Align Tricarboxylate transport protein TctC (characterized)
to candidate WP_017597374.1 D471_RS0103675 tripartite tricarboxylate transporter substrate-binding protein
Query= reanno::Dino:3609740 (326 letters) >NCBI__GCF_000341125.1:WP_017597374.1 Length = 330 Score = 185 bits (470), Expect = 1e-51 Identities = 110/326 (33%), Positives = 169/326 (51%), Gaps = 11/326 (3%) Query: 6 TRRTLIAA------AAALAMTGGAHAEGEQMLESIHFLIPGGAGGGWDGTARGTGEALTK 59 +RR ++AA AA L +TG G L ++P GGG+D TAR L + Sbjct: 5 SRRAVLAAGFVLPLAAFLPLTGCLPVRGPAELR---IMVPTPPGGGYDHTARTIKAVLEE 61 Query: 60 AGLVGSASYENMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTL 119 G V + N+ G G A+A L+ + G ++ ++ S S S + T Sbjct: 62 TGTVSEVTVFNLPGVSGTAALARLVYERGTP-GLILQMGLGVLANSHIESASHSATEATP 120 Query: 120 VAGTIGDYAAIVVGKDSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVMEAAG 179 +A I + A++V DSP +++ D+ A+ ADP++ +GGGS PGG DH+V ++ E G Sbjct: 121 LARLIEEPEALLVPPDSPFDTIDDMARAWRADPSSVVIGGGSTPGGPDHMVTMLLAEELG 180 Query: 180 KDALGVKYIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYD 239 D V Y YD GG AALLS E++ + G SE ++G+++++ VT + D Sbjct: 181 IDPAEVDYRTYDGGGPMQAALLSHEVSVAAAGPSEQRAAIDSGQLRVLAVTGADPDPGTD 240 Query: 240 SAPTMVEQGIDTTFVNWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIH 299 APT+ E GI F+NWRG A PGL A + ++D+PEW RN W + + Sbjct: 241 -APTLAEAGIPLHFLNWRGLLAPPGLSAADREELLAVVATLHDSPEWRAELERNRWTDAY 299 Query: 300 NSGADFQSFLEAQEAQIGDLMKKLGF 325 GA+F +FL +E ++G + +LGF Sbjct: 300 LEGAEFAAFLAEEEERVGTALNRLGF 325 Lambda K H 0.315 0.132 0.378 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: 328 Number of extensions: 19 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: 330 Length adjustment: 28 Effective length of query: 298 Effective length of database: 302 Effective search space: 89996 Effective search space used: 89996 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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