdb|3FX2|A Chain A, Comparison Of The Crystal Structures Of A Flavodoxin In
Its Three Oxidation States At Cryogenic Temperatures
pdb|4FX2|A Chain A, Comparison Of The Crystal Structures Of A Flavodoxin In
Its Three Oxidation States At Cryogenic Temperatures
pdb|5FX2|A Chain A, Comparison Of The Crystal Structures Of A Flavodoxin In
Its Three Oxidation States At Cryogenic Temperatures
Length = 147
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 43/121 (35%), Gaps = 20/121 (16%)
Query: 165 ASFTGDVE--AVNPANNLHFRGARVFQAVMEDLMAKGMKNAQNAVLSGCSAGGLTSILHC 222
S TG+ E A A L G V + A G+ + VL GCS G SI
Sbjct: 8 GSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQ 67
Query: 223 DNFRALFPV-------GTKVKCFADAGYFINAKDVSGASHIEQFYAQVVATHGSAKHLPA 275
D+F LF G KV CF G S E F V A K+L A
Sbjct: 68 DDFIPLFDSLEETGAQGRKVACFG-----------CGDSSYEYFCGAVDAIEEKLKNLGA 116
Query: 276 S 276
Sbjct: 117 E 117
>pdb|1FX1|A Chain A, A Crystallographic Structural Study Of The Oxidation
States Of Desulfovibrio Vulgaris Flavodoxin
Length = 148
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 43/121 (35%), Gaps = 20/121 (16%)
Query: 165 ASFTGDVE--AVNPANNLHFRGARVFQAVMEDLMAKGMKNAQNAVLSGCSAGGLTSILHC 222
S TG+ E A A L G V + A G+ + VL GCS G SI
Sbjct: 9 GSTTGNTEYTAETIARQLANAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQ 68
Query: 223 DNFRALFPV-------GTKVKCFADAGYFINAKDVSGASHIEQFYAQVVATHGSAKHLPA 275
D+F LF G KV CF G S E F V A K+L A
Sbjct: 69 DDFIPLFDSLEETGAQGRKVACFG-----------CGDSSYEYFCGAVDAIEEKLKNLGA 117
Query: 276 S 276
Sbjct: 118 E 118
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
0.324 0.136 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,546,636
Number of Sequences: 62578
Number of extensions: 496995
Number of successful extensions: 1227
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1226
Number of HSP's gapped (non-prelim): 8
length of query: 437
length of database: 14,973,337
effective HSP length: 102
effective length of query: 335
effective length of database: 8,590,381
effective search space: 2877777635
effective search space used: 2877777635
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)