Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_092057705.1 BQ4888_RS13095 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_900111775.1:WP_092057705.1 Length = 242 Score = 122 bits (305), Expect = 9e-33 Identities = 85/242 (35%), Positives = 121/242 (50%), Gaps = 7/242 (2%) Query: 10 LVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVADPQ 69 LVTGAS GIG A A+ A+ G D+ +NY A AEIEALG + DVAD + Sbjct: 8 LVTGASKGIGAAIALELAREGFDIWLNYGRDQQVAAQVAAEIEALGVACKRLPFDVADGE 67 Query: 70 TAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMVQAAAQQ 129 + + ++ V+V+NAG L M + V+L G Y + + Sbjct: 68 AVKAALEPLLDEAAPF-VLVNNAGFARDALLLWMTKEEWRDVLAVHLDGFYNVTKPVVNA 126 Query: 130 MVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSVLPGT 189 MV+ G I+ + S S G Q +Y+ KAG+ +S A + K + N+V PG Sbjct: 127 MVK-ARRGRIINIVSTSGESGIPGQVNYSAAKAGLIGATRSLAAEVAKRNVLVNAVSPGF 185 Query: 190 ILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAALLVDGGM 249 I TE+ KD +E + PLGRLG E++AG + FLASD A Y+TG V+GG Sbjct: 186 IDTEMLKD-----LPKERILPMIPLGRLGTVEEVAGLVAFLASDKATYITGQVFAVNGGA 240 Query: 250 YV 251 ++ Sbjct: 241 HM 242 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: 117 Number of extensions: 8 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: 242 Length adjustment: 24 Effective length of query: 230 Effective length of database: 218 Effective search space: 50140 Effective search space used: 50140 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: 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