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= 036679
         (294 letters)

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

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



>pdb|4GWP|D Chain D, Structure Of The Mediator Head Module From S. Cerevisiae
 pdb|4GWQ|D Chain D, Structure Of The Mediator Head Module From S. Cerevisiae
           In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
           Polymerase Ii Rpb1 Subunit
          Length = 121

 Score = 30.8 bits (68), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 6/95 (6%)

Query: 41  KIIDCRGLKSLEFLNLGKLSKFMVRNEDRLARVSICGPNVRL-VDISSLHAPCGINVALC 99
           K+   R + S++   L  ++    RN+D     S    N  L V  +S+       + L 
Sbjct: 9   KLEQTRTILSVKLAELINMTTIADRNDDDEG--SFAQENSELAVATTSVMMVNNQTMQLI 66

Query: 100 KNLKELKLFKLSITNEWLCNQFSELPFLEYLEIFR 134
           KN+++L +   SI  +WL NQ   +P  E+ ++ R
Sbjct: 67  KNVQDLLILTRSIKEKWLLNQ---IPVTEHSKVTR 98


>pdb|2ELL|A Chain A, Solution Structure Of The Leucine Rich Repeat Of Human
           Acidic Leucine- Rich Nuclear Phosphoprotein 32 Family
           Member B
 pdb|2RR6|A Chain A, Solution Structure Of The Leucine Rich Repeat Of Human
           Acidic Leucine- Rich Nuclear Phosphoprotein 32 Family
           Member B
          Length = 168

 Score = 27.7 bits (60), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 42/145 (28%), Positives = 67/145 (46%), Gaps = 24/145 (16%)

Query: 5   RNVTLSSLRELGLFKCAANDEAIRDIVAGCPLIERLKIIDCRGLKSLEFLNLGKLSKFMV 64
           RN T +++REL L  C +ND  I  + A    +E L +I+  GL S+  L      K + 
Sbjct: 19  RNRTPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINV-GLISVSNLPKLPKLKKLE 77

Query: 65  RNEDR--------------LARVSICGPNVRLVDISSLHAPCGINVALCKNLKELKLFKL 110
            +E+R              L  +++ G   +L DIS+L       +   + LK L LF  
Sbjct: 78  LSENRIFGGLDMLAEKLPNLTHLNLSGN--KLKDISTLEP-----LKKLECLKSLDLFNC 130

Query: 111 SIT--NEWLCNQFSELPFLEYLEIF 133
            +T  N++  + F  LP L YL+ +
Sbjct: 131 EVTNLNDYRESVFKLLPQLTYLDGY 155


>pdb|1XI4|A Chain A, Clathrin D6 Coat
 pdb|1XI4|B Chain B, Clathrin D6 Coat
 pdb|1XI4|C Chain C, Clathrin D6 Coat
 pdb|1XI4|D Chain D, Clathrin D6 Coat
 pdb|1XI4|E Chain E, Clathrin D6 Coat
 pdb|1XI4|F Chain F, Clathrin D6 Coat
 pdb|1XI4|G Chain G, Clathrin D6 Coat
 pdb|1XI4|H Chain H, Clathrin D6 Coat
 pdb|1XI4|I Chain I, Clathrin D6 Coat
 pdb|1XI5|A Chain A, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|B Chain B, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|C Chain C, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|D Chain D, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|E Chain E, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|F Chain F, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|G Chain G, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|H Chain H, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|I Chain I, Clathrin D6 Coat With Auxilin J-Domain
 pdb|3IYV|A Chain A, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|B Chain B, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|C Chain C, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|D Chain D, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|E Chain E, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|F Chain F, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|G Chain G, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|H Chain H, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|I Chain I, Clathrin D6 Coat As Full-Length Triskelions
          Length = 1630

 Score = 27.7 bits (60), Expect = 8.4,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 12/79 (15%)

Query: 115 EWLCNQFSELPFLEYLEIFRCM---KIRS-----IKISSPYLKKLLVRFCNKLYE-FKLD 165
           EWL N F  L   + LE  R M    IR      ++++S Y ++L  +   +L+E FK  
Sbjct: 649 EWLVNYFGSLSVEDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFK-- 706

Query: 166 TPNLSVFDYEGDMVSFSSN 184
                +F + G +V+FS +
Sbjct: 707 -SFEGLFYFLGSIVNFSQD 724


  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    0.139    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,929,784
Number of Sequences: 62578
Number of extensions: 290145
Number of successful extensions: 756
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 751
Number of HSP's gapped (non-prelim): 20
length of query: 294
length of database: 14,973,337
effective HSP length: 98
effective length of query: 196
effective length of database: 8,840,693
effective search space: 1732775828
effective search space used: 1732775828
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: 51 (24.3 bits)