Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_067073002.1 MCUHO_RS02500 glucose 1-dehydrogenase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_001602375.1:WP_067073002.1 Length = 270 Score = 178 bits (451), Expect = 1e-49 Identities = 98/256 (38%), Positives = 148/256 (57%), Gaps = 7/256 (2%) Query: 1 MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEAL------ 54 MK LEGK VLVTG STGIGR AI A GA+VAINY S+ A++ + +++ Sbjct: 1 MKRLEGKNVLVTGGSTGIGRETAIRFADEGANVAINYHSSETEAETTLEDVQDACSIIRE 60 Query: 55 -GQRAIAVKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFK 113 G R + V+GDVA + + + + +G++DV+++NAGI +M +D +R Sbjct: 61 RGCREMLVQGDVASEEDVERIFREVLGAWGRLDVLINNAGIQTASPTHEMTLDAYDRVLA 120 Query: 114 VNLHGAYFMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAI 173 VNL GA+ + A + + +G GG I+ +S+ + Y +KAG+ +L ++ A+ Sbjct: 121 VNLRGAFLCSREAVRHFLDRGGGGVILNNTSVHETIPKPQYAPYAASKAGIGALTRTLAL 180 Query: 174 ALGKHGIRCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASD 233 GIR N+V PG I T IN++ + D EK+ +E P+GR G P ++A FLASD Sbjct: 181 EYAGQGIRVNAVAPGAIATPINREWVDDPEKKAAVEGHIPMGRAGEPGEIAAVFAFLASD 240 Query: 234 MAAYVTGAALLVDGGM 249 AAY+TG + VDGG+ Sbjct: 241 EAAYITGQTIYVDGGL 256 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: 128 Number of extensions: 4 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: 270 Length adjustment: 25 Effective length of query: 229 Effective length of database: 245 Effective search space: 56105 Effective search space used: 56105 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