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= 029895
         (186 letters)

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

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



>pdb|2PT7|G Chain G, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
 pdb|2PT7|H Chain H, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
          Length = 152

 Score = 30.8 bits (68), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 119 EAIMRTANLSVPLKIYEIGGGSGTCAKGVMDYIMLNAPERVYNNMTYISVE 169
           E +M T   SV + ++E+G G      GV+ YI L    + + N  Y+S++
Sbjct: 86  EKVMDTQLQSVIMTVHEVGKGQMKAPDGVLTYIALKKLRKAFPN-KYVSIK 135


>pdb|3CQG|A Chain A, Nucleoporin Nup107/nup133 Interaction Complex, Delta
           Finger Mutant
          Length = 246

 Score = 30.0 bits (66), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 21/84 (25%)

Query: 101 SWFTPVELFKPWYAHGIAEAIMRTANLSVPLKIYEIGGGSGTCAKGVMDYIMLNAPERVY 160
           ++    E F  W+ H            SVP       GGSG   KG +D +  +  E++Y
Sbjct: 97  AYLEAHETFNEWFKHMN----------SVP-------GGSGGSWKGHLDALTADVKEKMY 139

Query: 161 NNMTYIS----VEIQSLTGRDTER 180
           N + ++     V+++     D ER
Sbjct: 140 NVLLFVDGGWMVDVREDAKEDHER 163


>pdb|2DPN|A Chain A, Crystal Structure Of The Glycerol Kinase From Thermus
           Thermophilus Hb8
 pdb|2DPN|B Chain B, Crystal Structure Of The Glycerol Kinase From Thermus
           Thermophilus Hb8
          Length = 495

 Score = 29.3 bits (64), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 136 IGGGSGTCAKGVMDYIMLNAPER-VYNNMTYISVEIQSLTGRDT 178
           +GGG G C  G   +++LN  +R V +    ++    SL GR T
Sbjct: 253 LGGGEGKCTYGTGAFLLLNTGKRPVLSEKGLLATVAWSLGGRAT 296


>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
           Complex Bound To Rna
          Length = 1003

 Score = 29.3 bits (64), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 23/43 (53%)

Query: 93  KIYKQSEISWFTPVELFKPWYAHGIAEAIMRTANLSVPLKIYE 135
           K++  SE S    VE+ K    + + E  M  AN+SV  KIY+
Sbjct: 704 KVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYD 746


>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
          Length = 977

 Score = 29.3 bits (64), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 23/43 (53%)

Query: 93  KIYKQSEISWFTPVELFKPWYAHGIAEAIMRTANLSVPLKIYE 135
           K++  SE S    VE+ K    + + E  M  AN+SV  KIY+
Sbjct: 678 KVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYD 720


  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    0.137    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,507,174
Number of Sequences: 62578
Number of extensions: 220641
Number of successful extensions: 387
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 383
Number of HSP's gapped (non-prelim): 7
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
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: 48 (23.1 bits)