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= 002884
(870 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2AVN|A Chain A, Crystal Structure Of A UbiquinoneMENAQUINONE BIOSYNTHESIS
Methyltransferase-Related Protein (Tm1389) From
Thermotoga Maritima Msb8 At 2.35 A Resolution
pdb|2AVN|B Chain B, Crystal Structure Of A UbiquinoneMENAQUINONE BIOSYNTHESIS
Methyltransferase-Related Protein (Tm1389) From
Thermotoga Maritima Msb8 At 2.35 A Resolution
Length = 260
Score = 32.0 bits (71), Expect = 1.5, Method: Composition-based stats.
Identities = 28/118 (23%), Positives = 50/118 (42%), Gaps = 6/118 (5%)
Query: 472 LDVGCGVASFGGYLFERDVLTMSFAPKDEHDAQIQFALERGIPAISAVMGTKRLQFPRNV 531
LD+G G + +L ER + P E ++ A E+G+ + + L FP
Sbjct: 59 LDLGGGTGKWSLFLQERGFEVVLVDPSKE---XLEVAREKGVKNVVEAKA-EDLPFPSGA 114
Query: 532 FDLVHCARCRVPWHIDGGKLLLELNRVLRPGGYFVWSATPVYQKLGEDVE--IWNAMS 587
F+ V + + + K E+ RVL P G + + Y L + +E W+ ++
Sbjct: 115 FEAVLALGDVLSYVENKDKAFSEIRRVLVPDGLLIATVDNFYTFLQQXIEKDAWDQIT 172
>pdb|3F29|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Sulfite
pdb|3F29|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Sulfite
pdb|2ZO5|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With Azide
pdb|2ZO5|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With Azide
pdb|3D1I|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With Nitrite
pdb|3D1I|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With Nitrite
pdb|3GM6|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Phosphate
pdb|3GM6|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Phosphate
pdb|3FO3|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase Reduced By Sodium
Dithionite (Sulfite Complex)
pdb|3FO3|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase Reduced By Sodium
Dithionite (Sulfite Complex)
pdb|3MMO|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Cyanide
pdb|3MMO|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Cyanide
pdb|3LG1|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase Reduced By Sodium
Borohydride (In Complex With Sulfite)
pdb|3LG1|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase Reduced By Sodium
Borohydride (In Complex With Sulfite)
pdb|3LGQ|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Sulfite
(Modified Tyr-303)
pdb|3LGQ|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In Complex With Sulfite
(Modified Tyr-303)
Length = 525
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 47/112 (41%), Gaps = 21/112 (18%)
Query: 494 SFAPKDEHDAQIQFALERGI------PAISAVMGTKRLQFPRNVFDL------------V 535
S P+ D I ++RG+ P S G ++ F R D V
Sbjct: 235 SAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNV 294
Query: 536 HCARCRVPWHIDGGKLLLELNRVL---RPGGYFVWSATPVYQKLGEDVEIWN 584
CA+C V ++ + G L + +RV R +F W+ Y++ ++++ ++
Sbjct: 295 MCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFD 346
>pdb|2OT4|A Chain A, Structure Of A Hexameric Multiheme C Nitrite Reductase
From The Extremophile Bacterium Thiolkalivibrio
Nitratireducens
pdb|2OT4|B Chain B, Structure Of A Hexameric Multiheme C Nitrite Reductase
From The Extremophile Bacterium Thiolkalivibrio
Nitratireducens
Length = 525
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 47/112 (41%), Gaps = 21/112 (18%)
Query: 494 SFAPKDEHDAQIQFALERGI------PAISAVMGTKRLQFPRNVFDL------------V 535
S P+ D I ++RG+ P S G ++ F R D V
Sbjct: 235 SAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNV 294
Query: 536 HCARCRVPWHIDGGKLLLELNRVL---RPGGYFVWSATPVYQKLGEDVEIWN 584
CA+C V ++ + G L + +RV R +F W+ Y++ ++++ ++
Sbjct: 295 MCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFD 346
>pdb|3UU9|A Chain A, Structure Of The Free Tvnirb Form Of Thioalkalivibrio
Nitratireducens Cytochrome C Nitrite Reductase
pdb|3UU9|B Chain B, Structure Of The Free Tvnirb Form Of Thioalkalivibrio
Nitratireducens Cytochrome C Nitrite Reductase
Length = 520
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 47/112 (41%), Gaps = 21/112 (18%)
Query: 494 SFAPKDEHDAQIQFALERGI------PAISAVMGTKRLQFPRNVFDL------------V 535
S P+ D I ++RG+ P S G ++ F R D V
Sbjct: 231 SAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNV 290
Query: 536 HCARCRVPWHIDGGKLLLELNRVL---RPGGYFVWSATPVYQKLGEDVEIWN 584
CA+C V ++ + G L + +RV R +F W+ Y++ ++++ ++
Sbjct: 291 MCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFD 342
>pdb|3SCE|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase With A Covalent Bond
Between The Ce1 Atom Of Tyr303 And The Cg Atom Of Gln360
(Tvnirb)
pdb|3SCE|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase With A Covalent Bond
Between The Ce1 Atom Of Tyr303 And The Cg Atom Of Gln360
(Tvnirb)
pdb|3S7W|A Chain A, Structure Of The Tvnirb Form Of Thioalkalivibrio
Nitratireducens Cytochrome C Nitrite Reductase With An
Oxidized Gln360 In A Complex With Hydroxylamine
pdb|3S7W|B Chain B, Structure Of The Tvnirb Form Of Thioalkalivibrio
Nitratireducens Cytochrome C Nitrite Reductase With An
Oxidized Gln360 In A Complex With Hydroxylamine
pdb|3OWM|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With
Hydroxylamine
pdb|3OWM|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With
Hydroxylamine
Length = 519
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 47/112 (41%), Gaps = 21/112 (18%)
Query: 494 SFAPKDEHDAQIQFALERGI------PAISAVMGTKRLQFPRNVFDL------------V 535
S P+ D I ++RG+ P S G ++ F R D V
Sbjct: 231 SAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNV 290
Query: 536 HCARCRVPWHIDGGKLLLELNRVL---RPGGYFVWSATPVYQKLGEDVEIWN 584
CA+C V ++ + G L + +RV R +F W+ Y++ ++++ ++
Sbjct: 291 MCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFD 342
>pdb|3RKH|A Chain A, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With Nitrite
(Full Occupancy)
pdb|3RKH|B Chain B, Structure Of The Thioalkalivibrio Nitratireducens
Cytochrome C Nitrite Reductase In A Complex With Nitrite
(Full Occupancy)
Length = 520
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 47/112 (41%), Gaps = 21/112 (18%)
Query: 494 SFAPKDEHDAQIQFALERGI------PAISAVMGTKRLQFPRNVFDL------------V 535
S P+ D I ++RG+ P S G ++ F R D V
Sbjct: 231 SAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNV 290
Query: 536 HCARCRVPWHIDGGKLLLELNRVL---RPGGYFVWSATPVYQKLGEDVEIWN 584
CA+C V ++ + G L + +RV R +F W+ Y++ ++++ ++
Sbjct: 291 MCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFD 342
>pdb|3BKW|A Chain A, Crystal Structure Of S-Adenosylmethionine Dependent
Methyltransferase (Np_104914.1) From Mesorhizobium Loti
At 1.60 A Resolution
pdb|3BKW|B Chain B, Crystal Structure Of S-Adenosylmethionine Dependent
Methyltransferase (Np_104914.1) From Mesorhizobium Loti
At 1.60 A Resolution
Length = 243
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 29/106 (27%), Positives = 51/106 (48%), Gaps = 8/106 (7%)
Query: 472 LDVGCGVASFGGYLFERD---VLTMSFAPKDEHDAQIQFALERGIPAISAVMGTKRLQFP 528
+D+GCG F + E VL + + K A+ + GI A + +L P
Sbjct: 48 VDLGCGFGWFCRWAHEHGASYVLGLDLSEKXLARARAA-GPDTGITYERADL--DKLHLP 104
Query: 529 RNVFDLVHCARCRVPWHIDGGKLLLELNRVLRPGGYFVWSAT-PVY 573
++ FDL + + + + D +L +++ L PGG+FV+S P+Y
Sbjct: 105 QDSFDLAYSSLA-LHYVEDVARLFRTVHQALSPGGHFVFSTEHPIY 149
>pdb|2GS9|A Chain A, Crystal Structure Of Tt1324 From Thermus Thermophilis Hb8
pdb|2GS9|B Chain B, Crystal Structure Of Tt1324 From Thermus Thermophilis Hb8
Length = 211
Score = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 12/63 (19%)
Query: 525 LQFPRNVFDLVHCARCRVPWHIDGGKLLLELNRVLRPGGYFV---------WSATPVYQK 575
L FP FD+V + + D ++LLE RVLRPGG V W+A +Y++
Sbjct: 89 LPFPGESFDVV-LLFTTLEFVEDVERVLLEARRVLRPGGALVVGVLEALSPWAA--LYRR 145
Query: 576 LGE 578
LGE
Sbjct: 146 LGE 148
>pdb|1YQ2|A Chain A, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2-
2-1)
pdb|1YQ2|B Chain B, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2-
2-1)
pdb|1YQ2|C Chain C, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2-
2-1)
pdb|1YQ2|D Chain D, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2-
2-1)
pdb|1YQ2|E Chain E, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2-
2-1)
pdb|1YQ2|F Chain F, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2-
2-1)
Length = 1024
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 43/204 (21%), Positives = 73/204 (35%), Gaps = 18/204 (8%)
Query: 509 LERGIPAISAVMGTKRLQFPRNVFDLVHCARCRVPWHIDGGKLLLELNRVLRPGGYFVWS 568
L R + ++A+ R++ D H W +DGG+L L ++ G VW
Sbjct: 811 LTRRVEDVAALPDGIRVRTRYAAADSTHSVAVEENWQLDGGELCLRIDITPSAGWNLVWP 870
Query: 569 ATPVYQKLGEDVE--IWNAMS---NLTVSMCWELVTIKMDKLNSAGFAIYRKPTTNECYE 623
V L DV+ W + SM +V L R T +
Sbjct: 871 RIGVRWDLPTDVDGAAWFGAGPRESYPDSMHATMVARHAASLEELNVPYARPQETGHRSD 930
Query: 624 KR----NQMTPPMCQNEEDPNAAWYVPLQACVHRVPVDKAERGSQWPEAWPHRLQRPPY- 678
R ++ P + + +P+AA P + + A G PH L P +
Sbjct: 931 VRWLELDRAGAPWLRIDAEPDAAGRRPGFSLARHTAQEIAAAGH------PHELPTPSHS 984
Query: 679 --WLNSSQMGIYGRPAPQDFTRDY 700
+++++Q G+ R D D+
Sbjct: 985 YLYVDAAQHGLGSRACGPDVWPDF 1008
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
0.316 0.134 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,796,960
Number of Sequences: 62578
Number of extensions: 1147311
Number of successful extensions: 2328
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2323
Number of HSP's gapped (non-prelim): 15
length of query: 870
length of database: 14,973,337
effective HSP length: 107
effective length of query: 763
effective length of database: 8,277,491
effective search space: 6315725633
effective search space used: 6315725633
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: 56 (26.2 bits)