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 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Miya:8501407 Length = 427 Score = 206 bits (525), Expect = 9e-58 Identities = 139/431 (32%), Positives = 226/431 (52%), Gaps = 17/431 (3%) Query: 9 LLLGGTTVLLFLGLPVAYS-----FFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLT 63 +L GG +L L PVA + F A+ G + +G + L V+ SF L Sbjct: 5 ILFGGMVLLFALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLA--VQRLYAGADSFPLL 62 Query: 64 PIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAM 123 +PLF+L GEL+ G+++R + D ++ LPG LA ++VV+ FF+ +SGS A TA Sbjct: 63 AVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADTAA 122 Query: 124 LGSLMLPMMLARGYEPKLGMGPIIAIGG-VDMLIPPSALAVLLGSLAGISISKLLIGGVL 182 +GS+++P M+ RGY L G + A GG + ++IPPS ++ G+L G SI +L GGVL Sbjct: 123 VGSILIPAMIRRGYPAPLA-GAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGVL 181 Query: 183 PGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVIS 242 PGLL+ S VA V A+ R P W R + L I I+ I Sbjct: 182 PGLLMGASLVALCVVEAR-RTGRVPERRFDARALWPAIRS-GAWALGAPAI---ILGTII 236 Query: 243 GGVATPTEAAAIGCAATLAITL-MYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQV 301 GGVAT TE+AA+ A L + L +R LRW+ L + S +++ II AA+ F V Sbjct: 237 GGVATATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVMLIIAAASLFGWV 296 Query: 302 LSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLG 361 ++ I + S ++ ++ +L+ +G F++ + +LL +P +P++ +LG Sbjct: 297 MALERLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLFVPVLVPLLPALG 356 Query: 362 IDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLIL 421 ID + GV+ ++ + +G+L PP G+ L +A I + + + +P + + L+L Sbjct: 357 IDLVHLGVIVVVNLAIGMLTPPLGVCLVVSCSIA--RIPLSAISRAIVPMLVVLIVDLLL 414 Query: 422 IFFWPGIATWL 432 + F+P + WL Sbjct: 415 VTFFPPLVLWL 425 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: 486 Number of extensions: 23 Number of successful extensions: 4 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: 427 Length adjustment: 32 Effective length of query: 407 Effective length of database: 395 Effective search space: 160765 Effective search space used: 160765 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