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= 005994
         (666 letters)

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

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



>pdb|3LLO|A Chain A, Crystal Structure Of The Stas Domain Of Motor Protein
           Prestin (Anion Transporter Slc26a5)
          Length = 143

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/143 (30%), Positives = 70/143 (48%), Gaps = 9/143 (6%)

Query: 456 NPHIAILGRLPGTTVYRNTQQYPEAYTYHGIVIVRIDAPIYFANISFLKDRLREYEVDVD 515
           +P   +LG+LP T VY +   Y E     GI I +I+APIY+AN       L+       
Sbjct: 1   SPSYTVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSSALKR------ 54

Query: 516 RSTRRGPEVERIYFVILEMAPVTYIDSSAVQALKDLYQEYKSRDIQIAISNLNHEVLLTL 575
           ++   G   E I+ VIL+   V ++DS  V+ L  + +EY    I + ++  + +V+  L
Sbjct: 55  KTGVNGS--ENIHTVILDFTQVNFMDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDL 112

Query: 576 SKSGVVDLIG-KEWYFVRAHDAV 597
           + +   +    KE  F   HDAV
Sbjct: 113 TSNRFFENPALKELLFHSIHDAV 135


>pdb|2KLN|A Chain A, Solution Structure Of Stas Domain Of Rv1739c From M.
           Tuberculosis
          Length = 130

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/122 (27%), Positives = 58/122 (47%), Gaps = 9/122 (7%)

Query: 477 YPEAYTYHGIVIVRIDAPIYFANISFLKDRLREYEVDVDRSTRRGPEVERIYFVILEMAP 536
           YP+A    G+V+ R DAP+ FAN    + R     VD D          ++ + +L    
Sbjct: 7   YPQAKRVPGLVVYRYDAPLCFANAEDFRRRALTV-VDQDPG--------QVEWFVLNAES 57

Query: 537 VTYIDSSAVQALKDLYQEYKSRDIQIAISNLNHEVLLTLSKSGVVDLIGKEWYFVRAHDA 596
              +D +A+ AL  L  E   R I  A++ +  ++  +L  + ++D IG++  F+    A
Sbjct: 58  NVEVDLTALDALDQLRTELLRRGIVFAMARVKQDLRESLRAASLLDKIGEDHIFMTLPTA 117

Query: 597 VQ 598
           VQ
Sbjct: 118 VQ 119


>pdb|3MGL|A Chain A, Crystal Structure Of Permease Family Protein From Vibrio
           Cholerae
 pdb|3MGL|B Chain B, Crystal Structure Of Permease Family Protein From Vibrio
           Cholerae
 pdb|4DGH|A Chain A, Structure Of Sulp Transporter Stas Domain From Vibrio
           Cholerae Refined To 1.9 Angstrom Resolution
 pdb|4DGH|B Chain B, Structure Of Sulp Transporter Stas Domain From Vibrio
           Cholerae Refined To 1.9 Angstrom Resolution
          Length = 130

 Score = 42.0 bits (97), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/121 (22%), Positives = 56/121 (46%), Gaps = 13/121 (10%)

Query: 486 IVIVRIDAPIYFANISFLKDRLREYEVDVDRSTRRGPEVERIYFVILEMAPVTYIDSSAV 545
           + +  ++ P +FA     +         V  S +  P++     +IL +  V + D + +
Sbjct: 21  LAVYALEGPFFFAAAETFER--------VXGSIQETPQI-----LILRLKWVPFXDITGI 67

Query: 546 QALKDLYQEYKSRDIQIAISNLNHEVLLTLSKSGVVDLIGKEWYFVRAHDAVQVCLQHVQ 605
           Q L++  Q +  R I++ IS  N  V   L K+G+V L+G++  +     A+   L  ++
Sbjct: 68  QTLEEXIQSFHKRGIKVLISGANSRVSQKLVKAGIVKLVGEQNVYPVFEGALSAALTEIE 127

Query: 606 S 606
           +
Sbjct: 128 A 128


>pdb|1VC1|A Chain A, Crystal Structure Of The Tm1442 Protein From Thermotoga
           Maritima, A Homolog Of The Bacillus Subtilis General
           Stress Response Anti-Anti-Sigma Factor Rsbv
 pdb|1VC1|B Chain B, Crystal Structure Of The Tm1442 Protein From Thermotoga
           Maritima, A Homolog Of The Bacillus Subtilis General
           Stress Response Anti-Anti-Sigma Factor Rsbv
 pdb|1SBO|A Chain A, Solution Structure Of Putative Anti Sigma Factor
           Antagonist From Thermotoga Maritima (Tm1442)
          Length = 110

 Score = 29.6 bits (65), Expect = 5.1,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 44/84 (52%), Gaps = 11/84 (13%)

Query: 488 IVRIDAPIYFANISFLKDRLREYEVDVDRSTRRGPEVERIYFVILEMAPVTYIDSSAVQA 547
           IVR+   I   N S LK++LR +   +  ++++         ++L+++ V+Y+DS+ +  
Sbjct: 16  IVRVQGDIDAYNSSELKEQLRNF---ISTTSKKK--------IVLDLSSVSYMDSAGLGT 64

Query: 548 LKDLYQEYKSRDIQIAISNLNHEV 571
           L  + ++ K    +  +S+L   +
Sbjct: 65  LVVILKDAKINGKEFILSSLKESI 88


  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
   0.323    0.138    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,209,643
Number of Sequences: 62578
Number of extensions: 651587
Number of successful extensions: 1310
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1303
Number of HSP's gapped (non-prelim): 7
length of query: 666
length of database: 14,973,337
effective HSP length: 105
effective length of query: 561
effective length of database: 8,402,647
effective search space: 4713884967
effective search space used: 4713884967
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)