Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate GFF1775 PGA1_c17990 D-malate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Phaeo:GFF1775 Length = 354 Score = 215 bits (547), Expect = 2e-60 Identities = 134/351 (38%), Positives = 197/351 (56%), Gaps = 24/351 (6%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETVEK 58 YRI I GDGIG EV+P RRV++ +++ E + E + G +PE+ +E+ Sbjct: 5 YRIAAIPGDGIGKEVLPVGRRVIDLVAQKHNFTVDWTEFDWSCERYHDTGRMMPEDGIEQ 64 Query: 59 ILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAK-----SRPVPG-SR 109 + + + GA P VP +G + LRR LD YANVRP + S P+ G Sbjct: 65 MKAFDSIYLGAVGFPG--VPDHVSLWGLLIPLRRELDQYANVRPVRLLKGISSPLAGRGA 122 Query: 110 PGVDLVIVRENTEGLYVEQERRYL-----DVAIADAVISKKASERIGRAALRIAEGRPRK 164 +D++IVREN EG Y E R + AI +++++++ ++RI A +A+ R RK Sbjct: 123 DDIDMIIVRENVEGEYSEIGGRVYQGTEHEAAIQESILTRRGTDRIMDYAFNVAKTRKRK 182 Query: 165 TLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTN 224 + A K+N + T + + A+ P + +D V+ P+ FDV+V +N Sbjct: 183 HVSSATKSNGIIHTMPFWDERFAAAAERHPAIGTAQFHIDIMTANFVLHPDWFDVVVASN 242 Query: 225 LLGDILSDLAAGLVGGLGLAPSGNI---GDTTAVFEPVHGSAPDIAGKGIANPTAAILSA 281 L GDILSDL + G +G+APS NI G ++FEPVHGSAPDIAGKG+ANP AA+ +A Sbjct: 243 LFGDILSDLGPAVAGSIGIAPSANINPEGKYPSMFEPVHGSAPDIAGKGVANPVAAVWTA 302 Query: 282 AMMLDYLGEKEAAKRVEKAVDLVL-ERGPRTPDLGGDATTEAFTEAVVEAL 331 AMML++LGE AA +E+A++ L +T DLGG A T A++ AL Sbjct: 303 AMMLEHLGEANAAADIEQAIETSLASPDTKTRDLGGTADTAGSEAAILAAL 353 Lambda K H 0.319 0.137 0.391 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: 284 Number of extensions: 11 Number of successful extensions: 5 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: 334 Length of database: 354 Length adjustment: 29 Effective length of query: 305 Effective length of database: 325 Effective search space: 99125 Effective search space used: 99125 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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