Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_011603795.1 FRAAL_RS11520 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000058485.1:WP_011603795.1 Length = 253 Score = 149 bits (377), Expect = 4e-41 Identities = 102/253 (40%), Positives = 139/253 (54%), Gaps = 14/253 (5%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L+G+ +VTGAS+G+G A G AQ GADV + D A + +E G+RA+AV Sbjct: 9 LDGRVAVVTGASSGLGVDFARGLAQAGADVVLGARRVDRLATTAET-VEKEGRRALAVAT 67 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 DVADP + V AVE FG+VD++V+NAGI L VNL+G Y+M Sbjct: 68 DVADPASCDALVVAAVEAFGRVDILVNNAGIGTAVPALRETPQQFRSVIDVNLNGCYWMA 127 Query: 124 QAAAQQMVRQGHGGSIVAVSSISAL-VGGEYQTHYTPTKAGVHSLMQSTAIA-LGKHGIR 181 QAAA+ M G SIV +SSI L G Q Y +KAG+ + + A G+ GIR Sbjct: 128 QAAARVM---RPGSSIVNISSILGLTTAGLPQAAYAASKAGLIGMTRDLAQQWTGRRGIR 184 Query: 182 CNSVLPGTILTEINKDDLADQEKREYMEA---RTPLGRLGAPEDLAGPIVFLASDMAAYV 238 N++ PG + ++ D+ + Y++A R GRLG PE+L +VFL SD ++V Sbjct: 185 VNALAPGFF-----RSEMTDEYQPGYLDAQMSRVLGGRLGEPEELTAALVFLTSDAGSFV 239 Query: 239 TGAALLVDGGMYV 251 TG L VDGG V Sbjct: 240 TGQTLAVDGGFTV 252 Lambda K H 0.318 0.133 0.379 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: 127 Number of extensions: 5 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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