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 3609776 Dshi_3159 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Dino:3609776 Length = 431 Score = 244 bits (622), Expect = 5e-69 Identities = 140/431 (32%), Positives = 234/431 (54%), Gaps = 32/431 (7%) Query: 28 FFAINVVGAWLFLGGDSALG-----------QLVRNGLVAVA---------SFSLTPIPL 67 F+++ + G F G ALG V NG VA SF+L+ IPL Sbjct: 4 FWSVFLGGLLAFAGSGLALGAALGLTGLLILHFVANGATFVAVDAVWNVLNSFTLSAIPL 63 Query: 68 FILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSL 127 FI++GE++ +G++ R + V R+PG L V T F A+SGS+++T A +GS+ Sbjct: 64 FIILGEIMLRSGVSARIYSALSPVFMRVPGGLLHTNVAVCTLFGAVSGSSLSTAAAVGSV 123 Query: 128 MLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLL 187 P M RGY+ + +G + G + +LIPPS ++ G+L SI +L + G++PGLL Sbjct: 124 AYPEMTRRGYDRRTVVGSLAGGGTLGLLIPPSLSLLIFGALTETSIGQLFLAGLVPGLLF 183 Query: 188 AISFVAYIVASAKLRPESAPREEL-----VVLRGWERWRELVVYVLPLSLIFVAIVAVIS 242 A F+ YI ++ P AP E +LRG V+ + P L+ ++I+ I+ Sbjct: 184 AAMFMVYIYLRCRITPSLAPAEAARPPGREILRG-------VLGLWPFLLLILSIMGSIT 236 Query: 243 GGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVL 302 G ATPTEAA IG AT+ I ++ L ++L +A+ + + G I F+++ AT +Q + Sbjct: 237 LGFATPTEAAGIGVIATIIIGRLWGTLTLRALAEAVYAAIRLYGAIAFVVIGATILAQAV 296 Query: 303 SFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGI 362 S G I++ V++S L P V+A+++ + + LG F D +S+M++TLP P++ LG Sbjct: 297 SLLGVPQAILETVRASDLGPLAVLAVVVLVYLVLGCFFDGLSLMIMTLPIVFPLLTGLGY 356 Query: 363 DQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILI 422 D IW GV+ I +++G + PP G+ L + V +++G+ + +PY + + ++ Sbjct: 357 DAIWLGVIITILIEIGQVTPPVGLNLSVLVSVTKNAVSLGEAAKATVPYWLILLAGVAIL 416 Query: 423 FFWPGIATWLP 433 P +A +LP Sbjct: 417 TALPALALFLP 427 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: 495 Number of extensions: 33 Number of successful extensions: 2 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: 431 Length adjustment: 32 Effective length of query: 407 Effective length of database: 399 Effective search space: 162393 Effective search space used: 162393 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