Align FcbT2, 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 8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q9RBR0 (181 letters) >FitnessBrowser__Miya:8501197 Length = 640 Score = 42.4 bits (98), Expect = 2e-08 Identities = 30/100 (30%), Positives = 50/100 (50%), Gaps = 5/100 (5%) Query: 60 VAEYSLYAITFLAAPLLLRKGQHIRVDLVLRAMPPRAAWLLEWAVDACGAAISG-LFLTS 118 ++ Y I++LA PL + K +IRVD++ +PPRA + VD C ++G L Sbjct: 84 LSRYLFIWISYLAVPLAIMKRSNIRVDVLCAKLPPRAQGMAWVVVDVCTLVLTGALCYMG 143 Query: 119 SVHVLVQ-SYSQSAMVMREMMFPEWWLYIPMPISLALLTI 157 HV +Q + Q+ M F Y+ +P+ L+T+ Sbjct: 144 FGHVQMQIAMPQTTPAMGIKYFIP---YMILPVGFFLMTL 180 Lambda K H 0.327 0.134 0.405 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: 278 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 181 Length of database: 640 Length adjustment: 28 Effective length of query: 153 Effective length of database: 612 Effective search space: 93636 Effective search space used: 93636 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: 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