RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3616
(143 letters)
>gnl|CDD|217059 pfam02480, Herpes_gE, Alphaherpesvirus glycoprotein E.
Glycoprotein E (gE) of Alphaherpesvirus forms a complex
with glycoprotein I (gI) (pfam01688), functioning as an
immunoglobulin G (IgG) Fc binding protein. gE is
involved in virus spread but is not essential for
propagation.
Length = 437
Score = 31.6 bits (72), Expect = 0.098
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 15/91 (16%)
Query: 29 IGPHCAQKSEFAYIAGGIAATVVFLIIIALFVWMICARSERRREPKKLVAQTNDQTGSQV 88
I P + + G+ V L+++ L W +C RRR+P ++
Sbjct: 340 IAPPSPGTRPYLLLLAGVLGAAVLLLVVGLLAW-VCVTRRRRRKPYAVIL---------- 388
Query: 89 NFYYGGAPYAESVAPSHHSTYAHYYDDEEDG 119
+P S+ P++ D E D
Sbjct: 389 ---NPFSPVYTSL-PTNELFEDVSSDSESDD 415
>gnl|CDD|204604 pfam11174, DUF2970, Protein of unknown function (DUF2970). This
short family is conserved in Proteobacteria. The
function is not known.
Length = 56
Score = 29.4 bits (67), Expect = 0.14
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 34 AQKSEFAYIAGGIAATVVFLIIIALFV 60
AQ S +I G+ +F+ + L V
Sbjct: 26 AQGSPLHFIIVGLVLAALFVGGLILLV 52
>gnl|CDD|238011 cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a
large number of membrane-bound and extracellular
(mostly animal) proteins. Many of these proteins
require calcium for their biological function and
calcium-binding sites have been found to be located at
the N-terminus of particular EGF-like domains;
calcium-binding may be crucial for numerous
protein-protein interactions. Six conserved core
cysteines form three disulfide bridges as in non
calcium-binding EGF domains, whose structures are very
similar. EGF_CA can be found in tandem repeat
arrangements.
Length = 38
Score = 27.6 bits (62), Expect = 0.44
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 6 CENKGTCVKDARGQPSCRCVGSFIGPHC 33
C+N GTCV + G C C + G +C
Sbjct: 11 CQNGGTCV-NTVGSYRCSCPPGYTGRNC 37
>gnl|CDD|225715 COG3174, COG3174, Predicted membrane protein [Function unknown].
Length = 371
Score = 29.6 bits (67), Expect = 0.47
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 39 FAYIAGGIAATVVFLIIIALFVWMICARSERR 70
AY++ + + V L AL V R++R
Sbjct: 14 TAYLSESLGSAVGLLAFAALAVLFYYHRADRD 45
>gnl|CDD|205044 pfam12725, DUF3810, Protein of unknown function (DUF3810). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 333 and 377 amino
acids in length. There is a conserved HEXXH sequence
motif that is characteristic of metallopeptidases. This
family may therefore belong to an as yet
uncharacterized family of peptidase enzymes.
Length = 317
Score = 29.8 bits (68), Expect = 0.47
Identities = 7/30 (23%), Positives = 17/30 (56%)
Query: 51 VFLIIIALFVWMICARSERRREPKKLVAQT 80
+L+II L ++I R +++ K+ + +
Sbjct: 30 YYLLIILLLRYLIKLRKRLKKKWKRFLLRV 59
>gnl|CDD|214452 MTH00195, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 307
Score = 29.3 bits (66), Expect = 0.71
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 50 VVFLIIIALFVWMICARSERRREPKKLVAQTNDQTGSQVNFYYGGAPYA 98
V+ L F+W + +E R P A+ + S N Y G P+A
Sbjct: 176 VILLCPPISFMWYVSTLAETNRAPFDF-AEGESELVSGFNVEYAGGPFA 223
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 29.1 bits (66), Expect = 0.84
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 45 GIAATVVFLIIIALFVWMICARSERRREPK 74
G A ++ L +IA VW +C S R +E
Sbjct: 653 GQAVIIIALALIAFLVWPLCRESWRDKESH 682
>gnl|CDD|221263 pfam11847, DUF3367, Domain of unknown function (DUF3367). This
domain is functionally uncharacterized. This domain is
found in bacteria and archaea. This presumed domain is
typically between 667 to 694 amino acids in length.
Length = 677
Score = 28.9 bits (65), Expect = 0.86
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 44 GGIAATVVFLIIIALFVWMICARSERRR 71
GG+ AT ++ +W++C RR
Sbjct: 165 GGVNATATLAALLPALLWLLCHARGRRW 192
>gnl|CDD|218316 pfam04893, Yip1, Yip1 domain. The Yip1 integral membrane domain
contains four transmembrane alpha helices. The domain
is characterized by the motifs DLYGP and GY. The Yip1
protein is a golgi protein involved in vesicular
transport that interacts with GTPases.
Length = 171
Score = 28.6 bits (64), Expect = 0.89
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 34 AQKSEFAYIAGGIAATVVFLIIIALFVWMIC 64
S I GG ++ L ++AL + +I
Sbjct: 57 TGGSALGSIIGGYLGLLLGLFLLALLLHLIA 87
>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 = 26.3 bits (59), Expect = 0.97
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 46 IAATVV----FLIIIALFVWMICARSERRRE 72
IAA VV L+I+ L V++ R +R+
Sbjct: 8 IAAGVVGGLLVLVILGLIVFLFRRRRHIKRK 38
>gnl|CDD|100085 cd06164, S2P-M50_SpoIVFB_CBS, SpoIVFB Site-2 protease (S2P), a zinc
metalloprotease (MEROPS family M50B), regulates
intramembrane proteolysis (RIP), and is involved in the
pro-sigmaK pathway of bacterial spore formation. In this
subgroup, SpoIVFB (sporulation protein, stage IV cell
wall formation, F locus, promoter-distal B) contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domain. SpoIVFB is one of 4 proteins involved in
endospore formation; the others are SpoIVFA (sporulation
protein, stage IV cell wall formation, F locus,
promoter-proximal A), BofA (bypass-of-forespore A), and
SpoIVB (sporulation protein, stage IV cell wall
formation, B locus). SpoIVFB is negatively regulated by
SpoIVFA and BofA and activated by SpoIVB. It is thought
that SpoIVFB, SpoIVFA, and BofA are located in the
mother-cell membrane that surrounds the forespore and
that SpoIVB is secreted from the forespore into the
space between the two where it activates SpoIVFB. It has
been proposed that the CBS domain may play a regulatory
role, although its exact function is unknown.
Length = 227
Score = 28.3 bits (64), Expect = 1.2
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 39 FAYIAGGIAATVVF--------LIIIALFVWMICARSERRR 71
FA + + +F LI+IA F+++ A +E R+
Sbjct: 187 FAVLLIILGLLSLFLNLLGGLWLILIAWFLYI-GAGAEARQ 226
>gnl|CDD|100082 cd06161, S2P-M50_SpoIVFB, SpoIVFB Site-2 protease (S2P), a zinc
metalloprotease (MEROPS family M50B), regulates
intramembrane proteolysis (RIP), and is involved in the
pro-sigmaK pathway of bacterial spore formation. SpoIVFB
(sporulation protein, stage IV cell wall formation, F
locus, promoter-distal B) is one of 4 proteins involved
in endospore formation; the others are SpoIVFA
(sporulation protein, stage IV cell wall formation, F
locus, promoter-proximal A), BofA (bypass-of-forespore
A), and SpoIVB (sporulation protein, stage IV cell wall
formation, B locus). SpoIVFB is negatively regulated by
SpoIVFA and BofA and activated by SpoIVB. It is thought
that SpoIVFB, SpoIVFA, and BofA are located in the
mother-cell membrane that surrounds the forespore and
that SpoIVB is secreted from the forespore into the
space between the two where it activates SpoIVFB.
Length = 208
Score = 28.3 bits (64), Expect = 1.2
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 39 FAYIAGGIAATVVF-------LIIIALFVWMICARSERRR 71
FA + + ++F L++IALF+++ A +E RR
Sbjct: 169 FAILLVVLGLFLLFLGLGNLWLLLIALFIYL-AAEAELRR 207
>gnl|CDD|238010 cd00053, EGF, Epidermal growth factor domain, found in epidermal
growth factor (EGF) presents in a large number of
proteins, mostly animal; the list of proteins currently
known to contain one or more copies of an EGF-like
pattern is large and varied; the functional
significance of EGF-like domains in what appear to be
unrelated proteins is not yet clear; a common feature
is that these repeats are found in the extracellular
domain of membrane-bound proteins or in proteins known
to be secreted (exception: prostaglandin G/H synthase);
the domain includes six cysteine residues which have
been shown to be involved in disulfide bonds; the main
structure is a two-stranded beta-sheet followed by a
loop to a C-terminal short two-stranded sheet;
Subdomains between the conserved cysteines vary in
length; the region between the 5th and 6th cysteine
contains two conserved glycines of which at least one
is present in most EGF-like domains; a subset of
these bind calcium.
Length = 36
Score = 26.3 bits (58), Expect = 1.3
Identities = 11/31 (35%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 4 GYCENKGTCVKDARGQPSCRCVGSFIGP-HC 33
C N GTCV + G C C + G C
Sbjct: 6 NPCSNGGTCV-NTPGSYRCVCPPGYTGDRSC 35
>gnl|CDD|224094 COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport
systems, permease components [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 289
Score = 28.4 bits (64), Expect = 1.4
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 9/41 (21%)
Query: 39 FAYIAGGIAATVVFLIIIALFVWMICAR-------SERRRE 72
I G ++ + +AL W AR S R RE
Sbjct: 140 LVAILGPGLLNLI--LALALVGWPGYARIVRGQVLSLRERE 178
>gnl|CDD|171510 PRK12452, PRK12452, cardiolipin synthetase; Reviewed.
Length = 509
Score = 28.3 bits (63), Expect = 1.7
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 50 VVFLIIIALFVWMICARSERRRE 72
+ L ++ + ++ I RS RR+
Sbjct: 65 LALLPVVGVLLYSIFGRSRWRRK 87
>gnl|CDD|226859 COG4452, CreD, Inner membrane protein involved in colicin E2
resistance [Defense mechanisms].
Length = 443
Score = 28.2 bits (63), Expect = 1.8
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 36 KSEFAYIAGGIAATVVFLIIIALFVW-MICARSERRREPKKLVAQTNDQTGSQV 88
KS + + ++ L+I L + +I R++ R + +A N +GSQ
Sbjct: 3 KSPLFWKLVTLFGAILLLLIPLLLIRGLIDERADYRSDVIDAIA--NSTSGSQK 54
>gnl|CDD|224535 COG1620, LldP, L-lactate permease [Energy production and
conversion].
Length = 522
Score = 28.0 bits (63), Expect = 2.0
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 40 AYIAGGIAATVVFLIIIALFVW 61
Y+A I + L IALF +
Sbjct: 27 GYVAAPITLLLTLL--IALFYF 46
>gnl|CDD|112053 pfam03222, Trp_Tyr_perm, Tryptophan/tyrosine permease family.
Length = 393
Score = 28.0 bits (63), Expect = 2.0
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 45 GIAATVVFLIIIALFVWMICARSERRREPKKL 76
G+AAT+ +I+ AL W AR P ++
Sbjct: 343 GLAATIWAVILPALLAWK--ARKRFPNAPYRV 372
>gnl|CDD|221295 pfam11893, DUF3413, Domain of unknown function (DUF3413). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is about 250
amino acids in length. This domain is found associated
with pfam00884.
Length = 253
Score = 27.6 bits (62), Expect = 2.0
Identities = 4/42 (9%), Positives = 21/42 (50%)
Query: 37 SEFAYIAGGIAATVVFLIIIALFVWMICARSERRREPKKLVA 78
E+ + + ++ +++A ++W + ++++ + + A
Sbjct: 133 VEWQLLFIVVPIILLLELLLANWLWKKLRKLKKKKLGRPVAA 174
>gnl|CDD|201668 pfam01219, DAGK_prokar, Prokaryotic diacylglycerol kinase.
Length = 104
Score = 26.6 bits (60), Expect = 2.4
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 28 FIGPHCAQKSEFAYIAGGIAATVVFL-IIIALFVWMI 63
I P + A A IAA V + I+A+ VW+I
Sbjct: 68 LISP---EYHPLAKRAKDIAAAAVLVAAILAVIVWLI 101
>gnl|CDD|233109 TIGR00739, yajC, preprotein translocase, YajC subunit. While
this protein is part of the preprotein translocase in
Escherichia coli, it is not essential for viability or
protein secretion. The N-terminus region contains a
predicted membrane-spanning region followed by a region
consisting almost entirely of residues with charged
(acidic, basic, or zwitterionic) side chains. This
small protein is about 100 residues in length, and is
restricted to bacteria; however, this protein is absent
from some lineages, including spirochetes and
Mycoplasmas [Protein fate, Protein and peptide
secretion and trafficking].
Length = 84
Score = 26.5 bits (59), Expect = 2.5
Identities = 6/26 (23%), Positives = 14/26 (53%)
Query: 50 VVFLIIIALFVWMICARSERRREPKK 75
+ ++I +F ++I +RR+ K
Sbjct: 7 LPLVLIFLIFYFLIIRPQRKRRKAHK 32
>gnl|CDD|222271 pfam13624, SurA_N_3, SurA N-terminal domain. This domain is
found at the N-terminus of the chaperone SurA. It is a
helical domain of unknown function. The C-terminus of
the SurA protein folds back and forms part of this
domain also but is not included in the current
alignment.
Length = 154
Score = 27.0 bits (60), Expect = 2.6
Identities = 8/45 (17%), Positives = 17/45 (37%)
Query: 46 IAATVVFLIIIALFVWMICARSERRREPKKLVAQTNDQTGSQVNF 90
+ ++ L+ +W K +VA+ N + S +F
Sbjct: 11 VFGVLIGLVTALFVLWFGAGSIFSDHSKKAVVAKVNGEKISATDF 55
>gnl|CDD|188086 TIGR00819, ydaH, p-Aminobenzoyl-glutamate transporter family. The
p-Aminobenzoyl-glutamate transporter family includes two
transporters, the AbgT (YdaH) protein of E. coli and
MtrF of Neisseria gonorrhoea. AbgT is apparently cryptic
in wild type cells, but when expressed on a high copy
number plasmid, or when expressed at higher levels due
to mutation, it allows utilization of
p-aminobenzoyl-glutamate as a source of p-aminobenzoate
for p-aminobenzoate auxotrophs. p-Aminobenzoate is a
constituent of and a precursor for the biosynthesis of
folic acid [Hypothetical proteins, Conserved].
Length = 525
Score = 27.6 bits (61), Expect = 2.9
Identities = 16/60 (26%), Positives = 22/60 (36%), Gaps = 14/60 (23%)
Query: 44 GGIAATVVFLIIIALFVWMICARSERRREPKKLVAQTNDQTGSQVNFYYGGAPYAESVAP 103
G I A VVF+ IA MI R+P N G+P+ + + P
Sbjct: 275 GLIIAGVVFIAFIAAIALMIIPADGILRDP--------------ENGLVAGSPFIKGIVP 320
>gnl|CDD|217153 pfam02628, COX15-CtaA, Cytochrome oxidase assembly protein. This
is a family of integral membrane proteins. CtaA is
required for cytochrome aa3 oxidase assembly in Bacillus
subtilis. COX15 is required for cytochrome c oxidase
assembly in yeast.
Length = 301
Score = 27.2 bits (61), Expect = 3.0
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 48 ATVVFLIIIALFVWMICARSERRREPKKLVA 78
A ++ L+I+ VW R RR L+
Sbjct: 75 ARLLGLLILVPLVWFWRRRRIPRRLKWLLLL 105
>gnl|CDD|233307 TIGR01195, oadG_fam, sodium pump decarboxylases, gamma subunit.
This model finds the subfamily of distantly related,
low complexity, hydrophobic small subunits of several
related sodium ion-pumping decarboxylases. These
include oxaloacetate decarboxylase gamma subunit and
methylmalonyl-CoA decarboxylase delta subunit. Most
sequences scoring between the noise and trusted cutoffs
are eukaryotic sodium channel proteins.
Length = 82
Score = 26.2 bits (58), Expect = 3.2
Identities = 5/31 (16%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 45 GIAATVVFLIIIALFVWMICARSERRREPKK 75
G+ +FL ++ V + + R++ +
Sbjct: 14 GMGIVFLFLSLLIYAVRGM-GKVVGRKKVPE 43
>gnl|CDD|218997 pfam06341, DUF1056, Protein of unknown function (DUF1056). This
family consists of several putative head-tail joining
bacteriophage proteins.
Length = 63
Score = 25.4 bits (56), Expect = 3.3
Identities = 7/28 (25%), Positives = 10/28 (35%), Gaps = 1/28 (3%)
Query: 39 FAYIAGGIAATVVFLIIIALFVWMICAR 66
AGGI +V + +I R
Sbjct: 33 INATAGGITISVTL-FLAGWLSEVISKR 59
>gnl|CDD|217024 pfam02417, Chromate_transp, Chromate transporter. Members of
this family probably act as chromate transporters.
Members of this family are found in both bacteria and
archaebacteria. The proteins are composed of one or two
copies of this region. The alignment contains two
conserved motifs, FGG and PGP.
Length = 169
Score = 26.7 bits (60), Expect = 3.5
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 11/42 (26%)
Query: 25 VGSFIGPHCAQKSEFAYIAGGIAATVV-----FLIIIALFVW 61
+ +FIG A G + AT+ FL+I+ L
Sbjct: 61 LATFIGYR------LAGFLGALVATLGFFLPSFLLILLLAPL 96
>gnl|CDD|227371 COG5038, COG5038, Ca2+-dependent lipid-binding protein, contains C2
domain [General function prediction only].
Length = 1227
Score = 27.0 bits (60), Expect = 3.9
Identities = 10/45 (22%), Positives = 21/45 (46%), Gaps = 11/45 (24%)
Query: 37 SEFAYIAGGIA-----------ATVVFLIIIALFVWMICARSERR 70
S + G +A A++ F+I++ ++V+ C + RR
Sbjct: 157 SVAIVLIGSVASWIFGYLGFSFASLFFIILVTMYVYRTCIKRVRR 201
>gnl|CDD|180606 PRK06525, PRK06525, hydrogenase 4 subunit D; Validated.
Length = 479
Score = 26.9 bits (60), Expect = 3.9
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 37 SEFAYIAGGIAATVVFLIIIALFVWMIC 64
S+F A G +V + I++ V ++
Sbjct: 394 SKFPIFAAGFELSVEYWILLPAMVLLLI 421
>gnl|CDD|201526 pfam00957, Synaptobrevin, Synaptobrevin.
Length = 89
Score = 26.0 bits (58), Expect = 4.0
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 41 YIAGGIAATVVFLIIIALFVW 61
I G+ ++ LIII +
Sbjct: 69 KIILGLVVLILILIIIIVICG 89
>gnl|CDD|178695 PLN03150, PLN03150, hypothetical protein; Provisional.
Length = 623
Score = 27.1 bits (60), Expect = 4.2
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 29/97 (29%)
Query: 5 YCENKGTCVKDARGQPSCR-CVGSFIGPHCAQKSEFAYIAGGIAATVVFLIIIALFVWMI 63
+ +N G C G P R C GPH + ++ IA G++ +FL+I A+ W
Sbjct: 522 FTDNAGLC-----GIPGLRAC-----GPHLSVGAKIG-IAFGVSVAFLFLVICAMCWW-- 568
Query: 64 CARSERRREPKKLVAQTNDQTGSQVNFYYGGAPYAES 100
R + +++ A+ APYA++
Sbjct: 569 -KRRQNILRAQRIAAR--------------EAPYAKA 590
>gnl|CDD|217741 pfam03806, ABG_transport, AbgT putative transporter family.
Length = 502
Score = 26.9 bits (60), Expect = 4.3
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 48 ATVVFLIIIALFVWMI 63
A V F++ IAL +
Sbjct: 260 AGVAFVVTIALLALTV 275
>gnl|CDD|201325 pfam00584, SecE, SecE/Sec61-gamma subunits of protein
translocation complex. SecE is part of the SecYEG
complex in bacteria which translocates proteins from
the cytoplasm. In eukaryotes the complex, made from
Sec61-gamma and Sec61-alpha translocates protein from
the cytoplasm to the ER. Archaea have a similar
complex.
Length = 56
Score = 25.2 bits (56), Expect = 4.3
Identities = 6/16 (37%), Positives = 14/16 (87%)
Query: 48 ATVVFLIIIALFVWMI 63
+VF++++ALF+W++
Sbjct: 30 VVLVFVLVMALFLWLV 45
>gnl|CDD|240537 cd13132, MATE_eukaryotic, Eukaryotic members of the multidrug and
toxic compound extrusion (MATE) family. 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. MATE has also been identified as a
large multigene family in plants, where the proteins are
linked to disease resistance. A number of family members
are involved in the synthesis of peptidoglycan
components in bacteria. This subfamily, which is
restricted to eukaryotes, contains vertebrate solute
transporters responsible for secretion of cationic drugs
across the brush border membranes, yeast proteins
located in the vacuole membrane, and plant proteins
involved in disease resistance and iron homeostatis
under osmotic stress.
Length = 436
Score = 26.8 bits (60), Expect = 4.5
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 42 IAGGIAATVVFLIIIALFVWMICAR 66
IAG I V+ L+II W A
Sbjct: 411 IAGLILQAVILLLIILRTDWDKEAE 435
>gnl|CDD|132557 TIGR03518, ABC_perm_GldF, gliding motility-associated ABC
transporter permease protein GldF. Members of this
protein family are exclusive to the Bacteroidetes
phylum (previously
Cytophaga-Flavobacteria-Bacteroides). GldF is believed
to be a ABC transporter permease protein (along with
ATP-binding subunit, GldA and a sunstrate-binding
subunit, GldG) and is linked to a type of rapid surface
gliding motility found in certain Bacteroidetes, such
as Flavobacterium johnsoniae and Cytophaga
hutchinsonii. Knockouts of GldF abolish the gliding
phenotype. Gliding motility appears closely linked to
chitin utilization in the model species Flavobacterium
johnsoniae. Bacteroidetes with members of this protein
family appear to have all of the genes associated with
gliding motility.
Length = 240
Score = 26.5 bits (59), Expect = 5.0
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 36 KSEF-AYIAGGIAATV--VFLIIIALFVW 61
K EF ++ + I V VFL+ LF+W
Sbjct: 6 KKEFNSFFSSPIGYLVIAVFLLANGLFLW 34
>gnl|CDD|217986 pfam04247, SirB, Invasion gene expression up-regulator, SirB.
SirB up-regulates Salmonella typhimurium invasion gene
transcription. It is, however, not essential for the
expression of these genes. Its function is unknown.
Length = 122
Score = 26.0 bits (58), Expect = 5.1
Identities = 6/37 (16%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 46 IAATVVFLIIIALFVWMICARSERRREPKKLVAQTND 82
+A +V+ ++ V M+ +++ K++ D
Sbjct: 13 VALSVLLFVL--RGVLMLRGSPWLQKKWVKILPHVID 47
>gnl|CDD|221690 pfam12650, DUF3784, Domain of unknown function (DUF3784). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
archaea. Proteins in this family are typically between
96 and 110 amino acids in length.
Length = 96
Score = 25.6 bits (57), Expect = 5.4
Identities = 7/26 (26%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 46 IAATVVFLIIIALFVWMICARSERRR 71
I A + F++++ V + A+ R+R
Sbjct: 72 IIAIIAFIVLLIFLVIYL-AKGNRKR 96
>gnl|CDD|236685 PRK10414, PRK10414, biopolymer transport protein ExbB; Provisional.
Length = 244
Score = 26.4 bits (58), Expect = 5.4
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 27 SFIGPHCAQKSEFAYIAGGIA----ATVVFLI--IIALFVWMICAR 66
SFIG Q + A +A GIA AT + L+ I A+ ++ + AR
Sbjct: 155 SFIGIAQTQTTNLAVVAPGIAEALLATAIGLVAAIPAVVIYNVFAR 200
>gnl|CDD|236732 PRK10662, PRK10662, beta-lactam binding protein AmpH;
Provisional.
Length = 378
Score = 26.5 bits (59), Expect = 5.5
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 52 FLIIIALFVWMIC-ARSERRREPKKLVAQTNDQTGSQVNFYYGGAP 96
L AL + A + + L + D+ + FY GA
Sbjct: 5 LLFSAALCAAALTSAHAAQPAADPLLASDIVDRYAEHI-FYGSGAT 49
>gnl|CDD|219677 pfam07974, EGF_2, EGF-like domain. This family contains EGF
domains found in a variety of extracellular proteins.
Length = 31
Score = 24.3 bits (53), Expect = 5.6
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 3/28 (10%)
Query: 6 CENKGTCVKDARGQPSCRCVGSFIGPHC 33
C +GTCV+ C C + G C
Sbjct: 7 CNGRGTCVRPCG---KCVCDSGYQGATC 31
>gnl|CDD|236845 PRK11099, PRK11099, putative inner membrane protein; Provisional.
Length = 399
Score = 26.4 bits (59), Expect = 5.9
Identities = 10/40 (25%), Positives = 15/40 (37%)
Query: 42 IAGGIAATVVFLIIIALFVWMICARSERRREPKKLVAQTN 81
GG+ T + L + L V R RR + A+
Sbjct: 359 PLGGLLITYLLLFLALLLVIGWEKRFFRRAKLTIRTAKEL 398
>gnl|CDD|226790 COG4340, COG4340, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 226
Score = 26.4 bits (58), Expect = 6.2
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 5/43 (11%)
Query: 106 HSTYAHYYDDEEDGW-EMPNFYNE----TYMKGEYRARNFSAV 143
T A + GW +N+ T+M G YR R FSA
Sbjct: 12 EETRALLGKEATAGWDAFAPSWNDLPLDTFMAGRYRLRRFSAF 54
>gnl|CDD|184883 PRK14889, PRK14889, VKOR family protein; Provisional.
Length = 143
Score = 25.8 bits (57), Expect = 6.3
Identities = 11/56 (19%), Positives = 16/56 (28%), Gaps = 4/56 (7%)
Query: 17 RGQPSCRCVGSFIGPHCAQKSEFAYIAG---GIAATVVFLIIIALFVWMICARSER 69
+ P C + S I S +A G F IAL + +
Sbjct: 35 KPPPFCT-INSVINCSSVLSSPYARFLGIPLDYLGAAWFSANIALALLGVGTLKRI 89
>gnl|CDD|223035 PHA03294, PHA03294, envelope glycoprotein H; Provisional.
Length = 835
Score = 26.6 bits (59), Expect = 6.7
Identities = 6/33 (18%), Positives = 14/33 (42%)
Query: 40 AYIAGGIAATVVFLIIIALFVWMICARSERRRE 72
Y+A + ++ + I+ M+C+ R
Sbjct: 803 TYLAASVGGALLAVAILYGIAKMLCSNVRNRGY 835
>gnl|CDD|206021 pfam13850, ERGIC_N, Endoplasmic Reticulum-Golgi Intermediate
Compartment (ERGIC). This family is the N-terminal of
ERGIC proteins, ER-Golgi intermediate compartment
clusters, otherwise known as Ervs, and is associated
with family COPIIcoated_ERV, pfam07970.
Length = 105
Score = 25.1 bits (56), Expect = 7.4
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 42 IAGGIAATVVFLIIIALFVW 61
+GGI + LIII LFV
Sbjct: 20 TSGGIITLISILIIIILFVS 39
>gnl|CDD|119324 cd06582, TM_PBP1_LivH_like, Transmembrane subunit (TM) of
Escherichia coli LivH and related proteins. LivH is one
of two TMs of the E. coli LIV-1/LS transporter, a
Periplasmic Binding Protein (PBP)-dependent ATP-Binding
Cassette (ABC) transporter involved in the uptake of
branched-chain amino acids (AAs). These types of
transporters generally bind type 1 PBPs. PBP-dependent
ABC transporters consist of a PBP, two TMs, and two
cytoplasmic ABCs, and are mainly involved in importing
solutes from the environment. The solute is captured by
the PBP, which delivers it to a gated translocation
pathway formed by the two TMs. The two ABCs bind and
hydrolyze ATP and drive the transport reaction. E. coli
LivH forms a heterodimer with another TM, LivM, to
generate the transmembrane pore. LivM is not included in
this subgroup. The LIV-1/LS transporter is comprised of
two TMs (LivM and LivH), two ABCs (LivG and LivF), and
one of two alternative PBPs, LivJ (LIV-BP) or LivK
(LS-BP). In addition to transporting branched-chain AAs
including leucine, isoleucine and valine, the E. coli
LIV-1/LS transporter is involved in the uptake of the
aromatic AA, phenylalanine.
Length = 272
Score = 25.9 bits (58), Expect = 7.4
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 40 AYIAGGIAATVVFLIIIALFVWM 62
AY++ G V F+++I + +
Sbjct: 245 AYLSSGYKDAVAFVLLILVLLVR 267
>gnl|CDD|223888 COG0818, DgkA, Diacylglycerol kinase [Cell envelope biogenesis,
outer membrane].
Length = 123
Score = 25.6 bits (57), Expect = 7.5
Identities = 8/30 (26%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 35 QKSEFAYIAGGIAATVVFL-IIIALFVWMI 63
+ E A A + + V + + A+ VW+I
Sbjct: 86 EYHELAKRAKDMGSAAVLIASLFAVIVWLI 115
>gnl|CDD|225142 COG2233, UraA, Xanthine/uracil permeases [Nucleotide transport and
metabolism].
Length = 451
Score = 26.0 bits (58), Expect = 7.6
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 27 SFIGPHCAQKSEF----AYIAGGIAATVVFLIIIALFVWMICAR 66
+F+ P A A + GGI A + +I+ V + AR
Sbjct: 89 AFVAPMIAIGGTTGDGIAALLGGIIAAGLVYFLISPIVKIRLAR 132
>gnl|CDD|233133 TIGR00801, ncs2, uracil-xanthine permease. The Nucleobase:Cation
Symporter-2 (NCS2) Family (TC 2.A.40) Most of the
functionally characterized members of the NCS2 family
are transporters specific for nucleobases including both
purines and pyrimidines. However, two closely related
rat members of the family, SVCT1 and SVCT2, localized to
different tissues of the body, cotransport L-ascorbate
and Na+ with a high degree of specificity and high
affinity for the vitamin. The NCS2 family appears to be
distantly related to the NCS1 family (TC #2.A.39)
[Transport and binding proteins, Nucleosides, purines
and pyrimidines].
Length = 412
Score = 26.1 bits (58), Expect = 7.6
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 27 SFIGPHCAQKSEFAY--IAGGIAATVVFLIIIALFVWMICARSERR 70
+F+ P A S I GG+ AT + +++L + + R +
Sbjct: 76 AFVSPMIAIGSGLGIPAIMGGLIATGLVYALLSLLIKKLGTRWLMK 121
>gnl|CDD|147692 pfam05675, DUF817, Protein of unknown function (DUF817). This
family consists of several bacterial proteins of
unknown function.
Length = 235
Score = 26.0 bits (58), Expect = 8.2
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 52 FLIIIALF--VWMICARSERRREPK 74
FL+I AL + M+ E E K
Sbjct: 39 FLLIAALLIQILMLATGLETWDELK 63
>gnl|CDD|224671 COG1757, NhaC, Na+/H+ antiporter [Energy production and
conversion].
Length = 485
Score = 26.1 bits (58), Expect = 8.3
Identities = 7/30 (23%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 34 AQKSEFAYIAGGIAATVVFLIIIALF-VWM 62
F + G + A ++ L I A W
Sbjct: 71 IIILIFLGLLGALTALLILLGIGAAIAAWA 100
>gnl|CDD|219377 pfam07333, SLR1-BP, S locus-related glycoprotein 1 binding pollen
coat protein (SLR1-BP). This family consists of a
number of cysteine rich SLR1 binding pollen coat like
proteins. Adhesion of pollen grains to the stigmatic
surface is a critical step during sexual reproduction
in plants. In Brassica, S locus-related glycoprotein 1
(SLR1), a stigma-specific protein belonging to the S
gene family of proteins, has been shown to be involved
in this step. SLR1-BP specifically binds SLR1 with high
affinity. The SLR1-BP gene is specifically expressed in
pollen at late stages of development and is a member of
the class A pollen coat protein (PCP) family, which
includes PCP-A1, an SLG (S locus glycoprotein)-binding
protein.
Length = 57
Score = 24.4 bits (53), Expect = 8.9
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 5/28 (17%)
Query: 2 CKGYCE-----NKGTCVKDARGQPSCRC 24
C C+ GTC+ +G+ C C
Sbjct: 26 CAALCKKKYKGGVGTCIPTPKGKKQCLC 53
>gnl|CDD|131844 TIGR02797, exbB, tonB-system energizer ExbB. This model describes
ExbB proteins, part of the MotA/TolQ/ExbB protein
family. The paired proteins MotA and MotB, TolQ and
TolR, and ExbB and ExbD harness the proton-motive force
to drive the flagellar motor, energize the Tol-Pal
system, or energize TonB, respectively. Tol-Pal and TonB
are both active at the outer membrane. Genomes may have
many different TonB-dependent receptors, of which many
of those characterized are involved in siderophore
transport across the outer membrane [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 211
Score = 25.8 bits (57), Expect = 9.1
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 27 SFIGPHCAQKSEFAYIAGGIA----ATVVFLI--IIALFVWMICARS 67
SFIG +Q + A +A GIA AT + L+ I A+ ++ + ARS
Sbjct: 144 SFIGISKSQTTNLAVVAPGIAEALLATAIGLVAAIPAVVIYNVFARS 190
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
0.321 0.135 0.438
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,141,096
Number of extensions: 609402
Number of successful extensions: 1148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1142
Number of HSP's successfully gapped: 69
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)