RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11692
(171 letters)
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 110 bits (278), Expect = 1e-30
Identities = 45/70 (64%), Positives = 56/70 (80%), Gaps = 1/70 (1%)
Query: 74 LILPTVLISFLCVLVFYLPAEAG-EKVTLGISILLSLVVFLLLVSKILPPTSLVLPLIAK 132
LI+P VLISFL LVF+LPA+AG EKVTLGI+ LL++ VFLLL+ + LP TS V+PLI K
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60
Query: 133 YLLFTFIMNT 142
YL+FT + T
Sbjct: 61 YLVFTMFVFT 70
>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 = 113 bits (284), Expect = 5e-30
Identities = 42/142 (29%), Positives = 69/142 (48%), Gaps = 4/142 (2%)
Query: 1 MKFGSWTFNGDQVSLALYNDKNF-VDLSDYWKSGTWDIIEVPAYLNVYDEHQPTE-TDIT 58
+KF SW + + + L VD S + ++++ V E E +T
Sbjct: 172 LKFESWGYTTNDIKLEWKEQGAVQVDDSLFISLPEFELLGVYGTRYCTSETNTGEYPCLT 231
Query: 59 FYIIIRRKTLFYTVNLILPTVLISFLCVLVFYLPAEA-GEKVTLGISILLSLVVFLLLVS 117
F ++RR+ L+Y + L +P++LI L + F+LPA+A G +V+LGI+ LL++ F V
Sbjct: 232 FSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADASGARVSLGITTLLTMTTFSSGVR 291
Query: 118 KILPPTSLVLPLIAKYLLFTFI 139
+ LP S V I Y
Sbjct: 292 ESLPAVSYV-KAIDVYFAVCMA 312
>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 = 65.7 bits (161), Expect = 1e-13
Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 7/74 (9%)
Query: 1 MKFGSWTFNGDQVSLALYNDKN-----FVDLSDYWKSGTWDIIEVPA--YLNVYDEHQPT 53
+KFGSWT+NG++V L +D +DLSD+ ++G WDI++VPA Y +
Sbjct: 142 LKFGSWTYNGEEVDLRWKDDTPPILDEEIDLSDFTENGEWDIVDVPAKRNEYPYGCYSEL 201
Query: 54 ETDITFYIIIRRKT 67
D+TFY ++RRK
Sbjct: 202 YPDVTFYFVLRRKP 215
>gnl|CDD|226427 COG3913, SciT, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 227
Score = 31.1 bits (70), Expect = 0.22
Identities = 19/51 (37%), Positives = 20/51 (39%), Gaps = 3/51 (5%)
Query: 3 FGSWTFNGDQVSLALYNDKNFVDLSDYW-KSGTWDIIEVPAYLNVYDEHQP 52
FG GD VS L VD D W SG E P +L YD P
Sbjct: 11 FGKLPSRGDFVSRGLPVQ--LVDTWDRWLASGAELDAEAPDWLATYDTSPP 59
>gnl|CDD|218122 pfam04515, Choline_transpo, Plasma-membrane choline transporter.
This family represents a high-affinity plasma-membrane
choline transporter in C.elegans which is thought to be
rate-limiting for ACh synthesis in cholinergic nerve
terminals.
Length = 327
Score = 29.1 bits (66), Expect = 0.94
Identities = 17/103 (16%), Positives = 34/103 (33%), Gaps = 23/103 (22%)
Query: 58 TFYIIIRRKTLFYTVN------LILPTVLISFLCVLVFYLPAEAGEKVTLGISILLSLVV 111
T+ ++ R + L L + +S L L+ YL + L + +
Sbjct: 231 TWELLKRNGLRALVNDGLGGFVLFLGKLFVSALTGLLAYLWLTYTDNSDLSYYAVPVALA 290
Query: 112 FLLLVSKILPPTSLVLPLIAKYLLFTFIMNTVKSACLHYFLLY 154
FL+ YL+ + M+ +S F+ +
Sbjct: 291 FLIS-----------------YLIASVFMSVYESGVDTIFVCF 316
>gnl|CDD|110122 pfam01098, FTSW_RODA_SPOVE, Cell cycle protein. This entry
includes the following members; FtsW, RodA, SpoVE.
Length = 356
Score = 28.8 bits (65), Expect = 1.5
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 54 ETDITFYIIIRRKTLFYTVNLILPTVLISFLCVLVFYLPAEA----GEKVTLGISILLSL 109
TD F +I + L+ L L F + +A G + +GIS+L+ +
Sbjct: 251 HTDFIFAVIGEELGFIGALLLLA---LFFLLIYRGFRIARKAKDRFGRLLAVGISLLIFI 307
Query: 110 VVFL--LLVSKILPPTSLVLPLI 130
F+ +VS +LP T L LP
Sbjct: 308 QSFINIGMVSGLLPVTGLPLPFF 330
>gnl|CDD|222645 pfam14280, DUF4365, Domain of unknown function (DUF4365). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria,
eukaryotes and viruses. Proteins in this family are
typically between 182 and 530 amino acids in length.
There is a single completely conserved residue D that
may be functionally important.
Length = 139
Score = 28.1 bits (63), Expect = 1.7
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 51 QPTETDITFYIIIRRKTLFYTVNLILPTVLI 81
ET F + R+ L Y +N LP +L+
Sbjct: 58 FYEETGGGFSFRLEREHLNYWLNHPLPVILV 88
>gnl|CDD|234721 PRK00302, lnt, apolipoprotein N-acyltransferase; Reviewed.
Length = 505
Score = 27.9 bits (63), Expect = 2.9
Identities = 15/49 (30%), Positives = 22/49 (44%)
Query: 80 LISFLCVLVFYLPAEAGEKVTLGISILLSLVVFLLLVSKILPPTSLVLP 128
+SFL VLV L A A K +++L L++ L + L P
Sbjct: 166 GLSFLVVLVNALLALALIKRRWRLALLALLLLLLAALGYGLRRLQWTTP 214
>gnl|CDD|218347 pfam04955, HupE_UreJ, HupE / UreJ protein. This family of proteins
are hydrogenase / urease accessory proteins. The
alignment contains many conserved histidines that are
likely to be involved in nickel binding. The members
usually have five membrane-spanning regions.
Length = 180
Score = 27.5 bits (62), Expect = 3.0
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 105 ILLSLVVF-LLLVSKILPPTSLVLPLIAKYLLF 136
I LS+++ LL+ P + L+A + LF
Sbjct: 85 IALSVLLLGLLVALARRLPLAAAAALVALFALF 117
>gnl|CDD|225245 COG2370, HupE, Hydrogenase/urease accessory protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 201
Score = 27.4 bits (61), Expect = 3.2
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 10/75 (13%)
Query: 64 RRKTLFYTVNLILPTVLISFLCVLVFYLP-AEAGEKVTLGISILLSLVVF-LLLVSKILP 121
R + + +L + L + +LP E G I S++ LLL
Sbjct: 68 IRAGWLVPLAFVATMILGALLGLSGVHLPFVEPG--------IAASVLGLGLLLALAARL 119
Query: 122 PTSLVLPLIAKYLLF 136
P V LI + LF
Sbjct: 120 PLPAVAALIGIFGLF 134
>gnl|CDD|223888 COG0818, DgkA, Diacylglycerol kinase [Cell envelope biogenesis,
outer membrane].
Length = 123
Score = 26.0 bits (58), Expect = 5.8
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 78 TVLISFLCVLVFYLPAEAGEKVTLGISILLSLVVFLL 114
+ VL F+L A E + L +SI L L+V LL
Sbjct: 36 LLAALVALVLAFFLGVSAIEWLLLILSIFLVLIVELL 72
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 27.0 bits (60), Expect = 6.5
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 93 AEAGEKVTLGISILLSLVVFLLLVSKIL 120
+EAGE ++G LLSL LL SKIL
Sbjct: 1369 SEAGENFSVGQRQLLSLARALLRRSKIL 1396
>gnl|CDD|233016 TIGR00546, lnt, apolipoprotein N-acyltransferase. This enzyme
transfers the acyl group to lipoproteins in the
lgt/lsp/lnt system which is found broadly in bacteria
but not in archaea. This model represents one component
of the "lipoprotein lgt/lsp/lnt system" genome property
[Protein fate, Protein modification and repair].
Length = 391
Score = 26.6 bits (59), Expect = 7.7
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 78 TVLISFLCVLVF-YLPAEAGEKVTLGISILLSLVVFLLLV 116
+SFL V + L +K + + +++VV L +
Sbjct: 103 VWGLSFLVVFLNALLALVLLKKESFKKLLAIAVVVLLAAL 142
>gnl|CDD|223055 PHA03361, PHA03361, UL7 tegument protein; Provisional.
Length = 302
Score = 26.5 bits (59), Expect = 8.0
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 68 LFYTVNLILPTVLISF-LCVLVFYLPAEAGEKVTLGISILLSLVVFLLLVSKILPP 122
L + + L P L+ F LC+L YL + T S+ + L FL + + P
Sbjct: 130 LPHRLVLFRPEDLLDFALCLLQMYLENCPRSRATA--SLFVQLSAFLRRAWRRITP 183
>gnl|CDD|200474 cd11335, AmyAc_MTase_N, Alpha amylase catalytic domain found in
maltosyltransferase. Maltosyltransferase (MTase), a
maltodextrin glycosyltransferase, acts on starch and
maltooligosaccharides. It catalyzes the transfer of
maltosyl units from alpha-1,4-linked glucans or
maltooligosaccharides to other alpha-1,4-linked glucans,
maltooligosaccharides or glucose. MTase is a homodimer.
The catalytic core domain has the (beta/alpha) 8 barrel
fold with the active-site cleft formed at the C-terminal
end of the barrel. Substrate binding experiments have
led to the location of two distinct maltose-binding
sites: one lies in the active-site cleft and the other
is located in a pocket adjacent to the active-site
cleft. It is a member of the alpha-amylase family, but
unlike typical alpha-amylases, MTase does not require
calcium for activity and lacks two histidine residues
which are predicted to be critical for binding the
glucose residue adjacent to the scissile bond in the
substrates. The common reaction chemistry of the
alpha-amylase family of enzymes is based on a two-step
acid catalytic mechanism that requires two critical
carboxylates: one acting as a general acid/base (Glu)
and the other as a nucleophile (Asp). Both hydrolysis
and transglycosylation proceed via the nucleophilic
substitution reaction between the anomeric carbon, C1
and a nucleophile. 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 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 = 538
Score = 26.5 bits (59), Expect = 8.8
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 37 IIEVPAYLNVYDEHQPTETDITFY 60
PA+ + ++ QP TD+T+
Sbjct: 264 CTTAPAFSDWINDPQPPWTDVTYL 287
>gnl|CDD|235159 PRK03784, PRK03784, vtamin B12-transporter permease; Provisional.
Length = 331
Score = 26.5 bits (59), Expect = 8.9
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 93 AEAGEKVTLGIS--ILLSLVVFLLLVSKILPPTSLVLPLIAKYLLFTFIM 140
AE G LG+S ++LV +LL +LPP +L L IA LL T I+
Sbjct: 88 AEPG---LLGVSNGAGVALVAAVLLGQGLLPPWALSLCAIAGALLITLIL 134
>gnl|CDD|223911 COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms].
Length = 1009
Score = 26.4 bits (59), Expect = 9.5
Identities = 10/30 (33%), Positives = 19/30 (63%), Gaps = 4/30 (13%)
Query: 99 VTLGISILLSLVVFLLLV----SKILPPTS 124
+T+ +++LLSL+V L L +++L P
Sbjct: 461 ITIAVAMLLSLLVALTLTPALCARLLKPVP 490
>gnl|CDD|182324 PRK10238, PRK10238, aromatic amino acid transporter; Provisional.
Length = 456
Score = 26.5 bits (58), Expect = 9.8
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 6/46 (13%)
Query: 72 VNLILPTVLISFLCVLVFYLPAEAGEKVTLGISILLSLVVFLLLVS 117
VN IL + L++ LCVL+ YL E+ +L++LVV L+++
Sbjct: 333 VNTILVSALVTALCVLINYLAPES------AFGLLMALVVSALVIN 372
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
0.327 0.143 0.433
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,898,860
Number of extensions: 852303
Number of successful extensions: 1722
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1675
Number of HSP's successfully gapped: 218
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.0 bits)