RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11108
         (106 letters)



>gnl|CDD|237089 PRK12398, PRK12398, pyruvoyl-dependent arginine decarboxylase;
           Provisional.
          Length = 162

 Score = 31.6 bits (72), Expect = 0.036
 Identities = 10/43 (23%), Positives = 23/43 (53%), Gaps = 6/43 (13%)

Query: 61  ALPDDIMKHAYIAQHQGRFQTAENYQLQADR------RTWKSK 97
           A+P+D   + Y++++ G  +T E+    A++       TW ++
Sbjct: 89  AIPEDQSLNGYLSEYHGYGETEEDAGKYAEKLAREMLSTWTNE 131


>gnl|CDD|219534 pfam07720, TPR_3, Tetratricopeptide repeat.  This Pfam entry
          includes tetratricopeptide-like repeats found in the
          LcrH/SycD-like chaperones.
          Length = 34

 Score = 25.9 bits (58), Expect = 0.79
 Identities = 4/23 (17%), Positives = 11/23 (47%)

Query: 63 PDDIMKHAYIAQHQGRFQTAENY 85
           + +   A +   +G++Q A + 
Sbjct: 1  LEYLYSLAAVFYLKGKYQEARHL 23


>gnl|CDD|233929 TIGR02563, cas_Csy4, CRISPR-associated protein Cas6/Csy4, subtype
           I-F/YPEST.  CRISPR (Clustered Regularly Interspaced
           Short Palindromic Repeats) is a widespread family of
           prokaryotic direct repeats with spacers of unique
           sequence between consecutive repeats. This protein
           family, typified by YPO2462 of Yersinia pestis, is a
           CRISPR-associated (Cas) family strictly associated with
           the Ypest subtype of CRISPR/Cas locus. This family is
           designated Csy4, for CRISPR/Cas Subtype Ypest protein 4
           [Mobile and extrachromosomal element functions, Other].
          Length = 185

 Score = 27.4 bits (61), Expect = 1.1
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 4/66 (6%)

Query: 31  SQKKERFYHVEQALVNCQDYAGLQLIKSLRALPDDIMKHAYIAQHQGRFQTAENYQLQAD 90
           + +     H  + L    DYA    I  +  +P D +K   + + Q    +A   + + +
Sbjct: 60  TAEDLDKLHSRRWLSGLSDYA---SISEISTVPADCVKRRTVRRKQ-TKSSAARLRRRLE 115

Query: 91  RRTWKS 96
           RR   +
Sbjct: 116 RRQGIN 121


>gnl|CDD|205996 pfam13825, Paramyxo_PNT, Paramyxovirus structural protein V/P
          N-terminus.  This family consists of several
          Paramyxoviridae structural protein P and V sequences.
          From a structural point of view, P is the
          best-characterized protein of the replicative complex.
          P is organised into two moieties that are functionally
          and structurally distinct: a C-terminal moiety (PCT)
          and an N-terminal moiety (PNT). PCT is the most
          conserved in sequence and contains all regions required
          for virus transcription, whereas PNT, which is poorly
          conserved, provides several additional functions
          required for replication. P protein plays a crucial
          role in the enzyme by positioning L onto the N/RNA
          template through an interaction with the C-terminal
          domain of N. Without P, L is not functional. The N, P,
          and L proteins of SeV and measles and mumps viruses are
          functionally equivalent. However, sequence identity
          between proteins from these viruses is limited, and the
          viruses have been placed in different genera
          (Respirovirus, Morbilivirus, and Rubulavirus,
          respectively). SeV P protein (568 aa) is a modular
          protein with distinct functional domains. The
          N-terminal part of P (PNT) is a chaperone for N and
          prevents it from binding to non-viral RNA in the
          infected cell.
          Length = 309

 Score = 26.3 bits (58), Expect = 3.0
 Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 9/32 (28%)

Query: 35 ERFYHVEQALVNCQDYAGLQLIKSLRALPDDI 66
          E+ YHV +         GL+ IK+LRA P D 
Sbjct: 1  EQAYHVNK---------GLECIKALRANPPDS 23


>gnl|CDD|185231 PRK15331, PRK15331, chaperone protein SicA; Provisional.
          Length = 165

 Score = 26.2 bits (57), Expect = 3.2
 Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 4/34 (11%)

Query: 56 IKSLRALPDDIMK----HAYIAQHQGRFQTAENY 85
          +K +  +P D+M     HAY   +QGR   AE +
Sbjct: 26 LKDVHGIPQDMMDGLYAHAYEFYNQGRLDEAETF 59


>gnl|CDD|217864 pfam04053, Coatomer_WDAD, Coatomer WD associated region.  This
           region is composed of WD40 repeats.
          Length = 429

 Score = 26.4 bits (59), Expect = 3.4
 Identities = 10/40 (25%), Positives = 19/40 (47%)

Query: 40  VEQALVNCQDYAGLQLIKSLRALPDDIMKHAYIAQHQGRF 79
            E+A    +D+  L L+       + + K A IA+ +G +
Sbjct: 352 AEEAYQKAKDFDKLLLLYLSTGNKEKLKKLAKIAEERGDY 391


>gnl|CDD|133383 cd01108, HTH_CueR, Helix-Turn-Helix DNA binding domain of
          CueR-like transcription regulators.  Helix-turn-helix
          (HTH) transcription regulators CueR and ActP, copper
          efflux regulators. In Bacillus subtilis, copper induced
          CueR regulates the copZA operon, preventing copper
          toxicity. In Rhizobium leguminosarum, ActP controls
          copper homeostasis; it detects cytoplasmic copper
          stress and activates transcription in response to
          increasing copper concentrations. These proteins are
          comprised of two distinct domains that harbor the
          regulatory (effector-binding) site and the active
          (DNA-binding) site. Their conserved N-terminal domains
          contain winged HTH motifs that mediate DNA binding,
          while the C-terminal domains have two conserved
          cysteines that define a monovalent copper ion binding
          site. These proteins share the N-terminal DNA binding
          domain with other transcription regulators of the MerR
          superfamily that promote transcription by reconfiguring
          the spacer between the -35 and -10 promoter elements.
          Length = 127

 Score = 25.6 bits (57), Expect = 4.0
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 22 GQASFLSGVSQKKERFYH 39
          G+A+ L+G+S K  R+Y 
Sbjct: 4  GEAAKLTGLSAKMIRYYE 21


>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
          Length = 502

 Score = 25.3 bits (56), Expect = 7.0
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 6   AVIASRHSFVLCPYVA-GQ-ASFLSGVSQKKERF 37
           A+I  + S V+C YVA GQ AS ++ V +     
Sbjct: 182 AIINQKDSDVICVYVAIGQKASAVARVIETLREH 215


>gnl|CDD|183516 PRK12416, PRK12416, protoporphyrinogen oxidase; Provisional.
          Length = 463

 Score = 25.2 bits (55), Expect = 9.5
 Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 1/33 (3%)

Query: 65  DIMKHAYIAQHQGRFQTAENYQLQADRRTWKSK 97
           DI+     A   G F   EN  L  D  TW S+
Sbjct: 310 DILDEQLPADGTG-FIVTENSDLHCDACTWTSR 341


  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
   0.322    0.131    0.404 

Gapped
Lambda     K      H
   0.267   0.0631    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,303,639
Number of extensions: 425932
Number of successful extensions: 342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 342
Number of HSP's successfully gapped: 16
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.4 bits)