Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_017617176.1 CDO52_RS11130 3-oxoacyl-ACP reductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_002263495.1:WP_017617176.1 Length = 254 Score = 136 bits (343), Expect = 4e-37 Identities = 93/257 (36%), Positives = 136/257 (52%), Gaps = 11/257 (4%) Query: 17 ERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALK 76 +R + +V ++TGA GIG+A AS+ +V D+ + E VA +E G A Sbjct: 2 QRYEGRVAVITGAGSGIGKATALRLASEGGTVVAVDLDRDAGEAVA---KETGGLYIA-- 56 Query: 77 ADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDP--LEMTEEDWRRCFAIDLDGAW 134 ADV++++ + A E +GR+DV N AG++ D L+ E WR+ ++L + Sbjct: 57 ADVTDEEAVKAAFAEVKEVYGRVDVAFNNAGISPPDDDSILDTGIEAWRKVQEVNLTSVY 116 Query: 135 YGCKAVLPQMIEQGVGSIINIAS-THSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGV 193 CK LP M EQG G+I+N AS + Y +K G+L ++R LG+++A GV Sbjct: 117 LCCKYALPYMREQGKGAIVNTASFVATMGAATSQISYTASKGGVLAMSRELGVQFARDGV 176 Query: 194 RVNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAP 253 RVNA++PG + T L + FA QR L P R +P E+A FLASD+A Sbjct: 177 RVNALSPGPVNTPLLKEL---FAKDPERAQRRLVHVPFGRFAEPEEIASAVAFLASDDAS 233 Query: 254 FINASCITIDGGRSVMY 270 FI AS +DGG S Y Sbjct: 234 FITASNFLVDGGISGAY 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: 134 Number of extensions: 8 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: 272 Length of database: 254 Length adjustment: 25 Effective length of query: 247 Effective length of database: 229 Effective search space: 56563 Effective search space used: 56563 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 24 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