RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10725
(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 = 65.7 bits (161), Expect = 8e-14
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 13/84 (15%)
Query: 21 EDYEVDLYLRQKWQDQRLK-----HHSITK-TLDLNDPNLVKAIWKPEVYFPNAKHAEFQ 74
+D +++LRQ+W D+RL + IT L + IWKP++ N K
Sbjct: 45 QDLTTNVWLRQQWTDERLAWDPEDYGGITSLRLPSDK------IWKPDIVLYN-KADGIH 97
Query: 75 YVTVPNVLVRINPDGEILYMLSII 98
+T PN VR+ PDG +L+ I
Sbjct: 98 DITTPNTNVRVYPDGTVLWSPPAI 121
Score = 44.9 bits (107), Expect = 3e-06
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 123 IWKPEVYFPNAKHAEFQYVTVPNVLVRINPDGEILYM 159
IWKP++ N K +T PN VR+ PDG +L+
Sbjct: 82 IWKPDIVLYN-KADGIHDITTPNTNVRVYPDGTVLWS 117
>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 = 67.4 bits (165), Expect = 8e-14
Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 12/83 (14%)
Query: 22 DYEVDLYLRQKWQDQRLKHHSITKTLDLNDPNLVKA------IWKPEVYFPNAKHAEFQY 75
DY +++LRQ+W D+RL+ + P + IW P+++F N K A F
Sbjct: 75 DYTTNIWLRQEWTDERLQWN------PEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHG 128
Query: 76 VTVPNVLVRINPDGEILYMLSII 98
+T+ NVLVRI+P+G +LY I
Sbjct: 129 ITMTNVLVRIHPNGSVLYSPRIT 151
Score = 50.5 bits (121), Expect = 5e-08
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 113 DLNDPNLVKA------IWKPEVYFPNAKHAEFQYVTVPNVLVRINPDGEILY 158
P + IW P+++F N K A F +T+ NVLVRI+P+G +LY
Sbjct: 95 PEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNVLVRIHPNGSVLY 146
>gnl|CDD|185688 cd02179, GH16_beta_GRP, beta-1,3-glucan recognition protein,
member of glycosyl hydrolase family 16. Beta-GRP
(beta-1,3-glucan recognition protein) is one of several
pattern recognition receptors (PRRs), also referred to
as biosensor proteins, that complexes with
pathogen-associated beta-1,3-glucans and then
transduces signals necessary for activation of an
appropriate innate immune response. They are present in
insects and lack all catalytic residues. This subgroup
also contains related proteins of unknown function that
still contain the active site. Their structures adopt a
jelly roll fold with a deep active site channel
harboring the catalytic residues, like those of other
glycosyl hydrolase family 16 members.
Length = 321
Score = 28.1 bits (63), Expect = 1.8
Identities = 12/40 (30%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 48 DLNDPNLVKAIWKPEVYFPNAKHAEFQ-YVTVPNVLVRIN 86
+ N L W EV FP EF Y P L +
Sbjct: 6 NFNGALLDLNKWTIEVRFPGEPDYEFVVYDDAPENLFVKD 45
Score = 28.1 bits (63), Expect = 1.8
Identities = 12/40 (30%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 113 DLNDPNLVKAIWKPEVYFPNAKHAEFQ-YVTVPNVLVRIN 151
+ N L W EV FP EF Y P L +
Sbjct: 6 NFNGALLDLNKWTIEVRFPGEPDYEFVVYDDAPENLFVKD 45
>gnl|CDD|77355 PRK09702, PRK09702, PTS system arbutin-specific transporter
subunit IIB; Provisional.
Length = 161
Score = 27.8 bits (61), Expect = 1.9
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 14 SLCTPAIEDYEVDLYLRQKWQDQR 37
++CTP ED EV LY + +++ R
Sbjct: 35 NMCTPGREDAEVKLYSKAEYKASR 58
>gnl|CDD|143506 cd06839, PLPDE_III_Btrk_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Btrk Decarboxylase. This
subfamily is composed of Bacillus circulans BtrK
decarboxylase and similar proteins. These proteins are
fold type III PLP-dependent enzymes that contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases, eukaryotic ornithine decarboxylases
and diaminopimelate decarboxylases. BtrK is presumed to
function as a PLP-dependent decarboxylase involved in
the biosynthesis of the aminoglycoside antibiotic
butirosin. Homodimer formation and the presence of the
PLP cofactor may be required for catalytic activity.
Length = 382
Score = 28.3 bits (64), Expect = 2.0
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 78 VPNVLVRINPDGEI 91
V V +RINPD E+
Sbjct: 122 VARVALRINPDFEL 135
Score = 28.3 bits (64), Expect = 2.0
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 143 VPNVLVRINPDGEI 156
V V +RINPD E+
Sbjct: 122 VARVALRINPDFEL 135
>gnl|CDD|240410 PTZ00418, PTZ00418, Poly(A) polymerase; Provisional.
Length = 593
Score = 28.2 bits (63), Expect = 2.0
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 41 HSITKTLDLNDPNLVKAIWKPEVYFPNAKH 70
H I K ++ N N + +P +F + KH
Sbjct: 383 HEIIKYIEKNSENTWTNVLEPLDFFTSYKH 412
>gnl|CDD|200496 cd11235, Sema_semaphorin, The Sema domain, a protein interacting
module, of semaphorins. Semaphorins are regulator
molecules in the development of the nervous system and
in axonal guidance. They also play important roles in
other biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. They can be
divided into 7 classes. Vertebrates have members in
classes 3-7, whereas classes 1 and 2 are known only in
invertebrates. Class 2 and 3 semaphorins are secreted
proteins; classes 1 and 4 through 6 are transmembrane
proteins; and class 7 is membrane associated via
glycosylphosphatidylinositol (GPI) linkage. The
semaphorins exert their function through their
receptors, the neuropilin and plexin families. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 437
Score = 27.4 bits (61), Expect = 3.5
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 97 IIENNTNKRKQKRKALDLNDPNLVKA-IWKPEVYF 130
+ +N R + + LN+P V A VYF
Sbjct: 142 TLGHNPPLRTEYHDSKWLNEPQFVGAFDIGDYVYF 176
>gnl|CDD|224235 COG1316, LytR, Transcriptional regulator [Transcription].
Length = 307
Score = 27.4 bits (61), Expect = 4.0
Identities = 8/49 (16%), Positives = 17/49 (34%), Gaps = 5/49 (10%)
Query: 69 KHAEFQYVTVPNVLVRINPDGEILYMLSI-----IENNTNKRKQKRKAL 112
A + +L+ +NP + ++SI + + K A
Sbjct: 60 TGAGQGGRSDSIMLLTLNPKNKKTTLISIPRDTYVPPIPGHGRDKINAA 108
>gnl|CDD|213275 cd05907, VL_LC_FACS_like, Long-chain fatty acid CoA synthetases and
Bubblegum-like very long-chain fatty acid CoA
synthetases. This family includes long-chain fatty acid
(C12-C20) CoA synthetases and Bubblegum-like very
long-chain (>C20) fatty acid CoA synthetases. FACS
catalyzes the formation of fatty acyl-CoA in a two-step
reaction: the formation of a fatty acyl-AMP molecule as
an intermediate, and the formation of a fatty acyl-CoA.
Eukaryotes generally have multiple isoforms of LC-FACS
genes with multiple splice variants. For example, nine
genes are found in Arabidopsis and six genes are
expressed in mammalian cells. Drosophila melanogaster
mutant bubblegum (BGM) have elevated levels of
very-long-chain fatty acids (VLCFA) caused by a
defective gene later named bubblegum. The human homolog
(hsBG) of bubblegum has been characterized as a very
long chain fatty acid CoA synthetase that functions
specifically in the brain; hsBG may play a central role
in brain VLCFA metabolism and myelinogenesis. Free fatty
acids must be "activated" to their CoA thioesters before
participating in most catabolic and anabolic reactions.
Length = 456
Score = 27.1 bits (61), Expect = 4.2
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 78 VPNVLVRINPDGEIL 92
+P V VRI DGEIL
Sbjct: 272 LPGVEVRIAEDGEIL 286
Score = 27.1 bits (61), Expect = 4.2
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 143 VPNVLVRINPDGEIL 157
+P V VRI DGEIL
Sbjct: 272 LPGVEVRIAEDGEIL 286
>gnl|CDD|225404 COG2848, COG2848, Uncharacterized conserved protein [Function
unknown].
Length = 445
Score = 27.1 bits (60), Expect = 5.3
Identities = 29/131 (22%), Positives = 43/131 (32%), Gaps = 20/131 (15%)
Query: 18 PAIEDYEVDLYLRQKWQDQRLKHHSITKTLDLNDPNLVKAIWKPEVYFPNAKHAEFQYVT 77
A ++ VD L H TK D L+++I PE ++ V
Sbjct: 101 KAAKEIGVDFIGGF----SALVHKGYTK----GDEALIRSI--PEALKSTSRVCSS--VN 148
Query: 78 VPNVLVRINPDGEILYMLSIIENNTNKRKQKRKALDLNDPNLVKAIWKPEVYFPNAKHAE 137
V + IN D +L M I+ + + N P + P A H
Sbjct: 149 VASTRTGINMD-AVLIMGEPIKATAELTGCAKLVVFANAVEDN-----P--FMPGAFHGV 200
Query: 138 FQYVTVPNVLV 148
+ V NV V
Sbjct: 201 GEADAVINVGV 211
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 26.8 bits (59), Expect = 6.1
Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 4/73 (5%)
Query: 26 DLYLRQKWQDQRLKHHSITKTLDLNDPNLVKAIWKPEVYFPNAKHAEFQYVTVPNVLVRI 85
D Y + L I + + N +++ K E+ A+ A N L R+
Sbjct: 198 DYYPGDFLEAHILMEPVIESSSEFNVSIVIEKNLKQELLDMEARLAYEANEERDNALRRL 257
Query: 86 NPDGEILYMLSII 98
E + LS +
Sbjct: 258 ----ENIQKLSDL 266
>gnl|CDD|181425 PRK08441, oorC, 2-oxoglutarate-acceptor oxidoreductase subunit
OorC; Reviewed.
Length = 183
Score = 26.2 bits (58), Expect = 6.2
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 88 DGEILYMLSIIENNTNKRKQ--KRKALDLNDPNLVK 121
+GEI +MLS + + N+ K K + + +PNLVK
Sbjct: 66 EGEIDFMLSTAQISYNQFKSGVKEGGIIVVEPNLVK 101
>gnl|CDD|225936 COG3401, COG3401, Fibronectin type 3 domain-containing protein
[General function prediction only].
Length = 343
Score = 26.0 bits (57), Expect = 9.8
Identities = 7/24 (29%), Positives = 8/24 (33%)
Query: 48 DLNDPNLVKAIWKPEVYFPNAKHA 71
L P VK W P K+
Sbjct: 79 SLERPKSVKVFWSPHPDVSVGKYI 102
Score = 26.0 bits (57), Expect = 9.8
Identities = 7/24 (29%), Positives = 8/24 (33%)
Query: 113 DLNDPNLVKAIWKPEVYFPNAKHA 136
L P VK W P K+
Sbjct: 79 SLERPKSVKVFWSPHPDVSVGKYI 102
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
0.319 0.136 0.411
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,449,732
Number of extensions: 766500
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 27
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 (21.8 bits)
S2: 55 (25.0 bits)