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= 048563
         (135 letters)

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

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



>pdb|2VK9|A Chain A, Crystal Structure Of The Catalytic Domain Of Alpha-Toxin
           From Clostridium Novyi
          Length = 551

 Score = 30.0 bits (66), Expect = 0.43,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 26/42 (61%)

Query: 17  SSNLLRLALLYKFGGIYLDPNVIVLENLSKLKNTIGAQTVDS 58
           +S++LR+A+L K+GG+Y D + +   NLS   +      +DS
Sbjct: 266 ASDILRIAILKKYGGVYCDLDFLPGVNLSLFNDISKPNGMDS 307


>pdb|4DMV|A Chain A, Crystal Structure Of The Gt Domain Of Clostridium
           Difficile Toxin A
 pdb|4DMW|A Chain A, Crystal Structure Of The Gt Domain Of Clostridium
           Difficile Toxin A (Tcda) In Complex With Udp And
           Manganese
          Length = 556

 Score = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 10/23 (43%), Positives = 18/23 (78%)

Query: 17  SSNLLRLALLYKFGGIYLDPNVI 39
           +S+++RL  L  FGG+YLD +++
Sbjct: 282 ASDIVRLLALKNFGGVYLDVDML 304


>pdb|3SRZ|A Chain A, Clostridium Difficile Toxin A (Tcda) Glucolsyltransferase
           Domain Bound To Udp-Glucose
 pdb|3SS1|A Chain A, Clostridium Difficile Toxin A (Tcda) Glucolsyltransferase
           Domain
          Length = 555

 Score = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 10/23 (43%), Positives = 18/23 (78%)

Query: 17  SSNLLRLALLYKFGGIYLDPNVI 39
           +S+++RL  L  FGG+YLD +++
Sbjct: 267 ASDIVRLLALKNFGGVYLDVDML 289


>pdb|1T90|A Chain A, Crystal Structure Of Methylmalonate Semialdehyde
           Dehydrogenase From Bacillus Subtilis
 pdb|1T90|B Chain B, Crystal Structure Of Methylmalonate Semialdehyde
           Dehydrogenase From Bacillus Subtilis
 pdb|1T90|C Chain C, Crystal Structure Of Methylmalonate Semialdehyde
           Dehydrogenase From Bacillus Subtilis
 pdb|1T90|D Chain D, Crystal Structure Of Methylmalonate Semialdehyde
           Dehydrogenase From Bacillus Subtilis
          Length = 486

 Score = 26.6 bits (57), Expect = 4.6,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 85  VNGRTRFNFTVLPPSAFYPVDWRRVQSFFMRPRNEQHSKLLHKKLELINK 134
           V G   FNF ++ P   +P+      +F ++P +E+   L  K +EL  K
Sbjct: 145 VGGIAPFNFPMMVPCWMFPMAIALGNTFILKP-SERTPLLTEKLVELFEK 193


>pdb|1HN0|A Chain A, Crystal Structure Of Chondroitin Abc Lyase I From Proteus
           Vulgaris At 1.9 Angstroms Resolution
          Length = 1021

 Score = 25.4 bits (54), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 5   NVDPGLISLGQN--SSNLLRLALLYKFGGIYLDPNVIVLENLSKLKNTIGA 53
           NV P L    +N  + +L+R  L+ +F G   + N+ + EN+SKLK+   A
Sbjct: 242 NVKPQLPVTPENLAAIDLIRQRLINEFVGGEKETNLALEENISKLKSDFDA 292


  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
   0.321    0.138    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,843,808
Number of Sequences: 62578
Number of extensions: 135196
Number of successful extensions: 263
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 256
Number of HSP's gapped (non-prelim): 8
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
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: 46 (22.3 bits)