Align Ectoine/proline transporter ProP (characterized)
to candidate HSERO_RS15670 HSERO_RS15670 major facilitator transporter
Query= SwissProt::Q79VC4 (504 letters) >FitnessBrowser__HerbieS:HSERO_RS15670 Length = 427 Score = 214 bits (544), Expect = 6e-60 Identities = 132/420 (31%), Positives = 220/420 (52%), Gaps = 20/420 (4%) Query: 30 RPAIKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVRPLGG 89 R AI + +GN +EW+D IYG V + F LL F VS+ +RPLG Sbjct: 18 RRAIISSSIGNALEWFDILIYGAFAVVIAKQFFPTGDDSVSLLLTFATFGVSFFMRPLGA 77 Query: 90 LVLGPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGG 149 +VLG D+ GR+ L +++ +M V TA+I +P+ ASIG A + L KM+QGFS GG Sbjct: 78 VVLGAYSDRAGRKAALMLSIMLMTVGTAMIAFMPSYASIGLLAPAGIALGKMIQGFSAGG 137 Query: 150 EYAGATTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTWVTTHFYGATAMEDFG 209 E+ +T ++ E AP RRGFF ++ + A A+ + T + +G Sbjct: 138 EFGSSTAFLVEHAP-HRRGFFSSWQVASQGISLLLAALFGAVLNNMLT----PEQLASWG 192 Query: 210 WRIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHW 269 WR+PF+ + + +Y+R + E P F+ + ++ NA + +DT H Sbjct: 193 WRVPFIFGLLIAPAGIYIRRHLDEAPEFKESSEKTNAPL-RDT------------FAHQK 239 Query: 270 RPLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMW 329 LLIG V + Y L+ Y+P Y +Q+GL + S+ A ++M + P VG Sbjct: 240 MRLLIGAGSVIMATVSVY-LSLYIPTYAVKQLGLPAWSSFAAMSVAGLIMFIGSPLVGAL 298 Query: 330 SDRVGRKPVYATAVAATLILMVPAFLIM-NTGTIGAVLIALSMVAIPTGLYVALSASALP 388 SD++GR P T+ A ++L P F+ + N+ +L+ +++ + +Y A + L Sbjct: 299 SDKIGRTPFMITSSALYIVLTYPMFVFLTNSPGFLQLLLLQTVIGVLMTMYFAAMPALLA 358 Query: 389 ALFPTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAIAGVALL 448 +FP A+R +GM ++YNI+V++FGG LI +L+ TG + + +++F + ++ +A L Sbjct: 359 DIFPVATRGTGMSLAYNIAVTIFGGFAGLIITWLIDFTGDKLSVSYFVIFGAVLSLIASL 418 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: 581 Number of extensions: 35 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: 427 Length adjustment: 33 Effective length of query: 471 Effective length of database: 394 Effective search space: 185574 Effective search space used: 185574 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