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 WP_086509202.1 BZY95_RS06745 C4-dicarboxylate ABC transporter permease
Query= TCDB::Q9RBQ9 (439 letters) >NCBI__GCF_002151265.1:WP_086509202.1 Length = 438 Score = 344 bits (882), Expect = 4e-99 Identities = 180/430 (41%), Positives = 274/430 (63%) Query: 1 MNWQLAAWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASF 60 M+W L L+LG L+ LGLPVA+SF A+N+VGA+LFLGG S + QLV N A+ SF Sbjct: 1 MDWWLTLSLILGALLTLMMLGLPVAFSFLAVNLVGAYLFLGGTSGIEQLVINTTDALTSF 60 Query: 61 SLTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIAT 120 +L PI +F++MGE++F +G+A +D +DK RL GRLA +AV G FS ++G+++ + Sbjct: 61 TLVPIAMFMIMGEVMFRSGIANDLMDTLDKWFGRLRGRLAYMAVGGGVLFSTLTGNSMGS 120 Query: 121 TAMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGG 180 A+LGS + P M RGY+ + +GPII G+ ++IPPSALAV+LG +A ISI +LLI Sbjct: 121 IALLGSSLTPEMEKRGYKKPMSLGPIIGSAGLAIMIPPSALAVVLGVVAEISIGRLLIAI 180 Query: 181 VLPGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAV 240 + PGLL+A+ + YI A L+P+ AP ++ + + +LP+ I A+V V Sbjct: 181 IAPGLLMAVLYAVYIWARCTLQPDVAPTFDVAPTPLKAKVTAGIRNILPIGFIVFAVVGV 240 Query: 241 ISGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQ 300 I G+ATPTEAAA G AT+ + L R L + +++ + IS M+L I+ A FSQ Sbjct: 241 IFLGLATPTEAAASGAVATILLALFKRRLTVDNFTRSMFESANISVMVLLIVAGAVAFSQ 300 Query: 301 VLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSL 360 +L+F+G T G++D V + + +V M+ ++ LG+F+ + +ML+TLP ++P+V L Sbjct: 301 LLAFTGTTFGLMDAVMNLPVNDHMIVLAMVFTVVLLGMFMGPLPIMLITLPIFVPVVDQL 360 Query: 361 GIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLI 420 G D IWF V++L+ ++ G PP G L+ MK VAP TMG ++ +A+P++ F + Sbjct: 361 GFDTIWFAVLFLLAIETGSTSPPLGAALFVMKAVAPVGTTMGSIYKAAIPFLICDFLAIG 420 Query: 421 LIFFWPGIAT 430 +IF +P I T Sbjct: 421 IIFAFPQIVT 430 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: 510 Number of extensions: 32 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: 438 Length adjustment: 32 Effective length of query: 407 Effective length of database: 406 Effective search space: 165242 Effective search space used: 165242 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 24 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