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= psy12486
         (148 letters)

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

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



>pdb|3F8M|A Chain A, Crystal Structure Of Phnf From Mycobacterium Smegmatis
 pdb|3F8M|B Chain B, Crystal Structure Of Phnf From Mycobacterium Smegmatis
          Length = 248

 Score = 29.6 bits (65), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 26/48 (54%)

Query: 1   MPKPKSSKPGDHTAYSELACAKQCSCGRVLPAHLWLPLSGCTAGILGL 48
           + +PK  +P    +Y+E A A+  S GR+L A   L      AG+LG+
Sbjct: 75  VARPKIRQPLGMGSYTEAAKAQGLSAGRILVAWSDLTADEVLAGVLGV 122


>pdb|3RYK|A Chain A, 1.63 Angstrom Resolution Crystal Structure Of
           Dtdp-4-Dehydrorhamnose 3,5-Epimerase (Rfbc) From
           Bacillus Anthracis Str. Ames With Tdp And Ppi Bound
 pdb|3RYK|B Chain B, 1.63 Angstrom Resolution Crystal Structure Of
           Dtdp-4-Dehydrorhamnose 3,5-Epimerase (Rfbc) From
           Bacillus Anthracis Str. Ames With Tdp And Ppi Bound
          Length = 205

 Score = 28.1 bits (61), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 12/80 (15%)

Query: 66  VLLLMRAGS----KWNRYFL----NRKSLLTNGFVGGLCTYVLFWTFFYTMGDKWIASHM 117
           V++ +R  S    +W  Y L    +R+ L+  GF  G CT V      Y + + + A H 
Sbjct: 108 VIVDLRKDSPTFKQWRGYILSADNHRQLLVPKGFAHGFCTLVPHTIVMYKVDEYYSADH- 166

Query: 118 TSQSLWEYLPNQSLCVYFPI 137
            S  LW    ++ L + +P+
Sbjct: 167 DSGVLWN---DKELAIPWPV 183


  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
   0.326    0.139    0.485 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,535,318
Number of Sequences: 62578
Number of extensions: 153632
Number of successful extensions: 251
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 250
Number of HSP's gapped (non-prelim): 2
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 bits)