RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12043
(143 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 = 114 bits (287), Expect = 1e-32
Identities = 40/107 (37%), Positives = 57/107 (53%)
Query: 24 KWYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETYHIASSDGLIS 83
+W D L WDP+ YG I + L ++W+PD+ +N A G T DG +
Sbjct: 56 QWTDERLAWDPEDYGGITSLRLPSDKIWKPDIVLYNKADGIHDITTPNTNVRVYPDGTVL 115
Query: 84 WVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFHFEDGN 130
W PP ++ C +DLTY+PFD Q C L GSW Y+G +D ++D
Sbjct: 116 WSPPAIYKSSCPMDLTYFPFDQQNCSLKFGSWTYNGEEVDLRWKDDT 162
>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 = 74.0 bits (182), Expect = 2e-16
Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 25 WYDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETYHI--ASSDGLI 82
W D LQW+P++Y + + +W PD+ +N T + +G +
Sbjct: 86 WTDERLQWNPEEYPGVTLVRTPDDSIWVPDIFFYNEKDAR-FHGITMTNVLVRIHPNGSV 144
Query: 83 SWVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDF 124
+ P + C +DL +PFD Q C L SW Y N+I
Sbjct: 145 LYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKL 186
>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 = 29.6 bits (67), Expect = 0.54
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 5/61 (8%)
Query: 27 DPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPFGETY----HIASSDGLI 82
D +L + Y + + + D F+++G D+ PF + Y G I
Sbjct: 253 DFLLHFGGNGYNSLFRNLNTDGG-HRRDNCYFDASGKGDIKPFVDEYLPQYEATKGKGYI 311
Query: 83 S 83
S
Sbjct: 312 S 312
>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 = 26.9 bits (59), Expect = 4.6
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 13/58 (22%)
Query: 43 IYLAPQEVWQPDLSTFNSAGGND----VSPFGETYHIASSDGL---------ISWVPP 87
+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 = 26.6 bits (59), Expect = 4.8
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 5/28 (17%)
Query: 25 WYDPVLQWDPKKYGDIKQIYLAPQEVWQ 52
WY +WDP++Y I+Q + +E W+
Sbjct: 151 WYT---EWDPEQYEQIQQ--MDFEEAWE 173
>gnl|CDD|119429 cd05169, PIKKc_TOR, TOR (Target of rapamycin), catalytic domain;
The TOR catalytic domain subfamily is part of a larger
superfamily that includes the catalytic domains of
other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
RIO kinases. TOR is a member of the phosphoinositide
3-kinase-related protein kinase (PIKK) subfamily. PIKKs
have intrinsic serine/threonine kinase activity and are
distinguished from other PKs by their unique catalytic
domain, similar to that of lipid PI3K, and their large
molecular weight (240-470 kDa). TOR contains a
rapamycin binding domain, a catalytic domain, and a
FATC (FRAP, ATM and TRRAP, C-terminal) domain at the
C-terminus. It is also called FRAP (FK506 binding
protein 12-rapamycin associated protein). TOR is a
central component of the eukaryotic growth regulatory
network. It controls the expression of many genes
transcribed by all three RNA polymerases. It associates
with other proteins to form two distinct complexes,
TORC1 and TORC2. TORC1 is involved in diverse
growth-related functions including protein synthesis,
nutrient use and transport, autophagy and stress
responses. TORC2 is involved in organizing cytoskeletal
structures.
Length = 280
Score = 26.0 bits (58), Expect = 8.0
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 72 TYHI---ASSDGLISWVPPCQ 89
TY + + + GLI WVP C
Sbjct: 72 TYSVIPLSPNVGLIGWVPGCD 92
>gnl|CDD|165102 PHA02735, PHA02735, putative DNA polymerase type B; Provisional.
Length = 716
Score = 26.2 bits (57), Expect = 8.0
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 67 SPFGETYHIASSDGLISWVPPCQFQVYCRLDLTYWPFDSQVCELILGSWVYDGNNIDFHF 126
S F E H+ +P +F+ + L W FD + ILG+ VY+ IDF
Sbjct: 557 SNFDENIHVPDDS-----LPESEFRKEAQDGLGAWDFDYEGDAFILGAGVYE---IDFDT 608
Query: 127 EDGNWRMNGDASEFKIK 143
+ N + + K K
Sbjct: 609 CQKGCKDNCNKFQGKHK 625
>gnl|CDD|225568 COG3024, COG3024, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 65
Score = 24.4 bits (53), Expect = 8.5
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 86 PPCQFQVYCRLDLTYWPFDSQVCELI-LGSW 115
P C V + + PF S+ C+LI LG W
Sbjct: 11 PTCGKPVVWGEESPFRPFCSKRCKLIDLGEW 41
>gnl|CDD|132431 TIGR03390, ascorbOXfungal, L-ascorbate oxidase, fungal type. This
model describes a family of fungal ascorbate oxidases,
within a larger family of multicopper oxidases that also
includes plant ascorbate oxidases (TIGR03388), plant
laccases and laccase-like proteins (TIGR03389), and
related proteins. The member from Acremonium sp. HI-25
is characterized.
Length = 538
Score = 26.0 bits (57), Expect = 9.0
Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 26 YDPVLQWDPKKYGDIKQIYLAPQEVWQPDLSTFNSAGGNDVSPF---GE-TYHIASSDGL 81
+DP + P K G++ +I VWQ S GG D PF G Y I DG
Sbjct: 407 FDPETRAFPAKVGEVLEI------VWQNTGSYTGPNGGVDTHPFHAHGRHFYDIGGGDGE 460
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 0.140 0.476
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: 7,309,745
Number of extensions: 628677
Number of successful extensions: 434
Number of sequences better than 10.0: 1
Number of HSP's gapped: 433
Number of HSP's successfully gapped: 19
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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 (21.8 bits)
S2: 54 (24.7 bits)