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= 001114
         (1154 letters)

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

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



>pdb|2YCU|A Chain A, Crystal Structure Of Human Non Muscle Myosin 2c In
           Pre-power Stroke State
          Length = 995

 Score = 30.8 bits (68), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 61/150 (40%), Gaps = 24/150 (16%)

Query: 615 LDGVLKNAAEKTAEALHL----------KDEYGKHIQAML---KAKQMQCVSYEKRIQEL 661
           +DG  K A EK  +AL L          K  +   + A L   +A +     Y KR  EL
Sbjct: 713 MDG--KQACEKMIQALELDPNLYRVGQSKIFFRAGVLAQLEEERASEQTKSDYLKRANEL 770

Query: 662 EQRLSDQYLMKQKHSNGKDVSDFALLVEKADDCKPESSGGGETHMPCISTSEPMDEVSCV 721
            Q ++D    KQ     +D  D    V+   +   E     +T  P     + + E+  +
Sbjct: 771 VQWIND----KQASLESRDFGDSIESVQSFMNAHKEYK---KTEKP--PKGQEVSELEAI 821

Query: 722 SNSFDAKLALLNRQPSKGREGVDENMLDSS 751
            NS   KL L+ R+P     G+  N +DS+
Sbjct: 822 YNSLQTKLRLIKREPFVAPAGLTPNEIDST 851


>pdb|4HAM|A Chain A, Crystal Structure Of Transcriptional Antiterminator From
           Listeria Monocytogenes Egd-E
          Length = 134

 Score = 30.4 bits (67), Expect = 6.5,   Method: Composition-based stats.
 Identities = 18/44 (40%), Positives = 28/44 (63%), Gaps = 6/44 (13%)

Query: 831 LADKSDQLS------ETQTKLKAVMEEVVMLGRELEMRQKLLDE 868
           +A+++D+LS      ET+TKLK  + ++V LG  +E   KL DE
Sbjct: 78  IANQTDKLSSPKKLAETRTKLKETILDLVYLGVNIEEIHKLADE 121


>pdb|2ZKR|5 Chain 5, Structure Of A Mammalian Ribosomal 60s Subunit Within An
           80s Complex Obtained By Docking Homology Models Of The
           Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 212

 Score = 30.0 bits (66), Expect = 8.7,   Method: Composition-based stats.
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 491 SMGLYDTPNQCDVNIAPSDTNLLDIDISDLEVYAPEYL---AGLRKGEKPVNVRDGSHSV 547
           S  L D P +          NL D+D++D      E +   AG  +    V   +G  ++
Sbjct: 11  SRALEDAPERNFRETVDLAVNLRDLDLNDPSNRVDESVVLPAGTGQETTIVVFAEGETAL 70

Query: 548 EAEEIALDALDREDPEEL 565
            AEE+A D LD ++ EEL
Sbjct: 71  RAEEVADDVLDEDELEEL 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
   0.316    0.131    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 30,244,679
Number of Sequences: 62578
Number of extensions: 1167307
Number of successful extensions: 3572
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 3564
Number of HSP's gapped (non-prelim): 20
length of query: 1154
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1045
effective length of database: 8,152,335
effective search space: 8519190075
effective search space used: 8519190075
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.6 bits)