Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_086511815.1 BZY95_RS20840 tricarboxylate transporter
Query= TCDB::Q9FA44 (504 letters) >NCBI__GCF_002151265.1:WP_086511815.1 Length = 500 Score = 422 bits (1086), Expect = e-122 Identities = 213/494 (43%), Positives = 321/494 (64%), Gaps = 6/494 (1%) Query: 9 QGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILLAT 68 QGFA ++T N++ AL+G +G IVG +PGLG + G+A+LLPL F + + +I+L Sbjct: 2 QGFATSLTFSNILAALVGAGLGIIVGAIPGLGSVTGIALLLPLTF--QMDPITGIIMLGA 59 Query: 69 VYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIAIG 128 +Y GC YGG S+ILLN+PGDA A++T+LDGYP++QQG GG AL + +SSF G + I Sbjct: 60 LYYGCMYGGSYSAILLNIPGDAPAVVTSLDGYPLSQQGHGGKALFTANISSFIGGTVGII 119 Query: 129 GIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGVDA 188 + P+LA L FGPAE AL++ A+ +G ++ NPLK ++ IG+ LAT+G+ Sbjct: 120 MLTFMGPILAHVGLMFGPAEVAALILLALCSIGWLLGDNPLKGLISTFIGVMLATIGIGT 179 Query: 189 NTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHT--SSGQTMVRKTG--RMLFN 244 G RFTFDS++L +G+ FI +VIG+F S++L+M+ + S + + + G L + Sbjct: 180 AFGQPRFTFDSMYLLNGISFIPLVIGMFGFSQVLVMMVNRVDPSAKGLSGRLGLKESLLD 239 Query: 245 LKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIRGVAA 304 KE + +LRS V+G VG+LPGAGAT S ++Y+ EKK+ N D GKG I+GVAA Sbjct: 240 RKEALSILPVSLRSGVLGNLVGILPGAGATTGSFLSYVLEKKVGRNGDELGKGRIQGVAA 299 Query: 305 PEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGLIAAL 364 EA NNA+A GSF P+L+LG+PGSGT AV++G L ++ + PGP +F PD VWGLI+++ Sbjct: 300 SEAGNNAAAAGSFAPLLSLGIPGSGTAAVLLGGLMMWGLQPGPLLFQNNPDFVWGLISSM 359 Query: 365 LIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVALGVL 424 + NVM ++ + +I ++L IP ++P IA V VG Y+V+++ FD+ M+ GV+ Sbjct: 360 YLGNVMAVLAALAIIPFLVKLLLIPASIMIPVIAVVCVVGSYSVNNSMFDVWFMLGAGVV 419 Query: 425 GYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAIMVIV 484 + + +P++PL+L FVL LE +LR+AL IS G+ I +S +A LL + ++ ++ Sbjct: 420 AFFMTAARYPIAPLLLAFVLTPRLETSLRQALDISRGDPMIFLRSPIAATLLTLILLFVL 479 Query: 485 VPPVLRLLRKHSRK 498 P RL R+ Sbjct: 480 YPLAKRLFMTVRRR 493 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: 786 Number of extensions: 54 Number of successful extensions: 4 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: 500 Length adjustment: 34 Effective length of query: 470 Effective length of database: 466 Effective search space: 219020 Effective search space used: 219020 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