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_020922288.1 RHE_RS18500 TRAP transporter large permease subunit
Query= TCDB::Q9RBQ9 (439 letters) >NCBI__GCF_000092045.1:WP_020922288.1 Length = 497 Score = 231 bits (588), Expect = 5e-65 Identities = 131/430 (30%), Positives = 220/430 (51%), Gaps = 13/430 (3%) Query: 13 GTTVLLFLGLPVAYSFFAIN----VVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIPLF 68 G + + G PVA+S A+ ++G ++ L L V++ L IP F Sbjct: 14 GMVIFMLYGFPVAFSLAAVGMFFGIIGIVTGHFSEAFLQALPLRFFGIVSNDLLLAIPFF 73 Query: 69 ILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLM 128 LMG +L GLA+ ++G K+ +PG LA ++ G AI+G+ A+ +G + Sbjct: 74 TLMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITGTVAASVITMGVIS 133 Query: 129 LPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLA 188 LP+ML GY P+L G I A G + +IPPS + V+L G S+ + +G + P +L Sbjct: 134 LPIMLRYGYSPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGDMYLGAIGPSILQV 193 Query: 189 ISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVL---PLSLIFVAIVAVISGGV 245 FV +++ + +RP+S P V RG W LV ++ P ++ ++ I G+ Sbjct: 194 TIFVLFVLVMSIVRPKSMPPLPKEV-RGDFNWALLVKVLMGMVPSIVLIFLVLGTIFMGL 252 Query: 246 ATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFS 305 ATPTEA A+G + + M R L W + +A+ T I+ M++ I++ +T FS V Sbjct: 253 ATPTEAGALGVVGAMLLAAMNRRLTWPLIREAMTSTTHITSMVVMILIGSTCFSLVFQGM 312 Query: 306 GATNGIVDLVQSSGLP--PAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGID 363 + I ++ SG+P P G + + + L F+D + + +P P+ SLGID Sbjct: 313 DGSRWIEHML--SGIPGGPVGFLIFVNIFIFVLAFFLDFFEIAFIVIPMLAPVASSLGID 370 Query: 364 QIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIF 423 IWFGV+ + MQ + PP G L+ ++ +A K + ++ A+P+VG+ ++ ++ Sbjct: 371 LIWFGVLICVNMQTSFMHPPFGFALFYLRSIASKDVKTSDIYMGALPWVGMQIILVAIVI 430 Query: 424 FWP-GIATWL 432 FWP + WL Sbjct: 431 FWPQSVTYWL 440 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: 642 Number of extensions: 41 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: 497 Length adjustment: 33 Effective length of query: 406 Effective length of database: 464 Effective search space: 188384 Effective search space used: 188384 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 Apr 09 2024. 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