Align L-dehydroascorbate transporter large permease subunit (characterized, see rationale)
to candidate Ac3H11_3227 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:A0A165IWV9 (425 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3227 Length = 434 Score = 823 bits (2125), Expect = 0.0 Identities = 425/425 (100%), Positives = 425/425 (100%) Query: 1 MAFVVFSLGMLVLMGTGMNMGLALVLTGAGMAWVLDFWDAQLLAQNLVAGVDSFPLLAVP 60 MAFVVFSLGMLVLMGTGMNMGLALVLTGAGMAWVLDFWDAQLLAQNLVAGVDSFPLLAVP Sbjct: 10 MAFVVFSLGMLVLMGTGMNMGLALVLTGAGMAWVLDFWDAQLLAQNLVAGVDSFPLLAVP 69 Query: 61 FFILAGELMNSGGISRRIIDMAQAWVGHIRGGLGYVAIGAAVLMASMSGSALADTAALAT 120 FFILAGELMNSGGISRRIIDMAQAWVGHIRGGLGYVAIGAAVLMASMSGSALADTAALAT Sbjct: 70 FFILAGELMNSGGISRRIIDMAQAWVGHIRGGLGYVAIGAAVLMASMSGSALADTAALAT 129 Query: 121 ILLPMMRQQGYPMNTSAGLIASGGIIAPIIPPSMPFVIYGVTTNTSISALFVSGIVPGLM 180 ILLPMMRQQGYPMNTSAGLIASGGIIAPIIPPSMPFVIYGVTTNTSISALFVSGIVPGLM Sbjct: 130 ILLPMMRQQGYPMNTSAGLIASGGIIAPIIPPSMPFVIYGVTTNTSISALFVSGIVPGLM 189 Query: 181 MGVGLIFAWRWVLRDLDLPQGEPLPVKDRLRATARAFWAMLMPLIIIGGMKTGVFTPTEA 240 MGVGLIFAWRWVLRDLDLPQGEPLPVKDRLRATARAFWAMLMPLIIIGGMKTGVFTPTEA Sbjct: 190 MGVGLIFAWRWVLRDLDLPQGEPLPVKDRLRATARAFWAMLMPLIIIGGMKTGVFTPTEA 249 Query: 241 AVVAAFYALVVALFIHREMKLADIYGVLVRAAKTTSIVMFLCAGAQVASYMITLADLPNV 300 AVVAAFYALVVALFIHREMKLADIYGVLVRAAKTTSIVMFLCAGAQVASYMITLADLPNV Sbjct: 250 AVVAAFYALVVALFIHREMKLADIYGVLVRAAKTTSIVMFLCAGAQVASYMITLADLPNV 309 Query: 301 LTSWLGPLVENPRLLMAVMMIVLVLIGTALDLTPTILIFAPVMLPIAVKAGIDPVYFGLM 360 LTSWLGPLVENPRLLMAVMMIVLVLIGTALDLTPTILIFAPVMLPIAVKAGIDPVYFGLM Sbjct: 310 LTSWLGPLVENPRLLMAVMMIVLVLIGTALDLTPTILIFAPVMLPIAVKAGIDPVYFGLM 369 Query: 361 FVLNGAIGLITPPVGTVLNVVAGVGRISMHSVIKGVNPFLFTYVLILALLVVFPQIVTAP 420 FVLNGAIGLITPPVGTVLNVVAGVGRISMHSVIKGVNPFLFTYVLILALLVVFPQIVTAP Sbjct: 370 FVLNGAIGLITPPVGTVLNVVAGVGRISMHSVIKGVNPFLFTYVLILALLVVFPQIVTAP 429 Query: 421 VVWLR 425 VVWLR Sbjct: 430 VVWLR 434 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: 792 Number of extensions: 25 Number of successful extensions: 1 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: 434 Length adjustment: 32 Effective length of query: 393 Effective length of database: 402 Effective search space: 157986 Effective search space used: 157986 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