Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_011842034.1 RSPH17029_RS15280 tripartite tricarboxylate transporter permease
Query= TCDB::Q9FA44 (504 letters) >NCBI__GCF_000015985.1:WP_011842034.1 Length = 658 Score = 315 bits (806), Expect = 4e-90 Identities = 174/482 (36%), Positives = 283/482 (58%), Gaps = 15/482 (3%) Query: 14 AMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILLATVYIGC 73 A+TP NL++AL+G +GT+VG LPGL VA+L+P F + PA + LI L +Y G Sbjct: 10 ALTPFNLMLALVGVVLGTVVGALPGLSATMAVAVLVPFTFTMD-PA-AGLIALGAIYTGA 67 Query: 74 EYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIAIGGIILF 133 YGG ++IL+N PG ++I T DGYPMA++G GG+A++++ +SS G ++ +++ Sbjct: 68 IYGGAFAAILVNTPGTPSSIATTFDGYPMARRGDGGLAITLATLSSVAGGIVGAIALLIL 127 Query: 134 APLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGVDANTGVY 193 AP LA+ +LAFGP EYF L +F + + ++ N LK + A +GL L+ VGV G Sbjct: 128 APPLARVALAFGPTEYFWLAIFGMTLIAALSVGNTLKGLIGACLGLFLSMVGVAVVGGDV 187 Query: 194 RFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGRMLFNLKEGAQCIG 253 R+T + G+ +IGL+ + ++L+ ++ +R L EG + Sbjct: 188 RYTLEMQRFLGGIDITSAIIGLYCIP---VILDLVATRDAHLRPAETHGLRLGEGLRIAW 244 Query: 254 ----TTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIRGVAAPEAAN 309 +RSSVIG VG+LPGAG +IA ++Y ++ S ++FGKG+ GV A EAAN Sbjct: 245 ARKVNVIRSSVIGTVVGILPGAGGSIAGLVSYAEARRSSRTPEAFGKGEPDGVIATEAAN 304 Query: 310 NASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGLIAALLIANV 369 NA+ G FIP L LG+PG+ A+++GAL + I GP +F+ + +V+ I LLIA V Sbjct: 305 NATVGGGFIPTLVLGIPGTPPDAIILGALLVQGIKIGPTLFSAEAGVVYTFIWGLLIATV 364 Query: 370 MLLIMNIPLIG--LFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVALGVLGYI 427 ++L + LIG + ++ IP + P +A ++ +G +A+HS D LMV LG++ ++ Sbjct: 365 LMLPAGL-LIGRYAYRTVVAIPKAMLAPTVALLTVIGSFAIHSNVQDAQLMVGLGLIAWV 423 Query: 428 LRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGN---MAILWQSGVAKALLIMAIMVIV 484 L + F SP++LG VLG++ EQ + I N + + + + ++ ++ A++ ++ Sbjct: 424 LARYGFAPSPIVLGLVLGQIAEQGFVQTYLIGNASDRTLEMFFGRPISIGIIFAALLTLL 483 Query: 485 VP 486 P Sbjct: 484 YP 485 Lambda K H 0.326 0.141 0.414 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: 1025 Number of extensions: 73 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 504 Length of database: 658 Length adjustment: 36 Effective length of query: 468 Effective length of database: 622 Effective search space: 291096 Effective search space used: 291096 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 (21.6 bits) S2: 53 (25.0 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