RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16470
(197 letters)
>gnl|CDD|216649 pfam01694, Rhomboid, Rhomboid family. This family contains
integral membrane proteins that are related to
Drosophila rhomboid protein. Members of this family are
found in bacteria and eukaryotes. Rhomboid promotes the
cleavage of the membrane-anchored TGF-alpha-like growth
factor Spitz, allowing it to activate the Drosophila EGF
receptor. Analysis has shown that Rhomboid-1 is an
intramembrane serine protease (EC:3.4.21.105).
Parasite-encoded rhomboid enzymes are also important for
invasion of host cells by Toxoplasma and the malaria
parasite.
Length = 146
Score = 73.4 bits (181), Expect = 7e-17
Identities = 46/127 (36%), Positives = 62/127 (48%), Gaps = 16/127 (12%)
Query: 1 MRDLEKLTGSFRIAIIYFGSGIGGNLASAIFVPYRADVGPAGAHFGLLACLIVEVGPAGA 60
LE++ GS R ++Y SG+ G+L S +F P VG +GA
Sbjct: 34 GIPLERILGSVRFLLLYLLSGLAGSLLSYLFSPA----------------SSPSVGASGA 77
Query: 61 HFGLLACLIVEVLNCWPLLKHPEQALMKLLTITFILLLFGLLPWVDNFAHLFGFLFGFLL 120
FGLL L+V + LL + AL+ LL I + LL G LP + NFAHL G + G LL
Sbjct: 78 IFGLLGALLVLLPRNRILLFNFPGALLLLLGIILLNLLLGFLPGISNFAHLGGLIAGLLL 137
Query: 121 SYALLPF 127
+ LL
Sbjct: 138 GFLLLRR 144
>gnl|CDD|185445 PTZ00101, PTZ00101, rhomboid-1 protease; Provisional.
Length = 278
Score = 41.4 bits (97), Expect = 1e-04
Identities = 33/122 (27%), Positives = 55/122 (45%), Gaps = 28/122 (22%)
Query: 4 LEKLTGSFRIAIIYFGSGIGGNL--ASAIFVPYRADVGPAGAHFGLLACLIVEVGPAGAH 61
LEK G +I I+YF +GI GN+ +S + P ++VG + +
Sbjct: 132 LEKNYGIVKIIILYFLTGIYGNILSSSVTYCP-------------------IKVGASTSG 172
Query: 62 FGLLACLIVEVLNCWPLLKHPEQALMKLLTITFILLLFGLL-----PWVDNFAHLFGFLF 116
GLL + E++ W +++H E+ + + I F L+ F +D+ HL G L
Sbjct: 173 MGLLGIVTSELILLWHVIRHRERVVFNI--IFFSLISFFYYFTFNGSNIDHVGHLGGLLS 230
Query: 117 GF 118
G
Sbjct: 231 GI 232
>gnl|CDD|223777 COG0705, COG0705, Membrane associated serine protease [Amino acid
transport and metabolism].
Length = 228
Score = 39.0 bits (91), Expect = 6e-04
Identities = 33/128 (25%), Positives = 50/128 (39%), Gaps = 13/128 (10%)
Query: 1 MRDLEKLTGSFRIAIIYFGSGIGGNLASAIFVP--YRADVGPAGAHFGLLACLIVEVGPA 58
+LE+ G+ R + Y SG+ LA +F P +G +GA FGLL +
Sbjct: 95 GSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPKGGAPSLGASGAIFGLLGAYFL----- 149
Query: 59 GAHFGLLACLIVEVLNCWPLLKHPEQALMKLLTITFILLLFGLLPWVDNFAHLFGFLFGF 118
F L++ + P L ++ L + P V AHL G + G
Sbjct: 150 --LFPFARILLLFLSLPRPAL----ILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGL 203
Query: 119 LLSYALLP 126
LL+ L
Sbjct: 204 LLAALLSR 211
>gnl|CDD|219026 pfam06432, GPI2, Phosphatidylinositol
N-acetylglucosaminyltransferase.
Glycosylphosphatidylinositol (GPI) represents an
important anchoring molecule for cell surface proteins.
The first step in its synthesis is the transfer of
N-acetylglucosamine (GlcNAc) from
UDP-N-acetylglucosamine to phosphatidylinositol (PI).
This step involves products of three or four genes in
both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG
A, PIG H and PIG C), respectively.
Length = 268
Score = 31.8 bits (73), Expect = 0.15
Identities = 13/70 (18%), Positives = 27/70 (38%)
Query: 92 ITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIFLIWVCLMFVII 151
+ F + LF LLP + +L++AL + + L+++ + I
Sbjct: 187 LLFAIQLFALLPILRRSIRKTSRRLHVVLTFALSILAVYLLLTLSPILALLFLLTVLFIS 246
Query: 152 FLVVLLLLFY 161
F+ L +
Sbjct: 247 FVCPLWFIRL 256
>gnl|CDD|225193 COG2311, COG2311, Predicted membrane protein [Function unknown].
Length = 394
Score = 31.9 bits (73), Expect = 0.18
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 78 LLKHPEQALMKLLTITFILLLFGLLPWVDNFAHLFGFLFG-FLLSYALLPFVSFGPYDRQ 136
+ + + +LLL GL+ H G LL+YAL + R+
Sbjct: 88 AARKGRRWVALYARRLLLLLLLGLI-------HALFIWDGDILLAYALTGLILLLFRRRK 140
Query: 137 KKIFLIWVCLMFVIIFLVVLLLLFYLIP 164
K LIW + ++ L+ +LLL L
Sbjct: 141 PKTLLIWATALLLLPVLLGVLLLLVLES 168
>gnl|CDD|237159 PRK12651, PRK12651, putative monovalent cation/H+ antiporter
subunit E; Reviewed.
Length = 158
Score = 29.8 bits (68), Expect = 0.60
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 8/75 (10%)
Query: 87 MKLLTITFILLLFG--LLPWVDNFAHLF-GFLFGFLLSYALLPFVSFGPYDRQKKIFLIW 143
M + I+L L + + GF+ G + + + Y R+ I+
Sbjct: 1 MAFQLLLNIILAVLWLFLTGSFSLGNFIIGFILGLFVLFLFRRLLPARFYLRR-----IY 55
Query: 144 VCLMFVIIFLVVLLL 158
+ V IFL L+
Sbjct: 56 KLIKLVPIFLKELIK 70
>gnl|CDD|233511 TIGR01654, bact_immun_7tm, bacteriocin-associated integral membrane
(putative immunity) protein. This model represents a
family of integral membrane proteins, most of which are
about 650 residues in size and predicted to span the
membrane seven times. Nearly half of the members of this
family are found in association with a member of the
lactococcin 972 family of bacteriocins (TIGR01653).
Others may be associated with uncharacterized proteins
that may also act as bacteriocins. Although this protein
is suggested to be an immunity protein, and the
bacteriocin is suggested to be exported by a
Sec-dependent process, the role of this protein is
unclear [Cellular processes, Toxin production and
resistance].
Length = 679
Score = 30.1 bits (68), Expect = 0.78
Identities = 21/94 (22%), Positives = 39/94 (41%), Gaps = 13/94 (13%)
Query: 85 ALMKLLTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIFLIWV 144
AL+ LL +F+L + G + ++ +F LL LL +SF K+ L
Sbjct: 224 ALLILLLSSFLLFIKGYTYLLKDY--IFMLSLSVLLLLLLLLIISFLTLLLLSKMSLANS 281
Query: 145 -----------CLMFVIIFLVVLLLLFYLIPIYD 167
+ +V ++++L++ LI I
Sbjct: 282 IKGKSSFKFLLIINYVCKLVLLVLVIATLITILS 315
>gnl|CDD|223701 COG0628, yhhT, Predicted permease, member of the PurR regulon
[General function prediction only].
Length = 355
Score = 29.9 bits (68), Expect = 0.79
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 77 PLLKHPEQALMKLLTITFILLLFGLLPWVDNFAHLF-GFLFGFLLSYALLPFVSFGPYDR 135
+ P L+ L + +LLL LL + F + L +L+Y L P V ++
Sbjct: 2 LMRWLPRTLLLGLRILLLLLLLLLLLAILYFFQPILLPLLLALVLAYLLNPLVRR--LEK 59
Query: 136 QKKIFLIWVCLMFVIIFLVVLLLLFYLIPI 165
+ L+ V L+ ++I L+++LL +IP
Sbjct: 60 RGIPRLLAVLLVLLLILLLIVLLGLLVIPS 89
>gnl|CDD|223885 COG0815, Lnt, Apolipoprotein N-acyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 518
Score = 29.3 bits (66), Expect = 1.3
Identities = 26/107 (24%), Positives = 36/107 (33%), Gaps = 16/107 (14%)
Query: 62 FGLLACLIVEVLNCWPLLKHPEQALMKLLTITFILLLFGLLPWVDNFAHLFGFLFGFLLS 121
FG L L + W L ++ +L L P GFLFGF
Sbjct: 24 FGALFALAFPPPDWWWLA---------WFSLAPLLWLVRGAPTSWEGLAKSGFLFGFGFF 74
Query: 122 YALLP--FVSFGPYDRQKKIFLIWVCLMFVIIFLVVLLLLFYLIPIY 166
A S G + L+ V L +++ L L LF L+
Sbjct: 75 LAGFYWLGTSLGVG-----LGLLAVALPLLVLLLAAWLALFLLLVAV 116
>gnl|CDD|165328 PHA03030, PHA03030, hypothetical protein; Provisional.
Length = 122
Score = 28.4 bits (63), Expect = 1.4
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 145 CLMFVIIFLVVLLLLFYLIPI 165
C+ ++IFL + L +F+ I I
Sbjct: 3 CIFLILIFLFIFLFIFFYIRI 23
>gnl|CDD|218184 pfam04632, FUSC, Fusaric acid resistance protein family. This
family includes a conserved region found in two proteins
associated with fusaric acid resistance,from
Burkholderia cepacia and Klebsiella oxytoca. These
proteins are likely to be membrane transporter proteins.
Length = 649
Score = 28.8 bits (65), Expect = 2.3
Identities = 14/31 (45%), Positives = 15/31 (48%)
Query: 95 ILLLFGLLPWVDNFAHLFGFLFGFLLSYALL 125
L LF +LP VD F L L LL LL
Sbjct: 404 FLYLFVVLPHVDGFPLLALVLAPPLLLGGLL 434
>gnl|CDD|193538 cd05662, M28_like_2, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions. This subfamily
is composed of uncharacterized proteins that do not
contain a protease-associated (PA) domain.
Length = 267
Score = 28.4 bits (64), Expect = 2.5
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 100 GLLPWVDNFAHLFGFLFGF 118
GL PW NF H F F F
Sbjct: 39 GLQPWGGNFEHPFSFSKRF 57
>gnl|CDD|131967 TIGR02921, PEP_integral, PEP-CTERM family integral membrane
protein. Members of this protein family, found in three
different species so far, have a PEP-CTERM sequence at
the carboxyl-terminus (see model TIGR02595), but are
unusual among PEP-CTERM proteins in having multiple
predicted transmembrane segments. The function is
unknown. It is proposed that a member of the EpsH
family, to be designated exosortase (see TIGR02602),
recognizes and cleaves PEP-CTERM proteins in a manner
analogous to the cleavage of LPXTG proteins by sortase
(see Haft, et al., 2006).
Length = 952
Score = 28.5 bits (63), Expect = 2.7
Identities = 38/139 (27%), Positives = 57/139 (41%), Gaps = 22/139 (15%)
Query: 45 FGLLACLIVEVGPAGAHFGLLACLIVEV------LNCWPLLKHPEQALMKL-----LTIT 93
FGL A L +G F L L++ + + LK+P AL+KL I
Sbjct: 32 FGLPAILAAAIGDHPIEFALALILLIAIPAICIGIGGTCFLKNP-TALIKLFYGVEAPIF 90
Query: 94 FILL--LFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIFLIWVCLMFVII 151
FI L LF + +H+ L ++ A FG + KI L W+ L+ ++
Sbjct: 91 FICLLRLFLIRELNPASSHI---LINIGIAIAAFAACLFGGVASRFKIGLQWLQLLAAML 147
Query: 152 FLVV-----LLLLFYLIPI 165
L+ LL F+ IP
Sbjct: 148 MLLFGIYAAALLAFFAIPA 166
>gnl|CDD|224428 COG1511, COG1511, Predicted membrane protein [Function unknown].
Length = 780
Score = 28.2 bits (63), Expect = 3.0
Identities = 18/84 (21%), Positives = 28/84 (33%), Gaps = 18/84 (21%)
Query: 87 MKLLTITFILL---------LFGLLPWVDNFAHLFGFLFGFL-LSYALLPF--VSFGPYD 134
K + I ++L L P F L L L+YA+ F V GP
Sbjct: 683 GKFIAIVLLVLQIAGSGGTFPIQLSPSF------FQILHPALPLTYAVNGFREVIGGPIP 736
Query: 135 RQKKIFLIWVCLMFVIIFLVVLLL 158
L+ + ++ + L L
Sbjct: 737 SNLWSGLLALIGFLILFIIGGLFL 760
>gnl|CDD|224476 COG1560, HtrB, Lauroyl/myristoyl acyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 308
Score = 28.0 bits (63), Expect = 3.0
Identities = 15/45 (33%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 79 LKHPEQALMKLLTITFILLLFGLLPW--VDNFAHLFGFLFGFLLS 121
L HP L L L L LLP+ + G L G LL
Sbjct: 10 LLHPRYWLTWLGV--GALWLLVLLPYPFLRRLGDGLGRLAGRLLK 52
>gnl|CDD|216594 pfam01594, UPF0118, Domain of unknown function DUF20. This
transmembrane region is found in putative permeases and
predicted transmembrane proteins it has no known
function. It is not clear what source suggested that
these proteins may be permeases and this information
should be treated with caution.
Length = 327
Score = 28.0 bits (63), Expect = 3.2
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 89 LLTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIFLIWVCLMF 148
LL + F+LLL ++ + L L +L+Y L P V F + I L+
Sbjct: 2 LLILIFLLLLLAFYWFIPDL--LVPLLIALVLAYLLNPVVRFLKRRGIPRSLAI--LLVL 57
Query: 149 VIIFLVVLLLLFYLIPI 165
++ + ++LL LIP+
Sbjct: 58 LLFLVALVLLGLLLIPL 74
>gnl|CDD|129428 TIGR00328, flhB, flagellar biosynthetic protein FlhB. FlhB and its
functionally equivalent orthologs, from among a larger
superfamily of proteins involved in type III protein
export systems, are specifically involved in flagellar
protein export. The seed members are restricted and the
trusted cutoff is set high such that the proteins
gathered by this model play roles specifically related
to flagellar structures. Full-length homologs scoring
below the trusted cutoff are involved in peptide export
but not necessarily in the creation of flagella
[Cellular processes, Chemotaxis and motility].
Length = 347
Score = 28.0 bits (63), Expect = 3.4
Identities = 16/77 (20%), Positives = 23/77 (29%), Gaps = 7/77 (9%)
Query: 90 LTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIFLIWV-CLMF 148
L + LLF D L F F S F L+
Sbjct: 32 LLAGVLSLLFFGDGLADLLVVLMSFFLSFETS------DILNLGSLVGIFFQSIREVLLL 85
Query: 149 VIIFLVVLLLLFYLIPI 165
++ V+LL++ L I
Sbjct: 86 LLPIFVLLLVVGVLSNI 102
>gnl|CDD|226884 COG4478, COG4478, Predicted membrane protein [Function unknown].
Length = 210
Score = 27.8 bits (62), Expect = 3.5
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 140 FLIWVCLMFVIIFLVVLLLLFYLIPIYDCELCSYFN 175
LI++ + +II L VLL +F IY E+ S
Sbjct: 4 KLIFIFSLLIIIALSVLLTIFLAWWIYPLEIHSLQL 39
>gnl|CDD|234093 TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl
glycosylphosphotransferase. Members of this family are
generally found near other genes involved in the
biosynthesis of a variety of exopolysaccharides. These
proteins consist of two fused domains, an N-terminal
hydrophobic domain of generally low conservation and a
highly conserved C-terminal sugar transferase domain
(pfam02397). Characterized and partially characterized
members of this subfamily include Salmonella WbaP
(originally RfbP) , E. coli WcaJ , Methylobacillus EpsB,
Xanthomonas GumD, Vibrio CpsA, Erwinia AmsG, Group B
Streptococcus CpsE (originally CpsD), and Streptococcus
suis Cps2E. Each of these is believed to act in
transferring the sugar from, for instance, UDP-glucose
or UDP-galactose, to a lipid carrier such as
undecaprenyl phosphate as the first (priming) step in
the synthesis of an oligosaccharide "block". This
function is encoded in the C-terminal domain. The
liposaccharide is believed to be subsequently
transferred through a "flippase" function from the
cytoplasmic to the periplasmic face of the inner
membrane by the N-terminal domain. Certain closely
related transferase enzymes such as Sinorhizobium ExoY
and Lactococcus EpsD lack the N-terminal domain and are
not found by this model.
Length = 445
Score = 27.9 bits (63), Expect = 3.5
Identities = 15/80 (18%), Positives = 26/80 (32%), Gaps = 10/80 (12%)
Query: 89 LLTITFIL--LLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKK------IF 140
L ++ +L LL G + L LL L G Y + +
Sbjct: 6 ALALSLLLAFLLRGGGLLPPPSFYSLLLLLILLLFLILFAA--SGLYRSWRGRSLLEELA 63
Query: 141 LIWVCLMFVIIFLVVLLLLF 160
+ + + V + L+ L L
Sbjct: 64 RVLLAWLLVFLLLLALAFLL 83
>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 = 27.5 bits (62), Expect = 4.1
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 111 LFGFLFGFLLSYALLPFVSFGPYDRQKKIF-LIWVCLMFVIIFLVVLLLLFYL 162
F F G LL Y L+ + +K++ L+ V+ +L VL LFYL
Sbjct: 20 WFPFSLGDLLYYLLIILLLRYLIKLRKRLKKKWKRFLLRVLAYLSVLYFLFYL 72
>gnl|CDD|149504 pfam08475, Baculo_VP91_N, Viral capsid protein 91 N-terminal. This
domain is found in Baculoviridae including the
nucleopolyhedrovirus at the N-terminus of the viral
capsid protein 91 (VP91).
Length = 185
Score = 27.2 bits (61), Expect = 4.4
Identities = 9/22 (40%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 146 LMFVIIFLVVLLLLFYLIPIYD 167
L+ V I L+++ L++YL IY+
Sbjct: 1 LLLVAIILLIIFLIYYLF-IYN 21
>gnl|CDD|221252 pfam11833, DUF3353, Protein of unknown function (DUF3353). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 205 to 258
amino acids in length.
Length = 193
Score = 27.2 bits (61), Expect = 4.7
Identities = 30/139 (21%), Positives = 49/139 (35%), Gaps = 30/139 (21%)
Query: 25 NLASAIFVPYRADVGPAGAHFGLLACLIVEVGPAGA-----HFGLLACLIVEVLNCWPLL 79
L + +P + FGLLA L++ GP G AC+ L
Sbjct: 80 RLLPSFDLPSGQGLLIRLVLFGLLALLLLLQGPPSGPQLQLALGTGACIY--------FL 131
Query: 80 KHPEQALMKLLTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKI 139
+ + L + L+ GL L G LL+ L PF+ G ++
Sbjct: 132 NRKGRRFGRALLWSLGGLVVGL-------------LLGSLLAVLLPPFILPGSLSPEQ-- 176
Query: 140 FLIWVCLMFVIIFLVVLLL 158
I +++++L L L
Sbjct: 177 --IQSLPAYLLLWLGSLFL 193
>gnl|CDD|181433 PRK08455, fliL, flagellar basal body-associated protein FliL;
Reviewed.
Length = 182
Score = 27.3 bits (61), Expect = 4.8
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 146 LMFVIIFLVVLLLL 159
L+ +II +VVLLLL
Sbjct: 19 LLIIIIGVVVLLLL 32
>gnl|CDD|232940 TIGR00361, ComEC_Rec2, DNA internalization-related competence
protein ComEC/Rec2. Apparant orthologs are found in 5
species so far (Haemophilus influenzae, Escherichia
coli, Bacillus subtilis, Neisseria gonorrhoeae,
Streptococcus pneumoniae), of which all but E. coli are
model systems for the study of competence for natural
transformation. This protein is a predicted multiple
membrane-spanning protein likely to be involved in DNA
internalization. In a large number of bacterial species
not known to exhibit competence, this protein is
replaced by a half-length N-terminal homolog of unknown
function, modelled by the related model ComEC_N-term.
The role for this protein in species that are not
naturally transformable is unknown [Cellular processes,
DNA transformation].
Length = 662
Score = 27.6 bits (61), Expect = 4.9
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 1/77 (1%)
Query: 90 LTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIF-LIWVCLMF 148
L+ +LL +F F +F +L Y++ P V + + L + L
Sbjct: 245 LSYIVLLLFDPYHLLSASFWLSFAAVFSLILWYSIFPQVKTQLGPVLRAVVSLTHLQLGA 304
Query: 149 VIIFLVVLLLLFYLIPI 165
+ L + L F+ +
Sbjct: 305 QLGSLPIQLYHFHGFSL 321
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 27.5 bits (62), Expect = 4.9
Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 12/82 (14%)
Query: 89 LLTITFIL---LLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKK------- 138
L+ + +L L FG D ++L L + LL F FG Y ++
Sbjct: 6 LILLALLLAYLLRFGSRGIPDIESYLALLLL--AVLLFLLIFALFGLYRSWRRRSRLREM 63
Query: 139 IFLIWVCLMFVIIFLVVLLLLF 160
+ I + + L +L L
Sbjct: 64 LLRILLAWTLTFLILALLAFLL 85
>gnl|CDD|219819 pfam08395, 7tm_7, 7tm Chemosensory receptor. This family includes
a number of gustatory and odorant receptors mainly from
insect species such as A. gambiae and D. melanogaster.
They are classified as G-protein-coupled receptors
(GPCRs), or seven-transmembrane receptors. They show
high sequence divergence, consistent with an ancient
origin for the family.
Length = 370
Score = 27.4 bits (61), Expect = 5.5
Identities = 18/99 (18%), Positives = 42/99 (42%)
Query: 65 LACLIVEVLNCWPLLKHPEQALMKLLTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYAL 124
L ++V +L+ + + L +LL + LL G F L L ++ L
Sbjct: 78 LLTVLVILLSLLFQRRRLARLLNELLRLDRRLLRLGSRRNFRRFNRLLLLLLVLIILLLL 137
Query: 125 LPFVSFGPYDRQKKIFLIWVCLMFVIIFLVVLLLLFYLI 163
+ + + + + L+ + + + L +L+L ++L+
Sbjct: 138 VSLLGYLLLSQYFLLVLLLLLYLLPYLVLNLLILQYFLL 176
>gnl|CDD|182289 PRK10179, PRK10179, formate dehydrogenase-N subunit gamma;
Provisional.
Length = 217
Score = 27.1 bits (60), Expect = 5.7
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 81 HPEQALM--KLLTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALL 125
+ Q +M ++++ F+LL+ G++ W FA F ++ Y+LL
Sbjct: 110 NAGQKMMFWSIMSMIFVLLVTGVIIWRPYFAQYFPMQ---VVRYSLL 153
>gnl|CDD|234931 PRK01265, PRK01265, heat shock protein HtpX; Provisional.
Length = 324
Score = 27.4 bits (61), Expect = 5.9
Identities = 19/56 (33%), Positives = 23/56 (41%), Gaps = 10/56 (17%)
Query: 86 LMKLLTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYALLPFVSF--------GPY 133
M L + +LL F L V + FG FG L +L FV F GPY
Sbjct: 11 NMALAGLGIVLLGFALAYAV--AYYAFGAQFGVGLILGILIFVFFLNIIQWLFGPY 64
>gnl|CDD|173239 PRK14778, PRK14778, lipoprotein signal peptidase; Provisional.
Length = 186
Score = 26.7 bits (59), Expect = 6.2
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 107 NFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIFLIWVCLMFVIIFLVVLLLLFYL 162
F + GFL A V+ G + + ++W ++FV++FL +L +F
Sbjct: 25 TFFIVPGFLR---FVKATNRGVALGLFSNLSEQ-VLWT-VLFVVVFLSLLPYIFRF 75
>gnl|CDD|233438 TIGR01494, ATPase_P-type, ATPase, P-type (transporting), HAD
superfamily, subfamily IC. The P-type ATPases are a
large family of trans-membrane transporters acting on
charged substances. The distinguishing feature of the
family is the formation of a phosphorylated intermediate
(aspartyl-phosphate) during the course of the reaction.
Another common name for these enzymes is the E1-E2
ATPases based on the two isolable conformations: E1
(unphosphorylated) and E2 (phosphorylated). Generally,
P-type ATPases consist of only a single subunit
encompassing the ATPase and ion translocation pathway,
however, in the case of the potassium (TIGR01497) and
sodium/potassium (TIGR01106) varieties, these functions
are split between two subunits. Additional small
regulatory or stabilizing subunits may also exist in
some forms. P-type ATPases are nearly ubiquitous in life
and are found in numerous copies in higher organisms (at
least 45 in Arabidopsis thaliana, for instance ).
Phylogenetic analyses have revealed that the P-type
ATPase subfamily is divided up into groups based on
substrate specificities and this is represented in the
various subfamily and equivalog models that have been
made: IA (K+) TIGR01497, IB (heavy metals) TIGR01525,
IIA1 (SERCA-type Ca++) TIGR01116, IIA2 (PMR1-type Ca++)
TIGR01522, IIB (PMCA-type Ca++) TIGR01517, IIC (Na+/K+,
H+/K+ antiporters) TIGR01106, IID (fungal-type Na+ and
K+) TIGR01523, IIIA (H+) TIGR01647, IIIB (Mg++)
TIGR01524, IV (phospholipid, flippase) TIGR01652 and V
(unknown specificity) TIGR01657. The crystal structure
of one calcium-pumping ATPase and an analysis of the
fold of the catalytic domain of the P-type ATPases have
been published. These reveal that the catalytic core of
these enzymes is a haloacid dehalogenase(HAD)-type
aspartate-nucleophile hydrolase. The location of the
ATP-binding loop in between the first and second HAD
conserved catalytic motifs defines these enzymes as
members of subfamily I of the HAD superfamily (see also
TIGR01493, TIGR01509, TIGR01549, TIGR01544 and
TIGR01545). Based on these classifications, the P-type
ATPase _superfamily_ corresponds to the IC subfamily of
the HAD superfamily.
Length = 543
Score = 27.3 bits (61), Expect = 6.7
Identities = 13/63 (20%), Positives = 19/63 (30%), Gaps = 10/63 (15%)
Query: 103 PWVDNFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIFLIWVCLMFVIIFLVVLLLLFYL 162
D + LF LL AL F+ W L L++L +
Sbjct: 152 SKRDRLENFIFILFLLLL--ALAVFLY--------LFIRGWDPNSIFKALLRALIVLVIV 201
Query: 163 IPI 165
+P
Sbjct: 202 VPP 204
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 27.1 bits (60), Expect = 6.9
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 87 MKLLTITFILLLFGLLPWVDNFAHLFGFLFGFLLSYA------LLPFVS--FGPYDRQKK 138
LL I I ++ G+ ++N +G LFG L +A L PF+ G DR
Sbjct: 997 TTLLIINIIGVIVGVSDAINNGYDSWGPLFGRLF-FALWVIVHLYPFLKGLLGKQDRMPT 1055
Query: 139 IFLIWVCLMFVIIFLV 154
I L+W L+ I+ L+
Sbjct: 1056 IILVWSILLASILTLL 1071
>gnl|CDD|234534 TIGR04286, MSEP-CTERM, MSEP-CTERM protein. Members of this protein
family average over 900 residues in length and appear to
have multiple membrane-spanning helices in the
N-terminal half. The extreme C-terminal region consists
of a motif with consensus sequence MSEP, then a
transmembrane alpha helix, then a short region with
several basic residues. This region, hereby dubbed
MSEP-CTERM, resembles other putative sorting signals
associated with the archaeosortase/exosortase protein
family (see TIGR04178). Genes for all members of this
family are found next to a gene for exosortase K.
Length = 920
Score = 27.4 bits (61), Expect = 6.9
Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 11/86 (12%)
Query: 89 LLTITFILLLFGLLPWVD--------NFAHLFGFLFGFLLSYALLPFVSFGPYDRQKKIF 140
LL+IT LL L + A LF G LL L + ++K
Sbjct: 10 LLSITLPQLLLLGLFYTSFDIIKGLLGPATLFTAFGGILLLLFLGIISYYVYKKIREKNI 69
Query: 141 LIWVCLMFVIIFLVVLLLLFYLIPIY 166
L ++ + + +++I +Y
Sbjct: 70 SKVYWL---LLLGLYICFSYFMIALY 92
>gnl|CDD|221309 pfam11912, DUF3430, Protein of unknown function (DUF3430). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 209 to 265 amino acids in
length.
Length = 204
Score = 26.7 bits (59), Expect = 6.9
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 147 MFVIIFLVVLLLLFYLIPIYDCELCSYFNCIPFTNEFC 184
M ++ L++L+LL I Y N IP+ + C
Sbjct: 1 MKLLFSLILLILLILNFVIS----QQYINFIPYQDGDC 34
>gnl|CDD|216181 pfam00902, TatC, Sec-independent protein translocase protein
(TatC). The bacterial Tat system has a remarkable
ability to transport folded proteins even enzyme
complexes across the cytoplasmic membrane. It is
structurally and mechanistically similar to the Delta
pH-driven thylakoidal protein import pathway. A
functional Tat system or Delta pH-dependent pathway
requires three integral membrane proteins: TatA/Tha4,
TatB/Hcf106 and TatC/cpTatC. The TatC protein is
essential for the function of both pathways. It might be
involved in twin-arginine signal peptide recognition,
protein translocation and proton translocation. Sequence
analysis predicts that TatC contains six transmembrane
helices (TMHs), and experimental data confirmed that N-
and C-termini of TatC or cpTatC are exposed to the
cytoplasmic or stromal face of the membrane. The
cytoplasmic N-terminus and the first cytoplasmic loop
region of the Escherichia coli TatC protein are
essential for protein export. At least two TatC
molecules co-exist within each Tat translocon.
Length = 212
Score = 26.7 bits (60), Expect = 6.9
Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 111 LFGFLFGF-LLSYALLPFVSFGPYDRQKKIFLIWVCLMFVIIFLVVLLLLFYLIPI 165
G + ++ Y + F++ G Y +++ L +V F++ L F ++PI
Sbjct: 68 FAGLILALPIILYQIWAFIAPGLYKNERRFLLPFVFASFLLFLLGAAFAYFVVLPI 123
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 27.3 bits (61), Expect = 7.2
Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 13/98 (13%)
Query: 77 PLLKHPEQALMKLLTITFILLLF------GLLPWVDN-FAHLFGFLFGFLLSYALLPFVS 129
+L HP L L + F++ L +D F L ++ L + + +
Sbjct: 266 RVLLHPVLGLPIFLLVMFLMFQLTFTIGGPLSDLIDGGFGALIEWVAQILPNLDIPSLLG 325
Query: 130 FGPYDRQKKIFLIWVCLMFVIIFLVVLLLLFYLIPIYD 167
D I + V++FL + +LF + + +
Sbjct: 326 SFLAD------GIIGGVGAVLVFLPQIFILFLFLSLLE 357
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 27.2 bits (61), Expect = 7.7
Identities = 23/140 (16%), Positives = 38/140 (27%), Gaps = 27/140 (19%)
Query: 12 RIAIIYFGSGIGGNLASAIFVPYRADVGPAGA---------HFGLLACLIV-------EV 55
+ + Y N+A A H + L++ V
Sbjct: 79 WVLLAYLVLAALLNVALLALGVNTAAETFGENSLSIIGFAVHVVAIVLLVLARREFPARV 138
Query: 56 GPAGAHFG----LLACLIVEVLNCWPLLK------HPEQALMKLLTITFILLLFGLLPWV 105
GA L+ L V +L W L++ P + L L L +
Sbjct: 139 RR-GALRKALAVLVGGLAVGILVGWGLVELFPGSLAPPERLGWALNRVVGFALADPDLFT 197
Query: 106 DNFAHLFGFLFGFLLSYALL 125
+ L G + AL+
Sbjct: 198 GHPPVWVNALLGLFGAAALI 217
>gnl|CDD|219117 pfam06638, Strabismus, Strabismus protein. This family consists of
several strabismus (STB) or Van Gogh-like (VANGL)
proteins 1 and 2. The exact function of this family is
unknown. It is thought, however that STB1 gene and STB2
may be potent tumour suppressor gene candidates.
Length = 507
Score = 27.0 bits (60), Expect = 8.5
Identities = 7/30 (23%), Positives = 14/30 (46%)
Query: 138 KIFLIWVCLMFVIIFLVVLLLLFYLIPIYD 167
+IF+ L+ ++ + LFY + I
Sbjct: 164 RIFVFRALLLVLVFLFLFSYWLFYGVRILG 193
>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 = 26.8 bits (60), Expect = 9.4
Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 7/83 (8%)
Query: 92 ITFILLLFGLLPWVDNFAHLF----GFL--FGFLLSYALLPFVSFGPYDRQKKIFLIWVC 145
+ L+L LP +D H F F F FL S+ +L + K++ + +
Sbjct: 311 LLLFLILSFYLPPLDLVWHGFQAPVWFPYRFSFLFSFLILLLAAEA-LLHLKQLKKLKIL 369
Query: 146 LMFVIIFLVVLLLLFYLIPIYDC 168
+ +++ L+ +L+ + +
Sbjct: 370 ISILLLVLLFILVFLLNLSKHYS 392
>gnl|CDD|191703 pfam07219, HemY_N, HemY protein N-terminus. This family represents
the N-terminus (approximately 150 residues) of bacterial
HemY porphyrin biosynthesis proteins. This is a membrane
protein involved in a late step of protoheme IX
synthesis.
Length = 108
Score = 25.7 bits (57), Expect = 9.4
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 140 FLIWVCLMFVIIFLVVLLLLFYLI 163
+ I L F +I L+++L + +L+
Sbjct: 10 YRIETSLTFAVILLLLVLAVLFLL 33
>gnl|CDD|205795 pfam13617, Lipoprotein_19, YnbE-like lipoprotein. This family
includes lipoproteins similar to E. coli YnbE. Protein
in this family are typically 60 amino acids in length
and contain an N-terminal lipid attachment site, which
has been included in the alignment to increase
sensitivity. The specific function of these proteins is
unknown.
Length = 59
Score = 24.5 bits (54), Expect = 9.4
Identities = 6/10 (60%), Positives = 8/10 (80%)
Query: 188 NINLNINIDH 197
INLN+ I+H
Sbjct: 30 TINLNVKIEH 39
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 0.153 0.507
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: 10,623,972
Number of extensions: 1080657
Number of successful extensions: 5208
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4738
Number of HSP's successfully gapped: 743
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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 (21.6 bits)
S2: 56 (25.3 bits)