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 3609772 Dshi_3155 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Dino:3609772 Length = 429 Score = 250 bits (639), Expect = 5e-71 Identities = 143/434 (32%), Positives = 239/434 (55%), Gaps = 11/434 (2%) Query: 8 WLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIPL 67 W + G LL L +PV F + G F + L + +L IP Sbjct: 3 WAISAGLLGLLALSIPVGIVLFLLGF-GVDAFFSPFPLIRGLGNLVWSTSNNATLIAIPF 61 Query: 68 FILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSL 127 F+L+GE+L +G+A R +D+ + LPG L V T FSA SGS++AT A + ++ Sbjct: 62 FVLLGEILVRSGIATRTYSALDRWVSWLPGGLVHANVATATMFSATSGSSVATAATVATV 121 Query: 128 MLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLL 187 +P GY+P+L G I A G + ++IPPS ++ G L SI +L + G++PG+ L Sbjct: 122 AMPQAEKLGYDPRLFSGAIAAGGTLGIMIPPSINLIVYGFLTQTSIPQLFLAGLVPGIAL 181 Query: 188 AISFVAYIVASAKLRPESAPREELVVLRGWERWRELV---VYVLPLSLIFVAIVAVISGG 244 A+ F+A V +RPE L LR + E++ + ++P+ L+F I+ I G Sbjct: 182 ALGFMAITVVICLIRPE------LGGLRRTFPFPEMLRALLQLIPIILLFTVIIGTIYKG 235 Query: 245 VATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSF 304 ATPTEAAA+G A + I ++ + + ++ GT+ I+ MI+ +++AA+ + L+ Sbjct: 236 WATPTEAAAVGVAGAVVIAALFGGVSVKMFADSILGTIKITSMIMLVVIAASFLNFTLAS 295 Query: 305 SGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQ 364 +G + L+ GL P G++ +++ I I LG F++ +S+M++T+P +P+V + G D Sbjct: 296 AGLGRELQSLLDGLGLTPTGLILVVVLIYIVLGFFIETLSLMVVTIPIIVPLVVAQGFDP 355 Query: 365 IWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFF 424 IWFG++ ++ +++ L+ PP G+ LY ++G A K M +V A+PYV M+ L+ Sbjct: 356 IWFGILMIVLIEMALITPPVGLNLYVVQG-ARKSGKMSEVMVGAIPYVIAMLIMVGLLIL 414 Query: 425 WPGIATWLPDVFVG 438 +P IA +LP V G Sbjct: 415 FPSIALYLPSVLSG 428 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: 480 Number of extensions: 24 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: 429 Length adjustment: 32 Effective length of query: 407 Effective length of database: 397 Effective search space: 161579 Effective search space used: 161579 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