RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10734
         (169 letters)



>gnl|CDD|185494 PTZ00168, PTZ00168, mitochondrial carrier protein; Provisional.
          Length = 259

 Score = 78.8 bits (194), Expect = 3e-18
 Identities = 51/158 (32%), Positives = 77/158 (48%), Gaps = 23/158 (14%)

Query: 2   GASAGVVVDVVLYPLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAAISSPIQGGVFFLTYD 61
           GA +GV+VD VLYP+D+IKT +Q++  F  S   K +Y G+ P  + +      F+  Y+
Sbjct: 10  GALSGVIVDAVLYPIDSIKTNIQAKKSFSFS-DIKKLYSGILPTLVGTVPASAFFYCFYE 68

Query: 62  GIKTFNSKYLNGHANLQLPLPLVHIMSASCAEAITCVVRVPTEIIKQRRQASMKNKTAFN 121
                 SK L       +    ++++S S AE   C+VR+P EI+KQ  Q S  N +   
Sbjct: 69  -----LSKKLLTEYRENISKTNLYLISTSIAEITACIVRLPFEIVKQNMQVS-GNISVLK 122

Query: 122 IVYSAIQQED----------------IPFSVIQFPIWE 143
            +Y   Q+E                 IPF  IQ+ +WE
Sbjct: 123 TIYEITQREGLPSFLGKSYFVMIVREIPFDCIQYFLWE 160


>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein. 
          Length = 96

 Score = 67.3 bits (165), Expect = 2e-15
 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 15/81 (18%)

Query: 1  AGASAGVVVDVVLYPLDTIKTRLQSQYGF---------------WRSGGFKAIYKGLGPA 45
          AG  AG +   V YPLD +KTRLQS                   ++  G + +YKGL P 
Sbjct: 11 AGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIYKEEGIRGLYKGLLPN 70

Query: 46 AISSPIQGGVFFLTYDGIKTF 66
           +       ++F TY+ +K  
Sbjct: 71 LLRVAPAAAIYFGTYETLKKL 91



 Score = 33.8 bits (78), Expect = 0.009
 Identities = 18/91 (19%), Positives = 29/91 (31%), Gaps = 20/91 (21%)

Query: 82  PLVHIMSASCAEAITCVVRVPTEIIKQRRQ-----ASMKNKTAFNIVYSAIQQE------ 130
            L  +++   A AI   V  P +++K R Q      S K K   +      ++E      
Sbjct: 5   FLASLLAGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIYKEEGIRGLY 64

Query: 131 ---------DIPFSVIQFPIWEYSMKSYTSY 152
                      P + I F  +E   K     
Sbjct: 65  KGLLPNLLRVAPAAAIYFGTYETLKKLLLKK 95


>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
           Provisional.
          Length = 300

 Score = 35.1 bits (81), Expect = 0.010
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 16/81 (19%)

Query: 1   AGASAGVVVDVVLYPLDTIKTRLQSQYG----------------FWRSGGFKAIYKGLGP 44
           +G  AG    +++YPLD  +TRL S  G                  +  GF ++Y+G G 
Sbjct: 119 SGGLAGASSLLIVYPLDFARTRLASDIGKGGDREFTGLFDCLMKISKQTGFLSLYQGFGV 178

Query: 45  AAISSPIQGGVFFLTYDGIKT 65
           +     +  G +F  YD  K 
Sbjct: 179 SVQGIIVYRGAYFGLYDSAKA 199


>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
           metabolism].
          Length = 750

 Score = 30.0 bits (68), Expect = 0.72
 Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 1/27 (3%)

Query: 12  VLYPLDTIKTRLQSQYGFWRSGGFKAI 38
           VLYP D+ + RL+ +Y F  S G + I
Sbjct: 227 VLYPGDSKELRLKQEY-FLGSAGVQDI 252


>gnl|CDD|218700 pfam05697, Trigger_N, Bacterial trigger factor protein (TF).  In
           the E. coli cytosol, a fraction of the newly synthesised
           proteins requires the activity of molecular chaperones
           for folding to the native state. The major chaperones
           implicated in this folding process are the
           ribosome-associated Trigger Factor (TF), and the DnaK
           and GroEL chaperones with their respective
           co-chaperones. Trigger Factor is an ATP-independent
           chaperone and displays chaperone and
           peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
           in vitro. It is composed of at least three domains, an
           N-terminal domain which mediates association with the
           large ribosomal subunit, a central substrate binding and
           PPIase domain with homology to FKBP proteins, and a
           C-terminal domain of unknown function. The positioning
           of TF at the peptide exit channel, together with its
           ability to interact with nascent chains as short as 57
           residues renders TF a prime candidate for being the
           first chaperone that binds to the nascent polypeptide
           chains. This family represents the N-terminal region of
           the protein.
          Length = 145

 Score = 27.5 bits (62), Expect = 2.6
 Identities = 6/37 (16%), Positives = 19/37 (51%), Gaps = 4/37 (10%)

Query: 100 RVPTEIIKQRRQASMKNKTAFNIV----YSAIQQEDI 132
           +VP  ++K+R    +  +   +++      A+++E +
Sbjct: 48  KVPRSVVKKRYGKEIYQEALEDLLQEAYEEALKEEKL 84


>gnl|CDD|173361 PTZ00066, PTZ00066, pyruvate kinase; Provisional.
          Length = 513

 Score = 28.2 bits (63), Expect = 2.6
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 75  ANLQLPLPLVHIMSASCAEAITCV 98
           AN + P+  V+IM+  C EA TC+
Sbjct: 353 ANGKFPVEAVNIMAKICFEAETCI 376


>gnl|CDD|222850 PHA02126, PHA02126, hypothetical protein.
          Length = 153

 Score = 27.6 bits (61), Expect = 2.7
 Identities = 12/45 (26%), Positives = 21/45 (46%)

Query: 7   VVVDVVLYPLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAAISSPI 51
           V++     PL  I+  L S+ GF +S  F A Y     + + + +
Sbjct: 98  VIIFNTQTPLTDIRIALYSKTGFSKSTEFTAYYVRYKESTMRNLV 142


>gnl|CDD|145308 pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29). 
          Length = 404

 Score = 26.8 bits (60), Expect = 5.9
 Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 3/40 (7%)

Query: 101 VPTEIIKQRRQASMKNKTAFNIVYSAIQQEDIPFSVIQFP 140
           V  E I   ++A      A     SA     + + V+ +P
Sbjct: 110 VDPERIAAYQKA---RGPALKPRRSATMSNKVSWCVVAYP 146


>gnl|CDD|176055 cd08410, C2B_Synaptotagmin-17, C2 domain second repeat present in
           Synaptotagmin 17.  Synaptotagmin is a
           membrane-trafficking protein characterized by a
           N-terminal transmembrane region, a linker, and 2
           C-terminal C2 domains. Synaptotagmin 17 is located in
           the brain, kidney, and prostate and is thought to be a
           peripheral membrane protein. Previously all
           synaptotagmins were thought to be calcium sensors in the
           regulation of neurotransmitter release and hormone
           secretion, but it has been shown that not all of them
           bind calcium.  Of the 17 identified synaptotagmins only
           8 bind calcium (1-3, 5-7, 9, 10).  The function of the
           two C2 domains that bind calcium are: regulating the
           fusion step of synaptic vesicle exocytosis (C2A) and
           binding to phosphatidyl-inositol-3,4,5-triphosphate
           (PIP3) in the absence of calcium ions and to
           phosphatidylinositol bisphosphate (PIP2) in their
           presence (C2B).  C2B also regulates also the recycling
           step of synaptic vesicles.  C2 domains fold into an
           8-standed beta-sandwich that can adopt 2 structural
           arrangements: Type I and Type II, distinguished by a
           circular permutation involving their N- and C-terminal
           beta strands. Many C2 domains are Ca2+-dependent
           membrane-targeting modules that bind a wide variety of
           substances including bind phospholipids, inositol
           polyphosphates, and intracellular proteins.  Most C2
           domain proteins are either signal transduction enzymes
           that contain a single C2 domain, such as protein kinase
           C, or membrane trafficking proteins which contain at
           least two C2 domains, such as synaptotagmin 1.  However,
           there are a few exceptions to this including RIM
           isoforms and some splice variants of piccolo/aczonin and
           intersectin which only have a single C2 domain.  C2
           domains with a calcium binding region have negatively
           charged residues, primarily aspartates, that serve as
           ligands for calcium ions. This cd contains the second C2
           repeat, C2B, and has a type-I topology.
          Length = 135

 Score = 26.0 bits (57), Expect = 7.3
 Identities = 11/54 (20%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 104 EIIKQRRQASMKNKT--AFNIVYS-AIQQEDIPFSVIQFPIWEYSMKSYTSYTG 154
           ++IK ++ + M+      +N  +S  + QE++    + F ++ +++KS   + G
Sbjct: 48  KLIKTKKTSCMRGTIDPFYNESFSFKVPQEELENVSLVFTVYGHNVKSSNDFIG 101


>gnl|CDD|234309 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase.  This family of
           alanyl-tRNA synthetases is limited to the archaea, and
           is a subset of those sequences identified by the model
           pfam07973 covering the second additional domain (SAD) of
           alanyl and threonyl tRNA synthetases.
          Length = 902

 Score = 26.5 bits (59), Expect = 9.3
 Identities = 9/30 (30%), Positives = 18/30 (60%)

Query: 100 RVPTEIIKQRRQASMKNKTAFNIVYSAIQQ 129
            V  EI  +RR   M++ TA +++ +A ++
Sbjct: 580 EVKGEIDWERRLRLMRHHTATHVLLAAARR 609


  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
   0.321    0.136    0.409 

Gapped
Lambda     K      H
   0.267   0.0705    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,446,472
Number of extensions: 738487
Number of successful extensions: 548
Number of sequences better than 10.0: 1
Number of HSP's gapped: 543
Number of HSP's successfully gapped: 14
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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: 55 (25.0 bits)