Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate RR42_RS03285 RR42_RS03285 tricarboxylic transport membrane protein
Query= TCDB::Q9FA46 (325 letters) >FitnessBrowser__Cup4G11:RR42_RS03285 Length = 318 Score = 389 bits (1000), Expect = e-113 Identities = 187/315 (59%), Positives = 237/315 (75%) Query: 11 ASILLMSTSVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIEKPMRVTYMPGG 70 A L + A+ A + ECI PAKPGGGFDLTCKL Q +LLE G E+P+R+ YMPGG Sbjct: 4 ACAALALAAACARPAAAAPECIVPAKPGGGFDLTCKLAQRALLEAGFTEQPVRLAYMPGG 63 Query: 71 VGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASVGTDYGMIAVR 130 +GAVAYN+IVAQRP EP T+VAFS GSLL L+QGKFG+YG DVRW+ ++GTDYG+IAVR Sbjct: 64 IGAVAYNSIVAQRPAEPDTIVAFSDGSLLALAQGKFGKYGAADVRWVGALGTDYGVIAVR 123 Query: 131 ADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPHKMRYVAFEGG 190 ADSP+KTLKDL+ A+ DP+ V+ GAG +IG+QDWMK+A++A++A V +MR+V FEGG Sbjct: 124 ADSPFKTLKDLVAALRSDPDQVLFGAGGTIGNQDWMKAAMVARQAGVGYKRMRFVGFEGG 183 Query: 191 GEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANIPTAKEQGYDLV 250 GE TAL G HVQ VSGD SE LG IR+LAV + RLPG+LA +PTA+EQG+D+V Sbjct: 184 GEAFTALQGGHVQAVSGDASEAAMQLGAGGIRILAVLAAQRLPGRLAGVPTAREQGFDIV 243 Query: 251 WPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMTGQQLDDYVKKQ 310 WPI+RGFY+GPKV+ ADYQ W + F++LQ + F + R +GLF D+ G LD YV++ Sbjct: 244 WPILRGFYMGPKVAQADYQRWAERFERLQASPAFARLRAEQGLFPADLGGADLDTYVQRT 303 Query: 311 VTDYREQAKAFGLAK 325 V YR AK FGL + Sbjct: 304 VQRYRTLAKEFGLTR 318 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: 418 Number of extensions: 12 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: 325 Length of database: 318 Length adjustment: 28 Effective length of query: 297 Effective length of database: 290 Effective search space: 86130 Effective search space used: 86130 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