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= 033611
         (115 letters)

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

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



>pdb|3UX3|A Chain A, Crystal Structure Of Domain-Swapped Fam96a Minor Dimer
 pdb|3UX3|B Chain B, Crystal Structure Of Domain-Swapped Fam96a Minor Dimer
          Length = 130

 Score = 86.7 bits (213), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 57/76 (75%), Gaps = 3/76 (3%)

Query: 40  EVFDHVRDIKDPEHPYSLEELKVITEDAIEV---DDERSYVRVTFTPTVEHCSMATVIGL 96
           EV+D +R I+DPE P +LEEL+V++E  +EV   ++E   V + FTPTV HCS+AT+IGL
Sbjct: 12  EVYDLIRTIRDPEKPNTLEELEVVSESCVEVQEINEEEYLVIIRFTPTVPHCSLATLIGL 71

Query: 97  CLRVKLMRSLPPRFKV 112
           CLRVKL R LP + K+
Sbjct: 72  CLRVKLQRCLPFKHKL 87


>pdb|3UX2|A Chain A, Crystal Structure Of Domain-Swapped Fam96a Major Dimer
          Length = 130

 Score = 86.7 bits (213), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 57/76 (75%), Gaps = 3/76 (3%)

Query: 40  EVFDHVRDIKDPEHPYSLEELKVITEDAIEV---DDERSYVRVTFTPTVEHCSMATVIGL 96
           EV+D +R I+DPE P +LEEL+V++E  +EV   ++E   V + FTPTV HCS+AT+IGL
Sbjct: 12  EVYDLIRTIRDPEKPNTLEELEVVSESCVEVQEINEEEYLVIIRFTPTVPHCSLATLIGL 71

Query: 97  CLRVKLMRSLPPRFKV 112
           CLRVKL R LP + K+
Sbjct: 72  CLRVKLQRCLPFKHKL 87


>pdb|2ZXT|A Chain A, Crystal Structure Of Tim40MIA40, A DISULFIDE RELAY SYSTEM
           IN Mitochondria, Solved As Mbp Fusion Protein
          Length = 465

 Score = 26.9 bits (58), Expect = 2.9,   Method: Composition-based stats.
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 5/49 (10%)

Query: 21  RSASSC-VNDEYAAEQIDQQEVFDHVRDI--KDPEHPYSLEELKVITED 66
           +SA SC V  E   + ID  E F H++D   K PEH Y+ E+LK  ++D
Sbjct: 412 KSAFSCFVYSEAEPKGIDCVEKFQHMQDCFRKYPEH-YA-EQLKETSDD 458


>pdb|2OCB|A Chain A, Crystal Structure Of Human Rab9b In Complex With A Gtp
           Analogue
          Length = 180

 Score = 25.8 bits (55), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 7/53 (13%)

Query: 21  RSASSC-----VNDEYAAEQI-DQQEVFDHVRDIKDPEH-PYSLEELKVITED 66
           R A  C     V+D  + E + + Q+ F +  D+KDPEH P+ +   KV  ED
Sbjct: 78  RGADCCLLTFSVDDRQSFENLGNWQKEFIYYADVKDPEHFPFVVLGNKVDKED 130


>pdb|4IUJ|A Chain A, Structure Of Polymerase Acid Protein (pa) From
           Influenzavirus A Influenza A Virus A, Wilson-smith/1933
           (h1n1)
          Length = 464

 Score = 25.4 bits (54), Expect = 8.7,   Method: Composition-based stats.
 Identities = 23/84 (27%), Positives = 31/84 (36%), Gaps = 19/84 (22%)

Query: 13  YEKKERRARSASSCVNDEY--AAEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEV 70
           Y+  E   RS +S + +E+  A E  D   +                 EL  I EDA  +
Sbjct: 141 YDSDEPELRSLASWIQNEFNKACELTDSSWI-----------------ELDEIGEDAAPI 183

Query: 71  DDERSYVRVTFTPTVEHCSMATVI 94
           +   S  R  FT  V HC     I
Sbjct: 184 EHIASMRRNYFTAEVSHCRATEYI 207


  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
   0.319    0.134    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,239,139
Number of Sequences: 62578
Number of extensions: 116376
Number of successful extensions: 312
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 301
Number of HSP's gapped (non-prelim): 14
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)