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= 043376
         (348 letters)

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

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



>pdb|1E8C|A Chain A, Structure Of Mure The Udp-N-Acetylmuramyl Tripeptide
           Synthetase From E. Coli
 pdb|1E8C|B Chain B, Structure Of Mure The Udp-N-Acetylmuramyl Tripeptide
           Synthetase From E. Coli
          Length = 498

 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 26/38 (68%)

Query: 270 DSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVA 307
           DSRV +AGDLFV  VG + DG  Y+ +A  +G  A++A
Sbjct: 27  DSRVAAAGDLFVAVVGHQADGRRYIPQAIAQGVAAIIA 64


>pdb|2AM1|A Chain A, Sp Protein Ligand 1
 pdb|2AM2|A Chain A, Sp Protein Ligand 2
          Length = 454

 Score = 38.5 bits (88), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 3/58 (5%)

Query: 254 VSVYGDLEVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEI 311
           +S++ D ++E    + DSR++  GDLFV   G + DGH ++  A + GA   ++ KE+
Sbjct: 18  ISIFEDTQLE--KAEFDSRLIGTGDLFVPLKGAR-DGHDFIETAFENGAAVTLSEKEV 72


>pdb|2WTZ|A Chain A, Mure Ligase Of Mycobacterium Tuberculosis
 pdb|2WTZ|B Chain B, Mure Ligase Of Mycobacterium Tuberculosis
 pdb|2WTZ|C Chain C, Mure Ligase Of Mycobacterium Tuberculosis
 pdb|2WTZ|D Chain D, Mure Ligase Of Mycobacterium Tuberculosis
 pdb|2XJA|A Chain A, Structure Of Mure From M.Tuberculosis With Dipeptide And
           Adp
 pdb|2XJA|B Chain B, Structure Of Mure From M.Tuberculosis With Dipeptide And
           Adp
 pdb|2XJA|C Chain C, Structure Of Mure From M.Tuberculosis With Dipeptide And
           Adp
 pdb|2XJA|D Chain D, Structure Of Mure From M.Tuberculosis With Dipeptide And
           Adp
          Length = 535

 Score = 35.4 bits (80), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 264 ITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCKALV 323
           +TG+   ++ VS GDLF    G  T G  ++ +A  RGAVAV+ +    + E  G  A+ 
Sbjct: 62  VTGVTLRAQDVSPGDLFAALTGSTTHGARHVGDAIARGAVAVL-TDPAGVAEIAGRAAVP 120

Query: 324 IV 325
           ++
Sbjct: 121 VL 122


>pdb|1GG4|A Chain A, Crystal Structure Of Escherichia Coli Udpmurnac-Tripeptide
           D-Alanyl-D-Alanine-Adding Enzyme (Murf) At 2.3 Angstrom
           Resolution
 pdb|1GG4|B Chain B, Crystal Structure Of Escherichia Coli Udpmurnac-Tripeptide
           D-Alanyl-D-Alanine-Adding Enzyme (Murf) At 2.3 Angstrom
           Resolution
          Length = 452

 Score = 35.0 bits (79), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 8/79 (10%)

Query: 261 EVEITGIQHDSRVVSAGDLFVCCVGRKTDGHLYLSEADKRGAVAVVASKEIDIEETLGCK 320
           ++ +  +  D+R ++ G LFV   G + D H +  +A   GA A++ S+ +DI+      
Sbjct: 21  DITLDAVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAGGAGALLVSRPLDID-----L 75

Query: 321 ALVIVEDTNLV---LPHWL 336
             +IV+DT L    L  W+
Sbjct: 76  PQLIVKDTRLAFGELAAWV 94


>pdb|2X9P|A Chain A, X-Ray Structure Of The Substrate-Free Cytochrome P450 Pimd
           - A Polyene Macrolide Antibiotic Pimaricin Epoxidase
 pdb|2XBK|A Chain A, X-Ray Structure Of The Substrate-Bound Cytochrome P450
           Pimd - A Polyene Macrolide Antibiotic Pimaricin
           Epoxidase
          Length = 404

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 3/44 (6%)

Query: 90  KANQSTYLNAIADVDDPPVNTGDVSEQDDFFGEIDKAVAMKRDE 133
           +A  +T L  IA +DD     G V  QDD FG +   V  KR E
Sbjct: 172 RAELTTLLAGIAKLDD---REGAVRAQDDLFGYVAGLVEHKRAE 212


  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
   0.318    0.136    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,687,712
Number of Sequences: 62578
Number of extensions: 258593
Number of successful extensions: 486
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 482
Number of HSP's gapped (non-prelim): 6
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)