RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16987
         (110 letters)



>gnl|CDD|172503 PRK14002, PRK14002, potassium-transporting ATPase subunit C;
          Provisional.
          Length = 186

 Score = 31.6 bits (72), Expect = 0.047
 Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 9/56 (16%)

Query: 5  GVYSSVVLIAVGVYFNSLGGDLVHDDIVALARNQDVLGGTSVGQMFTND--FWGTP 58
            Y   +     +  N   G+ +         N  V+G  ++GQ FT D  FWG P
Sbjct: 20 VFYILALWGFAQLAPNKGNGETI-------TLNGKVVGYANIGQSFTQDIYFWGRP 68


>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
           Validated.
          Length = 882

 Score = 29.4 bits (67), Expect = 0.33
 Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 3/28 (10%)

Query: 50  FTNDFWGTPLSDPASHKSYRPLTTLTFR 77
           F N+  G P   PA H+S RPL TL  R
Sbjct: 279 FDNEIPGIP---PARHRSGRPLKTLAQR 303


>gnl|CDD|147008 pfam04639, Baculo_E56, Baculoviral E56 protein, specific to ODV
           envelope.  This family represents the E56 protein, which
           is localises to the occlusion derived virus (ODV)
           envelope, but not to the budded virus (BV) envelope.
          Length = 308

 Score = 28.4 bits (64), Expect = 0.64
 Identities = 13/27 (48%), Positives = 15/27 (55%)

Query: 10  VVLIAVGVYFNSLGGDLVHDDIVALAR 36
           V L+ VGVY      DLV D + AL R
Sbjct: 119 VTLLGVGVYLVFNAADLVQDIVDALNR 145


>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
           This family consists of the archaeal A' subunit of the
           DNA-directed RNA polymerase. The example from
           Methanocaldococcus jannaschii contains an intein.
          Length = 867

 Score = 27.8 bits (62), Expect = 1.2
 Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 3/32 (9%)

Query: 46  VGQMFTNDFWGTPLSDPASHKSYRPLTTLTFR 77
           V   F N+  G P   PA H+S RPL TL  R
Sbjct: 271 VATYFDNELPGIP---PARHRSGRPLKTLAQR 299


>gnl|CDD|176888 cd08879, RHO_alpha_C_AntDO-like, C-terminal catalytic domain of the
           oxygenase alpha subunit of Pseudomonas resinovorans
           strain CA10 anthranilate 1,2-dioxygenase and related
           aromatic ring hydroxylating dioxygenases.  C-terminal
           catalytic domain of the oxygenase alpha subunit of
           anthranilate 1,2-dioxygenase (AntDO) and related
           Rieske-type non-heme iron aromatic ring-hydroxylating
           oxygenases (RHOs, also known as aromatic ring
           hydroxylating dioxygenases). RHOs utilize non-heme
           Fe(II) to catalyze the addition of hydroxyl groups to
           the aromatic ring, an initial step in the oxidative
           degradation of aromatic compounds. RHOs are composed of
           either two or three protein components, and are
           comprised of an electron transport chain (ETC) and an
           oxygenase. The ETC transfers reducing equivalents from
           the electron donor to the oxygenase component, which in
           turn transfers electrons to the oxygen molecules. The
           oxygenase components are oligomers, either (alpha)n or
           (alpha)n(beta)n.  The alpha subunits are the catalytic
           components and have an N-terminal domain, which binds a
           Rieske-like 2Fe-2S cluster, and the C-terminal catalytic
           domain which binds the non-heme Fe(II). The Fe(II) is
           co-ordinated by conserved His and Asp residues.
           Oxygenases belonging to this subgroup include the alpha
           subunits of AntDO, aniline dioxygenase, Acinetobacter
           calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate
           1,2-dioxygenase from Pseudomonas cepacia 2CBS,
           2,4,5-trichlorophenoxyacetic acid oxygenase from
           Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic
           acid oxygenase from Bradyrhizobium sp. strain HW13,
           p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase
           form Pseudomonas cepacia 2CBS, and Pseudomonas putida
           IacC, which may be involved in the catabolism of the
           plant hormone indole 3-acetic acid. This subfamily
           belongs to the SRPBCC
           (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
           superfamily of proteins that bind hydrophobic ligands.
           SRPBCC domains have a deep hydrophobic ligand-binding
           pocket.
          Length = 237

 Score = 26.2 bits (58), Expect = 4.3
 Identities = 7/21 (33%), Positives = 8/21 (38%)

Query: 18  YFNSLGGDLVHDDIVALARNQ 38
            F    G    DD+ A  R Q
Sbjct: 167 DFFGPSGFATPDDLEAFERCQ 187


>gnl|CDD|217044 pfam02451, Nodulin, Nodulin.  Nodulin is a plant protein of unknown
           function. It is induced during nodulation in legume
           roots after rhizobium infection.
          Length = 177

 Score = 25.4 bits (55), Expect = 6.9
 Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 6/44 (13%)

Query: 52  NDFWGTPLSDPASHKSYRPLT------TLTFRTVLGISSCVSSR 89
              +   +S        +P        T+ FRTVL   S VS+R
Sbjct: 95  KSPFEPSISRVIPWPPIQPRDQGLLIETVQFRTVLKTCSHVSAR 138


  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
   0.322    0.136    0.413 

Gapped
Lambda     K      H
   0.267   0.0902    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,539,416
Number of extensions: 459792
Number of successful extensions: 348
Number of sequences better than 10.0: 1
Number of HSP's gapped: 348
Number of HSP's successfully gapped: 16
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (23.9 bits)