RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17211
(72 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 = 68.9 bits (169), Expect = 5e-16
Identities = 26/70 (37%), Positives = 43/70 (61%)
Query: 1 MRTVTNYYLVNLSLADLFMAVFNCVFNFIYMLYSHWPFGEMYCKVNYFITNITVAASVFT 60
+RT TN +L+NL++ADL + + Y++ WPFG+ CK+ F+ + AS+
Sbjct: 9 LRTPTNIFLLNLAVADLLFLLTLPPWALYYLVGGDWPFGDALCKLVGFLFVVNGYASILL 68
Query: 61 LVAISLDRFV 70
L AIS+DR++
Sbjct: 69 LTAISIDRYL 78
>gnl|CDD|222976 PHA03087, PHA03087, G protein-coupled chemokine receptor-like
protein; Provisional.
Length = 335
Score = 34.8 bits (80), Expect = 0.001
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 2 RTVTNYYLVNLSLADL-FMAVFNCVFNFIYMLYSHWPFGEMYCKVNYFITNITVAASVFT 60
+T + YL+NL+++DL F+ F Y + W FGE CK+ + I S+
Sbjct: 71 KTPMDIYLLNLAVSDLLFVMTLP--FQIYYYILFQWSFGEFACKIVSGLYYIGFYNSMNF 128
Query: 61 LVAISLDRFV 70
+ +S+DR++
Sbjct: 129 ITVMSVDRYI 138
>gnl|CDD|165021 PHA02638, PHA02638, CC chemokine receptor-like protein;
Provisional.
Length = 417
Score = 32.7 bits (74), Expect = 0.007
Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 4/70 (5%)
Query: 1 MRTVTNYYLVNLSLADLFMAVFNCVFNF-IYMLYSHWPFGEMYCKVNYFITNITVAASVF 59
++T+T+ Y+ NL+++DL +F F F IY + W FG+ CKV I +++F
Sbjct: 128 IKTITDIYIFNLAISDL---IFVIDFPFIIYNEFDQWIFGDFMCKVISASYYIGFFSNMF 184
Query: 60 TLVAISLDRF 69
+ +S+DR+
Sbjct: 185 LITLMSIDRY 194
>gnl|CDD|213356 cd12822, TmCorA-like, Thermotoga maritima CorA-like family. This
family belongs to the MIT superfamily of essential
membrane proteins involved in transporting divalent
cations (uptake or efflux) across membranes. Members of
the Thermotoga maritima CorA_like family are found in
all three kingdoms of life. It is a functionally diverse
family, in addition to the CorA Co2+ transporter from
the hyperthermophilic Thermotoga maritima, it includes
three Saccharomyces cerevisiae members: two plasma
membrane proteins, the Mg2+ transporter Alr1p/Swc3p and
the putative Mg2+ transporter, Alr2p, and the vacuole
membrane protein Mnr2p, a putative Mg2+ transporter.
Thermotoga maritima CorA forms funnel-shaped
homopentamers, the tip of the funnel is formed from two
C-terminal transmembrane (TM) helices from each monomer,
and the large opening of the funnel from the N-terminal
cytoplasmic domains. The GMN signature motif of the MIT
superfamily occurs just after TM1, mutation within this
motif is known to abolish Mg2+ transport by Alr1p.
Natural variants in this signature sequence may be
associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 289
Score = 26.8 bits (60), Expect = 0.73
Identities = 12/38 (31%), Positives = 15/38 (39%), Gaps = 7/38 (18%)
Query: 27 NFIYMLYSHWPFGEMYCKVNYFITNITVAASVFTLVAI 64
NF YM HWP+G YFI + L+
Sbjct: 252 NFEYMPELHWPYG-------YFIVLGIMLLIAGGLLWW 282
>gnl|CDD|165177 PHA02834, PHA02834, chemokine receptor-like protein; Provisional.
Length = 323
Score = 26.4 bits (58), Expect = 1.3
Identities = 22/67 (32%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 4 VTNYYLVNLSLADLFMAVFNCVFNFIYMLYSHWPFGEMYCKVNYFITNITVAASVFTLVA 63
V + YL N++++DL M VF+ F I+ + W FGE CK+ + + +++F +
Sbjct: 61 VVDVYLFNIAMSDL-MLVFSFPF-IIHNDLNEWIFGEFMCKLVLGVYFVGFFSNMFFVTL 118
Query: 64 ISLDRFV 70
IS+DR++
Sbjct: 119 ISIDRYI 125
>gnl|CDD|181509 PRK08629, PRK08629, coproporphyrinogen III oxidase; Provisional.
Length = 433
Score = 25.8 bits (57), Expect = 1.8
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 30 YMLYSHWPFGEMYC 43
YMLY+H PF C
Sbjct: 53 YMLYAHVPFCHTLC 66
>gnl|CDD|239219 cd02889, SQCY, Squalene cyclase (SQCY) domain; found in class II
terpene cyclases that have an alpha 6 - alpha 6 barrel
fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene
cyclase (OSQCY) are integral membrane proteins that
catalyze a cationic cyclization cascade converting
linear triterpenes to fused ring compounds. Bacterial
SQCY catalyzes the convertion of squalene to hopene or
diplopterol. Eukaryotic OSQCY transforms the 2,3-epoxide
of squalene to compounds such as, lanosterol (a
metabolic precursor of cholesterol and steroid hormones)
in mammals and fungi or, cycloartenol in plants.
Deletion of a single glycine residue of Alicyclobacillus
acidocaldarius SQCY alters its substrate specificity
into that of eukaryotic OSQCY. Both enzymes have a
second minor domain, which forms an alpha-alpha barrel
that is inserted into the major domain. This group also
contains SQCY-like archael sequences and some bacterial
SQCY's which lack this minor domain.
Length = 348
Score = 25.6 bits (57), Expect = 2.5
Identities = 10/37 (27%), Positives = 13/37 (35%), Gaps = 7/37 (18%)
Query: 8 YLVNLSLAD------LFMAVFNCVFNFIYMLYSH-WP 37
YL+N D VF F Y Y + +P
Sbjct: 305 YLLNTQQEDGDWPQEEITGVFFKNFYIRYHNYRNYFP 341
>gnl|CDD|233033 TIGR00583, mre11, DNA repair protein (mre11). All proteins in this
family for which functions are known are subunits of a
nuclease complex made up of multiple proteins including
MRE11 and RAD50 homologs. The functions of this nuclease
complex include recombinational repair and non-homolgous
end joining. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University). The proteins in this family are distantly
related to proteins in the SbcCD complex of bacteria
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 402
Score = 24.8 bits (54), Expect = 5.0
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 39 GEMYCKVNYFITNITVAASVFTL 61
+C VNY NI VA VF++
Sbjct: 94 DTAFCNVNYEDPNINVAIPVFSI 116
>gnl|CDD|219281 pfam07059, DUF1336, Protein of unknown function (DUF1336). This
family represents the C-terminus (approximately 250
residues) of a number of hypothetical plant proteins of
unknown function.
Length = 215
Score = 24.2 bits (53), Expect = 7.2
Identities = 12/35 (34%), Positives = 14/35 (40%)
Query: 37 PFGEMYCKVNYFITNITVAASVFTLVAISLDRFVE 71
P GE Y V YF V + L RFV+
Sbjct: 74 PGGEGYSLVLYFALEEPVEKELSPAFGSLLRRFVD 108
>gnl|CDD|237910 PRK15103, PRK15103, paraquat-inducible membrane protein A;
Provisional.
Length = 419
Score = 23.8 bits (52), Expect = 9.3
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 13 SLADLFMAVFNCVFNFIYM 31
+L+ LFM + +F F+ M
Sbjct: 55 ALSALFMLLLANLFPFVNM 73
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
0.335 0.142 0.448
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,542,163
Number of extensions: 260808
Number of successful extensions: 517
Number of sequences better than 10.0: 1
Number of HSP's gapped: 514
Number of HSP's successfully gapped: 31
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 53 (24.1 bits)