Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_013537152.1 THEAM_RS02025 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000185805.1:WP_013537152.1 Length = 242 Score = 150 bits (380), Expect = 2e-41 Identities = 101/245 (41%), Positives = 141/245 (57%), Gaps = 12/245 (4%) Query: 8 VIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGADA 67 V+VTG +RGIGRA A GA+V I +G+++ RA A+ A EI A G V D Sbjct: 10 VLVTGGTRGIGRAIAERFVEVGAKVYI--TGTNQERAEAV--AREIGAVG-----VKMDV 60 Query: 68 ADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYFTVQA 127 + + ++++ +E G +DVLVNNAGI F+ M E + + TNL G Y +A Sbjct: 61 FNREEVKEVIFDILEKEGQIDVLVNNAGITRDSLFIRMKDEDWDAVINTNLTGVYNVTRA 120 Query: 128 AARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRCNAV 187 M ++ R G II +SS+ G Q +Y+ TK+ L+ +S A LG GIR NAV Sbjct: 121 VVPSMVKK-RKGVIINISSVVGFTGNVGQVNYSATKSALIGFTKSLAKELGGRGIRVNAV 179 Query: 188 LPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGASLLV 247 PG I TD+ K + + K E + S +PL R GEP ++A +FLASDMA Y+TG +L V Sbjct: 180 APGYITTDMTKA-IPEKIKAELLKS-IPLRREGEPREVADACLFLASDMASYITGTTLHV 237 Query: 248 DGGLF 252 +GGLF Sbjct: 238 NGGLF 242 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: 165 Number of extensions: 11 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: 242 Length adjustment: 24 Effective length of query: 232 Effective length of database: 218 Effective search space: 50576 Effective search space used: 50576 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: 46 (22.3 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