RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16442
         (116 letters)



>gnl|CDD|219280 pfam07052, Hep_59, Hepatocellular carcinoma-associated antigen 59. 
           This family represents a conserved region approximately
           100 residues long within mammalian hepatocellular
           carcinoma-associated antigen 59 and similar proteins.
           Family members are found in a variety of eukaryotes,
           mainly as hypothetical proteins.
          Length = 102

 Score =  102 bits (256), Expect = 8e-30
 Identities = 48/90 (53%), Positives = 62/90 (68%), Gaps = 4/90 (4%)

Query: 1   MKYIEEQLSKRKKGEETKEGGQGEEGGVNYCSPEEAALQAVPDHLRQSSTHQSEEMLSNQ 60
           MKYIEE+L+KRK G+      +  +   N     E  L A+P+HL+     ++EEMLSNQ
Sbjct: 17  MKYIEEELAKRK-GQAADADAEDSDKAANNLKRAEDELYALPEHLK---VKKNEEMLSNQ 72

Query: 61  MLSGIPEVDLGIEAKIRNIEATEEAKLKLL 90
           ML GIPEVDLGIEAK++NIE TE+AK +LL
Sbjct: 73  MLGGIPEVDLGIEAKLKNIERTEKAKRRLL 102


>gnl|CDD|176105 cd08413, PBP2_CysB_like, The C-terminal substrate domain of
          LysR-type transcriptional regulators CysB-like contains
          type 2 periplasmic binding fold.  CysB is a
          transcriptional activator of genes involved in sulfate
          and thiosulfate transport, sulfate reduction, and
          cysteine synthesis. In Escherichia coli, the regulation
          of transcription in response to sulfur source is
          attributed to two transcriptional regulators, CysB and
          Cbl. CysB, in association with Cbl, downregulates the
          expression of ssuEADCB operon which is required for the
          utilization of sulfur from aliphatic sulfonates, in the
          presence of cysteine. Also, Cbl and CysB together
          directly function as transcriptional activators of
          tauABCD genes, which are required for utilization of
          taurine as sulfur source for growth. Like many other
          members of the LTTR family, CysB is composed of two
          functional domains joined by a linker helix involved in
          oligomerization: an N-terminal HTH (helix-turn-helix)
          domain, which is responsible for the DNA-binding
          specificity, and a C-terminal substrate-binding domain,
          which is structurally homologous to the type 2
          periplasmic binding proteins. As also observed in the
          periplasmic binding proteins, the C-terminal domain of
          the bacterial transcriptional repressor undergoes a
          conformational change upon substrate binding which in
          turn changes the DNA binding affinity of the repressor.
           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.  Besides transport
          proteins, the PBP2 superfamily includes the
          substrate-binding domains from ionotropic glutamate
          receptors, LysR-like transcriptional regulators, and
          unorthodox sensor proteins involved in signal
          transduction.
          Length = 198

 Score = 28.0 bits (63), Expect = 0.93
 Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 14/40 (35%)

Query: 44 HLRQSSTHQSEEMLSNQMLSGIPEVDLGIEAKIRNIEATE 83
           L Q +  Q  EM+         E D+ I        ATE
Sbjct: 32 SLHQGTPSQIAEMVLKG------EADIAI--------ATE 57


>gnl|CDD|223654 COG0581, PstA, ABC-type phosphate transport system, permease
           component [Inorganic ion transport and metabolism].
          Length = 292

 Score = 27.2 bits (61), Expect = 1.9
 Identities = 9/15 (60%), Positives = 13/15 (86%)

Query: 35  EAALQAVPDHLRQSS 49
           E AL+AVPD LR+++
Sbjct: 164 EEALRAVPDSLREAA 178


>gnl|CDD|225600 COG3058, FdhE, Uncharacterized protein involved in formate
           dehydrogenase formation [Posttranslational modification,
           protein turnover, chaperones].
          Length = 308

 Score = 26.7 bits (59), Expect = 3.0
 Identities = 10/38 (26%), Positives = 15/38 (39%)

Query: 33  PEEAALQAVPDHLRQSSTHQSEEMLSNQMLSGIPEVDL 70
              AA  A  + L ++S  + E M S  + S    V  
Sbjct: 116 EANAAALAAIEQLEKASEQELESMASALLASDFSLVSS 153


>gnl|CDD|183573 PRK12524, PRK12524, RNA polymerase sigma factor; Provisional.
          Length = 196

 Score = 26.4 bits (58), Expect = 3.0
 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 35  EAALQAVPDHLRQSSTHQSEEMLSNQMLSGIPEVDLGIEA 74
           +AAL A+P+  RQ+   +  E LSN  ++ + E+  G+EA
Sbjct: 131 DAALAALPERQRQAVVLRHIEGLSNPEIAEVMEI--GVEA 168


>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
          Length = 381

 Score = 25.8 bits (57), Expect = 6.3
 Identities = 9/24 (37%), Positives = 15/24 (62%)

Query: 62  LSGIPEVDLGIEAKIRNIEATEEA 85
           +S +PEV L +   + + E T+EA
Sbjct: 143 ISNVPEVPLVVSDSVESYEKTKEA 166


>gnl|CDD|223479 COG0402, SsnA, Cytosine deaminase and related metal-dependent
           hydrolases [Nucleotide transport and metabolism /
           General function prediction only].
          Length = 421

 Score = 25.9 bits (57), Expect = 6.7
 Identities = 13/57 (22%), Positives = 20/57 (35%)

Query: 34  EEAALQAVPDHLRQSSTHQSEEMLSNQMLSGIPEVDLGIEAKIRNIEATEEAKLKLL 90
              A     + L   +     EML N   +    VD+  E+     EA  E  L+ +
Sbjct: 90  PREARLLTEEDLYARALLALLEMLRNGTTTARTHVDVVAESADAAFEAALEVGLRAV 146


>gnl|CDD|217481 pfam03303, WTF, WTF protein.  This is a family of hypothetical
          Schizosaccharomyces pombe proteins. Their function is
          unknown.
          Length = 240

 Score = 25.6 bits (56), Expect = 7.2
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 4  IEEQLSKRKKGEETKEGGQGEEGGVNYCSPEEAALQAVPDHLRQSSTHQSE 54
          ++E    +   E   E G   E    Y S EE  L    D  + S+T  +E
Sbjct: 12 LDELDELKTDHEIDLEKGPLPE----YNSEEEGTLPPYSDIAKLSNTGPTE 58


>gnl|CDD|150575 pfam09919, DUF2149, Uncharacterized conserved protein (DUF2149). 
          This domain, found in various hypothetical prokaryotic
          proteins, has no known function.
          Length = 91

 Score = 24.5 bits (54), Expect = 7.7
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 2/32 (6%)

Query: 1  MKYIEEQLSKRKKGEETKE--GGQGEEGGVNY 30
          M+ IE++  + K+ +ET +  GG+GE  G  Y
Sbjct: 48 MEIIEKKGKEIKRYKETGQDGGGEGERLGTAY 79


  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
   0.308    0.127    0.353 

Gapped
Lambda     K      H
   0.267   0.0752    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,742,636
Number of extensions: 483303
Number of successful extensions: 300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 297
Number of HSP's successfully gapped: 14
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 53 (24.1 bits)