RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8686
(176 letters)
>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 = 93.6 bits (233), Expect = 8e-23
Identities = 43/170 (25%), Positives = 70/170 (41%), Gaps = 36/170 (21%)
Query: 8 LDLILKDEAGGDLTTFITNGEWYLLVCKQISSKKNEVQYECCPETYVDITFTIQIRRRTL 67
L+ + D + FI+ E+ LL + + E Y +TF+ +RRR L
Sbjct: 186 LEWKEQGAVQVDDSLFISLPEFELL---GVYGTRYC-TSETNTGEYPCLTFSFVLRRRPL 241
Query: 68 YYFFNLIVPCVLISSMALLGFTLPPD-SGEKLTLVYKGFLRTSAFFNNSVQCTRDFSGLP 126
YY L +P +LI ++ + F LP D SG +++L
Sbjct: 242 YYLLQLYIPSILIVILSWVSFWLPADASGARVSL-------------------------- 275
Query: 127 LILSGVTILLSLTVFLNLVAESMPTTSDAVPLIGTHHRLIFLIIYYLLLV 176
G+T LL++T F + V ES+P S V I + + ++ LL
Sbjct: 276 ----GITTLLTMTTFSSGVRESLPAVS-YVKAIDVYFAVCMAFVFLALLE 320
>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 = 71.5 bits (176), Expect = 1e-15
Identities = 40/105 (38%), Positives = 54/105 (51%), Gaps = 33/105 (31%)
Query: 73 LIVPCVLISSMALLGFTLPPDSG-EKLTLVYKGFLRTSAFFNNSVQCTRDFSGLPLILSG 131
LI+PCVLIS ++ L F LP D+G EK+TL G
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTL------------------------------G 30
Query: 132 VTILLSLTVFLNLVAESMPTTSDAVPLIGTHHRLIFLIIYYLLLV 176
+T LL++TVFL L+ ES+P TS VPLIG + L+F + + V
Sbjct: 31 ITTLLTMTVFLLLIRESLPKTSYVVPLIGKY--LVFTMFVFTASV 73
>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 = 53.4 bits (129), Expect = 4e-09
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 9/67 (13%)
Query: 6 NTLDLILKDEAGG------DLTTFITNGEWYLLVCKQISSKKNEVQYECCPETYVDITFT 59
+DL KD+ DL+ F NGEW ++ + +K+NE Y C E Y D+TF
Sbjct: 152 EEVDLRWKDDTPPILDEEIDLSDFTENGEWDIV---DVPAKRNEYPYGCYSELYPDVTFY 208
Query: 60 IQIRRRT 66
+RR+
Sbjct: 209 FVLRRKP 215
>gnl|CDD|220437 pfam09844, DUF2071, Uncharacterized conserved protein (COG2071).
This conserved protein (similar to YgjF), found in
various prokaryotes, has no known function.
Length = 217
Score = 28.8 bits (65), Expect = 1.3
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 69 YFFNLIVPCVLISSMALLGFTLP 91
FF+L P +L+ A F LP
Sbjct: 82 VFFSLDAPRLLVVFGARTLFGLP 104
>gnl|CDD|233838 TIGR02366, DHAK_reg, probable dihydroxyacetone kinase regulator.
The seed alignment for this family was built from a set
of closely related uncharacterized proteins associated
with operons for the type of bacterial dihydroxyacetone
kinase that transfers PEP-derived phosphate from a
phosphoprotein, as in phosphotransferase system
transport, rather than from ATP. Members have a TetR
transcriptional regulator domain (pfam00440) at the
N-terminus and sequence homology throughout.
Length = 176
Score = 26.6 bits (59), Expect = 5.2
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 54 VDITFTIQIRRRTLYYFF 71
DI T QIRR+T Y F
Sbjct: 27 SDIMQTAQIRRQTFYNHF 44
>gnl|CDD|221256 pfam11837, DUF3357, Domain of unknown function (DUF3357). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 96 to 119 amino acids in length.
Length = 106
Score = 25.8 bits (57), Expect = 7.6
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 120 RDFSGLPLILSGVTILLSLTVFLNLVAES 148
R GL +LS + LLSL L L +
Sbjct: 27 RPLKGLLAVLSSLLFLLSLVALLILNGQP 55
>gnl|CDD|237156 PRK12647, PRK12647, putative monovalent cation/H+ antiporter
subunit A; Reviewed.
Length = 761
Score = 26.8 bits (60), Expect = 8.4
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 124 GLPLILSGVTILLSLTVFLNL 144
LPL+LS +T+LL + ++L
Sbjct: 486 NLPLLLSLLTLLLGIGLYLLR 506
>gnl|CDD|182282 PRK10171, PRK10171, hydrogenase 1 b-type cytochrome subunit;
Provisional.
Length = 235
Score = 26.5 bits (58), Expect = 8.9
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 67 LYYFFNLIVPCVLISSMALLGFTLPPDSGEKLTLVYKGFLRTSAF 111
++++ ++ VL+ + +G LP SGE L Y G++R F
Sbjct: 20 IWHWLTVLCMAVLMVTGYFIGKPLPSVSGEATYLFYMGYIRLIHF 64
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 0.142 0.424
Gapped
Lambda K H
0.267 0.0773 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,926,311
Number of extensions: 822525
Number of successful extensions: 911
Number of sequences better than 10.0: 1
Number of HSP's gapped: 908
Number of HSP's successfully gapped: 38
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
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: 56 (25.3 bits)