Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate Ac3H11_1732 Tricarboxylate transport membrane protein TctA
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1732 Length = 503 Score = 402 bits (1033), Expect = e-116 Identities = 204/501 (40%), Positives = 326/501 (65%), Gaps = 7/501 (1%) Query: 1 MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60 MD LS GF VA T +NL+ +GC +GT++G+LPG+GP+ +A+LLP +AL P Sbjct: 1 MDLINNLSLGFGVAFTFQNLIYCFVGCLLGTLIGVLPGIGPVATIAMLLPATYAL--PPV 58 Query: 61 SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120 +ALI+LA +Y G +YGG ++IL+N+PG++++++T +DGY MA++G+ G AL+ + + SF Sbjct: 59 AALIMLAGIYYGAQYGGSTTAILVNLPGESSSVVTVIDGYQMARKGRAGPALAAAGLGSF 118 Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180 F + + FAP L + + FGPAEYF+LMV + + + + LK+ ++GL Sbjct: 119 FAGCVGTLILAAFAPPLTEVAFKFGPAEYFSLMVLGLIGAVVLASGSLLKAVGMIVLGLL 178 Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGR 240 + VG D N+GV RF+FD L+DG+ F+ + +G+F EI+ L + + Sbjct: 179 MGLVGTDVNSGVARFSFDIPELTDGIGFVTIAMGVFGYGEIIANLSRPDEDREVFTAKVE 238 Query: 241 MLFNLKEG-AQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKK--LSGNSDSFGKG 297 LF K+ + I LR + +G +G+LPG GA +A+ Y EKK L FG+G Sbjct: 239 GLFPTKDDFKRMIPAVLRGTSLGAALGILPGGGALLAAFAAYTVEKKTKLQPGEVPFGQG 298 Query: 298 DIRGVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIV 357 +IRGVAAPE+ANNA + SFIP+LTLG+P + A+M+GA+T++NI PGP + T P++ Sbjct: 299 NIRGVAAPESANNAGSQTSFIPLLTLGIPPNAVMALMVGAMTIHNIQPGPQVMTSNPELF 358 Query: 358 WGLIAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVL 417 WGLIA++ I N ML+++N+PLIG++ ++LT+P ++ P+I AVGVY+ ++ TFD+ + Sbjct: 359 WGLIASMWIGNAMLIVLNLPLIGIWIKLLTVPYRWLFPSIVLFCAVGVYSTNNNTFDIWM 418 Query: 418 MVALGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLI 477 + G++GYI K+ +PL+LGF+LG M+E+NLRRAL +S G+ ++ ++ LL Sbjct: 419 VGIFGLIGYIFHKLGTEPAPLLLGFILGPMMEENLRRALLLSRGDWSVFVTRPLSAGLLA 478 Query: 478 MA--IMVIVVPPVLRLLRKHS 496 A +++IV+ P ++ R+ + Sbjct: 479 AAALLLIIVLLPAVKNKREEA 499 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: 795 Number of extensions: 45 Number of successful extensions: 5 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: 503 Length adjustment: 34 Effective length of query: 470 Effective length of database: 469 Effective search space: 220430 Effective search space used: 220430 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 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