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= 029475
         (193 letters)

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

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



>pdb|3SQG|C Chain C, Crystal Structure Of A Methyl-Coenzyme M Reductase
           Purified From Black Sea Mats
 pdb|3SQG|F Chain F, Crystal Structure Of A Methyl-Coenzyme M Reductase
           Purified From Black Sea Mats
 pdb|3SQG|I Chain I, Crystal Structure Of A Methyl-Coenzyme M Reductase
           Purified From Black Sea Mats
          Length = 279

 Score = 31.2 bits (69), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 31/141 (21%), Positives = 59/141 (41%), Gaps = 13/141 (9%)

Query: 24  QRVAGNFHISVHGLNIYVAQMIFGGAKNVNVSHVIHDLSF---GPKYPGIHNPLDGTVRM 80
           Q  AGN H++ +  N           +++    ++  L+    G +Y  IH PL+     
Sbjct: 3   QFTAGNSHVAQNRRNYMDPSYKLEKLRDIPEEDIVRLLAHRAPGEEYKSIHPPLE----E 58

Query: 81  LHDTSGTFKYYIKIVPTEYRYISKDVLPTNQFSVTEYFSTINEFDRTWPAVYFLYDLSPI 140
           + +     +  +K  PTE    + D +   Q++ + +FS I  + R W A+     + P 
Sbjct: 59  MEEPDCAVRQIVK--PTEG-AAAGDRIRYVQYTDSMFFSPITPYQRAWEALNRYKGVDPG 115

Query: 141 TV---TIKEERRSFLHLITRL 158
            +   TI E R   +  I ++
Sbjct: 116 VLSGRTIIEARERDIEKIAKI 136


>pdb|3P1W|A Chain A, Crystal Structure Of Rab Gdi From Plasmodium Falciparum,
           Pfl2060c
          Length = 475

 Score = 26.9 bits (58), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 16/73 (21%)

Query: 101 YISKDVLPTNQFSVTE----YFSTINEFDRTWPAVYFLYDLSPITVTIKEERRSFLHLIT 156
           Y++ D L    +   E    Y  +I+ F ++ P +Y LY L  I               +
Sbjct: 216 YLNDDYLKQPAYLTLERIKLYMQSISAFGKS-PFIYPLYGLGGIP-----------EGFS 263

Query: 157 RLCAVLGGTFALT 169
           R+CA+ GGTF L 
Sbjct: 264 RMCAINGGTFMLN 276


>pdb|2GFT|A Chain A, Crystal Structure Of The E263a Nucleophile Mutant Of
           Bacillus Licheniformis Endo-beta-1,4-galactanase In
           Complex With Galactotriose
 pdb|2GFT|B Chain B, Crystal Structure Of The E263a Nucleophile Mutant Of
           Bacillus Licheniformis Endo-beta-1,4-galactanase In
           Complex With Galactotriose
          Length = 399

 Score = 26.6 bits (57), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 19/87 (21%), Positives = 36/87 (41%)

Query: 19  GVLDVQRVAGNFHISVHGLNIYVAQMIFGGAKNVNVSHVIHDLSFGPKYPGIHNPLDGTV 78
           G   V+    N  +++H  N   +      A+ ++  HV +D+     YP  H  L    
Sbjct: 186 GSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLT 245

Query: 79  RMLHDTSGTFKYYIKIVPTEYRYISKD 105
            +L   + T+   + +  T Y Y ++D
Sbjct: 246 SVLTSVADTYGKKVMVAATSYTYTAED 272


  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
   0.325    0.140    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,070,417
Number of Sequences: 62578
Number of extensions: 260098
Number of successful extensions: 722
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 716
Number of HSP's gapped (non-prelim): 11
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)