Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate N515DRAFT_2489 N515DRAFT_2489 alcohol dehydrogenase, propanol-preferring
Query= BRENDA::Q2K0Q7 (347 letters) >FitnessBrowser__Dyella79:N515DRAFT_2489 Length = 343 Score = 94.4 bits (233), Expect = 4e-24 Identities = 89/292 (30%), Positives = 127/292 (43%), Gaps = 31/292 (10%) Query: 1 MTKVRALVLERQHELALRDIDLPLET-GAGQVKIKIHTVGVCGSDVHYYTHGKIGPFVVN 59 M+K + R L ++P+ T G G+V +KI GVC +D+H P Sbjct: 1 MSKTMKAAVVRAFGQPLSIDEVPVPTPGLGEVLVKIEACGVCHTDLHAVDGD--WPVKPK 58 Query: 60 APMVLGHEAAGTVVEVGSGVRHLKVGDRVCMEPGIPDPNSKASRLGMYNIDPAVSFWAT- 118 P + GHE G VV +G GV HLK GDRV GIP S + + + W T Sbjct: 59 PPFIPGHEGVGYVVAIGPGVTHLKEGDRV----GIPWLYSACG-----HCEHCLGGWETL 109 Query: 119 --------PPVHGVLTPEVVHPANYTFKLPDNVSFAEGAMVEPFAVGMQAASKAKIA--- 167 V+G + A+Y LPD + F E A V G+ K+ Sbjct: 110 CESQQNTGYSVNGGFAEYALAAADYVGHLPDGIGFVEIAPV--LCAGVTVYKGLKVTDTR 167 Query: 168 PGDTAIVLGAGPIGTMVAIAALAGGCARAIVADLAQPKLDIAAQYQGVIPVNIRETNLIE 227 PG+ ++ G G +G M A A G A V D+ KLD+A + + +N R + + Sbjct: 168 PGNWVVISGIGGLGHMAVQYAAAMGLNVAAV-DIDDAKLDLARRLGAQLIINARHADPVA 226 Query: 228 EVGQLTDGWGADVVFECSGSPKAWETIMALPRPGGVIVAVGLPVNPVGFDVS 279 V + + GA + SPKA+ M + R GG + GLP P FD+S Sbjct: 227 VVKK--EIGGAHGALVTAVSPKAFGQAMNMVRRGGTVSLNGLP--PGSFDLS 274 Lambda K H 0.319 0.137 0.405 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: 313 Number of extensions: 14 Number of successful extensions: 5 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: 343 Length adjustment: 29 Effective length of query: 318 Effective length of database: 314 Effective search space: 99852 Effective search space used: 99852 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 (21.7 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