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= 034321
         (98 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1H3Q|A Chain A, Crystal Sturcture Of Sedl At 2.4 Angstroms Resolution
          Length = 140

 Score = 76.3 bits (186), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 54/81 (66%), Gaps = 3/81 (3%)

Query: 1  MATTACFIIVSRNEIPIYEAEV---GSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMF 57
          M+ +  F+IV  ++ P++E E    G A  ++D   L+QFI HAALD+V +  W ++ M+
Sbjct: 1  MSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMY 60

Query: 58 LKAIDRFNDLVVSVYVTAGHI 78
          LK +D+FN+  VS +VTAGH+
Sbjct: 61 LKTVDKFNEWFVSAFVTAGHM 81


>pdb|2J3W|A Chain A, The Crystal Structure Of The Bet3-Trs31-Sedlin Complex.
 pdb|2J3W|C Chain C, The Crystal Structure Of The Bet3-Trs31-Sedlin Complex
          Length = 142

 Score = 76.3 bits (186), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 54/81 (66%), Gaps = 3/81 (3%)

Query: 1  MATTACFIIVSRNEIPIYEAEV---GSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMF 57
          M+ +  F+IV  ++ P++E E    G A  ++D   L+QFI HAALD+V +  W ++ M+
Sbjct: 3  MSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMY 62

Query: 58 LKAIDRFNDLVVSVYVTAGHI 78
          LK +D+FN+  VS +VTAGH+
Sbjct: 63 LKTVDKFNEWFVSAFVTAGHM 83


>pdb|1TF6|A Chain A, Co-crystal Structure Of Xenopus Tfiiia Zinc Finger Domain
           Bound To The 5s Ribosomal Rna Gene Internal Control
           Region
 pdb|1TF6|D Chain D, Co-crystal Structure Of Xenopus Tfiiia Zinc Finger Domain
           Bound To The 5s Ribosomal Rna Gene Internal Control
           Region
          Length = 190

 Score = 27.3 bits (59), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 17/26 (65%)

Query: 48  DLAWTTSAMFLKAIDRFNDLVVSVYV 73
           DL +TT A   K  +RF+++ + VYV
Sbjct: 81  DLRFTTKANMKKHFNRFHNIKICVYV 106


>pdb|3ZWL|B Chain B, Structure Of Eukaryotic Translation Initiation Factor
           Eif3i Complex With Eif3b C-Terminus (655-700)
 pdb|3ZWL|D Chain D, Structure Of Eukaryotic Translation Initiation Factor
           Eif3i Complex With Eif3b C-Terminus (655-700)
          Length = 369

 Score = 26.6 bits (57), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 15  IPIYEAEVGSA---VKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKA 60
           I IYE E  SA   + +     +H+ I H  LD      W+T   ++ A
Sbjct: 144 INIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIA 192


>pdb|3H3F|A Chain A, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|3H3F|B Chain B, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|3H3F|C Chain C, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|3H3F|D Chain D, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|3H3F|E Chain E, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|3H3F|F Chain F, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|3H3F|G Chain G, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|3H3F|H Chain H, Rabbit Muscle L-Lactate Dehydrogenase In Complex With Nadh
           And Oxamate
 pdb|4I8X|A Chain A, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I8X|B Chain B, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I8X|C Chain C, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I8X|D Chain D, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I8X|E Chain E, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I8X|F Chain F, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I8X|G Chain G, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I8X|H Chain H, Crystal Structure Of Rabbit Ldha In Complex With Ap27460
 pdb|4I9H|A Chain A, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9H|B Chain B, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9H|C Chain C, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9H|D Chain D, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9H|E Chain E, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9H|F Chain F, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9H|G Chain G, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9H|H Chain H, Crystal Structure Of Rabbit Ldha In Complex With Ap28669
 pdb|4I9N|A Chain A, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9N|B Chain B, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9N|C Chain C, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9N|D Chain D, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9N|E Chain E, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9N|F Chain F, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9N|G Chain G, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9N|H Chain H, Crystal Structure Of Rabbit Ldha In Complex With Ap28161
           And Ap28122
 pdb|4I9U|A Chain A, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
 pdb|4I9U|B Chain B, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
 pdb|4I9U|C Chain C, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
 pdb|4I9U|D Chain D, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
 pdb|4I9U|E Chain E, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
 pdb|4I9U|F Chain F, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
 pdb|4I9U|G Chain G, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
 pdb|4I9U|H Chain H, Crystal Structure Of Rabbit Ldha In Complex With A
           Fragment Inhibitor Ap26256
          Length = 331

 Score = 26.2 bits (56), Expect = 4.7,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 25/42 (59%)

Query: 21  EVGSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAID 62
           E+G+   +E   Q+H+ ++ +A ++++   +TT A+ L   D
Sbjct: 216 ELGTDADKEQWKQVHKQVVDSAYEVIKLKGYTTWAIGLSVAD 257


>pdb|3KQH|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQH|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQK|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQK|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
          Length = 436

 Score = 25.8 bits (55), Expect = 6.0,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 4/73 (5%)

Query: 11  SRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVS 70
           S  EIP Y    G A+  E        I   +     +LA   S + L A+  +  L VS
Sbjct: 155 STGEIPFY----GKAIPIETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVS 210

Query: 71  VYVTAGHILHTST 83
           V  T+G ++  +T
Sbjct: 211 VIPTSGDVIVVAT 223


>pdb|3KQL|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQL|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQN|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQU|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQU|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQU|C Chain C, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQU|D Chain D, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQU|E Chain E, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
 pdb|3KQU|F Chain F, Three Conformational Snapshots Of The Hepatitis C Virus
           Ns3 Helicase Reveal A Ratchet Translocation Mechanism
          Length = 437

 Score = 25.8 bits (55), Expect = 6.2,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 4/73 (5%)

Query: 11  SRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVS 70
           S  EIP Y    G A+  E        I   +     +LA   S + L A+  +  L VS
Sbjct: 155 STGEIPFY----GKAIPIETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVS 210

Query: 71  VYVTAGHILHTST 83
           V  T+G ++  +T
Sbjct: 211 VIPTSGDVIVVAT 223


>pdb|3JTF|A Chain A, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
           Efflux Protein From Bordetella Parapertussis In Complex
           With Amp
 pdb|3JTF|B Chain B, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
           Efflux Protein From Bordetella Parapertussis In Complex
           With Amp
          Length = 129

 Score = 25.4 bits (54), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 5   ACFIIVSRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRF 64
           A  I  + +  P+YE +  + +    A  L ++ L  ALDI    +    A+F+  + R 
Sbjct: 31  ATIIETAHSRFPVYEDDRDNIIGILLAKDLLRYXLEPALDI---RSLVRPAVFIPEVKRL 87

Query: 65  NDLVVSVYVTAGHI 78
           N L+     +  H+
Sbjct: 88  NVLLREFRASRNHL 101


  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
   0.331    0.138    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,244,068
Number of Sequences: 62578
Number of extensions: 68075
Number of successful extensions: 192
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 186
Number of HSP's gapped (non-prelim): 9
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)