RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13288
         (200 letters)



>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
           replication, recombination, and repair / Transcription /
           Translation, ribosomal structure and biogenesis].
          Length = 513

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 4/59 (6%)

Query: 135 IATFPLTVKNFMEKHLKDPYEINL---MEELTLKGVTQYYAFV-QERQKVHCLNTLFSK 189
            AT P  ++    ++L DP EI +     E TLK + Q+Y  V  E +K+  L  L   
Sbjct: 212 SATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKD 270


>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
          Length = 401

 Score = 35.6 bits (82), Expect = 0.013
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 112 FNGQILVPKHVLRSLEPKTKVSAI-ATFPLTVKNFMEKHLKDPYEINL-MEELTLKGVTQ 169
           F GQI     V + L P  +V+   AT P  +     K ++DP  I +  +ELTL+G+ Q
Sbjct: 187 FKGQI---YDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQ 243

Query: 170 YYAFVQERQ 178
           +Y  V++ +
Sbjct: 244 FYVAVEKEE 252


>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
           involved in ATP-dependent RNA unwinding, needed in a
           variety of cellular processes including splicing,
           ribosome biogenesis and RNA degradation. The name
           derives from the sequence of the Walker  B motif (motif
           II). This domain contains the ATP- binding region.
          Length = 203

 Score = 33.6 bits (78), Expect = 0.032
 Identities = 8/22 (36%), Positives = 12/22 (54%)

Query: 136 ATFPLTVKNFMEKHLKDPYEIN 157
           AT P  V++   K L++P  I 
Sbjct: 182 ATMPKEVRDLARKFLRNPVRIL 203


>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
          Length = 456

 Score = 29.0 bits (65), Expect = 1.8
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 120 KHVLRSLEPKTK-VSAIATFPLTVKNFMEKHLKDPYEINLMEELTL-KGVTQYYAFVQER 177
           + VL  L  K + +   ATF   +K   EK L +P EI +    T  + VTQ+  FV ++
Sbjct: 171 RRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKK 230

Query: 178 QKVHCLNTLFSK 189
           +K   L+ +  K
Sbjct: 231 RKRELLSQMIGK 242


>gnl|CDD|132991 cd06917, STKc_NAK1_like, Catalytic domain of Fungal Nak1-like
           Protein Serine/Threonine Kinases.  Serine/threonine
           kinases (STKs), Nak1 subfamily, catalytic (c) domain.
           STKs catalyze the transfer of the gamma-phosphoryl group
           from ATP to serine/threonine residues on protein
           substrates. The Nak1 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. This subfamily is composed of
           Schizosaccharomyces pombe Nak1, Saccharomyces cerevisiae
           Kic1p (kinase that interacts with Cdc31p) and related
           proteins. Nak1 (also known as N-rich kinase 1), is
           required by fission yeast for polarizing the tips of
           actin cytoskeleton and is involved in cell growth, cell
           separation, cell morphology and cell-cycle progression.
           Kic1p is required by budding yeast for cell integrity
           and morphogenesis. Kic1p interacts with Cdc31p, the
           yeast homologue of centrin, and phosphorylates
           substrates in a Cdc31p-dependent manner.
          Length = 277

 Score = 28.2 bits (63), Expect = 3.0
 Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 11/65 (16%)

Query: 42  CVIFREVLLKISSWEKVNL--------PLYVESQGTSKFRSFGKGDIFNAGSVSRITRHT 93
            VI REVL+ +    KV +         + V + G  K   FG   + N  S  R    T
Sbjct: 104 SVIIREVLVALKYIHKVGVIHRDIKAANILVTNTGNVKLCDFGVAALLNQNSSKRS---T 160

Query: 94  FAMTP 98
           F  TP
Sbjct: 161 FVGTP 165


>gnl|CDD|240310 PTZ00200, PTZ00200, cysteine proteinase; Provisional.
          Length = 448

 Score = 27.4 bits (61), Expect = 5.4
 Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 1/37 (2%)

Query: 123 LRSLEPKTKVSAIATFPLTVKNFMEKHLKDP-YEINL 158
            R L P  KV   +       +F  +H+ +P Y  NL
Sbjct: 181 FRKLFPVIKVPPKSNSTSHNNDFKARHVSNPTYLKNL 217


>gnl|CDD|233603 TIGR01862, N2-ase-Ialpha, nitrogenase component I, alpha chain.
           This model represents the alpha chain of all three
           varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of
           nitrogenase [Central intermediary metabolism, Nitrogen
           fixation].
          Length = 443

 Score = 27.4 bits (61), Expect = 5.6
 Identities = 8/46 (17%), Positives = 16/46 (34%)

Query: 146 MEKHLKDPYEINLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKCC 191
            EK +   Y++N++ E  + G         E   +  + T      
Sbjct: 184 REKEITTEYDVNIIGEYNIGGDAWVMRIYLEEMGIQVVATFTGDGT 229


>gnl|CDD|234243 TIGR03523, GldN, gliding motility associated protien GldN.
          Members of this protein family are exclusive to the
          Bacteroidetes phylum (previously
          Cytophaga-Flavobacteria-Bacteroides). GldN is a protein
          linked to a type of rapid surface gliding motility
          found in certain Bacteroidetes, such as Flavobacterium
          johnsoniae and Cytophaga hutchinsonii. Knockouts of
          GldN abolish the gliding phenotype. Gliding motility
          appears closely linked to chitin utilization in the
          model species Flavobacterium johnsoniae. Bacteroidetes
          with members of this protein also include those which
          are not believed to express the gliding phenotype, such
          as Prevotella intermedia and Porphyromonas gingivales.
          Length = 280

 Score = 27.0 bits (60), Expect = 5.9
 Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 4/33 (12%)

Query: 43 VIFREVLLKISSWEKVNLPLYVESQGTSKFRSF 75
          V++R + L+    EK+NLPLY  +      RS 
Sbjct: 61 VVWRRIDLR----EKINLPLYYPTDPVGDRRSL 89


  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    0.138    0.404 

Gapped
Lambda     K      H
   0.267   0.0652    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,730,072
Number of extensions: 884812
Number of successful extensions: 784
Number of sequences better than 10.0: 1
Number of HSP's gapped: 784
Number of HSP's successfully gapped: 12
Length of query: 200
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 108
Effective length of database: 6,857,034
Effective search space: 740559672
Effective search space used: 740559672
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: 56 (25.5 bits)