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= 031660
(155 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JYA|A Chain A, Nmr Solution Structure Of Protein Atu1810 From
Agrobacterium Tumefaciens. Northeast Structural Genomics
Consortium Target Atr23, Ontario Centre For Structural
Proteomics Target Atc1776
Length = 106
Score = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 36/92 (39%), Positives = 52/92 (56%), Gaps = 4/92 (4%)
Query: 56 IYTPARTATQQGSGKLGRWKINF-MSTQKWENPLMGWTSTGDPYANVGDAGLSFDSKEAA 114
IY PA+TA Q G+ K W + F + +P+MG+TS+ D V L+F+++E A
Sbjct: 8 IYRPAKTAMQSGTAKTNVWVLEFDAEVPRKIDPIMGYTSSSDMKQQVK---LTFETQEQA 64
Query: 115 REFAERHGWEYVVRKPHRPLLKVKSYADNFKW 146
+A+R G EY V P KV SY DNF++
Sbjct: 65 EAYAQRKGIEYRVILPKEATRKVVSYTDNFRF 96
>pdb|2LJU|A Chain A, Solution Structure Of Putative Oxidoreductase From
Ehrlichia Chaffeensis, Seattle Structural Genomics
Center For Infectious Disease (Ssgcid)
Length = 108
Score = 62.4 bits (150), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 36/93 (38%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 53 RVVIYTPARTATQQGSGKLGRWKINFM-STQKWENPLMGWTSTGDPYANVGDAGLSFDSK 111
R IY PA++ Q G KL WK+ F S ++ PLM WT + D V LSF ++
Sbjct: 13 RARIYKPAKSTMQSGHSKLKAWKLEFEPSCTQYTEPLMNWTGSHDTKQQVC---LSFTTR 69
Query: 112 EAAREFAERHGWEYVVRKPHRPLLKVKSYADNF 144
E A +A H +Y V + + + KSYADNF
Sbjct: 70 ELAIAYAVAHKIDYTVLQDNPRTIVPKSYADNF 102
>pdb|3K6U|A Chain A, M. Acetivorans Molybdate-binding Protein (moda) In
Unliganded Open Form
pdb|3K6V|A Chain A, M. Acetivorans Molybdate-Binding Protein (Moda) In
Citrate-Bound Open Form
pdb|3K6W|A Chain A, Apo And Ligand Bound Structures Of Moda From The Archaeon
Methanosarcina Acetivorans
pdb|3K6X|A Chain A, M. Acetivorans Molybdate-Binding Protein (Moda) In
Molybdate-Bound Close Form With 2 Molecules In
Asymmetric Unit Forming Beta Barrel
pdb|3K6X|B Chain B, M. Acetivorans Molybdate-Binding Protein (Moda) In
Molybdate-Bound Close Form With 2 Molecules In
Asymmetric Unit Forming Beta Barrel
Length = 354
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 115 REFAERHGWEYVVRKPHRPLLKVKSYADNFK 145
R AE+HG+EYV P L ++ YADN+
Sbjct: 248 RSVAEQHGFEYVALPPAIDLSSLE-YADNYS 277
>pdb|3CFX|A Chain A, Crystal Structure Of M. Acetivorans Periplasmic Binding
Protein Moda/wtpa With Bound Tungstate
pdb|3CFX|B Chain B, Crystal Structure Of M. Acetivorans Periplasmic Binding
Protein Moda/wtpa With Bound Tungstate
Length = 296
Score = 30.0 bits (66), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 115 REFAERHGWEYVVRKPHRPLLKVKSYADNFK 145
R AE+HG+EYV P L ++ YADN+
Sbjct: 210 RSVAEQHGFEYVALPPAIDLSSLE-YADNYS 239
>pdb|4A8J|B Chain B, Crystal Structure Of The Elongator Subcomplex Elp456
pdb|4A8J|E Chain E, Crystal Structure Of The Elongator Subcomplex Elp456
Length = 270
Score = 29.6 bits (65), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 49 HLRRRVVIYTPARTATQQGSGKLGRWKINFMSTQ 82
HL ++++ Y PA TATQ + +N++ST+
Sbjct: 82 HLVKQIISYLPAATATQAKKHXVIIDSLNYISTE 115
>pdb|4EJS|B Chain B, Structure Of Yeast Elongator Subcomplex Elp456
Length = 242
Score = 29.3 bits (64), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 49 HLRRRVVIYTPARTATQQGSGKLGRWKINFMSTQ 82
HL ++++ Y PA TATQ + +N++ST+
Sbjct: 86 HLVKQIISYLPAATATQAKKHMVIIDSLNYISTE 119
>pdb|1JDQ|A Chain A, Solution Structure Of Tm006 Protein From Thermotoga
Maritima
Length = 98
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 15 VRGTVCPFSRAFSADALVEVKPGEI 39
VRG VCP + AL +KPGEI
Sbjct: 31 VRGEVCPVPDVETKRALQNMKPGEI 55
>pdb|3JUX|A Chain A, Structure Of The Translocation Atpase Seca From Thermotoga
Maritima
Length = 822
Score = 27.7 bits (60), Expect = 2.4, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 104 AGLSFDSKEAAREFAERHGWEYVVRKPHRPLLK 136
AG++ +K EF + +G E VV H+P+++
Sbjct: 413 AGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIR 445
>pdb|3DIN|A Chain A, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
pdb|3DIN|B Chain B, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
Length = 871
Score = 27.7 bits (60), Expect = 2.5, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 104 AGLSFDSKEAAREFAERHGWEYVVRKPHRPLLK 136
AG++ +K EF + +G E VV H+P+++
Sbjct: 413 AGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIR 445
>pdb|2LQM|A Chain A, Solution Structures Of Rada Intein From Pyrococcus
Horikoshii
pdb|4E2T|A Chain A, Crystal Structures Of Rada Intein From Pyrococcus
Horikoshii
pdb|4E2T|B Chain B, Crystal Structures Of Rada Intein From Pyrococcus
Horikoshii
Length = 174
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 18/23 (78%), Gaps = 2/23 (8%)
Query: 33 EVKPGEIGMVSGIPEEHLRRRVV 55
EVKPG++ V G+ EE LRRR++
Sbjct: 109 EVKPGDV--VVGVREEVLRRRII 129
>pdb|1Z6L|A Chain A, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|1Z6L|B Chain B, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|3BI2|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI2|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BNM|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNM|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNU|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3BNU|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3CN8|B Chain B, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CN8|A Chain A, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CND|B Chain B, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CND|A Chain A, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CNP|B Chain B, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNP|A Chain A, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNS|A Chain A, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNS|B Chain B, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNT|B Chain B, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
pdb|3CNT|A Chain A, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
Length = 516
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 24/52 (46%)
Query: 20 CPFSRAFSADALVEVKPGEIGMVSGIPEEHLRRRVVIYTPARTATQQGSGKL 71
C ++AD ++ P + +S PE++LR R+ P + Q K+
Sbjct: 238 CEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKI 289
>pdb|1YY5|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1YY5|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|C Chain C, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|D Chain D, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
Length = 513
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 24/52 (46%)
Query: 20 CPFSRAFSADALVEVKPGEIGMVSGIPEEHLRRRVVIYTPARTATQQGSGKL 71
C ++AD ++ P + +S PE++LR R+ P + Q K+
Sbjct: 238 CEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKI 289
>pdb|4ECH|A Chain A, Yeast Polyamine Oxidase Fms1, H67q Mutant
pdb|4ECH|B Chain B, Yeast Polyamine Oxidase Fms1, H67q Mutant
Length = 516
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 24/52 (46%)
Query: 20 CPFSRAFSADALVEVKPGEIGMVSGIPEEHLRRRVVIYTPARTATQQGSGKL 71
C ++AD ++ P + +S PE++LR R+ P + Q K+
Sbjct: 238 CEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKI 289
>pdb|4GDP|A Chain A, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|B Chain B, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|C Chain C, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|D Chain D, Yeast Polyamine Oxidase Fms1, N195a Mutant
Length = 516
Score = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 24/52 (46%)
Query: 20 CPFSRAFSADALVEVKPGEIGMVSGIPEEHLRRRVVIYTPARTATQQGSGKL 71
C ++AD ++ P + +S PE++LR R+ P + Q K+
Sbjct: 238 CEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKI 289
>pdb|2IPC|A Chain A, Crystal Structure Of The Translocation Atpase Seca From
Thermus Thermophilus Reveals A Parallel, Head-To-Head
Dimer
pdb|2IPC|B Chain B, Crystal Structure Of The Translocation Atpase Seca From
Thermus Thermophilus Reveals A Parallel, Head-To-Head
Dimer
pdb|2IPC|C Chain C, Crystal Structure Of The Translocation Atpase Seca From
Thermus Thermophilus Reveals A Parallel, Head-To-Head
Dimer
pdb|2IPC|D Chain D, Crystal Structure Of The Translocation Atpase Seca From
Thermus Thermophilus Reveals A Parallel, Head-To-Head
Dimer
Length = 997
Score = 26.2 bits (56), Expect = 7.6, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 104 AGLSFDSKEAAREFAERHGWEYVVRKPHRPLLKVKSYAD 142
AG++ +K +EF E +G + VV +RP+++ K + D
Sbjct: 382 AGMTGTAKTEEKEFQEIYGMDVVVVPTNRPVIR-KDFPD 419
>pdb|3MVE|A Chain A, Crystal Structure Of A Novel Pyruvate Decarboxylase
pdb|3MVE|B Chain B, Crystal Structure Of A Novel Pyruvate Decarboxylase
Length = 415
Score = 26.2 bits (56), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 68 SGKLGRWKIN---FMSTQKWENPLMGWTSTGDPYANVGD 103
SG++ W + F+S++K + P++ + GDP + D
Sbjct: 335 SGQMAAWSLKVQGFLSSRKTKVPILAMSLEGDPVSPYSD 373
>pdb|3OUR|A Chain A, Crystal Structure Of Complex Between Eiia And A Novel
Pyruvate Decarboxylase
pdb|3OUR|C Chain C, Crystal Structure Of Complex Between Eiia And A Novel
Pyruvate Decarboxylase
pdb|3OUR|E Chain E, Crystal Structure Of Complex Between Eiia And A Novel
Pyruvate Decarboxylase
pdb|3OUR|G Chain G, Crystal Structure Of Complex Between Eiia And A Novel
Pyruvate Decarboxylase
Length = 435
Score = 26.2 bits (56), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 68 SGKLGRWKIN---FMSTQKWENPLMGWTSTGDPYANVGD 103
SG++ W + F+S++K + P++ + GDP + D
Sbjct: 355 SGQMAAWSLKVQGFLSSRKTKVPILAMSLEGDPVSPYSD 393
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
0.317 0.133 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,210,388
Number of Sequences: 62578
Number of extensions: 206852
Number of successful extensions: 417
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 404
Number of HSP's gapped (non-prelim): 19
length of query: 155
length of database: 14,973,337
effective HSP length: 91
effective length of query: 64
effective length of database: 9,278,739
effective search space: 593839296
effective search space used: 593839296
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: 47 (22.7 bits)