RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13691
         (103 letters)



>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor
          (CBF/NF-Y) and archaeal histone.  This family includes
          archaebacterial histones and histone like transcription
          factors from eukaryotes.
          Length = 65

 Score = 45.7 bits (109), Expect = 4e-08
 Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A ++R++K            +S+D +    +    FI  + +EA  I  ++ RKT++
Sbjct: 3  LPIARVKRIMKSD-----PDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTIN 57

Query: 70 GVDVI 74
             + 
Sbjct: 58 AEHIK 62


>gnl|CDD|227479 COG5150, COG5150, Class 2 transcription repressor NC2, beta
          subunit (Dr1) [Transcription].
          Length = 148

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 4/82 (4%)

Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
          D+ +LP A +Q+++   LPKD    +  +K+ R     A   FI  L++EA     E+ +
Sbjct: 8  DENSLPKATVQKMVSSILPKD----LVFTKEAREIFINACIEFINMLSSEANEACEEEAK 63

Query: 66 KTLSGVDVIEGVKQIGFEVIIE 87
          KT++   VI+ ++ + FE  IE
Sbjct: 64 KTIAYEHVIKALENLEFEEYIE 85


>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
          dynamics].
          Length = 91

 Score = 40.8 bits (96), Expect = 6e-06
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
           DL LP A ++R++++A  +       VS        +A   ++  +  +A+ +A    R
Sbjct: 16 TDLLLPKAPVRRILRKAGAE------RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKR 69

Query: 66 KTLSGVDVIEGVKQIGFEVIIE 87
          KT+   D+   +K++G  +  E
Sbjct: 70 KTVKAEDIKLALKRLGRRIYGE 91


>gnl|CDD|227533 COG5208, HAP5, CCAAT-binding factor, subunit C [Transcription].
          Length = 286

 Score = 40.0 bits (93), Expect = 5e-05
 Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 6/88 (6%)

Query: 5   LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN 64
           L D NLP A I++++K       E    +S +  +   K   +FI  LT  A   A E  
Sbjct: 105 LKDHNLPLARIKKVMKTD-----EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENK 159

Query: 65  RKTLSGVDVIEGVKQIG-FEVIIEILGK 91
           R+TL   D+   VK+   F+ +I+I+ +
Sbjct: 160 RRTLQKSDIAAAVKKSEMFDFLIDIVPR 187


>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
           eukaryotic snRNP [Transcription].
          Length = 564

 Score = 28.9 bits (65), Expect = 0.38
 Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 65  RKTLSGVDVIEGVKQIGFEVIIEI 88
           RK L G   IE ++Q+GF+ I+E+
Sbjct: 82  RKHLKG-ARIEKIEQLGFDRILEL 104


>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
           This family consists of the N-terminal region of the
          prokaryotic fibronectin-binding protein. Fibronectin
          binding is considered to be an important virulence
          factor in streptococcal infections. Fibronectin is a
          dimeric glycoprotein that is present in a soluble form
          in plasma and extracellular fluids; it is also present
          in a fibrillar form on cell surfaces. Both the soluble
          and cellular forms of fibronectin may be incorporated
          into the extracellular tissue matrix. While fibronectin
          has critical roles in eukaryotic cellular processes,
          such as adhesion, migration and differentiation, it is
          also a substrate for the attachment of bacteria. The
          binding of pathogenic Streptococcus pyogenes and
          Staphylococcus aureus to epithelial cells via
          fibronectin facilitates their internalisation and
          systemic spread within the host.
          Length = 447

 Score = 26.4 bits (59), Expect = 2.8
 Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 1/24 (4%)

Query: 65 RKTLSGVDVIEGVKQIGFEVIIEI 88
          RK L G   I  ++QIGF+ I+E 
Sbjct: 77 RKHLEG-GRIVDIEQIGFDRIVEF 99


>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4. 
          Length = 75

 Score = 25.2 bits (56), Expect = 3.1
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 7  DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK 66
           L +      R+++E L +    ++ +S    +A  +A    +  +  +A  +A    RK
Sbjct: 3  RLLILKLPFSRVVRE-LKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRK 61

Query: 67 TLS 69
          T++
Sbjct: 62 TIT 64


>gnl|CDD|213289 cd05922, FACL_like_6, Uncharacterized subfamily of fatty acid CoA
           ligase (FACL).  Fatty acyl-CoA ligases catalyze the
           ATP-dependent activation of fatty acids in a two-step
           reaction. The carboxylate substrate first reacts with
           ATP to form an acyl-adenylate intermediate, which then
           reacts with CoA to produce an acyl-CoA ester. This is a
           required step before free fatty acids can participate in
           most catabolic and anabolic reactions.
          Length = 350

 Score = 26.0 bits (58), Expect = 4.1
 Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 3/34 (8%)

Query: 2   AESLDDLNLPSAIIQRLIKEALPKDAEGKINVSK 35
            + L +  +P+ I+     ++LPK+A GK++ S 
Sbjct: 318 RKHLPNYMVPAEIVFV---DSLPKNANGKVDRSA 348


>gnl|CDD|233694 TIGR02033, D-hydantoinase, D-hydantoinase.  This model represents
           the D-hydantoinase (dihydropyrimidinase) which primarily
           converts 5,6-dihydrouracil to 3-ureidopropanoate but
           also acts on dihydrothymine and hydantoin. The enzyme is
           a metalloenzyme.
          Length = 454

 Score = 25.4 bits (56), Expect = 7.2
 Identities = 8/25 (32%), Positives = 15/25 (60%)

Query: 27  AEGKINVSKDVRLAAGKAASLFILH 51
           A+G+I + K V L +   A +F ++
Sbjct: 354 AKGRITLEKFVELTSTNPAKIFNMY 378


>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.  This
           model describes the DndB protein encoded by an operon
           associated with a sulfur-containing modification to DNA.
           The operon is sporadically distributed in bacteria, much
           like some restriction enzyme operons. DndD is described
           as a putative ATPase. The small number of examples known
           so far include species from among the Firmicutes,
           Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
           metabolism, Restriction/modification].
          Length = 650

 Score = 25.0 bits (55), Expect = 8.7
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 8/80 (10%)

Query: 1   MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFIL--------HL 52
           + ESL  L LP+  ++ +  E    D     +     RL+  +   L +L          
Sbjct: 332 LLESLPKLALPAEHVKEIAAELAEIDKPATTDSEIPHRLSGSELTQLEVLIQQVKRELQD 391

Query: 53  TTEALSIANEKNRKTLSGVD 72
               L     +  + L+ VD
Sbjct: 392 AKSQLLKELRELEEELAEVD 411


  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
   0.314    0.132    0.338 

Gapped
Lambda     K      H
   0.267   0.0867    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,143,566
Number of extensions: 444284
Number of successful extensions: 387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 383
Number of HSP's successfully gapped: 34
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
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: 42 (22.0 bits)
S2: 53 (23.9 bits)