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 SM_b20035 SM_b20035 ABC transporter permease
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Smeli:SM_b20035 Length = 426 Score = 198 bits (504), Expect = 2e-55 Identities = 134/435 (30%), Positives = 235/435 (54%), Gaps = 17/435 (3%) Query: 9 LLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLV-RNGLVAVASFSLTPIPL 67 + LG + LG+P+A++ ++ V L+LG A Q+V +N L SF L +P Sbjct: 5 IFLGALLGPMALGVPIAFALI-LSGVALMLYLGLFDA--QIVAQNVLNGADSFPLMAVPF 61 Query: 68 FILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSL 127 F+L GE++ GL++R + ++ + G L +A+ A S++SGS +A A LG+L Sbjct: 62 FLLAGEVMNTGGLSRRIVALAMAMVGHIRGGLGFVAIFAACILSSLSGSAVADAAALGAL 121 Query: 128 MLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLL 187 +LPMML G++P G I + + +IPPS +L G + G+SI+KL + G+ PGL++ Sbjct: 122 LLPMMLKSGHDPARASGLIASASIIGPIIPPSIGFILFGVVGGVSITKLFLAGIFPGLMI 181 Query: 188 AISF-VAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGGVA 246 A + + +++ + K + E PR+ G R R V + L L V I+A + GV Sbjct: 182 AAALSITWLIVARKEQFELPPRQS-----GRLRLRAFVDSLWALFLP-VIIIAGLKFGVF 235 Query: 247 TPTEAAAIGCAATLAITL-MYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFS 305 TPTEA I +L +++ +YR L L IS +++F++ A + +++ + Sbjct: 236 TPTEAGVIAAVYSLFVSMVVYRELAPAQLFHVFVSAAKISAVVMFLVACAAVSAWLITVA 295 Query: 306 GATNGIVDLVQS-SGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQ 364 + L++ G A ++AIM+ I+I +G +D +L+ P MP++K GID Sbjct: 296 DVPGALAALLEPLMGNQTALLIAIMVLIVI-VGTAMDMTPTILIMTPVLMPVIKQAGIDP 354 Query: 365 IWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFF 424 ++FGV+++I +GL+ PP G +L + GV+ ++M + MP++ +L L+ Sbjct: 355 VYFGVLFIINNSIGLITPPVGTVLNVICGVS--KLSMEDLMKGVMPFLFAELIVLFLLVL 412 Query: 425 WPGIATWLPDVFVGR 439 +P + T +P + GR Sbjct: 413 FPELVT-VPVSWFGR 426 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: 486 Number of extensions: 30 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: 426 Length adjustment: 32 Effective length of query: 407 Effective length of database: 394 Effective search space: 160358 Effective search space used: 160358 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