Align TctB aka STM2787, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_090445405.1 BLS63_RS13845 tripartite tricarboxylate transporter TctB family protein
Query= TCDB::Q9FA45 (144 letters) >NCBI__GCF_900100495.1:WP_090445405.1 Length = 151 Score = 96.3 bits (238), Expect = 2e-25 Identities = 59/144 (40%), Positives = 83/144 (57%), Gaps = 5/144 (3%) Query: 2 MSDRIFAGIWLLLCIAGLFIAWQIQSEYSYEPVGPRPFPLGIIGLMALCALALLLR---H 58 M DRIFAG LL+C +AW + ++YEPVGPR FPL ++ L+A AL L + H Sbjct: 1 MHDRIFAGSNLLICTVLAVLAWGYHAPFAYEPVGPRAFPLLLLLLIAGAALYQLFKPLGH 60 Query: 59 PDTVSWPR--RHVLQKLITMIIILLMYAWGFEWLGFPIATALLTMVIGMLFGATIPAAGI 116 P RHV +K+ I +L YA FE LGF ++ L + + L+GA+ +G+ Sbjct: 61 APAKEEPGLDRHVSRKISLCIAAMLAYAAVFEVLGFIPSSVLFAVAMARLYGASGLQSGV 120 Query: 117 SGAVLGILLWYAFDRLLDVTLPLG 140 GA++ + L+ FD LDV LPLG Sbjct: 121 GGALIAVGLYLLFDYGLDVPLPLG 144 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: 78 Number of extensions: 3 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: 151 Length adjustment: 16 Effective length of query: 128 Effective length of database: 135 Effective search space: 17280 Effective search space used: 17280 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