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= 004138
         (771 letters)

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

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



>pdb|3D0F|A Chain A, Structure Of The Big_1156.2 Domain Of Putative
           Penicillin-Binding Protein Mrca From Nitrosomonas
           Europaea Atcc 19718
 pdb|3D0F|B Chain B, Structure Of The Big_1156.2 Domain Of Putative
           Penicillin-Binding Protein Mrca From Nitrosomonas
           Europaea Atcc 19718
          Length = 106

 Score = 30.8 bits (68), Expect = 3.2,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 226 GQLFRSKNDGSVTSRRFVCSKEGFQHPSRVGCGAFMRIKRKEFGSWIVDRL 276
           G+  R   DG   + RF+ +        R+  GA +R+K+ E GSW + +L
Sbjct: 56  GETIRITGDGLKAAHRFLSNDPKIGE-KRIRPGALIRVKKTEKGSWQIVQL 105


>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
          Length = 1054

 Score = 30.4 bits (67), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 240  RRFVCSKEGFQHPSRVGCGAFMRIKRKEFGSWIVDRLQKDHNHDLECQMGANKKTFATSK 299
            R +V  K G   P+++G   F  + R+ +  ++     +D   DLE +M A ++      
Sbjct: 986  RNYVVEKYGRMIPTKLGIDVFRFLVRR-YAKFV----SEDRTRDLESRMDAIERGELDYL 1040

Query: 300  KFIEDVSGGLDSVD 313
            K +ED+   + S+D
Sbjct: 1041 KALEDMYAEIKSID 1054


>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
 pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
          Length = 1054

 Score = 30.0 bits (66), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 240  RRFVCSKEGFQHPSRVGCGAFMRIKRKEFGSWIVDRLQKDHNHDLECQMGANKKTFATSK 299
            R +V  K G   P+++G   F  + R+ +  ++     +D   DLE +M A ++      
Sbjct: 986  RNYVVEKYGRMIPTKLGIDVFRFLVRR-YAKFV----SEDRTRDLESRMDAIERGELDYL 1040

Query: 300  KFIEDVSGGLDSVD 313
            K +ED+   + S+D
Sbjct: 1041 KALEDMYAEIKSID 1054


>pdb|3QR3|A Chain A, Crystal Structure Of Cel5a (Eg2) From Hypocrea Jecorina
           (Trichoderma Reesei)
 pdb|3QR3|B Chain B, Crystal Structure Of Cel5a (Eg2) From Hypocrea Jecorina
           (Trichoderma Reesei)
          Length = 340

 Score = 30.0 bits (66), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 10/30 (33%), Positives = 17/30 (56%)

Query: 505 AQFSTMWTALIEKYGQRDNIWLKEMYEKRE 534
           AQF+++W+ L  KY  +  +W   M E  +
Sbjct: 123 AQFTSLWSQLASKYASQSRVWFGIMNEPHD 152


  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
   0.321    0.134    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,847,633
Number of Sequences: 62578
Number of extensions: 937700
Number of successful extensions: 1719
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1716
Number of HSP's gapped (non-prelim): 10
length of query: 771
length of database: 14,973,337
effective HSP length: 106
effective length of query: 665
effective length of database: 8,340,069
effective search space: 5546145885
effective search space used: 5546145885
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: 55 (25.8 bits)