RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4880
         (137 letters)



>gnl|CDD|197836 smart00704, ZnF_CDGSH, CDGSH-type zinc finger. Function unknown. 
          Length = 38

 Score = 38.5 bits (90), Expect = 3e-05
 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)

Query: 63 KIVDYFDKPNLTDFTAFCRCWRSRDFPYCNGFH 95
          K  D  +        A CRC RS++FPYC+G H
Sbjct: 1  KRPDEVEVEKRKK-YALCRCGRSKNFPYCDGSH 32


>gnl|CDD|220203 pfam09360, zf-CDGSH, Iron-binding zinc finger CDGSH type.  The
          CDGSH-type zinc finger domain binds iron rather than
          zinc as a redox-active pH-labile 2Fe-2S cluster. The
          conserved sequence
          C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining
          feature of this family. The domain is oriented towards
          the cytoplasm and is tethered to the mitochondrial
          membrane by a more N-terminal domain found in higher
          vertebrates, MitoNEET_N, pfam10660. The domain forms a
          uniquely folded homo-dimer and spans the outer
          mitochondrial membrane, orienting the iron-binding
          residues towards the cytoplasm.
          Length = 34

 Score = 36.0 bits (84), Expect = 3e-04
 Identities = 10/18 (55%), Positives = 14/18 (77%)

Query: 78 AFCRCWRSRDFPYCNGFH 95
          A CRC RS++ P+C+G H
Sbjct: 16 ALCRCGRSKNQPFCDGSH 33


>gnl|CDD|192389 pfam09808, SNAPc_SNAP43, Small nuclear RNA activating complex
          (SNAPc), subunit SNAP43.  Members of this family are
          part of the SNAPc complex required for the
          transcription of both RNA polymerase II and III
          small-nuclear RNA genes. They bind to the proximal
          sequence element (PSE), a non-TATA-box basal promoter
          element common to these 2 types of genes. Furthermore,
          they also recruit TBP and BRF2 to the U6 snRNA TATA
          box.
          Length = 194

 Score = 29.2 bits (66), Expect = 0.56
 Identities = 6/29 (20%), Positives = 13/29 (44%)

Query: 62 DKIVDYFDKPNLTDFTAFCRCWRSRDFPY 90
          D+++  F + +   F  F   W+   F +
Sbjct: 7  DELLGRFQEADSVRFEDFKEVWKEMGFSH 35


>gnl|CDD|225018 COG2107, COG2107, Predicted periplasmic solute-binding protein
           [General function prediction only].
          Length = 272

 Score = 28.4 bits (64), Expect = 1.1
 Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 3/26 (11%)

Query: 102 LGDNVGPILIRRSK---LKPFTLATP 124
           LG   GPI++ +S+   LK   +A P
Sbjct: 76  LGIGYGPIVVAKSEVKDLKGKRVAVP 101


>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
          Length = 292

 Score = 28.2 bits (64), Expect = 1.4
 Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 2/28 (7%)

Query: 48  VLVHVNPDIHKNHADKIVDYFDKPNLTD 75
           VL     +I   + D+I ++F  P +TD
Sbjct: 215 VLEERGFEIE--NYDEIREFFLNPPVTD 240


>gnl|CDD|225904 COG3369, COG3369, Zinc finger domain containing protein
          (CDGSH-type) [Function unknown].
          Length = 78

 Score = 26.7 bits (59), Expect = 1.5
 Identities = 9/19 (47%), Positives = 12/19 (63%)

Query: 77 TAFCRCWRSRDFPYCNGFH 95
           A CRC  S + P+C+G H
Sbjct: 31 AALCRCGHSENKPFCDGTH 49


>gnl|CDD|218863 pfam06030, DUF916, Bacterial protein of unknown function
          (DUF916).  This family consists of several hypothetical
          bacterial proteins of unknown function.
          Length = 121

 Score = 27.2 bits (61), Expect = 1.7
 Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 3/26 (11%)

Query: 52 VNPDIHKNHADKIVDYFD---KPNLT 74
          V P + +N  DK   YFD   KP  T
Sbjct: 3  VTPVLPENQVDKNASYFDLKVKPGQT 28


>gnl|CDD|223538 COG0462, PrsA, Phosphoribosylpyrophosphate synthetase [Nucleotide
           transport and metabolism / Amino acid transport and
           metabolism].
          Length = 314

 Score = 27.6 bits (62), Expect = 2.3
 Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 6/33 (18%)

Query: 39  FMTMAGPTHVLVHVNPDIHKNHADKIVDYFDKP 71
            +  AG   VL  V+      HA +I  +FD P
Sbjct: 116 LLETAGADRVLT-VDL-----HAPQIQGFFDIP 142


>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
           Endonuclease that cleaves the 5'-overhanging flap
           structure that is generated by displacement synthesis
           when DNA polymerase encounters the 5'-end of a
           downstream Okazaki fragment. Has 5'-endo-/exonuclease
           and 5'-pseudo-Y-endonuclease activities. Cleaves the
           junction between single and double-stranded regions of
           flap DNA.
          Length = 338

 Score = 26.4 bits (59), Expect = 5.1
 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 2/28 (7%)

Query: 48  VLVHVNPDIHKNHADKIVDYFDKPNLTD 75
           VL     DI   + D+I ++F  P +TD
Sbjct: 262 VLKARGEDI--ENYDEIREFFLNPPVTD 287


>gnl|CDD|132656 TIGR03617, F420_MSMEG_2256, probable F420-dependent oxidoreductase,
           MSMEG_2256 family.  Coenzyme F420 has a limited
           phylogenetic distribution, including methanogenic
           archaea, Mycobacterium tuberculosis and related species,
           Colwellia psychrerythraea 34H, Rhodopseudomonas
           palustris HaA2, and others. Partial phylogenetic
           profiling identifies protein subfamilies, within the
           larger family called luciferase-like monooxygenanases
           (pfam00296), that appear only in F420-positive genomes
           and are likely to be F420-dependent. This model
           describes one such subfamily, exemplified by MSMEG_2256
           from Mycobacterium smegmatis [Unknown function, Enzymes
           of unknown specificity].
          Length = 318

 Score = 26.2 bits (58), Expect = 5.6
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 1   MREDRSFLICLWTALVGGAYGEFRGDPNYHTETPSPPFF 39
           MRE    L  +W A   G   +FRG+  ++T T   PFF
Sbjct: 94  MREYILALRAIWDAWQDGTRLDFRGE--FYTHTLMTPFF 130


>gnl|CDD|215073 PLN00142, PLN00142, sucrose synthase.
          Length = 815

 Score = 26.5 bits (59), Expect = 6.5
 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 7/41 (17%)

Query: 37  PFFMTM-AGPTHVLV------HVNPDIHKNHADKIVDYFDK 70
           P F T   GP  ++V      H++P      A+KI D+F+K
Sbjct: 692 PTFATCQGGPAEIIVDGVSGFHIDPYHGDEAANKIADFFEK 732


  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
   0.326    0.143    0.487 

Gapped
Lambda     K      H
   0.267   0.0713    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,247,765
Number of extensions: 629723
Number of successful extensions: 630
Number of sequences better than 10.0: 1
Number of HSP's gapped: 630
Number of HSP's successfully gapped: 15
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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 (21.6 bits)
S2: 54 (24.6 bits)