RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy13330
         (289 letters)



>gnl|CDD|130645 TIGR01583, formate-DH-gamm, formate dehydrogenase, gamma subunit.
           This model represents the gamma chain of the gamma
           proteobacteria (and Aquifex aolicus) formate
           dehydrogenase. This subunit is integral to the
           cytoplasmic membrane, consisting of 4 transmembrane
           helices, and receives electrons from the beta subunit.
           The entire E. coli formate dehydrogenase N
           (nitrate-inducible form) has been crystallized. The
           gamma subunit contains two cytochromes, heme b(P) and
           heme b(C) near the periplasmic and cytoplasmic sides of
           the membrane respectively. The electron acceptor quinone
           binds at the cytoplasmic heme histidine ligand.
           NiFe-hydrogenase and thiosulfate reductase contain
           homologous gamma subunits, and these can be found
           scoring in the noise of this model [Energy metabolism,
           Anaerobic, Energy metabolism, Electron transport].
          Length = 204

 Score = 30.5 bits (69), Expect = 0.73
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 6/49 (12%)

Query: 162 KNDNQWRYNL--FLAKNPVPVRCPIAGKFNFTQRGDALFETRILGGVTL 208
           K D +W   +  +L+K   PV  P AGK+N  Q+  + +   +LGG  +
Sbjct: 78  KYDIRWMMKVGGYLSKIKRPV--PSAGKYNAGQK--SWYWILVLGGFLM 122


>gnl|CDD|224630 COG1716, COG1716, FOG: FHA domain [Signal transduction mechanisms].
          Length = 191

 Score = 28.0 bits (62), Expect = 5.1
 Identities = 6/25 (24%), Positives = 10/25 (40%)

Query: 127 VCFDFVPRHHNVIRYRKGIAVIKDN 151
           +  D V R H  +R       ++D 
Sbjct: 103 LDDDVVSRRHAELRREGNEVFLEDL 127


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.324    0.140    0.445 

Gapped
Lambda     K      H
   0.267   0.0508    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,897,343
Number of extensions: 1406458
Number of successful extensions: 1284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1284
Number of HSP's successfully gapped: 6
Length of query: 289
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 193
Effective length of database: 6,679,618
Effective search space: 1289166274
Effective search space used: 1289166274
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 58 (26.6 bits)