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= psy8227
         (125 letters)

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

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



>pdb|3H7H|A Chain A, Crystal Structure Of The Human Transcription Elongation
           Factor Dsif, Hspt4HSPT5 (176-273)
          Length = 120

 Score = 79.0 bits (193), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 6   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 61


>pdb|2EXU|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae
           Transcription Elongation Factors Spt4-Spt5ngn Domain
          Length = 200

 Score = 34.7 bits (78), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 81  RACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           RAC+ C  ++T ++F  DGC NC        +  +   CTS +F+
Sbjct: 5   RACMLCGIVQTTNEFNRDGCPNCQGIFE--EAGVSTMECTSPSFE 47


>pdb|3HD6|A Chain A, Crystal Structure Of The Human Rhesus Glycoprotein Rhcg
          Length = 490

 Score = 28.5 bits (62), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 44  LWFLWTLVHSATMVHGTSNNNAKIDDFNNLA 74
           LW  W   +SA   HG S + A I+ + +LA
Sbjct: 233 LWMYWPSFNSAISYHGDSQHRAAINTYCSLA 263


>pdb|2XIO|A Chain A, Structure Of Putative Deoxyribonuclease Tatdn1 Isoform A
          Length = 301

 Score = 27.3 bits (59), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 56  MVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFD-QFEFDGCDNCDEFLHMKNSRD 114
           +++   NN  K+         F + + C   +Q+K F+ QFE         FLH +NS  
Sbjct: 93  LLNLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKYFEKQFELSEQTKLPMFLHCRNSHA 152

Query: 115 NVYNCTSSNFD 125
              + T  N D
Sbjct: 153 EFLDITKRNRD 163


>pdb|4ATM|A Chain A, Crystal Structure Of The Bar Domain Of Human Amphiphysin,
           Isoform 1 At 1.8 Angstrom Resolution Featuring Increased
           Order At The N-Terminus
          Length = 243

 Score = 27.3 bits (59), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 4   RDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWT 49
           ++E+  LW+  R   +V   +   SL AKF + + +LC+ L+ + T
Sbjct: 189 QEELPSLWSR-RVGFYVNTFKNVSSLEAKFHKEIAVLCHKLYEVMT 233


>pdb|3SOG|A Chain A, Crystal Structure Of The Bar Domain Of Human Amphiphysin,
           Isoform 1
          Length = 205

 Score = 26.9 bits (58), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 4   RDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWT 49
           ++E+  LW+  R   +V   +   SL AKF + + +LC+ L+ + T
Sbjct: 157 QEELPSLWSR-RVGFYVNTFKNVSSLEAKFHKEIAVLCHKLYEVMT 201


>pdb|2K16|A Chain A, Solution Structure Of The Free Taf3 Phd Domain
 pdb|2K17|A Chain A, Solution Structure Of The Taf3 Phd Domain In Complex With
           A H3k4me3 Peptide
          Length = 75

 Score = 25.8 bits (55), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 75  KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLH 108
           ++  Q   C GC+  K  D     GCD+CD++ H
Sbjct: 13  EWGNQIWICPGCN--KPDDGSPMIGCDDCDDWYH 44


  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
   0.327    0.135    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,784,691
Number of Sequences: 62578
Number of extensions: 132243
Number of successful extensions: 287
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 283
Number of HSP's gapped (non-prelim): 9
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)