RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16087
(252 letters)
>gnl|CDD|215646 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family).
This family contains, amongst other G-protein-coupled
receptors (GCPRs), members of the opsin family, which
have been considered to be typical members of the
rhodopsin superfamily. They share several motifs, mainly
the seven transmembrane helices, GCPRs of the rhodopsin
superfamily. All opsins bind a chromophore, such as
11-cis-retinal. The function of most opsins other than
the photoisomerases is split into two steps: light
absorption and G-protein activation. Photoisomerases, on
the other hand, are not coupled to G-proteins - they are
thought to generate and supply the chromophore that is
used by visual opsins.
Length = 251
Score = 115 bits (291), Expect = 2e-31
Identities = 44/165 (26%), Positives = 77/165 (46%), Gaps = 10/165 (6%)
Query: 56 FLLSVYLPF--VYLQVNGKWGLPDFVCDFYIAMDVMCSTSSIFNLVAISIDRYIAVTQPI 113
L + LP +Y V G W D +C + V+ +SI L AISIDRY+A+ P+
Sbjct: 25 LLFLLTLPPWALYYLVGGDWPFGDALCKLVGFLFVVNGYASILLLTAISIDRYLAIVHPL 84
Query: 114 KYAKHKNNRRVWLTIVLVWAISVAIGSPIVLGLNNT--PDRVPDLCLF------YSSDFI 165
+Y + + RR + I++VW +++ + P +L + CL +
Sbjct: 85 RYRRIRTPRRAKVLILVVWVLALLLSLPPLLFSWLRTVEEGNVTTCLIDFPEESTKRSYT 144
Query: 166 IYSSLSSFYIPCIIMVFLYYNIFKALSKRAKKAKAARKPHLSEMK 210
+ S+L F +P ++++ Y I + L KRA+ + + S K
Sbjct: 145 LLSTLLGFVLPLLVILVCYTLILRTLRKRARSGASQARAKRSSSK 189
Score = 46.9 bits (112), Expect = 2e-06
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 7 QVNGKWGLPDFVCDFYIAMDVMCSTSSIFNLVAISIDR 44
V G W D +C + V+ +SI L AISIDR
Sbjct: 39 LVGGDWPFGDALCKLVGFLFVVNGYASILLLTAISIDR 76
>gnl|CDD|222976 PHA03087, PHA03087, G protein-coupled chemokine receptor-like
protein; Provisional.
Length = 335
Score = 55.2 bits (133), Expect = 7e-09
Identities = 35/155 (22%), Positives = 70/155 (45%), Gaps = 9/155 (5%)
Query: 57 LLSVYLPF-VYLQVNGKWGLPDFVCDFYIAMDVMCSTSSIFNLVAISIDRYIAVTQPIKY 115
L + LPF +Y + +W +F C + + +S+ + +S+DRYIA+ P+K
Sbjct: 87 LFVMTLPFQIYYYILFQWSFGEFACKIVSGLYYIGFYNSMNFITVMSVDRYIAIVHPVKS 146
Query: 116 AKHKNNRRVWLTIVLVWAISVAIGSPIVLGLNNTPDRVPDLC-LFYSSDFIIYS------ 168
K + ++ +++W IS+ +PI+ D +C +FY++ + +
Sbjct: 147 NKINTVKYGYIVSLVIWIISIIETTPILFVYTTKKDHETLICCMFYNNKTMNWKLFINFE 206
Query: 169 -SLSSFYIPCIIMVFLYYNIFKALSKRAKKAKAAR 202
++ IP I+++ Y I L K K +
Sbjct: 207 INIIGMLIPLTILLYCYSKILITLKGINKSKKNKK 241
>gnl|CDD|165021 PHA02638, PHA02638, CC chemokine receptor-like protein;
Provisional.
Length = 417
Score = 38.8 bits (90), Expect = 0.002
Identities = 38/166 (22%), Positives = 69/166 (41%), Gaps = 23/166 (13%)
Query: 60 VYLPFVYLQVNGKWGLPDFVCDFYIAMDVMCSTSSIFNLVAISIDRYIAVTQPIKYAKHK 119
+ PF+ +W DF+C A + S++F + +SIDRY A+ PI + K++
Sbjct: 148 IDFPFIIYNEFDQWIFGDFMCKVISASYYIGFFSNMFLITLMSIDRYFAILYPISFQKYR 207
Query: 120 NNRRVWLTIVLVWAISVAIGSP---------IVLGLNNTPDRVPDL-CLFY----SSDFI 165
+ ++ W +S+ I SP I+ ++ + + + C ++
Sbjct: 208 TFNIGIILCIISWILSLIITSPAYFIFEASNIIFSAQDSNETISNYQCTLIEDNEKNNIS 267
Query: 166 IYSSLSSF-------YIPCIIMVFLYYNIFKALS--KRAKKAKAAR 202
+ F +IP II F Y I L K++KK K+
Sbjct: 268 FLGRILQFEINILGMFIPIIIFAFCYIKIILKLKQLKKSKKTKSII 313
>gnl|CDD|165177 PHA02834, PHA02834, chemokine receptor-like protein; Provisional.
Length = 323
Score = 38.3 bits (89), Expect = 0.002
Identities = 35/144 (24%), Positives = 58/144 (40%), Gaps = 9/144 (6%)
Query: 56 FLLSVYLPFVYLQVNGKWGLPDFVCDFYIAMDVMCSTSSIFNLVAISIDRYIAVTQPIKY 115
+L PF+ +W +F+C + + + S++F + ISIDRYI V K
Sbjct: 74 LMLVFSFPFIIHNDLNEWIFGEFMCKLVLGVYFVGFFSNMFFVTLISIDRYILVVNATKI 133
Query: 116 AKHKNNRRVWLTIVLVWAISVAIGSPIVLGLNNTPDRVPDLCLF--YSSDFIIYSSLS-- 171
+ V L+ V W SV + P ++ C+F Y +F + +
Sbjct: 134 KNKSISLSVLLS-VAAWVCSVILSMPAMVLYYVDNTDNLKQCIFNDYHENFSWSAFFNFE 192
Query: 172 ----SFYIPCIIMVFLYYNIFKAL 191
IP II+++ Y I L
Sbjct: 193 INIFGIVIPLIILIYCYSKILYTL 216
>gnl|CDD|192535 pfam10320, 7TM_GPCR_Srsx, Serpentine type 7TM GPCR chemoreceptor
Srsx. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srsx is a solo family
amongst the superfamilies of chemoreceptors.
Chemoperception is one of the central senses of soil
nematodes like C. elegans which are otherwise 'blind'
and 'deaf'.
Length = 257
Score = 34.5 bits (80), Expect = 0.036
Identities = 37/160 (23%), Positives = 63/160 (39%), Gaps = 9/160 (5%)
Query: 48 CFTKFSNVFLLSVYLPFVYLQVNGKWGLPDFVCDFYIAMDVMCSTSSIFNLVAISIDRYI 107
C +++ LS + FV L G L C I + T+ ++ I IDR I
Sbjct: 30 CVQCLADLLCLSGEIIFVVLLFTGT-QLTRNECFLIIIPYIFGQTAQSPLMLMIGIDRLI 88
Query: 108 AVTQPIKYAKHKNNRRVWLTIVLVWAISVAIGSPIVLGLNNTPDRVPDLCL----FYSSD 163
AV PI Y +++ +++ ++ S I +V G D +C +
Sbjct: 89 AVKFPIFYRLLSSSKYLFIQLIFPVIYSSFI---LVYGFLERDDETIIVCAPPLALNGTA 145
Query: 164 FIIYSSLSSFYIPCIIMVFLYYNIFKALSKRAKKAKAARK 203
F I+ +LSS I I+++ I K ++K
Sbjct: 146 FRIF-TLSSVIINVIVLIVYIILIIIFKKKGQTTNSDSKK 184
>gnl|CDD|220691 pfam10323, 7TM_GPCR_Srv, Serpentine type 7TM GPCR chemoreceptor
Srv. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srv is a member of the
Srg superfamily of chemoreceptors. Chemoperception is
one of the central senses of soil nematodes like C.
elegans which are otherwise 'blind' and 'deaf'.
Length = 283
Score = 33.4 bits (77), Expect = 0.084
Identities = 22/103 (21%), Positives = 46/103 (44%), Gaps = 4/103 (3%)
Query: 99 VAISIDRYIAVTQPI-KYAKHKNNRRVWLTIVLVWAISVAIGSPIVLGLNNTPDRVPDLC 157
+S +RY+A+ PI + K + R+W I++ W + I ++ + D ++
Sbjct: 94 SFLSTNRYLAICFPISRLTKIWQSARLWKIILIYWLPGLLISLVVLKNTDIYYDNEENMP 153
Query: 158 LFYSSDFIIYSSLSSF---YIPCIIMVFLYYNIFKALSKRAKK 197
+ D I +L + ++ CI + Y +F + K+ K
Sbjct: 154 VVADKDVIQRFTLIALIFVFVTCIYCIIAYGALFFVIRKKFNK 196
>gnl|CDD|220695 pfam10328, 7TM_GPCR_Srx, Serpentine type 7TM GPCR chemoreceptor
Srx. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srx is part of the Srg
superfamily of chemoreceptors. Chemoperception is one of
the central senses of soil nematodes like C. elegans
which are otherwise 'blind' and 'deaf'.
Length = 275
Score = 32.9 bits (76), Expect = 0.11
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 9/100 (9%)
Query: 45 GKLCFTK-FSNVFLLSVYL----PFVYLQVNGKWGLPDFVCDFYIAMDVM-CSTSSIFNL 98
G LC K SN + +++L P L ++ LP+ + + ++ S
Sbjct: 29 GILCANKAISNAIICTIFLFYVVPMTLLDLSF---LPELLNSHIGGLILLGLYEISPLTH 85
Query: 99 VAISIDRYIAVTQPIKYAKHKNNRRVWLTIVLVWAISVAI 138
+ IS++R+ AV P KY K + + + I +W I++ I
Sbjct: 86 LLISLNRFCAVFFPFKYKKIFSIKNTKIIITFIWIIAIII 125
>gnl|CDD|224775 COG1862, YajC, Preprotein translocase subunit YajC [Intracellular
trafficking and secretion].
Length = 97
Score = 30.3 bits (69), Expect = 0.28
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 168 SSLSSFYIPCIIMVFLYYNIFKALSKRAKKAKAARKPHLSEMKPG 212
S L +I Y+ I + KR K+ + L+ +K G
Sbjct: 7 SGLVLLLPLVLIFAIFYFLIIRPQRKRMKE----HQELLNSLKKG 47
>gnl|CDD|133014 cd02523, PC_cytidylyltransferase, Phosphocholine
cytidylyltransferases catalyze the synthesis of
CDP-choline. This family contains proteins similar to
prokaryotic phosphocholine (P-cho)
cytidylyltransferases. Phosphocholine (PC)
cytidylyltransferases catalyze the transfer of a
cytidine monophosphate from CTP to phosphocholine to
form CDP-choline. PC is the most abundant phospholipid
in eukaryotic membranes and it is also important in
prokaryotic membranes. For pathogenic prokaryotes, the
cell surface PC facilitates the interaction with host
surface and induces attachment and invasion. In addition
cell wall PC serves as scaffold for a group of
choline-binding proteins that are secreted from the
cells. Phosphocholine (PC) cytidylyltransferase is a key
enzyme in the prokaryotic choline metabolism pathway. It
has been hypothesized to consist of a choline transport
system, a choline kinase, CTP:phosphocholine
cytidylyltransferase, and a choline phosphotransferase
that transfers P-Cho from CDP-Cho to either lipoteichoic
acid or lipopolysaccharide.
Length = 229
Score = 29.1 bits (66), Expect = 1.7
Identities = 11/88 (12%), Positives = 28/88 (31%), Gaps = 10/88 (11%)
Query: 151 DRVPDLCLFYSSDFIIYSSLSSFYI-------PCIIM---VFLYYNIFKALSKRAKKAKA 200
+ P++ Y+ D+ +++ S Y+ +++ V +I + L
Sbjct: 63 KKYPNIKFVYNPDYAETNNIYSLYLARDFLDEDFLLLEGDVVFDPSILERLLSSPADNAI 122
Query: 201 ARKPHLSEMKPGIVIENVAQTRRLAETT 228
E + V + L +
Sbjct: 123 LVDKKTKEWEDEYVKDLDDAGVLLGIIS 150
>gnl|CDD|222709 pfam14362, DUF4407, Domain of unknown function (DUF4407). This
family of proteins is found in bacteria. Proteins in
this family are typically between 366 and 597 amino
acids in length. There is a single completely conserved
residue R that may be functionally important.
Length = 297
Score = 28.8 bits (65), Expect = 2.3
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 95 IFNLVAISIDRYIAVTQPIKYAKHKNNRRVWLT----IVLVWAISVAIGSPIVL 144
++ LV ++DR+I T K + RR L ++L I+V I P+ L
Sbjct: 54 VWGLVIFNLDRFIVSTI----KKRDSGRRRLLQALPRLLLAVLIAVVISEPLEL 103
>gnl|CDD|217191 pfam02699, YajC, Preprotein translocase subunit. See.
Length = 83
Score = 26.2 bits (59), Expect = 5.4
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 168 SSLSSFYIPCIIMVFLYYNIFKALSKRAKKAKAARKPHLSEMKPG 212
S LSS +I Y+ + + KR K+ K LS +K G
Sbjct: 1 SGLSSLLPLVLIFAIFYFLLIRPQQKRQKEHKEM----LSSLKKG 41
>gnl|CDD|220687 pfam10316, 7TM_GPCR_Srbc, Serpentine type 7TM GPCR chemoreceptor
Srbc. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srbc is a solo family
amongst the superfamilies of chemoreceptors.
Chemoperception is one of the central senses of soil
nematodes like C. elegans which are otherwise 'blind'
and 'deaf'.
Length = 272
Score = 27.5 bits (62), Expect = 6.4
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 99 VAISIDRYIAVTQPIKYAKHKNNRRVWLTIVLVWAISVAIGSPIVL 144
+ ISI+R IAV PI Y H ++ I+L+ AIS + VL
Sbjct: 99 LLISIERVIAVYFPIFY--HNYRPKIPNFIILILAISYGLFEQYVL 142
>gnl|CDD|238833 cd01663, Cyt_c_Oxidase_I, Cytochrome C oxidase subunit I.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Only subunits I
and II are essential for function, but subunit III,
which is also conserved, may play a role in assembly or
oxygen delivery to the active site. Subunits I, II, and
III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Subunit I contains a
heme-copper binuclear center (the active site where O2
is reduced to water) formed by a high-spin heme (heme
a3) and a copper ion (CuB). It also contains a low-spin
heme (heme a), believed to participate in the transfer
of electrons to the binuclear center. For every
reduction of an O2 molecule, eight protons are taken
from the inside aqueous compartment and four electrons
are taken from cytochrome c on the opposite side of the
membrane. The four electrons and four of the protons
are used in the reduction of O2; the four remaining
protons are pumped across the membrane. This charge
separation of four charges contributes to the
electrochemical gradient used for ATP synthesis. Two
proton channels, the D-pathway and K-pathway, leading to
the binuclear center have been identified in subunit I.
A well-defined pathway for the transfer of pumped
protons beyond the binuclear center has not been
identified. Electrons are transferred from cytochrome c
(the electron donor) to heme a via the CuA binuclear
site in subunit II, and directly from heme a to the
binuclear center.
Length = 488
Score = 27.4 bits (62), Expect = 7.5
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 144 LGLNNTPDRVPDLCLFYSSDFIIYSSLSSF--YIPCIIMVFLYYNIFKALSKRAK 196
LGL P R PD Y + ++ +SS I + ++ + ++++ K
Sbjct: 422 LGLAGMPRRYPD----YPDAYAGWNMISSIGSLISFVSVLLFLFIVWESFVSGRK 472
>gnl|CDD|222477 pfam13965, SID-1_RNA_chan, dsRNA-gated channel SID-1. This is a
family of proteins that are transmembrane dsRNA-gated
channels. They passively transport dsRNA into cells and
do not act as ATP-dependent pumps. They are required for
systemic RNA interference.
Length = 567
Score = 27.4 bits (61), Expect = 9.0
Identities = 6/39 (15%), Positives = 15/39 (38%)
Query: 173 FYIPCIIMVFLYYNIFKALSKRAKKAKAARKPHLSEMKP 211
C++ + +IF+ + + +P SE +
Sbjct: 126 LLSFCLLFIVFVIHIFRNRRDLRSRDIISFEPSPSEQRA 164
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
0.326 0.139 0.428
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,644,421
Number of extensions: 1188576
Number of successful extensions: 1659
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1650
Number of HSP's successfully gapped: 65
Length of query: 252
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 157
Effective length of database: 6,723,972
Effective search space: 1055663604
Effective search space used: 1055663604
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 (21.7 bits)
S2: 58 (26.1 bits)