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Searching for up to 100 curated homologs for WP_011384964.1 AMB_RS13000 C4-dicarboxylate ABC transporter (486 a.a.)

Found high-coverage hits (≥70%) to 24 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 2.A.56.3.1 / P74224 GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (see paper)
    53% identity, 91% coverage of query (442 bits)

TC 2.A.56.3.3 / Q8YSQ7 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids from Nostoc sp. (strain PCC 7120 / UTEX 2576) (see paper)
    56% identity, 91% coverage of query (421 bits)

TC 2.A.56.3.2 / Q9RBQ9 FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (see paper)
    32% identity, 79% coverage of query (168 bits)

Build an alignment

Build an alignment for WP_011384964.1 and 3 homologs with ≥ 30% identity

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Additional hits (identity < 30%)

TC 2.A.56.1.10 / Q6N8W8 TrapT family, dctM subunit, C4-dicarboxylate transport, component of Transporter for lignin derived aromatic compounds, TarPQM from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
    27% identity, 91% coverage of query (166 bits)

DCTM_PSEAE / Q9HU16 C4-dicarboxylate TRAP transporter large permease protein DctM from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
    29% identity, 79% coverage of query (142 bits)

Sama_2211 alpha-ketoglutarate TRAP transporter, large permease component from Shewanella amazonensis SB2B
    30% identity, 79% coverage of query (139 bits)

Shew_1444 dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component from Shewanella loihica PV-4
    29% identity, 79% coverage of query (137 bits)

DCTM_RHOCA / O07838 C4-dicarboxylate TRAP transporter large permease protein DctM from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (see paper)
TC 2.A.56.1.1 / O07838 DctM, component of Tripartite dicarboxylate:H+ symporter (substrates include: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate and mesaconate) from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (see 2 papers)
    27% identity, 80% coverage of query (137 bits)

TC 2.A.56.1.7 / Q930W3 Putative uncharacterized protein, component of The malonate uptake transporter, MatPQM. Regulated by the GtrA transcriptional activator (Chen et al. 2010). MatM is fused in a single protein C-terminal to MatA (malonyl-CoA decarboxylase) from Rhizobium meliloti (strain 1021)
    27% identity, 83% coverage of query (134 bits)

SIAT2_HAEIF / Q4TVS0 Sialic acid TRAP transporter permease protein SiaT; N-acetylneuraminic acid permease; N-acetylneuraminic acid transporter; Neu5Ac permease from Haemophilus influenzae (see paper)
    24% identity, 89% coverage of query (126 bits)

SIAT1_HAEIN / P44543 Sialic acid TRAP transporter permease protein SiaT; N-acetylneuraminic acid permease; N-acetylneuraminic acid transporter; Neu5Ac permease from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see paper)
TC 2.A.56.1.3 / P44543 SiaT aka Sialic acid TRAP transporter permease protein, component of Na+-dependent (smf-driven) sialic acid (N-acetyl neuraminic acid) transporter, SiaTP (Allen et al., 2005; Severi et al., 2005; Johnston et al., 2008). SiaT is also called SiaQM from Haemophilus influenzae (see 2 papers)
    24% identity, 89% coverage of query (125 bits)

DCTMQ_OLEA2 / Q312S1 Isethionate TRAP transporter permease protein DctMQ; TRAP transporter, fused DctMQ subunit from Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20) (Desulfovibrio alaskensis) (see paper)
    27% identity, 83% coverage of query (124 bits)

Psest_2124 D-gluconate TRAP transporter, large permease component from Pseudomonas stutzeri RCH2
    26% identity, 90% coverage of query (119 bits)

PGA1_c20660 TRAP transporter for fumarate, succinate, L-malate, and 2-oxogulatarate, large permease component from Phaeobacter inhibens BS107
    29% identity, 81% coverage of query (117 bits)

Ac3H11_3227 gluconate TRAP transporter, large permease component from Acidovorax sp. GW101-3H11
    25% identity, 82% coverage of query (113 bits)

AZOBR_RS15920 Large component of TRAP-type D-gluconate transporter from Azospirillum brasilense Sp245
    25% identity, 89% coverage of query (106 bits)

8b01B / Q6LPW1 Cryo-em structure of the tripartite atp-independent periplasmic (trap) transporter siaqm from photobacterium profundum in a nanodisc (see paper)
    26% identity, 88% coverage of query (100 bits)

PP_1167 D-glucuronate / D-galacturonate TRAP transporter, large permease component from Pseudomonas putida KT2440
    27% identity, 80% coverage of query (99.4 bits)

TEAC_HALED / E1VBK3 Ectoine TRAP transporter large permease protein TeaC from Halomonas elongata (strain ATCC 33173 / DSM 2581 / NBRC 15536 / NCIMB 2198 / 1H9) (see paper)
    26% identity, 85% coverage of query (99.0 bits)

YiaN / b3578 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit from Escherichia coli K-12 substr. MG1655 (see 2 papers)
yiaN / P37675 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit from Escherichia coli (strain K12) (see paper)
YIAN_ECOLI / P37675 2,3-diketo-L-gulonate TRAP transporter large permease protein YiaN from Escherichia coli (strain K12) (see paper)
TC 2.A.56.1.2 / P37675 YiaN, component of The 2,3-diketo-L-gulonate (2,3-DKG) transporter, YiaMNO [2,3-KDG is a breakdown product of L-ascorbate] from Escherichia coli (see 7 papers)
    26% identity, 80% coverage of query (90.5 bits)

UEHC_RUEPO / Q5LUA9 Ectoine/5-hydroxyectoine TRAP transporter large permease protein UehC; Uptake of ectoine and hydroxyectoine protein C from Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter pomeroyi) (see paper)
    25% identity, 80% coverage of query (89.4 bits)

SIAM_VIBCH / Q9KR66 Sialic acid TRAP transporter large permease protein SiaM from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see 2 papers)
TC 2.A.56.1.6 / B9TSM9 TRAP dicarboxylate transporter DctM subunit, component of The Na+-dependent sialic acid uptake porter, SiaPQM. SiaQ and SiaM form a 1:1 stoichiometric complex from Vibrio cholerae (see paper)
    27% identity, 88% coverage of query (88.6 bits)

TC 2.A.56.1.9 / R4JQ65 TRAP transporter DctM subunit, component of The possible disulfide 3,3'-dithiodipropionic acid (DTDP) tripartite transporter, DctMPQ from Advenella mimigardefordensis DPN7
    27% identity, 90% coverage of query (74.3 bits)

TC 2.A.56.2.1 / O83924 Dicarboxylate transporter (DctM), component of TRAP transporter for a hydrophobic substrate (3-d structure known; tp0958 has 18-20 TMSs) (Deka et al., 2012). The substrate could be a lipoprotein, tp0956 (O83922) which is encoded in the same operon with tp0957 and tp058. This protein differs from all other members of the TRAP-T family in having 19 predicted TMSs with extra TMSs at its N-terminus from Treponema pallidum (strain Nichols) (see paper)
    26% identity, 71% coverage of query (70.1 bits)

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by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory