Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_012044687.1 BBTA_RS21880 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000015165.1:WP_012044687.1 Length = 253 Score = 159 bits (402), Expect = 5e-44 Identities = 100/249 (40%), Positives = 140/249 (56%), Gaps = 6/249 (2%) Query: 2 KLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAV 61 ++L G+ LVTGA+ G GRA A+G A GAD+ I DG A+ C EI G++A A Sbjct: 5 QMLAGRLALVTGAANGNGRAIALGLAGRGADLVITDIDVDG-AERCATEIRDHGRKAWAH 63 Query: 62 KGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMP--VDVVERTFKVNLHGA 119 + DV D A+ G + ++V+NAGI +D P +R VNL+G Sbjct: 64 RLDVTDAAGCTALAAQLRAEVGAISILVNNAGII-IRENIDSPRAAQNWQRVLDVNLNGV 122 Query: 120 YFMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHG 179 F V A +R+ G +IV ++S+++ +G Y+P+K GV SL Q+ A L G Sbjct: 123 -FNVTYAFLGALRETRG-TIVNIASVASFIGISNTLGYSPSKGGVKSLTQALARELAPDG 180 Query: 180 IRCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVT 239 IR N++ PG I T + + D E+ +RTPLGR+G PE+LAGP+ FL SDMA+YV Sbjct: 181 IRVNAIAPGVIATAMTESTRNDPERLAGFMSRTPLGRVGQPEELAGPVAFLVSDMASYVN 240 Query: 240 GAALLVDGG 248 G L VDGG Sbjct: 241 GVTLPVDGG 249 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: 126 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: 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