Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_176342950.1 BZY95_RS20840 tripartite tricarboxylate transporter permease
Query= TCDB::Q9FA44 (504 letters) >NCBI__GCF_002151265.1:WP_176342950.1 Length = 507 Score = 425 bits (1092), Expect = e-123 Identities = 216/502 (43%), Positives = 324/502 (64%), Gaps = 6/502 (1%) Query: 1 MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60 MD L QGFA ++T N++ AL+G +G IVG +PGLG + G+A+LLPL F + Sbjct: 1 MDILQSLMQGFATSLTFSNILAALVGAGLGIIVGAIPGLGSVTGIALLLPLTF--QMDPI 58 Query: 61 SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120 + +I+L +Y GC YGG S+ILLN+PGDA A++T+LDGYP++QQG GG AL + +SSF Sbjct: 59 TGIIMLGALYYGCMYGGSYSAILLNIPGDAPAVVTSLDGYPLSQQGHGGKALFTANISSF 118 Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180 G + I + P+LA L FGPAE AL++ A+ +G ++ NPLK ++ IG+ Sbjct: 119 IGGTVGIIMLTFMGPILAHVGLMFGPAEVAALILLALCSIGWLLGDNPLKGLISTFIGVM 178 Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHT--SSGQTMVRKT 238 LAT+G+ G RFTFDS++L +G+ FI +VIG+F S++L+M+ + S + + + Sbjct: 179 LATIGIGTAFGQPRFTFDSMYLLNGISFIPLVIGMFGFSQVLVMMVNRVDPSAKGLSGRL 238 Query: 239 G--RMLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGK 296 G L + KE + +LRS V+G VG+LPGAGAT S ++Y+ EKK+ N D GK Sbjct: 239 GLKESLLDRKEALSILPVSLRSGVLGNLVGILPGAGATTGSFLSYVLEKKVGRNGDELGK 298 Query: 297 GDIRGVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDI 356 G I+GVAA EA NNA+A GSF P+L+LG+PGSGT AV++G L ++ + PGP +F PD Sbjct: 299 GRIQGVAASEAGNNAAAAGSFAPLLSLGIPGSGTAAVLLGGLMMWGLQPGPLLFQNNPDF 358 Query: 357 VWGLIAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLV 416 VWGLI+++ + NVM ++ + +I ++L IP ++P IA V VG Y+V+++ FD+ Sbjct: 359 VWGLISSMYLGNVMAVLAALAIIPFLVKLLLIPASIMIPVIAVVCVVGSYSVNNSMFDVW 418 Query: 417 LMVALGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALL 476 M+ GV+ + + +P++PL+L FVL LE +LR+AL IS G+ I +S +A LL Sbjct: 419 FMLGAGVVAFFMTAARYPIAPLLLAFVLTPRLETSLRQALDISRGDPMIFLRSPIAATLL 478 Query: 477 IMAIMVIVVPPVLRLLRKHSRK 498 + ++ ++ P RL R+ Sbjct: 479 TLILLFVLYPLAKRLFMTVRRR 500 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: 788 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: 507 Length adjustment: 34 Effective length of query: 470 Effective length of database: 473 Effective search space: 222310 Effective search space used: 222310 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 Apr 09 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