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 3607632 Dshi_1041 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Dino:3607632 Length = 439 Score = 387 bits (993), Expect = e-112 Identities = 191/433 (44%), Positives = 290/433 (66%) Query: 1 MNWQLAAWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASF 60 M W AA L+LG L+ L +PVA++F N++GA++F+GG + QLV N AV+SF Sbjct: 3 MEWWEAALLMLGMVIGLMALCVPVAFAFLIANLIGAYIFMGGLIGVEQLVANTGEAVSSF 62 Query: 61 SLTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIAT 120 L +P+F+LMG L FH+G+A + I+ +D+ + R GRL+ I+V+ GT F+A+SGS +A Sbjct: 63 VLVTVPMFVLMGNLFFHSGIALKIIETLDRSMGRSTGRLSYISVLCGTIFAALSGSNMAN 122 Query: 121 TAMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGG 180 TAM+G L+LP M R Y+ + +GPII GG+ +LIPPS LAVLLGS+A ISI+ LL+ G Sbjct: 123 TAMMGGLLLPQMEERKYQRHMSIGPIIGSGGLALLIPPSTLAVLLGSIAQISIADLLLAG 182 Query: 181 VLPGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAV 240 VLPGL+LA+ +VA I + P++AP ++V WE+ R + Y+LP+SL+ +V + Sbjct: 183 VLPGLVLALLYVATIWLQLRRNPQAAPAYDVVTAPFWEKIRLICTYILPMSLVVFCVVGL 242 Query: 241 ISGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQ 300 I G+ TP+EAAA G + L ++++Y W + ++L+GT+ +S M+ FII+A+ TFSQ Sbjct: 243 ILLGITTPSEAAAFGVLSVLVLSILYGRFSWDMVAKSLEGTLRVSVMVFFIIIASKTFSQ 302 Query: 301 VLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSL 360 VL+FSGAT+G++ S P ++ IM +L+ LG+FVD +SMMLLT+P + PI ++ Sbjct: 303 VLAFSGATSGMIAWATSYEFAPITMLLIMFVVLLILGMFVDAISMMLLTIPIFFPIAAAM 362 Query: 361 GIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLI 420 G D IWFG++ L+ +++ PP G+LL+ M+GVAP T + +A PY+ +L+ Sbjct: 363 GFDPIWFGLVMLLAIEMSGTTPPFGLLLFVMQGVAPPGTTYWTIVRAAAPYLICDLILLV 422 Query: 421 LIFFWPGIATWLP 433 + P +A WLP Sbjct: 423 GLIAVPALALWLP 435 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: 518 Number of extensions: 26 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: 439 Length adjustment: 32 Effective length of query: 407 Effective length of database: 407 Effective search space: 165649 Effective search space used: 165649 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