RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12195
         (254 letters)



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

 Score = 32.2 bits (73), Expect = 0.10
 Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 113 LFHNKATLYKHLYLEHKATSLSIQ---CNMCSLVLDSKESLVTHISQT-HTLMFTCRRCP 168
           L +N   L +  YL    TS ++    C +C +   S  SL  HI  T H+    C  C 
Sbjct: 49  LIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCG 106

Query: 169 STFLNSATLSKHVKMEHN 186
             F N+ +   HV  +HN
Sbjct: 107 KEFRNTDSTLDHVCKKHN 124



 Score = 27.5 bits (61), Expect = 3.4
 Identities = 10/24 (41%), Positives = 13/24 (54%)

Query: 216 SVHQIQCPYCITDFSEDKNLIQHI 239
           +V    CP C+  FS   +L QHI
Sbjct: 70  AVSPYVCPLCLMPFSSSVSLKQHI 93


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

 Score = 27.4 bits (61), Expect = 0.76
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 177 LSKHVKMEHNSKSYQCNECPESFER 201
           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 = 1.4
 Identities = 28/110 (25%), Positives = 43/110 (39%), Gaps = 19/110 (17%)

Query: 129 KATSLSIQCNMCSLVLDSKESLVTHISQTHTLMFTCRRCPSTFLNSATLSKHVKMEHNSK 188
           K  SL I C +CSL L     L TH+++++  ++  +     F+     +       N K
Sbjct: 317 KVCSLPISCPICSLQL----ILSTHLARSYHHLYPLK----PFVEKPEGT-------NPK 361

Query: 189 SYQCNECPESFERLNKLKRHKFQAHNDSVHQIQCPYCITDFSEDKNLIQH 238
           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 = 29.8 bits (68), Expect = 1.5
 Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 2/23 (8%)

Query: 227 TDFSEDKNLIQHIVSVHLGKEGT 249
           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 = 3.1
 Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 5/33 (15%)

Query: 218 HQIQCPYCITDFSED-----KNLIQHIVSVHLG 245
           H +QCPYCI  +++       N  Q + +VH+ 
Sbjct: 53  HAVQCPYCIDAYTQTSLEKGANKEQMMEAVHVA 85


>gnl|CDD|217357 pfam03079, ARD, ARD/ARD' family.  The two acireductone
          dioxygenase enzymes (ARD and ARD', previously known as
          E-2 and E-2') from Klebsiella pneumoniae share the same
          amino acid sequence, but bind different metal ions: ARD
          binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be
          experimentally interconverted by removal of the bound
          metal ion and reconstitution with the appropriate metal
          ion. The two enzymes share the same substrate,
          1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield
          different products. ARD' yields the alpha-keto
          precursor of methionine (and formate), thus forming
          part of the ubiquitous methionine salvage pathway that
          converts 5'-methylthioadenosine (MTA) to methionine.
          This pathway is responsible for the tight control of
          the concentration of MTA, which is a powerful inhibitor
          of polyamine biosynthesis and transmethylation
          reactions. ARD yields methylthiopropanoate, carbon
          monoxide and formate, and thus prevents the conversion
          of MTA to methionine. The role of the ARD catalyzed
          reaction is unclear: methylthiopropanoate is cytotoxic,
          and carbon monoxide can activate guanylyl cyclase,
          leading to increased intracellular cGMP levels. This
          family also contains other members, whose functions are
          not well characterized.
          Length = 157

 Score = 27.7 bits (62), Expect = 3.7
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 8  LEEHKVVIIRCETCTRNYESLESLTTHLSFKHSNQFLMKCTNCNVLVPR-DEIL 60
           E  K+ ++  +    + E+ E L     +KH +   +  T C    P  DE L
Sbjct: 28 DELAKLGVLYWKLDADDEETAEELLRIRKYKHYDDVDIDVTVCPETTPNFDEKL 81


>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3.  The
          reovirus inner capsid protein lambda-1 displays
          nucleoside triphosphate phosphohydrolase (NTPase),
          RNA-5'-triphosphatase (RTPase), and RNA helicase
          activity and may play a role in the transcription of
          the virus genome, the unwinding or reannealing of
          double-stranded RNA during RNA synthesis. The RTPase
          activity constitutes the first step in the capping of
          RNA, resulting in a 5'-diphosphorylated RNA
          plus-strand. lambda1 is an Orthoreovirus core protein,
          VP3 is the homologous core protein in Aquareoviruses.
          Length = 1166

 Score = 27.4 bits (61), Expect = 9.1
 Identities = 7/24 (29%), Positives = 10/24 (41%)

Query: 17 RCETCTRNYESLESLTTHLSFKHS 40
           C  C   + S++ L  H    HS
Sbjct: 75 VCNVCMAEFSSMDQLAEHQRTTHS 98


  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    0.130    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: 11,361,462
Number of extensions: 945913
Number of successful extensions: 855
Number of sequences better than 10.0: 1
Number of HSP's gapped: 851
Number of HSP's successfully gapped: 36
Length of query: 254
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 159
Effective length of database: 6,723,972
Effective search space: 1069111548
Effective search space used: 1069111548
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: 58 (26.3 bits)