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_086508651.1 BZY95_RS03775 C4-dicarboxylate ABC transporter
Query= TCDB::Q9RBQ9 (439 letters) >NCBI__GCF_002151265.1:WP_086508651.1 Length = 456 Score = 251 bits (640), Expect = 4e-71 Identities = 146/446 (32%), Positives = 235/446 (52%), Gaps = 16/446 (3%) Query: 10 LLGGTTVLLFLGLPVAYSFFAINVV------------GAWLFLGGDSALGQLVRNGLVAV 57 + G LL +G PVA++ I + GA L+ +G L R + Sbjct: 11 MFAGFMGLLLIGFPVAWALAGIGFLFAVIGHVLVEHMGADLWFSWGGTIGVLDRRLYGII 70 Query: 58 ASFSLTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGST 117 A+ + +PLFI MG +L +G+A+R ++ + +V+ L G AV V+ G +A +G Sbjct: 71 ANELMVALPLFIFMGIMLDRSGIAERLMNSLVRVLGGLRGGYAVTVVIVGVLLAASTGIV 130 Query: 118 IATTAMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGIS---IS 174 A+ +LG L + ML Y L +G ++G + +L+PPS + VL+ G S + Sbjct: 131 GASVVLLGMLSIGPMLQAKYNKSLAVGTACSVGTLGILVPPSIMLVLMADRLGTSEASVG 190 Query: 175 KLLIGGVLPGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIF 234 +L +G ++PG++L + ++AYIV +A ++ + AP E E+++ VLP + Sbjct: 191 RLFMGALIPGIMLGVMYIAYIVIAAYIKKDLAPAPENRQPLNARALLEVLIAVLPPLALI 250 Query: 235 VAIVAVISGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVA 294 VA++ I G AT TEA+A+G + + L R L + + +AL T + I I V Sbjct: 251 VAVLGSIFTGFATTTEASAVGALGAVLLALFNRRLNFDVVSKALYQTTRTTAFIFGIFVG 310 Query: 295 ATTFSQVLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYM 354 AT F+ VL G + I + + PAGVV ++ ++ LG F+D V + L+ LP Sbjct: 311 ATVFAVVLRGLGGDDVIRNAITGLPFGPAGVVLTIMLVVFLLGFFLDWVEITLIILPLVA 370 Query: 355 PIVKSLGIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGL 414 P+V SLG+D +WF +++ IC+Q L PP G L+ +KGV P IT ++ P+V L Sbjct: 371 PVVFSLGVDPVWFAILFAICLQTSFLTPPVGFALFYIKGVCPPGITTLDIYKGVAPFVAL 430 Query: 415 SFTMLILIFFWPGIATWLP-DVFVGR 439 L L+FF+ +ATWLP V+ GR Sbjct: 431 QMLGLFLVFFYEPLATWLPAQVYSGR 456 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: 509 Number of extensions: 29 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: 456 Length adjustment: 33 Effective length of query: 406 Effective length of database: 423 Effective search space: 171738 Effective search space used: 171738 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