RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4851
         (62 letters)



>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
          Length = 706

 Score = 36.2 bits (84), Expect = 2e-04
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 15  RYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVL 54
           R P G  V  LG +GD   + E +L +H +P  +F + VL
Sbjct: 192 RPPFGEVVEVLGDLGDPGADIEAILRDHGIPS-EFPEKVL 230


>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R.  This family consists of an
           exoribonuclease, ribonuclease R, also called VacB. It is
           one of the eight exoribonucleases reported in E. coli
           and is broadly distributed throughout the bacteria. In
           E. coli, double mutants of this protein and
           polynucleotide phosphorylase are not viable. Scoring
           between trusted and noise cutoffs to the model are
           shorter, divergent forms from the Chlamydiae, and
           divergent forms from the Campylobacterales (including
           Helicobacter pylori) and Leptospira interrogans
           [Transcription, Degradation of RNA].
          Length = 709

 Score = 27.2 bits (61), Expect = 0.37
 Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 17  PQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSY 56
             G  V  LG   D   +  +++ +H +P+  F + VL  
Sbjct: 192 AIGKVVEILGHADDPGIDILIIIRKHGIPYE-FPEEVLDE 230


>gnl|CDD|183048 PRK11239, PRK11239, hypothetical protein; Provisional.
          Length = 215

 Score = 25.5 bits (56), Expect = 1.8
 Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 5/36 (13%)

Query: 20 HFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLS 55
          H++R +   G     N V   E    +S+F DL LS
Sbjct: 66 HYLRTVSGFG-----NRVTKYEQRFCNSEFGDLKLS 96


>gnl|CDD|221694 pfam12658, Ten1, Telomere capping.  Stn1 and Ten1 are DNA-binding
          proteins with specificity for telomeric DNA substrates
          and both protect chromosome termini from unregulated
          resection and regulate telomere length. Stn1 complexes
          with Ten1 and Cdc13 to function as a telomere-specific
          replication protein A (RPA)-like complex. These three
          interacting proteins associate with the telomeric
          overhang in budding yeast, whereas a single protein
          known as Pot1 (protection of telomeres-1) performs this
          function in fission yeast, and a two-subunit complex
          consisting of POT1 and TPP1 associates with telomeric
          ssDNA in humans. S.pombe has Stn1- and Ten1-like
          proteins that are essential for chromosome end
          protection. Stn1 orthologues exist in all species that
          have Pot1, whereas Ten1-like proteins can be found in
          all fungi. Fission yeast Stn1 and Ten1 localise at
          telomeres in a manner that correlates with the length
          of the ssDNA overhang, suggesting that they
          specifically associate with the telomeric ssDNA. Two
          separate protein complexes are required for chromosome
          end protection in fission yeast. Protection of
          telomeres by multiple proteins with OB-fold domains is
          conserved in eukaryotic evolution.
          Length = 116

 Score = 25.0 bits (55), Expect = 1.9
 Identities = 14/36 (38%), Positives = 18/36 (50%)

Query: 17 PQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDL 52
            G  VR LG + D D    VL LEH+ P +  +D 
Sbjct: 22 SNGDKVRFLGCVSDYDPTTGVLTLEHNYPSTSSADE 57


>gnl|CDD|184713 PRK14502, PRK14502, bifunctional mannosyl-3-phosphoglycerate
           synthase/mannosyl-3 phosphoglycerate phosphatase;
           Provisional.
          Length = 694

 Score = 24.1 bits (52), Expect = 5.2
 Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 7/36 (19%)

Query: 1   MIFALIKPLII-------HHMRYPQGHFVRALGPIG 29
           M+  +  P+++       H MR     +V+ +GP G
Sbjct: 646 MLETVDSPILVQRPGNKWHKMRLRNPSYVKGVGPEG 681


  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    0.146    0.473 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,293,610
Number of extensions: 238007
Number of successful extensions: 219
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 5
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
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: 53 (24.2 bits)