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= 015418
         (407 letters)

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

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



>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 = 1.4,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 196 PNLKLAGPTSFAPVIEMAMSIVEQSGGQYHVLLIIADGQVTRSVDTV 242
           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 = 30.0 bits (66), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 285 DNIPARAFDNFQFVNFTEIMSKNHDQTRKETEFALSALMEIPSQYKATIELNILGRRKGN 344
           D +P    D F  V   ++ S+  +  R   E  L AL+E+ +        ++  RR+  
Sbjct: 104 DGLPGLVVDRFGEVLVLQVRSRGMEALR---EVWLPALLEVVAPKGVYERSDVEARRQEG 160

Query: 345 VPERVALPPPVYG 357
           +PERV +   VYG
Sbjct: 161 LPERVGV---VYG 170


>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 = 29.6 bits (65), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 52/135 (38%), Gaps = 36/135 (26%)

Query: 151 DEDNLIPCYGFGDASTHDQDVFSFYSGGRFCYGFEEVLSRYREIVPNLKLAGPTSFAP-- 208
           ++D LIP YG                  RF Y   E+  RY   V  L+    T F P  
Sbjct: 86  EDDVLIPIYG------------------RFGYLLTEIAERYGANVHMLECEWGTVFDPED 127

Query: 209 VIE---------MAMSIVEQSGGQYHVLLIIADGQVTR-------SVDTVRGCLSPQEQK 252
           +I          +AM   E S G+ H L  I +   T        +V T+ GC    ++ 
Sbjct: 128 IIREIKKVKPKIVAMVHGETSTGRIHPLKAIGEACRTEDALFIVDAVATIGGCEVKVDEW 187

Query: 253 TVDAIVKASELPLSI 267
            +DA +  ++  LS+
Sbjct: 188 KIDAAIGGTQKCLSV 202


>pdb|3PG5|A Chain A, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
 pdb|3PG5|B Chain B, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
 pdb|3PG5|C Chain C, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
 pdb|3PG5|D Chain D, Crystal Structure Of Protein Dip2308 From Corynebacterium
           Diphtheriae, Northeast Structural Genomics Consortium
           Target Cdr78
          Length = 361

 Score = 29.6 bits (65), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 23/97 (23%), Positives = 44/97 (45%), Gaps = 11/97 (11%)

Query: 107 IDFTKSNEWT---GKRSFNRRSLHYIGDGLNP------YEQAISIIGKTLAVFDEDNLIP 157
           I+   S+ W    G+++   R +H+ G   +       Y+     +G +L  F+   L+ 
Sbjct: 116 IEDLXSDSWQSALGRQTGPFRRIHWAGQLAHAXERDDRYDVIFFDVGPSLGPFNRTVLLG 175

Query: 158 CYGFGDASTHDQDVFSFYSGGRFCYGFEEVLSRYREI 194
           C  F   +    D+FSF++ G     F+  +++Y EI
Sbjct: 176 CDAF--VTPTATDLFSFHAFGNLARWFDAWVTQYAEI 210


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

 Score = 28.9 bits (63), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 3/37 (8%)

Query: 124 RSLHYIGDGLNP---YEQAISIIGKTLAVFDEDNLIP 157
           R+L+ IG   N    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
   0.317    0.134    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,707,357
Number of Sequences: 62578
Number of extensions: 420805
Number of successful extensions: 935
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 933
Number of HSP's gapped (non-prelim): 19
length of query: 407
length of database: 14,973,337
effective HSP length: 101
effective length of query: 306
effective length of database: 8,652,959
effective search space: 2647805454
effective search space used: 2647805454
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: 53 (25.0 bits)