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 Ac3H11_155 TRAP dicarboxylate transporter, DctM subunit, unknown substrate 5
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_155 Length = 432 Score = 242 bits (618), Expect = 1e-68 Identities = 135/428 (31%), Positives = 233/428 (54%), Gaps = 15/428 (3%) Query: 13 GTTVLLFL----GLPVAYSFFAINVVGAWLFLG---GDSALGQLVRNGLVAVASFSLTPI 65 G V+LF GL + S A+ +VG LF GDS + + + +S++LT + Sbjct: 8 GLIVVLFAVLGSGLWIGLSLLAVALVGMELFTNRPVGDSMMLTIWGS----TSSWTLTAL 63 Query: 66 PLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLG 125 PLF+ MGE+LF + L+ G+ + RLPGRL + VV T F+AISGS+ AT A +G Sbjct: 64 PLFLWMGEILFRSKLSSSMFKGLAPWLERLPGRLLHVNVVGCTIFAAISGSSAATCATIG 123 Query: 126 SLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGL 185 + LP + RGY ++ +G + G + +LIPPS + ++ G A +SISKL + GV+PGL Sbjct: 124 KITLPELKQRGYPEEISVGTLAGAGTLGLLIPPSIIMIVYGVAANVSISKLFLAGVIPGL 183 Query: 186 LLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGGV 245 LLA F+ YI+ A + P + + + + +++P+ + V ++ I G+ Sbjct: 184 LLAALFMGYIIVWALFNKDKVPAPDAQLSFAQKLYASR--HLIPVVSLIVVVLGAIYSGI 241 Query: 246 ATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFS 305 AT TEAAA+G A +L + + +L W + L + MI I+ A + + F Sbjct: 242 ATATEAAALGVAGSLILAKIEGSLNWARFKEGLVAACRVYCMIGLILAGAAFLTLAMGFI 301 Query: 306 GATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQI 365 G + + + + L P ++ +++ I LG F+D +SM++LT+ +P V++ G D + Sbjct: 302 GLPRHLAEFIGALHLSPFALMLLLIVFFILLGCFLDGISMVVLTIAVLLPTVEAAGFDLV 361 Query: 366 WFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFW 425 WFG+ ++ +++ + PP G L+ ++G+ + +T + +A+P L +I+ +F Sbjct: 362 WFGIFIVLVVEMAQITPPVGFNLFVLQGMTRREVTW--IARTALPLFALMIVAVIMTYFV 419 Query: 426 PGIATWLP 433 P + WLP Sbjct: 420 PDVVLWLP 427 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: 507 Number of extensions: 30 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: 432 Length adjustment: 32 Effective length of query: 407 Effective length of database: 400 Effective search space: 162800 Effective search space used: 162800 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