RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10100
         (65 letters)



>gnl|CDD|213903 TIGR04290, meth_Rta_06860, methyltransferase, Rta_06860 family.
           Members of this family are methyltransferases that mark
           a widely distributed large conserved gene neighborhood
           of unknown function. It appears most common in soil and
           rhizosphere bacteria.
          Length = 226

 Score = 28.5 bits (64), Expect = 0.16
 Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 2/36 (5%)

Query: 26  MGVFYHIRSVALIEDLPGEETHFASIDDFYQTVERG 61
           MGV YH+R   L  DL  E  H A     +QT+ RG
Sbjct: 122 MGVLYHLRHPLLALDLLRE--HVAGDLLLFQTLTRG 155


>gnl|CDD|219818 pfam08393, DHC_N2, Dynein heavy chain, N-terminal region 2.
           Dyneins are described as motor proteins of eukaryotic
           cells, as they can convert energy derived from the
           hydrolysis of ATP to force and movement along
           cytoskeletal polymers, such as microtubules. This region
           is found C-terminal to the dynein heavy chain N-terminal
           region 1 (pfam08385) in many members of this family. No
           functions seem to have been attributed specifically to
           this region.
          Length = 408

 Score = 25.6 bits (57), Expect = 1.9
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 10/57 (17%)

Query: 7   KLSLCGVIISAWGIVQ---LALMGVFYH--IRSVALIEDLPGEETHFASIDDFYQTV 58
           KL+L   ++  W  VQ   + L  +F    I+       LP E   F+++D  ++ +
Sbjct: 212 KLNLIQEVLELWLKVQRKWVYLEPIFSSSDIKK-----QLPEESKRFSNVDKEWKKL 263


>gnl|CDD|235504 PRK05562, PRK05562, precorrin-2 dehydrogenase; Provisional.
          Length = 223

 Score = 25.0 bits (55), Expect = 2.6
 Identities = 11/33 (33%), Positives = 15/33 (45%)

Query: 30  YHIRSVALIEDLPGEETHFASIDDFYQTVERGY 62
             IR+ A   +L  E   F   DDFY   ++G 
Sbjct: 171 TKIRNKAKKNELKDEIIEFICSDDFYFFYKKGK 203


>gnl|CDD|222428 pfam13872, AAA_34, P-loop containing NTP hydrolase pore-1. 
          Length = 303

 Score = 24.8 bits (55), Expect = 3.6
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 43  GEETHFASIDDFYQTVERG 61
           G  T FA+ +DF   +E+G
Sbjct: 237 GPGTPFATREDFVSAMEKG 255


>gnl|CDD|176161 cd08472, PBP2_CrgA_like_3, The C-terminal substrate binding domain
           of an uncharacterized LysR-type transcriptional
           regulator CrgA-like, contains the type 2 periplasmic
           binding fold.  This CD represents the substrate binding
           domain of an uncharacterized LysR-type transcriptional
           regulator (LTTR) CrgA-like 3. The LTTRs are acting as
           both auto-repressors and activators of target promoters,
           controlling operons involved in a wide variety of
           cellular processes such as amino acid biosynthesis, CO2
           fixation, antibiotic resistance, degradation of aromatic
           compounds, nodule formation of nitrogen-fixing bacteria,
           and synthesis of virulence factors, to name a few. In
           contrast to the tetrameric form of other LTTRs, CrgA
           from Neisseria meningitides assembles into an octameric
           ring, which can bind up to four 63-bp DNA
           oligonucleotides. Phylogenetic cluster analysis showed
           that the CrgA-like regulators form a subclass of the
           LTTRs that function as octamers. The CrgA is an
           auto-repressor of its own gene and activates the
           expression of the mdaB gene which coding for an
           NADPH-quinone reductase and that its action is increased
           by MBL (alpha-methylene-gamma-butyrolactone), an inducer
           of NADPH-quinone oxidoreductase.  The structural
           topology of this substrate-binding domain is most
           similar to that of the type 2 periplasmic binding
           proteins (PBP2), which are responsible for the uptake of
           a variety of substrates such as phosphate, sulfate,
           polysaccharides, lysine/arginine/ornithine, and
           histidine. The PBP2 bind their ligand in the cleft
           between these domains in a manner resembling a Venus
           flytrap. After binding their specific ligand with high
           affinity, they can interact with a cognate membrane
           transport complex comprised of two integral membrane
           domains and two cytoplasmically located ATPase domains.
           This interaction triggers the ligand translocation
           across the cytoplasmic membrane energized by ATP
           hydrolysis.
          Length = 202

 Score = 24.4 bits (54), Expect = 3.8
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 19  GIVQLALMGVFYHIRSVALIEDLPG 43
           GI+Q+    V  H+ S  L+E LP 
Sbjct: 146 GIIQVPRFMVRPHLASGRLVEVLPD 170


>gnl|CDD|173945 cd08186, Fe-ADH8, Iron-containing alcohol dehydrogenase.  Type III
           Iron-containing alcohol dehydrogenases (ADH). Alcohol
           dehydrogenase catalyzes the reduction of acetaldehyde to
           alcohol with NADP as cofactor. The ADH of
           hyperthermophilic archaeon Thermococcus hydrothermalis
           oxidizes a series of primary aliphatic and aromatic
           alcohols preferentially from C2 to C8 but is also active
           towards methanol and glycerol and stereospecific for
           monoterpenes. It was suggested that the type III ADHs in
           microorganisms are involved in acetaldehyde detoxication
           rather than in alcohol turnover.
          Length = 383

 Score = 24.3 bits (53), Expect = 4.8
 Identities = 12/30 (40%), Positives = 15/30 (50%)

Query: 30  YHIRSVALIEDLPGEETHFASIDDFYQTVE 59
           Y I   AL   LP ++T + SID     VE
Sbjct: 169 YSIDDPALTTTLPPDQTIYTSIDALNHVVE 198


>gnl|CDD|234497 TIGR04199, exosort_xrtJ, exosortase J.  Exosortase J occurs as a
          three-member paralogous family in Acidobacterium sp.
          MP5ACTX8. It contains an N-terminal
          exosortase/archaeosortase domain and a novel C-terminal
          domain comprising about half of total protein length.
          The presumptive target, found as an adjacent gene for
          two of the three paralogs, consists of a possible
          lipoprotein signal peptide followed almost immediately
          by a C-terminal region with some PEP-CTERM-like
          characteristics.
          Length = 522

 Score = 24.1 bits (52), Expect = 7.2
 Identities = 10/24 (41%), Positives = 14/24 (58%)

Query: 16 SAWGIVQLALMGVFYHIRSVALIE 39
          S WGI  LAL  +  H+R V+ + 
Sbjct: 57 SWWGIALLALSILLAHLRDVSNLV 80


>gnl|CDD|235660 PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
          Length = 472

 Score = 23.7 bits (52), Expect = 7.6
 Identities = 10/17 (58%), Positives = 10/17 (58%)

Query: 45  ETHFASIDDFYQTVERG 61
           E  F  IDDF QT ER 
Sbjct: 296 EGGFIQIDDFCQTKERH 312


  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
   0.328    0.144    0.449 

Gapped
Lambda     K      H
   0.267   0.0789    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,354,697
Number of extensions: 247847
Number of successful extensions: 339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 339
Number of HSP's successfully gapped: 11
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)