Align Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase (characterized, see rationale)
to candidate WP_072905143.1 BUB13_RS02370 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:Q92MG1 (307 letters) >NCBI__GCF_900142125.1:WP_072905143.1 Length = 288 Score = 257 bits (656), Expect = 3e-73 Identities = 126/281 (44%), Positives = 188/281 (66%), Gaps = 1/281 (0%) Query: 8 IALIGIGLIGSSIARDIREKQLAGTIVVTTRSEATLKRAGELGLGDRYTLSAAEAVEGAD 67 +A+IG+GLIG S++ ++E G +V R + L++A ELG+ DRY+ +AV+ AD Sbjct: 9 LAIIGVGLIGGSLSLALKEAGAVGEVVGCGRGKPNLEKALELGVVDRYSRDPLDAVKDAD 68 Query: 68 LVVVSVPVGASGAVAAEIAAHLKPGAIVTDVGSTKGSVIAQMAPHLPKDVHFVPGHPIAG 127 ++ ++ PV V E+ KPGAI+TD GS KG+V A + P +P +V+FVPGHPIAG Sbjct: 69 VIFLATPVKTLATVTEELLPACKPGAIITDGGSVKGAVSAAIDPLMPDNVYFVPGHPIAG 128 Query: 128 TEHSGPDAGFAGLFRGRWCILTPPAGTDEEAVARLRLFWETLGSMVDEMDPKHHDKVLAI 187 TE SG +A F L+RG+ CILTP T+ +A+A + W+ GS V +M + HD+VLA Sbjct: 129 TEKSGAEAAFPTLYRGKRCILTPTENTNADALALVEKMWQIAGSEVVKMSLEKHDRVLAA 188 Query: 188 VSHLPHIIAYNIVGTADDLETVTESEVIKYSASGFRDFTRLAASDPTMWRDVCLHNKDAI 247 +SHLPH++AY++V + E +++YSA GFRDFTR+A+SDPTMWRD+ N+D + Sbjct: 189 ISHLPHMVAYSLVNAVGSYDHY-EENILEYSAGGFRDFTRIASSDPTMWRDIAETNRDGL 247 Query: 248 LEMLARFSEDLASLQRAIRWGDGDKLFDLFTRTRAIRRSIV 288 LEM+ +F + A L+ I G G+KLF+ F R++ +R +I+ Sbjct: 248 LEMMEQFEKFFAELKTDIAEGSGEKLFEFFLRSKQLRDAIL 288 Lambda K H 0.320 0.135 0.398 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: 226 Number of extensions: 3 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: 307 Length of database: 288 Length adjustment: 26 Effective length of query: 281 Effective length of database: 262 Effective search space: 73622 Effective search space used: 73622 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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