RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17187
         (123 letters)



>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain.  Cyclins regulate
           cyclin dependent kinases (CDKs). Human cyclin-O is a
           Uracil-DNA glycosylase that is related to other cyclins.
           Cyclins contain two domains of similar all-alpha fold,
           of which this family corresponds with the N-terminal
           domain.
          Length = 127

 Score = 77.2 bits (191), Expect = 1e-19
 Identities = 28/83 (33%), Positives = 44/83 (53%)

Query: 14  LYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHAL 73
           L   L+++ EE     +    AV+ +DRFL   P+ +++LQL    CLLIA+K  E +  
Sbjct: 34  LIDWLVEVHEEFKLLPETLYLAVNYLDRFLSKQPVPRTKLQLVGVTCLLIAAKYEEIYPP 93

Query: 74  CVEDLVYYSDYTFSPHTLKTTEK 96
            VED VY +D  ++   +   E 
Sbjct: 94  SVEDFVYITDNAYTKEEILRMEL 116


>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold. Protein binding domain
          functioning in cell-cycle and transcription control.
          Present in cyclins, TFIIB and Retinoblastoma (RB).The
          cyclins consist of 8 classes of cell cycle regulators
          that regulate cyclin dependent kinases (CDKs). TFIIB is
          a transcription factor that binds the TATA box.
          Cyclins, TFIIB and RB contain 2 copies of the domain.
          Length = 88

 Score = 51.9 bits (125), Expect = 5e-10
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 13 FLYSSLLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHA 72
               L ++ +      +    AV+++DRFL    +      L A+A L +A+K+ E   
Sbjct: 4  TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPP 63

Query: 73 LCVEDLVYYSDYTFSPHTLKTTEK 96
            ++DLV+ + Y  +   +   EK
Sbjct: 64 W-LKDLVHVTGY-ATEEEILRMEK 85


>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and
          Retinoblastoma.  A helical domain present in cyclins
          and TFIIB (twice) and Retinoblastoma (once). A protein
          recognition domain functioning in cell-cycle and
          transcription control.
          Length = 83

 Score = 47.6 bits (114), Expect = 2e-08
 Identities = 20/68 (29%), Positives = 33/68 (48%)

Query: 18 LLQLCEERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTASACLLIASKIRECHALCVED 77
          L ++C+  + + +    AV+++DRFL      K    L A+A L +ASK  E      E 
Sbjct: 3  LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKEL 62

Query: 78 LVYYSDYT 85
          + Y   +T
Sbjct: 63 VHYTGYFT 70


>gnl|CDD|227357 COG5024, COG5024, Cyclin [Cell division and chromosome
           partitioning].
          Length = 440

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 32  FPYAVSIMDRFLCY--CPMEKSQLQLTASACLLIASKIRECHALCVEDLVYYSDYTFSPH 89
              A++I+DRFL      +EK QL     + L IASK  E +   ++DLVY +D  F+  
Sbjct: 234 LFLAINIIDRFLSSRVVSLEKYQLV--GISALFIASKYEEVNCPSIKDLVYATDGAFTRD 291

Query: 90  TLKTTEK 96
            +   E+
Sbjct: 292 DIIRAER 298


>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
           ribosomal structure and biogenesis].
          Length = 239

 Score = 27.2 bits (61), Expect = 2.1
 Identities = 7/22 (31%), Positives = 11/22 (50%)

Query: 46  CPMEKSQLQLTASACLLIASKI 67
           C  E+SQ    A A  ++  K+
Sbjct: 147 CQNERSQHLNKALARKMLKGKL 168


>gnl|CDD|143490 cd06815, PLPDE_III_AR_like_1, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzyme Alanine Racemase-like 1.  This
           subfamily is composed of uncharacterized bacterial
           proteins with similarity to bacterial alanine racemases
           (AR), which are fold type III PLP-dependent enzymes
           containing an N-terminal PLP-binding TIM-barrel domain
           and a C-terminal beta-sandwich domain. AR exists as
           homodimers with active sites that lie at the interface
           between the TIM barrel domain of one subunit and the
           beta-sandwich domain of the other subunit. It catalyzes
           the interconversion between L- and D-alanine, which is
           an essential component of the peptidoglycan layer of
           bacterial cell walls. Members of this subfamily may act
           as PLP-dependent enzymes.
          Length = 353

 Score = 26.7 bits (60), Expect = 3.3
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 4/44 (9%)

Query: 75  VEDLVYYSDYTF--SPHTLKTTEKPAVYLNNTH--VIMKKVKDL 114
           VED+V Y+D +      T+K   + A      H  ++M  + DL
Sbjct: 85  VEDVVKYADISLNSELETIKALSEEAKKQGKIHKIILMVDLGDL 128


>gnl|CDD|189028 cd09858, PIN_MKT1, PIN domain of Mkt1: A global regulator of mRNAs
           encoding mitochondrial proteins and eukaryotic homologs.
            The Mkt1 gene product interacts with the
           Poly(A)-binding protein associated factor, Pbp1, and is
           present at the 3' end of RNA transcripts during
           translation. The Mkt1-Pbp1 complex is involved in the
           post-transcriptional regulation of HO endonuclease
           expression. Mkt1 and eukaryotic homologs are atypical
           members of the structure-specific, 5' nuclease family.
           Conical members of this family possess a PIN (PilT N
           terminus) domain with a helical arch/clamp region/I
           domain (approximately 40 to 55 residues in MKT1 PIN
           domains) and inserted within the PIN domain is a H3TH
           (helix-3-turn-helix) domain, an atypical
           helix-hairpin-helix-2-like region. Although Mkt1 appears
           to possess both a PIN and H3TH domain, the Mkt1 PIN
           domain lacks several of the active site residues
           necessary to bind essential divalent metal ion cofactors
           (Mg2+/Mn2+) required for nuclease activity in this
           family. Also, Mkt1 lacks the glycine-rich loop in the
           H3TH domain which is proposed to facilitate duplex DNA
           binding.
          Length = 215

 Score = 26.0 bits (58), Expect = 5.7
 Identities = 9/21 (42%), Positives = 14/21 (66%)

Query: 14  LYSSLLQLCEERHCEYQVFPY 34
           LY  L+++ +E+  EY V PY
Sbjct: 133 LYRFLIRILKEKGIEYLVAPY 153


>gnl|CDD|197483 smart00038, COLFI, Fibrillar collagens C-terminal domain.  Found
          at C-termini of fibrillar collagens: Ephydatia muelleri
          procollagen EMF1alpha, vertebrate collagens
          alpha(1)III, alpha(1)II, alpha(2)V etc.
          Length = 232

 Score = 25.5 bits (56), Expect = 8.0
 Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 2/42 (4%)

Query: 19 LQLC--EERHCEYQVFPYAVSIMDRFLCYCPMEKSQLQLTAS 58
          L+LC  E +  EY V P    I D    +C  E  +  ++ S
Sbjct: 35 LKLCHPEWKSGEYWVDPNQGCIRDAIKVFCNFETGETCVSPS 76


  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
   0.326    0.133    0.402 

Gapped
Lambda     K      H
   0.267   0.0783    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,702,392
Number of extensions: 453248
Number of successful extensions: 417
Number of sequences better than 10.0: 1
Number of HSP's gapped: 417
Number of HSP's successfully gapped: 11
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)