Align 3-hydroxypropanonate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate AZOBR_RS26815 AZOBR_RS26815 3-hydroxyisobutyrate dehydrogenase
Query= metacyc::MONOMER-18957 (354 letters) >FitnessBrowser__azobra:AZOBR_RS26815 Length = 299 Score = 117 bits (292), Expect = 5e-31 Identities = 94/318 (29%), Positives = 146/318 (45%), Gaps = 38/318 (11%) Query: 21 FIGLGLMGQHMARHVYNQLEPSDKLYVYDVDPKHTTQFLTEVTSQTPQNAPLLTPLNSLK 80 FIGLG MG+ M N + + YDV P + + Sbjct: 6 FIGLGNMGRPMCD---NLTKAGHDVVGYDVVPAARDAYAAAG--------------GRVA 48 Query: 81 DFTTEVDSQLDFIVTMVPEGKHVKSVVSELVGHYKSTGNYDPSIK--TTFLDSSTIDIPT 138 E + D +++M+P GKHV++ Y+ G + T +D STID+ + Sbjct: 49 STLAEALADADTVISMIPTGKHVRAA-------YEDEGGVLAHARPGTMLIDCSTIDVES 101 Query: 139 SRDVHQLVKSSIPEFDFIDTPVSGGVAGARKGTLSFML--SRETHDDIDPSLTALLSKMG 196 +R V + + F +D PVSG V A+ GTL+FM+ + E + P LTA MG Sbjct: 102 ARAVSKAAADA--GFVMVDAPVSGAVPAAQAGTLTFMVGGTAEGFERARPVLTA----MG 155 Query: 197 INIFPCGATHGTGLAAKLANNYLLAITNIAAADSFQLAESFGLNLQNYAKLVAVSTGKSW 256 IF GA+ G G+A K+ NN + ++ +A ++ F LAE GL+ Q ++ VS+G W Sbjct: 156 PKIFHVGAS-GNGVALKICNNMMAGMSMVAISEVFALAEKLGLDHQTVYDVMTVSSGNCW 214 Query: 257 ASVDNCPIPGVYPDNNLPSDVNYEGGFITKLTRKDVVLATESAKFNNRFLMLGDIGRHWY 316 A CP+PG P + P++ +Y+ GF + KD+ L+ +A + L Y Sbjct: 215 ALQSYCPVPGPVPAS--PANRDYQPGFAAAMMLKDMRLSQNAAATSGAATPLAGSAAALY 272 Query: 317 DKACEREDIANRDLSVLF 334 E N+D S +F Sbjct: 273 QMLVEHGH-GNKDFSAVF 289 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: 215 Number of extensions: 14 Number of successful extensions: 4 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: 354 Length of database: 299 Length adjustment: 28 Effective length of query: 326 Effective length of database: 271 Effective search space: 88346 Effective search space used: 88346 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