Align Ectoine/proline transporter ProP (characterized)
to candidate BWI76_RS04280 BWI76_RS04280 MFS transporter
Query= SwissProt::Q79VC4 (504 letters) >FitnessBrowser__Koxy:BWI76_RS04280 Length = 436 Score = 172 bits (435), Expect = 3e-47 Identities = 120/404 (29%), Positives = 195/404 (48%), Gaps = 18/404 (4%) Query: 38 VGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFG-FAVSYLVRPLGGLVLGPLG 96 +G +E+YDF I+ + + +F EW FG FA YL RPLGG+++ G Sbjct: 21 LGGALEFYDFIIFVFFAAVVGELFFPADIPEWLRQVQTFGIFAAGYLARPLGGIIMAHFG 80 Query: 97 DKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGGEYAGATT 156 D VGR+K+ +++ +MA+ T IGLLPT AS+G A +LL ++++QG + GGE GA Sbjct: 81 DLVGRKKMFTLSILLMALPTLAIGLLPTYASVGIVAPLLLLFMRILQGAAIGGEVPGAWV 140 Query: 157 YVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTWVTTHFYGATAMEDFGWRIPFLT 216 +VAE P++R G L G +G G SVVA T + T+ + + GWRIPFL Sbjct: 141 FVAEHVPEKRIGIACGTLTAGLTVGILLG-SVVA--TLINTNL-TPQGIHEGGWRIPFLL 196 Query: 217 AIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHWRPLLIGI 276 G++A+YLR + ETP F Q E L + V H + + + + Sbjct: 197 GGAFGLVAMYLRRWLQETPVFLEMQQRKALAQE---------LPVKAVALKHQKAVAVSM 247 Query: 277 AIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMWSDRVGRK 336 + + + PV+L++ G A +++ + G+ +DR G Sbjct: 248 LLTWLLSAGVVVVILMSPVWLQKHYGFAPAITLQANSIATIMLCIGCLLAGLAADRFGAS 307 Query: 337 PVYATAVAATLILMVPAFLIMNTGTIGAVLIALSMVAIPTGLYVALSASALPALFPTASR 396 + + L AF ++ + + + V + G+ A+ + A FP R Sbjct: 308 RTFIVG-SVFLAAASWAFYHLSGASPQRLFLLYGTVGLCVGVVGAVPYVMVRA-FPAEVR 365 Query: 397 FSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFS 440 F+G+ SYN+S ++FGG TP+ L+ + + PA Y++ S Sbjct: 366 FTGISFSYNVSYAIFGGLTPIAVTMLMGVS--PMAPAWYVLALS 407 Lambda K H 0.322 0.138 0.407 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: 627 Number of extensions: 36 Number of successful extensions: 4 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: 436 Length adjustment: 33 Effective length of query: 471 Effective length of database: 403 Effective search space: 189813 Effective search space used: 189813 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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