Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate PP_1418 PP_1418 putative Tricarboxylate transport protein TctC
Query= TCDB::Q9FA46 (325 letters) >FitnessBrowser__Putida:PP_1418 Length = 326 Score = 406 bits (1044), Expect = e-118 Identities = 193/316 (61%), Positives = 251/316 (79%), Gaps = 2/316 (0%) Query: 9 LTASILLMSTSVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIEKPMRVTYMP 68 L LL++ + LA E P R ECIAPA PGGGFDLTCKL+Q +L++ + KPMRVTYMP Sbjct: 10 LATGCLLLAGNALAAE-PKRPECIAPASPGGGFDLTCKLVQSALVQEKILSKPMRVTYMP 68 Query: 69 GGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASVGTDYGMIA 128 GGVGAVAYNA+VAQRP + GT+VA+S GSLLNL+QGKFGR+ + V+WLA+VGT YG IA Sbjct: 69 GGVGAVAYNAVVAQRPADAGTLVAWSSGSLLNLAQGKFGRFDENAVKWLAAVGTSYGAIA 128 Query: 129 VRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPHKMRYVAFE 188 V++DSP+KTL DL+ A++KDP+ VVIG+G ++GSQDWM++AL+A+ A ++P +RYVA E Sbjct: 129 VKSDSPYKTLDDLVAALKKDPSKVVIGSGGTVGSQDWMQTALIAKAAGINPRDLRYVALE 188 Query: 189 GGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRL-PGQLANIPTAKEQGY 247 GGGE TAL+G H+QV S D+S+ +P++ +R+LAVFSENRL ++ +IPTAKEQGY Sbjct: 189 GGGEIATALLGGHIQVGSTDISDSMPHIQSGNMRILAVFSENRLNEPEMKDIPTAKEQGY 248 Query: 248 DLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMTGQQLDDYV 307 D+VWP++RGFY+GPKVSD DY WW +F K+ +++F K RD R LF F MTG++LD YV Sbjct: 249 DIVWPVVRGFYLGPKVSDEDYAWWKASFDKMLASEDFAKLRDQRELFPFAMTGEELDGYV 308 Query: 308 KKQVTDYREQAKAFGL 323 KKQV DY+ AK FGL Sbjct: 309 KKQVADYKALAKEFGL 324 Lambda K H 0.318 0.135 0.401 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: 401 Number of extensions: 9 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: 325 Length of database: 326 Length adjustment: 28 Effective length of query: 297 Effective length of database: 298 Effective search space: 88506 Effective search space used: 88506 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: 41 (21.7 bits) S2: 48 (23.1 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