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 GFF1039 Psest_1072 TRAP transporter, DctM subunit
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__psRCH2:GFF1039 Length = 456 Score = 231 bits (590), Expect = 3e-65 Identities = 149/437 (34%), Positives = 227/437 (51%), Gaps = 23/437 (5%) Query: 17 LLFLGLPVAYSFFAINVV------------GAWLFLGGDSALGQLVRNGLVAVASFSLTP 64 LL LG PVA+S I ++ A L+ D +G L VA+ + Sbjct: 18 LLLLGFPVAWSLAGIGLLFAVLGYVLVEHFDANLWFTWDGTIGVLDARIYGIVANELMVA 77 Query: 65 IPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAML 124 +PLFI MG +L +G+A+R + + +V+ L G AV VV G +A +G A+ A+L Sbjct: 78 LPLFIFMGIMLDRSGIAERLMHSLVRVLGPLRGGYAVTVVVVGILLAASTGIVGASVALL 137 Query: 125 GSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGIS---ISKLLIGGV 181 G L + ML Y L +G ++G + +LIPPS + VL+ G S + KL +G + Sbjct: 138 GMLSIGPMLQANYNKSLAVGTACSVGTLGILIPPSIMLVLMADRLGTSEASVGKLFMGAL 197 Query: 182 LPGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELV----VYVLPLSLIFVAI 237 +PG++LA+ ++ YIV A L+ + AP V R R L+ V PL+LIF A+ Sbjct: 198 IPGMMLALMYILYIVIVAWLKKDFAPAP---VNRPKLDARALLDVFWAVVPPLALIF-AV 253 Query: 238 VAVISGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATT 297 + I G+AT TEA+A+G L + R L L AL T + I I + AT Sbjct: 254 LGSIFFGIATTTEASAVGAFGALLMAAASRRLNLPVLKDALYQTSRTAAFIFGIFIGATV 313 Query: 298 FSQVLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIV 357 F+ VL G + I + GV+ +LAI LG F+D V + L+ LP P++ Sbjct: 314 FAAVLRGLGGDDVIRAALTGLPFGQTGVLLTVLAITFLLGFFLDWVEITLIILPLVAPVL 373 Query: 358 KSLGIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFT 417 S+G+D +WF +++ +C+Q L PP G L+ +KGV P IT V+ +PY+ + Sbjct: 374 FSMGVDPLWFAILFALCLQTSFLTPPVGFALFYIKGVCPPGITTRDVYLGVLPYIVIQLI 433 Query: 418 MLILIFFWPGIATWLPD 434 L L+F++ +ATWLP+ Sbjct: 434 GLALVFYFAPLATWLPN 450 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: 518 Number of extensions: 31 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: 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 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