RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6104
(118 letters)
>gnl|CDD|240549 cd13144, MATE_like_4, Uncharacterized subfamily of the multidrug
and toxic compound extrusion (MATE) proteins. The
integral membrane proteins from the MATE family are
involved in exporting metabolites across the cell
membrane and are responsible for multidrug resistance
(MDR) in many bacteria and animals. A number of family
members are involved in the synthesis of peptidoglycan
components in bacteria.
Length = 434
Score = 32.2 bits (74), Expect = 0.046
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 33 WWCFLLSSIFTFILGLVIVLLWRL 56
WW F ++ I +F+L L + L RL
Sbjct: 413 WWSFPIAEIVSFLLSL--LFLKRL 434
>gnl|CDD|238832 cd01662, Ubiquinol_Oxidase_I, Ubiquinol oxidase subunit I.
Ubiquinol oxidase, the terminal oxidase in the
respiratory chains of aerobic bacteria, is a multi-chain
transmembrane protein located in the cell membrane. It
catalyzes the reduction of O2 and simultaneously pumps
protons across the membrane. The number of subunits in
ubiquinol oxidase varies from two to five. Subunit I
contains a heme-copper binuclear center (the active site
where O2 is reduced to water) formed by a high-spin heme
and a copper ion. It also contains a low-spin heme,
believed to participate in the transfer of electrons
from ubiquinol 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 ubiquinol 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.
It is generally believed that the channels contain water
molecules that act as 'proton wires' to transfer the
protons. A well-defined pathway for the transfer of
pumped protons beyond the binuclear center has not been
identified. Electrons are believed to be transferred
directly from ubiquinol (the electron donor) to the
low-spin heme, and directly from the low-spin heme to
the binuclear center.
Length = 501
Score = 28.3 bits (64), Expect = 0.85
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 34 WCFLLSSIFTFILGL-VIVLLWRLFAFICCRKEPELSPNDP 73
L+S+I F++ V++ L + I RK + DP
Sbjct: 444 PLNLISTIGAFLIAAGVLLFLINVIVSI--RKGKRDATGDP 482
>gnl|CDD|119392 cd06174, MFS, The Major Facilitator Superfamily (MFS) is a large
and diverse group of secondary transporters that
includes uniporters, symporters, and antiporters. MFS
proteins facilitate the transport across cytoplasmic or
internal membranes of a variety of substrates including
ions, sugar phosphates, drugs, neurotransmitters,
nucleosides, amino acids, and peptides. They do so using
the electrochemical potential of the transported
substrates. Uniporters transport a single substrate,
while symporters and antiporters transport two
substrates in the same or in opposite directions,
respectively, across membranes. MFS proteins are
typically 400 to 600 amino acids in length, and the
majority contain 12 transmembrane alpha helices (TMs)
connected by hydrophilic loops. The N- and C-terminal
halves of these proteins display weak similarity and may
be the result of a gene duplication/fusion event. Based
on kinetic studies and the structures of a few bacterial
superfamily members, GlpT (glycerol-3-phosphate
transporter), LacY (lactose permease), and EmrD
(multidrug transporter), MFS proteins are thought to
function through a single substrate binding site,
alternating-access mechanism involving a rocker-switch
type of movement. Bacterial members function primarily
for nutrient uptake, and as drug-efflux pumps to confer
antibiotic resistance. Some MFS proteins have medical
significance in humans such as the glucose transporter
Glut4, which is impaired in type II diabetes, and
glucose-6-phosphate transporter (G6PT), which causes
glycogen storage disease when mutated.
Length = 352
Score = 28.0 bits (63), Expect = 1.0
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 33 WWCFLLSSIFTFILGLVIVLLWRLFAFICC 62
W FL+ +I +L L+++ L RL +
Sbjct: 153 RWLFLILAILGLLLALLLLFLLRLLLLLAL 182
>gnl|CDD|221311 pfam11915, DUF3433, Protein of unknown function (DUF3433). This
is a family of functionally uncharacterized proteins.
The family is found in eukaryotes, and represents the
conserved central region of the member proteins.
Length = 92
Score = 26.8 bits (60), Expect = 1.4
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 34 WCFLLSSIFTFILGLVIVLLWRLFAFICCRKEP 66
FL S + T ++ +++ LLW+ F R +P
Sbjct: 1 SNFLYSFLPT-LVAVILGLLWQSIDFDVRRLQP 32
>gnl|CDD|220443 pfam09852, DUF2079, Predicted membrane protein (DUF2079). This
domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 451
Score = 27.3 bits (61), Expect = 1.9
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 9/38 (23%)
Query: 27 CLQERKWWCFLLSSIFTF---------ILGLVIVLLWR 55
L RKWW FLL + + GL + LL R
Sbjct: 129 ALLRRKWWLFLLLLLLLLLVKEDLGLVVAGLGLWLLLR 166
>gnl|CDD|218619 pfam05510, Sarcoglycan_2, Sarcoglycan alpha/epsilon. Sarcoglycans
are a subcomplex of transmembrane proteins which are
part of the dystrophin-glycoprotein complex. They are
expressed in the skeletal, cardiac and smooth muscle.
Although numerous studies have been conducted on the
sarcoglycan subcomplex in skeletal and cardiac muscle,
the manner of the distribution and localisation of these
proteins along the nonjunctional sarcolemma is not
clear. This family contains alpha and epsilon members.
Length = 398
Score = 26.7 bits (59), Expect = 3.2
Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 14/81 (17%)
Query: 10 KPTESILISTATSDIDICLQERKWWC----------FLLSSIFTF--ILGLVIVLLWRLF 57
KP E +S A D L + + + TF L + ++L+ L
Sbjct: 259 KPKEEEPLSKANGDGI--LFHDPEYAPPRELVPYRDYGDEFVVTFAIPLLVFLLLVLLLA 316
Query: 58 AFICCRKEPELSPNDPKQKEQ 78
+C ++E + Q
Sbjct: 317 YIMCFQREGRKKRDSRTSDSQ 337
>gnl|CDD|130156 TIGR01084, mutY, A/G-specific adenine glycosylase. This equivalog
model identifies mutY members of the pfam00730
superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro
rich loop followed by a conserved aspartate). The major
members of the superfamily are nth and mutY [DNA
metabolism, DNA replication, recombination, and repair].
Length = 275
Score = 26.6 bits (59), Expect = 3.4
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 78 QKAIRQGKQEFEGTFMTEAKDWAGELISGQTTTGRIL 114
KA ++ +EF G F + +D A G+ T G IL
Sbjct: 86 HKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAIL 122
>gnl|CDD|176248 cd08288, MDR_yhdh, Yhdh putative quinone oxidoreductases. Yhdh
putative quinone oxidoreductases (QOR). QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 324
Score = 26.3 bits (59), Expect = 3.7
Identities = 7/23 (30%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 93 MTEAKDWAGELISGQTTTGRILV 115
+ + D A +++GQ GR++V
Sbjct: 301 LADVPDAAEAILAGQ-VRGRVVV 322
>gnl|CDD|177862 PLN02214, PLN02214, cinnamoyl-CoA reductase.
Length = 342
Score = 26.6 bits (58), Expect = 3.7
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 13 ESILISTATSDIDICLQERKWWCF 36
E+++ + SD+D C + W+C+
Sbjct: 140 EAVVDESCWSDLDFCKNTKNWYCY 163
>gnl|CDD|143653 cd07912, Tweety_N, N-terminal domain of the protein encoded by
the Drosophila tweety gene and related proteins, a
family of chloride ion channels. The protein product
of the Drosophila tweety (tty) gene is thought to form
a trans-membrane protein with five membrane-spanning
regions and a cytoplasmic C-terminus. This N-terminal
domain contains the putative transmembrane spanning
regions. Tweety has been suggested as a candidate for a
large conductance chloride channel, both in vertebrate
and insect cells. Three human homologs have been
identified and designated TTYH1-3. TTYH2 has been
associated with the progression of cancer, and
Drosophila melanogaster tweety has been assumed to play
a role in development. TTYH2, and TTYH3 bind to and are
ubiquinated by Nedd4-2, a HECT type E3 ubiquitin
ligase, which most likely plays a role in controlling
the cellular levels of tweety family proteins.
Length = 418
Score = 26.1 bits (58), Expect = 5.2
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 37 LLSSIFTFILGL-VIVLLWRLFAFICCRKEPELSPN 71
+L+SI L L ++ LL L C RK E P
Sbjct: 41 ILASIPAACLILSLLFLLVYLITRCCDRKPTEERPR 76
>gnl|CDD|224839 COG1928, PMT1, Dolichyl-phosphate-mannose--protein O-mannosyl
transferase [Posttranslational modification, protein
turnover, chaperones].
Length = 699
Score = 26.3 bits (58), Expect = 5.2
Identities = 6/29 (20%), Positives = 8/29 (27%), Gaps = 3/29 (10%)
Query: 32 KWWCFLLSSIFTFILGLVIVLLWRLFAFI 60
KW + L + LW L
Sbjct: 209 KWVGLF---TTGVVGLLAVYELWSLLYDK 234
>gnl|CDD|163462 TIGR03750, conj_TIGR03750, conjugative transfer region protein,
TIGR03750 family. Members of this protein family are
found occasionally on plasmids. Usually, however, they
are found on the bacterial main chromosome in regions
flanked by markers of conjugative transfer and/or
transposition [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 111
Score = 25.3 bits (56), Expect = 5.2
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 33 WWCFLLSSIFTFILGLVIVLLWRLFAFIC 61
+ +LGL++ LL +A I
Sbjct: 24 GVAAGVGLAAGLVLGLLLALLAGPWALIP 52
>gnl|CDD|220432 pfam09835, DUF2062, Uncharacterized protein conserved in bacteria
(DUF2062). This domain, found in various prokaryotic
proteins, has no known function.
Length = 148
Score = 25.6 bits (57), Expect = 5.7
Identities = 4/23 (17%), Positives = 11/23 (47%)
Query: 35 CFLLSSIFTFILGLVIVLLWRLF 57
+L + + +++ LWR +
Sbjct: 118 SLVLGLVLALLGYFLVLRLWRAY 140
>gnl|CDD|220420 pfam09815, XK-related, XK-related protein. Members of this family
comprise various XK-related proteins, that are involved
in sodium-dependent transport of neutral amino acids or
oligopeptides. These proteins are responsible for the Kx
blood group system - defects results in McLeod syndrome,
an X-linked multi-system disorder characterized by late
onset abnormalities in the neuromuscular and
hematopoietic systems.
Length = 334
Score = 26.1 bits (58), Expect = 5.7
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 37 LLSSIFTFILGLVIVLLWRLFAFICCRKEPE 67
L +S+F + V++L W + F R++ +
Sbjct: 210 LFASVFPLYVAAVLLLHWLVMTFWVSRQQTD 240
>gnl|CDD|223567 COG0493, GltD, NADPH-dependent glutamate synthase beta chain and
related oxidoreductases [Amino acid transport and
metabolism / General function prediction only].
Length = 457
Score = 26.1 bits (58), Expect = 5.9
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 1/45 (2%)
Query: 71 NDPKQKEQKAIRQGKQEFEGTFMTEAKDWAGELISGQTTTGRILV 115
+P + R+G GT T+A D I G +
Sbjct: 348 VEPGEYVDGWGRRGPVGVIGTEKTDAADTVILAI-GFEGDATDGL 391
>gnl|CDD|235559 PRK05684, flgJ, flagellar rod assembly protein/muramidase FlgJ;
Validated.
Length = 312
Score = 25.6 bits (57), Expect = 6.2
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 74 KQKEQKAIRQGKQEFEGTFM 93
+ + +R Q+FEG F+
Sbjct: 25 GKDPKANLRAVAQQFEGMFV 44
>gnl|CDD|224491 COG1575, MenA, 1,4-dihydroxy-2-naphthoate octaprenyltransferase
[Coenzyme metabolism].
Length = 303
Score = 25.7 bits (57), Expect = 6.4
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 31 RKWWCFLLSSIFTFILGLVIVLLWRLFAFI 60
RK + LL + I+ VI+ L+ ++ +
Sbjct: 222 RKLYAALLVVAYLAIVIFVILGLFPVWGLL 251
>gnl|CDD|223152 COG0074, SucD, Succinyl-CoA synthetase, alpha subunit [Energy
production and conversion].
Length = 293
Score = 25.2 bits (56), Expect = 8.2
Identities = 15/38 (39%), Positives = 18/38 (47%)
Query: 76 KEQKAIRQGKQEFEGTFMTEAKDWAGELISGQTTTGRI 113
K+ K I QG +GTF TE G I G T G+
Sbjct: 7 KDTKVIVQGITGKQGTFHTEQMLAYGTKIVGGVTPGKG 44
>gnl|CDD|233141 TIGR00820, zip, ZIP zinc/iron transport family. The Zinc
(Zn2+)-Iron (Fe2+) Permease (ZIP) Family (TC
2.A.5)Members of the ZIP family consist of proteins with
eight putative transmembrane spanners. They are derived
from animals, plants and yeast. Theycomprise a diverse
family, with several paralogues in any one organism
(e.g., at least five in Caenorabditis elegans, at least
five in Arabidopsis thaliana and two inSaccharomyces
cervisiae. The two S. cerevisiae proteins, Zrt1 and
Zrt2, both probably transport Zn2+ with high
specificity, but Zrt1 transports Zn2+ with ten-fold
higher affinitythan Zrt2. Some members of the ZIP family
have been shown to transport Zn2+ while others transport
Fe2+, and at least one transports a range of metal ions.
The energy source fortransport has not been
characterized, but these systems probably function as
secondary carriers [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 324
Score = 25.4 bits (56), Expect = 8.5
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 25 DICLQERKWWCFLLSSIFTFILGLVIVLLWRLFA 58
CL+ W F + I ++ LL LFA
Sbjct: 82 SPCLESTPWGKFPFAGFIAMI-SAILTLLVDLFA 114
>gnl|CDD|220467 pfam09911, DUF2140, Uncharacterized protein conserved in bacteria
(DUF2140). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 187
Score = 25.2 bits (56), Expect = 8.7
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 14/57 (24%)
Query: 32 KWWCFLLSSIFTFILGLVIVLLWRLFAFICCRKEPELSPNDPKQKEQKAIRQGKQEF 88
KW F+L ++ L + V+ +RLFA P +P K + F
Sbjct: 4 KWAFFVLLAL---NLASIAVVFFRLFA-----------PVEPVTKPSAKESKSDAVF 46
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 25.4 bits (55), Expect = 8.7
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 4/31 (12%)
Query: 6 CVLCK-PTESILISTATSDIDICLQERKWWC 35
C LC+ TE+++ T+ + +R+ W
Sbjct: 100 CPLCRTETEAVVF---TASSPADITDRRQWK 127
>gnl|CDD|150923 pfam10327, 7TM_GPCR_Sri, Serpentine type 7TM GPCR chemoreceptor
Sri. 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. Sri is part of the Str
superfamily of chemoreceptors. Chemoperception is one of
the central senses of soil nematodes like C. elegans
which are otherwise 'blind' and 'deaf'.
Length = 303
Score = 25.2 bits (56), Expect = 8.7
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 33 WWCFLLSSIFTFILGLVIVLLWRLFAFI 60
L +IF F+L + L L F+
Sbjct: 88 ISSHYLMTIFVFLLSFQLESL--LLCFV 113
>gnl|CDD|223939 COG1007, NuoN, NADH:ubiquinone oxidoreductase subunit 2 (chain N)
[Energy production and conversion].
Length = 475
Score = 25.3 bits (56), Expect = 9.0
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 36 FLLSSIFTFILGLVIVLLWRLFA 58
L+++I +LG++ + L A
Sbjct: 446 LLVAAILVLVLGILPQPVIDLAA 468
>gnl|CDD|149223 pfam08019, DUF1705, Domain of unknown function (DUF1705). Some
members of this family are putative bacterial membrane
proteins. This domain is found immediately N terminal to
the sulfatase domain in many sulfatases.
Length = 156
Score = 25.2 bits (56), Expect = 9.2
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 28 LQERKWWCFLLSSIFTFILGLVIVLLWRLFAF 59
++ R W LL + + + L+++LL +
Sbjct: 88 IRYRPWLRELLQRLLSILASLLVILLIAFLFY 119
>gnl|CDD|220299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 25.3 bits (56), Expect = 9.7
Identities = 8/44 (18%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 24 IDICLQERKWWCFLLSSIFTFI----------LGLVIVLLWRLF 57
++ ++E+K ++++ I + LV+ L+RL
Sbjct: 159 LERLIREKKPGLYIIALALLLISNFYFGYMICIFLVLYFLYRLI 202
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 0.138 0.447
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,785,567
Number of extensions: 490438
Number of successful extensions: 1407
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1401
Number of HSP's successfully gapped: 87
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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: 53 (24.1 bits)