RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13007
(128 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 = 63.1 bits (154), Expect = 5e-13
Identities = 32/85 (37%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 44 VVIARNKHMHTATNYYLFSLAVSDLLMLFWGIPSEIIYIWHKYPYMFDETICIMVSFLSE 103
+VI R K + T TN +L +LAV+DLL L +P +Y + F + +C +V FL
Sbjct: 1 LVILRTKKLRTPTNIFLLNLAVADLLFLL-TLPPWALYYLVGGDWPFGDALCKLVGFLFV 59
Query: 104 TSANATVLTITAFTVERYIAICHPF 128
+ A++L +TA +++RY+AI HP
Sbjct: 60 VNGYASILLLTAISIDRYLAIVHPL 84
>gnl|CDD|222976 PHA03087, PHA03087, G protein-coupled chemokine receptor-like
protein; Provisional.
Length = 335
Score = 43.6 bits (103), Expect = 5e-06
Identities = 37/106 (34%), Positives = 53/106 (50%), Gaps = 3/106 (2%)
Query: 22 FPVTVIYVIILVTGCFGNLCTCVVIARNKHMHTATNYYLFSLAVSDLLMLFWGIPSEIIY 81
+ V+Y I G GN+ V+ + K + T + YL +LAVSDLL F IY
Sbjct: 41 TILIVVYSTIFFFGLVGNIIVIYVLTKTK-IKTPMDIYLLNLAVSDLL--FVMTLPFQIY 97
Query: 82 IWHKYPYMFDETICIMVSFLSETSANATVLTITAFTVERYIAICHP 127
+ + + F E C +VS L ++ IT +V+RYIAI HP
Sbjct: 98 YYILFQWSFGEFACKIVSGLYYIGFYNSMNFITVMSVDRYIAIVHP 143
>gnl|CDD|165021 PHA02638, PHA02638, CC chemokine receptor-like protein;
Provisional.
Length = 417
Score = 41.2 bits (96), Expect = 4e-05
Identities = 30/104 (28%), Positives = 55/104 (52%), Gaps = 4/104 (3%)
Query: 24 VTVIYVIILVTGCFGNLCTCVVIARNKHMHTATNYYLFSLAVSDLLMLFWGIPSEIIYIW 83
+ + Y+II + G FGN ++I K + T T+ Y+F+LA+SDL+ + I I
Sbjct: 101 IKIFYIIIFILGLFGNAAI-IMILFCKKIKTITDIYIFNLAISDLIFV---IDFPFIIYN 156
Query: 84 HKYPYMFDETICIMVSFLSETSANATVLTITAFTVERYIAICHP 127
++F + +C ++S + + IT +++RY AI +P
Sbjct: 157 EFDQWIFGDFMCKVISASYYIGFFSNMFLITLMSIDRYFAILYP 200
>gnl|CDD|165177 PHA02834, PHA02834, chemokine receptor-like protein; Provisional.
Length = 323
Score = 34.5 bits (79), Expect = 0.009
Identities = 26/103 (25%), Positives = 53/103 (51%), Gaps = 8/103 (7%)
Query: 24 VTVIYVIILVTGCFGNLCTCVVIARNKHMHTATNYYLFSLAVSDLLMLFWGIPSEIIYIW 83
V V Y+++ + G GN+ V+ + M + YLF++A+SDL+++F +I
Sbjct: 31 VIVFYILLFIFGLIGNVLVIAVLIVKRFMFV-VDVYLFNIAMSDLMLVF-----SFPFII 84
Query: 84 HK--YPYMFDETICIMVSFLSETSANATVLTITAFTVERYIAI 124
H ++F E +C +V + + + +T +++RYI +
Sbjct: 85 HNDLNEWIFGEFMCKLVLGVYFVGFFSNMFFVTLISIDRYILV 127
>gnl|CDD|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases. RNase
PH-like 3'-5' exoribonucleases are enzymes that catalyze
the 3' to 5' processing and decay of RNA substrates.
Evolutionarily related members can be fond in
prokaryotes, archaea, and eukaryotes. Bacterial
ribonuclease PH contains a single copy of this domain,
and removes nucleotide residues following the -CCA
terminus of tRNA. Polyribonucleotide
nucleotidyltransferase (PNPase) contains two tandem
copies of the domain and is involved in mRNA degradation
in a 3'-5' direction. Archaeal exosomes contain two
individually encoded RNase PH-like 3'-5'
exoribonucleases and are required for 3' processing of
the 5.8S rRNA. The eukaryotic exosome core is composed
of six individually encoded RNase PH-like subunits, but
it is not a phosphorolytic enzyme per se; it directly
associates with Rrp44 and Rrp6, which are hydrolytic
exoribonucleases related to bacterial RNase II/R and
RNase D. All members of the RNase PH-like family form
ring structures by oligomerization of six domains or
subunits, except for a total of 3 subunits with tandem
repeats in the case of PNPase, with a central channel
through which the RNA substrate must pass to gain access
to the phosphorolytic active sites.
Length = 218
Score = 29.2 bits (66), Expect = 0.45
Identities = 9/26 (34%), Positives = 10/26 (38%)
Query: 22 FPVTVIYVIILVTGCFGNLCTCVVIA 47
P V+YV I V G L A
Sbjct: 95 KPSWVLYVDIQVLSRDGGLLDACWNA 120
>gnl|CDD|206772 cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryotic exosome. The
RRP42 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 272
Score = 26.8 bits (60), Expect = 3.6
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 26 VIYVIILVTGCFGNLCTCVVIA 47
V+YV +LV GNL + IA
Sbjct: 130 VLYVDVLVLESGGNLLDAISIA 151
>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 = 25.6 bits (57), Expect = 7.1
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 32 LVTGCFGNLCTCVVIARNKHMHTATNYYLFSLAVSDLLMLFWGIPS 77
V G FGN+ ++ + K + + +Y + ++DLL L I
Sbjct: 1 SVIGIFGNVIMIILTFKKKKLRSKCSYLICVQCLADLLCLSGEIIF 46
>gnl|CDD|152415 pfam11980, DUF3481, Domain of unknown function (DUF3481). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is about 80
amino acids in length. This domain is found associated
with pfam00754, pfam00431, pfam00629. This domain has
two completely conserved residues (Y and E) that may be
functionally important.
Length = 84
Score = 24.4 bits (53), Expect = 9.8
Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 2/59 (3%)
Query: 7 EDLAWGPQHDPLYVIFPVTVIYVIILVTGCFGNL--CTCVVIARNKHMHTATNYYLFSL 63
+ DP+ ++L C G + C C A +K H+A Y F L
Sbjct: 10 QPGNMLKTLDPILYTIIAMSGLGVLLGAVCLGVVLYCHCSHNAMSKRNHSALENYNFEL 68
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
0.330 0.142 0.470
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,472,971
Number of extensions: 552851
Number of successful extensions: 669
Number of sequences better than 10.0: 1
Number of HSP's gapped: 662
Number of HSP's successfully gapped: 27
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
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 (21.9 bits)
S2: 53 (24.4 bits)