RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4697
(383 letters)
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 62.3 bits (152), Expect = 3e-12
Identities = 36/97 (37%), Positives = 52/97 (53%), Gaps = 8/97 (8%)
Query: 49 EYSVSALENLPVNYVLLTVTTN---KPRDLRVKY-WLSNDYGERFSISRQ-GDISLMQCL 103
Y VS EN P V+LTV+ + V Y +S + FSI G+I+ + L
Sbjct: 1 SYEVSVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTAKPL 60
Query: 104 DYETEDSYRFTVYATD---TLMTTSATVNISVVNVND 137
D E + SY TV ATD ++++ATV I+V++VND
Sbjct: 61 DREEQSSYTLTVTATDGGGPPLSSTATVTITVLDVND 97
Score = 51.5 bits (124), Expect = 2e-08
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 158 DLTPGSVIGKVEAADGDKGD--RVTLSL-RGPYEKMFSIN-DSGHISIVD-LSALNTSTI 212
+ PG+V+ V A D D G+ VT S+ G + +FSI+ +G I+ L S+
Sbjct: 9 NAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTAKPLDREEQSSY 68
Query: 213 QLVVVATDTGNPPRQASVP 231
L V ATD G PP ++
Sbjct: 69 TLTVTATDGGGPPLSSTAT 87
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 51.9 bits (125), Expect = 8e-09
Identities = 35/92 (38%), Positives = 45/92 (48%), Gaps = 10/92 (10%)
Query: 50 YSVSALENLPVNYVLLTVTTNKPRDL----RVKYW-LSNDYGERFSISRQ-GDISLMQCL 103
YS S EN PV +LTVT DL R+ Y L G F I GD+S + L
Sbjct: 1 YSASVPENAPVGTEVLTVTATDA-DLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTKPL 59
Query: 104 DYETEDSYRFTVYATD---TLMTTSATVNISV 132
D E+ Y TV ATD ++++ TV I+V
Sbjct: 60 DRESIGEYELTVLATDSGGPPLSSTTTVTITV 91
Score = 39.2 bits (92), Expect = 3e-04
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 158 DLTPGSVIGKVEAADGDKGDRVTLS---LRGPYEKMFSIN-DSGHISIVD-LSALNTSTI 212
+ G+ + V A D D G + L G F I+ D+G +S L +
Sbjct: 8 NAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTKPLDRESIGEY 67
Query: 213 QLVVVATDTGNPPRQASVPAI 233
+L V+ATD+G PP ++
Sbjct: 68 ELTVLATDSGGPPLSSTTTVT 88
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 50.0 bits (120), Expect = 3e-08
Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 5/67 (7%)
Query: 76 RVKYWL-SNDYGERFSI-SRQGDISLMQCLDYETEDSYRFTVYATD---TLMTTSATVNI 130
+V Y + S + FSI G+I+ + LD E + Y TV ATD ++++ATV I
Sbjct: 12 KVTYSILSGNDDGLFSIDPETGEITTTKPLDREEQPEYTLTVEATDGGGPPLSSTATVTI 71
Query: 131 SVVNVND 137
+V++VND
Sbjct: 72 TVLDVND 78
Score = 33.9 bits (78), Expect = 0.017
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 170 AADGDKGD--RVTLSL-RGPYEKMFSIN-DSGHISIVD-LSALNTSTIQLVVVATDTGNP 224
A D D G+ +VT S+ G + +FSI+ ++G I+ L L V ATD G P
Sbjct: 2 ATDADSGENGKVTYSILSGNDDGLFSIDPETGEITTTKPLDREEQPEYTLTVEATDGGGP 61
Query: 225 PRQASVP 231
P ++
Sbjct: 62 PLSSTAT 68
>gnl|CDD|216842 pfam02009, Rifin_STEVOR, Rifin/stevor family. Several multicopy
gene families have been described in Plasmodium
falciparum, including the stevor family of subtelomeric
open reading frames and the rif interspersed repetitive
elements. Both families contain three predicted
transmembrane segments. It has been proposed that stevor
and rif are members of a larger superfamily that code
for variant surface antigens.
Length = 290
Score = 34.3 bits (79), Expect = 0.082
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 252 TSSTVLIILGVVLIVLGFVIILLIL-YIHKNKHTK 285
+ +++IVL +II LIL Y K K K
Sbjct: 246 FEPIYASAIAILIIVLVMLIIYLILRYRRKKKMKK 280
>gnl|CDD|182152 PRK09932, PRK09932, glycerate kinase II; Provisional.
Length = 381
Score = 34.1 bits (78), Expect = 0.11
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 11/80 (13%)
Query: 154 IPLADLTPGSVIGKVEAADGDKGDRVTLSLRGPY-EKM---FSINDSGHISIVDLSALNT 209
+P+AD G+V V A G+ VTL + GP EK+ + + G ++++++A +
Sbjct: 39 LPIADGGEGTVDAMVAATG---GNIVTLEVCGPMGEKVNAFYGLTGDGKTAVIEMAAASG 95
Query: 210 STIQLVVVATDTGNPPRQAS 229
L++VA + NP +S
Sbjct: 96 ----LMLVAPEKRNPLLASS 111
>gnl|CDD|99957 cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA
domains. Bromodomains are 110 amino acid long domains,
that are found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine. The structure(2DKW) in this alignment is an
uncharacterized protein predicted from analysis of cDNA
clones from human fetal liver.
Length = 112
Score = 31.6 bits (72), Expect = 0.22
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 2 INEDDFLQPITLVVRAIQYDNQDRYALATLIVSKA 36
+ DFL+ I L+V N DR LI S+A
Sbjct: 59 LTAKDFLKDIDLIVTNALEYNPDRDPADKLIRSRA 93
>gnl|CDD|213052 cd12087, TM_EGFR-like, Transmembrane domain of the Epidermal Growth
Factor Receptor family of Protein Tyrosine Kinases.
PTKs catalyze the transfer of the gamma-phosphoryl group
from ATP to tyrosine (tyr) residues in protein
substrates. EGFR (HER, ErbB) subfamily members include
EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4
(ErbB4), and similar proteins. They are receptor PTKs
(RTKs) containing an extracellular EGF-related
ligand-binding region, a transmembrane (TM) helix, and a
cytoplasmic region with a tyr kinase domain and a
regulatory C-terminal tail. They are activated by
ligand-induced dimerization, resulting in the
phosphorylation of tyr residues in the C-terminal tail,
which serve as binding sites for downstream signaling
molecules. Collectively, they can recognize a variety of
ligands including EGF, TGFalpha, and neuregulins, among
others. All four subfamily members can form homo- or
heterodimers. HER3 contains an impaired kinase domain
and depends on its heterodimerization partner for
activation. EGFR subfamily members are involved in
signaling pathways leading to a broad range of cellular
responses including cell proliferation, differentiation,
migration, growth inhibition, and apoptosis. The TM
domain not only serves as a membrane anchor, but also
plays an important role in receptor dimerization and
optimal activation. Mutations in the TM domain of EGFR
family RTKs have been associated with increased breast
cancer risk.
Length = 38
Score = 29.4 bits (67), Expect = 0.22
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 252 TSSTVLIILGVVLIVLGFVIILLILYI-----HKNKH 283
TS T I GVV +L VI+ LI+++ H +
Sbjct: 2 TSKTTSIAAGVVGGLLVLVILGLIVFLFRRRRHIKRK 38
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 30.5 bits (69), Expect = 0.87
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 253 SSTVLIILGVVLIVLGFVIILLILYIH 279
S +LIILG++LI G I LL+L+
Sbjct: 7 ISIILIILGLLLIASG--IALLVLFGA 31
>gnl|CDD|223646 COG0573, PstC, ABC-type phosphate transport system, permease
component [Inorganic ion transport and metabolism].
Length = 310
Score = 31.1 bits (71), Expect = 0.98
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 256 VLIILGVVLIVLGFVIILLILYIHKNKHTKN 286
L LG+VL V+ ++ +L YI + + K
Sbjct: 280 ALFALGLVLFVITLLLNILARYIVRRRRRKY 310
>gnl|CDD|224188 COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase subunit I [Energy
production and conversion].
Length = 660
Score = 31.2 bits (71), Expect = 1.1
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 253 SSTVLIILGVVLIVLG--FVIILLIL--YIH 279
S IILG+++++ G I L IL +H
Sbjct: 595 SVPFGIILGIIILIFGHLLNIALSILGAGVH 625
>gnl|CDD|224945 COG2034, COG2034, Predicted membrane protein [Function unknown].
Length = 85
Score = 28.8 bits (65), Expect = 1.2
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 254 STVLIILGVVLIVLGFVIILL 274
S LII G++LI +GF++I L
Sbjct: 4 SEDLIIAGLILIFIGFLLIFL 24
>gnl|CDD|176491 cd08761, Cyt_b561_CYB561D2_like, Eukaryotic cytochrome b(561),
including the CYB561D2 gene product. Cytochrome b(561),
as found in eukaryotes, similar to and including the
human CYB561D2 gene product. CYB561D2 is a candidate
tumor suppressor. The protein might act as a
ferric-chelate reductase, catalyzing the reduction of
Fe(3+) to Fe(2+), such as associated with the transport
of iron from the endosome to the cytoplasm. It is
assumed that this protein uses ascorbate as the electron
donor. Belongs to the cytochrome b(561) family, which
are secretory vesicle-specific electron transport
proteins. Cytochromes b(561) are integral membrane
proteins that bind two heme groups non-covalently, and
may have six alpha-helical trans-membrane segments.
Length = 183
Score = 30.0 bits (68), Expect = 1.5
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 256 VLIILGVVLIVLGFVIILLILYIHKNKHTKN 286
+L +L ++ I+ G V I Y +K ++ K
Sbjct: 63 ILQLLALLCILAGLVAI----YYNKERNGKP 89
>gnl|CDD|222017 pfam13273, DUF4064, Protein of unknown function (DUF4064).
Length = 96
Score = 28.8 bits (65), Expect = 1.5
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 242 QQASSKLNSGTSSTVLIILGVVLIVLGFVIILLILYIHKN 281
Q + + ST+ LG+ I+L + I+ + + K
Sbjct: 39 QNSMVETILDALSTLGTGLGIGAIILSILGIIGSILVKKK 78
>gnl|CDD|241486 cd13332, FERM_C_JAK1, Janus kinase 1 FERM domain C-lobe. JAK1 is a
tyrosine kinase protein essential in signaling type I
and type II cytokines. It interacts with the gamma chain
of type I cytokine receptors to elicit signals from the
IL-2 receptor family, the IL-4 receptor family, the
gp130 receptor family, ciliary neurotrophic factor
receptor (CNTF-R), neurotrophin-1 receptor (NNT-1R) and
Leptin-R). It also is involved in transducing a signal
by type I (IFN-alpha/beta) and type II (IFN-gamma)
interferons, and members of the IL-10 family via type II
cytokine receptors. JAK (also called Just Another
Kinase) is a family of intracellular, non-receptor
tyrosine kinases that transduce cytokine-mediated
signals via the JAK-STAT pathway. The JAK family in
mammals consists of 4 members: JAK1, JAK2, JAK3 and
TYK2. JAKs are composed of seven JAK homology (JH)
domains (JH1-JH7) . The C-terminal JH1 domain is the
main catalytic domain, followed by JH2, which is often
referred to as a pseudokinase domain, followed by
JH3-JH4 which is homologous to the SH2 domain, and
lastly JH5-JH7 which is a FERM domain. Named after
Janus, the two-faced Roman god of doorways, JAKs possess
two near-identical phosphate-transferring domains; one
which displays the kinase activity (JH1), while the
other negatively regulates the kinase activity of the
first (JH2). The FERM domain has a cloverleaf tripart
structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe,A-lobe, B-lobe, C-lobe/F1, F2, F3). The
C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 198
Score = 29.8 bits (67), Expect = 1.7
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 11/58 (18%)
Query: 72 PRDLRVKYW-----LSNDYG-ERF-----SISRQGDISLMQCLDYETEDSYRFTVYAT 118
DL+VKY L+ YG E F IS + +++ D + Y V
Sbjct: 18 LYDLKVKYLSTLETLTKGYGAEIFETSSLLISSESELNNFNYGDGDNSHDYEVLVTGN 75
>gnl|CDD|217699 pfam03729, DUF308, Short repeat of unknown function (DUF308).
Family of short repeats that occurs in a limited number
of membrane proteins. It may divide further in short
repeats of around 7-10 residues of the pattern
G-#-X(2)-#(2)-X (#=hydrophobic).
Length = 72
Score = 27.8 bits (63), Expect = 1.7
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 252 TSSTVLIILGVVLIVLGFVIILLILYIHKNKHTKN 286
++I++G++L+V G I+ +I + K
Sbjct: 20 ALLALVILIGILLLVSG--ILQIIAAFQRRKGGGG 52
>gnl|CDD|187762 cd09322, TDT_TehA_like, The Tellurite-resistance/Dicarboxylate
Transporter (TDT) family includes TehA proteins. The
Tellurite-resistance/Dicarboxylate Transporter (TDT)
family includes members from all three kingdoms, but
only three members of the family have been functionally
characterized: the TehA protein of E. coli functioning
as a tellurite-resistance uptake permease, the Mae1
protein of S. pombe functioning in the uptake of malate
and other dicarboxylates, and the sulfite efflux pump
(SSU1) of Saccharomyces cerevisiae. In plants, the
plasma membrane protein SLAC1 (Slow Anion
Channel-Associated 1), which is preferentially expressed
in guard cells, encodes a distant homolog of fungal and
bacterial dicarboxylate/malic acid transport proteins.
SLAC1 is essential in mediating stomatal responses to
physiological and stress stimuli. Members of the TDT
family exhibit 10 putative transmembrane a-helical
spanners (TMSs).
Length = 289
Score = 29.8 bits (68), Expect = 2.1
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 236 FPEAIVQQASSKLNSGTSSTVLIILGVVLIVLGFVIILLIL 276
FP A + A K+ + S L +L +VL+ L +IL++
Sbjct: 249 FPLAALAIALLKMAAYLGSGFLQLLALVLLELLTAVILVLY 289
>gnl|CDD|99881 cd05806, CBM20_laforin, Laforin protein tyrosine phosphatase,
N-terminal CBM20 (carbohydrate-binding module, family
20) domain. Laforin, encoded by the EPM2A gene, is a
dual-specificity phosphatase that dephosphorylates
complex carbohydrates. Mutations in the gene encoding
laforin result in Lafora disease, a fatal autosomal
recessive neurodegenerative disorder characterized by
the presence of intracellular deposits of insoluble,
abnormally branched, glycogen-like polymers, known as
Lafora bodies, in neurons, muscle, liver, and other
tissues. The molecular basis for the formation of these
Lafora bodies is unknown. Laforin is one of the only
phosphatases that contains a carbohydrate-binding
module. The CBM20 domain is found in a large number of
starch degrading enzymes including alpha-amylase,
beta-amylase, glucoamylase, and CGTase (cyclodextrin
glucanotransferase). CBM20 is also present in proteins
that have a regulatory role in starch metabolism in
plants (e.g. alpha-amylase) or glycogen metabolism in
mammals (e.g. laforin). CBM20 folds as an antiparallel
beta-barrel structure with two starch binding sites.
These two sites are thought to differ functionally with
site 1 acting as the initial starch recognition site and
site 2 involved in the specific recognition of
appropriate regions of starch.
Length = 112
Score = 28.6 bits (64), Expect = 2.2
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 3/68 (4%)
Query: 111 YRFTVYATDTLMTTSATVNISVVNVNDWDPRFRYPQYELFLPHIPLADLTPGSVIGKVEA 170
+RF V T T V S + WDP+ P + L+ P +G+VE
Sbjct: 3 FRFGVVLTFADRDTELLVLGSRPELGSWDPQRAVP---MRPARKALSPQEPSLWLGEVEL 59
Query: 171 ADGDKGDR 178
++ D
Sbjct: 60 SEPGSEDT 67
>gnl|CDD|205807 pfam13630, SdpI, SdpI/YhfL protein family. This family of proteins
includes the SdpI and YhfL proteins from B. subtilis.
The SdpI protein is a multipass integral membrane
protein that protects toxin-producing cells from being
killed. Killing is mediated by the exported toxic
protein SdpC an extracellular protein that induces the
synthesis of an immunity protein.
Length = 72
Score = 27.5 bits (62), Expect = 2.5
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 253 SSTVLIILGVVLIVLGFVIILLILYI 278
+ + II G++L++LG +I+ ++ I
Sbjct: 30 AGKLFIIGGLILLLLGLLILDILFLI 55
>gnl|CDD|217631 pfam03595, C4dic_mal_tran, C4-dicarboxylate transporter/malic acid
transport protein. This family of transporters have ten
alpha helical transmembrane segments. The structure of a
bacterial homologue of SLAC1 shows it to have a trimeric
arrangement. The pore is composed of five helices with a
conserved phe residue involved in gating. One homologue,
Mae1 from the yeast Schizosaccharomyces pombe, functions
as a malate uptake transporter; another, Ssu1 from
Saccharomyces cerevisiae and other fungi including
Aspergillus fumigatus, is characterized as a sulphite
efflux pump; and TehA from Escherichia coli is
identified as a tellurite resistance protein by virtue
of its association in the tehA/tehB operon. Many
homologues are incorrectly annotated as tellurite
resistance/dicarboxylate transporter (TDT) proteins.
Length = 314
Score = 29.5 bits (67), Expect = 3.1
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 236 FPEAIVQQASSKLNSGTSSTVLIILGVVLIVL--GFVIILLILYIH 279
FP A+ L S +LG +L+V+ +I+L+ +
Sbjct: 269 FPLGAYALATLLLAKALGSPAFRVLGTILLVIAVLIWLIVLVRTLR 314
>gnl|CDD|205301 pfam13120, DUF3974, Domain of unknown function (DUF3974). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
130 amino acids in length.
Length = 126
Score = 28.5 bits (63), Expect = 3.1
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 255 TVLIILGVVLIVLGFVIILLILYIHKNKHTKNNGPPGSSHSKNDSFLSNVILP 307
VL+++G +L++ F I++L++Y + + P +H D LSN +P
Sbjct: 6 MVLLLIGTLLLI-AFTIVVLLVYFGRKLYFSWAKPYKRAHDSIDK-LSNKSIP 56
>gnl|CDD|233130 TIGR00797, matE, putative efflux protein, MATE family. The Multi
Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The
MATE family consists of probable efflux proteins
including a functionally characterized multi drug efflux
system from Vibrio parahaemolyticus, a putative
ethionine resistance protein of Saccharomyces
cerevisiae, and the functionally uncharacterized DNA
damage-inducible protein F (DinF) of E. coli. These
proteins have 12 probable TMS [Transport and binding
proteins, Other].
Length = 342
Score = 29.5 bits (67), Expect = 3.4
Identities = 18/89 (20%), Positives = 42/89 (47%), Gaps = 14/89 (15%)
Query: 197 GHISIVDLSALN-----TSTIQLVVVATDTGNPPRQA-SVPAIMHFPEAIVQQASSKLNS 250
GH+ VDL+A++ + +++ T A +V A + + + +QA
Sbjct: 21 GHLGPVDLAAVSLGSSVFMFLFSILMGLGTATTALVAQAVGAGNY--QRLGRQAQ----- 73
Query: 251 GTSSTVLIILGVVLIVLGFVIILLILYIH 279
S + ++LG+ ++++G+ I +L +
Sbjct: 74 -QSLLLALLLGLPVLLVGYFFIDPLLSLM 101
>gnl|CDD|150844 pfam10233, Cg6151-P, Uncharacterized conserved protein CG6151-P.
This is a family of small, less than 200 residue long,
proteins which are named as CG6151-P proteins that are
conserved from fungi to humans. The function is unknown.
The fungal members have a characteristic ICP sequence
motif. Some members are annotated as putative
clathrin-coated vesicle protein but this could not be
defined.
Length = 113
Score = 28.0 bits (63), Expect = 3.5
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 252 TSSTVLIILGVVLIVLGFVIILL 274
T S V I+ G++ IV GFV+I +
Sbjct: 19 TISAVCIVFGILCIVQGFVVIFI 41
>gnl|CDD|238847 cd01714, ETF_beta, The electron transfer flavoprotein (ETF) serves
as a specific electron acceptor for various
mitochondrial dehydrogenases. ETF transfers electrons to
the main respiratory chain via ETF-ubiquinone
oxidoreductase. ETF is an heterodimer that consists of
an alpha and a beta subunit which binds one molecule of
FAD per dimer . A similar system also exists in some
bacteria. The homologous pair of proteins (FixA/FixB)
are essential for nitrogen fixation. The beta subunit
protein is distantly related to and forms a heterodimer
with the alpha subunit.
Length = 202
Score = 29.1 bits (66), Expect = 3.5
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 215 VVVATDTG-NPPRQASVPAIM 234
V+ D G N PR S+P IM
Sbjct: 171 AVITVDLGINEPRYPSLPGIM 191
>gnl|CDD|233337 TIGR01273, speA, arginine decarboxylase, biosynthetic. Two
alternative pathways can convert arginine to putrescine.
One is decarboxylation by this enzyme followed by
removal of the urea moeity by agmatinase. In the other,
the ureohydrolase (arginase) acts first, followed by
ornithine decarboxylase. This pathway leads to
spermidine biosynthesis, hence the gene symbol speA. A
distinct biodegradative form is also pyridoxal
phosphate-dependent but is not similar in sequence
[Central intermediary metabolism, Polyamine
biosynthesis].
Length = 624
Score = 29.6 bits (67), Expect = 3.5
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 191 FSINDSGHISIV---DLSALNTSTIQLVVVATDTGNPPRQASVPAIMHFPEAIVQQASSK 247
F++N G++S+ D + ++LV G +P ++ FP+ I+Q
Sbjct: 20 FAVNKLGNVSVRPGGDDTLQRIDLLELVKQVEARG-----LQLPLLVRFPD-ILQHRIRS 73
Query: 248 LNS 250
LN+
Sbjct: 74 LNA 76
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 29.1 bits (66), Expect = 4.1
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 12/48 (25%)
Query: 77 VKYWLSNDYGE----------RFSISRQGDISLMQCLDYETED--SYR 112
KY L + E R D++ MQC+ + TED +Y+
Sbjct: 268 AKYMLRANENEEAEKTASLFTRDGTGPLADLNDMQCMWFLTEDGEAYQ 315
>gnl|CDD|151515 pfam11070, DUF2871, Protein of unknown function (DUF2871). This
family of proteins has no known function.
Length = 131
Score = 28.0 bits (63), Expect = 4.2
Identities = 14/42 (33%), Positives = 21/42 (50%)
Query: 246 SKLNSGTSSTVLIILGVVLIVLGFVIILLILYIHKNKHTKNN 287
+K N T T L ++ L+VLGF L++L + K N
Sbjct: 26 TKANGFTGRTQLSLVHTHLLVLGFFFFLIVLLLEKVFKLSKN 67
>gnl|CDD|240242 PTZ00046, PTZ00046, rifin; Provisional.
Length = 358
Score = 29.1 bits (66), Expect = 4.3
Identities = 15/28 (53%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 259 ILGVVLIVLGFVIILLIL-YIHKNKHTK 285
I+ +V+IVL VII LIL Y K K K
Sbjct: 321 IVAIVVIVLIMVIIYLILRYRRKKKMKK 348
>gnl|CDD|218853 pfam06011, TRP, Transient receptor potential (TRP) ion channel.
This family of proteins are transient receptor potential
(TRP) ion channels. They are essential for cellular
viability and are involved in cell growth and cell wall
synthesis. The genes for these proteins are homologous
to polycystic kidney disease related ion channel genes.
Length = 531
Score = 29.1 bits (66), Expect = 4.6
Identities = 19/65 (29%), Positives = 27/65 (41%), Gaps = 18/65 (27%)
Query: 251 GTSSTVLIILGVVLIVL--GFVIILLIL--------YIHKNKHTKNNGPPGSSHSKND-- 298
G S V ++GVV+ V+ + LLIL KN + K+D
Sbjct: 471 GQSEIVRGVMGVVIFVINAAVALFLLILIAINTIIALFRKNPDAR------YQPMKDDRV 524
Query: 299 SFLSN 303
SFLS+
Sbjct: 525 SFLSS 529
>gnl|CDD|223701 COG0628, yhhT, Predicted permease, member of the PurR regulon
[General function prediction only].
Length = 355
Score = 28.8 bits (65), Expect = 4.7
Identities = 7/40 (17%), Positives = 24/40 (60%)
Query: 238 EAIVQQASSKLNSGTSSTVLIILGVVLIVLGFVIILLILY 277
+A++ S L S S + ++ ++ +++ +++L++L+
Sbjct: 130 DALLSALLSILQSILGSLLSLLSSLLSLIVSLLLVLVLLF 169
>gnl|CDD|213523 TIGR00304, TIGR00304, TIGR00304 family protein. The member of this
family from Pyrococcus horikoshii scores only 13.91
bits, largely because it is at least 15 residues shorter
than other members of this family of small proteins and
is penalized for not matching to the N-terminal section
of the model. Cutoff scores are set so this hit is
between noise and trusted cutoffs [Hypothetical
proteins, Conserved].
Length = 77
Score = 27.0 bits (60), Expect = 4.8
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 254 STVLIILGVVLIVLGFVIILLILYI 278
S +LI LG++LIV+GF++ L +
Sbjct: 3 SEILIPLGIILIVIGFLLTFLGGAL 27
>gnl|CDD|233430 TIGR01477, RIFIN, variant surface antigen, rifin family. This
model represents the rifin branch of the rifin/stevor
family (pfam02009) of predicted variant surface antigens
as found in Plasmodium falciparum. This model is based
on a set of rifin sequences kindly provided by Matt
Berriman from the Sanger Center. This is a global model
and assesses a penalty for incomplete sequence.
Additional fragmentary sequences may be found with the
fragment model and a cutoff of 20 bits.
Length = 353
Score = 28.9 bits (65), Expect = 4.9
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 249 NSGTSSTVLI--ILGVVLIVLGFVIILLIL-YIHKNKHTK 285
+ T +I I+ +++IVL VII LIL Y K K K
Sbjct: 304 TTTNYYTPIIASIIAILIIVLIMVIIYLILRYRRKKKMKK 343
>gnl|CDD|129443 TIGR00343, TIGR00343, pyridoxal 5'-phosphate synthase, synthase
subunit Pdx1. This protein had been believed to be a
singlet oxygen resistance protein. Subsequent work
showed that it is a protein of pyridoxine (vitamin B6)
biosynthesis, and that pyridoxine quenches the highly
toxic singlet form of oxygen produced by light in the
presence of certain chemicals [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridoxine].
Length = 287
Score = 28.6 bits (64), Expect = 5.0
Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 17/87 (19%)
Query: 179 VTLSLRGPYEKMFSINDSGHISIVDLSALNTST-------IQL----VVVAT---DTGNP 224
V LR P E + + G + +V+ +A +T +QL V V + + NP
Sbjct: 178 VAKELRVPVELLLEVLKLGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSSNP 237
Query: 225 PRQAS--VPAIMHFPE-AIVQQASSKL 248
+ A V A H+ + + S L
Sbjct: 238 EKLAKAIVEATTHYDNPEKLAEVSKDL 264
>gnl|CDD|220473 pfam09925, DUF2157, Predicted membrane protein (DUF2157). This
domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 144
Score = 28.0 bits (63), Expect = 5.1
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 238 EAIVQQASSKLNSGTSSTVLIILGVVLIVLGFVIIL 273
EAI+ + + +L+ LG +L+ G + +
Sbjct: 16 EAILARYGEDPARSSLVRILLWLGALLLGAGVIFFV 51
>gnl|CDD|239734 cd03765, proteasome_beta_bacterial, Bacterial proteasome, beta
subunit. The 20S proteasome, multisubunit proteolytic
complex, is the central enzyme of nonlysosomal protein
degradation in both the cytosol and nucleus. It is
composed of 28 subunits arranged as four homoheptameric
rings that stack on top of one another forming an
elongated alpha-beta-beta-alpha cylinder with a central
cavity. The proteasome alpha and beta subunits are
members of the N-terminal nucleophile (Ntn)-hydrolase
superfamily. Their N-terminal threonine residues are
exposed as a nucleophile in peptide bond hydrolysis.
Mammals have 7 alpha and 7 beta proteasome subunits
while archaea have one of each.
Length = 236
Score = 28.3 bits (64), Expect = 5.1
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 187 YEKMFSINDSGHISIVDLSALNTSTIQLVV----VATDTGNPPRQASVP 231
Y KMF + G IV L+A N +T Q V+ + + P
Sbjct: 30 YRKMFVFSVPGERVIVLLTAGNLATTQAVISLLQRDLEDPEETNLLNAP 78
>gnl|CDD|217757 pfam03840, SecG, Preprotein translocase SecG subunit.
Length = 74
Score = 26.7 bits (60), Expect = 5.7
Identities = 7/25 (28%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 258 IILGVVLIVLGFVIILLILYIHKNK 282
IL V+ +++ ++I+L+L + K
Sbjct: 2 TILLVLHVIVAILLIILVL-LQSGK 25
>gnl|CDD|99851 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of Drosophila
Egalitarian (Egl) and similar proteins. The Egalitarian
(Egl) protein subfamily is composed of Drosophila Egl
and similar proteins. Egl is a component of an
mRNA-binding complex which is required for oocyte
specification. Egl contains a DEDDy-type DnaQ-like 3'-5'
exonuclease domain possessing three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
YX(3)D pattern at ExoIII. The motifs are clustered
around the active site and contain four conserved acidic
residues that serve as ligands for the two metal ions
required for catalysis. The conservation of this
subfamily throughout eukaryotes suggests that its
members may be part of ancient RNA processing complexes
that are likely to participate in the regulated
processing of specific mRNAs. Some members of this
subfamily do not have a completely conserved YX(3)D
pattern at the ExoIII motif.
Length = 197
Score = 28.0 bits (63), Expect = 5.7
Identities = 7/36 (19%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 91 ISRQGDISLMQCLDYETEDSYRFTVYATDTLMTTSA 126
+ R+G + L+Q T Y F + +++ +
Sbjct: 22 LGRKGKLCLVQIA-TRTGQIYLFDILKLGSIVFING 56
>gnl|CDD|114838 pfam06143, Baculo_11_kDa, Baculovirus 11 kDa family. Family of
uncharacterized Baculovirus proteins that are all about
11 kDa in size.
Length = 84
Score = 26.5 bits (59), Expect = 6.7
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 256 VLIILGVVLIVLGFVIILLILYIHKNKHT 284
VL+I G V+ V+ + ILL++ I+KN
Sbjct: 37 VLVICGFVVFVMIVLFILLLVNINKNAEL 65
>gnl|CDD|214769 smart00665, B561, Cytochrome b-561 / ferric reductase transmembrane
domain. Cytochrome b-561 recycles ascorbate for the
generation of norepinephrine by
dopamine-beta-hydroxylase in the chromaffin vesicles of
the adrenal gland. It is a transmembrane heme protein
with the two heme groups being bound to conserved
histidine residues. A cytochrome b-561 homologue, termed
Dcytb, is an iron-regulated ferric reductase in the
duodenal mucosa. Other homologues of these are also
likely to be ferric reductases. SDR2 is proposed to be
important in regulating the metabolism of iron in the
onset of neurodegenerative disorders.
Length = 129
Score = 27.2 bits (61), Expect = 7.0
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 256 VLIILGVVLIVLGFVIILLILYIHKNKHTKNN 287
VL IL +VL V+G + I I N+ N
Sbjct: 39 VLQILALVLGVIGLLAIF----ISHNESGIAN 66
>gnl|CDD|220712 pfam10355, Ytp1, Protein of unknown function (Ytp1). This is a
family of proteins found in fungi. The region appears to
contain regions similar to mitochondrial electron
transport proteins. The C-terminal domain is hydrophobic
and negatively charged. There are consensus sites for
both N-linked glycosylation and cAMP-dependent protein
kinase phosphorylation.
Length = 272
Score = 28.0 bits (63), Expect = 7.6
Identities = 4/27 (14%), Positives = 15/27 (55%)
Query: 253 SSTVLIILGVVLIVLGFVIILLILYIH 279
+L+++G+ +++ + +L+ L
Sbjct: 246 MFYLLVLVGLAFLLMAWETVLIALKDW 272
>gnl|CDD|222035 pfam13303, PTS_EIIC_2, Phosphotransferase system, EIIC. The
bacterial phosphoenolpyruvate: sugar phosphotransferase
system (PTS) is a multi-protein system involved in the
regulation of a variety of metabolic and transcriptional
processes. The sugar-specific permease of the PTS
consists of three domains (IIA, IIB and IIC). The IIC
domain catalyzes the transfer of a phosphoryl group from
IIB to the sugar substrate.
Length = 329
Score = 28.3 bits (64), Expect = 8.2
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 248 LNSGTSSTVLIILGVVLIVLGFVIILLI--LYIHKNKHTKNN 287
LN GT + ++++ +V VL V+ LLI L+I K K
Sbjct: 284 LNMGTGPSNILLIILVFFVLPAVLALLIYKLFIKKLGLIKPG 325
>gnl|CDD|153009 pfam12575, DUF3753, Protein of unknown function (DUF3753). This
family of proteins is found in viruses. Proteins in this
family are approximately 70 amino acids in length. There
is a conserved YLK sequence motif. There are two
completely conserved residues (D and F) that may be
functionally important.
Length = 72
Score = 26.1 bits (58), Expect = 8.5
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 245 SSKLNSGTSSTVLIILGVVLIVLGFVIILLILYI 278
K S +++ IIL + +I + +++L LY+
Sbjct: 36 KLKRRSSNTNSNWIILIITIIAVVIIVLLTFLYL 69
>gnl|CDD|237245 PRK12879, PRK12879, 3-oxoacyl-(acyl carrier protein) synthase III;
Reviewed.
Length = 325
Score = 27.9 bits (63), Expect = 8.7
Identities = 15/46 (32%), Positives = 15/46 (32%), Gaps = 2/46 (4%)
Query: 157 ADLTPGSVIGKVEAADGDKGDRVTLSLRGPYEKMFSINDSGHISIV 202
A I V DGD GD L G M SG IV
Sbjct: 170 ATENEPGFIDYVLGTDGDGGD--ILYRTGLGTTMDRDALSGDGYIV 213
>gnl|CDD|236412 PRK09204, secY, preprotein translocase subunit SecY; Reviewed.
Length = 426
Score = 28.2 bits (64), Expect = 9.0
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 236 FPEAIVQQASSKLNSGTSSTVLIILGVVLIVLGFVIILLILYI 278
P AI Q +G+ S ++ +L LIVL +I ++++
Sbjct: 195 LPSAI-GQTFELARTGSLSILVFLL---LIVLFLAVIAFVVFV 233
>gnl|CDD|200247 TIGR03150, fabF, beta-ketoacyl-acyl-carrier-protein synthase II.
3-oxoacyl-[acyl-carrier-protein] synthase 2 (KAS-II,
FabF) is involved in the condensation step of fatty acid
biosynthesis in which the malonyl donor group is
decarboxylated and the resulting carbanion used to
attack and extend the acyl group attached to the acyl
carrier protein. Most genomes encoding fatty acid
biosynthesis contain a number of condensing enzymes,
often of all three types: 1, 2 and 3. Synthase 2 is
mechanistically related to synthase 1 (KAS-I, FabB)
containing a number of absolutely conserved catalytic
residues in common. This model is based primarily on
genes which are found in apparent operons with other
essential genes of fatty acid biosynthesis
(GenProp0681). The large gap between the trusted cutoff
and the noise cutoff contains many genes which are not
found adjacent to genes of the fatty acid pathway in
genomes that often also contain a better hit to this
model. These genes may be involved in other processes
such as polyketide biosyntheses. Some genomes contain
more than one above-trusted hit to this model which may
result from recent paralogous expansions. Second hits to
this model which are not next to other fatty acid
biosynthesis genes may be involved in other processes.
FabB sequences should fall well below the noise cutoff
of this model [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 407
Score = 27.8 bits (63), Expect = 9.2
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 65 LTVTTNKPRDLRVKYWLSNDYG 86
L N+ R+ ++ Y LSN +G
Sbjct: 375 LDYVPNEAREAKIDYALSNSFG 396
>gnl|CDD|227084 COG4741, COG4741, Predicted secreted endonuclease distantly related
to archaeal Holliday junction resolvase [Nucleotide
transport and metabolism].
Length = 175
Score = 27.4 bits (61), Expect = 9.7
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 258 IILGVVLIVLGFVIILLILYI 278
+IL +++ +L V+ LL YI
Sbjct: 4 VILILIVFILALVLYLLRAYI 24
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 27.8 bits (62), Expect = 9.8
Identities = 15/53 (28%), Positives = 22/53 (41%)
Query: 311 VNVVAIPKIQENPVFNGSQEELQTQRGGTNSSIYTATVKKTLSGKPELDPEVG 363
+ Q+N +G Q Q+ T S+I V + SG ELD +G
Sbjct: 36 ERLHRSLGAQKNRRNSGKAGIPQAQKSQTISAIELEEVPRFSSGFGELDRVLG 88
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
0.316 0.133 0.377
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,033,106
Number of extensions: 1806823
Number of successful extensions: 3118
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3089
Number of HSP's successfully gapped: 77
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.8 bits)