Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_086510301.1 BZY95_RS12740 tartrate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_002151265.1:WP_086510301.1 Length = 353 Score = 221 bits (563), Expect = 2e-62 Identities = 141/346 (40%), Positives = 200/346 (57%), Gaps = 22/346 (6%) Query: 2 AYRICLIEGDGIGHEVIPAARRVLEATG-----LPLEFVEAEAGWETFERRGTSVPEETV 56 ++RI +I GDGIG EVI A ++VL A L EFV+ + + + +G +P + Sbjct: 3 SHRIAVIPGDGIGQEVIEAGKKVLSALAEKSGDLRFEFVDFDWSSQRYLEKGEYIPAGGL 62 Query: 57 EKILSCHATLFGAATSPTRKVPGFFGAIRY---LRRRLDLYANVRPAKSRPVPGSR---- 109 +++ A FGA S + VP + + D YANVRPA+ P SR Sbjct: 63 DELSRFDAIYFGAVGS--QDVPDHISLWELRLAICQGFDQYANVRPARVLPGVNSRLKGA 120 Query: 110 PGVDLVIVRENTEGLYVEQERRYL-----DVAIADAVISKKASERIGRAALRIAEGRPRK 164 +D +IVREN+EG Y R +V +V ++K ERI R A ++A+ RPRK Sbjct: 121 EDIDWIIVRENSEGEYSGNGGRVHQGFPDEVGTEVSVFTRKGVERIHRFAFQLAQSRPRK 180 Query: 165 TLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTN 224 L + K+N L+ + EVAKD+P V++ +VD ++V++PE DVIV TN Sbjct: 181 QLTLVTKSNAQRYGMVLWDEVFFEVAKDYPDVSIDRELVDAVTTRMVLKPETMDVIVATN 240 Query: 225 LLGDILSDLAAGLVGGLGLAPSGNI---GDTTAVFEPVHGSAPDIAGKGIANPTAAILSA 281 L DILSDLAA L G LG+AP+ N+ G ++FEP+HGSA DIAGKGIANP + +A Sbjct: 241 LHADILSDLAAALSGSLGIAPTANLNPAGTFPSMFEPIHGSAFDIAGKGIANPVGSFWTA 300 Query: 282 AMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAV 327 AMML++LGE AA+R+ A++ + G +T DLGG ATT T+A+ Sbjct: 301 AMMLEHLGESTAAERLMAAIERLTASGLQTKDLGGTATTRDVTQAI 346 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: 307 Number of extensions: 16 Number of successful extensions: 6 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: 353 Length adjustment: 29 Effective length of query: 305 Effective length of database: 324 Effective search space: 98820 Effective search space used: 98820 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 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