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 CCNA_01515 CCNA_01515 C4-dicarboxylate transporter large subunit
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__Caulo:CCNA_01515 Length = 426 Score = 206 bits (525), Expect = 9e-58 Identities = 134/430 (31%), Positives = 220/430 (51%), Gaps = 17/430 (3%) Query: 9 LLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIPLF 68 LLLG +LL +G+PVA FA+ + F+ D A + V FSL IP F Sbjct: 5 LLLGLLALLLIIGVPVA---FALGLASLVTFIFMDIAPVVAFQRIATGVNVFSLMAIPFF 61 Query: 69 ILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLM 128 I G+L+ G+A+R + D + R+ G L V+ V A F +SGS +A+ + LGS + Sbjct: 62 IFAGDLMQQAGIAERLVRVADAAMGRIRGGLGVVDVGASMMFGGVSGSAVASVSALGSTL 121 Query: 129 LPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISIS--KLLIGGVLPGLL 186 +P+M +GY+ + + +LIPPS ++ + AG+S+S L + GVLPG+L Sbjct: 122 IPLMKEKGYDADYAVNVTSTSAILGILIPPSHNMIIYAAAAGVSVSVADLFLAGVLPGIL 181 Query: 187 LAI--SFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGG 244 I + A+I+A + P+ GW + LP L V I + GG Sbjct: 182 TGIFLAAAAWIIAVRRGYPKGE-------FPGWPAFAAAFASALPGLLTAVIIFGGVLGG 234 Query: 245 VATPTEAAAIGCAATLAI-TLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLS 303 V TPTE++A+ TL I ++YR L ++ A Q V + M++ II +A F +L+ Sbjct: 235 VFTPTESSAVAVIYTLVIAVIVYRTLGFRGFTTAAQNAVKTTAMVMLIIGSAAAFGWLLA 294 Query: 304 FSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGID 363 A + L+Q+ P ++ ++ IL+ LG F+D ++++T P ++P+ + G+D Sbjct: 295 LLEAPEQLATLLQTLTDNPILILLLINLILLILGTFMDMAPLIVITSPIFLPVAMATGMD 354 Query: 364 QIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIF 423 + FG+M ++ + +GL+ PP G +L+ G A I + Q + P+ F L+ I Sbjct: 355 PVQFGIMMMLNLGIGLVTPPVGSVLFV--GCAVGKIKVEQAVRTIWPFYLALFAALMAIT 412 Query: 424 FWPGIATWLP 433 F P + LP Sbjct: 413 FVPALTLTLP 422 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: 461 Number of extensions: 31 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: 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