Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_090445408.1 BLS63_RS13850 tripartite tricarboxylate transporter substrate binding protein
Query= TCDB::Q9FA46 (325 letters) >NCBI__GCF_900100495.1:WP_090445408.1 Length = 327 Score = 372 bits (954), Expect = e-108 Identities = 183/318 (57%), Positives = 232/318 (72%), Gaps = 2/318 (0%) Query: 6 LRTLTASILLMSTSVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIEKPMRVT 65 L L ++LL S + A E PSR ECIAP+KPGGGFDLTCKL+Q L + G +E PMRVT Sbjct: 9 LLPLACALLLGSFNAAANE-PSRPECIAPSKPGGGFDLTCKLVQAGLKDHGLLEAPMRVT 67 Query: 66 YMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASVGTDYG 125 YMPGG+GAVAYNAI A R EPGT+VAFSG SLLNL+ GK+GRY + V+WL ++GTDYG Sbjct: 68 YMPGGIGAVAYNAIAANRRNEPGTLVAFSGASLLNLALGKYGRYDENAVQWLTTIGTDYG 127 Query: 126 MIAVRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPHKMRYV 185 +AVR DSP+KTL D++ A++KDP SV +G G SIG Q W K ALLA+ A VDP +RY Sbjct: 128 TLAVREDSPFKTLDDVIQALKKDPKSVAVGGGGSIGGQGWAKIALLAKAAGVDPRALRYA 187 Query: 186 AFEGGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANIPTAKEQ 245 AFEGG E ALMG HV +V+G SE + G+KIR L V+SE RLPG+LA++PTAKEQ Sbjct: 188 AFEGGAEHYMALMGGHVDLVTGSASE-IRAQKGNKIRALVVYSEERLPGELASVPTAKEQ 246 Query: 246 GYDLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMTGQQLDD 305 GYD+ WP+IRG+Y+GP+V WW ++F KLQ + EF++ R + ++GQ+L + Sbjct: 247 GYDIQWPLIRGYYMGPEVKPEVVAWWRESFAKLQNSAEFQQYLQDRDVIPLSVSGQELKE 306 Query: 306 YVKKQVTDYREQAKAFGL 323 VKKQV DYR+ + FGL Sbjct: 307 LVKKQVEDYRKLGEEFGL 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: 405 Number of extensions: 13 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: 327 Length adjustment: 28 Effective length of query: 297 Effective length of database: 299 Effective search space: 88803 Effective search space used: 88803 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 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