RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3908
         (170 letters)



>gnl|CDD|221744 pfam12736, CABIT, Cell-cycle sustaining, positive selection,.  The
           'CABIT' domain (for 'cysteine-containing, all- in
           Themis') is found in a newly identified gene family that
           has three mammalian homologues (Themis, Icb1 and
           9130404H23Rik) that encode proteins with two CABIT
           domains and a highly conserved proline-rich region. In
           contrast, Fam59A, Fam59B and related proteins from
           mammals to cnidarians, including the insect Serrano
           proteins, have a single copy of the CABIT domain, a
           proline-rich region and often a C-terminal SAM
           (sterile-motif) domain. Multiple-sequence alignment has
           predicted that the CABIT domain adopts an all-strand
           structure with at least 12 strands, ie a dyad of
           six-stranded beta-barrel units. The CABIT domain
           contains a nearly absolutely conserved cysteine residue
           which is likely to be central to its function. CABIT
           domain proteins function downstream of tyrosine kinase
           signalling and interact with GRB2.
          Length = 251

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 40/131 (30%), Positives = 61/131 (46%), Gaps = 16/131 (12%)

Query: 30  LPTVVKIIKGQYGNLGVPTLPSPGLQSTVLLVSAGKRQKIIAQAVKLKEGRRFVGVGSRI 89
           LP VVK+  G+Y   GV  L        +LL S  + +K++A+ V+ + GR    VG ++
Sbjct: 1   LPQVVKVTSGEYFEGGVYLLKGQ----ELLLHSGDRIKKVVARCVEREGGR----VGPKL 52

Query: 90  DIPENYPGYFELLSEEGKSMRCCETVLEISRRKIEAGCLIREAIKGIVAKYDEEGNLQSD 149
            IP +YPG F+LL  +    R  E+V E+  R      L+ E I+            Q  
Sbjct: 53  LIPLSYPGKFKLLPRD----RSFESVEELLARVFPGRVLVTEDIRTSSDLSSSSDVDQ-- 106

Query: 150 GARIVNIGEVL 160
              +V  G+ L
Sbjct: 107 --ILVPAGDEL 115


>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
           transport and metabolism].
          Length = 428

 Score = 28.7 bits (65), Expect = 1.5
 Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 1   MATD-GQILLATAKWSDEGQYLREFVSKNSLPTVVKIIKGQYGNLGVPTLPSPGLQSTVL 59
           + +D  ++LLA      +   +      +    V  ++  +    G P  P  G   T  
Sbjct: 301 LESDLVELLLAAVDGKLDEVEILF---WDKGAAVGVVLAAE----GYPGDPEKGDVITGD 353

Query: 60  LVSAGKRQKIIAQAVKLKEGRRFVGVGSR 88
             +  +  K+    VKL +G + V  G R
Sbjct: 354 EEAEEEGAKVFHAGVKLDDGGQLVTSGGR 382


>gnl|CDD|163561 TIGR03849, arch_ComA, phosphosulfolactate synthase.  This model
           finds the ComA (Coenzyme M biosynthesis A) protein,
           phosphosulfolactate synthase, in methanogenic archaea.
           The ComABC pathway is one of at least two pathways to
           the intermediate sulfopyruvate. Coenzyme M occurs rarely
           and sporadically outside of the archaea, as for expoxide
           metabolism in Xanthobacter autotrophicus Py2, but
           candidate phosphosulfolactate synthases from that and
           other species occur fall below the cutoff and outside
           the scope of this model. This model deliberately is
           narrower in scope than pfam02679 [Biosynthesis of
           cofactors, prosthetic groups, and carriers, Other,
           Energy metabolism, Methanogenesis].
          Length = 237

 Score = 27.4 bits (61), Expect = 3.6
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 12/62 (19%)

Query: 99  FELLSEEGKSMRCCETVLEISRR------KIEAGC---LI--REAIKGIVAKYDEEGNLQ 147
           F +LSE GK     ++ L    R       +EAG    +I  RE+ K I   +DE+GN++
Sbjct: 114 FMVLSEVGKKSPEKDSELTPDDRIKLINKDLEAGADYVIIEGRESGKNI-GLFDEKGNVK 172

Query: 148 SD 149
            D
Sbjct: 173 ED 174


>gnl|CDD|188022 TIGR00095, TIGR00095, RNA methyltransferase, RsmD family.  This
          model represents a family of uncharacterized bacterial
          proteins. Members are present in nearly every complete
          bacterial genome, always in a single copy. PSI-BLAST
          analysis shows homology to several families of
          SAM-dependent methyltransferases, including ribosomal
          RNA adenine dimethylases [Protein synthesis, tRNA and
          rRNA base modification].
          Length = 190

 Score = 27.0 bits (60), Expect = 3.9
 Identities = 9/28 (32%), Positives = 13/28 (46%)

Query: 34 VKIIKGQYGNLGVPTLPSPGLQSTVLLV 61
          ++II GQY    +   P P  + T   V
Sbjct: 10 IRIIGGQYRGRKLKVPPGPSTRPTTDRV 37


>gnl|CDD|221489 pfam12252, SidE, Dot/Icm substrate protein.  This family of
           proteins is found in bacteria. Proteins in this family
           are typically between 397 and 1543 amino acids in
           length. This family is the SidE protein in the Dot/Icm
           pathway of Legionella pneumophila bacteria. There is
           little literature describing the family.
          Length = 1443

 Score = 27.5 bits (61), Expect = 5.0
 Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 3/34 (8%)

Query: 68  KIIAQAVKLKEGRRFVGVGSRIDIPE---NYPGY 98
           K   Q  KLKE  RF+ V   + +PE    +PG 
Sbjct: 499 KFFPQTYKLKENERFMRVDEFLKLPEVQSTFPGS 532


>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
          recombination, and repair].
          Length = 187

 Score = 26.8 bits (60), Expect = 5.0
 Identities = 8/24 (33%), Positives = 13/24 (54%)

Query: 34 VKIIKGQYGNLGVPTLPSPGLQST 57
          ++II G+Y    + T   PG + T
Sbjct: 2  MRIIGGKYKGRKLKTPDGPGTRPT 25


>gnl|CDD|235610 PRK05788, PRK05788, cobalamin biosynthesis protein CbiG; Validated.
          Length = 315

 Score = 26.4 bits (59), Expect = 9.2
 Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 18/92 (19%)

Query: 74  VKLKEGRRFVGVGSRIDIPENYPGYFELLSEEGKSMRCCETVLEISRRKIEAGCLIREAI 133
           VKL+     +G+G R  +        E ++E  +  R  E  L I  R +       +AI
Sbjct: 188 VKLRPKNVVLGIGCRKGVS------AEEIAEAVE--RALEA-LNIDPRAV-------KAI 231

Query: 134 KGIVAKYDEEGNLQSDGARIVNIGEVLLPKSE 165
             I  K DE G LQ   A  + +  +   K E
Sbjct: 232 ASITLKKDEPGLLQ--LAEELGVPFITFSKEE 261


>gnl|CDD|200548 cd10922, CE4_PelA_like_C, C-terminal Putative NodB-like catalytic
          domain of PelA-like uncharacterized hypothetical
          proteins found in bacteria.  This family is represented
          by a protein PelA of unknown function that is encoded
          by a gene in the pelA-G gene cluster for pellicle
          production and biofilm formation in Pseudomonas
          aeruginosa. PelA and most of the family members contain
          a domain of unknown function, DUF297, in the N-terminus
          and a C-terminal domain that shows high sequence
          similarity to the catalytic domain of the six-stranded
          barrel rhizobial NodB-like proteins, which remove
          N-linked or O-linked acetyl groups from cell wall
          polysaccharides and belong to the larger carbohydrate
          esterase 4 (CE4) superfamily.
          Length = 266

 Score = 26.1 bits (58), Expect = 9.4
 Identities = 13/31 (41%), Positives = 17/31 (54%)

Query: 19 QYLREFVSKNSLPTVVKIIKGQYGNLGVPTL 49
            LRE + K  LPT V +I+G+    G P L
Sbjct: 30 VLLREILEKYPLPTTVSVIEGELDPDGYPKL 60


  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    0.136    0.383 

Gapped
Lambda     K      H
   0.267   0.0668    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,732,867
Number of extensions: 815931
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 571
Number of HSP's successfully gapped: 13
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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: 42 (22.0 bits)
S2: 55 (25.1 bits)