Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate AZOBR_RS24695 AZOBR_RS24695 3-oxoacyl-ACP reductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__azobra:AZOBR_RS24695 Length = 256 Score = 155 bits (391), Expect = 1e-42 Identities = 92/251 (36%), Positives = 136/251 (54%), Gaps = 13/251 (5%) Query: 18 RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77 RL +V +TG GIG A+ A++ A +V++DI AE ETVAA R GA HA Sbjct: 10 RLAGRVAFVTGGGGGIGRAVCERLAAEGAAVVVADIGAEVAETVAAALRAEGAQAHATAL 69 Query: 78 DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 +V++++ A E +D++VN AG+ R +MT+ +W ++L G W GC Sbjct: 70 NVADRESWGAAVTGLPEAFRGVDIMVNVAGIVRDRSLPKMTDAEWSAVIDVNLRGTWLGC 129 Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCF---PYPVAKHGLLGLTRALGIEYAPKGVR 194 + + ++G G I+NIAST I G F Y +K G++GLTR +E A +G+ Sbjct: 130 QTAFRLVGDRGWGRIVNIAST----AILGTFGQANYSASKAGVVGLTRTAALEGARRGIL 185 Query: 195 VNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPF 254 VNA+APG +ET + P A R + L+ P R+G+P E+A FLASD+A + Sbjct: 186 VNAVAPGVVETAIVEGV------PDAVRSQWLEKTPIGRLGKPAEIAAVVAFLASDDAAY 239 Query: 255 INASCITIDGG 265 + I DGG Sbjct: 240 VTGQTIVADGG 250 Lambda K H 0.321 0.137 0.419 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: 181 Number of extensions: 6 Number of successful extensions: 3 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: 272 Length of database: 256 Length adjustment: 25 Effective length of query: 247 Effective length of database: 231 Effective search space: 57057 Effective search space used: 57057 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: 47 (22.7 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