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= 031896
         (151 letters)

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

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



>pdb|1WWH|A Chain A, Crystal Structure Of The Mppn Domain Of Mouse Nup35
 pdb|1WWH|B Chain B, Crystal Structure Of The Mppn Domain Of Mouse Nup35
 pdb|1WWH|C Chain C, Crystal Structure Of The Mppn Domain Of Mouse Nup35
 pdb|1WWH|D Chain D, Crystal Structure Of The Mppn Domain Of Mouse Nup35
          Length = 119

 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/68 (44%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 9  IVPFRFPPADTNLVLREFEKCGVILKHVPGPRDANWMHILYQNRSDAQKALSKNGMQING 68
          +  F FP A  + +L +F + G ILKHV      NWMHI YQ++  A+KALSK+G     
Sbjct: 27 VTVFGFPQASASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALSKDGRIFGE 85

Query: 69 VLIVGVKP 76
           +++GVKP
Sbjct: 86 SIMIGVKP 93


>pdb|3P3D|A Chain A, Crystal Structure Of The Nup53 Rrm Domain From Pichia
           Guilliermondii
          Length = 132

 Score = 37.0 bits (84), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 41/99 (41%), Gaps = 20/99 (20%)

Query: 9   IVPFRFPPADTNLVLREFEKCGVILKH-------------------VPGPRDANWMHILY 49
           I+ F +P    N V+  F++ G IL+                    VP     +W  I Y
Sbjct: 10  ILVFGYPETMANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITY 69

Query: 50  QNRSDAQKALSKNGMQINGVLIVGVKPLDPMQRQALNER 88
            N + A  AL +NG   NGVL+ GV P      + L +R
Sbjct: 70  DNPASAVDALLENGAVFNGVLL-GVIPYTKDAVERLQKR 107


>pdb|3IC1|A Chain A, Crystal Structure Of Zinc-Bound Succinyl-Diaminopimelate
           Desuccinylase From Haemophilus Influenzae
 pdb|3IC1|B Chain B, Crystal Structure Of Zinc-Bound Succinyl-Diaminopimelate
           Desuccinylase From Haemophilus Influenzae
 pdb|3ISZ|A Chain A, Crystal Structure Of Mono-zinc Form Of
           Succinyl-diaminopimelate Desuccinylase From Haemophilus
           Influenzae
 pdb|3ISZ|B Chain B, Crystal Structure Of Mono-zinc Form Of
           Succinyl-diaminopimelate Desuccinylase From Haemophilus
           Influenzae
          Length = 377

 Score = 26.2 bits (56), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 19/76 (25%), Positives = 31/76 (40%)

Query: 74  VKPLDPMQRQALNERINSQGFMTLPPPSSRTSELNSFRASSRPYYLQNGHTSTGQSGGAI 133
           + P D   +Q + ER+   GF     P + T  L +   +S P     GHT    +G   
Sbjct: 18  ISPNDEGCQQIIAERLEKLGFQIEWMPFNDTLNLWAKHGTSEPVIAFAGHTDVVPTGDEN 77

Query: 134 ASPAKSMVSKIMDLMF 149
              +    ++I+D M 
Sbjct: 78  QWSSPPFSAEIIDGML 93


  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    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,293,190
Number of Sequences: 62578
Number of extensions: 154412
Number of successful extensions: 316
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 306
Number of HSP's gapped (non-prelim): 10
length of query: 151
length of database: 14,973,337
effective HSP length: 90
effective length of query: 61
effective length of database: 9,341,317
effective search space: 569820337
effective search space used: 569820337
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: 47 (22.7 bits)