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= 025946
         (245 letters)

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

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



>pdb|2F00|A Chain A, Escherichia Coli Murc
 pdb|2F00|B Chain B, Escherichia Coli Murc
          Length = 491

 Score = 28.5 bits (62), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESV-RFSNESTTFG 214
           +I  D       DF+  K T  + L   P+  +    VDD  +RE + R   ++TT+G
Sbjct: 194 NIEADHXDTYQGDFENLKQTFINFLHNLPFYGRAVXCVDDPVIRELLPRVGRQTTTYG 251


>pdb|4HV4|A Chain A, 2.25 Angstrom Resolution Crystal Structure Of
           Udp-N-Acetylmuramate--L- Alanine Ligase (Murc) From
           Yersinia Pestis Co92 In Complex With Amp
 pdb|4HV4|B Chain B, 2.25 Angstrom Resolution Crystal Structure Of
           Udp-N-Acetylmuramate--L- Alanine Ligase (Murc) From
           Yersinia Pestis Co92 In Complex With Amp
          Length = 494

 Score = 28.5 bits (62), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESV-RFSNESTTFGQA 216
           +I  D       DF+  K T  + L   P+  +    +DD  VRE + R     TT+G  
Sbjct: 197 NIEADHMDTYQGDFENLKQTFINFLHNLPFYGRAVMCIDDPVVRELLPRVGRHITTYG-- 254

Query: 217 FSD 219
           FSD
Sbjct: 255 FSD 257


  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
   0.323    0.138    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,174,582
Number of Sequences: 62578
Number of extensions: 221869
Number of successful extensions: 411
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 411
Number of HSP's gapped (non-prelim): 4
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)