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= psy17180
         (130 letters)

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

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



>pdb|3QNQ|A Chain A, Crystal Structure Of The Transporter Chbc, The Iic
           Component From The N,n'-diacetylchitobiose-specific
           Phosphotransferase System
 pdb|3QNQ|B Chain B, Crystal Structure Of The Transporter Chbc, The Iic
           Component From The N,n'-diacetylchitobiose-specific
           Phosphotransferase System
 pdb|3QNQ|C Chain C, Crystal Structure Of The Transporter Chbc, The Iic
           Component From The N,n'-diacetylchitobiose-specific
           Phosphotransferase System
 pdb|3QNQ|D Chain D, Crystal Structure Of The Transporter Chbc, The Iic
           Component From The N,n'-diacetylchitobiose-specific
           Phosphotransferase System
          Length = 442

 Score = 27.7 bits (60), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 9/56 (16%)

Query: 63  GDVFRPS------PHPMLFSALIGTGYQITTVTLSVILFAIVGDLYTEYFIFTSFW 112
           G V RPS        P+LFS  +G+G +I+ V L ++ FA+    +  Y  F   W
Sbjct: 370 GLVARPSGAAVTWTTPILFSGYLGSGGKISGVILQLVNFALA---FVIYLPFLKIW 422


>pdb|3HJH|A Chain A, A Rigid N-Terminal Clamp Restrains The Motor Domains Of
           The Bacterial Transcription-Repair Coupling Factor
          Length = 483

 Score = 26.6 bits (57), Expect = 3.5,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)

Query: 46  DDMERDLGDEYGWKQVHGDVFRPSPHPMLFSALIGTGYQITTVTLSVILFAI 97
           D M  +L D   W+ +  D F  SPH  + S+ + T YQ+ T+   V++  +
Sbjct: 64  DQMVMNLAD---WETLPYDSF--SPHQDIISSRLSTLYQLPTMQRGVLIVPV 110


>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
           Coupling Factor
 pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
           Coupling Factor
          Length = 1151

 Score = 26.6 bits (57), Expect = 3.5,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)

Query: 46  DDMERDLGDEYGWKQVHGDVFRPSPHPMLFSALIGTGYQITTVTLSVILFAI 97
           D M  +L D   W+ +  D F  SPH  + S+ + T YQ+ T+   V++  +
Sbjct: 67  DQMVMNLAD---WETLPYDSF--SPHQDIISSRLSTLYQLPTMQRGVLIVPV 113


  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
   0.333    0.147    0.464 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,763,813
Number of Sequences: 62578
Number of extensions: 139382
Number of successful extensions: 407
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 406
Number of HSP's gapped (non-prelim): 5
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 45 (21.9 bits)