Align FcbT1, 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 3607282 Dshi_0697 TRAP dicarboxylate transporter- DctP subunit (RefSeq)
Query= TCDB::Q9RBR1 (326 letters) >FitnessBrowser__Dino:3607282 Length = 336 Score = 164 bits (415), Expect = 3e-45 Identities = 99/318 (31%), Positives = 170/318 (53%), Gaps = 23/318 (7%) Query: 9 SIAAAASVASAALPVRAQELVLRAVSAFPEKTSQSIHFEKFIERVNSTGKGVLRINYVGG 68 ++AA + AA +A E L AV AFP + F +F+++VN+ G+GV++I GG Sbjct: 9 ALAAGLGLGGAA---QATE-TLTAVHAFPTTLIYTQSFLEFVDKVNAAGEGVVQIEVRGG 64 Query: 69 PRAIPTFEVGNAVKSGVVDIANCHGGYYANLFPEADALKLMQVTPQELRRSGGFDAINRI 128 P AI F+ +AV+ G+VD+ G +Y PE DA+ +T E R +GG D +N+I Sbjct: 65 PEAIGMFQQPDAVRDGIVDMVYTPGSFYGGTVPEKDAMVASNLTAVEARENGGTDLMNQI 124 Query: 129 WNAKGNMQYLAMIYGYSPFHLFL--NKKISKPSELA--GMKIRISPLYRDFLSA-LGVQV 183 K + YL ++L+ + + +L+ G+K+R + +Y F + LG QV Sbjct: 125 HQEKMGVYYLGWFDSGVSYNLWTKDEPQFEENGDLSVEGIKLRGNAVYNAFFTEYLGAQV 184 Query: 184 VNVAPGEIYTALERGVVEGYGWPIYSIFDLGWHEKTKYRVEPGFYNTETSIIMNLDSYKR 243 +++ ++Y ALERGVV+ GW + DL W+E YR+EP F++T+ +I+NL+ ++ Sbjct: 185 IDLPTTDVYAALERGVVDATGWTQIGLIDLKWNEFLNYRIEPNFFSTDLGVIVNLEKWES 244 Query: 244 LTSAQRAVLDPALAYAEGLNEDYKTINAREEKKQAD------AGIQVIRFEGEEGREFVR 297 L+ + +L + + ++ A K+ AD G+QV+ EGE ++ Sbjct: 245 LSDEAKTILQDV-----AIQHERDSVEALRAKRDADFAALEEGGMQVVSLEGEAKERYLA 299 Query: 298 RAYDEGW---KGIIARAP 312 A ++ W +G++A P Sbjct: 300 AAREKTWERMRGLMAEHP 317 Lambda K H 0.320 0.136 0.400 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: 300 Number of extensions: 12 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: 326 Length of database: 336 Length adjustment: 28 Effective length of query: 298 Effective length of database: 308 Effective search space: 91784 Effective search space used: 91784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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