RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12196
         (150 letters)



>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
          Length = 128

 Score = 32.2 bits (73), Expect = 0.038
 Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 9   LFHNKATLYKHLYLEHKATSLSIQ---CNMCSLVLDSKESLVTHISQT-HTLMFTCRRCP 64
           L +N   L +  YL    TS ++    C +C +   S  SL  HI  T H+    C  C 
Sbjct: 49  LIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCG 106

Query: 65  STFLNSATLSKHVKMEHN 82
             F N+ +   HV  +HN
Sbjct: 107 KEFRNTDSTLDHVCKKHN 124



 Score = 27.9 bits (62), Expect = 1.4
 Identities = 10/24 (41%), Positives = 13/24 (54%)

Query: 112 SVHQIQCPYCITDFSEDKNLIQHI 135
           +V    CP C+  FS   +L QHI
Sbjct: 70  AVSPYVCPLCLMPFSSSVSLKQHI 93



 Score = 25.6 bits (56), Expect = 8.6
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 2/53 (3%)

Query: 58  FTCRRCPSTFLNSATLSKHVKMEHNSKSYQCNECPESFERLNKLKRHKFQAHN 110
           + C  C   F +S +L +H++   +SK   C  C + F   +    H  + HN
Sbjct: 74  YVCPLCLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEFRNTDSTLDHVCKKHN 124


>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain. 
          Length = 26

 Score = 27.4 bits (61), Expect = 0.40
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 73 LSKHVKMEHNSKSYQCNECPESFER 97
          L +H++     K Y+C  C +SF  
Sbjct: 2  LRRHMRTHTGEKPYKCPVCGKSFSS 26


>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
           initiation/nucleotide excision repair factor TFIIH,
           subunit SSL1 [Transcription / DNA replication,
           recombination, and repair].
          Length = 421

 Score = 30.0 bits (67), Expect = 0.53
 Identities = 28/110 (25%), Positives = 43/110 (39%), Gaps = 19/110 (17%)

Query: 25  KATSLSIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKMEHNSK 84
           K  SL I C +CSL L     L TH+++++  ++  +     F+     +       N K
Sbjct: 317 KVCSLPISCPICSLQL----ILSTHLARSYHHLYPLK----PFVEKPEGT-------NPK 361

Query: 85  SYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQH 134
           S  C  C   F    K     F     S  + QC  C + F  D ++  H
Sbjct: 362 STHCFVCQGPFP---KPPVSPFDESTSSG-RYQCELCKSTFCSDCDVFIH 407


>gnl|CDD|212673 cd10231, YegD_like, Escherichia coli YegD, a putative chaperone
           protein, and related proteins.  This bacterial subfamily
           includes the uncharacterized Escherichia coli YegD. It
           belongs to the heat shock protein 70 (HSP70) family of
           chaperones that assist in protein folding and assembly
           and can direct incompetent "client" proteins towards
           degradation. Typically, HSP70s have a nucleotide-binding
           domain (NBD) and a substrate-binding domain (SBD). The
           nucleotide sits in a deep cleft formed between the two
           lobes of the NBD. The two subdomains of each lobe change
           conformation between ATP-bound, ADP-bound, and
           nucleotide-free states. ATP binding opens up the
           substrate-binding site; substrate-binding increases the
           rate of ATP hydrolysis. YegD lacks the SBD. HSP70
           chaperone activity is regulated by various
           co-chaperones: J-domain proteins and nucleotide exchange
           factors (NEFs). Some family members are not chaperones
           but instead, function as NEFs for their Hsp70 partners,
           other family members function as both chaperones and
           NEFs.
          Length = 415

 Score = 29.0 bits (66), Expect = 0.87
 Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 2/23 (8%)

Query: 123 TDFSEDKNLIQHIVSVHLGKEGT 145
           TDF  D+ L  H V   LGK  T
Sbjct: 219 TDF--DRRLSLHAVMPLLGKGST 239


>gnl|CDD|200420 TIGR04169, perox_w_seleSAM,
           alkylhydroperoxidase/carboxymuconolactone decarboxylase
           family protein.  Members of this family are usually
           annotated as putative carboxymuconolactone
           decarboxylases, are related also to alkylhydroperoxidase
           AhpD, and contain a peroxidase-like Cys-X-X-Cys putative
           redox-active disulfide. All members occur in genomes
           with a radical SAM protein of family TIGR04167, which
           occasionally are selenoproteins.
          Length = 109

 Score = 27.5 bits (61), Expect = 1.5
 Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 5/33 (15%)

Query: 114 HQIQCPYCITDFSED-----KNLIQHIVSVHLG 141
           H +QCPYCI  +++       N  Q + +VH+ 
Sbjct: 53  HAVQCPYCIDAYTQTSLEKGANKEQMMEAVHVA 85


>gnl|CDD|182445 PRK10420, PRK10420, L-lactate permease; Provisional.
          Length = 551

 Score = 28.3 bits (63), Expect = 1.6
 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)

Query: 28  SLSIQCNMCSLVLDSKESLVTHISQTHTLMFTC 60
           S++I C    LV   KES +   +  H+L+FTC
Sbjct: 503 SIAIACAAVGLV--GKESDLFRFTVKHSLIFTC 533


  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    0.130    0.405 

Gapped
Lambda     K      H
   0.267   0.0655    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,524,746
Number of extensions: 501258
Number of successful extensions: 462
Number of sequences better than 10.0: 1
Number of HSP's gapped: 460
Number of HSP's successfully gapped: 45
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
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: 54 (24.7 bits)