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= 023605
         (280 letters)

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

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



>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
           Bound To Ssrna And Amp-Pnp
          Length = 512

 Score = 30.4 bits (67), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 67  IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 124
           I ++  + E+F   + +  E  KK I  R+  +++++     K    LC  L N+FK + 
Sbjct: 257 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 316

Query: 125 NIIELHGQ 132
            I+E HG+
Sbjct: 317 PILEFHGK 324


>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
 pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
           5-Bru And Amp- Pnp
 pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
           Fluoride
 pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
           Fluoride
          Length = 563

 Score = 30.4 bits (67), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 67  IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 124
           I ++  + E+F   + +  E  KK I  R+  +++++     K    LC  L N+FK + 
Sbjct: 308 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 367

Query: 125 NIIELHGQ 132
            I+E HG+
Sbjct: 368 PILEFHGK 375


>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
           Amp-Pnp
          Length = 579

 Score = 30.4 bits (67), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 67  IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 124
           I ++  + E+F   + +  E  KK I  R+  +++++     K    LC  L N+FK + 
Sbjct: 257 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 316

Query: 125 NIIELHGQ 132
            I+E HG+
Sbjct: 317 PILEFHGK 324


>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
 pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
          Length = 257

 Score = 30.0 bits (66), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 67  IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 124
           I ++  + E+F   + +  E  KK I  R+  +++++     K    LC  L N+FK + 
Sbjct: 2   IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 61

Query: 125 NIIELHGQ 132
            I+E HG+
Sbjct: 62  PILEFHGK 69


>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
           Rna-Dna Duplex
 pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
           Rna-Dna Duplex
          Length = 256

 Score = 30.0 bits (66), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 67  IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 124
           I ++  + E+F   + +  E  KK I  R+  +++++     K    LC  L N+FK + 
Sbjct: 2   IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 61

Query: 125 NIIELHGQ 132
            I+E HG+
Sbjct: 62  PILEFHGK 69


>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
 pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
          Length = 257

 Score = 30.0 bits (66), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 67  IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 124
           I ++  + E+F   + +  E  KK I  R+  +++++     K    LC  L N+FK + 
Sbjct: 2   IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 61

Query: 125 NIIELHGQ 132
            I+E HG+
Sbjct: 62  PILEFHGK 69


>pdb|1P2Z|A Chain A, Refinement Of Adenovirus Type 2 Hexon With Cns
          Length = 967

 Score = 30.0 bits (66), Expect = 1.6,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 94  EIGFESLLELRCGKLKRKLCHW--LVNQFKPERNIIELHGQKLELCPKMFS-KIMGVKDG 150
           E+ ++ LL+   G   R    W   V+ + P+  IIE HG + EL    F    +GV D 
Sbjct: 378 ELSYQLLLD-SIGDRTRYFSMWNQAVDSYDPDVRIIENHGTEDELPNYCFPLGGIGVTDT 436

Query: 151 GMAIKING 158
             AIK NG
Sbjct: 437 YQAIKANG 444


>pdb|2WP4|A Chain A, Crystal Structure Of Rv3119 From Mycobacterium
           Tuberculosis
 pdb|2WP4|B Chain B, Crystal Structure Of Rv3119 From Mycobacterium
           Tuberculosis
          Length = 147

 Score = 28.5 bits (62), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 139 KMFSKIMGVKDGGMAIKINGASDHIA--EVRRIFQPTVKGIRIRTLEEVIEQLDEANKIF 196
           ++ + + G + GG+ I +    DH A  +V R+F      + IRTL  +I + ++  +  
Sbjct: 24  EVLAAVSGPEQGGIVIFVGNVRDHNAGHDVTRLFYEAYPPMVIRTLMSIIGRCEDKAEGV 83

Query: 197 KVAFT 201
           +VA  
Sbjct: 84  RVAVA 88


>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
          Factor Sox-17
          Length = 82

 Score = 28.1 bits (61), Expect = 5.3,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 6  SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 52
          + +E KRL  +N DL     L K +GK++K L   +K  + +  ER+
Sbjct: 19 AKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERL 64


>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
          Length = 71

 Score = 27.3 bits (59), Expect = 9.9,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 6  SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 52
          + +E KRL  +N DL     L K +GK++K L   +K  + +  ER+
Sbjct: 14 AKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERL 59


  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
   0.325    0.140    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,168,837
Number of Sequences: 62578
Number of extensions: 258049
Number of successful extensions: 909
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 909
Number of HSP's gapped (non-prelim): 12
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)