RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12705
(204 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 = 108 bits (272), Expect = 7e-28
Identities = 49/105 (46%), Positives = 67/105 (63%), Gaps = 4/105 (3%)
Query: 100 YSSLTLTFILNRQYGFYLMDFYAPSILLVCISWVSFWMAPDAVPGRTILGASTMLTF--F 157
Y LT +F+L R+ +YL+ Y PSIL+V +SWVSFW+ DA R LG +T+LT F
Sbjct: 227 YPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADASGARVSLGITTLLTMTTF 286
Query: 158 QLGIETGSSLPNVSYIRSNDVWFFACTVFIFLSLAEFAFVNTIWR 202
G+ SLP VSY+++ DV+F C F+FL+L E AFVN +
Sbjct: 287 SSGVR--ESLPAVSYVKAIDVYFAVCMAFVFLALLETAFVNYVHH 329
Score = 40.5 bits (95), Expect = 3e-04
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 17 QEFKVQLLLQLHWKDPRLEYRHY-APHITEMVGERNFIQNIWTPHIYLTNERDSLVLGLY 75
++ + L+ W D RL++ P +T + +IW P I+ NE+D+ G+
Sbjct: 74 MDYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPD---DSIWVPDIFFYNEKDARFHGIT 130
Query: 76 RRDMLVSILPDGDMLFSTR 94
++LV I P+G +L+S R
Sbjct: 131 MTNVLVRIHPNGSVLYSPR 149
>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 = 75.0 bits (185), Expect = 1e-16
Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 121 YAPSILLVCISWVSFWMAPDAVPGRTILGASTML--TFFQLGIETGSSLPNVSYIRSNDV 178
P +L+ +SW+ FW+ DA P + LG +T+L T F L I SLP SY+
Sbjct: 2 IIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIR--ESLPKTSYVVPLIG 59
Query: 179 WFFACTVFIFLSLAEFAFVN 198
+ T+F+F + E+A V
Sbjct: 60 KYLVFTMFVFTASVEYAVVV 79
>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 = 46.9 bits (112), Expect = 1e-06
Identities = 21/83 (25%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 16 QQEFKVQLLLQLHWKDPRLEYRHYAPHITEMVGERNFI----QNIWTPHIYLTNERDSLV 71
Q+ + L+ W D RL + E G + IW P I L N+ D +
Sbjct: 44 NQDLTTNVWLRQQWTDERLAWDP------EDYGGITSLRLPSDKIWKPDIVLYNKADGIH 97
Query: 72 LGLYRRDMLVSILPDGDMLFSTR 94
+ V + PDG +L+S
Sbjct: 98 DITT-PNTNVRVYPDGTVLWSPP 119
>gnl|CDD|226945 COG4579, COG4579, Isocitrate dehydrogenase kinase/phosphatase
[Signal transduction mechanisms].
Length = 578
Score = 29.0 bits (65), Expect = 2.1
Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 15/96 (15%)
Query: 10 IGNLSFQQEFKVQLLLQLHWKDPRL--EYRHYAPHITEMVGERNFIQNIW-----TP-HI 61
+G ++ QEF+ + P L E AP +G++ I++++ TP +I
Sbjct: 366 VGRMADTQEFE-NFVFPKSRISPALMAELLQEAPEKVTDLGDQIVIRHLYIERRMTPLNI 424
Query: 62 YLTNERDSLV------LGLYRRDMLVSILPDGDMLF 91
+L + G + + + + GDMLF
Sbjct: 425 WLEQVEGQQLRDAIEEYGNAIKQLAAANIFPGDMLF 460
>gnl|CDD|239298 cd03000, PDI_a_TMX3, PDIa family, TMX3 subfamily; composed of
eukaryotic proteins similar to human TMX3, a TRX related
transmembrane protein containing one redox active TRX
domain at the N-terminus and a classical ER retrieval
sequence for type I transmembrane proteins at the
C-terminus. The TMX3 transcript is found in a variety of
tissues with the highest levels detected in skeletal
muscle and the heart. In vitro, TMX3 showed oxidase
activity albeit slightly lower than that of protein
disulfide isomerase.
Length = 104
Score = 26.6 bits (59), Expect = 4.6
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 107 FILNRQYGFYLMDFYAP 123
F R+ +L+DFYAP
Sbjct: 9 FKDVRKEDIWLVDFYAP 25
>gnl|CDD|165586 PHA03342, PHA03342, US22 family homolog; Provisional.
Length = 511
Score = 26.9 bits (59), Expect = 8.9
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 15/75 (20%)
Query: 89 MLFSTRSRAYMYSSLTLT-------------FILNRQYGFYL--MDFYAPSILLVCISWV 133
ML + R Y+Y + T F ++R+ Y+ MD P L C++W+
Sbjct: 107 MLAGEQGRIYVYCARDDTLHLVARDIEEFARFGISRRAFAYIEDMDAILPPADLECLNWI 166
Query: 134 SFWMAPDAVPGRTIL 148
+ D PG +L
Sbjct: 167 ASCDVHDGAPGMELL 181
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 0.141 0.447
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,562,289
Number of extensions: 986992
Number of successful extensions: 1043
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1039
Number of HSP's successfully gapped: 34
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
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: 57 (25.7 bits)