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= 037863
(672 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DFD|A Chain A, Crystal Structure Of Human Malate Dehydrogenase Type 2
pdb|2DFD|B Chain B, Crystal Structure Of Human Malate Dehydrogenase Type 2
pdb|2DFD|C Chain C, Crystal Structure Of Human Malate Dehydrogenase Type 2
pdb|2DFD|D Chain D, Crystal Structure Of Human Malate Dehydrogenase Type 2
Length = 342
Score = 37.7 bits (86), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 62/147 (42%), Gaps = 25/147 (17%)
Query: 332 GLYNFLKILSLTVINIYGTIKTKNLNAGQLRSLKSFSTYKSLEDLKHNEIFLRENIPMWI 391
G+YN KI +T ++I +R+ + K L+ R N+P+
Sbjct: 163 GVYNPNKIFGVTTLDI-------------VRANTFVAELKGLDPA-------RVNVPVIG 202
Query: 392 GVAGYLVFSILSIIVIPIMFPQLKWYYVVIAYILAPSLSFCNAYGAGLTDINMAYNYGKV 451
G AG + ++S + FPQ + + A + GAG ++MAY +
Sbjct: 203 GHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARF 262
Query: 452 ALFVLAALSGRENGLVAGMVGCGLVKS 478
++ A++G+E G+V C VKS
Sbjct: 263 VFSLVDAMNGKE-----GVVECSFVKS 284
>pdb|1MLD|A Chain A, Refined Structure Of Mitochondrial Malate Dehydrogenase
From Porcine Heart And The Consensus Structure For
Dicarboxylic Acid Oxidoreductases
pdb|1MLD|B Chain B, Refined Structure Of Mitochondrial Malate Dehydrogenase
From Porcine Heart And The Consensus Structure For
Dicarboxylic Acid Oxidoreductases
pdb|1MLD|C Chain C, Refined Structure Of Mitochondrial Malate Dehydrogenase
From Porcine Heart And The Consensus Structure For
Dicarboxylic Acid Oxidoreductases
pdb|1MLD|D Chain D, Refined Structure Of Mitochondrial Malate Dehydrogenase
From Porcine Heart And The Consensus Structure For
Dicarboxylic Acid Oxidoreductases
Length = 314
Score = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 35/147 (23%), Positives = 62/147 (42%), Gaps = 25/147 (17%)
Query: 332 GLYNFLKILSLTVINIYGTIKTKNLNAGQLRSLKSFSTYKSLEDLKHNEIFLRENIPMWI 391
G+YN KI +T ++I +R+ + K L+ R ++P+
Sbjct: 135 GVYNPNKIFGVTTLDI-------------VRANAFVAELKGLDPA-------RVSVPVIG 174
Query: 392 GVAGYLVFSILSIIVIPIMFPQLKWYYVVIAYILAPSLSFCNAYGAGLTDINMAYNYGKV 451
G AG + ++S + FPQ + + A + GAG ++MAY +
Sbjct: 175 GHAGKTIIPLISQCTPKVDFPQDQLSTLTGRIQEAGTEVVKAKAGAGSATLSMAYAGARF 234
Query: 452 ALFVLAALSGRENGLVAGMVGCGLVKS 478
++ A++G+E G+V C VKS
Sbjct: 235 VFSLVDAMNGKE-----GVVECSFVKS 256
>pdb|1Q3B|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The R252a Mutant
At 2.05 Resolution.
pdb|2OPF|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli (R252a) In Complex
With Ap-Site Containing Dna Substrate
Length = 262
Score = 32.3 bits (72), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 15/72 (20%)
Query: 332 GLYNFLKILSLTVINIYGTIKTKNLNAGQLRSLK---------SFSTYKSLEDLKHN--- 379
GL N+L++ L + + G K K+LNA QL +L S++T +++ KH+
Sbjct: 165 GLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGAL 224
Query: 380 ---EIFLRENIP 388
++F R+ P
Sbjct: 225 FRFKVFHRDGEP 236
>pdb|1Q3C|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The E2a Mutant At
2.3 Resolution
Length = 262
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 15/72 (20%)
Query: 332 GLYNFLKILSLTVINIYGTIKTKNLNAGQLRSLK---------SFSTYKSLEDLKHN--- 379
GL N+L++ L + + G K K+LNA QL +L S++T +++ KH+
Sbjct: 165 GLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGAL 224
Query: 380 ---EIFLRENIP 388
++F R+ P
Sbjct: 225 FRFKVFHRDGEP 236
>pdb|2OQ4|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
pdb|2OQ4|B Chain B, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
Length = 262
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 15/72 (20%)
Query: 332 GLYNFLKILSLTVINIYGTIKTKNLNAGQLRSLK---------SFSTYKSLEDLKHN--- 379
GL N+L++ L + + G K K+LNA QL +L S++T +++ KH+
Sbjct: 165 GLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGAL 224
Query: 380 ---EIFLRENIP 388
++F R+ P
Sbjct: 225 FRFKVFHRDGEP 236
>pdb|1K3W|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of
The Dna Repair Enzyme Endonuclease Viii With Dna
pdb|1K3X|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of
The Dna Repair Enzyme Endonuclease Viii With
Brominated-Dna
pdb|1Q39|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The Wt Enzyme At
2.8 Resolution.
pdb|2EA0|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-viii (nei) From E. Coli In Complex With
Ap-site Containing Dna Substrate
Length = 262
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 15/72 (20%)
Query: 332 GLYNFLKILSLTVINIYGTIKTKNLNAGQLRSLK---------SFSTYKSLEDLKHN--- 379
GL N+L++ L + + G K K+LNA QL +L S++T +++ KH+
Sbjct: 165 GLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGAL 224
Query: 380 ---EIFLRENIP 388
++F R+ P
Sbjct: 225 FRFKVFHRDGEP 236
>pdb|1Y9I|A Chain A, Crystal Structure Of Low Temperature Requirement C Protein
From Listeria Monocytogenes
pdb|1Y9I|B Chain B, Crystal Structure Of Low Temperature Requirement C Protein
From Listeria Monocytogenes
pdb|1Y9I|C Chain C, Crystal Structure Of Low Temperature Requirement C Protein
From Listeria Monocytogenes
pdb|1Y9I|D Chain D, Crystal Structure Of Low Temperature Requirement C Protein
From Listeria Monocytogenes
Length = 178
Score = 29.6 bits (65), Expect = 5.4, Method: Composition-based stats.
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 331 DGLYNFLKILSLTVINIYGTIKTKN 355
+GLY +IL+L+++N+YG+I N
Sbjct: 92 EGLYGVDEILALSIVNVYGSIGFTN 116
>pdb|1RFZ|A Chain A, Structure Of Protein Of Unknown Function From Bacillus
Stearothermophilus
pdb|1RFZ|B Chain B, Structure Of Protein Of Unknown Function From Bacillus
Stearothermophilus
pdb|1RFZ|C Chain C, Structure Of Protein Of Unknown Function From Bacillus
Stearothermophilus
pdb|1RFZ|D Chain D, Structure Of Protein Of Unknown Function From Bacillus
Stearothermophilus
Length = 168
Score = 29.6 bits (65), Expect = 5.4, Method: Composition-based stats.
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 331 DGLYNFLKILSLTVINIYGTIKTKN 355
+GLY +IL+L+++N+YG+I N
Sbjct: 94 EGLYGVDEILALSIVNVYGSIGFTN 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
0.326 0.141 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,835,112
Number of Sequences: 62578
Number of extensions: 686934
Number of successful extensions: 1479
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1472
Number of HSP's gapped (non-prelim): 8
length of query: 672
length of database: 14,973,337
effective HSP length: 105
effective length of query: 567
effective length of database: 8,402,647
effective search space: 4764300849
effective search space used: 4764300849
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.8 bits)