Align TctB aka STM2787, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_090447894.1 BLS63_RS21755 tripartite tricarboxylate transporter TctB family protein
Query= TCDB::Q9FA45 (144 letters) >NCBI__GCF_900100495.1:WP_090447894.1 Length = 147 Score = 100 bits (249), Expect = 9e-27 Identities = 61/139 (43%), Positives = 87/139 (62%), Gaps = 6/139 (4%) Query: 5 RIFAGIWLLLCIAGLFIAWQIQSEYSYEPVGPRPFPLGIIGLMALCALALLLRHPDTVSW 64 R+F+ IWLL C +AW Q+ ++Y+PVGPR +PL ++ LM +L LL++ V Sbjct: 4 RLFSAIWLLFCAWLAVLAWGFQAPFAYDPVGPRAYPLLLLALMGAGSLWLLIK--PGVLT 61 Query: 65 PRRHVLQKL--ITMIIILLMYAWGFEWLGFPIATALLTMVIGMLF-GATIPAAGISGAVL 121 + HV L ++ LL YA FE LGF ++TAL+ +G+LF G +P A ISG ++ Sbjct: 62 QQLHVPSALRATLCVLALLAYALLFEPLGFILSTALVGFALGVLFTGRPMPCA-ISGVLM 120 Query: 122 GILLWYAFDRLLDVTLPLG 140 G+LL+ FD LLDV LPLG Sbjct: 121 GLLLYGLFDYLLDVPLPLG 139 Lambda K H 0.332 0.147 0.498 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: 117 Number of extensions: 10 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: 144 Length of database: 147 Length adjustment: 16 Effective length of query: 128 Effective length of database: 131 Effective search space: 16768 Effective search space used: 16768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 42 (20.8 bits)
This GapMind analysis is from Sep 24 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