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= 020904
(320 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SJ5|A Chain A, Crystal Structure Of A Duf151 Family Protein (tm0160) From
Thermotoga Maritima At 2.8 A Resolution
pdb|1SJ5|B Chain B, Crystal Structure Of A Duf151 Family Protein (tm0160) From
Thermotoga Maritima At 2.8 A Resolution
Length = 164
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 33/117 (28%), Positives = 54/117 (46%), Gaps = 7/117 (5%)
Query: 140 PAIVLKMEDGTGLLLPIIVLEMPSVLLMAAMRNVQIARPTLYQVVKEMIEKMGYEVRLVR 199
P ++L +E GT +LPI + L AM ++ RP + ++ ++E + V V
Sbjct: 30 PVVILGIE-GTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVI 88
Query: 200 VTKRVHEAYFAQL------YLTKVGNETECVSFDLRPSDAINIAVRCKVPIQVNKYL 250
+ ++A L Y + E + D RPSDAI +AV+ PI V+ L
Sbjct: 89 IHSLKDNTFYATLVIRDLTYTDEEDEEAALIDIDSRPSDAIILAVKTGAPIFVSDNL 145
>pdb|1VJL|A Chain A, Crystal Structure Of A Duf151 Family Protein (Tm0160) From
Thermotoga Maritima At 1.90 A Resolution
pdb|1VJL|B Chain B, Crystal Structure Of A Duf151 Family Protein (Tm0160) From
Thermotoga Maritima At 1.90 A Resolution
Length = 164
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 52/117 (44%), Gaps = 7/117 (5%)
Query: 140 PAIVLKMEDGTGLLLPIIVLEMPSVLLMAAMRNVQIARPTLYQVVKEMIEKMGYEVRLVR 199
P ++L +E GT +LPI + L A + RP + ++ ++E + V V
Sbjct: 30 PVVILGIE-GTNRVLPIWIGACEGHALALAXEKXEFPRPLTHDLLLSVLESLEARVDKVI 88
Query: 200 VTKRVHEAYFAQL------YLTKVGNETECVSFDLRPSDAINIAVRCKVPIQVNKYL 250
+ ++A L Y + E + D RPSDAI +AV+ PI V+ L
Sbjct: 89 IHSLKDNTFYATLVIRDLTYTDEEDEEAALIDIDSRPSDAIILAVKTGAPIFVSDNL 145
>pdb|1VL2|A Chain A, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
pdb|1VL2|B Chain B, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
pdb|1VL2|C Chain C, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
pdb|1VL2|D Chain D, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
Length = 421
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 231 SDAINIAVRCKVPIQVNKYLAYSDGMRVI----ESGKLS--THSPGSDGLLFTELDKPSG 284
+D IN A+ +PI+V+K YS+ ++ E+GKL H P D +FT P
Sbjct: 168 TDLINYAMEKGIPIKVSKKRPYSEDENLMHISHEAGKLEDPAHIPDED--VFTWTVSPKD 225
Query: 285 QPCLDT 290
P +T
Sbjct: 226 APDEET 231
>pdb|1JVN|A Chain A, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1JVN|B Chain B, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1OX4|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 9/100 (9%)
Query: 182 QVVKEMIEKMGYEVRLVRVTKRVHEAYFAQLYLTKVGNETECVS--FDLRPSDAINIAVR 239
Q + IE +GYEV+LV+ K + + ++L L VGN V F+ I +
Sbjct: 18 QSLTNAIEHLGYEVQLVKSPKDFNISGTSRLILPGVGNYGHFVDNLFNRGFEKPIREYIE 77
Query: 240 CKVPIQVNKYLAYSDGMRVIESGKLSTHSPGSDGLLFTEL 279
PI + G++ + +G S SP S GL + +
Sbjct: 78 SGKPI-----MGIXVGLQALFAG--SVESPKSTGLNYIDF 110
>pdb|1OX4|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 9/100 (9%)
Query: 182 QVVKEMIEKMGYEVRLVRVTKRVHEAYFAQLYLTKVGNETECVS--FDLRPSDAINIAVR 239
Q + IE +GYEV+LV+ K + + ++L L VGN V F+ I +
Sbjct: 18 QSLTNAIEHLGYEVQLVKSPKDFNISGTSRLILPGVGNYGHFVDNLFNRGFEKPIREYIE 77
Query: 240 CKVPIQVNKYLAYSDGMRVIESGKLSTHSPGSDGLLFTEL 279
PI + G++ + +G S SP S GL + +
Sbjct: 78 SGKPI-----MGICVGLQALFAG--SVESPKSTGLNYIDF 110
>pdb|1DBG|A Chain A, Crystal Structure Of Chondroitinase B
pdb|1DBO|A Chain A, Crystal Structure Of Chondroitinase B
Length = 506
Score = 28.1 bits (61), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 33/125 (26%), Positives = 56/125 (44%), Gaps = 17/125 (13%)
Query: 150 TGLLLPIIVLEMPSVLLMAAMRNVQIARPTLYQVVKEMIEKMGYEVRLVRVTKRVHEAYF 209
G LLPI+VL + + + V + TLYQVVKE+ K G V++ T +
Sbjct: 8 AGYLLPIMVL----LNVAPCLGQVVASNETLYQVVKEV--KPGGLVQIADGTYKD----- 56
Query: 210 AQLYLTKVGNETECVSFDLRPSDAINIAVRCKVPIQ----VNKYLAYSDGMRVIESGKLS 265
QL ++ G ++ + KV ++ + + + + DG R I++ K
Sbjct: 57 VQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRAIQAWK-- 114
Query: 266 THSPG 270
+H PG
Sbjct: 115 SHGPG 119
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
0.320 0.135 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,787,042
Number of Sequences: 62578
Number of extensions: 336921
Number of successful extensions: 732
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: 726
Number of HSP's gapped (non-prelim): 8
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)