Align 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) (characterized)
to candidate GFF3083 HP15_3026 TRAP dicarboxylate transporter, DctM subunit
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Marino:GFF3083 Length = 499 Score = 246 bits (627), Expect = 2e-69 Identities = 143/448 (31%), Positives = 249/448 (55%), Gaps = 22/448 (4%) Query: 8 WLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAV-ASFSLTPIP 66 +L+ G V L +GLP+A+ + V+ +++L GD+ + +V + + A+ + IP Sbjct: 57 YLMFGSLAVALMMGLPLAFVTGGLGVM--FIYLVGDAMMLNIVPGRIFPLMANPDIAAIP 114 Query: 67 LFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGS 126 LFI M +L GL + + K + + G LA +VA T +A+ G A +G Sbjct: 115 LFIFMASMLERAGLIEEMFSVVYKWMGGISGGLAAATIVASTILAAMVGVIGAAVVTMGI 174 Query: 127 LMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLL 186 + LP ML R Y+ K+ +G I+A G + +LIPPS LA+L +A S+ +L +G +LPGL+ Sbjct: 175 IALPAMLKRHYDHKIAIGSIMAGGTLGILIPPSILAILYAVVAQQSVGELYLGSLLPGLM 234 Query: 187 LAISFVAYIVASAKLRPESAPR---EELVVLRGWERWRELVVYVLPLSLIFVAIVAVISG 243 L+ ++ Y++ + L P+ P E+ + L+ E+ + L + PL+L+ + ++ ++ G Sbjct: 235 LSGLYLTYVLVRSWLNPKLGPPIPVEDRISLK--EKLKLLGNLIAPLALVGL-VLGLLFG 291 Query: 244 GVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLS 303 G+ATP EAA IG + + +M++ L +A T S M+L+I+ A+ F Sbjct: 292 GIATPVEAAGIGSFGAIIVAMMHKKFSIAGLREASVTTAKASAMVLWIMFGASVFVGFYI 351 Query: 304 FSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSL--- 360 G + D + +G+ G++ +++ +L+ LG+F+D V ++LL +P ++PIVK+L Sbjct: 352 LQGGQQFVTDAILGTGMSAYGILFLLMVLLVVLGMFLDWVGILLLAVPIFIPIVKALEFP 411 Query: 361 ---------GIDQI-WFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMP 410 G D + WFGV+YL+ MQ+ L PP G L+ ++GV P I+MG +F S++ Sbjct: 412 GLFGFPPVAGDDVVLWFGVLYLVNMQMSFLSPPFGYALFYIRGVCPPEISMGTIFKSSLV 471 Query: 411 YVGLSFTMLILIFFWPGIATWLPDVFVG 438 ++ + L + PGI TWLP + G Sbjct: 472 FLAIQAFGLFMCVLIPGIVTWLPGLVYG 499 Lambda K H 0.329 0.143 0.433 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 623 Number of extensions: 46 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 439 Length of database: 499 Length adjustment: 33 Effective length of query: 406 Effective length of database: 466 Effective search space: 189196 Effective search space used: 189196 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory