Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 7023089 Shewana3_0327 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__ANA3:7023089 Length = 241 Score = 134 bits (336), Expect = 2e-36 Identities = 80/241 (33%), Positives = 125/241 (51%), Gaps = 5/241 (2%) Query: 9 VLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVADP 68 VLVTG+S GIG+A A+ A G D+A++Y + A + AE+ ALG +K DVAD Sbjct: 5 VLVTGSSRGIGKAIALKLAAAGYDIALHYHSNQAAADASAAELSALGVNVSLLKFDVADR 64 Query: 69 QTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMVQAAAQ 128 + + +E G ++ NAGI +AF M + NL G Y ++ Sbjct: 65 AAVKAAIEADIEANGAYYGVILNAGINRDNAFPAMSEAEWDSVIHTNLDGFYNVIHPCVM 124 Query: 129 QMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSVLPG 188 MV+ GG I+ ++S+S + G Q +Y+ +KAG+ ++ ++ L K I N + PG Sbjct: 125 PMVQGRKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRKITVNCIAPG 184 Query: 189 TILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAALLVDGG 248 I T D+ ++ +E P+ R+G P ++A FL SD AAY+T + V+GG Sbjct: 185 LIET-----DMVADIPKDMVEQLVPMRRMGKPNEIAALAAFLMSDDAAYITRQVISVNGG 239 Query: 249 M 249 M Sbjct: 240 M 240 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: 130 Number of extensions: 7 Number of successful extensions: 2 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: 241 Length adjustment: 24 Effective length of query: 230 Effective length of database: 217 Effective search space: 49910 Effective search space used: 49910 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 17 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