RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7487
(439 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 = 247 bits (633), Expect = 2e-77
Identities = 109/248 (43%), Positives = 144/248 (58%), Gaps = 17/248 (6%)
Query: 14 DFTLDFYFRQFWTDPRLAFR--QRPGVETLSVGSDFIKNIWVPDTFFVNEKQSYFHIATT 71
D+T + + RQ WTD RL + + PGV + D +IWVPD FF NEK + FH T
Sbjct: 75 DYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDD---SIWVPDIFFYNEKDARFHGITM 131
Query: 72 SNEFIRIHHSGSITRSIRLTITASCPMNLQYFPMDRQLCHIEIESFGYTMRDIRYKWNE- 130
+N +RIH +GS+ S R+T+T +CPM+L+ FP D Q C ++ ES+GYT DI+ +W E
Sbjct: 132 TNVLVRIHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQ 191
Query: 131 GPNSVGVSNEVSLPQFKVLGHRQKDLEIS-LTTGNYSRLACEIQFVRSMGYYLIQIYIPS 189
G V S +SLP+F++LG S TG Y L R YYL+Q+YIPS
Sbjct: 192 GAVQVDDSLFISLPEFELLGVYGTRYCTSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPS 251
Query: 190 SLIVAISWVSFWLNRNATPARVALGVTTVLTMTTLQVLSFS----------IDVYLGTCF 239
LIV +SWVSFWL +A+ ARV+LG+TT+LTMTT IDVY C
Sbjct: 252 ILIVILSWVSFWLPADASGARVSLGITTLLTMTTFSSGVRESLPAVSYVKAIDVYFAVCM 311
Query: 240 VMVFASLL 247
VF +LL
Sbjct: 312 AFVFLALL 319
Score = 137 bits (347), Expect = 6e-36
Identities = 52/95 (54%), Positives = 64/95 (67%)
Query: 343 GNYSRLACEIQFVRSMGYYLIQIYIPSGLIVIISWVSFWLNRNATPARVALGVTTVLTMT 402
G Y L R YYL+Q+YIPS LIVI+SWVSFWL +A+ ARV+LG+TT+LTMT
Sbjct: 225 GEYPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADASGARVSLGITTLLTMT 284
Query: 403 TLMSSTNAALPKISYVKSIDVYLGTCFVMVFASLL 437
T S +LP +SYVK+IDVY C VF +LL
Sbjct: 285 TFSSGVRESLPAVSYVKAIDVYFAVCMAFVFLALL 319
Score = 127 bits (321), Expect = 2e-32
Identities = 51/95 (53%), Positives = 62/95 (65%)
Query: 248 GNYSRLACEIQFVRSMGYYLIQIYVPSILIVAISWVSFWLNRVATVARVNLGVTTVLTMT 307
G Y L R YYL+Q+Y+PSILIV +SWVSFWL A+ ARV+LG+TT+LTMT
Sbjct: 225 GEYPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADASGARVSLGITTLLTMT 284
Query: 308 TLMSSTNAALPKVSYIKSIDVYLGTCFVMVFACLL 342
T S +LP VSY+K+IDVY C VF LL
Sbjct: 285 TFSSGVRESLPAVSYVKAIDVYFAVCMAFVFLALL 319
>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 = 154 bits (391), Expect = 1e-44
Identities = 51/179 (28%), Positives = 83/179 (46%), Gaps = 11/179 (6%)
Query: 2 LESVLKLKFRSEDFTLDFYFRQFWTDPRLAF--RQRPGVETLSVGSDFIKNIWVPDTFFV 59
L ++ + +++D T + + RQ WTD RLA+ G+ +L + SD IW PD
Sbjct: 34 LTQIIDVDEKNQDLTTNVWLRQQWTDERLAWDPEDYGGITSLRLPSD---KIWKPDIVLY 90
Query: 60 NEKQSYFHIATTSNEFIRIHHSGSITRSIRLTITASCPMNLQYFPMDRQLCHIEIESFGY 119
N K H TT N +R++ G++ S +SCPM+L YFP D+Q C ++ S+ Y
Sbjct: 91 N-KADGIHDITTPNTNVRVYPDGTVLWSPPAIYKSSCPMDLTYFPFDQQNCSLKFGSWTY 149
Query: 120 TMRDIRYKWNEGPNSVGVSNEVSLPQFKVLGHRQKDLEISL----TTGNYSRLACEIQF 174
++ +W + + E+ L F G + G YS L ++ F
Sbjct: 150 NGEEVDLRWKDDTP-PILDEEIDLSDFTENGEWDIVDVPAKRNEYPYGCYSELYPDVTF 207
>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 = 112 bits (282), Expect = 8e-29
Identities = 28/73 (38%), Positives = 41/73 (56%)
Query: 365 IYIPSGLIVIISWVSFWLNRNATPARVALGVTTVLTMTTLMSSTNAALPKISYVKSIDVY 424
+ IP LI +SW+ FWL +A P +V LG+TT+LTMT + +LPK SYV +
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60
Query: 425 LGTCFVMVFASLL 437
+ VF + +
Sbjct: 61 YLVFTMFVFTASV 73
Score = 102 bits (256), Expect = 5e-25
Identities = 25/73 (34%), Positives = 39/73 (53%)
Query: 270 IYVPSILIVAISWVSFWLNRVATVARVNLGVTTVLTMTTLMSSTNAALPKVSYIKSIDVY 329
+ +P +LI +SW+ FWL A +V LG+TT+LTMT + +LPK SY+ +
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60
Query: 330 LGTCFVMVFACLL 342
+ VF +
Sbjct: 61 YLVFTMFVFTASV 73
Score = 82.3 bits (204), Expect = 5e-18
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 10/73 (13%)
Query: 185 IYIPSSLIVAISWVSFWLNRNATPARVALGVTTVLTMTTLQVL--------SFS--IDVY 234
+ IP LI +SW+ FWL +A P +V LG+TT+LTMT +L S+ +
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60
Query: 235 LGTCFVMVFASLL 247
+ VF + +
Sbjct: 61 YLVFTMFVFTASV 73
>gnl|CDD|143285 cd05877, Ig_LP_like, Immunoglobulin (Ig)-like domain of human
cartilage link protein (LP). Ig_LP_like: immunoglobulin
(Ig)-like domain similar to that that found in human
cartilage link protein (LP). In cartilage,
chondroitin-keratan sulfate proteoglycan (CSPG),
aggrecan, forms cartilage link protein stabilized
aggregates with hyaluronan (HA). These aggregates
contribute to the tissue's load bearing properties.
Aggregates having other CSPGs substituting for aggrecan
may contribute to the structural integrity of many
different tissues. Members of the vertebrate HPLN
(hyaluronan/HA and proteoglycan binding link) protein
family are physically linked adjacent to CSPG genes.
Length = 106
Score = 28.8 bits (65), Expect = 1.7
Identities = 19/83 (22%), Positives = 26/83 (31%), Gaps = 24/83 (28%)
Query: 110 CHIEIESFGYTMRDIRYKWNEGPNSVGVSNEVSLPQFKVLGHRQK--------------- 154
C E R IR KW + + +V +G R K
Sbjct: 9 CRYHYEPELSAPRKIRVKWTKLESDYLKEEDV----LVAIGTRHKSYGSYQGRVFLRRAH 64
Query: 155 DLEISL-----TTGNYSRLACEI 172
DL+ SL +Y R CE+
Sbjct: 65 DLDASLVITDLRLEDYGRYRCEV 87
>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 89
Score = 27.9 bits (63), Expect = 2.9
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 59 VNEKQSYFHIATTSNEFIRIHHSGSITRSIRL 90
VN+ + Y H+ + N FIR GS+ R ++L
Sbjct: 44 VNDPEKYPHLLSVKNCFIR----GSVVRYVQL 71
>gnl|CDD|227143 COG4806, RhaA, L-rhamnose isomerase [Carbohydrate transport and
metabolism].
Length = 419
Score = 29.4 bits (66), Expect = 4.2
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 12 SEDFTL---DFYFRQFWTDPRLAFRQRPGVETLSVGSDFIKNIWVPD 55
++ FTL D RQFW D A R+ +G+ + NIW+PD
Sbjct: 142 ADGFTLSHPDDEIRQFWIDHCKASRRVSAYFGEQLGTPSVMNIWIPD 188
>gnl|CDD|130809 TIGR01748, rhaA, L-rhamnose isomerase. This enzyme interconverts
L-rhamnose and L-rhamnulose. In some species, including
E. coli, this is the first step in rhamnose catabolism.
Sequential steps are catalyzed by rhamnulose kinase
(rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to
yield glycerone phosphate and (S)-lactaldehyde.
Characterization of this family is based on members in
E. coli and Salmonella [Energy metabolism, Sugars].
Length = 414
Score = 29.5 bits (66), Expect = 4.4
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 12 SEDFTL---DFYFRQFWTDPRLAFRQRPGVETLSVGSDFIKNIWVPD 55
++ FTL D RQFW D A R+ +G+ + NIW+PD
Sbjct: 138 ADGFTLSHPDDSIRQFWIDHCKASRRISEYFGKELGTPSVMNIWIPD 184
>gnl|CDD|191458 pfam06134, RhaA, L-rhamnose isomerase (RhaA). This family consists
of several bacterial L-rhamnose isomerase proteins
(EC:5.3.1.14).
Length = 417
Score = 29.0 bits (65), Expect = 5.0
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 15 FTL---DFYFRQFWTDPRLAFRQRPGVETLSVGSDFIKNIWVPD 55
TL D RQFW D +A R+ +G+ + NIW+PD
Sbjct: 144 LTLAHPDKEIRQFWIDHCIASRKISEYFGKELGTPSLTNIWIPD 187
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 0.138 0.422
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,035,090
Number of extensions: 2118733
Number of successful extensions: 2523
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2493
Number of HSP's successfully gapped: 66
Length of query: 439
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 339
Effective length of database: 6,502,202
Effective search space: 2204246478
Effective search space used: 2204246478
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 (21.8 bits)
S2: 60 (26.9 bits)