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= 020304
(328 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1R30|A Chain A, The Crystal Structure Of Biotin Synthase, An S-
Adenosylmethionine-dependent Radical Enzyme
pdb|1R30|B Chain B, The Crystal Structure Of Biotin Synthase, An S-
Adenosylmethionine-dependent Radical Enzyme
Length = 369
Score = 31.6 bits (70), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 28/117 (23%), Positives = 54/117 (46%), Gaps = 17/117 (14%)
Query: 199 VETLVHSGLDVFAHNIETVKRLQRIVRDPRAGYEQSLEVLKHAKLSKKGLITKSSIMLGL 258
+ L ++GLD + HN++T + R Y++ L+ L+ K+ G+ S ++GL
Sbjct: 162 AQRLANAGLDYYNHNLDTSPEFYGNIITTRT-YQERLDTLE--KVRDAGIKVCSGGIVGL 218
Query: 259 GESDDDLKEAMADLRSIDVDILTLGQYLQPTPLHLTVKEYVTP-------EKFDFWK 308
GE+ + D + + + L + P+++ VK TP + FDF +
Sbjct: 219 GET-------VKDRAGLLLQLANLPTPPESVPINMLVKVKGTPLADNDDVDAFDFIR 268
>pdb|3IIZ|A Chain A, X-Ray Structure Of The Fefe-Hydrogenase Maturase Hyde From
T. Maritima In Complex With S-Adenosyl-L-Methionine
Length = 348
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 52/199 (26%), Positives = 82/199 (41%), Gaps = 18/199 (9%)
Query: 98 GDGIATATIMLLGDTCTRGCRFCAVKTSRNPAPPDPMEPENT---AKAIASWGVDYIVLT 154
GD + I+ + C + C +C ++ M PE A+ +G IVL
Sbjct: 48 GDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQ 107
Query: 155 S-VDRDDIPDGGSGHFARTVKAMKKQKPDIMVECLTSDFRGDLRAVETLVHSGLDVFAHN 213
S D +PD + VK +KK + V S E +G D +
Sbjct: 108 SGEDPYXMPD----VISDIVKEIKK----MGVAVTLSLGEWPREYYEKWKEAGADRYLLR 159
Query: 214 IETVK-RLQRIVRDPRAGYEQSLEVLKHAKLSKKGLITKSSIMLGL-GESDDDLKEAMAD 271
ET L R +R P +E L L L + G T + M+GL G++ DDL + +
Sbjct: 160 HETANPVLHRKLR-PDTSFENRLNXL--LTLKELGYETGAGSMVGLPGQTIDDLVDDLLF 216
Query: 272 LRSIDVDILTLGQYLQPTP 290
L+ D D++ +G ++ P P
Sbjct: 217 LKEHDFDMVGIGPFI-PHP 234
>pdb|3CIW|A Chain A, X-Ray Structure Of The [fefe]-Hydrogenase Maturase Hyde
From Thermotoga Maritima
pdb|3IIX|A Chain A, X-Ray Structure Of The Fefe-Hydrogenase Maturase Hyde From
T. Maritima In Complex With Methionine And
5'deoxyadenosine
Length = 348
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 52/199 (26%), Positives = 82/199 (41%), Gaps = 18/199 (9%)
Query: 98 GDGIATATIMLLGDTCTRGCRFCAVKTSRNPAPPDPMEPENT---AKAIASWGVDYIVLT 154
GD + I+ + C + C +C ++ M PE A+ +G IVL
Sbjct: 48 GDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQ 107
Query: 155 S-VDRDDIPDGGSGHFARTVKAMKKQKPDIMVECLTSDFRGDLRAVETLVHSGLDVFAHN 213
S D +PD + VK +KK + V S E +G D +
Sbjct: 108 SGEDPYXMPD----VISDIVKEIKK----MGVAVTLSLGEWPREYYEKWKEAGADRYLLR 159
Query: 214 IETVK-RLQRIVRDPRAGYEQSLEVLKHAKLSKKGLITKSSIMLGL-GESDDDLKEAMAD 271
ET L R +R P +E L L L + G T + M+GL G++ DDL + +
Sbjct: 160 HETANPVLHRKLR-PDTSFENRLNXL--LTLKELGYETGAGSMVGLPGQTIDDLVDDLLF 216
Query: 272 LRSIDVDILTLGQYLQPTP 290
L+ D D++ +G ++ P P
Sbjct: 217 LKEHDFDMVGIGPFI-PHP 234
>pdb|1UAS|A Chain A, Crystal Structure Of Rice Alpha-Galactosidase
Length = 362
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 8/66 (12%)
Query: 123 KTSRNPAPPDPMEPENTAKAIASWGVDYIVLTSVDRDDIPDGGSG---HFARTVKAMKKQ 179
+T N P E K ASWGVDY+ D+ D G + R AMK
Sbjct: 99 QTCSNKMPGSLDHEEQDVKTFASWGVDYL-----KYDNCNDAGRSVMERYTRMSNAMKTY 153
Query: 180 KPDIMV 185
+I
Sbjct: 154 GKNIFF 159
>pdb|1D1N|A Chain A, Solution Structure Of The Fmet-Trnafmet Binding Domain Of
Becillus Stearothermophillus Translation Initiation
Factor If2
Length = 99
Score = 29.3 bits (64), Expect = 3.3, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 170 ARTVKAMKKQKPDIMVECLTSDFRGDLRAVETLVHSGLDVFAHNIETVKRLQRIVRDPRA 229
A + K K + C +D + + L+ G+ V+ I+++KR + VR+
Sbjct: 9 AEVRQTFKVSKVGTIAGCYVTDGKITRDSKVRLIRQGIVVYEGEIDSLKRYKDDVREVAQ 68
Query: 230 GYEQSLEVLKHAKLSKKGLITKSSIM 255
GYE L + K+ K+G + ++ +M
Sbjct: 69 GYECGLTI-KNFNDIKEGDVIEAYVM 93
>pdb|3CIX|A Chain A, X-ray Structure Of The [fefe]-hydrogenase Maturase Hyde
From Thermotoga Maritima In Complex With Thiocyanate
Length = 348
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 52/199 (26%), Positives = 82/199 (41%), Gaps = 18/199 (9%)
Query: 98 GDGIATATIMLLGDTCTRGCRFCAVKTSRNPAPPDPMEPENT---AKAIASWGVDYIVLT 154
GD + I+ + C + C +C ++ M PE A+ +G IVL
Sbjct: 48 GDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQ 107
Query: 155 S-VDRDDIPDGGSGHFARTVKAMKKQKPDIMVECLTSDFRGDLRAVETLVHSGLDVFAHN 213
S D +PD + VK +KK + V S E +G D +
Sbjct: 108 SGEDPYYMPD----VISDIVKEIKK----MGVAVTLSLGEWPREYYEKWKEAGADRYLLR 159
Query: 214 IETVK-RLQRIVRDPRAGYEQSLEVLKHAKLSKKGLITKSSIMLGL-GESDDDLKEAMAD 271
ET L R +R P +E L L L + G T + M+GL G++ DDL + +
Sbjct: 160 HETANPVLHRKLR-PDTSFENRLNXL--LTLKELGYETGAGSMVGLPGQTIDDLVDDLLF 216
Query: 272 LRSIDVDILTLGQYLQPTP 290
L+ D D++ +G ++ P P
Sbjct: 217 LKEHDFDMVGIGPFI-PHP 234
>pdb|3RAZ|A Chain A, The Crystal Structure Of Thioredoxin-Related Protein From
Neisseria Meningitidis Serogroup B
Length = 151
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 266 KEAMADLRSIDVDIL-TLGQYLQPTPLHLTVKEYVTPEKFDFWKAYGESIG 315
K+ D I +D +G +L+ TP+ + Y +F K YG ++G
Sbjct: 54 KKGSVDXVGIALDTSDNIGNFLKQTPVSYPIWRYTGANSRNFXKTYGNTVG 104
>pdb|2L5H|A Chain A, Solution Structure Of The H189q Mutant Of The Enzyme I
Dimer Using Residual Dipolar Couplings And Small Angle
X-Ray Scattering
pdb|2L5H|B Chain B, Solution Structure Of The H189q Mutant Of The Enzyme I
Dimer Using Residual Dipolar Couplings And Small Angle
X-Ray Scattering
Length = 573
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 191 DFRGDLRAVETLVHSGLDVFAHNIETVKRLQRIVR-----DPRAGYEQSL 235
+ GD RA L+ GLD F+ + ++ R+++I+R D + EQ+L
Sbjct: 504 ELAGDERATLLLLGMGLDEFSMSAISIPRIKKIIRNTNFEDAKVLAEQAL 553
>pdb|2KX9|A Chain A, Solution Structure Of The Enzyme I Dimer Using Residual
Dipolar Couplings And Small Angle X-Ray Scattering
pdb|2KX9|B Chain B, Solution Structure Of The Enzyme I Dimer Using Residual
Dipolar Couplings And Small Angle X-Ray Scattering
pdb|2XDF|A Chain A, Solution Structure Of The Enzyme I Dimer Complexed With
Hpr Using Residual Dipolar Couplings And Small Angle
X-Ray Scattering
pdb|2XDF|B Chain B, Solution Structure Of The Enzyme I Dimer Complexed With
Hpr Using Residual Dipolar Couplings And Small Angle
X-Ray Scattering
Length = 573
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 191 DFRGDLRAVETLVHSGLDVFAHNIETVKRLQRIVR-----DPRAGYEQSL 235
+ GD RA L+ GLD F+ + ++ R+++I+R D + EQ+L
Sbjct: 504 ELAGDERATLLLLGMGLDEFSMSAISIPRIKKIIRNTNFEDAKVLAEQAL 553
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
0.318 0.134 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,210,658
Number of Sequences: 62578
Number of extensions: 421673
Number of successful extensions: 1120
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1111
Number of HSP's gapped (non-prelim): 20
length of query: 328
length of database: 14,973,337
effective HSP length: 99
effective length of query: 229
effective length of database: 8,778,115
effective search space: 2010188335
effective search space used: 2010188335
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: 52 (24.6 bits)