Align L-dehydroascorbate transporter large permease subunit (characterized, see rationale)
to candidate Ac3H11_163 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:A0A165IWV9 (425 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_163 Length = 425 Score = 300 bits (768), Expect = 6e-86 Identities = 159/423 (37%), Positives = 263/423 (62%), Gaps = 27/423 (6%) Query: 6 FSLGMLVLMGTGMNMGLALVLTGAGMAWVLDFWDAQLLAQNLVAGVDSFPLLAVPFFILA 65 F+L + V + G+ L + + A M + + + A ++ FPL A+PFFILA Sbjct: 13 FALTISVAVSIGLASILGIQASNANML---------ISVKEMFASINKFPLAAIPFFILA 63 Query: 66 GELMNSGGISRRIIDMAQAWVGHIRGGLGYVAIGAAVLMASMSGSALADTAALATILLPM 125 G LM +GGISRR+++ A++ VG ++GGL + ++ A++SGS++A T A+ IL+P Sbjct: 64 GNLMETGGISRRLVEFAKSIVGGVQGGLPMTCVLTCMIFAAVSGSSVATTFAIGAILIPA 123 Query: 126 MRQQGYPMNTSAGLIASGGIIAPIIPPSMPFVIYGVTTNTSISALFVSGIVPGLMM-GVG 184 + + GYP + +A L A+ + IIPPS+P ++YGV+ SI LF++G PGL++ G Sbjct: 124 LIKHGYPTSYAAALQATSAELGVIIPPSIPMILYGVSAEVSIGELFIAGFGPGLLISGAL 183 Query: 185 LIFAWR------WVLRDLD--LPQGEPLPVKDRLRATARAFWAMLMPLIIIGGMKTGVFT 236 ++F W W D D +P G +AT +A WA+LMP+II+GG+ GVFT Sbjct: 184 MLFVWAYCKYKGWGKNDGDGRMPFG---------KATLQAGWALLMPVIILGGIYGGVFT 234 Query: 237 PTEAAVVAAFYALVVALFIHREMKLADIYGVLVRAAKTTSIVMFLCAGAQVASYMITLAD 296 PTEA+ VA FYAL+V + I+RE+KL D+Y +L ++A +++++MF+ A A + +++IT A Sbjct: 235 PTEASAVAVFYALLVGVVIYREIKLRDLYAILRKSAISSAVIMFIIANAGLFAFLITRAG 294 Query: 297 LPNVLTSWLGPLVENPRLLMAVMMIVLVLIGTALDLTPTILIFAPVMLPIAVKAGIDPVY 356 +P+ + WL ++++P L + + L +IG ++ + I++ AP++ P+A+ GIDPV+ Sbjct: 295 VPDAIGRWLEAVLQSPALFLLGVNAALFVIGMFIETSAAIIVLAPILAPVAMHFGIDPVH 354 Query: 357 FGLMFVLNGAIGLITPPVGTVLNVVAGVGRISMHSVIKGVNPFLFTYVLILALLVVFPQI 416 FGL+ V+N A+G+ITPP G L V +IS+ +IK + PF+ ++ L ++ P I Sbjct: 355 FGLIMVVNLALGMITPPFGVNLFAACTVAKISLDRIIKHLLPFVCVILVCLLVITYVPSI 414 Query: 417 VTA 419 A Sbjct: 415 SLA 417 Lambda K H 0.329 0.143 0.431 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: 464 Number of extensions: 19 Number of successful extensions: 3 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: 425 Length of database: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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 (21.8 bits) S2: 51 (24.3 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