RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2472
         (571 letters)



>gnl|CDD|215581 PLN03109, PLN03109, ETHYLENE-INSENSITIVE3-like3 protein;
           Provisional.
          Length = 599

 Score = 30.6 bits (69), Expect = 2.8
 Identities = 13/40 (32%), Positives = 18/40 (45%)

Query: 351 IRLERTIQRNLLLAQQAKDNLKTAGNGQQPSEGKKTRPQD 390
           I+L+R  +R   L Q A +  K      Q    K +R QD
Sbjct: 51  IKLKRIKERQKKLQQAALEKSKPKKISDQARRKKMSRAQD 90


>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175). 
          Length = 820

 Score = 30.6 bits (70), Expect = 3.1
 Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 11/59 (18%)

Query: 363 LAQQAKDNLKTAGNGQQPSEGKKTRPQDLVRLYEIILQNLGE----------LQQLSGM 411
           LA+QA+ N +            +   QDL R+ + I + L E          L+QL  M
Sbjct: 512 LAEQAQRNPQQGDQPPDQGNSMELTQQDLQRMMDRI-EELMESGRRAEAQQLLEQLQQM 569


>gnl|CDD|233691 TIGR02027, rpoA, DNA-directed RNA polymerase, alpha subunit,
           bacterial and chloroplast-type.  This family consists of
           the bacterial (and chloroplast) DNA-directed RNA
           polymerase alpha subunit, encoded by the rpoA gene. The
           RNA polymerase catalyzes the transcription of DNA into
           RNA using the four ribonucleoside triphosphates as
           substrates. The amino terminal domain is involved in
           dimerizing and assembling the other RNA polymerase
           subunits into a transcriptionally active enzyme. The
           carboxy-terminal domain contains determinants for
           interaction with DNA and with transcriptional activator
           proteins [Transcription, DNA-dependent RNA polymerase].
          Length = 297

 Score = 29.5 bits (67), Expect = 4.1
 Identities = 32/110 (29%), Positives = 50/110 (45%), Gaps = 12/110 (10%)

Query: 158 EAQAYVSWIVGVLHFELKLWKSAMKNLKEAQVVYEKLMSALNEEDAL--LYKQKVEELTP 215
           +A A  + I+ + H E         NL E    +E+      EE     L   K+EEL  
Sbjct: 190 DAIAEAAKIL-IEHLEP------FVNLDEEIEAFEEEQEEEEEELEDAKLLSIKIEELDL 242

Query: 216 SLRYCAYNIGDQAGIEDLMQLRSQTHGDLLHSLDSLMIQSKEHSAEVLSE 265
           S+R  +YN   +AGI  L +L S++  +LL  + +   +S     E L+E
Sbjct: 243 SVR--SYNCLKRAGIHTLGELVSKSEEELL-KIKNFGKKSLTEIKEKLAE 289


>gnl|CDD|221062 pfam11290, DUF3090, Protein of unknown function (DUF3090).  This
           family of proteins with unknown function appears to be
           restricted to Actinobacteria.
          Length = 171

 Score = 28.9 bits (65), Expect = 4.7
 Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)

Query: 269 RGRSVAVRSERVRVFLLAERSLDASLGQAGA 299
            GR V+V  E+ +V  LAER +D  L + G 
Sbjct: 29  GGRLVSVALEKQQVAALAER-IDELLDEVGR 58


>gnl|CDD|223368 COG0291, RpmI, Ribosomal protein L35 [Translation, ribosomal
          structure and biogenesis].
          Length = 65

 Score = 27.2 bits (61), Expect = 4.9
 Identities = 9/23 (39%), Positives = 14/23 (60%)

Query: 61 TRRIRRLRKTLHLPQGDKRHFKK 83
          T+R R LRKT  + + D +  K+
Sbjct: 38 TKRKRHLRKTAVVSKADLKRVKR 60


>gnl|CDD|188530 TIGR04015, WcaC, colanic acid biosynthesis glycosyl transferase
           WcaC.  This gene is one of the glycosyl transferases
           involved in the biosynthesis of colanic acid, an
           exopolysaccharide expressed in Enterobacteraceae
           species.
          Length = 405

 Score = 29.5 bits (66), Expect = 5.4
 Identities = 11/19 (57%), Positives = 16/19 (84%)

Query: 193 KLMSALNEEDALLYKQKVE 211
           KLMSALN+ DAL++  +V+
Sbjct: 299 KLMSALNQMDALVFSSRVD 317


>gnl|CDD|173690 cd05599, STKc_NDR_like, Catalytic domain of Nuclear Dbf2-Related
           kinase-like Protein Serine/Threonine Kinases.
           Serine/Threonine Kinases (STKs), Nuclear Dbf2-Related
           (NDR) kinase subfamily, catalytic (c) domain. STKs
           catalyze the transfer of the gamma-phosphoryl group from
           ATP to serine/threonine residues on protein substrates.
           The NDR subfamily is part of a larger superfamily that
           includes the catalytic domains of other protein STKs,
           protein tyrosine kinases, RIO kinases, aminoglycoside
           phosphotransferase, choline kinase, and phosphoinositide
           3-kinase. NDR kinase contains an N-terminal regulatory
           (NTR) domain and an insert within the catalytic domain
           that contains an auto-inhibitory sequence. Like many
           other AGC kinases, NDR kinase requires phosphorylation
           at two sites, the activation loop (A-loop) and the
           hydrophobic motif (HM), for activity. NDR kinases
           regulate mitosis, cell growth, embryonic development,
           and neurological processes. They are also required for
           proper centrosome duplication. Higher eukaryotes contain
           two NDR isoforms, NDR1 and NDR2. This subfamily also
           contains fungal NDR-like kinases.
          Length = 364

 Score = 28.9 bits (65), Expect = 7.0
 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 454 SRATAYASDAASSLPSSGELATLKPELATLEAAIDSNKYSALAYSVLGTEGTPD 507
           S  T +    + +LPS+      KP  +  +A        ALAYS   T GTPD
Sbjct: 154 SHRTEFYRILSHALPSNFLDFISKPMSSKRKAETWKRNRRALAYS---TVGTPD 204


>gnl|CDD|151921 pfam11483, DUF3209, Protein of unknown function (DUF3209).  This
           family of proteins has no known function.
          Length = 122

 Score = 27.8 bits (62), Expect = 7.1
 Identities = 29/115 (25%), Positives = 41/115 (35%), Gaps = 15/115 (13%)

Query: 194 LMSALNEEDALLYKQKVEELTPSLRYCAYNIGDQAGIEDLMQLRSQTHGDLLHSLDSLMI 253
           LM+ L  +D    +   EEL   L      I   A  + L  L       L+  L+  + 
Sbjct: 12  LMNVLGTKDDHARQHAREELEGVLEP---PIEALAEAKTLAALERHLDAALVD-LEEEIA 67

Query: 254 QSKEHSAEVLSEVSWRGRSVAVRSERVRVFLLAERSLDASLGQAGADKIELLESH 308
            ++    E       RGR VAVR         AE +L        A   +L E+H
Sbjct: 68  ATEPEDPEY---DYLRGRLVAVRD--------AEGALKRLRMHGEAVLDDLGETH 111


>gnl|CDD|183270 PRK11670, PRK11670, antiporter inner membrane protein; Provisional.
          Length = 369

 Score = 28.5 bits (64), Expect = 9.9
 Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 155 TKLEAQAYVSWIVGVLHFELKL---WKSAMKNLKEA 187
           T L+A  +V+ +   LH EL +   W SA + LKE 
Sbjct: 34  TTLKALHHVALLDDTLHIELVMPFVWNSAFEELKEQ 69


  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
   0.316    0.131    0.368 

Gapped
Lambda     K      H
   0.267   0.0735    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,781,826
Number of extensions: 2814682
Number of successful extensions: 2529
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2529
Number of HSP's successfully gapped: 23
Length of query: 571
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 469
Effective length of database: 6,413,494
Effective search space: 3007928686
Effective search space used: 3007928686
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: 41 (21.6 bits)
S2: 62 (27.6 bits)