Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate RR42_RS33755 RR42_RS33755 tartrate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Cup4G11:RR42_RS33755 Length = 358 Score = 216 bits (549), Expect = 9e-61 Identities = 141/351 (40%), Positives = 194/351 (55%), Gaps = 26/351 (7%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEAT-----GLPLEFVEAEAGWETFERRGTSVPEETVE 57 Y+I I GDGIG EVI A +VLE G L + + +G +PE +E Sbjct: 4 YKIAAIPGDGIGPEVISAGLQVLETLAGQDGGFKLGVEHFPWSSDYYLEKGYYIPEGGLE 63 Query: 58 KILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAKSRPVPGSRP---- 110 ++ A FGA + VP +G + + D YANVRPA R +PG + Sbjct: 64 RLKQFDAIFFGAVGA--LNVPDHVSLWGLRLPIAQGFDQYANVRPA--RVLPGVKSPLAN 119 Query: 111 --GVDLVIVRENTEGLYVEQERRY-----LDVAIADAVISKKASERIGRAALRIAEGRPR 163 +D VI+REN+EG Y R ++ AV ++ ERI R A IA+ RPR Sbjct: 120 GKDIDWVIIRENSEGEYAGNGGRTHRGLPIETGTETAVFTRAGVERIHRFAFEIAQKRPR 179 Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223 K L + K+N ++ + EVAKD+P V V +VD ++V++P DV+V T Sbjct: 180 KHLTLVTKSNAQRFGMVMWDEIFYEVAKDYPDVKVDRELVDAVTTRMVLKPHTLDVVVAT 239 Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIGDTT---AVFEPVHGSAPDIAGKGIANPTAAILS 280 NL DILSDLAA L G LG+AP+ N+ ++FEP+HGSA DI GKG+ANP A + Sbjct: 240 NLHADILSDLAAALSGSLGIAPTANLNPERLFPSMFEPIHGSAFDITGKGVANPIATFWT 299 Query: 281 AAMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 AAMML++LGEK AA+R+ A++ + G TPDLGG ATT + TEA+ + L Sbjct: 300 AAMMLEHLGEKPAAERLMAAIEQITANGVFTPDLGGHATTASVTEAICKVL 350 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: 288 Number of extensions: 19 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: 358 Length adjustment: 29 Effective length of query: 305 Effective length of database: 329 Effective search space: 100345 Effective search space used: 100345 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