Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_086509281.1 BZY95_RS07240 hypothetical protein
Query= TCDB::Q9FA44 (504 letters) >NCBI__GCF_002151265.1:WP_086509281.1 Length = 506 Score = 335 bits (858), Expect = 3e-96 Identities = 177/484 (36%), Positives = 296/484 (61%), Gaps = 10/484 (2%) Query: 17 PENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILLATVYIGCEYG 76 P L++ IG G + +PG + + LPL FA+ P + ++ +VY+G G Sbjct: 15 PYTLLLMAIGALAGIVSAAIPGFTITMAIVLTLPLTFAM--PPLQGIAVMLSVYVGGLSG 72 Query: 77 GRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIAIGGIILFAPL 136 G S+ LL +PG +++ T D +PMA+ G G AL++ SSFFGSLI+I +IL AP Sbjct: 73 GLFSAALLGIPGTPSSVATTFDAFPMARSGLPGKALALGLWSSFFGSLISIVVLILAAPP 132 Query: 137 LAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGVDANTGVYRFT 196 LA ++ GP EYFAL+VFA+ + S++ + L+ +A L+G+GLATVG D G RFT Sbjct: 133 LALLAVKLGPWEYFALIVFALTVIASLVGDSLLRGLIAGLVGIGLATVGPDPLMGRERFT 192 Query: 197 FDSVHLSDGVQFIVVVIGLFSVSEILLMLEHT----SSGQTMVRKTGRMLFNLKEGAQCI 252 F LS G+ F+VV+IG+++VS++L LE + + G T + NL+ + Sbjct: 193 FGYEMLSAGIPFLVVLIGMYAVSQLLSELETSPKQQAQGSTSLISGDMRPHNLETLKAIV 252 Query: 253 ---GTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIRGVAAPEAAN 309 +RSS+IG F+G +PGAG++I++ + Y K+ S + ++FGKG+ +GV A E+ N Sbjct: 253 LRPVNVIRSSLIGVFIGAVPGAGSSISNLLAYDQAKRSSSHPENFGKGEPQGVIASESGN 312 Query: 310 NASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGLIAALLIANV 369 +++A G IP++ LG+PGS AV+M A+ ++ I+ GP + + P++V+G+ ++ +A+V Sbjct: 313 SSTAGGGLIPLIALGIPGSAVDAVLMAAIMVHGISIGPRLILDNPELVYGMFLSMAVASV 372 Query: 370 MLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVALGVLGYILR 429 ++L + + L+ F +L +P +F+VP + + +G + +++ DL L+ +GV+GY+ + Sbjct: 373 LMLCIGLLLMRAFLNLLNVPKYFIVPVVLSCCVIGAFTLNNRITDLYLLAGVGVVGYLFK 432 Query: 430 KMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAIMVIVVPPVL 489 K+ +P++PL+LG VLG + E NLRRA S + + + ++ ALL +A+ IV V Sbjct: 433 KLDYPLAPLVLGVVLGPIAETNLRRAFQTST-DWTLFFTRPISAALLALAVASIVYSIVA 491 Query: 490 RLLR 493 L R Sbjct: 492 YLRR 495 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: 731 Number of extensions: 34 Number of successful extensions: 3 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: 504 Length of database: 506 Length adjustment: 34 Effective length of query: 470 Effective length of database: 472 Effective search space: 221840 Effective search space used: 221840 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: 52 (24.6 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