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= 027690
         (220 letters)

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

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



>pdb|2DNX|A Chain A, Solution Structure Of Rsgi Ruh-063, An N-Terminal Domain
           Of Syntaxin 12 From Human Cdna
          Length = 130

 Score = 39.7 bits (91), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 2/102 (1%)

Query: 23  QAVAAGIFQINTAVAAFRRLVDAIGTSKDTLDHRQKLHNTRQRILQLVKDTSAKLKSVS- 81
           Q  +  I +I+ A A  + L+  +GT +D+   ++ L   +    QL K+T+  LK +  
Sbjct: 17  QTCSGNIQRISQATAQIKNLMSQLGTKQDSSKLQENLQQLQHSTNQLAKETNELLKELGS 76

Query: 82  -ESDRDTDVNQNKKVEDAKLARDFQTVLQEFQKIQQLASERE 122
                 T   + ++++  +L  DF   L  FQ +Q+  SE+E
Sbjct: 77  LPLPLSTSEQRQQRLQKERLMNDFSAALNNFQAVQRRVSEKE 118


>pdb|1GL2|B Chain B, Crystal Structure Of An Endosomal Snare Core Complex
          Length = 65

 Score = 32.7 bits (73), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 13/18 (72%), Positives = 16/18 (88%)

Query: 196 NEIFKDLAVLVHEQGVVI 213
           NEIFKDL +++HEQG VI
Sbjct: 22  NEIFKDLGMMIHEQGDVI 39


>pdb|2NPS|B Chain B, Crystal Structure Of The Early Endosomal Snare Complex
          Length = 71

 Score = 30.4 bits (67), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 11/18 (61%), Positives = 17/18 (94%)

Query: 196 NEIFKDLAVLVHEQGVVI 213
           N+IFKDLA+++H+QG +I
Sbjct: 19  NQIFKDLAMMIHDQGDLI 36


>pdb|1W36|C Chain C, Recbcd:dna Complex
 pdb|1W36|F Chain F, Recbcd:dna Complex
 pdb|3K70|C Chain C, Crystal Structure Of The Complete Initiation Complex Of
           Recbcd
 pdb|3K70|F Chain F, Crystal Structure Of The Complete Initiation Complex Of
           Recbcd
          Length = 1122

 Score = 28.9 bits (63), Expect = 2.3,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 56  RQKLHNTRQRILQLVKDTSAKLKSVSESDRDTDVNQNKKVEDAKLARDFQTVLQEFQKIQ 115
           RQ+ H+   R L L +D S     +  SD + DV         KL RD+  +L + +  Q
Sbjct: 263 RQRRHSFEDRELPLFRD-SENAGQLFNSDGEQDVGNPLLASWGKLGRDYIYLLSDLESSQ 321

Query: 116 QL 117
           +L
Sbjct: 322 EL 323


  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    0.131    0.344 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,755,302
Number of Sequences: 62578
Number of extensions: 91882
Number of successful extensions: 304
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: 300
Number of HSP's gapped (non-prelim): 10
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
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)