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= 003890
         (788 letters)

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

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



>pdb|2ZW9|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZW9|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZWA|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZWA|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZZK|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZZK|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
          Length = 695

 Score = 30.4 bits (67), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 30/117 (25%), Positives = 55/117 (47%), Gaps = 3/117 (2%)

Query: 194 REELFDLLIEGPSGLSVVAILNGSGFDKTAFAADTYNNNHIKFYFDCLAWVRVSIAYDSG 253
           R  L  ++ + P    +V +  G G+D   F     NN   + Y D ++++ +  + D  
Sbjct: 93  RSRLNSIIEQTPQDKKIVVVNLGCGYDPLPFQLLDTNNIQSQQYHDRVSFIDIDYS-DLL 151

Query: 254 KILDDIIKSVMPPSRVSVIIGEDYKLKKTILRDYLTNKKYFIVLDDVFNDSDIWDDL 310
           KI  ++IK++   S++ + + ED         D+LT  KY     D+ NDS ++  L
Sbjct: 152 KIKIELIKTIPELSKI-IGLSEDKDYVDDSNVDFLTTPKYLARPCDL-NDSKMFSTL 206


>pdb|3H7N|A Chain A, Structure Of Nup120
 pdb|3H7N|B Chain B, Structure Of Nup120
 pdb|3H7N|C Chain C, Structure Of Nup120
 pdb|3H7N|D Chain D, Structure Of Nup120
          Length = 729

 Score = 29.6 bits (65), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 7/48 (14%)

Query: 522 LQSFLNHSSESDHLALIDCENFCEKFK-------HLRILNLGSAVLVQ 562
           L  F + SS+SD+ ++I C+ F E++        HL+I +L S  L+Q
Sbjct: 208 LTRFFSRSSKSDYDSVISCKLFHERYLIVLTQNCHLKIWDLTSFTLIQ 255


>pdb|3F7F|A Chain A, Structure Of Nup120
 pdb|3F7F|B Chain B, Structure Of Nup120
 pdb|3F7F|C Chain C, Structure Of Nup120
 pdb|3F7F|D Chain D, Structure Of Nup120
          Length = 729

 Score = 29.6 bits (65), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 7/48 (14%)

Query: 522 LQSFLNHSSESDHLALIDCENFCEKFK-------HLRILNLGSAVLVQ 562
           L  F + SS+SD+ ++I C+ F E++        HL+I +L S  L+Q
Sbjct: 208 LTRFFSRSSKSDYDSVISCKLFHERYLIVLTQNCHLKIWDLTSFTLIQ 255


>pdb|3HXR|A Chain A, Nucleoporin Nup120 From S.Cerevisiae (Aa 1-757)
          Length = 761

 Score = 29.3 bits (64), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 7/48 (14%)

Query: 522 LQSFLNHSSESDHLALIDCENFCEKFK-------HLRILNLGSAVLVQ 562
           L  F + SS+SD+ ++I C+ F E++        HL+I +L S  L+Q
Sbjct: 212 LTRFFSRSSKSDYDSVISCKLFHERYLIVLTQNCHLKIWDLTSFTLIQ 259


  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
   0.322    0.139    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,883,077
Number of Sequences: 62578
Number of extensions: 815960
Number of successful extensions: 1811
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1811
Number of HSP's gapped (non-prelim): 5
length of query: 788
length of database: 14,973,337
effective HSP length: 107
effective length of query: 681
effective length of database: 8,277,491
effective search space: 5636971371
effective search space used: 5636971371
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)