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= 000952
         (1210 letters)

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

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



>pdb|1R30|A Chain A, The Crystal Structure Of Biotin Synthase, An S-
           Adenosylmethionine-dependent Radical Enzyme
 pdb|1R30|B Chain B, The Crystal Structure Of Biotin Synthase, An S-
           Adenosylmethionine-dependent Radical Enzyme
          Length = 369

 Score = 33.5 bits (75), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 38/140 (27%), Positives = 56/140 (40%), Gaps = 21/140 (15%)

Query: 210 FAGSPSASRQALPTLSSLLSRSFNSQIIPANVVESAENKDSATLSVSTLSNIEEADGMED 269
           F GS    R  L  ++ L  +     +  A  V   ++ D   + VSTL +I+     ED
Sbjct: 21  FQGSAHRPRWTLSQVTELFEKPLLDLLFEAQQVHR-QHFDPRQVQVSTLLSIKTGACPED 79

Query: 270 LDYIALDVLKWRWLDESQSSSMST--EGDRVATIQEMSSLNFLEVGAAALLLGDMEAKMK 327
             Y              QSS   T  E +R+  ++++     LE    A   G     M 
Sbjct: 80  CKYC------------PQSSRYKTGLEAERLMEVEQV-----LESARKAKAAGSTRFCM- 121

Query: 328 GQPWKYIGTNDMPYLDQLLQ 347
           G  WK     DMPYL+Q++Q
Sbjct: 122 GAAWKNPHERDMPYLEQMVQ 141


>pdb|1KNY|A Chain A, Kanamycin Nucleotidyltransferase
 pdb|1KNY|B Chain B, Kanamycin Nucleotidyltransferase
          Length = 253

 Score = 30.8 bits (68), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 3/47 (6%)

Query: 1152 RVAYYSSAFLLKRMMTEK--PEKYQHMLQNLVFKAQQSNNEKLLENL 1196
            R+ Y +SA +L   + +   P  Y H+ Q  V   Q S++EKLLE+L
Sbjct: 182  RICYTTSASVLTEAVKQSDLPSGYDHLCQ-FVMSGQLSDSEKLLESL 227


>pdb|3MTJ|A Chain A, The Crystal Structure Of A Homoserine Dehydrogenase From
           Thiobacillus Denitrificans To 2.15a
          Length = 444

 Score = 30.4 bits (67), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 45/182 (24%), Positives = 73/182 (40%), Gaps = 26/182 (14%)

Query: 112 VALLKRYLLRYKPSEE-----TLLQIDRFCLNTISECAITPNRKVSPWSRSLNQQSGAST 166
           ++ L R  +RY  +EE      LL I R   N I E  + P   + P  R +    GA  
Sbjct: 234 ISQLTREDVRY--AEELGYRIKLLGIARRAENGI-ELRVHPT--LIPERRLIANVDGAXN 288

Query: 167 ASV----NASPSL---------PVSSFTSGTLVKSLNYVRSLVAQHIPRRSFQPASFAGS 213
           A +       P+L         P +S     LV       +     +P  +FQP   A +
Sbjct: 289 AVLVKGDAVGPTLYYGAGAGSEPTASAVVADLVDVTRLHTADPHHRVPHLAFQPDQLADT 348

Query: 214 PSASRQALPTLSSLLSRSFNSQIIPANVVESAENKDSATLSVSTLSNIEEADGMEDLDYI 273
           P    +A+ T   L  R+F+   + A++     +   +++S+      E A+G E +D I
Sbjct: 349 PILPXEAVRTAYYLRLRAFDRPGVLADITRILAD---SSISIDAXVQKEPAEGEEQVDII 405

Query: 274 AL 275
            L
Sbjct: 406 LL 407


>pdb|1KAN|A Chain A, Molecular Structure Of Kanamycin Nucleotidyltransferase
            Determined To 3.0-Angstroms Resolution
 pdb|1KAN|B Chain B, Molecular Structure Of Kanamycin Nucleotidyltransferase
            Determined To 3.0-Angstroms Resolution
          Length = 253

 Score = 30.4 bits (67), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 3/47 (6%)

Query: 1152 RVAYYSSAFLLKRMMTEK--PEKYQHMLQNLVFKAQQSNNEKLLENL 1196
            R+ Y +SA +L   + +   P  Y H+ Q  V   Q S++EKLLE+L
Sbjct: 182  RICYTTSASVLTEAVKQSDLPSGYDHLCQ-FVMSGQLSDSEKLLESL 227


  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    0.132    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 30,534,270
Number of Sequences: 62578
Number of extensions: 1143835
Number of successful extensions: 2333
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2331
Number of HSP's gapped (non-prelim): 6
length of query: 1210
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1100
effective length of database: 8,089,757
effective search space: 8898732700
effective search space used: 8898732700
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: 57 (26.6 bits)