Sites on a Tree

 

Searching for up to 100 curated homologs for RR42_RS04820 FitnessBrowser__Cup4G11:RR42_RS04820 (215 a.a.)

Found high-coverage hits (≥70%) to 42 curated proteins.

You can add additional sequences or change the %identity threshold for inclusion. Once you have selected sequences, you can build an alignment and a tree.

Hits with ≥ 30% identity

TC 3.A.1.12.10 / Q87WH4 OpuC aka PSPTO4576, component of The OpuC transporter selective for glycine betaine > choline, acetylcholine, carnitine and proline betaine (contains tandem cystathionine-β-synthase (CBS) domains in the ABC component of OpuC that are required for osmoregulatory function (Chen and Beattie, 2007)) from Pseudomonas syringae pv. tomato (see paper)
    67% identity, 100% coverage of query (271 bits)

OSMW_SALTY / Q8ZPK3 Osmoprotectant import permease protein OsmW from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
TC 3.A.1.12.14 / Q8ZPK3 Putative binding-protein-dependent transport system, component of OsmU (OsmVWXY) transporter for glycine betaine and choline-O-sulfate uptake. Induced by osmotic stress (0.3M NaCl) (Frossard et al., 2012). Also called OpuCA/CB1/CB2/CC from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    61% identity, 100% coverage of query (228 bits)

U5LHK3 ABC-type quaternary amine transporter (subunit 2/3) (EC 7.6.2.9) from Bacillus infantis (see paper)
    43% identity, 96% coverage of query (166 bits)

OPUCB_BACSU / O34878 Glycine betaine/carnitine/choline transport system permease protein OpuCB from Bacillus subtilis (strain 168) (see 3 papers)
TC 3.A.1.12.4 / O34878 OPCB aka OpuCB, component of Uptake system for choline, L-carnitine, D-carnitine, glycine betaine, proline betaine, crotonobetaine, γ-butyrobetaine, dimethylsulfonioacetate, dimethylsulfoniopropionate, ectoine and choline-O-sulfate from Bacillus subtilis (see 2 papers)
    41% identity, 100% coverage of query (162 bits)

OPUBB_BACSU / Q45461 Choline transport system permease protein OpuBB from Bacillus subtilis (strain 168) (see 2 papers)
TC 3.A.1.12.3 / Q45461 OPBB aka OpuBB aka PROW, component of Choline porter from Bacillus subtilis (see 3 papers)
    40% identity, 100% coverage of query (147 bits)

OPUCD_LISM4 / G2JZ41 Carnitine transport permease protein OpuCD from Listeria monocytogenes serotype 1/2a (strain 10403S) (see 4 papers)
OPUCD_LISMN / Q9KHT6 Carnitine transport permease protein OpuCD from Listeria monocytogenes (see paper)
    37% identity, 98% coverage of query (145 bits)

OPUBD_BACSU / P39775 Choline transport system permease protein OpuBD from Bacillus subtilis (strain 168) (see 2 papers)
TC 3.A.1.12.3 / P39775 OPBD aka OpuBD aka PROZ, component of Choline porter from Bacillus subtilis (see 4 papers)
    36% identity, 98% coverage of query (140 bits)

OPUCB_LISM4 / G2JZ43 Carnitine transport permease protein OpuCB from Listeria monocytogenes serotype 1/2a (strain 10403S) (see 4 papers)
OPUCB_LISMN / Q9KHT8 Carnitine transport permease protein OpuCB from Listeria monocytogenes (see paper)
    39% identity, 100% coverage of query (140 bits)

EGTUB_STAA3 / A0A0H2XK79 Probable ergothioneine transporter EgtUBC from Staphylococcus aureus (strain USA300) (see paper)
    43% identity, 90% coverage of query (138 bits)

OPUCD_BACSU / O34742 Glycine betaine/carnitine/choline transport system permease protein OpuCD from Bacillus subtilis (strain 168) (see 3 papers)
TC 3.A.1.12.4 / O34742 OPCD aka OpuCD, component of Uptake system for choline, L-carnitine, D-carnitine, glycine betaine, proline betaine, crotonobetaine, γ-butyrobetaine, dimethylsulfonioacetate, dimethylsulfoniopropionate, ectoine and choline-O-sulfate from Bacillus subtilis (see 2 papers)
    35% identity, 96% coverage of query (137 bits)

EGTUB_STRP2 / A0A0H2ZQB9 Ergothioneine transporter EgtUBC from Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (see paper)
    45% identity, 74% coverage of query (132 bits)

OSMY_SALTY / Q8ZPK1 Osmoprotectant import permease protein OsmY from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
TC 3.A.1.12.14 / Q8ZPK1 ABC-type transport system protein, component of OsmU (OsmVWXY) transporter for glycine betaine and choline-O-sulfate uptake. Induced by osmotic stress (0.3M NaCl) (Frossard et al., 2012). Also called OpuCA/CB1/CB2/CC from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    40% identity, 93% coverage of query (131 bits)

EGTUB_LISMO / Q8Y775 Probable ergothioneine transporter EgtUBC from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (see 2 papers)
    45% identity, 87% coverage of query (127 bits)

TC 3.A.1.12.8 / Q93A34 BilEB aka OpuBB protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) from Listeria monocytogenes (see paper)
    45% identity, 87% coverage of query (127 bits)

U5LFB4 ABC-type quaternary amine transporter (subunit 3/3) (EC 7.6.2.9) from Bacillus infantis (see paper)
    39% identity, 87% coverage of query (122 bits)

YehW / b2128 glycine betaine ABC transporter membrane subunit YehW from Escherichia coli K-12 substr. MG1655 (see 3 papers)
yehW / P33359 glycine betaine ABC transporter membrane subunit YehW from Escherichia coli (strain K12) (see 2 papers)
YEHW_ECOLI / P33359 Glycine betaine uptake system permease protein YehW from Escherichia coli (strain K12) (see 3 papers)
    38% identity, 95% coverage of query (119 bits)

TC 3.A.1.12.11 / Q8Q043 Glycine betaine transport system, permease protein, component of The glycine betaine uptake porter, GbpABCD from Methanosarcina mazei (see paper)
    34% identity, 94% coverage of query (118 bits)

YehY / b2130 glycine betaine ABC transporter membrane subunit YehY from Escherichia coli K-12 substr. MG1655 (see 4 papers)
yehY / P33361 glycine betaine ABC transporter membrane subunit YehY from Escherichia coli (strain K12) (see 2 papers)
YEHY_ECOLI / P33361 Glycine betaine uptake system permease protein YehY from Escherichia coli (strain K12) (see 3 papers)
    39% identity, 90% coverage of query (117 bits)

EGTUB_ENTFA / Q837Z8 Probable ergothioneine transporter EgtUBC from Enterococcus faecalis (strain ATCC 700802 / V583) (see paper)
    38% identity, 87% coverage of query (116 bits)

AO356_09615 ABC transporter for L-Histidine, permease component from Pseudomonas fluorescens FW300-N2C3
    36% identity, 86% coverage of query (99.0 bits)

TC 3.A.1.12.11 / Q8Q042 Glycine betaine transport system, permease protein, component of The glycine betaine uptake porter, GbpABCD from Methanosarcina mazei (see paper)
    34% identity, 98% coverage of query (92.4 bits)

TC 3.A.1.12.9 / Q8U4S4 OtaB, component of The salt-induced glycine betaine OtaABC transporter from Methanosarcina mazei (see paper)
    34% identity, 93% coverage of query (91.7 bits)

TC 3.A.1.12.6 / Q9KKE2 HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine from Rhizobium meliloti (Sinorhizobium meliloti) (see paper)
    34% identity, 87% coverage of query (91.7 bits)

A0A077T980 ABC-type quaternary amine transporter (subunit 3/3) (EC 7.6.2.9) from Vibrio anguillarum serotype O1 (see paper)
    34% identity, 85% coverage of query (91.3 bits)

TC 3.A.1.12.7 / Q92N36 ChoW, component of High affinity (3 μM) choline-specific uptake system from Rhizobium meliloti (Sinorhizobium meliloti) (see 2 papers)
    32% identity, 85% coverage of query (89.0 bits)

OPUAB_BACSU / P46921 Glycine betaine transport system permease protein OpuAB from Bacillus subtilis (strain 168) (see 2 papers)
P46921 ABC-type quaternary amine transporter (EC 7.6.2.9) from Bacillus subtilis (see 2 papers)
TC 3.A.1.12.2 / P46921 OPAB aka OpuAB, component of Glycine betaine OpuAA/AB/AC porter (also transports dimethylsulfonioacetate and dimethylsulfoniopropionate) from Bacillus subtilis (see 3 papers)
    34% identity, 93% coverage of query (87.0 bits)

OUSW_DICD3 / E0SCY2 Glycine betaine/choline transport system permease protein OusW from Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937)) (see paper)
    33% identity, 90% coverage of query (86.7 bits)

OsrA / b2678 glycine betaine ABC transporter membrane subunit ProW (EC 7.6.2.9) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
proW / P14176 glycine betaine ABC transporter membrane subunit ProW (EC 7.6.2.9) from Escherichia coli (strain K12) (see paper)
PROW_ECOLI / P14176 Glycine betaine/proline betaine transport system permease protein ProW from Escherichia coli (strain K12) (see 4 papers)
TC 3.A.1.12.1 / P14176 ProW aka B2678, component of Glycine betaine/proline porter, ProU or ProVWX (also transports proline betaine, carnitine, dimethyl proline, homobetaine, γ-butyrobetaine and choline with low affinity) from Escherichia coli (see 5 papers)
    34% identity, 86% coverage of query (85.9 bits)

TC 3.A.1.12.13 / Q7CXG1 ABC transporter, membrane spanning protein (Proline/glycine betaine), component of High affinity (2mμM) choline uptake porter. The choline binding receptor exhibits a venus fly trap mechanism of substrate binding. (ChoX binds acetyl choline and betaine with low affinity (80μM and 470μM, respectively) (Aktas et al., 2011) (most similar to 3.A.1.12.7) from Agrobacterium tumefaciens (strain C58 / ATCC 33970) (see 2 papers)
    30% identity, 86% coverage of query (83.6 bits)

TC 3.A.1.12.12 / Q9HTI7 Probable permease of ABC transporter, component of The CbcWV/CbcX (choline)/CaiX (carnitine)/BetX (betaine) transporter with 3 binding receptors for distinct quaternary ammonium compounds. Only the ligand-bound receptor binds to the transporter with high affinity from Pseudomonas aeruginosa (see paper)
    32% identity, 77% coverage of query (82.8 bits)

GBUB_LISM4 / Q9RR45 Glycine betaine/carnitine transport permease protein GbuB from Listeria monocytogenes serotype 1/2a (strain 10403S) (see 4 papers)
    32% identity, 75% coverage of query (81.3 bits)

TC 3.A.1.12.5 / Q9RQ05 BusAB aka OPUABC, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport from Lactococcus lactis (see 2 papers)
    32% identity, 78% coverage of query (77.0 bits)

Q7DAU8 ABC-type quaternary amine transporter (EC 7.6.2.9) from Lactococcus lactis (see paper)
    32% identity, 78% coverage of query (76.3 bits)

Build an alignment

Build an alignment for RR42_RS04820 and 33 homologs with ≥ 30% identity

Select sequences

Add sequences from UniProt, PDB, RefSeq, or MicrobesOnline (separate identifiers with commas or spaces):

Or download the sequences

Change minimum %identity:

Additional hits (identity < 30%)

TMOV_RUEPO / Q5LT64 Trimethylamine N-oxide transport system permease protein TmoV; TMAO transport system permease protein TmoV from Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter pomeroyi) (see paper)
    29% identity, 83% coverage of query (73.9 bits)

AO356_13810 ABC transporter for Carnitine, permease component from Pseudomonas fluorescens FW300-N2C3
    28% identity, 87% coverage of query (72.4 bits)

Pf6N2E2_4682 ABC transporter for Carnitine, permease component from Pseudomonas fluorescens FW300-N2E2
    28% identity, 87% coverage of query (72.4 bits)

AO353_07785 ABC transporter for Carnitine, permease component from Pseudomonas fluorescens FW300-N2E3
    27% identity, 87% coverage of query (70.9 bits)

EGTU_HELPG / B5Z7I3 Ergothioneine transport permease/ergothioneine binding protein EgtU from Helicobacter pylori (strain G27) (see paper)
    32% identity, 95% coverage of query (64.7 bits)

TMOV_PELUB / Q4FL38 Trimethylamine N-oxide transport system permease protein TmoV; TMAO transport system permease protein TmoV from Pelagibacter ubique (strain HTCC1062) (see paper)
    28% identity, 71% coverage of query (61.2 bits)

RIBX_CHLAA / A9WGD1 Riboflavin transport system permease protein RibX from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (see paper)
TC 3.A.1.17.14 / A9WGD1 Riboflavin transport system permease protein RibX, component of Riboflavin uptake porter, RibXY (RibX, 168 aas and 6 TMSs; RibY, 351 aas) from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
    34% identity, 71% coverage of query (58.5 bits)

CMPB_SYNE7 / Q55106 Bicarbonate transport system permease protein CmpB from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (Anacystis nidulans R2) (see paper)
TC 3.A.1.16.3 / Q55106 CmpB, component of Bicarbonate porter (activated by low [CO2] mediated by CmpR; (Nishimura et al., 2008)) (see 2 papers)
    24% identity, 92% coverage of query (53.1 bits)

TC 3.A.1.17.2 / O85765 SsuC, component of Aromatic sulfonate porter from Pseudomonas putida (see paper)
    31% identity, 87% coverage of query (53.1 bits)

Or start over

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory