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_011382867.1 AMB_RS02190 C4-dicarboxylate ABC transporter
Query= TCDB::Q9RBQ9 (439 letters) >NCBI__GCF_000009985.1:WP_011382867.1 Length = 651 Score = 216 bits (551), Expect = 1e-60 Identities = 136/438 (31%), Positives = 224/438 (51%), Gaps = 17/438 (3%) Query: 14 TTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIPLFILMGE 73 T +++F G+P+A++ + ++ LF+ S + + +N +A+ + IPLFIL G Sbjct: 218 TLLVMFSGMPIAFALGVVALIFMLLFMPAAS-VDTIAQNFYEELANVIILAIPLFILKGA 276 Query: 74 LLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLMLPMML 133 + + + + + R+PG L V +A F+A++GS+ AT + +GS +P M Sbjct: 277 TIGRSNAGKDLYSALHAWLHRIPGGLGVANTIACGLFAAMAGSSPATCSAIGSAGIPEMR 336 Query: 134 ARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLAISFVA 193 ARGY P G I A G + +L+PPS +L A +S+ +L + G+ PGLLL F Sbjct: 337 ARGYSPGFAAGIIAAGGTLGILLPPSVTMLLYAVAAEVSLGRLFLAGIGPGLLLITLFAG 396 Query: 194 YIVASAKLRPESAPREELVVLRGWE------------RWRELVVYVLPLSLIFVAIVAVI 241 Y V + R E E G + +VV+V P I ++ V+ Sbjct: 397 YSVL--RYRHEYRRAERAAASHGTHSALLADEHYTTRQKIRMVVWVAPFVTILAGVMVVL 454 Query: 242 SGGVATPTEAAAIGCA-ATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQ 300 G ATP+E A +G A L I LMY R + L+ L GT+ S M+L II + ++ Sbjct: 455 YAGWATPSETAGVGAVLALLVIGLMYGIWRPRLLMPILTGTLRESTMLLMIIGMSLLYAY 514 Query: 301 VLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSL 360 V+S + D + L ++A +L + LG F+ VS++L+T P +P +K+ Sbjct: 515 VMSHLRISQAAADWIIGLALSKWFLLAAILLFTVVLGFFLPPVSIILMTAPIILPPLKAA 574 Query: 361 GIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLI 420 G D IWFGV+ + M++GL+ PP G+ ++ +K +AP I + + +P+V + ++ Sbjct: 575 GFDLIWFGVVMTVVMEMGLIHPPVGLNIFVIKNIAP-DIPLRDIIWGTLPFVLIMMVAVV 633 Query: 421 LIFFWPGIATWLPDVFVG 438 PGIATWLP +G Sbjct: 634 ACCLIPGIATWLPGAVMG 651 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: 704 Number of extensions: 42 Number of successful extensions: 4 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: 651 Length adjustment: 35 Effective length of query: 404 Effective length of database: 616 Effective search space: 248864 Effective search space used: 248864 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: 52 (24.6 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