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 1937061 b3578 predicted transporter (NCBI)
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Keio:1937061 Length = 425 Score = 194 bits (492), Expect = 6e-54 Identities = 128/422 (30%), Positives = 227/422 (53%), Gaps = 18/422 (4%) Query: 10 LLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVA-SFSLTPIPLF 68 LLGG + GLP+A+ A+ + GA L D Q++ LV A SFSL IP F Sbjct: 10 LLGGIAI----GLPIAW---ALLLCGAALMFWLDMFDVQIMAQTLVNGADSFSLLAIPFF 62 Query: 69 ILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLM 128 +L GE++ GL++R +D K++ PG L + V+A +++SGS +A TA + +L+ Sbjct: 63 VLAGEIMNAGGLSKRIVDLPMKLVGHKPGGLGYVGVLAAMIMASLSGSAVADTAAVAALL 122 Query: 129 LPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLL- 187 +PMM + Y G I + G + +IPPS ++ G +G+SISKL + G+ PG+++ Sbjct: 123 VPMMRSANYPVNRAAGLIASGGIIAPIIPPSIPFIIFGVSSGLSISKLFMAGIAPGMMMG 182 Query: 188 AISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGGVAT 247 A + + +++L + PR++ ++ E W V + L L V I+ G+ T Sbjct: 183 ATLMLTWWWQASRL---NLPRQQKATMQ--EIWHSFVSGIWALFLP-VIIIGGFRSGLFT 236 Query: 248 PTEAAAIGCAATLAI-TLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFSG 306 PTEA A+ L + T++YR + + +L L G + +++F++ +A + +++ + Sbjct: 237 PTEAGAVAAFYALFVATVIYREMTFATLWHVLIGAAKTTSVVMFLVASAQVSAWLITIAE 296 Query: 307 ATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQIW 366 + DL+Q P + +++ ++ +G+ +D +L+ P MP+VK GID I+ Sbjct: 297 LPMMVSDLLQPLVDSPRLLFIVIMVAILIVGMVMDLTPTVLILTPVLMPLVKEAGIDPIY 356 Query: 367 FGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFWP 426 FGVM++I +GL+ PP G +L + GVA + PYV + +++L++ F P Sbjct: 357 FGVMFIINCSIGLITPPIGNVLNVISGVA--KLKFDDAVRGVFPYVLVLYSLLVVFVFIP 414 Query: 427 GI 428 + Sbjct: 415 DL 416 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: 510 Number of extensions: 36 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: 425 Length adjustment: 32 Effective length of query: 407 Effective length of database: 393 Effective search space: 159951 Effective search space used: 159951 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