RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5812
(365 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 = 442 bits (1138), Expect = e-154
Identities = 146/320 (45%), Positives = 199/320 (62%), Gaps = 6/320 (1%)
Query: 33 CHKKSATTERLANVT-QTISQLLHGYDIRLRPNFGGDPLYVGMDLTIASFDSISEVSMDY 91
L V + + +LL YD R+RP FGG P+ V +L + S + E +MDY
Sbjct: 17 VSLAGNAKSNLKEVERKLLDELLKNYDARVRPVFGGPPVTVSFNLFLRSIMDVDEKNMDY 76
Query: 92 TITMYLNQYWKDDRLAFS-SEDEVLTLSGDFAEKIWVPDTFFANDKNSFLHDVTERNKLV 150
T ++L Q W D+RL ++ E +TL + IWVPD FF N+K++ H +T N LV
Sbjct: 77 TTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNVLV 136
Query: 151 RLNGDGSITYGMRFTTTLACMMDLHYYPLDNQNCTVEIESYGYTVLDVVMYWKET-PVRG 209
R++ +GS+ Y R T TLAC MDL +P D QNC+++ ES+GYT D+ + WKE V+
Sbjct: 137 RIHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQGAVQV 196
Query: 210 VEEAQ--LPQFTILGH-ETNDRKEKLATGTYQRLSLSFKLQRNIGYFVFQTYLPSILIVM 266
+ LP+F +LG T + TG Y L+ SF L+R Y++ Q Y+PSILIV+
Sbjct: 197 DDSLFISLPEFELLGVYGTRYCTSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPSILIVI 256
Query: 267 LSWVSFWINHEATSARVALGITTVLTMTTISTGVRSSLPRISYVKAIDIYLVMCFVFVFA 326
LSWVSFW+ +A+ ARV+LGITT+LTMTT S+GVR SLP +SYVKAID+Y +C FVF
Sbjct: 257 LSWVSFWLPADASGARVSLGITTLLTMTTFSSGVRESLPAVSYVKAIDVYFAVCMAFVFL 316
Query: 327 ALLEYAAVNYSYWADRAKKK 346
ALLE A VNY + D A+ K
Sbjct: 317 ALLETAFVNYVHHKDPAQGK 336
>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 = 188 bits (479), Expect = 2e-58
Identities = 71/218 (32%), Positives = 102/218 (46%), Gaps = 18/218 (8%)
Query: 47 TQTISQLLHGYDIRLRP-NFGGDPLYVGMDLTIASFDSISEVSMDYTITMYLNQYWKDDR 105
+ + LL YD R+RP G DP+ V + L + + E + D T ++L Q W D+R
Sbjct: 2 ERLLDDLLENYDKRVRPVKNGSDPVTVSVGLYLTQIIDVDEKNQDLTTNVWLRQQWTDER 61
Query: 106 LAFSSED----EVLTLSGDFAEKIWVPDTFFANDKNSFLHDVTERNKLVRLNGDGSITYG 161
LA+ ED L L D KIW PD N K +HD+T N VR+ DG++ +
Sbjct: 62 LAWDPEDYGGITSLRLPSD---KIWKPDIVLYN-KADGIHDITTPNTNVRVYPDGTVLWS 117
Query: 162 MRFTTTLACMMDLHYYPLDNQNCTVEIESYGYTVLDVVMYWKE-TPVRGVEEAQLPQFTI 220
+C MDL Y+P D QNC+++ S+ Y +V + WK+ TP EE L FT
Sbjct: 118 PPAIYKSSCPMDLTYFPFDQQNCSLKFGSWTYNGEEVDLRWKDDTPPILDEEIDLSDFTE 177
Query: 221 LG-----HETNDRKEKLA---TGTYQRLSLSFKLQRNI 250
G R E + Y ++ F L+R
Sbjct: 178 NGEWDIVDVPAKRNEYPYGCYSELYPDVTFYFVLRRKP 215
>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 = 147 bits (373), Expect = 2e-42
Identities = 34/80 (42%), Positives = 48/80 (60%)
Query: 257 TYLPSILIVMLSWVSFWINHEATSARVALGITTVLTMTTISTGVRSSLPRISYVKAIDIY 316
+P +LI LSW+ FW+ +A +V LGITT+LTMT +R SLP+ SYV +
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60
Query: 317 LVMCFVFVFAALLEYAAVNY 336
++ +FVF A +EYA V
Sbjct: 61 YLVFTMFVFTASVEYAVVVL 80
>gnl|CDD|233469 TIGR01564, S_layer_MJ, S-layer protein, MJ0822 family. This model
represents one of several families of proteins
associated with the formation of prokaryotic S-layers.
Members of this family are found in archaeal species,
including Pyrococcus horikoshii (split into two tandem
reading frames), Methanococcus jannaschii, and related
species. Some local similarity can be found to other
S-layer protein families [Cell envelope, Surface
structures].
Length = 571
Score = 29.9 bits (67), Expect = 2.3
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 118 SGDFAEKIWVPDTFFANDKNSFLHDVTERNKLVRL 152
D++E W F AN S L+D T+ +LV L
Sbjct: 118 DLDYSEAWWNGTAFSANYTASVLNDGTKSGELVNL 152
>gnl|CDD|232845 TIGR00145, TIGR00145, FTR1 family protein. A characterized member
from yeast acts as oxidase-coupled high affinity iron
transporter. Note that the apparent member from E. coli
K12-MG1655 has a frameshift by homology with member
sequences from other species [Unknown function,
General].
Length = 283
Score = 29.3 bits (66), Expect = 2.9
Identities = 10/40 (25%), Positives = 19/40 (47%)
Query: 246 LQRNIGYFVFQTYLPSILIVMLSWVSFWINHEATSARVAL 285
LQ++ + + I +VMLS++ W+ RV +
Sbjct: 66 LQKDEFKELLEGIFGVIAVVMLSYMGLWMLRMQRKWRVKI 105
>gnl|CDD|183561 PRK12504, PRK12504, putative monovalent cation/H+ antiporter
subunit B; Reviewed.
Length = 178
Score = 28.4 bits (64), Expect = 4.0
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 279 TSARVALGITTVLTMTTISTGVRSSLPRISYVKAIDIYLVMCFVFVFAALL 329
T A V GI+TVL + T++ R + ++ + I++ V+ + +F ALL
Sbjct: 56 TEAAVGAGISTVLLLLTLALTGRPDVDKV--FERINVPAVLIALVLFVALL 104
>gnl|CDD|193608 cd09641, Cas3''_I, CRISPR/Cas system-associated protein Cas3''.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
HD-like nuclease, specifically digesting double-stranded
oligonucleotides and preferably cleaving at G:C pairs;
signature gene for Type I.
Length = 200
Score = 27.6 bits (61), Expect = 7.6
Identities = 14/81 (17%), Positives = 23/81 (28%), Gaps = 14/81 (17%)
Query: 219 TILGH--ETNDRKEKLATGTYQRLSLSFKLQRNIGYFV------------FQTYLPSILI 264
+L H + +LA ++L L L R + FQ YL
Sbjct: 8 PLLEHLLDVAAWDAELAEEFARKLGLELGLSRELLALAGLLHDLGKATPAFQKYLRGGKE 67
Query: 265 VMLSWVSFWINHEATSARVAL 285
+ + H A +
Sbjct: 68 ALREGKRKEVRHSLLGALLLY 88
>gnl|CDD|233123 TIGR00770, Dcu, anaerobic c4-dicarboxylate membrane transporter
family protein. These proteins are members of th
C4-Dicarboxylate Uptake (Dcu) Family (TC 2.A.13). Most
proteins in this family have 12 GES predicted
transmembrane regions; however one member has 10
experimentally determined transmembrane regions with
both the N- and C-termini localized to the periplasm.
The two Escherichia coli proteins, DcuA and DcuB,
transport aspartate, malate, fumarate and succinate, and
function as antiporters with any two of these
substrates. Since DcuA is encoded in an operon with the
gene for aspartase, and DcuB is encoded in an operon
with the gene for fumarase, their physiological
functions may be to catalyze aspartate:fumarate and
fumarate:malate exchange during the anaerobic
utilization of aspartate and fumarate, respectively
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 430
Score = 28.2 bits (63), Expect = 8.4
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 54 LHGYDIRLRPNFGGDPLYVGMDLTIASF 81
L+ I RP F G P+ +GMD I F
Sbjct: 236 LYAAAISKRPGFVGKPI-LGMDHAIVMF 262
>gnl|CDD|130539 TIGR01474, ubiA_proteo, 4-hydroxybenzoate polyprenyl transferase,
proteobacterial. This model represents a family of
integral membrane proteins that condenses
para-hydroxybenzoate with any of several
polyprenyldiphosphates. Heterologous expression studies
suggest that for, many but not all members, the activity
seen (e.g. octaprenyltransferase in E. coli) reflects
available host isoprenyl pools rather than enzyme
specificity. A fairly deep split by both clustering
(UPGMA) and phylogenetics (NJ tree) separates this group
(mostly Proteobacterial and mitochondrial), with several
characterized members, from another group (mostly
archaeal and Gram-positive bacterial) lacking
characterized members [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 281
Score = 27.7 bits (62), Expect = 9.4
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 283 VALGITTVLTMTTISTGVRSSLPRISY--VKAIDIY--LVMCFVFVFAALLEYAAV 334
VALG+ L TI GV S +Y +K I + LV+ F + AL+ +AAV
Sbjct: 99 VALGVLLQLNPLTILLGVASLALVATYPFMKRITYWPQLVLGLAFGWGALMGWAAV 154
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
0.321 0.135 0.404
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,408,337
Number of extensions: 1752099
Number of successful extensions: 1517
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1512
Number of HSP's successfully gapped: 34
Length of query: 365
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 267
Effective length of database: 6,590,910
Effective search space: 1759772970
Effective search space used: 1759772970
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 (21.9 bits)
S2: 60 (27.0 bits)