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= 029889
         (186 letters)

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

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



>pdb|4DGK|A Chain A, Crystal Structure Of Phytoene Desaturase Crti From Pantoea
           Ananatis
          Length = 501

 Score = 29.3 bits (64), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 34/89 (38%), Gaps = 22/89 (24%)

Query: 57  HNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYR 116
           H    GP YR L+D  F +  +     L       L+A   PC+TD  +A  E  G  Y 
Sbjct: 323 HTVCFGPRYRELIDEIFNHDGLAEDFSL------YLHA---PCVTDSSLAP-EGCGSYYV 372

Query: 117 VALRIAKDPRFERLPCTHKGTYADDCLVE 145
           +A            P  H GT   D  VE
Sbjct: 373 LA------------PVPHLGTANLDWTVE 389


>pdb|3SIU|B Chain B, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
           Monomeric Form
 pdb|3SIU|E Chain E, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
           Monomeric Form
 pdb|3SIV|B Chain B, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
           Dimeric Form
 pdb|3SIV|E Chain E, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
           Dimeric Form
 pdb|3SIV|H Chain H, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
           Dimeric Form
 pdb|3SIV|K Chain K, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
           Dimeric Form
          Length = 254

 Score = 28.9 bits (63), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 62  GPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCV 104
            P YRV+VD N +   I+N+L++    +   Y+K  P +   V
Sbjct: 8   APEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLV 50


>pdb|2OZB|B Chain B, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
 pdb|2OZB|E Chain E, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
          Length = 260

 Score = 28.9 bits (63), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 62  GPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCV 104
            P YRV+VD N +   I+N+L++    +   Y+K  P +   V
Sbjct: 14  APEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLV 56


>pdb|3W3S|A Chain A, Crystal Structure Of A. Aeolicus Trnasec In Complex With
           M. Kandleri Serrs
          Length = 527

 Score = 26.6 bits (57), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 9/54 (16%)

Query: 109 EKLGQKYRVALRIAKDPRFE-RLPCTHKGTY--------ADDCLVERVTQHKCF 153
           E+LG+K+RV +R  K PR+E  L    + TY        ADD +VE  T    F
Sbjct: 86  ERLGRKHRVGVRDLKIPRYEVVLRFDREVTYDYVGYVPVADDVVVEDGTVRLTF 139


  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
   0.324    0.139    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,884,276
Number of Sequences: 62578
Number of extensions: 180172
Number of successful extensions: 440
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 437
Number of HSP's gapped (non-prelim): 4
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)