RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7944
         (231 letters)



>gnl|CDD|221571 pfam12423, KIF1B, Kinesin protein 1B.  This domain family is
          found in eukaryotes, and is approximately 50 amino
          acids in length. The family is found in association
          with pfam00225, pfam00498. KIF1B is an anterograde
          motor for transport of mitochondria in axons of
          neuronal cells.
          Length = 42

 Score = 48.7 bits (117), Expect = 2e-08
 Identities = 15/47 (31%), Positives = 19/47 (40%), Gaps = 6/47 (12%)

Query: 40 RQRLEMMREMYHNEAEMSPTSPDYNIESLTGGDPFYDRFPWFRLVGR 86
            RL +MREMY N  E          +     DPFY+      L+G 
Sbjct: 2  ENRLFLMREMYQNYDE------PEYSQHFKEEDPFYEPPENHSLIGV 42


>gnl|CDD|203377 pfam06018, CodY, CodY GAF-like domain.  This domain is a GAF-like
           domain found at the N-terminus of several bacterial
           GTP-sensing transcriptional pleiotropic repressor CodY
           proteins. Presumably this domain is involved in GTP
           binding. CodY has been found to repress the dipeptide
           transport operon (dpp) of Bacillus subtilis in
           nutrient-rich conditions. The CodY protein also has a
           repressor effect on many genes in Lactococcus lactis
           during growth in milk.
          Length = 177

 Score = 28.0 bits (63), Expect = 3.5
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 7/48 (14%)

Query: 169 EENPPCTSSMYAFPEENGLWFPEKLTYL-------DKIGTVLKLRLQE 209
             N P  S +  FP EN   FP  LT +       +++GT++  R+ +
Sbjct: 85  SANLPIDSELTVFPVENKELFPNGLTTIVPIYGGGERLGTLILARVDK 132


>gnl|CDD|240529 cd13124, MATE_SpoVB_like, Stage V sporulation protein B, also known
           as Stage III sporulation protein F, and related
           proteins.  The integral membrane protein SpoVB has been
           implicated in the biosynthesis of the peptidoglycan
           component of the spore cortex in Bacillus subtilis. This
           model represents a subfamily of the multidrug and toxic
           compound extrusion (MATE)-like proteins. Proteins from
           the MATE family are involved in exporting metabolites
           across the cell membrane and are often responsible for
           multidrug resistance (MDR).
          Length = 434

 Score = 28.2 bits (64), Expect = 4.5
 Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 15/60 (25%)

Query: 74  FYDRFPWFRLVGRAFVYLSNLMYPI------------PL-IQK-VAIVNEKGDVKGHLKI 119
            Y R P   ++G   + L  + YPI            P+ I K VA  N  GD KG  +I
Sbjct: 16  IY-RIPLQNIIGDEGMGLYQMAYPIYGIFLTLATAGIPVAISKLVAEYNALGDYKGARRI 74


>gnl|CDD|131834 TIGR02787, codY_Gpos, GTP-sensing transcriptional pleiotropic
           repressor CodY.  This model represents the full length
           of CodY, a pleiotropic repressor in Bacillus subtilis
           and other Firmicutes (low-GC Gram-positive bacteria)
           that responds to intracellular levels of GTP and
           branched chain amino acids. The C-terminal
           helix-turn-helix DNA-binding region is modeled by
           pfam08222 in Pfam [Regulatory functions, DNA
           interactions].
          Length = 251

 Score = 27.8 bits (62), Expect = 4.9
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 10/66 (15%)

Query: 154 NKKAVEDSGHQGDKVEE---NPPCTSSMYAFPEENGLWFPEKLTYL-------DKIGTVL 203
           ++K  E+       + +   N P  S +  FPEE+   FP+ LT +       +++GT++
Sbjct: 66  DRKFPEEYNSALMMIYDTEANIPVDSELTVFPEESRDLFPKGLTTIVPIYGGGERLGTLI 125

Query: 204 KLRLQE 209
             R  +
Sbjct: 126 LARSDK 131


>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
          glucokinase family.  This model represents a subfamily
          of proteins that includes thermoresistant and
          thermosensitve isozymes of gluconate kinase
          (gluconokinase) in E. coli and other related proteins;
          members of this family are often named by similarity to
          the thermostable isozyme. These proteins show homology
          to shikimate kinases and adenylate kinases but not to
          gluconate kinases from the FGGY family of carbohydrate
          kinases.
          Length = 163

 Score = 27.0 bits (60), Expect = 6.3
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 2/29 (6%)

Query: 61 PDYNIESLTGGDPFYD--RFPWFRLVGRA 87
          P  NIE ++ G P  D  R+PW + +  A
Sbjct: 34 PAANIEKMSAGIPLNDDDRWPWLQNLNDA 62


>gnl|CDD|223822 COG0751, GlyS, Glycyl-tRNA synthetase, beta subunit [Translation,
           ribosomal structure and biogenesis].
          Length = 691

 Score = 27.2 bits (61), Expect = 8.2
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 2/63 (3%)

Query: 83  LVGRAFVYLSNLMYPIPLIQKVAIVNEKG--DVKGHLKIAVQIVTDEESTDLTGTVKQSA 140
            +GR   YL +  Y   +I  V  +N     D+    +   + +   E+  L    K+ +
Sbjct: 529 FLGRLRTYLQDEGYRKDIIDAVLALNPTDLLDIIARAEALQEFLDLPEAKALAAANKRVS 588

Query: 141 RII 143
            I+
Sbjct: 589 NIL 591


>gnl|CDD|221779 pfam12803, G-7-MTase, mRNA (guanine-7-)methyltransferase
           (G-7-MTase).  The Sendai virus RNA-dependent RNA
           polymerase complex, which consists of L and P proteins,
           participates in the synthesis of viral mRNAs that
           possess a methylated cap structure. The N-terminal of
           the L protein acts as the RNA-dependent RNA polymerase
           part of the molecule, family Paramyx_RNA_pol, pfam00946.
           This domain is the C-terminal part of the L protein and
           it catalyzes cap methylation through its mRNA
           (guanine-7-)methyltransferase (G-7-MTase) activity.
          Length = 320

 Score = 27.2 bits (61), Expect = 8.6
 Identities = 5/32 (15%), Positives = 15/32 (46%)

Query: 37  LPSRQRLEMMREMYHNEAEMSPTSPDYNIESL 68
           L   ++  ++ +   +EA+  P+   +N+   
Sbjct: 136 LTPIEKCAVLTDYLESEAQEDPSGLSWNLSPP 167


>gnl|CDD|130804 TIGR01743, purR_Bsub, pur operon repressor, Bacillus subtilis type.
            This model represents the puring operon repressor PurR
           of low-GC Gram-positive bacteria. This homodimeric
           repressor contains a large region homologous to
           phosphoribosyltransferases and is inhibited by
           5-phosphoribosyl 1-pyrophosphate [Purines, pyrimidines,
           nucleosides, and nucleotides, Purine ribonucleotide
           biosynthesis, Regulatory functions, DNA interactions].
          Length = 268

 Score = 27.1 bits (60), Expect = 8.8
 Identities = 4/26 (15%), Positives = 16/26 (61%)

Query: 82  RLVGRAFVYLSNLMYPIPLIQKVAIV 107
           R++   ++YL++++    ++ K+  +
Sbjct: 94  RILPGGYLYLTDILGKPSILSKIGKI 119


>gnl|CDD|226871 COG4465, CodY, Pleiotropic transcriptional repressor
           [Transcription].
          Length = 261

 Score = 26.6 bits (59), Expect = 9.9
 Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 7/47 (14%)

Query: 169 EENPPCTSSMYAFPEENGLWFPEKLTYLDKI-------GTVLKLRLQ 208
             N P  S +  FP EN   FP  LT +  I       GT++  RL 
Sbjct: 90  SANLPVDSELTIFPVENKDLFPNGLTTIVPIYGGGERLGTLILWRLD 136


  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
   0.320    0.138    0.419 

Gapped
Lambda     K      H
   0.267   0.0769    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,054,080
Number of extensions: 1122638
Number of successful extensions: 813
Number of sequences better than 10.0: 1
Number of HSP's gapped: 812
Number of HSP's successfully gapped: 13
Length of query: 231
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 137
Effective length of database: 6,768,326
Effective search space: 927260662
Effective search space used: 927260662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.7 bits)