Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate Ac3H11_2748 Putative short-chain dehydrogenase/reductase (EC 1.1.1.100)
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2748 Length = 266 Score = 135 bits (340), Expect = 9e-37 Identities = 88/252 (34%), Positives = 134/252 (53%), Gaps = 7/252 (2%) Query: 2 LLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAI 61 LL DK ++TGA GIGR AR AR+GA V+I G L + G A+ Sbjct: 3 LLKDKVALITGAGGGIGRGIARCYAREGAAVLIAELDPVTGAEAEAELQQ----MGARAL 58 Query: 62 AVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYL-KTVGTNLNG 120 V D DS E + AA ++FG +D+L+NNA + + L+ + L +T+ + + Sbjct: 59 FVPTDVLRKDSVEAAIQAAADSFGGLDILINNAFVPSENVLLEDKTDAMLERTLTSTVWA 118 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 +++ ++AA M+ +G GG II +SI +G Y K+G++ L +S A G + Sbjct: 119 SWWAMRAALPHMRARG-GGRIINFTSIDVDIGAWQHADYNTGKSGVVGLTRSAAAEWGRF 177 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPI-VFLASDMARY 239 I CNA+ P + +K ER + P+GR G+P+ GP+ VFL S+MAR+ Sbjct: 178 NITCNAIAPTAMGATFHKLAAEIPGFAERSAAARPMGRSGDPELDIGPVAVFLGSEMARF 237 Query: 240 VTGASLLVDGGL 251 VTG ++ VDGGL Sbjct: 238 VTGITMHVDGGL 249 Lambda K H 0.319 0.136 0.383 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: 161 Number of extensions: 6 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: 256 Length of database: 266 Length adjustment: 25 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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