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 SMa0151 SMa0151 hypothetical protein
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Smeli:SMa0151 Length = 909 Score = 213 bits (543), Expect = 2e-59 Identities = 129/426 (30%), Positives = 223/426 (52%), Gaps = 9/426 (2%) Query: 16 VLLFLGLPVAYSFFAINVVGAWLFLGGDS--ALGQLVRNGLVAVASFSLTPIPLFILMGE 73 VLL G+P+A++ ++ G LG + +G +A+ + IP+F+LMG Sbjct: 8 VLLATGMPIAFALGLAAFAALYMQSGAGIFYVLGDTMFSG---IANLAYVSIPMFVLMGA 64 Query: 74 LLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLMLPMML 133 + + +D+ + R+PG L + + A FS ++GS+ AT A +G + +P M+ Sbjct: 65 AVASSPAGSDLYTSLDRWLNRIPGGLILSNIGACAIFSGMTGSSPATCAAIGKMGIPEMM 124 Query: 134 ARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLAISFVA 193 RGY + G I A G + +LIPPS ++ G SI +L + G+LPG+LL I F+ Sbjct: 125 RRGYPASVASGSIAAGGTLGILIPPSVTLIVYGIATETSIGRLFMAGILPGILLTIMFMT 184 Query: 194 YIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGGVATPTEAAA 253 + V K + E +V + ++ +LP LI + V+ GG+ATP+EAA Sbjct: 185 WAVIDCKRK--GYEFEARLVRYSMKERLAVLPRILPFLLIIAGTLYVLYGGIATPSEAAG 242 Query: 254 IGCAATLAITLM-YRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFSGATNGIV 312 G TLA+ ++ YR R++ + + S MI+ I+ AA F+ LS T + Sbjct: 243 AGAFLTLAVVIVAYRLFRFRPVAGIFGSAMKESVMIMMIMAAAELFAFALSSLFITQTVA 302 Query: 313 DLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQIWFGVMYL 372 + + ++A++ L+ G+F+ V+++++T P PIV G D WF ++ Sbjct: 303 AAIADMEVNRWVLMAVINVFLLICGMFLPPVAVIVMTSPMLFPIVTQAGFDPYWFAIVLT 362 Query: 373 ICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFWPGIATWL 432 I M++GL+ PP G+ L+ + +AP+ I + ++PYV + F +IL+ +P +ATWL Sbjct: 363 INMEVGLITPPIGLNLFVINAIAPQ-IPTKDILWGSLPYVLVMFLAIILLCVFPDVATWL 421 Query: 433 PDVFVG 438 P+ +G Sbjct: 422 PNQMLG 427 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: 767 Number of extensions: 31 Number of successful extensions: 4 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: 909 Length adjustment: 38 Effective length of query: 401 Effective length of database: 871 Effective search space: 349271 Effective search space used: 349271 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: 54 (25.4 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