Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000425265.1:WP_027723082.1 Length = 240 Score = 127 bits (319), Expect = 2e-34 Identities = 81/245 (33%), Positives = 131/245 (53%), Gaps = 9/245 (3%) Query: 7 KTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVA 66 K L+TGAS GIG A A+ A+ G D+ +NY D A +I+ GQ+ +K DV Sbjct: 3 KIALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDVT 62 Query: 67 DPQTAQDFVAKAVETFGKVD-VMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMVQA 125 D + ++ ++ +E KV ++V+NAG + M + +V+L G + + + Sbjct: 63 DEKAVEENLSSLLEK--KVPYIVVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNVTKP 120 Query: 126 AAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSV 185 +M+R+ G I+ ++S S G QT+Y KAG+ +S A+ + K I N+V Sbjct: 121 VVSRMLRK-RTGRIINIASTSGETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAV 179 Query: 186 LPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAALLV 245 PG I T++ + D+ K PL RLG P+++AG + FL SD A+Y+TG + V Sbjct: 180 TPGFIDTDMLSELPVDEIKN-----TIPLKRLGTPKEVAGVVSFLCSDKASYITGQTIAV 234 Query: 246 DGGMY 250 +GG+Y Sbjct: 235 NGGIY 239 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: 99 Number of extensions: 4 Number of successful extensions: 3 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: 240 Length adjustment: 24 Effective length of query: 230 Effective length of database: 216 Effective search space: 49680 Effective search space used: 49680 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 Apr 09 2024. 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