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= 029470
         (193 letters)

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

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



>pdb|2LJU|A Chain A, Solution Structure Of Putative Oxidoreductase From
           Ehrlichia Chaffeensis, Seattle Structural Genomics
           Center For Infectious Disease (Ssgcid)
          Length = 108

 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 53  RVVIYTPARTATQQGSGKLGRWKINFM-STQKWENPLMGWTSTGDPYANVGDAGLSFDSK 111
           R  IY PA++  Q G  KL  WK+ F  S  ++  PLM WT + D    V    LSF ++
Sbjct: 13  RARIYKPAKSTMQSGHSKLKAWKLEFEPSCTQYTEPLMNWTGSHDTKQQV---CLSFTTR 69

Query: 112 EAAREFAERHGWEYVAAGDIFRTF 135
           E A  +A  H  +Y    D  RT 
Sbjct: 70  ELAIAYAVAHKIDYTVLQDNPRTI 93


>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 = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 4/71 (5%)

Query: 56  IYTPARTATQQGSGKLGRWKINF-MSTQKWENPLMGWTSTGDPYANVGDAGLSFDSKEAA 114
           IY PA+TA Q G+ K   W + F     +  +P+MG+TS+ D    V    L+F+++E A
Sbjct: 8   IYRPAKTAMQSGTAKTNVWVLEFDAEVPRKIDPIMGYTSSSDMKQQV---KLTFETQEQA 64

Query: 115 REFAERHGWEY 125
             +A+R G EY
Sbjct: 65  EAYAQRKGIEY 75


>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 = 1.2,   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 = 1.3,   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 = 2.2,   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|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 = 4.4,   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


  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    0.133    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,825,494
Number of Sequences: 62578
Number of extensions: 215580
Number of successful extensions: 421
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 415
Number of HSP's gapped (non-prelim): 11
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
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: 49 (23.5 bits)