RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4296
         (103 letters)



>gnl|CDD|227416 COG5084, YTH1, Cleavage and polyadenylation specificity factor
           (CPSF) Clipper subunit and related makorin family
           Zn-finger proteins [General function prediction only].
          Length = 285

 Score = 78.0 bits (192), Expect = 1e-18
 Identities = 32/70 (45%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 21  VPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTK--MPECYFYSRFNACHN-KE 77
            P    +     SVVCK +LRGLCK G  CEFLHEYD+     P C  +S   +C +   
Sbjct: 92  TPNNHVNPVLSSSVVCKFFLRGLCKSGFSCEFLHEYDLRSSQGPPCRSFSLKGSCSSGPS 151

Query: 78  CPFLHIDPDS 87
           C + HIDPDS
Sbjct: 152 CGYSHIDPDS 161


>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger. 
          Length = 27

 Score = 36.1 bits (84), Expect = 1e-04
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 32 RSVVCKHWLRGLCKKGDQCEFLHEY 56
          ++ +CK + RG C +GD+C+F H  
Sbjct: 3  KTELCKFFKRGYCPRGDRCKFAHPL 27


>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and
          similar). 
          Length = 27

 Score = 28.7 bits (65), Expect = 0.082
 Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 1/22 (4%)

Query: 34 VVCKHWLR-GLCKKGDQCEFLH 54
           +C+ + R G CK GD+C+F H
Sbjct: 4  ELCRFFSRTGTCKYGDRCKFAH 25



 Score = 24.8 bits (55), Expect = 2.0
 Identities = 9/24 (37%), Positives = 11/24 (45%), Gaps = 1/24 (4%)

Query: 60 KMPECYFYSRFNAC-HNKECPFLH 82
          K   C F+SR   C +   C F H
Sbjct: 2  KTELCRFFSRTGTCKYGDRCKFAH 25


>gnl|CDD|227577 COG5252, COG5252, Uncharacterized conserved protein, contains
           CCCH-type Zn-finger protein [General function prediction
           only].
          Length = 299

 Score = 30.4 bits (68), Expect = 0.12
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 32  RSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPE 63
           ++VVC  +L   C KGD C+F H  +  +  E
Sbjct: 84  KTVVCALFLNKTCAKGDACKFAHGKEEARKTE 115


>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
           and CCCH-type Zn-fingers [General function prediction
           only].
          Length = 259

 Score = 28.9 bits (64), Expect = 0.43
 Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 1/28 (3%)

Query: 34  VVCKHW-LRGLCKKGDQCEFLHEYDMTK 60
            VCK +   G C  GD C+FLH+    K
Sbjct: 142 DVCKDYKETGYCGYGDSCKFLHDRSDFK 169


>gnl|CDD|238874 cd01836, FeeA_FeeB_like, SGNH_hydrolase subfamily, FeeA, FeeB and
           similar esterases/lipases. FeeA and FeeB are part of a
           biosynthetic gene cluster and may participate in the
           biosynthesis of long-chain N-acyltyrosines by providing
           saturated and unsaturated fatty acids, which it turn are
           loaded onto the acyl carrier protein FeeL. SGNH
           hydrolases are a diverse family of lipases and
           esterases. The tertiary fold of the enzyme is
           substantially different from that of the alpha/beta
           hydrolase family and unique among all known hydrolases;
           its active site closely resembles the Ser-His-Asp(Glu)
           triad found in other serine hydrolases.
          Length = 191

 Score = 28.4 bits (64), Expect = 0.50
 Identities = 9/34 (26%), Positives = 15/34 (44%)

Query: 21  VPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLH 54
           +P PLR + G R+ +    L  L  +  +   L 
Sbjct: 123 LPQPLRWLLGRRARLLNRALERLASEAPRVTLLP 156


>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
          Length = 480

 Score = 26.6 bits (58), Expect = 2.8
 Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 2/27 (7%)

Query: 56  YDMTKMPECYFYSRFNACHNKECPFLH 82
           Y  TK   C  Y R   C N +C +LH
Sbjct: 199 YGTTKY--CTSYLRNAVCPNPDCMYLH 223


>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
           regulator (CFTR).  The model describes the cystis
           fibrosis transmembrane conductor regulator (CFTR) in
           eukaryotes. The principal role of this protein is
           chloride ion conductance. The protein is predicted to
           consist of 12 transmembrane domains. Mutations or
           lesions in the genetic loci have been linked to the
           aetiology of asthma, bronchiectasis, chronic obstructive
           pulmonary disease etc. Disease-causing mutations have
           been studied by 36Cl efflux assays in vitro cell
           cultures and electrophysiology, all of which point to
           the impairment of chloride channel stability and not the
           biosynthetic processing per se [Transport and binding
           proteins, Anions].
          Length = 1490

 Score = 26.0 bits (57), Expect = 5.1
 Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 6/36 (16%)

Query: 45  KKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPF 80
           KK D+   LHE        CYFY  F+    K   F
Sbjct: 612 KKADKILLLHE------GVCYFYGTFSELQAKRPDF 641


>gnl|CDD|185681 cd09286, NMNAT_Eukarya, Nicotinamide/nicotinate mononucleotide
           adenylyltransferase, Eukaryotic.
           Nicotinamide/nicotinate mononucleotide (NMN/
           NaMN)adenylyltransferase (NMNAT).  NMNAT represents the
           primary bacterial and eukaryotic adenylyltransferases
           for nicotinamide-nucleotide and for the deamido form,
           nicotinate nucleotide.  It is an indispensable enzyme in
           the biosynthesis of NAD(+) and NADP(+).
           Nicotinamide-nucleotide adenylyltransferase synthesizes
           NAD via the salvage pathway, while nicotinate-nucleotide
           adenylyltransferase synthesizes the immediate precursor
           of NAD via the de novo pathway. Human NMNAT displays
           unique dual substrate specificity toward both NMN and
           NaMN, and can participate in both de novo and salvage
           pathways of NAD synthesis.  This subfamily consists
           strictly of eukaryotic members and includes secondary
           structural elements not found in all NMNATs.
          Length = 225

 Score = 25.3 bits (56), Expect = 5.8
 Identities = 12/46 (26%), Positives = 16/46 (34%), Gaps = 5/46 (10%)

Query: 12  PSFQAPGVLVPFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYD 57
            SF  PG+     L  I G+  +V     R      D   F+   D
Sbjct: 132 ESFGIPGLWKDADLEEILGEFGLVVVE--RT---GSDPENFIASSD 172


>gnl|CDD|213271 cd05903, CHC_CoA_lg, Cyclohexanecarboxylate-CoA ligase (also called
           cyclohex-1-ene-1-carboxylate:CoA ligase).
           Cyclohexanecarboxylate-CoA ligase activates the
           aliphatic ring compound, cyclohexanecarboxylate, for
           degradation. It catalyzes the synthesis of
           cyclohexanecarboxylate-CoA thioesters in a two-step
           reaction involving the formation of
           cyclohexanecarboxylate-AMP anhydride, followed by the
           nucleophilic substitution of AMP by CoA.
          Length = 437

 Score = 24.9 bits (55), Expect = 8.9
 Identities = 9/12 (75%), Positives = 10/12 (83%)

Query: 19  VLVPFPLRHITG 30
           VL+P PL HITG
Sbjct: 137 VLMPSPLAHITG 148


  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
   0.328    0.143    0.495 

Gapped
Lambda     K      H
   0.267   0.0763    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,141,127
Number of extensions: 395331
Number of successful extensions: 340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 17
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: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)