Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate RR42_RS03695 RR42_RS03695 hypothetical protein
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__Cup4G11:RR42_RS03695 Length = 500 Score = 400 bits (1028), Expect = e-116 Identities = 199/498 (39%), Positives = 320/498 (64%), Gaps = 4/498 (0%) Query: 1 MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60 M+ + +L+ GF+ A+T +N+ +GC +GT++G+LPG+GP+ +A+LLP+ + L P Sbjct: 1 MELFEHLALGFSTALTLQNVGYCFLGCVLGTLIGVLPGIGPLATIAMLLPVTYTL--PPV 58 Query: 61 SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120 +ALI+LA +Y G +YGG ++IL+N+PG++++++T +DGY MA++G+ GVAL+ + + SF Sbjct: 59 AALIMLAGIYYGAQYGGSTTAILVNLPGESSSVVTTIDGYQMARRGRAGVALATAGLGSF 118 Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180 F +A + FA L++ + FGPAEYF+LM + + + + K+ ++GL Sbjct: 119 FAGCVATLILAAFATPLSELAFKFGPAEYFSLMCLGLIGAVVLASGSLPKAVAMIVLGLL 178 Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGR 240 L VG D N+G RF+FD L+DGV F+ + +G+F +EI+ LE + +T Sbjct: 179 LGLVGTDVNSGAARFSFDVPELTDGVDFVALAMGMFGFAEIIANLEQKENRETFTDHVSN 238 Query: 241 MLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300 + + + + LR + +G +G+LPG GA +AS Y EKK S S FGKG I Sbjct: 239 LWPSRADFKRMAPAVLRGTALGSILGILPGGGAALASFAAYSLEKKTSKYSHEFGKGAIE 298 Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360 GVA PE+ANNA+A SFIP+LTLG+P + A+M+GA+T++NI PGP + T P + WGL Sbjct: 299 GVAGPESANNAAAQTSFIPLLTLGIPPNAVMALMVGAMTIHNIQPGPQVMTSNPALFWGL 358 Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420 IA++ I N+ML+I+N+PLIG++ ++L +P ++ PAI +GV++V++ TFD+ Sbjct: 359 IASMWIGNLMLIILNLPLIGIWVKLLQVPYRYLYPAILVFCCIGVFSVNNQTFDVFTAAG 418 Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMA- 479 GV+GY+ K+ +PL+LGFVLG M+E+N RRAL +S G + ++ LLI A Sbjct: 419 FGVIGYLFIKLKCEPAPLLLGFVLGPMMEENFRRALLLSRGTFTVFLTRPLSLGLLIAAG 478 Query: 480 -IMVIVVPPVLRLLRKHS 496 ++ IV P ++ R+ + Sbjct: 479 LLVCIVALPSIKAKREEA 496 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: 741 Number of extensions: 37 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: 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 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