RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6242
         (541 letters)



>gnl|CDD|201954 pfam01753, zf-MYND, MYND finger. 
          Length = 39

 Score = 48.6 bits (116), Expect = 6e-08
 Identities = 19/39 (48%), Positives = 22/39 (56%), Gaps = 2/39 (5%)

Query: 15 CAVC--RETALHKCSACKEVAYCGKQHQKEHWKLHKPKC 51
          CAVC      L +CS CK V YC K+ QK  W  HK +C
Sbjct: 1  CAVCGKEALKLLRCSRCKSVYYCSKECQKADWPYHKKEC 39


>gnl|CDD|235636 PRK05886, yajC, preprotein translocase subunit YajC; Validated.
          Length = 109

 Score = 29.8 bits (67), Expect = 1.2
 Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 7/31 (22%)

Query: 66 RYLQATLDLH----PGDRIARESPL---IVG 89
          + +QAT+DLH    PGDR+   S L   IVG
Sbjct: 27 KAMQATIDLHESLQPGDRVHTTSGLQATIVG 57


>gnl|CDD|216337 pfam01159, Ribosomal_L6e, Ribosomal protein L6e. 
          Length = 108

 Score = 28.7 bits (65), Expect = 2.5
 Identities = 9/22 (40%), Positives = 12/22 (54%)

Query: 58  IKSSPLLGRYLQATLDLHPGDR 79
           IK  P L +YL++   L  GD 
Sbjct: 81  IKKHPDLKQYLKSRFSLRKGDY 102


>gnl|CDD|171539 PRK12492, PRK12492, long-chain-fatty-acid--CoA ligase;
          Provisional.
          Length = 562

 Score = 30.2 bits (68), Expect = 3.4
 Identities = 12/19 (63%), Positives = 13/19 (68%)

Query: 67 YLQATLDLHPGDRIARESP 85
          YLQ   DL PGDRIA + P
Sbjct: 65 YLQQHTDLVPGDRIAVQMP 83


>gnl|CDD|232847 TIGR00155, pqiA_fam, integral membrane protein, PqiA family.  This
           family consists of uncharacterized predicted integral
           membrane proteins found, so far, only in the
           Proteobacteria. Of two members in E. coli, one is
           induced by paraquat and is designated PqiA,
           paraquat-inducible protein A [Unknown function,
           General].
          Length = 403

 Score = 29.8 bits (67), Expect = 4.1
 Identities = 15/45 (33%), Positives = 17/45 (37%), Gaps = 5/45 (11%)

Query: 78  DRIARESPLIVGPKLALAEPICLGCHKPLNPNLADNARCPRCFWP 122
           D    E P +  P   L    C  CH  + P  A    CPRC  P
Sbjct: 200 DDFYPEMPELRQP---LKLRSCSACHTTILP--AQEPVCPRCSTP 239



 Score = 28.6 bits (64), Expect = 7.9
 Identities = 10/25 (40%), Positives = 11/25 (44%), Gaps = 2/25 (8%)

Query: 455 ICLGCHKPLNPNLADNARCPRCFWP 479
            C  CH  + P  A    CPRC  P
Sbjct: 217 SCSACHTTILP--AQEPVCPRCSTP 239


>gnl|CDD|168170 PRK05677, PRK05677, long-chain-fatty-acid--CoA ligase; Validated.
          Length = 562

 Score = 29.7 bits (67), Expect = 4.3
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 67 YLQATLDLHPGDRIARESP 85
          +LQ   DL PGDRIA + P
Sbjct: 65 WLQQHTDLKPGDRIAVQLP 83


>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
          Length = 1337

 Score = 29.7 bits (67), Expect = 4.9
 Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 3/42 (7%)

Query: 446 PNLKATDEPI--CLGCHKPLNPNLADNARCPRCFWPA-CSAR 484
           P+     EP+  C  C   + P+ +    CPRC        R
Sbjct: 683 PDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPYQR 724


>gnl|CDD|236547 PRK09521, PRK09521, exosome complex RNA-binding protein Csl4;
           Provisional.
          Length = 189

 Score = 28.4 bits (64), Expect = 6.2
 Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 3/43 (6%)

Query: 80  IARESPL---IVGPKLALAEPICLGCHKPLNPNLADNARCPRC 119
           I+   PL     G  L +   +C  C  PL     +  +CP C
Sbjct: 130 ISYTDPLQLSTKGKDLGVIYAMCSRCRTPLVKKGENELKCPNC 172


  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
   0.321    0.135    0.441 

Gapped
Lambda     K      H
   0.267   0.0677    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,231,253
Number of extensions: 2408063
Number of successful extensions: 2121
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2121
Number of HSP's successfully gapped: 27
Length of query: 541
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 439
Effective length of database: 6,413,494
Effective search space: 2815523866
Effective search space used: 2815523866
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 (21.9 bits)
S2: 61 (27.4 bits)