RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14129
         (160 letters)



>gnl|CDD|217293 pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand
           binding domain.  This family is the extracellular ligand
           binding domain of these ion channels. This domain forms
           a pentameric arrangement in the known structure.
          Length = 215

 Score =  110 bits (278), Expect = 4e-31
 Identities = 39/101 (38%), Positives = 54/101 (53%)

Query: 38  KWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETYHIASSDGLIS 97
           +W D  L WDP+ YG I  + L   ++W+PD+  +N A G        T      DG + 
Sbjct: 56  QWTDERLAWDPEDYGGITSLRLPSDKIWKPDIVLYNKADGIHDITTPNTNVRVYPDGTVL 115

Query: 98  WVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDF 138
           W PP  ++  C +DLTY+PFD Q C L  GSW Y+G  +D 
Sbjct: 116 WSPPAIYKSSCPMDLTYFPFDQQNCSLKFGSWTYNGEEVDL 156


>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein.  The
           Ligand-gated Ion Channel (LIC) Family of
           Neurotransmitter Receptors TC 1.A.9)Members of the LIC
           family of ionotropic neurotransmitter receptors are
           found only in vertebrate and invertebrate animals. They
           exhibit receptor specificity for (1)acetylcholine, (2)
           serotonin, (3) glycine, (4) glutamate and (5)
           g-aminobutyric acid (GABA). All of these receptor
           channels are probably hetero- orhomopentameric. The best
           characterized are the nicotinic acetyl-choline receptors
           which are pentameric channels of a2bgd subunit
           composition. All subunits arehomologous. The three
           dimensional structures of the protein complex in both
           the open and closed configurations have been solved at
           0.9 nm resolution.The channel protein complexes of the
           LIC family preferentially transport cations or anions
           depending on the channel (e.g., the acetylcholine
           receptors are cationselective while glycine receptors
           are anion selective) [Transport and binding proteins,
           Cations and iron carrying compounds].
          Length = 459

 Score = 78.6 bits (194), Expect = 1e-17
 Identities = 38/135 (28%), Positives = 57/135 (42%), Gaps = 10/135 (7%)

Query: 13  HPVHRCTQTSLHSI----EKKVDQTLNF---KKWYDPVLQWDPKKYGDIKQIYLAPQEVW 65
            PV       L SI    EK +D T N    ++W D  LQW+P++Y  +  +      +W
Sbjct: 53  PPVTVSFNLFLRSIMDVDEKNMDYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDDSIW 112

Query: 66  QPDLSTFNSAGGNDVSPFGETYHI--ASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCE 123
            PD+  +N            T  +     +G + + P     + C +DL  +PFD Q C 
Sbjct: 113 VPDIFFYNEKDAR-FHGITMTNVLVRIHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCS 171

Query: 124 LILGSWVYDGNNIDF 138
           L   SW Y  N+I  
Sbjct: 172 LKFESWGYTTNDIKL 186


>gnl|CDD|224999 COG2088, SpoVG, Uncharacterized protein, involved in the regulation
           of septum location [Cell envelope biogenesis, outer
           membrane].
          Length = 95

 Score = 31.3 bits (71), Expect = 0.063
 Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 130 VYDGNNIDFLACPSRSMPLIRWARRDTIHPI 160
           V +GNN  F+A PSR  P   +  RD  HPI
Sbjct: 36  VIEGNNGLFVAMPSRRTPDGEF--RDIAHPI 64


>gnl|CDD|237321 PRK13259, PRK13259, regulatory protein SpoVG; Reviewed.
          Length = 94

 Score = 29.2 bits (66), Expect = 0.35
 Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 130 VYDGNNIDFLACPSRSMPLIRWARRDTIHPI 160
           V +GNN  F+A PS+  P   +  RD  HPI
Sbjct: 36  VIEGNNGLFIAMPSKRTPDGEF--RDIAHPI 64


>gnl|CDD|200486 cd11348, AmyAc_2, Alpha amylase catalytic domain found in an
           uncharacterized protein family.  The Alpha-amylase
           family comprises the largest family of glycoside
           hydrolases (GH), with the majority of enzymes acting on
           starch, glycogen, and related oligo- and
           polysaccharides. These proteins catalyze the
           transformation of alpha-1,4 and alpha-1,6 glucosidic
           linkages with retention of the anomeric center. The
           protein is described as having 3 domains: A, B, C. A is
           a (beta/alpha) 8-barrel; B is a loop between the beta 3
           strand and alpha 3 helix of A; C is the C-terminal
           extension characterized by a Greek key. The majority of
           the enzymes have an active site cleft found between
           domains A and B where a triad of catalytic residues
           (Asp, Glu and Asp) performs catalysis. Other members of
           this family have lost the catalytic activity as in the
           case of the human 4F2hc, or only have 2 residues that
           serve as the catalytic nucleophile and the acid/base,
           such as Thermus A4 beta-galactosidase with 2 Glu
           residues (GH42) and human alpha-galactosidase with 2 Asp
           residues (GH31). The catalytic triad (DED) is not
           present here. The family members are quite extensive and
           include: alpha amylase, maltosyltransferase,
           cyclodextrin glycotransferase, maltogenic amylase,
           neopullulanase, isoamylase, 1,4-alpha-D-glucan
           maltotetrahydrolase, 4-alpha-glucotransferase,
           oligo-1,6-glucosidase, amylosucrase, sucrose
           phosphorylase, and amylomaltase.
          Length = 429

 Score = 30.4 bits (69), Expect = 0.37
 Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 41  DPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETY----HIASSDGLI 96
           D +L +    Y  + +         + D   F+++G  D+ PF + Y          G I
Sbjct: 253 DFLLHFGGNGYNSLFRNLNTDGG-HRRDNCYFDASGKGDIKPFVDEYLPQYEATKGKGYI 311

Query: 97  S 97
           S
Sbjct: 312 S 312


>gnl|CDD|165102 PHA02735, PHA02735, putative DNA polymerase type B; Provisional.
          Length = 716

 Score = 28.1 bits (62), Expect = 2.7
 Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 8/61 (13%)

Query: 81  SPFGETYHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSWVYDGNNIDFLA 140
           S F E  H+         +P  +F+      L  W FD +    ILG+ VY+   IDF  
Sbjct: 557 SNFDENIHVPDDS-----LPESEFRKEAQDGLGAWDFDYEGDAFILGAGVYE---IDFDT 608

Query: 141 C 141
           C
Sbjct: 609 C 609


>gnl|CDD|173650 cd05094, PTKc_TrkC, Catalytic domain of the Protein Tyrosine
           Kinase, Tropomyosin Related Kinase C.  Protein Tyrosine
           Kinase (PTK) family; Tropomyosin Related Kinase C
           (TrkC); catalytic (c) domain. The PTKc family is part of
           a larger superfamily that includes the catalytic domains
           of other kinases such as protein serine/threonine
           kinases, RIO kinases, and phosphoinositide 3-kinase
           (PI3K). PTKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to tyrosine (tyr)
           residues in protein substrates. TrkC is a member of the
           Trk subfamily of proteins, which are receptor tyr
           kinases (RTKs) containing an extracellular region with
           arrays of leucine-rich motifs flanked by two
           cysteine-rich clusters followed by two
           immunoglobulin-like domains, a transmembrane segment,
           and an intracellular catalytic domain. Binding of TrkC
           to its ligand, neurotrophin 3 (NT3), results in receptor
           oligomerization and activation of the catalytic domain.
           TrkC is broadly expressed in the nervous system and in
           some non-neural tissues including the developing heart.
           NT3/TrkC signaling plays an important role in the
           innervation of the cardiac conducting system and the
           development of smooth muscle cells. Mice deficient with
           NT3 and TrkC have multiple heart defects. NT3/TrkC
           signaling is also critical for the development and
           maintenance of enteric neurons that are important for
           the control of gut peristalsis.
          Length = 291

 Score = 26.5 bits (58), Expect = 6.4
 Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 13/58 (22%)

Query: 57  IYLAPQEVWQPDLSTFNSAGGND----VSPFGETYHIASSDGL---------ISWVPP 101
           +YLA Q     DL+T N   G +    +  FG +  + S+D           I W+PP
Sbjct: 137 VYLASQHFVHRDLATRNCLVGANLLVKIGDFGMSRDVYSTDYYRVGGHTMLPIRWMPP 194


>gnl|CDD|221471 pfam12227, DUF3603, Protein of unknown function (DUF3603).  This
           protein is found in bacteria and eukaryotes. Proteins in
           this family are about 250 amino acids in length.
          Length = 214

 Score = 26.2 bits (58), Expect = 6.7
 Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 5/28 (17%)

Query: 39  WYDPVLQWDPKKYGDIKQIYLAPQEVWQ 66
           WY    +WDP++Y  I+Q  +  +E W+
Sbjct: 151 WYT---EWDPEQYEQIQQ--MDFEEAWE 173


>gnl|CDD|165177 PHA02834, PHA02834, chemokine receptor-like protein; Provisional.
          Length = 323

 Score = 26.4 bits (58), Expect = 7.4
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 4/43 (9%)

Query: 87  YHIASSDGLISWVPPCQFQVYCHLDLTYWPFDSQVCELILGSW 129
           ++IA SD ++ +     F    H DL  W F   +C+L+LG +
Sbjct: 67  FNIAMSDLMLVF----SFPFIIHNDLNEWIFGEFMCKLVLGVY 105


  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
   0.322    0.137    0.469 

Gapped
Lambda     K      H
   0.267   0.0685    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,119,160
Number of extensions: 699133
Number of successful extensions: 473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 472
Number of HSP's successfully gapped: 14
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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 (25.1 bits)