RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy176
         (101 letters)



>gnl|CDD|111612 pfam02736, Myosin_N, Myosin N-terminal SH3-like domain.  This
          domain has an SH3-like fold. It is found at the
          N-terminus of many but not all myosins. The function of
          this domain is unknown.
          Length = 42

 Score = 39.8 bits (94), Expect = 4e-06
 Identities = 17/32 (53%), Positives = 20/32 (62%)

Query: 44 VWVPDPADGFVLGRILDLGMDEVTVQPLDSKK 75
          VWVPDP +GFV G I     D+VTV+  D K 
Sbjct: 4  VWVPDPKEGFVKGEIKSREGDKVTVKTEDGKT 35


>gnl|CDD|240361 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain;
           Provisional.
          Length = 494

 Score = 28.0 bits (63), Expect = 0.89
 Identities = 10/19 (52%), Positives = 13/19 (68%)

Query: 75  KPKAAFSLDRVYTAEEHDS 93
           KPK  FS+DRV+  E  D+
Sbjct: 356 KPKKYFSIDRVFRNETLDA 374


>gnl|CDD|234095 TIGR03030, CelA, cellulose synthase catalytic subunit
           (UDP-forming).  Cellulose synthase catalyzes the
           beta-1,4 polymerization of glucose residues in the
           formation of cellulose. In bacteria, the substrate is
           UDP-glucose. The synthase consists of two subunits (or
           domains in the frequent cases where it is encoded as a
           single polypeptide), the catalytic domain modelled here
           and the regulatory domain (pfam03170). The regulatory
           domain binds the allosteric activator cyclic di-GMP. The
           protein is membrane-associated and probably assembles
           into multimers such that the individual cellulose
           strands can self-assemble into multi-strand fibrils.
          Length = 713

 Score = 27.3 bits (61), Expect = 1.5
 Identities = 11/73 (15%), Positives = 22/73 (30%), Gaps = 2/73 (2%)

Query: 8   NLTWYT-SLISISVVVGAVDFESVVYKFKPYLMENQKVWVPDPADGFVLGRILDLGMDEV 66
            L W   +LI +   +  V  E    +  P +       V      +V   + D  +  +
Sbjct: 545 VLGWNLLNLILLGAALAVV-AERRQRRSSPRIPCKIPAEVQRDGGRWVEATVEDASVGGL 603

Query: 67  TVQPLDSKKPKAA 79
            ++      P   
Sbjct: 604 GIKINAQGAPGPQ 616


>gnl|CDD|217261 pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family,
          beta-barrel domain.  This family includes the ATP
          synthase alpha and beta subunits the ATP synthase
          associated with flagella.
          Length = 69

 Score = 25.6 bits (57), Expect = 2.1
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 9/60 (15%)

Query: 18 ISVVVGAV----DFESVVYKFKPYLMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDS 73
          I  V+G V         +      L    +V + +  +G +LG +L+LG D+V V  +  
Sbjct: 1  IVQVIGPVVDVEFGIGRLPG----LYNALEVELVEFGNG-LLGEVLNLGGDKVRVVVMGG 55


>gnl|CDD|202886 pfam04096, Nucleoporin2, Nucleoporin autopeptidase. 
          Length = 137

 Score = 26.0 bits (58), Expect = 2.8
 Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 2/33 (6%)

Query: 47 PDPAD--GFVLGRILDLGMDEVTVQPLDSKKPK 77
            P D  G  L +I+D G   V V P D  KP 
Sbjct: 38 LGPVDLSGIDLDKIVDFGPRSVEVYPDDENKPP 70


>gnl|CDD|226467 COG3958, COG3958, Transketolase, C-terminal subunit [Carbohydrate
           transport and metabolism].
          Length = 312

 Score = 25.3 bits (56), Expect = 6.9
 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 13/55 (23%)

Query: 50  ADGFVLGRIL-------DLGMD-EV----TVQPLDSK-KPKAAFSLDRVYTAEEH 91
           A G ++   L         G+   V    T++P+D +   KAA    R+ TAEEH
Sbjct: 199 ATGVMVAEALEAAEILKKEGISAAVINMFTIKPIDEQAILKAARETGRIVTAEEH 253


>gnl|CDD|239099 cd02418, Peptidase_C39B, A sub-family of peptidase family C39.
           Peptidase family C39 mostly contains
           bacteriocin-processing endopeptidases from bacteria. The
           cysteine peptidases in family C39 cleave the
           "double-glycine" leader peptides from the precursors of
           various bacteriocins (mostly non-lantibiotic). The
           cleavage is mediated by the transporter as part of the
           secretion process. Bacteriocins are antibiotic proteins
           secreted by some species of bacteria that inhibit the
           growth of other bacterial species. The bacteriocin is
           synthesized as a precursor with an N-terminal leader
           peptide, and processing involves removal of the leader
           peptide by cleavage at a Gly-Gly bond, followed by
           translocation of the mature bacteriocin across the
           cytoplasmic membrane. Most endopeptidases of family C39
           are N-terminal domains in larger proteins (ABC
           transporters) that serve both functions. The proposed
           protease active site is conserved in this sub-family.
          Length = 136

 Score = 24.9 bits (55), Expect = 7.6
 Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 5/25 (20%)

Query: 30  VVYKFKPYLMENQKVWVPDPADGFV 54
           VVYK K      +K+ + DPA G  
Sbjct: 94  VVYKIK-----KKKILIADPAVGIT 113


  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
   0.315    0.134    0.391 

Gapped
Lambda     K      H
   0.267   0.0787    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,186,794
Number of extensions: 439182
Number of successful extensions: 278
Number of sequences better than 10.0: 1
Number of HSP's gapped: 278
Number of HSP's successfully gapped: 19
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 53 (24.1 bits)