Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate SMc01992 SMc01992 alcohol dehydrogenase
Query= reanno::Dino:3607129 (347 letters) >FitnessBrowser__Smeli:SMc01992 Length = 346 Score = 495 bits (1275), Expect = e-145 Identities = 245/346 (70%), Positives = 287/346 (82%) Query: 1 MARALVLEAARKLALRDIDLPDELGPEDVRIAIDTVGVCGSDVHYYTHGKIGPFVVKQPM 60 MA+ALVLE +L+LRDI + +L P DV I I TVGVCGSDVHYYTHGKIGPFVV +PM Sbjct: 1 MAKALVLEKKGQLSLRDIPVRRDLSPTDVLIGIRTVGVCGSDVHYYTHGKIGPFVVNEPM 60 Query: 61 VLGHEAAGIVTEIGAAVTHLALGDRVCMEPGIPNGSSKASKLGVYNVDPAVQFWATPPVH 120 +LGHEAAG+V E+G+ V HL GDRVCMEPGIP+ SS++SKLG+YNVDP+V+FWATPPVH Sbjct: 61 ILGHEAAGVVLEVGSQVRHLKKGDRVCMEPGIPDLSSRSSKLGIYNVDPSVRFWATPPVH 120 Query: 121 GCLTPSVVHPAAFTFKLPDHVSFAEGAMVEPFAIGMQAAAKARIKPGDVALVTGAGPIGV 180 GCLTP VVHPAAFT++LPDHVSFAEGAMVEPFAIG+QAA +A I+PGDV V GAGPIG+ Sbjct: 121 GCLTPEVVHPAAFTYRLPDHVSFAEGAMVEPFAIGVQAALRAGIRPGDVGAVMGAGPIGM 180 Query: 181 MVALAALAGGCAKVFVSDLVEDKLAIAAGYDNIHPILIPRDNPAEVLQEATEGWGADVVF 240 M ALAALAGGC+KV+V+DL + KL + Y+ I I + + +E L AT GWGADVVF Sbjct: 181 MTALAALAGGCSKVYVADLAQPKLDVIGAYEGIETINVRQQAVSEALAGATGGWGADVVF 240 Query: 241 ECAGAAASIQAALEAAAPAGCVVWVGMPVDPVPVDIVLAQSRELRMETVFRYANMYDRAI 300 EC+GAA +I A A P G VV VGMPV+PVP DIV Q++ELR+ETVFRYAN+YDRAI Sbjct: 241 ECSGAAPAILALPSLARPGGTVVLVGMPVEPVPFDIVGMQAKELRIETVFRYANVYDRAI 300 Query: 301 ALLASGKVDLKPLISATFPFEDSIAAFDRAVEARPTDVKIQIKMGA 346 L+ASGKVDLKPLISAT PF++SIAAFDRAVEARPTDVKIQI+M A Sbjct: 301 ELIASGKVDLKPLISATIPFDESIAAFDRAVEARPTDVKIQIEMPA 346 Lambda K H 0.321 0.137 0.408 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: 447 Number of extensions: 17 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: 347 Length of database: 346 Length adjustment: 29 Effective length of query: 318 Effective length of database: 317 Effective search space: 100806 Effective search space used: 100806 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 (21.8 bits) S2: 49 (23.5 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