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= 016250
         (392 letters)

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

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



>pdb|3ISL|A Chain A, Crystal Structure Of Ureidoglycine-Glyoxylate
           Aminotransferase (Pucg) From Bacillus Subtilis
 pdb|3ISL|B Chain B, Crystal Structure Of Ureidoglycine-Glyoxylate
           Aminotransferase (Pucg) From Bacillus Subtilis
          Length = 416

 Score = 35.0 bits (79), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 52/122 (42%), Gaps = 23/122 (18%)

Query: 151 DEDNLIPCYGFGDGGRFCYGFEEVLSRYREIVPNLKLAGPTSFAP--VIE---------M 199
           ++D LIP YG     RF Y   E+  RY   V  L+    T F P  +I          +
Sbjct: 86  EDDVLIPIYG-----RFGYLLTEIAERYGANVHMLECEWGTVFDPEDIIREIKKVKPKIV 140

Query: 200 AMSIVEQSGGQYHVLLIIADGQVTR-------SVDTVRGCLSPQEQKTVDAIVKASELPL 252
           AM   E S G+ H L  I +   T        +V T+ GC    ++  +DA +  ++  L
Sbjct: 141 AMVHGETSTGRIHPLKAIGEACRTEDALFIVDAVATIGGCEVKVDEWKIDAAIGGTQKCL 200

Query: 253 SI 254
           S+
Sbjct: 201 SV 202


>pdb|1S1M|A Chain A, Crystal Structure Of E. Coli Ctp Synthetase
 pdb|1S1M|B Chain B, Crystal Structure Of E. Coli Ctp Synthetase
 pdb|2AD5|A Chain A, Mechanisms Of Feedback Regulation And Drug Resistance Of
           Ctp Synthetases: Structure Of The E. Coli Ctps/ctp
           Complex At 2.8- Angstrom Resolution.
 pdb|2AD5|B Chain B, Mechanisms Of Feedback Regulation And Drug Resistance Of
           Ctp Synthetases: Structure Of The E. Coli Ctps/ctp
           Complex At 2.8- Angstrom Resolution
          Length = 545

 Score = 31.6 bits (70), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 75  RYSRIADDYKSLDQVTEALARAGLESSNLIVGIDFTKSNEWTGKRSFNRRSLHYI----G 130
           +Y  + D YKS   V EAL   GL++  + V I    S +   +     + L  I    G
Sbjct: 297 KYIELPDAYKS---VIEALKHGGLKN-RVSVNIKLIDSQDVETRGVEILKGLDAILVPGG 352

Query: 131 DGLNPYEQAISIIGKTLAVFDEDNLIPCYGFGDGGRFCYGFEEVLSRYREIVPNLKLAGP 190
            G    E  I     T A F  +N IP  G       C G +  L  Y   V N++ A  
Sbjct: 353 FGYRGVEGMI-----TTARFARENNIPYLGI------CLGMQVALIDYARHVANMENANS 401

Query: 191 TSFAP 195
           T F P
Sbjct: 402 TEFVP 406


>pdb|1KRH|A Chain A, X-Ray Stucture Of Benzoate Dioxygenase Reductase
 pdb|1KRH|B Chain B, X-Ray Stucture Of Benzoate Dioxygenase Reductase
          Length = 338

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 183 PNLKLAGPTSFAPVIEMAMSIVEQSGGQYHVLLIIADGQVTRSVDTV 229
           P L LAG T  AP + M + ++EQ G ++ V L+     VT+  D V
Sbjct: 212 PVLMLAGGTGIAPFLSM-LQVLEQKGSEHPVRLVFG---VTQDCDLV 254


>pdb|4DMG|A Chain A, Thermus Thermophilus M5c1942 Methyltransferase Rlmo
 pdb|4DMG|B Chain B, Thermus Thermophilus M5c1942 Methyltransferase Rlmo
          Length = 393

 Score = 30.4 bits (67), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 272 DNIPARAFDNFQFVNFTEIMSKNHDQTRKETEFALSALMEIPSQYKATIELNILGRRKGN 331
           D +P    D F  V   ++ S+  +  R   E  L AL+E+ +        ++  RR+  
Sbjct: 104 DGLPGLVVDRFGEVLVLQVRSRGMEALR---EVWLPALLEVVAPKGVYERSDVEARRQEG 160

Query: 332 VPERVALPPPVYG 344
           +PERV +   VYG
Sbjct: 161 LPERVGV---VYG 170


>pdb|3ULQ|A Chain A, Crystal Structure Of The Anti-Activator Rapf Complexed
           With The Response Regulator Coma Dna Binding Domain
          Length = 383

 Score = 28.5 bits (62), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 3/37 (8%)

Query: 124 RSLHYIG---DGLNPYEQAISIIGKTLAVFDEDNLIP 157
           R+L+ IG   +  + YE AI    + +AVF+E N++P
Sbjct: 225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILP 261


  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
   0.316    0.134    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,289,535
Number of Sequences: 62578
Number of extensions: 407090
Number of successful extensions: 986
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 969
Number of HSP's gapped (non-prelim): 40
length of query: 392
length of database: 14,973,337
effective HSP length: 101
effective length of query: 291
effective length of database: 8,652,959
effective search space: 2518011069
effective search space used: 2518011069
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)