Align Ectoine/proline transporter ProP (characterized)
to candidate N515DRAFT_0974 N515DRAFT_0974 MFS transporter, MHS family, proline/betaine transporter
Query= SwissProt::Q79VC4 (504 letters) >FitnessBrowser__Dyella79:N515DRAFT_0974 Length = 433 Score = 194 bits (494), Expect = 4e-54 Identities = 129/431 (29%), Positives = 204/431 (47%), Gaps = 20/431 (4%) Query: 26 PKKIRPAIKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVR 85 P+ R ++ + +EWYDF +Y Y ++ VF G E LLA + GFA+SY +R Sbjct: 8 PEISRGSMAVAALSTVVEWYDFTLYLYFATVLSRVFFGG--GESSLLATLAGFAISYAMR 65 Query: 86 PLGGLVLGPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGF 145 PLG +V G +GD++GR++ L ++M +M ++ LLP+ A G A LL LL+ F Sbjct: 66 PLGAVVFGHIGDRIGRRRTLLLSMMLMTLAMLATALLPSHAVAGPAAGALLLLLRCFMAF 125 Query: 146 STGGEYAGATTYVAEFAPDRRRGFFGAFLDMGSYLG--FAAGASVVAITTWVTTHFYGAT 203 S GGEY G Y+ E A RRG + S +G A G S + ++ T Sbjct: 126 SVGGEYTGVVAYLLEGARKDRRGLITSLASAASEIGALLAVGVSALTVSAMSTAQ----- 180 Query: 204 AMEDFGWRIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAG 263 ++ +GWRIPF L R+ + E+P F Q E + V + L Sbjct: 181 -LDSWGWRIPFFVGAALAGCVWIARSTMEESPDFV-RQVEQHTVPDSP---------LGH 229 Query: 264 VIRHHWRPLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLL 323 ++ +H L AI A + Y +Y+P +L L + ++ V + L+ Sbjct: 230 MLANHRPALFRTFAISALGSITYYVGITYVPAFLSSSGILAEERSLWLSTLAAVAVILVT 289 Query: 324 PFVGMWSDRVGRKPVYATAVAATLILMVPAFLIMNTGTIGAVLIALSMVAIPTGLYVALS 383 P G SDRVGR+PV A+++L + F +M + + ++A G A+ Sbjct: 290 PLAGALSDRVGRRPVLVWLAVASVLLPLAMFQLMARAMELNIALGAIVLACLAGGVSAVG 349 Query: 384 ASALPALFPTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAIA 443 A A FP R SG+ + ++ ++FGG TP + + L++ TG VP I + + Sbjct: 350 APATAEQFPGEGRLSGLALGVTMATAIFGGLTPFLAELLIKMTGWHAVPGAMIGLVAIVV 409 Query: 444 GVALLFMTESS 454 LL M E++ Sbjct: 410 LPVLLAMPETN 420 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: 538 Number of extensions: 20 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: 433 Length adjustment: 33 Effective length of query: 471 Effective length of database: 400 Effective search space: 188400 Effective search space used: 188400 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