RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8797
         (122 letters)



>gnl|CDD|202203 pfam02319, E2F_TDP, E2F/DP family winged-helix DNA-binding domain. 
           This family contains the transcription factor E2F and
           its dimerisation partners TDP1 and TDP2, which stimulate
           E2F-dependent transcription. E2F binds to DNA as a
           homodimer or as a heterodimer in association with
           TDP1/2, the heterodimer having increased binding
           efficiency. The crystal structure of an E2F4-DP2-DNA
           complex shows that the DNA-binding domains of the E2F
           and DP proteins both have a fold related to the
           winged-helix DNA-binding motif. Recognition of the
           central c/gGCGCg/c sequence of the consensus DNA-binding
           site is symmetric, and amino acids that contact these
           bases are conserved among all known E2F and DP proteins.
          Length = 67

 Score = 97.6 bits (244), Expect = 3e-28
 Identities = 44/66 (66%), Positives = 54/66 (81%), Gaps = 1/66 (1%)

Query: 57  RYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKSK 115
           R + SLGLLT+KF+KL + SP G+ DLN A++ LDV QKRRIYDITNVLEGIG++EKKSK
Sbjct: 1   RKEKSLGLLTQKFLKLCEKSPDGITDLNEAAKELDVKQKRRIYDITNVLEGIGLIEKKSK 60

Query: 116 NNIQCK 121
           N I+  
Sbjct: 61  NEIRWI 66


>gnl|CDD|227927 COG5640, COG5640, Secreted trypsin-like serine protease
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 413

 Score = 28.3 bits (63), Expect = 1.0
 Identities = 16/81 (19%), Positives = 26/81 (32%), Gaps = 6/81 (7%)

Query: 23  NLDQD----DEESPFKTPKSVKKMRVNPPTTPAKEKGT-RYDTSLGLLTKKFVKLLQSSP 77
           NL  D    +       P+ VK    +   T      T    T+          + +SSP
Sbjct: 121 NLGNDIAVLELARAASLPR-VKITSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSP 179

Query: 78  QGVVDLNVASESLDVQKRRIY 98
           +G +   VA   + +     Y
Sbjct: 180 KGTILHEVAVLFVPLSTCAQY 200


>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
           replication, recombination, and repair /
           Posttranslational modification, protein turnover,
           chaperones].
          Length = 366

 Score = 27.7 bits (62), Expect = 1.7
 Identities = 11/28 (39%), Positives = 15/28 (53%)

Query: 86  ASESLDVQKRRIYDITNVLEGIGILEKK 113
             E L   +RR  DI + LEG+GI+   
Sbjct: 307 LCERLRTSQRRFSDIISELEGLGIVSAS 334


>gnl|CDD|223207 COG0129, IlvD, Dihydroxyacid dehydratase/phosphogluconate
           dehydratase [Amino acid transport and metabolism /
           Carbohydrate transport and metabolism].
          Length = 575

 Score = 27.1 bits (61), Expect = 2.4
 Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 20/78 (25%)

Query: 4   TIRIRLKLKFHSNMVKRRLNLDQDDEESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLG 63
            IRI        ++  R L+L   +EE       + +     P        G       G
Sbjct: 512 IIRI--------DIPNRTLDLLVSEEEL-----AARRAEWPAPGDPAWPRYGR------G 552

Query: 64  LLTKKFVKLLQSSPQGVV 81
           LL   + KL+ S+ +G V
Sbjct: 553 LL-AAYRKLVSSADKGAV 569


>gnl|CDD|235641 PRK05904, PRK05904, coproporphyrinogen III oxidase; Provisional.
          Length = 353

 Score = 27.1 bits (60), Expect = 2.9
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 64  LLTKKFVKLLQSSPQGVVDLNVASESLDVQK--RRIYDITNVLEGIGILEKKSKNNIQC 120
           L+T+  + LL+ +    + L V S + ++ K   R + I +  E I +L K    NI C
Sbjct: 100 LITQSQINLLKKNKVNRISLGVQSMNNNILKQLNRTHTIQDSKEAINLLHKNGIYNISC 158


>gnl|CDD|218866 pfam06039, Mqo, Malate:quinone oxidoreductase (Mqo).  This family
           consists of several bacterial Malate:quinone
           oxidoreductase (Mqo) proteins (EC:1.1.99.16). Mqo takes
           part in the citric acid cycle. It oxidises L-malate to
           oxaloacetate and donates electrons to ubiquinone-1 and
           other artificial acceptors or, via the electron transfer
           chain, to oxygen. NAD is not an acceptor and the natural
           direct acceptor for the enzyme is most likely a quinone.
           The enzyme is therefore called malate:quinone
           oxidoreductase, abbreviated to Mqo. Mqo is a peripheral
           membrane protein and can be released from the membrane
           by addition of chelators.
          Length = 489

 Score = 26.5 bits (59), Expect = 3.7
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 4/43 (9%)

Query: 53  EKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKR 95
           ++GT  D + G LT++  K LQ  P   V+L    E  D+++ 
Sbjct: 174 DEGT--DVNFGALTRQLFKYLQQKPN--VELQYNHEVRDIKRN 212


>gnl|CDD|220409 pfam09797, NatB_MDM20, N-acetyltransferase B complex (NatB) non
           catalytic subunit.  This is the non-catalytic subunit of
           the N-terminal acetyltransferase B complex (NatB). The
           NatB complex catalyzes the acetylation of the
           amino-terminal methionine residue of all proteins
           beginning with Met-Asp or Met-Glu and of some proteins
           beginning with Met-Asn or Met-Met. In Saccharomyces
           cerevisiae this subunit is called MDM20 and in
           Schizosaccharomyces pombe it is called Arm1. NatB
           acetylates the Tpm1 protein and regulates and
           tropomyocin-actin interactions. This subunit is required
           by the NatB complex for the N-terminal acetylation of
           Tpm1.
          Length = 364

 Score = 26.2 bits (58), Expect = 4.9
 Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%)

Query: 99  DITNVLEGIGILE---KKSKNNIQCK 121
           D+  +LE I +LE   KKS +N   K
Sbjct: 190 DLEYLLEAIALLENGLKKSPHNYDLK 215


>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
           division and chromosome partitioning].
          Length = 272

 Score = 26.0 bits (58), Expect = 5.7
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 13/51 (25%)

Query: 60  TSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV----QKRRIYDITNVLEG 106
           T+L  L KK V         ++D ++   +LD+    + R +YD+ +V+EG
Sbjct: 25  TALAQLGKKVV---------LIDFDIGLRNLDLIMGLENRIVYDLVDVIEG 66


>gnl|CDD|180743 PRK06912, acoL, dihydrolipoamide dehydrogenase; Validated.
          Length = 458

 Score = 25.8 bits (57), Expect = 7.5
 Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)

Query: 81  VDLNVASESLD---VQKRRIYDITNVLEGIGILEKKSK 115
           + L   S S+D   +Q R+   +T +++GI  L KK+K
Sbjct: 67  ITLPNGSISIDWKQMQARKSQIVTQLVQGIQYLMKKNK 104


>gnl|CDD|237654 PRK14278, PRK14278, chaperone protein DnaJ; Provisional.
          Length = 378

 Score = 25.8 bits (57), Expect = 7.7
 Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 1/20 (5%)

Query: 82  DLNVASESL-DVQKRRIYDI 100
           +++VA E L D +KRRI D+
Sbjct: 47  EISVAYEVLSDPEKRRIVDL 66


  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    0.361 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,906,076
Number of extensions: 489988
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 276
Number of HSP's successfully gapped: 26
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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 (24.1 bits)