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 7024207 Shewana3_1414 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__ANA3:7024207 Length = 465 Score = 181 bits (458), Expect = 6e-50 Identities = 133/467 (28%), Positives = 228/467 (48%), Gaps = 47/467 (10%) Query: 5 LAAWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTP 64 +A L V +FLG+P+A + +++ LF DS ++ + ++L Sbjct: 1 MAIATLFTALLVCMFLGMPIAIALGFSSMLTI-LFFSNDSLASVALKLYESSSEHYTLLA 59 Query: 65 IPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAML 124 IP FIL L G+A+R ID I + G LA+ +V+A F+A+SGS+ AT A + Sbjct: 60 IPFFILSSAFLSTGGVARRIIDFAMDSIGHIRGGLAMASVMACMLFAAVSGSSPATVAAI 119 Query: 125 GSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPG 184 GS+++ M+ GY K G I G + +LIPPS + ++ + +S +++ + G++PG Sbjct: 120 GSIVIVGMVKAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPG 179 Query: 185 LLLA--ISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVIS 242 L++ + V YIVA K P S P G+++ L + + ++ I Sbjct: 180 LMMGFLLMIVIYIVARFKNLP-SRP------FPGFKQLGISSAKALGGLALIIIVLGSIY 232 Query: 243 GGVATPTEAAAIGCAATLAITLM-YRAL------RWQSLVQALQGTVA------------ 283 GGVA+PTEA+A+ C I + YR + W++ + + + Sbjct: 233 GGVASPTEASAVACMYAYFIAVFGYRDIGPLKNVAWRNPNEPIPSAIVRNLGHMALGLIK 292 Query: 284 ----------------ISGMILFIIVAATTFSQVLSFSGATNGIVDLVQSSGLPPAGVVA 327 +S M+LFII A F+ VL+ + I + + GLP G + Sbjct: 293 TPIDKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAEHIVGMGLPAWGFLI 352 Query: 328 IMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQIWFGVMYLICMQLGLLMPPHGML 387 I+ +L+ G F++ +++L+ P PI LGID I G++ ++ M++G+L PP G+ Sbjct: 353 IVNLLLLAAGNFMEPSAIVLIMAPILFPIATHLGIDPIHLGIIMVVNMEIGMLTPPVGLN 412 Query: 388 LYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFWPGIATWLPD 434 L+ G+ + I G V S +P++ L L LI + P I+ +LP+ Sbjct: 413 LFVTAGITGRSI--GWVIQSVLPWLALMLAFLALITYVPQISLFLPE 457 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: 471 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 439 Length of database: 465 Length adjustment: 33 Effective length of query: 406 Effective length of database: 432 Effective search space: 175392 Effective search space used: 175392 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