RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8685
(70 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 = 70.1 bits (172), Expect = 4e-16
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 2 PGKKNEVQYECCPETYVDITFTIQIRRRTLYYFFNLIVPCVLISSMALLGFTLPPD-SGE 60
G + E Y +TF+ +RRR LYY L +P +LI ++ + F LP D SG
Sbjct: 213 YGTRYC-TSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADASGA 271
Query: 61 KLTLVINVLL 70
+++L I LL
Sbjct: 272 RVSLGITTLL 281
>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 = 50.0 bits (120), Expect = 4e-09
Identities = 21/35 (60%), Positives = 26/35 (74%), Gaps = 1/35 (2%)
Query: 37 LIVPCVLISSMALLGFTLPPDSG-EKLTLVINVLL 70
LI+PCVLIS ++ L F LP D+G EK+TL I LL
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLL 35
>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 = 42.6 bits (101), Expect = 1e-06
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 1 MPGKKNEVQYECCPETYVDITFTIQIRRRT 30
+P K+NE Y C E Y D+TF +RR+
Sbjct: 186 VPAKRNEYPYGCYSELYPDVTFYFVLRRKP 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 = 0.15
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 33 YFFNLIVPCVLISSMALLGFTLP 55
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 = 27.4 bits (61), Expect = 0.44
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 18 VDITFTIQIRRRTLYYFF 35
DI T QIRR+T Y F
Sbjct: 27 SDIMQTAQIRRQTFYNHF 44
>gnl|CDD|238646 cd01321, ADGF, Adenosine deaminase-related growth factors (ADGF), a
novel family of secreted growth-factors with sequence
similarty to adenosine deaminase.
Length = 345
Score = 26.1 bits (58), Expect = 1.5
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 4 KKNEVQYECCPETYVDITFTIQIRRRTLYYFFNLIVPCVLISS 46
KK + E CP + + +R VP V ISS
Sbjct: 243 KKKNIAIEVCPISNQVLGLVSDLRNHPAAALLARGVPVV-ISS 284
>gnl|CDD|185065 PRK15110, PRK15110, antimicrobial peptide ABC transporter permease
SapB; Provisional.
Length = 321
Score = 24.6 bits (54), Expect = 4.7
Identities = 9/13 (69%), Positives = 13/13 (100%)
Query: 43 LISSMALLGFTLP 55
LIS++ALLGF++P
Sbjct: 110 LISALALLGFSIP 122
>gnl|CDD|232942 TIGR00366, TIGR00366, TIGR00366 family protein. [Hypothetical
proteins, Conserved].
Length = 438
Score = 24.0 bits (52), Expect = 7.5
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 30 TLYYFFNLIVPCVLISSMALLGFTLPPDSGE 60
T++ +NLI+ ++I + + + + P GE
Sbjct: 184 TIFSGYNLIITAIIIVFLPFITYMMMPKRGE 214
>gnl|CDD|111553 pfam02667, SCFA_trans, Short chain fatty acid transporter. This
family consists of two sequences annotated as short
chain fatty acid transporters, however, there are no
references giving details of experimental
characterisation of this function.
Length = 453
Score = 24.0 bits (52), Expect = 8.4
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 30 TLYYFFNLIVPCVLISSMALLGFTLPPDSGE 60
T++ +NLI+ ++I + + + + P GE
Sbjct: 187 TIFSGYNLIITAIIIIFLPFITYMMMPKRGE 217
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
0.328 0.145 0.444
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: 3,577,504
Number of extensions: 270065
Number of successful extensions: 318
Number of sequences better than 10.0: 1
Number of HSP's gapped: 317
Number of HSP's successfully gapped: 19
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
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: 53 (24.1 bits)