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= 037691
         (337 letters)

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

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



>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Termination Factor 3
          Length = 298

 Score = 35.4 bits (80), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 63/133 (47%), Gaps = 17/133 (12%)

Query: 166 GSDLKRVISRRPR----LLVSAVKTRLRPTLYFLQSMGIAE------VNKHTYLLSCSVE 215
           G DL + I + P     LL    +  ++  L FL+ +GI +      + K+  + S  +E
Sbjct: 44  GVDLSK-IEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLE 102

Query: 216 DKLIPRLQYFQKIGFSKREATAMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDLKELKE- 274
           + L  R+ Y     FSK +   M R+ P L N+SV +  + +L +F   +   +K+ ++ 
Sbjct: 103 N-LKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSV-ERLDNRLGFFQKELELSVKKTRDL 160

Query: 275 ---FPQYFSFSLE 284
               P+  + SLE
Sbjct: 161 VVRLPRLLTGSLE 173


>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Termination Factor 3
          Length = 270

 Score = 35.0 bits (79), Expect = 0.059,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 63/133 (47%), Gaps = 17/133 (12%)

Query: 166 GSDLKRVISRRPR----LLVSAVKTRLRPTLYFLQSMGIAE------VNKHTYLLSCSVE 215
           G DL + I + P     LL    +  ++  L FL+ +GI +      + K+  + S  +E
Sbjct: 16  GVDLSK-IEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLE 74

Query: 216 DKLIPRLQYFQKIGFSKREATAMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDLKELKE- 274
           + L  R+ Y     FSK +   M R+ P L N+SV +  + +L +F   +   +K+ ++ 
Sbjct: 75  N-LKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSV-ERLDNRLGFFQKELELSVKKTRDL 132

Query: 275 ---FPQYFSFSLE 284
               P+  + SLE
Sbjct: 133 VVRLPRLLTGSLE 145


>pdb|3ERR|A Chain A, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
           As A Fusion With Seryl-Trna Synthetase
 pdb|3ERR|B Chain B, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
           As A Fusion With Seryl-Trna Synthetase
          Length = 536

 Score = 33.5 bits (75), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 12/59 (20%)

Query: 268 DLKELKEFPQYFSFSLENRIKPRHQACVDKGVCFPLNVLLKTSEAQFHRRLDVCCNSSM 326
           DLK L++ P+ F           H+A  +KGV   L  LL   E Q H++ +V  +  M
Sbjct: 3   DLKRLRQEPEVF-----------HRAIREKGVALDLEALLAVDE-QLHKQQEVIADKQM 49


>pdb|3EAP|A Chain A, Crystal Structure Of The Rhogap Domain Of Arhgap11a
 pdb|3EAP|B Chain B, Crystal Structure Of The Rhogap Domain Of Arhgap11a
 pdb|3EAP|C Chain C, Crystal Structure Of The Rhogap Domain Of Arhgap11a
 pdb|3EAP|D Chain D, Crystal Structure Of The Rhogap Domain Of Arhgap11a
          Length = 271

 Score = 30.8 bits (68), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 16/38 (42%), Positives = 20/38 (52%)

Query: 188 LRPTLYFLQSMGIAEVNKHTYLLSCSVEDKLIPRLQYF 225
           L   L   Q +G  E NK T LLSC + D  +  L+YF
Sbjct: 155 LHEALLKAQQLGTEEKNKATLLLSCLLADHTVHVLRYF 192


>pdb|4B3N|A Chain A, Crystal Structure Of Rhesus Trim5alpha PrySPRY DOMAIN
 pdb|4B3N|B Chain B, Crystal Structure Of Rhesus Trim5alpha PrySPRY DOMAIN
          Length = 602

 Score = 27.7 bits (60), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 27/112 (24%), Positives = 51/112 (45%), Gaps = 17/112 (15%)

Query: 164 VNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQSMGIAEVNKHTYLLSCSVEDKLIPRLQ 223
           V   D ++V SR P+++  A  T     L+   S+     N  T +L      + I   +
Sbjct: 423 VIAEDKRQVSSRNPQIMYQAPGT-----LFTFPSL--TNFNYCTGVLGS----QSITSGK 471

Query: 224 YFQKIGFSKREAT-----AMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDLK 270
           ++ ++  SK+ A      A F+    ++N    +NY+ K  Y+V+G+   +K
Sbjct: 472 HYWEVDVSKKSAWILGVCAGFQS-DAMYNIEQNENYQPKYGYWVIGLQEGVK 522


  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    0.138    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,489,203
Number of Sequences: 62578
Number of extensions: 297399
Number of successful extensions: 704
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 699
Number of HSP's gapped (non-prelim): 8
length of query: 337
length of database: 14,973,337
effective HSP length: 99
effective length of query: 238
effective length of database: 8,778,115
effective search space: 2089191370
effective search space used: 2089191370
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: 52 (24.6 bits)