RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12993
         (243 letters)



>gnl|CDD|227585 COG5260, TRF4, DNA polymerase sigma [DNA replication,
           recombination, and repair].
          Length = 482

 Score = 95.2 bits (237), Expect = 2e-22
 Identities = 57/218 (26%), Positives = 86/218 (39%), Gaps = 57/218 (26%)

Query: 23  LFVVGSTMTGFGLDSSDVDMCLGIRPYEFDRGQAIRVLCVLETSDVDMCLEIFKKADLIH 82
           L V GST TG  L  SD+D+C+                     SD     E      L  
Sbjct: 98  LKVFGSTETGLALPKSDIDLCI--------------------ISDPRGYKETRNAGSLAS 137

Query: 83  AKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQKIFKKADLI-HAKVPILKFQDS 141
                                            + + + + K+  ++  A+VPI+K  D 
Sbjct: 138 ---------------------------------HLFKKNLAKEVVVVSTARVPIIKLVDP 164

Query: 142 SFKLEVDLNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLVKLWAQAHNINDAKNMTISSYS 201
              L  D++ NN  G+ N  L+  Y + D R+RPLVL++K W +   +ND    T+SSY+
Sbjct: 165 QSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYT 224

Query: 202 FTLMVIHFLQCGTSPPVLPNLVAQYPTKFSPNSNIDNI 239
            + MV+ FLQ         N +    +    N NIDN+
Sbjct: 225 ISCMVLSFLQMHPPFLFFDNGLL---SPLKYNKNIDNL 259


>gnl|CDD|143392 cd05402, NT_PAP_TUTase, Nucleotidyltransferase (NT) domain of
           poly(A) polymerases and terminal uridylyl transferases. 
           Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail
           synthesis, and terminal uridylyl transferases (TUTases)
           uridylate RNA. PAPs in this subgroup include human PAP
           alpha, mouse testis-specific cytoplasmic PAP beta, human
           nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4
           and-5, Schizosaccharomyces pombe caffeine-induced death
           proteins -1, and -14, Caenorhabditis elegans Germ Line
           Development-2, and Chlamydomonas reinhardtii MUT68. This
           family also includes human U6 snRNA-specific TUTase1,
           and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This
           family belongs to the Pol beta-like NT superfamily. In
           the majority of enzymes in this superfamily, two
           carboxylates, Dx[D/E], together with a third more distal
           carboxylate, coordinate two divalent metal cations
           involved in a two-metal ion mechanism of nucleotide
           addition. For the majority of proteins in this family,
           these carboxylate residues are conserved.
          Length = 114

 Score = 80.7 bits (200), Expect = 1e-19
 Identities = 39/102 (38%), Positives = 59/102 (57%), Gaps = 6/102 (5%)

Query: 19  AHVRLFVVGSTMTGFGLDSSDVDMCLGIRPYEFDRGQAIRVLC-VLETSDVDMCLEIFKK 77
              +L+  GS +TG GL  SD+D+CL    +  DR   +R L  +L+ S     +E+   
Sbjct: 18  PGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSG--EVVEVEP- 74

Query: 78  ADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYA 119
             +I+A+VPI+KF D    +EVD++ NN+ G+RNT LL  Y 
Sbjct: 75  --IINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114


>gnl|CDD|150167 pfam09404, DUF2003, Eukaryotic protein of unknown function
           (DUF2003).  This is a family of proteins of unknown
           function which adopt an alpha helical and beta sheet
           structure.
          Length = 447

 Score = 30.7 bits (69), Expect = 0.64
 Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 10/46 (21%)

Query: 134 PILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQM-DWRIRPLVL 178
           PIL   +SSF+LEVD+          T LL C AQ+ +W+  P +L
Sbjct: 179 PILSRLESSFQLEVDV---------LTQLLRCQAQISEWKFLPSLL 215



 Score = 27.3 bits (60), Expect = 9.0
 Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 9/35 (25%)

Query: 86  PILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQ 120
           PIL   +SSF+LEVD+          T LL C AQ
Sbjct: 179 PILSRLESSFQLEVDV---------LTQLLRCQAQ 204


>gnl|CDD|115879 pfam07252, DUF1433, Protein of unknown function (DUF1433).  This
           family contains a number of hypothetical bacterial
           proteins of unknown function approximately 100 residues
           in length.
          Length = 88

 Score = 27.7 bits (62), Expect = 2.1
 Identities = 6/24 (25%), Positives = 16/24 (66%)

Query: 187 HNINDAKNMTISSYSFTLMVIHFL 210
           +NI + K++T +++  + M I+ +
Sbjct: 15  YNIKNYKSVTFTNFEKSPMGIYSI 38


>gnl|CDD|226368 COG3850, NarQ, Signal transduction histidine kinase,
           nitrate/nitrite-specific [Signal transduction
           mechanisms].
          Length = 574

 Score = 29.2 bits (66), Expect = 2.3
 Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 6/57 (10%)

Query: 176 LVLLVKLWAQAHNINDAKNMTISSYSFTLMVIHFLQCGTSPPVLPNLVAQYPTKFSP 232
           L+LL      A  IN A ++ + SY     V          P L   VA + T    
Sbjct: 28  LLLLASSQGDAEAINIAGSLRMQSYRLLYAV------QLGSPQLDAHVALFQTSLHS 78


>gnl|CDD|216779 pfam01909, NTP_transf_2, Nucleotidyltransferase domain.  Members
          of this family belong to a large family of
          nucleotidyltransferases. This family includes kanamycin
          nucleotidyltransferase (KNTase) which is a
          plasmid-coded enzyme responsible for some types of
          bacterial resistance to aminoglycosides. KNTase
          in-activates antibiotics by catalyzing the addition of
          a nucleotidyl group onto the drug.
          Length = 92

 Score = 26.7 bits (59), Expect = 4.7
 Identities = 7/37 (18%), Positives = 13/37 (35%)

Query: 7  VEEYVRFTLRDPAHVRLFVVGSTMTGFGLDSSDVDMC 43
          + +             + + GS   G  L  SD+D+ 
Sbjct: 1  LSKIKEILKELYGVAEVVLFGSYARGTYLPGSDIDLL 37


>gnl|CDD|215585 PLN03115, PLN03115, ferredoxin--NADP(+) reductase; Provisional.
          Length = 367

 Score = 28.0 bits (62), Expect = 5.1
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 18  PAHVRLFVVGSTMTG-FGLDSSDVDMCLGIRPYEFDRGQAIRVLC 61
           P  +RL+ + S+  G FG DS  V +C+    Y  D+G+ ++ +C
Sbjct: 142 PHKLRLYSIASSALGDFG-DSKTVSLCVKRLVYTNDQGEIVKGVC 185


>gnl|CDD|217491 pfam03320, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase,
           glpX-encoded. 
          Length = 308

 Score = 27.0 bits (61), Expect = 9.1
 Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 19/61 (31%)

Query: 3   LSKAVEEYVRFTLRDPAH-------------VRLF----VVGSTMTGFGLDSSDVDMCLG 45
           L K VE+     L  P H             V+L     V G+  T      + VD+ +G
Sbjct: 148 LGKDVEDLTVVVLDRPRHAELIEEIREAGARVKLISDGDVAGAIATALP--DTGVDILMG 205

Query: 46  I 46
           I
Sbjct: 206 I 206


  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
   0.325    0.139    0.422 

Gapped
Lambda     K      H
   0.267   0.0556    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,955,906
Number of extensions: 1086511
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1008
Number of HSP's successfully gapped: 18
Length of query: 243
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 149
Effective length of database: 6,768,326
Effective search space: 1008480574
Effective search space used: 1008480574
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 (21.6 bits)
S2: 58 (26.5 bits)