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= 003989
         (781 letters)

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

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



>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
           Star-Gsg Quaking Protein
          Length = 140

 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/98 (33%), Positives = 51/98 (52%), Gaps = 7/98 (7%)

Query: 174 IPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA-DTGEKVEISTSDANVQST 232
           +PVKEYP +NF+G I GP   T K+LE ET   I V G  +    +K E +    N +  
Sbjct: 8   VPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHL 67

Query: 233 YEEFHISISA-DSYEKVD-----AATDLIELLVTSVSG 264
            E+ H+ I+  D+  + +     A  ++ +LLV +  G
Sbjct: 68  NEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEG 105


>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
           Rna By Splicing Factor 1
          Length = 131

 Score = 42.7 bits (99), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 29/85 (34%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 172 VPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQS 231
           V IP  EYP  NF+GL+ GP  +T K +EKE    I + G  +    KV     D  +  
Sbjct: 11  VMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKV--GRKDGQMLP 68

Query: 232 TYEE-FHISISADSYEKVDAATDLI 255
             +E  H  ++A++ E V  A + I
Sbjct: 69  GEDEPLHALVTANTMENVKKAVEQI 93


>pdb|3U1N|A Chain A, Structure Of The Catalytic Core Of Human Samhd1
 pdb|3U1N|B Chain B, Structure Of The Catalytic Core Of Human Samhd1
 pdb|3U1N|C Chain C, Structure Of The Catalytic Core Of Human Samhd1
 pdb|3U1N|D Chain D, Structure Of The Catalytic Core Of Human Samhd1
          Length = 528

 Score = 33.5 bits (75), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 20/35 (57%)

Query: 417 QPQPTGPIHIGRPSMPSLPQAVSSVGPRPLPDRPL 451
           + QPTG I I R    SLP+ V+S  P+ L D  L
Sbjct: 361 ETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKL 395


  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
   0.311    0.129    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,193,913
Number of Sequences: 62578
Number of extensions: 869369
Number of successful extensions: 1259
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1209
Number of HSP's gapped (non-prelim): 29
length of query: 781
length of database: 14,973,337
effective HSP length: 106
effective length of query: 675
effective length of database: 8,340,069
effective search space: 5629546575
effective search space used: 5629546575
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)