Align 3-hydroxypropanonate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF1712 PGA1_c17360 3-hydroxyisobutyrate dehydrogenase MmsB
Query= metacyc::MONOMER-18957 (354 letters) >FitnessBrowser__Phaeo:GFF1712 Length = 291 Score = 127 bits (319), Expect = 4e-34 Identities = 96/318 (30%), Positives = 147/318 (46%), Gaps = 41/318 (12%) Query: 18 NYGFIGLGLMGQHMARHVYNQLEPSDKLYVYDVDPKHTTQFLTEVTSQTPQNAPLLTPLN 77 N GFIGLG MG MA ++ + DV + T + Sbjct: 2 NIGFIGLGNMGGPMAANLAKAGHDVTGFDMADVSIEGVTMAAS----------------- 44 Query: 78 SLKDFTTEVDSQLDFIVTMVPEGKHVKSVVSELVGHYKSTGNYDPSIKTTFLDSSTIDIP 137 E + + ++TM+P G+ +++V +++ S T +D ST+D+ Sbjct: 45 -----AAEAATDAEVVITMLPNGQILRAVADDVIPAM--------SAGATLVDCSTVDVD 91 Query: 138 TSRDVHQLVKSSIPEFDFIDTPVSGGVAGARKGTLSFML--SRETHDDIDPSLTALLSKM 195 ++R V S+ F+D PVSGG+ GA GTL+FM S +P L M Sbjct: 92 SARAVADQAGSA--NLMFVDAPVSGGIGGASGGTLTFMAGGSAAAFAAAEP----LFDIM 145 Query: 196 GINIFPCGATHGTGLAAKLANNYLLAITNIAAADSFQLAESFGLNLQNYAKLVAVSTGKS 255 G CG G G AAK+ NN +L IT I ++F LA+ GL+ Q +V+ S+G S Sbjct: 146 GQKAVHCGEA-GAGQAAKICNNMILGITMIGTCEAFALADKLGLDRQKMFDVVSTSSGYS 204 Query: 256 WASVDNCPIPGVYPDNNLPSDVNYEGGFITKLTRKDVVLATESAKFNNRFLMLGDIGRHW 315 W+ CP PGV P + P+D +Y+ GF +L KD+ LA ++A + +G + + Sbjct: 205 WSMNAYCPAPGVGPQS--PADNDYQPGFAAELMLKDLRLAQQAAHSADADTPMGALAQAL 262 Query: 316 YDKACEREDIANRDLSVL 333 Y E E A +D S + Sbjct: 263 YSMFVEDEGGAGKDFSAM 280 Lambda K H 0.317 0.134 0.392 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: 210 Number of extensions: 10 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 354 Length of database: 291 Length adjustment: 28 Effective length of query: 326 Effective length of database: 263 Effective search space: 85738 Effective search space used: 85738 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 (21.6 bits) S2: 48 (23.1 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