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= 022068
         (303 letters)

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

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



>pdb|1M2B|A Chain A, Crystal Structure At 1.25 Angstroms Resolution Of The
           Cys55ser Variant Of The Thioredoxin-Like [2fe-2s]
           Ferredoxin From Aquifex Aeolicus
 pdb|1M2B|B Chain B, Crystal Structure At 1.25 Angstroms Resolution Of The
           Cys55ser Variant Of The Thioredoxin-Like [2fe-2s]
           Ferredoxin From Aquifex Aeolicus
          Length = 110

 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 46/103 (44%), Gaps = 15/103 (14%)

Query: 190 YVFVCSH----GSRDKRCGVCGPALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYA---G 242
           +VFVC      G     C   G    E F A ++      Q+F+       G   A   G
Sbjct: 5   HVFVCVQDRPPGHPQGSCAQRGSR--EVFQAFMEKIQTDPQLFMTTVITPTGSMNACMMG 62

Query: 243 NLIVYSPDSEGKIMGHWYGYVTPDDVPAILDQHIAKGEIIERL 285
            ++V  PD      G WYG V P+DV  I+++H+  GE +ERL
Sbjct: 63  PVVVVYPD------GVWYGQVKPEDVDEIVEKHLKGGEPVERL 99


>pdb|1M2D|A Chain A, Crystal Structure At 1.05 Angstroms Resolution Of The
           Cys59ser Variant Of The Thioredoxin-Like [2fe-2s]
           Ferredoxin From Aquifex Aeolicus
 pdb|1M2D|B Chain B, Crystal Structure At 1.05 Angstroms Resolution Of The
           Cys59ser Variant Of The Thioredoxin-Like [2fe-2s]
           Ferredoxin From Aquifex Aeolicus
          Length = 110

 Score = 40.0 bits (92), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 46/103 (44%), Gaps = 15/103 (14%)

Query: 190 YVFVCSH----GSRDKRCGVCGPALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYA---G 242
           +VFVC      G     C   G    E F A ++      Q+F+       G   A   G
Sbjct: 5   HVFVCVQDRPPGHPQGSCAQRGSR--EVFQAFMEKIQTDPQLFMTTVITPTGCMNASMMG 62

Query: 243 NLIVYSPDSEGKIMGHWYGYVTPDDVPAILDQHIAKGEIIERL 285
            ++V  PD      G WYG V P+DV  I+++H+  GE +ERL
Sbjct: 63  PVVVVYPD------GVWYGQVKPEDVDEIVEKHLKGGEPVERL 99


>pdb|1F37|A Chain A, Structure Of A Thioredoxin-Like [2fe-2s] Ferredoxin From
           Aquifex Aeolicus
 pdb|1F37|B Chain B, Structure Of A Thioredoxin-Like [2fe-2s] Ferredoxin From
           Aquifex Aeolicus
 pdb|1M2A|A Chain A, Crystal Structure At 1.5 Angstroms Resolution Of The Wild
           Type Thioredoxin-Like [2fe-2s] Ferredoxin From Aquifex
           Aeolicus
 pdb|1M2A|B Chain B, Crystal Structure At 1.5 Angstroms Resolution Of The Wild
           Type Thioredoxin-Like [2fe-2s] Ferredoxin From Aquifex
           Aeolicus
          Length = 110

 Score = 39.7 bits (91), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 33/104 (31%), Positives = 46/104 (44%), Gaps = 15/104 (14%)

Query: 189 SYVFVCSH----GSRDKRCGVCGPALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYA--- 241
            +VFVC      G     C   G    E F A ++      Q+F+       G   A   
Sbjct: 4   KHVFVCVQDRPPGHPQGSCAQRGSR--EVFQAFMEKIQTDPQLFMTTVITPTGCMNACMM 61

Query: 242 GNLIVYSPDSEGKIMGHWYGYVTPDDVPAILDQHIAKGEIIERL 285
           G ++V  PD      G WYG V P+DV  I+++H+  GE +ERL
Sbjct: 62  GPVVVVYPD------GVWYGQVKPEDVDEIVEKHLKGGEPVERL 99


>pdb|2R6H|A Chain A, Crystal Structure Of The Domain Comprising The Nad Binding
           And The Fad Binding Regions Of The Nadh:ubiquinone
           Oxidoreductase, Na Translocating, F Subunit From
           Porphyromonas Gingivalis
 pdb|2R6H|B Chain B, Crystal Structure Of The Domain Comprising The Nad Binding
           And The Fad Binding Regions Of The Nadh:ubiquinone
           Oxidoreductase, Na Translocating, F Subunit From
           Porphyromonas Gingivalis
 pdb|2R6H|C Chain C, Crystal Structure Of The Domain Comprising The Nad Binding
           And The Fad Binding Regions Of The Nadh:ubiquinone
           Oxidoreductase, Na Translocating, F Subunit From
           Porphyromonas Gingivalis
 pdb|2R6H|D Chain D, Crystal Structure Of The Domain Comprising The Nad Binding
           And The Fad Binding Regions Of The Nadh:ubiquinone
           Oxidoreductase, Na Translocating, F Subunit From
           Porphyromonas Gingivalis
          Length = 290

 Score = 28.1 bits (61), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 12/40 (30%), Positives = 21/40 (52%)

Query: 178 WASGVQEGLTGSYVFVCSHGSRDKRCGVCGPALIEKFNAE 217
           W +G++ G++ SY+F    G +    G  G   I+  +AE
Sbjct: 119 WKAGIKPGISSSYIFSLKPGDKVXXSGPYGDFHIQDTDAE 158


  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    0.142    0.453 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,064,846
Number of Sequences: 62578
Number of extensions: 361954
Number of successful extensions: 654
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 648
Number of HSP's gapped (non-prelim): 10
length of query: 303
length of database: 14,973,337
effective HSP length: 98
effective length of query: 205
effective length of database: 8,840,693
effective search space: 1812342065
effective search space used: 1812342065
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: 51 (24.3 bits)