RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15859
         (175 letters)



>gnl|CDD|204498 pfam10484, MRP-S23, Mitochondrial ribosomal protein S23.  MRP-S23
          is one of the proteins that makes up the 55S ribosome
          in eukaryotes from nematodes to humans. It does not
          appear to carry any common motifs, either RNA binding
          or ribosomal protein motifs. All of the mammalian MRPs
          are encoded in nuclear genes that are evolving more
          rapidly than those encoding cytoplasmic ribosomal
          proteins. The MRPs are imported into mitochondria where
          they assemble coordinately with mitochondrially
          transcribed rRNAs into ribosomes that are responsible
          for translating the 13 mRNAs for essential proteins of
          the oxidative phosphorylation system. MRP-S23 is
          significantly up-regulated in uterine cancer cells.
          Length = 74

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 13/14 (92%), Positives = 13/14 (92%)

Query: 2  ASSRLEKIGTIFTR 15
          A SRLEKIGTIFTR
Sbjct: 1  AGSRLEKIGTIFTR 14



 Score = 27.0 bits (60), Expect = 2.0
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 70  KLHKALGKKMPGYNLLEKNRPTVSQKIILQTLQHQKEDPSLSEDEALAKAIETYNSE 126
           K HK  G+     NL + N  + SQ+ + Q     K   +L E+E   +  +    E
Sbjct: 15  KFHKY-GRGQETINLFDMNNRSQSQQFV-QKYDELKSQGALDEEELFEETAKALLEE 69


>gnl|CDD|222356 pfam13741, MRP-S25, Mitochondrial ribosomal protein S25.  This is
          the family of fungal 37S mitochondrial ribosomal S25
          proteins.
          Length = 229

 Score = 29.3 bits (66), Expect = 0.96
 Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 12 IFTRVTGLLRAGAMNVNEKPIWYDVYRAFPPKVEPLYSRPI 52
          +  R +  L+AG +   +KP WYDV    PP        P 
Sbjct: 10 VLQRTSAYLKAGLLK--KKPAWYDVVADIPPTTLLTRKPPP 48


>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
          Length = 869

 Score = 28.4 bits (64), Expect = 2.6
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 5/78 (6%)

Query: 42  PKVEPLYSRPIADVPIKEIIYPEDSIRAKLHKALGKKMPGY-----NLLEKNRPTVSQKI 96
           P++E ++ +          I  E+ I  K  KA G ++  Y     N LE       ++ 
Sbjct: 780 PRIEIVFGKGDGKERPNLEIDLEEFIAVKGIKAKGNRLTTYKVKTINELEPLPYEEPEEE 839

Query: 97  ILQTLQHQKEDPSLSEDE 114
             +  +    +   SED+
Sbjct: 840 TAEEPEEVDPEDVKSEDD 857


>gnl|CDD|200393 TIGR04142, PCisTranLspir, putative peptidyl-prolyl cis-trans
           isomerase, LIC12922 family.  Members of this protein
           family have a known crystal structure (3NRK) showing
           similarity to the peptidyl-prolyl cis-trans isomerase
           SurA. Members are found in Leptospira species next to an
           uncharacterized radical SAM enzyme and a
           cytidylyltransferase family protein.
          Length = 315

 Score = 27.4 bits (60), Expect = 3.9
 Identities = 13/99 (13%), Positives = 34/99 (34%), Gaps = 4/99 (4%)

Query: 62  YPEDSIRAKLHKA----LGKKMPGYNLLEKNRPTVSQKIILQTLQHQKEDPSLSEDEALA 117
              +  R          L  +     + E+    V+++ +   ++ + E   ++  +   
Sbjct: 34  LKHEDYRKSFRTRIIDFLIDRAIVDVVAEEESIQVNEQRVDSEIEKRMEVMGITNRKQFE 93

Query: 118 KAIETYNSEIRQVKADDIPEDFNKPKFGYYKTKPSLANE 156
           K +ET +    ++   ++P    K +    K      NE
Sbjct: 94  KTMETSSGMPFELWVTELPYQIKKGQLLQLKIAVPPPNE 132


>gnl|CDD|184003 PRK13364, PRK13364, protocatechuate 4,5-dioxygenase subunit beta;
          Provisional.
          Length = 278

 Score = 27.4 bits (61), Expect = 4.6
 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 6/56 (10%)

Query: 9  IGTIFT-RVTGLLRAGAMNVNEKPIWYDVYRAFPPKVEPLY-SRPIADVPIKEIIY 62
          IG I T  V  +  A A  + + P W   +  FPP  E L   +P  DV +  + Y
Sbjct: 5  IGGITTSHVPAIGGAIAKGLQQDPYWKPFFDGFPPVREWLEKVKP--DVAV--VFY 56


>gnl|CDD|241263 cd01229, PH_Ect2, Epithelial cell transforming 2 (Ect2) pleckstrin
           homology (PH) domain.  Ect2, a mammalian ortholog of
           Drosophila pebble, plays a role in neuronal
           differentiation and brain development. Pebble and Ect2
           have been identified as Rho-family guanine nucleotide
           exchange factors (GEF) that mediate activation of Rho
           during cytokinesis, but are proposed to play slightly
           different roles. PH domains have diverse functions, but
           in general are involved in targeting proteins to the
           appropriate cellular location or in the interaction with
           a binding partner. They share little sequence
           conservation, but all have a common fold, which is
           electrostatically polarized. Less than 10% of PH domains
           bind phosphoinositide phosphates (PIPs) with high
           affinity and specificity. PH domains are distinguished
           from other PIP-binding domains by their specific
           high-affinity binding to PIPs with two vicinal phosphate
           groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
           which results in targeting some PH domain proteins to
           the plasma membrane. A few display strong specificity in
           lipid binding. Any specificity is usually determined by
           loop regions or insertions in the N-terminus of the
           domain, which are not conserved across all PH domains.
           PH domains are found in cellular signaling proteins such
           as serine/threonine kinase, tyrosine kinases, regulators
           of G-proteins, endocytotic GTPases, adaptors, as well as
           cytoskeletal associated molecules and in lipid
           associated enzymes.
          Length = 180

 Score = 26.9 bits (60), Expect = 4.9
 Identities = 8/16 (50%), Positives = 9/16 (56%)

Query: 154 ANEFKRAVETKVDMFD 169
            NE KR  E +  MFD
Sbjct: 8   INEDKRKTEGQAQMFD 23


>gnl|CDD|226930 COG4564, COG4564, Signal transduction histidine kinase [Signal
           transduction mechanisms].
          Length = 459

 Score = 27.1 bits (60), Expect = 6.2
 Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 12/89 (13%)

Query: 47  LYSRPIADVPIKE----IIYPEDSIRAKLHKALGKKMPGYNLLEKNRPTVSQKIILQTLQ 102
           L    +AD  +KE    ++  ++  RA+L + L   +        ++  VS K  L+   
Sbjct: 226 LREHRLADKKLKELAQRVVDTQEDERARLARELHDGI--------SQNLVSVKCALELAA 277

Query: 103 HQKEDPSLSEDEALAKAIETYNSEIRQVK 131
            Q   P      A+ KA +  N  I++V+
Sbjct: 278 RQLNPPKGGAHPAIEKAADALNGAIKEVR 306


>gnl|CDD|225619 COG3077, RelB, DNA-damage-inducible protein J [DNA replication,
           recombination, and repair].
          Length = 88

 Score = 25.8 bits (57), Expect = 6.6
 Identities = 6/33 (18%), Positives = 13/33 (39%)

Query: 107 DPSLSEDEALAKAIETYNSEIRQVKADDIPEDF 139
           D  L  +    +AI+  +   + V+     +D 
Sbjct: 50  DLRLPSNAETLQAIKELDKAGKGVEVSKTVDDL 82


>gnl|CDD|163495 TIGR03783, Bac_Flav_CT_G, Bacteroides conjugation system ATPase,
           TraG family.  Members of this family include the
           predicted ATPase, TraG, encoded by transfer region genes
           of conjugative transposons of Bacteroides, such as
           CTnDOT, found on the main chromosome. Members also
           include TraG homologs borne on plasmids in Bacteroides.
           The protein family is related to the conjugative
           transfer system ATPase VirB4 [Cellular processes, DNA
           transformation].
          Length = 829

 Score = 27.1 bits (60), Expect = 6.8
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 12/74 (16%)

Query: 93  SQKIILQTL-QHQKEDPSLSEDEALAKAIETYNSEIRQVKADD-IPEDFNKPKFGYYKTK 150
           S K ++ TL + + E P+ SE+ AL+ A+  Y   IR +  D  I   FN     +Y+  
Sbjct: 524 SIKTLILTLWKREDEPPTRSEEVALSNAVSAY---IRLISEDRGIAPSFN----TFYEY- 575

Query: 151 PSLANEFKRAVETK 164
             + ++++  +E K
Sbjct: 576 --VKDDYRAELEEK 587


>gnl|CDD|177643 PHA03415, PHA03415, putative internal virion protein; Provisional.
          Length = 1019

 Score = 26.9 bits (59), Expect = 7.0
 Identities = 28/95 (29%), Positives = 38/95 (40%), Gaps = 9/95 (9%)

Query: 59  EIIYPEDSIRAKLHKALGKKMPGYNLLEKNRPT------VSQKIILQTLQHQKEDPSLSE 112
           +I  P D  +A L+ A    + G N L             +Q +    L+  K D  LS 
Sbjct: 8   KIQLPADEFQAALNAAAASGLSGDNSLVDGGLAGAAAEDKAQALAAAPLEEAKADAKLST 67

Query: 113 -DEALAKAIETYNSEIRQVKADDIPEDFNK--PKF 144
            D+  A A ET  + I +   DD  E FN   P F
Sbjct: 68  TDKVQAAAQETETAYILEAMDDDRDEMFNDFDPNF 102


>gnl|CDD|182695 PRK10747, PRK10747, putative protoheme IX biogenesis protein;
           Provisional.
          Length = 398

 Score = 26.6 bits (59), Expect = 7.9
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 11/58 (18%)

Query: 84  LLEKNRPTVSQKIILQTLQHQKED------PSL--SEDEALAKAIETYNSEIRQVKAD 133
           L+E +    +Q+IIL  L+ Q ++      P L  +  E L K +     +I+Q    
Sbjct: 273 LIECDDHDTAQQIILDGLKRQYDERLVLLIPRLKTNNPEQLEKVL---RQQIKQHGDT 327


>gnl|CDD|187867 cd09736, Csy2_I-F, CRISPR/Cas system-associated RAMP superfamily
           protein Csy2.  CRISPR (Clustered Regularly Interspaced
           Short Palindromic Repeats) and associated Cas proteins
           comprise a system for heritable host defense by
           prokaryotic cells against phage and other foreign DNA;
           RAMP superfamily protein; predicted Cas5 ortholog.
          Length = 289

 Score = 26.1 bits (58), Expect = 9.4
 Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 7/98 (7%)

Query: 47  LYSRPIADVPIKEIIYPE-DSIRAKLHKALGKKMPGYNLLEKNRPTVSQKIILQTLQHQK 105
           L    +A   I  I   E  S   +L K L + +PG+ LL++    +++   LQ LQ   
Sbjct: 124 LQQMRLAGGSIIPIGPVEIKSDEKELRKLLRRLLPGFALLDR-SDLLAE--ALQRLQTTN 180

Query: 106 EDPSLSEDEALAKAIETYNSEIRQVKADDIPEDFNKPK 143
            + +L  D  L  A   +     + + + I   +++ K
Sbjct: 181 PEATLL-DAWLDFAALNHQPL--RDEEEAIESAYSRKK 215


  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
   0.316    0.134    0.387 

Gapped
Lambda     K      H
   0.267   0.0748    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,059,169
Number of extensions: 848918
Number of successful extensions: 800
Number of sequences better than 10.0: 1
Number of HSP's gapped: 799
Number of HSP's successfully gapped: 38
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.3 bits)