Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate RR42_RS34870 RR42_RS34870 hypothetical protein
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__Cup4G11:RR42_RS34870 Length = 500 Score = 403 bits (1036), Expect = e-117 Identities = 197/493 (39%), Positives = 321/493 (65%), Gaps = 4/493 (0%) Query: 6 YLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALIL 65 +L+ GF+ A++ +NL A +GC +GT++G+LPGLGP+ +A+LLP+ + L P +ALI+ Sbjct: 6 HLALGFSTALSLQNLAYAFLGCVLGTLIGVLPGLGPLATIAMLLPVTYTL--PPVAALIM 63 Query: 66 LATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLI 125 LA +Y G +YGG ++IL+N+PG++++++T +DGY MA++G+ GVAL+ + + SFF + Sbjct: 64 LAGIYYGAQYGGSTTAILVNLPGESSSVVTTIDGYQMARRGRAGVALATAGLGSFFAGCV 123 Query: 126 AIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVG 185 A + FA L++ + FGPAEYF+LM + + + + K+ ++GL L +G Sbjct: 124 ATLILAAFATPLSELAFKFGPAEYFSLMCLGLIGAVVLASGSLPKAVAMIVLGLLLGLIG 183 Query: 186 VDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGRMLFNL 245 D N+G RF+FD L+DG+ F+ + +G+F +EI+ LE + +T + Sbjct: 184 TDVNSGAARFSFDIPELTDGIDFVALAMGMFGFAEIIANLEQKEARETFTDSVTNLWPTR 243 Query: 246 KEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIRGVAAP 305 ++ + I LR + +G +G+LPG GA +AS Y EKK S + FGKG I GVA P Sbjct: 244 EDFRRMIPAVLRGTFLGSALGILPGGGAALASFAAYSLEKKTSKYAHEFGKGAIEGVAGP 303 Query: 306 EAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGLIAALL 365 E+ANNA+A SFIP+LTLG+P + A+M+GA+T++NI PGP + T P + WGLIA++ Sbjct: 304 ESANNAAAQTSFIPLLTLGIPPNAVMALMVGAMTIHNIQPGPQVMTSNPALFWGLIASMW 363 Query: 366 IANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVALGVLG 425 I N+ML+I+N+P+IG++ ++LT+P ++ PAI +GVY+V++ TFD+ + G++G Sbjct: 364 IGNLMLIILNLPMIGVWVKLLTVPYRYLYPAILVFCGIGVYSVNNQTFDVFMAAGFGIIG 423 Query: 426 YILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMA--IMVI 483 Y+ K+ +PL+LGFVLG M+E+N RR+L +S G + ++ LLI A ++ I Sbjct: 424 YLFLKLKCEPAPLLLGFVLGPMMEENFRRSLLLSRGEFTVFVTRPLSLGLLIAAASLVAI 483 Query: 484 VVPPVLRLLRKHS 496 V P ++ R+ + Sbjct: 484 VALPSIKAKREEA 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: 731 Number of extensions: 33 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