RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy34
         (190 letters)



>gnl|CDD|203409 pfam06205, GT36_AF, Glycosyltransferase 36 associated family. 
          Length = 90

 Score = 27.5 bits (62), Expect = 1.6
 Identities = 10/31 (32%), Positives = 14/31 (45%)

Query: 144 ARNPPDQELMQATSTRGAVAGMSSYTSDEEE 174
           ARN  + E     +  G     +SYT+D  E
Sbjct: 1   ARNEYNPEFAHRVAFAGVSEPATSYTTDRAE 31


>gnl|CDD|179626 PRK03660, PRK03660, anti-sigma F factor; Provisional.
          Length = 146

 Score = 27.6 bits (62), Expect = 2.5
 Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 13/69 (18%)

Query: 113 SIVYATDKKHTKVEFPEARIYEETLNIILY-EARNPPDQEL-MQATSTRGAVAGMSSYTS 170
           +I++  +     V + E  I EE L I +  E +   D E  MQ             YT+
Sbjct: 51  AIIHGYENNPDGVVYIEVEIEEEELEITVRDEGKGIEDIEEAMQPL-----------YTT 99

Query: 171 DEEEERSGL 179
             E ERSG+
Sbjct: 100 KPELERSGM 108


>gnl|CDD|235056 PRK02627, PRK02627, acetylornithine aminotransferase; Provisional.
          Length = 396

 Score = 27.0 bits (61), Expect = 7.3
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 23  PLITSLKEEQLLLNATAKPVVKLL 46
            ++    E+ LL+N T   V++LL
Sbjct: 348 EIVKKALEKGLLINVTGDNVLRLL 371


>gnl|CDD|197388 cd10153, RcnR-FrmR-like_DUF156, Transcriptional regulators RcnR and
           FrmR, and related domains; this domain family was
           previously known as part of DUF156.  This domain family
           includes various transcriptional regulators that respond
           to different stressors. It includes Escherichia coli
           RncR (formally known as YohL, nickel and
           cobalt-sensitive), and E. coli FrmR (formally known as
           YaiN, formaldehyde sensitive). Escherichia coli RncR
           represses expression of the gene encoding the nickel and
           cobalt-efflux protein RcnA; RcnA may act through
           modulating NikR, to repress the NIkABCDE nickel
           transporter. In vitro, purified RncR binds to the rncA
           promoter DNA fragment in the absence of Ni2+ or Co2+,
           and the affinity of RncR for this promoter is reduced in
           the presence of excess nickel.  Escherichia coli FrmR
           regulates the formaldehyde degradation frmRAB operon.
           This family belongs to a larger superfamily that
           includes CsoRs (copper-sensitive operon repressors).
           CsoRs form homotetramers (dimer of dimers). In
           Mycobacterium tuberculosis CsoR, within each dimer, two
           Cys residues on opposite subunits, along with a His
           residue, bind the Cu(I) ion (forming a triagonal S2N
           coordination complex, C-H-C). These residues are
           conserved in the majority of members of this
           superfamily. In this family, however, not all these
           residues are conserved; in E.coli RcnR and FrmR there is
           a His or a Thr instead of the second Cys (C-H-H or
           C-H-T) respectively. For E. coli FrmR, an N-terminal His
           residue, not conserved in all members of this family, is
           also involved in metal binding (H-C-H-H). A conserved
           Tyr and a Glu residue that facilitate allosteric
           regulation of DNA binding for CsoRs are poorly conserved
           in this family.
          Length = 88

 Score = 25.2 bits (56), Expect = 9.5
 Identities = 9/23 (39%), Positives = 11/23 (47%)

Query: 143 EARNPPDQELMQATSTRGAVAGM 165
           EA       L Q  + RGAV G+
Sbjct: 28  EAEADCAAVLQQIAAVRGAVNGL 50


  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    0.132    0.374 

Gapped
Lambda     K      H
   0.267   0.0626    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,388,258
Number of extensions: 857367
Number of successful extensions: 634
Number of sequences better than 10.0: 1
Number of HSP's gapped: 634
Number of HSP's successfully gapped: 14
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
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 (25.6 bits)