Align Tricarboxylate transport protein TctB (characterized)
to candidate WP_049763402.1 RSPH17029_RS15400 tripartite tricarboxylate transporter TctB family protein
Query= reanno::Dino:3609739 (162 letters) >NCBI__GCF_000015985.1:WP_049763402.1 Length = 146 Score = 49.3 bits (116), Expect = 3e-11 Identities = 43/150 (28%), Positives = 68/150 (45%), Gaps = 11/150 (7%) Query: 4 DRWIALVLLGVCLIYGYTAWFTMDADLAPFMRRNPIWPSTFPKVLSVLGAVAALVILLGL 63 D W + LL C G+ AW T+ L + I F L ++G ++ L I L L Sbjct: 7 DIWAGIGLLAFC---GFVAWRTL---LVRTVASGTIAGPVFVPWL-MIGGLSLLAIALIL 59 Query: 64 EGPQKPPKAGDIDYRRLGDYKIGQAALLLGLMVGYALLLRPAGFLVSTTSFLILGSVILG 123 + ++ RR + + LL L+V YA P G+LVST +LG ++ Sbjct: 60 RSILRGSSPVELPTRRT----LVRMGLLALLLVAYAAAFEPLGYLVSTLVTFVLGLLLFN 115 Query: 124 ERNWPVMIGVAVVATGAIWYLVQEVLGIFL 153 ER V+I V + TG ++ +L ++L Sbjct: 116 ERRPLVLILVPLALTGGVYLGFTRLLQVWL 145 Lambda K H 0.329 0.147 0.467 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: 64 Number of extensions: 1 Number of successful extensions: 1 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: 162 Length of database: 146 Length adjustment: 17 Effective length of query: 145 Effective length of database: 129 Effective search space: 18705 Effective search space used: 18705 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: 43 (21.2 bits)
This GapMind analysis is from Apr 10 2024. 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