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 GFF1282 PGA1_c12980 TRAP transporter, subunit DctM
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Phaeo:GFF1282 Length = 466 Score = 179 bits (455), Expect = 1e-49 Identities = 140/474 (29%), Positives = 226/474 (47%), Gaps = 55/474 (11%) Query: 4 QLAAWLLLGGTTVLLFLGLPVAYSFFAINVVG-AWLF---LGGD------------SALG 47 ++ W+ G + LG+ VA++ +VG W+F G D G Sbjct: 5 EIGLWVS-GFLLATVLLGMRVAFAAGLAGLVGLVWIFWAKFGYDPERFTKAVTIAVKTAG 63 Query: 48 QLVRNGLVAVASFSLTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAG 107 Q+ + V+S +L+ IP FIL+G L ++ GL + + + + +PG LAV V A Sbjct: 64 QVPHS---KVSSQALSLIPTFILIGYLAYYAGLTKALFEAAKRWLAWVPGGLAVSTVFAT 120 Query: 108 TFFSAISGSTIATTAMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGS 167 F+A+SG+++AT+A+ + +P ML GY+ + G + A G + LIPPSA+ V+ Sbjct: 121 AGFAAVSGASVATSAVFARIAIPEMLKIGYDKRFAAGVVAAGGTLASLIPPSAILVIYAI 180 Query: 168 LAGISISKLLIGGVLPGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYV 227 + + KLL+ G +PG A+ + I+ A P + G+ W+E +V + Sbjct: 181 IVEQDVGKLLLAGFIPGAFSAVVYGLLIIGMAMTIKGFGP-----AVTGF-TWKERLVSL 234 Query: 228 LP-LSLIFVAIVAVI-----SGGVA--TPTEAAAIGCAATLAITLMYRALRWQSLVQALQ 279 P L ++FV ++ GG A TPTE AIG A + + +YR +RW L AL Sbjct: 235 PPALPILFVVATIILFVYNPFGGDAWGTPTEGGAIG-AFVVFLMALYRGMRWAELKDALL 293 Query: 280 GTVAISGMILFIIVAATTFSQVLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLF 339 T +S MI II + + L F+ D + S L P ++ +L LG+F Sbjct: 294 ETAKLSVMIFTIIWGVLIYVRFLGFAELPAAFSDWITSLTLSPMLILICILLAYAVLGMF 353 Query: 340 VDQVSMMLLTLPFYMPIVKSLG-----------------IDQIWFGVMYLICMQLGLLMP 382 +D + M+LLTLP P V +L + IWFG++ + + L+ P Sbjct: 354 MDAIGMLLLTLPVVYPAVMALNGGEYVSAAESTFGMSGPMCAIWFGILVVKMAEFCLITP 413 Query: 383 PHGMLLYTMKGVAPKHITMGQVFASAMP-YVGLSFTMLILIFFWPGIATWLPDV 435 P G+ + + GV +T+ VF P ++ T+ IL+ F P I WLP + Sbjct: 414 PIGLNCFVVAGVR-DDLTVQDVFKGVTPFFIADGITIAILVAF-PSIVLWLPSL 465 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: 515 Number of extensions: 29 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: 466 Length adjustment: 33 Effective length of query: 406 Effective length of database: 433 Effective search space: 175798 Effective search space used: 175798 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