Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate Pf1N1B4_4412 Tartrate dehydrogenase (EC 1.1.1.93) @ Tartrate decarboxylase (EC 4.1.1.73) @ D-malic enzyme (EC 1.1.1.83)
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4412 Length = 351 Score = 222 bits (565), Expect = 1e-62 Identities = 144/348 (41%), Positives = 199/348 (57%), Gaps = 25/348 (7%) Query: 2 AYRICLIEGDGIGHEVIPAARRVLEA----TGLPLEFVEAEAGWETFERRGTSVPEETVE 57 AY+I + GDGIG EVI A VL+A +G L F + + + + G +PE +E Sbjct: 3 AYKIAAVPGDGIGVEVIAAGVEVLQALSKKSGFDLTFKHYDWNSDNYLKNGYYIPEGGLE 62 Query: 58 KILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAKSRPVPGSRPG--- 111 ++ + A FGA + VP +G + + D YANVRPA R +PG + Sbjct: 63 ELKTFDAIFFGAVGA--LNVPDHISLWGLRLPICQGFDQYANVRPA--RVLPGVKSPLLN 118 Query: 112 ---VDLVIVRENTEGLYVEQERRYL-----DVAIADAVISKKASERIGRAALRIAEGRPR 163 +D V+VREN+EG Y R +VA +V ++ ERI R A +A RPR Sbjct: 119 GDQIDWVVVRENSEGEYSGNGGRVHRGLPEEVATEVSVFTRAGVERIHRFAFELARSRPR 178 Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223 K L + K+N L+ + EVAKDFP V + +VD ++V++P DVIV T Sbjct: 179 KHLTMVTKSNAQRHGMVLWDEIFYEVAKDFPDVKIDKELVDAVTTRMVLKPSTLDVIVAT 238 Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIGDTT---AVFEPVHGSAPDIAGKGIANPTAAILS 280 NL DILSDLAA L G LG+AP+ N+ + ++FEP+HGSA DI GKG+ANP A + Sbjct: 239 NLHADILSDLAAALSGSLGIAPTANLNPSRKFPSMFEPIHGSAFDITGKGVANPIATFWT 298 Query: 281 AAMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVV 328 AAMML++LGE AAK++ A++ V E G TPDLGG+ATT T+AV+ Sbjct: 299 AAMMLEHLGETTAAKQLMSAIEAVTESGLHTPDLGGNATTRQITDAVI 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: 273 Number of extensions: 15 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: 351 Length adjustment: 29 Effective length of query: 305 Effective length of database: 322 Effective search space: 98210 Effective search space used: 98210 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