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 GFF3978 HP15_3918 trap-type mannitol/chloroaromatic compound transport system, large permease component
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Marino:GFF3978 Length = 436 Score = 273 bits (697), Expect = 1e-77 Identities = 155/436 (35%), Positives = 242/436 (55%), Gaps = 3/436 (0%) Query: 1 MNWQLAAWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASF 60 M+ + L G L LGLP+A+ ++VV + G DS + + SF Sbjct: 1 MSIEALTLLFFGSLLFFLLLGLPLAFVLGGVSVVFLYFTWGFDSFY-MVASQIWGTMGSF 59 Query: 61 SLTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIAT 120 +L IPLF+ M +L TG+A+ + L G LA+ + F+A+ G + A Sbjct: 60 TLVAIPLFVFMAMILERTGVARDLYRMMHLWCGGLRGGLALGTLGICAVFAAMVGISGAA 119 Query: 121 TAMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGG 180 +G++ LP ML RGY+ + +G I GG +LIPPS L +L + G+S+ K+ G Sbjct: 120 VVAMGTIALPSMLERGYDKSMALGVINTGGGWGILIPPSILMILYALITGVSVGKMFAAG 179 Query: 181 VLPGLLLAISFVAYIVASAKLRPESAPREELVVLRGW-ERWRELVVYVLPLSLIFVAIVA 239 ++PG+LL + YI+ L+PE AP W E++R L +LP+ ++ + + + Sbjct: 180 IMPGVLLMVLTAIYIIVRCHLQPELAPALPKEDRGTWPEKFRALRAVLLPIGVVVMVLGS 239 Query: 240 VISGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFS 299 +I GG+ TPTEAAA+G L +YR +W L +A T ++GMI++I+ AA FS Sbjct: 240 II-GGITTPTEAAAMGVLGALISAAVYRQFKWSILKEAAIRTFKLTGMIMWILFAAHAFS 298 Query: 300 QVLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKS 359 GA I L+ P G++ M+ I+ L + +D V +ML+TLP +MPIV+S Sbjct: 299 AAYQSMGAQELIEGLMNMVPGGPWGIIIAMMVIVFLLAMVLDPVGIMLITLPVFMPIVES 358 Query: 360 LGIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTML 419 LG D IWFG++++I M++G + PP G L+ +KG+ P ITM ++ S +P+V + + Sbjct: 359 LGFDPIWFGILFVINMEIGYMTPPFGFNLFYLKGIVPPSITMKDIYKSIIPFVIVEIVGI 418 Query: 420 ILIFFWPGIATWLPDV 435 ILI +P IATWLPD+ Sbjct: 419 ILIMVFPEIATWLPDL 434 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: 555 Number of extensions: 28 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: 436 Length adjustment: 32 Effective length of query: 407 Effective length of database: 404 Effective search space: 164428 Effective search space used: 164428 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