Align L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized)
to candidate AZOBR_RS31390 AZOBR_RS31390 3-ketoacyl-ACP reductase
Query= SwissProt::Q9HK58 (254 letters) >FitnessBrowser__azobra:AZOBR_RS31390 Length = 252 Score = 122 bits (307), Expect = 5e-33 Identities = 80/248 (32%), Positives = 128/248 (51%), Gaps = 3/248 (1%) Query: 3 DFKGKNAVITGGSRGIGRAIALGLAKQGANILISYASHDSEADEVLETASKYGVKAHKVK 62 D GK A++TGG+ GIG+AIA+ LA+ GA+I ++ + E ++E G + + Sbjct: 6 DLTGKTALVTGGNGGIGQAIAVALARAGADIAVAGRTPPDETRALVEGL---GRRFAAIP 62 Query: 63 VDQSDPYESIRFAEKAIETFGKVHILVDNAGICPFEDFFRISVDLFEKVWKVNVESHYFI 122 D S E+ + T G + ILV+NAG+ +D + ++ V VN++S +F+ Sbjct: 63 ADLSSIAPIPALMEETVGTLGGLDILVNNAGLIRRDDPLDFTEADWDAVLDVNLKSVFFL 122 Query: 123 TQRIAKNMIENKINGRILLISSISAHVGGEFQTHYTTTKSALNGFMHSIAIVLGKYGILV 182 Q + + N G+I+ I+S+ + GG Y +KS + G +A GI V Sbjct: 123 CQAFGRYALGNGRKGKIINIASMLSFQGGIRVPSYAASKSGIAGITRLLANEWAGKGINV 182 Query: 183 NSLEPGTILTDINKEDLSNQEKRAYMERRTVVGRLGLPEDMVAPALFLLSDDNTYVTGTE 242 N++ PG + T + +++ + A + R GR P DM PA+FL SD + YV GT Sbjct: 183 NAIAPGYVATSVTTALRADERRNAEILARIPAGRWSEPADMGGPAVFLASDASDYVHGTI 242 Query: 243 LLADGGML 250 L DGG L Sbjct: 243 LPVDGGWL 250 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: 6 Number of successful extensions: 2 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: 252 Length adjustment: 24 Effective length of query: 230 Effective length of database: 228 Effective search space: 52440 Effective search space used: 52440 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