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= 024877
         (261 letters)

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

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



>pdb|3LMD|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Corynebacterium Glutamicum Atcc 13032
 pdb|3Q2Q|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Corynebacterium Glutamicum Complexed With Calcium
           And Isoprenyl Diphosphate
          Length = 360

 Score = 30.4 bits (67), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 75  YDSSIPEHREALRALWNAAFPDEELRDLISEQWKEMGWQGKDPSTDFRGGGFISLENLLY 134
           +  + PEH +AL+    A     ++ D I + + E    GK P TD R G F +L  L  
Sbjct: 214 HAGAAPEHIDALKNFGAAVGMIFQIVDDIIDIFSETHESGKTPGTDLREGVF-TLPVLYA 272

Query: 135 LARNFP 140
           L  + P
Sbjct: 273 LREDTP 278


>pdb|2X1L|A Chain A, Crystal Structure Of Mycobacterium Smegmatis
           Methionyl-Trna Synthetase In Complex With Methionine And
           Adenosine
 pdb|2X1L|B Chain B, Crystal Structure Of Mycobacterium Smegmatis
           Methionyl-Trna Synthetase In Complex With Methionine And
           Adenosine
 pdb|2X1L|C Chain C, Crystal Structure Of Mycobacterium Smegmatis
           Methionyl-Trna Synthetase In Complex With Methionine And
           Adenosine
 pdb|2X1M|A Chain A, Crystal Structure Of Mycobacterium Smegmatis
           Methionyl-Trna Synthetase In Complex With Methionine
          Length = 524

 Score = 28.9 bits (63), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 26/44 (59%), Gaps = 4/44 (9%)

Query: 52  PSFDLTPAQEECLQRLQLRIDVAYD----SSIPEHREALRALWN 91
           P+ +L     +  QRLQ ++++++D    +S  +H EA +A+W 
Sbjct: 75  PAAELARRNSDVFQRLQEKLNISFDRFIRTSDADHYEASKAIWK 118


>pdb|2LF2|A Chain A, Solution Nmr Structure Of The Ahsa1-Like Protein Chu_1110
           From Cytophaga Hutchinsonii, Northeast Structural
           Genomics Consortium Target Chr152
          Length = 175

 Score = 28.1 bits (61), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 12/66 (18%)

Query: 69  LRIDVAYDSSIPEHRE---------ALRALWNAAFPDEELRDLISEQWKEMGWQGKDPST 119
           +R D+A D S+ +  +         A+RA+   AF   E+ D   + W    W+ K  S 
Sbjct: 1   MRTDLALDFSVNKENKTITIKREFAAVRAIVWEAFTRAEILD---QWWAPKPWKAKTKSM 57

Query: 120 DFRGGG 125
           DF+ GG
Sbjct: 58  DFKEGG 63


  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
   0.322    0.136    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,536,710
Number of Sequences: 62578
Number of extensions: 298608
Number of successful extensions: 634
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 623
Number of HSP's gapped (non-prelim): 13
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)