RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16242
(383 letters)
>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 = 231 bits (590), Expect = 1e-74
Identities = 100/239 (41%), Positives = 139/239 (58%), Gaps = 16/239 (6%)
Query: 115 IIIPCMGISFLTVLTFYLPSDSG-EKVTLSISILISLHVFFLLVVEIIPPTSLVVPLLGK 173
+IIPC+ ISFL+ L F+LP+D+G EKVTL I+ L+++ VF LL+ E +P TS VVPL+GK
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60
Query: 174 YLIFAMILVSISICVTVVVLNVHFRSPQTHKMAPWVKRVFIQFLPRILVMRRPLYNPDGS 233
YL+F M + + S+ VVVLNVH RSP THKM WV+++F++ LPR+L M+RP +
Sbjct: 61 YLVFTMFVFTASVEYAVVVLNVHHRSPSTHKMPEWVRKLFLRKLPRLLFMKRPPESLSPP 120
Query: 234 HLADGPLIGGSGGSCKIHGHVSLSNILTEAILSSSPQDDSKHLRP---PAFSHAQCPPVM 290
+ S G V E+ P+ S S + P +
Sbjct: 121 AAPNLRRSSSS------SGSVLEPASGKESKGVGGPETSSGLPGGSGSGLGSPFRLSPEL 174
Query: 291 HRSCFCVRFIAEHTRMQDDSTKESTLIMVKEDWKYVALVLDRLFLWIFTLAVLGGTAGI 349
++ VRFIAEH R +D+ + VKEDWKYVA+V+DRL WIF +A + GT
Sbjct: 175 KKALEGVRFIAEHLRSRDEFDE------VKEDWKYVAMVIDRLSRWIFPIAFVLGTLVY 227
>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 = 156 bits (396), Expect = 2e-43
Identities = 72/294 (24%), Positives = 114/294 (38%), Gaps = 29/294 (9%)
Query: 57 RRERVGVDLSEFYMSVEWDILEVPAVRNEKFYTCCDEPYLDITFNITMRRKTLFYTVNII 116
+ V VD S F E+++L V R Y +TF+ +RR+ L+Y + +
Sbjct: 190 EQGAVQVDDSLFISLPEFELLGVYGTRYC-TSETNTGEYPCLTFSFVLRRRPLYYLLQLY 248
Query: 117 IPCMGISFLTVLTFYLPSD-SGEKVTLSISILISLHVFFLLVVEIIPPTSLVVPLLGKYL 175
IP + I L+ ++F+LP+D SG +V+L I+ L+++ F V E +P S V + Y
Sbjct: 249 IPSILIVILSWVSFWLPADASGARVSLGITTLLTMTTFSSGVRESLPAVS-YVKAIDVYF 307
Query: 176 IFAMILVSISICVTVVVLNVHFRSPQTHKMAPWVKRVFIQFLPRILVMRRPLYNPDGSHL 235
M V +++ T V VH + P K + ++ L + P
Sbjct: 308 AVCMAFVFLALLETAFVNYVHHKDPAQGKRH-----LLLERCAWRLCKQEP--------- 353
Query: 236 ADGPLIGGSGGSCKIHGHVSLSNILTEAILSSSPQDDSKHLRPPAFSHAQCPPVMHRSCF 295
G H SLS++ A + H+ P
Sbjct: 354 -------GEDYRRPALDHASLSSVEMRA--KDGGRGLESPTERQRLLHSPPPAEGDLD-- 402
Query: 296 CVRFIAEHTRMQDDSTKESTLIMVKEDWKYVALVLDRLFLWIFTLAVLGGTAGI 349
+ I E R+ K V DWK+ A V+D+L F LA L G
Sbjct: 403 -LAGILEEVRIAHRFRKRDESEEVVRDWKFRAKVIDKLSRMAFPLAFLLFNIGY 455
>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 = 70.7 bits (174), Expect = 3e-14
Identities = 26/61 (42%), Positives = 34/61 (55%)
Query: 48 DLSPRRPPHRRERVGVDLSEFYMSVEWDILEVPAVRNEKFYTCCDEPYLDITFNITMRRK 107
DL + +DLS+F + EWDI++VPA RNE Y C E Y D+TF +RRK
Sbjct: 155 DLRWKDDTPPILDEEIDLSDFTENGEWDIVDVPAKRNEYPYGCYSELYPDVTFYFVLRRK 214
Query: 108 T 108
Sbjct: 215 P 215
>gnl|CDD|218276 pfam04814, HNF-1_N, Hepatocyte nuclear factor 1 (HNF-1), N
terminus. This family consists of the N terminus of
homeobox-containing transcription factor HNF-1. This
region contains a dimerisation sequence and an acidic
region that may be involved in transcription activation.
Mutations and the common Ala/Val 98 polymorphism in
HNF-1 cause the type 3 form of maturity-onset diabetes
of the young (MODY3).
Length = 177
Score = 30.6 bits (69), Expect = 0.78
Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 1/63 (1%)
Query: 6 SCVPAKDEHHHHPESF-YPYHTAARSTEDLSRFKRESSRKNKDDLSPRRPPHRRERVGVD 64
+ + H P + ++ED + K + LSP H+R V
Sbjct: 49 LNLDKGESCHALPNGLGEGRLSEDETSEDGEDDRPPPILKELERLSPEEAAHQRAEVDRL 108
Query: 65 LSE 67
L E
Sbjct: 109 LRE 111
>gnl|CDD|214444 MTH00165, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 573
Score = 31.3 bits (72), Expect = 0.98
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 4/80 (5%)
Query: 108 TLFYTVNIIIPCMGISFLTVLTFYLPSDSGEKVTLSISILISLHVFF--LLVVEIIP-PT 164
T+ Y+ +I M F L SD + + S+ +L+ + +F +L I P P
Sbjct: 388 TVSYSFRLIYYSMSGDFNLKSLNNL-SDESKFMLKSMILLLFMSIFGGSMLSWLIFPEPY 446
Query: 165 SLVVPLLGKYLIFAMILVSI 184
+ +P K L +IL+
Sbjct: 447 MICLPFYLKLLTLFVILLGG 466
>gnl|CDD|221096 pfam11368, DUF3169, Protein of unknown function (DUF3169). Some
members in this family of proteins are annotated as
membrane proteins however this cannot be confirmed.
Currently there is no known function.
Length = 248
Score = 30.7 bits (70), Expect = 1.0
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 85 EKFYTCCDEPYLDITFNITMRRKTLFYTVNIIIPCMGISFLTVLTFYLPSDSGEKVTLSI 144
+KF DE N K F +N +I + FL +++ +GE L+I
Sbjct: 174 KKFANSLDEGERQA--NYESSYKIYF-VLNQVILPLLYVFLFIISI----LTGENQILAI 226
Query: 145 SILISLHVFFLL 156
++I +H++ +
Sbjct: 227 LLVIIIHIYINV 238
>gnl|CDD|222060 pfam13347, MFS_2, MFS/sugar transport protein. This family is part
of the major facilitator superfamily of membrane
transport proteins.
Length = 425
Score = 30.3 bits (69), Expect = 1.9
Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 5/63 (7%)
Query: 295 FCVRFIAEHTRMQDDSTKESTLIMVKEDWKYVALVLDRLFLWIFTLAVLGGTAGIILQAP 354
C E + + ++ +L ++ +K AL +R L + L +L A +
Sbjct: 190 ICFAGTKERVSVPPEQKEKVSL---RDMFK--ALFKNRPLLILLLLYLLNALAMAVRNGL 244
Query: 355 SLY 357
LY
Sbjct: 245 LLY 247
Score = 28.7 bits (65), Expect = 6.0
Identities = 26/126 (20%), Positives = 48/126 (38%), Gaps = 22/126 (17%)
Query: 100 FNITMRRKTLFYTV-----NIIIPCMGISF---LTVLTFYLPSDSGEKVTLSISILISLH 151
F ++M K ++ + + + I + + VLT D E+ +L+ I
Sbjct: 92 FGLSMTAKLIYAFITYILLGLAYTFVNIPYWSLIPVLT----RDPKERTSLASYRRIGAT 147
Query: 152 VFFLLVVEIIPPTSLVVPLLGK------YLIFAMILVSIS-ICVTVVVLNVHFRSPQTHK 204
+ LLV I PP +V LLG Y + A+I+ ++ + + R +
Sbjct: 148 IGGLLVAVIAPP---LVALLGGGNGAKGYFLAALIIAILAVVGFLICFAGTKERVSVPPE 204
Query: 205 MAPWVK 210
V
Sbjct: 205 QKEKVS 210
>gnl|CDD|190932 pfam04284, DUF441, Protein of unknown function (DUF441). Predicted
to be an integral membrane protein.
Length = 140
Score = 29.0 bits (66), Expect = 1.9
Identities = 12/55 (21%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 145 SILISLHVFFLLVVEIIPPTSLVVPLLGKYLIFA-MILVSISICVTVVVLNVHFR 198
S+ I+ LL++++ P + P L K I + +++I++ V + + F+
Sbjct: 17 SLTIA--AAVLLLIKLTPLDQKIFPFLEKKGINWGVTILTIAVLVPIATGKIGFK 69
>gnl|CDD|215815 pfam00244, 14-3-3, 14-3-3 protein.
Length = 236
Score = 29.5 bits (67), Expect = 2.7
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 299 FIAEHTRMQDDSTKESTLIMVKEDWKYVALVLDRLFLW 336
IAE + ++S K+STLIM L+ D L LW
Sbjct: 199 AIAELDTLSEESYKDSTLIM--------QLLRDNLTLW 228
>gnl|CDD|224596 COG1682, TagG, ABC-type polysaccharide/polyol phosphate export
systems, permease component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 263
Score = 29.5 bits (67), Expect = 3.0
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 144 ISILISLHVFFLLVVEIIPPTSLVVPLLGKYLIFAMILVSISICVTVVVLNVHFR 198
+ LI L + + ++ + S LL + +IL S+ + + + L V FR
Sbjct: 120 FNFLIHLIIILIFLIILGVEPSWHWLLL-LPALLLLILFSVGLGLILASLGVRFR 173
>gnl|CDD|172788 PRK14300, PRK14300, chaperone protein DnaJ; Provisional.
Length = 372
Score = 29.6 bits (66), Expect = 3.1
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 1 MSMMRSCVPAKDEHHHHPESFYPYHTAARSTEDLSRFKRESSRKNKDDLS 50
MS MRS + H H E P + + R E L FK+ES + ++D S
Sbjct: 315 MSKMRSTIRGDMLTHIHVE--VPKNLSKRQRELLEEFKKESINEKENDGS 362
>gnl|CDD|182964 PRK11102, PRK11102, bicyclomycin/multidrug efflux system;
Provisional.
Length = 377
Score = 29.5 bits (67), Expect = 3.1
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 153 FFLLVVEIIPPTSLVVPLLGKYLIF----AMILVSISICVTVVVLNVHFRSPQTHK 204
F LV+ I P L+ P++G +L+ I +++ + V F P+T
Sbjct: 119 FVTLVMTIAP---LLAPIIGGWLLVWFSWHAIFWVLALAAILAAALVFFFIPETLP 171
>gnl|CDD|234052 TIGR02900, spore_V_B, stage V sporulation protein B. SpoVB is the
stage V sporulation protein B of the bacterial endopore
formation program in Bacillus subtilis and various other
Firmcutes. It is nearly universal among
endospore-formers. Paralogs with rather high sequence
similarity to SpoVB exist, including YkvU in B. subtilis
and a number of proteins in the genus Clostridium.
Member sequences for the seed alignment were chosen to
select those proteins, no more than one to a genome,
closest to B. subtilis SpoVB in a neighbor joining tree
[Cellular processes, Sporulation and germination].
Length = 488
Score = 28.8 bits (65), Expect = 6.1
Identities = 10/67 (14%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 96 LDITFNITMRRKTLFYTVNI------IIPCMGISFLTVLTFYLPSDSGEKVTLSISILIS 149
L N+ +K + T+++ + + + L Y+ + + L + I++
Sbjct: 422 LVTILNLAEIKKNIRITIDLSDFLIFALLGILVYLGLSLLKYIIFNPNILINLLLIIILG 481
Query: 150 LHVFFLL 156
++ LL
Sbjct: 482 FSLYILL 488
>gnl|CDD|234638 PRK00108, mraY, phospho-N-acetylmuramoyl-pentapeptide-transferase;
Provisional.
Length = 344
Score = 28.6 bits (65), Expect = 6.5
Identities = 13/47 (27%), Positives = 21/47 (44%)
Query: 146 ILISLHVFFLLVVEIIPPTSLVVPLLGKYLIFAMILVSISICVTVVV 192
ILI+L LL + TSL +P + +++ I V+V
Sbjct: 123 ILIALIFALLLYLLGSTSTSLTIPFFKDLSLDLGVILYIPFAYFVIV 169
>gnl|CDD|237748 PRK14537, PRK14537, 50S ribosomal protein L20/unknown domain fusion
protein; Provisional.
Length = 230
Score = 28.0 bits (62), Expect = 7.3
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 2/40 (5%)
Query: 15 HHHPESFYPYHTAARSTEDLSRFKRESSRKNKDDLSPRRP 54
H PE F Y A+ LS+F+ + K K L
Sbjct: 100 HLQPEVFVQYVELAKKF--LSQFQSTTITKPKKVLINEVL 137
>gnl|CDD|218624 pfam05529, Bap31, B-cell receptor-associated protein 31-like.
Bap31 is a polytopic integral protein of the endoplasmic
reticulum membrane and a substrate of caspase-8. Bap31
is cleaved within its cytosolic domain, generating
pro-apoptotic p20 Bap31.
Length = 149
Score = 27.5 bits (62), Expect = 7.8
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 152 VFFLLVVEIIPPTSLVVPLLGKYLIFAMILVSIS 185
VF LL E+ LV+PL I I S+S
Sbjct: 8 VFGLLYAEMAVFLLLVLPL--PSPIRRKIFKSVS 39
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
0.325 0.139 0.432
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,808,507
Number of extensions: 1947542
Number of successful extensions: 2456
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2438
Number of HSP's successfully gapped: 61
Length of query: 383
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 284
Effective length of database: 6,546,556
Effective search space: 1859221904
Effective search space used: 1859221904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 60 (26.7 bits)