RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15424
         (153 letters)



>gnl|CDD|221146 pfam11597, Med13_N, Mediator complex subunit 13 N-terminal.
           Mediator is a large complex of up to 33 proteins that is
           conserved from plants through fungi to humans - the
           number and representation of individual subunits varying
           with species. It is arranged into four different
           sections, a core, a head, a tail and a kinase-activity
           part, and the number of subunits within each of these is
           what varies with species. Overall, Mediator regulates
           the transcriptional activity of RNA polymerase II but it
           would appear that each of the four different sections
           has a slightly different function. Med13 is part of the
           ancillary kinase module, together with Med12, CDK8 and
           CycC, which in yeast is implicated in transcriptional
           repression, though most of this activity is likely
           attributable to the CDK8 kinase. The large Med12 and
           Med13 proteins are required for specific developmental
           processes in Drosophila, zebrafish, and Caenorhabditis
           elegans but their biochemical functions are not
           understood.
          Length = 370

 Score = 76.5 bits (188), Expect = 4e-17
 Identities = 42/104 (40%), Positives = 50/104 (48%), Gaps = 28/104 (26%)

Query: 41  TDLCGIKWRKLVHGDSAGTGYSPGSEPLEDPVLASYAKCLAGDILCVWRRVGTPQNGGSG 100
            DL GIKWR  V G       S G + LEDP+L+SY++CLA D L VWRR   P      
Sbjct: 15  ADLTGIKWRIYVWGGPP----SRGPDLLEDPILSSYSRCLAADDLEVWRRKQGP------ 64

Query: 101 GGGGGLFDSIGLPQVTSVPPLSLQAAKELWIFWYGEEPDLSSIV 144
                                +  A KELWIFWYG EP+L  +V
Sbjct: 65  ------------------LVYNDPARKELWIFWYGPEPELLDLV 90


>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger.  [Transport and
           binding proteins, Cations and iron carrying compounds].
          Length = 1096

 Score = 31.5 bits (71), Expect = 0.14
 Identities = 16/30 (53%), Positives = 19/30 (63%)

Query: 3   GRGGGGGGEREGGKVRETEEEEEEEVEKWE 32
           G GG  GG+ E  +  E EEEEEEE E+ E
Sbjct: 854 GGGGSDGGDSEEEEEEEEEEEEEEEEEEEE 883



 Score = 30.3 bits (68), Expect = 0.36
 Identities = 16/29 (55%), Positives = 19/29 (65%)

Query: 4   RGGGGGGEREGGKVRETEEEEEEEVEKWE 32
           +G  GGG  +GG   E EEEEEEE E+ E
Sbjct: 850 KGVDGGGGSDGGDSEEEEEEEEEEEEEEE 878


>gnl|CDD|223036 PHA03295, PHA03295, envelope glycoprotein H; Provisional.
          Length = 714

 Score = 29.3 bits (66), Expect = 0.97
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 113 PQVTSVPPLSLQAAKELWIFWYGEEPDLSSIVTP 146
            Q  +VPP  L   +++++       ++S I  P
Sbjct: 133 TQALTVPPPELLPMQDVYMTGSPYVVNVSEIHRP 166


>gnl|CDD|220404 pfam09789, DUF2353, Uncharacterized coiled-coil protein (DUF2353). 
           Members of this family of uncharacterized proteins have
           no known function.
          Length = 319

 Score = 28.7 bits (64), Expect = 1.3
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 11  EREGGKVRETEEEEEEEVEKWERLGER 37
           E  GG VRE+ EE  + V + E+L E+
Sbjct: 115 EFMGGGVRESFEERNDLVSQLEKLREK 141


>gnl|CDD|225339 COG2718, COG2718, Uncharacterized conserved protein [Function
           unknown].
          Length = 423

 Score = 27.8 bits (62), Expect = 2.2
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 3   GRGGGGGGEREGGKVRETEEEEEEEVEKWERL 34
           G GGGG G+ +     E E+E   ++ + E L
Sbjct: 93  GGGGGGSGKGQAAGDGEGEDEFVFQISREEVL 124


>gnl|CDD|182044 PRK09717, PRK09717, stationary phase growth adaptation protein;
          Provisional.
          Length = 179

 Score = 27.4 bits (60), Expect = 2.8
 Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 7/61 (11%)

Query: 25 EEEVEKWERLGERGGDT-DLCGIKWRKLVHGDSAGTGYSPGSEPLEDPVLASYA-KCLAG 82
          ++EVEKW   G   GD  DL  +   + V+       +  G EPLE     +Y+  C   
Sbjct: 2  KQEVEKWRPFGHPDGDIRDLSFLDAHQAVY-----VQHHEGKEPLEYRFWVTYSLHCFTK 56

Query: 83 D 83
          D
Sbjct: 57 D 57


>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
           Validated.
          Length = 882

 Score = 27.5 bits (62), Expect = 2.9
 Identities = 17/31 (54%), Positives = 21/31 (67%)

Query: 12  REGGKVRETEEEEEEEVEKWERLGERGGDTD 42
           RE G+++ TEEE EE +EK ERL E G   D
Sbjct: 102 RECGRLKLTEEEIEEYLEKLERLKEWGSLAD 132


>gnl|CDD|217829 pfam03985, Paf1, Paf1.  Members of this family are components of
           the RNA polymerase II associated Paf1 complex. The Paf1
           complex functions during the elongation phase of
           transcription in conjunction with Spt4-Spt5 and
           Spt16-Pob3i.
          Length = 431

 Score = 27.4 bits (61), Expect = 3.5
 Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)

Query: 15  GKVRETEEEEEEEVEKWERLGERGGD 40
            +V E E+EEEE+    E   E G D
Sbjct: 368 EEVDEDEDEEEEQRS-DEHEEEEGED 392


>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5).  This
           family consists of apoptosis inhibitory protein 5 (API5)
           sequences from several organisms. Apoptosis or
           programmed cell death is a physiological form of cell
           death that occurs in embryonic development and organ
           formation. It is characterized by biochemical and
           morphological changes such as DNA fragmentation and cell
           volume shrinkage. API5 is an anti apoptosis gene located
           in human chromosome 11, whose expression prevents the
           programmed cell death that occurs upon the deprivation
           of growth factors.
          Length = 543

 Score = 27.3 bits (60), Expect = 3.8
 Identities = 11/17 (64%), Positives = 11/17 (64%)

Query: 2   RGRGGGGGGEREGGKVR 18
           RGRG GGGG R  G  R
Sbjct: 524 RGRGRGGGGGRGRGYNR 540


>gnl|CDD|198151 smart01083, Cir_N, N-terminal domain of CBF1 interacting
          co-repressor CIR.  This is a 45 residue conserved
          region at the N-terminal end of a family of proteins
          referred to as CIRs (CBF1-interacting co-repressors).
          CBF1 (centromere-binding factor 1) acts as a
          transcription factor that causes repression by binding
          specifically to GTGGGAA motifs in responsive promoters,
          and it requires CIR as a co-repressor. CIR binds to
          histone deacetylase and to SAP30 and serves as a linker
          between CBF1 and the histone deacetylase complex.
          Length = 37

 Score = 24.4 bits (54), Expect = 4.9
 Identities = 7/19 (36%), Positives = 12/19 (63%)

Query: 16 KVRETEEEEEEEVEKWERL 34
          +V + E++ EEE +K E  
Sbjct: 12 RVWKAEQKAEEEKKKIEER 30


>gnl|CDD|219796 pfam08325, WLM, WLM domain.  This is a predicted metallopeptidase
           domain called WLM (Wss1p-like metalloproteases). These
           are linked to the Ub-system by virtue of fusions with
           the UB-binding PUG (PUB), Ub-like, and Little Finger
           domains. More specifically, genetic evidence implicates
           the WLM family in de-SUMOylation.
          Length = 183

 Score = 26.1 bits (58), Expect = 6.4
 Identities = 12/41 (29%), Positives = 13/41 (31%), Gaps = 4/41 (9%)

Query: 5   GGGGGGEREGGKVRETEEEEEEEVEKWERLGERGGDTDLCG 45
           G    G R GG+      E  E        G  GG   L G
Sbjct: 124 GFLSSGRRLGGRGSYNSAEGREL----GGNGLSGGGERLGG 160


>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
           subunit G; Reviewed.
          Length = 197

 Score = 26.2 bits (57), Expect = 7.1
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 11  EREGGKVRETEEEEEEEVEKWERLGERGGD 40
           ER   K+ E E++EE+E E+ E+  E   D
Sbjct: 145 ERREEKIDEREDQEEQEREREEQTIEEQSD 174


>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional.
          Length = 584

 Score = 26.5 bits (59), Expect = 7.3
 Identities = 12/44 (27%), Positives = 15/44 (34%)

Query: 63  PGSEPLEDPVLASYAKCLAGDILCVWRRVGTPQNGGSGGGGGGL 106
                LE+ VL +    L  D+L      G      S GG G  
Sbjct: 292 AEDRALEEIVLEAVRAALPPDLLARLAAGGARARARSAGGAGAA 335


>gnl|CDD|165587 PHA03343, PHA03343, US22 family homolog; Provisional.
          Length = 578

 Score = 26.1 bits (57), Expect = 9.1
 Identities = 14/44 (31%), Positives = 18/44 (40%)

Query: 2   RGRGGGGGGEREGGKVRETEEEEEEEVEKWERLGERGGDTDLCG 45
           +G GG            E  EEEEE  +K E    RG  + + G
Sbjct: 101 KGPGGETAAAAAAAAAAEKGEEEEEAGDKIEPPAVRGSVSPIRG 144


  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
   0.311    0.139    0.436 

Gapped
Lambda     K      H
   0.267   0.0812    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,438,174
Number of extensions: 785081
Number of successful extensions: 1098
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1077
Number of HSP's successfully gapped: 37
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (24.8 bits)