Align L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized)
to candidate CCNA_01747 CCNA_01747 3-oxoacyl-(acyl-carrier protein) reductase
Query= SwissProt::Q9HK58 (254 letters) >FitnessBrowser__Caulo:CCNA_01747 Length = 246 Score = 119 bits (299), Expect = 4e-32 Identities = 82/250 (32%), Positives = 134/250 (53%), Gaps = 8/250 (3%) Query: 1 MLDFKGKNAVITGGSRGIGRAIALGLAKQGANILISYASHDSEADEVLETASKYGVKAHK 60 M D GK A++TG + GIG AIA L QGA++++S + A E ++ G +A Sbjct: 1 MFDLTGKTALVTGATGGIGGAIARALHAQGAHVVLSGTRESALA----ELKAELGERAST 56 Query: 61 VKVDQSDPYESIRFAEKAIETFGK-VHILVDNAGICPFEDFFRISVDLFEKVWKVNVESH 119 V + SD + KA E G + I++ NAG+ R+ + ++ V KVN+E + Sbjct: 57 VVANLSDAEQVDGLVAKAEEAAGAPLDIVIANAGVTRDGLIVRMKDEDWDTVIKVNLEGY 116 Query: 120 YFITQRIAKNMIENKINGRILLISSISAHVGGEFQTHYTTTKSALNGFMHSIAIVLGKYG 179 + +++ AK M++ + GRI+ I+SI G QT+Y +K+ + GF ++A L G Sbjct: 117 FRLSRAAAKGMMKRRA-GRIIGITSIVGVTGNPGQTNYAASKAGMIGFSKALAQELASRG 175 Query: 180 ILVNSLEPGTILTDINKEDLSNQEKRAYMERRTVVGRLGLPEDMVAPALFLLSDDNTYVT 239 + VN + PG I + + D N++++A + G+LG D+ A ++L SD YVT Sbjct: 176 VTVNCVAPGFIASPMT--DALNEQQKAGILSTIPAGKLGEGADIAAACVYLASDQAGYVT 233 Query: 240 GTELLADGGM 249 G L +GGM Sbjct: 234 GQTLHVNGGM 243 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: 136 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: 254 Length of database: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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: 46 (22.3 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