Align L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized)
to candidate Ac3H11_2518 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::Q9HK58 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2518 Length = 263 Score = 120 bits (300), Expect = 4e-32 Identities = 81/257 (31%), Positives = 132/257 (51%), Gaps = 11/257 (4%) Query: 1 MLDFKGKNAVITGGSRGIGRAIALGLAKQGANILISYASHDSEADEVLETASKYGVKAHK 60 + D GK A++TGGSRG+G +A L + GA I++S + S+ +E G+ A Sbjct: 8 LFDLTGKTALVTGGSRGLGLQLAHALGEAGAKIMLS-SRKASDLEEATAELQAAGIDARW 66 Query: 61 VKVDQSDPYESIRFAEKAIETFGKVHILVDNAGI---CPFEDFFRISVDLFEKVWKVNVE 117 + D ++ + R A++ +E G V IL++NAG P ED VD ++KV +NV Sbjct: 67 IAADCANETDIRRLADETLECLGHVDILINNAGAAWGAPAEDH---PVDAWDKVMNLNVR 123 Query: 118 SHYFITQRIAKNMIENKINGRILLISSISAHVG---GEFQTHYTTTKSALNGFMHSIAIV 174 ++ ++Q IAK+ + + +G I+ ++SI+ G G Y T+K A+ F ++A Sbjct: 124 GYFILSQHIAKHSMIGRRSGSIINVASIAGLGGNPKGMNTIAYNTSKGAVINFTRALAAE 183 Query: 175 LGKYGILVNSLEPGTILTDINKEDLSNQEKRAYMERRTVVGRLGLPEDMVAPALFLLSDD 234 G Y I VN++ PG + + L + A + +GRLG ED+ SD Sbjct: 184 WGAYNIRVNAICPGFFPSKMTVGTLKAMGEEA-LAAHAPLGRLGDDEDLKGLCALYASDA 242 Query: 235 NTYVTGTELLADGGMLI 251 ++TG L DGG+ I Sbjct: 243 GKHITGQWLAVDGGVSI 259 Lambda K H 0.318 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: 150 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: 254 Length of database: 263 Length adjustment: 24 Effective length of query: 230 Effective length of database: 239 Effective search space: 54970 Effective search space used: 54970 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: 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