RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6190
         (87 letters)



>gnl|CDD|233147 TIGR00840, b_cpa1, sodium/hydrogen exchanger 3.  The Monovalent
           Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36)The
           CPA1 family is a large family of proteins derived from
           Gram-positive and Gram-negative bacteria, blue green
           bacteria, yeast, plants and animals.Transporters from
           eukaryotes have been functionally characterized, and all
           of these catalyze Na+:H+ exchange. Their primary
           physiological functions may be in(1) cytoplasmic pH
           regulation, extruding the H+ generated during
           metabolism, and (2) salt tolerance (in plants), due to
           Na+ uptake into vacuoles.This model is specific for the
           eukaryotic members members of this family [Transport and
           binding proteins, Cations and iron carrying compounds].
          Length = 559

 Score = 76.4 bits (188), Expect = 5e-18
 Identities = 29/45 (64%), Positives = 38/45 (84%)

Query: 1   MKNYVEANISHKSHTTVKYAMKMLSSSSETIIFMFLGISTISDAH 45
           MK YVEAN+S +S TT+KY MKMLSS SET+IF+FLG+S +++ H
Sbjct: 272 MKKYVEANMSRRSQTTIKYFMKMLSSLSETLIFIFLGVSLVTENH 316


>gnl|CDD|181661 PRK09124, PRK09124, pyruvate dehydrogenase; Provisional.
          Length = 574

 Score = 29.6 bits (67), Expect = 0.14
 Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 6/37 (16%)

Query: 38  ISTISDAHVCWTCDVDRPYKYVIEEVWTVRLTSMNGR 74
           IS  +     +TCDV  P       VW  R   MNG+
Sbjct: 368 ISEFAADDAIFTCDVGTP------TVWAARYLKMNGK 398


>gnl|CDD|185677 cd00817, ValRS_core, catalytic core domain of valyl-tRNA
           synthetases.  Valine amino-acyl tRNA synthetase (ValRS)
           catalytic core domain. This enzyme is a monomer which
           aminoacylates the 2'-OH of the nucleotide at the 3' of
           the appropriate tRNA. The core domain is based on the
           Rossman fold and is responsible for the ATP-dependent
           formation of the enzyme bound aminoacyl-adenylate. It
           contains the characteristic class I HIGH and KMSKS
           motifs, which are involved in ATP binding.  ValRS has an
           insertion in the core domain, which is subject to both
           deletions and rearrangements. This editing region
           hydrolyzes mischarged cognate tRNAs and thus prevents
           the incorporation of chemically similar amino acids.
          Length = 382

 Score = 28.4 bits (64), Expect = 0.42
 Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 2/33 (6%)

Query: 39  STISDAHVCWTCDVDRPYKYVIEEVWTVRLTSM 71
           + ISD  VC         + +++  W V++  +
Sbjct: 148 TAISDIEVCSRSGD--VIEPLLKPQWFVKVKDL 178


>gnl|CDD|216235 pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family.  Na/H
           antiporters are key transporters in maintaining the pH
           of actively metabolising cells. The molecular mechanisms
           of antiport are unclear. These antiporters contain 10-12
           transmembrane regions (M) at the amino-terminus and a
           large cytoplasmic region at the carboxyl terminus. The
           transmembrane regions M3-M12 share identity with other
           members of the family. The M6 and M7 regions are highly
           conserved. Thus, this is thought to be the region that
           is involved in the transport of sodium and hydrogen
           ions. The cytoplasmic region has little similarity
           throughout the family.
          Length = 370

 Score = 26.0 bits (58), Expect = 2.7
 Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 8/41 (19%)

Query: 1   MKNYVEAN-ISHKSHTTVKYAMKMLSSSSETIIFMFLGIST 40
           + NY  AN +S K                  + F+ +G+S 
Sbjct: 244 LSNYAFANELSEKLE-------PFGYGLFLPLFFVSVGLSL 277


>gnl|CDD|220758 pfam10443, RNA12, RNA12 protein.  This family includes RNA12 from
           S. cerevisiae. That protein contains an RRM domain. This
           region is C-terminal to that and includes a P-loop motif
           suggesting this region binds to NTP. The RNA12 proteins
           is involved in pre-rRNA maturation.
          Length = 428

 Score = 25.7 bits (57), Expect = 3.8
 Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 12  KSHTTVKYAM-KMLSSSSETIIFMFLGISTISDAHVCWT 49
           KS  + + A+  ++S ++  I+ MFLG S    + + WT
Sbjct: 280 KSGESPEEAVSDIISQAASEILKMFLGDSKGGASDLKWT 318


>gnl|CDD|233149 TIGR00845, caca, sodium/calcium exchanger 1.  The Ca2+:Cation
          Antiporter (CaCA) Family (TC 2.A.19)Proteins of the
          CaCA family are found ubiquitously, having been
          identified in animals, plants, yeast, archaea and
          widely divergent bacteria.All of the characterized
          animal proteins catalyze Ca2+:Na+ exchange although
          some also transport K+. The NCX1 plasma membrane
          protein exchanges 3 Na+ for 1 Ca2+. The E. coli ChaA
          protein catalyzes Ca2+:H+ antiport but may also
          catalyze Na+:H+ antiport. All remaining
          well-characterized members of the family catalyze
          Ca2+:H+ exchange.This model is specific for the
          eukaryotic sodium ion/calcium ion exchangers of the
          Caca family [Transport and binding proteins, Other].
          Length = 928

 Score = 25.1 bits (55), Expect = 6.2
 Identities = 7/13 (53%), Positives = 12/13 (92%)

Query: 31 IIFMFLGISTISD 43
          +++MFLG+S I+D
Sbjct: 82 MVYMFLGVSIIAD 94


>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
           regulator (CFTR).  The model describes the cystis
           fibrosis transmembrane conductor regulator (CFTR) in
           eukaryotes. The principal role of this protein is
           chloride ion conductance. The protein is predicted to
           consist of 12 transmembrane domains. Mutations or
           lesions in the genetic loci have been linked to the
           aetiology of asthma, bronchiectasis, chronic obstructive
           pulmonary disease etc. Disease-causing mutations have
           been studied by 36Cl efflux assays in vitro cell
           cultures and electrophysiology, all of which point to
           the impairment of chloride channel stability and not the
           biosynthetic processing per se [Transport and binding
           proteins, Anions].
          Length = 1490

 Score = 24.5 bits (53), Expect = 9.4
 Identities = 8/37 (21%), Positives = 21/37 (56%)

Query: 3   NYVEANISHKSHTTVKYAMKMLSSSSETIIFMFLGIS 39
           NYV+   ++ S   V+  + +  +S+  I ++++G +
Sbjct: 899 NYVDQQHANASSPDVQKPVIITPTSAYYIFYIYVGTA 935


  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    0.127    0.385 

Gapped
Lambda     K      H
   0.267   0.0756    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,979,401
Number of extensions: 289862
Number of successful extensions: 216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 216
Number of HSP's successfully gapped: 10
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
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 (21.9 bits)
S2: 53 (24.1 bits)