Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_086508767.1 BZY95_RS04410 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_002151265.1:WP_086508767.1 Length = 359 Score = 215 bits (547), Expect = 2e-60 Identities = 142/358 (39%), Positives = 200/358 (55%), Gaps = 33/358 (9%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVL---EATGLPLEFVEAEAGWETFERRGTSVPEETVE 57 M +I ++ GDGIG E+ A R+L +A GL +E + G ++ G +P T++ Sbjct: 1 MTRKILVLPGDGIGPEITAEASRILAACQAHGLDIEIEQGLVGGSAYDEHGEPLPAVTLD 60 Query: 58 KILSCHATLFGAATSPT---------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGS 108 K + A L GA P R G G LR+ L L+AN+RPA + P S Sbjct: 61 KAKAADAILLGAVGGPKWDKLEDLAKRPEKGLLG----LRKNLGLFANLRPAITYPQLAS 116 Query: 109 RP--------GVDLVIVRENTEGLYVEQERRY-----LDVAIADAVISKKASERIGRAAL 155 G+D++IVRE T G+Y Q R V + S+ ERIGR A Sbjct: 117 ASSLKPELVAGLDIMIVRELTGGIYFGQPRGIEVRDGQRVGFNTYIYSESEIERIGRVAF 176 Query: 156 RIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPE 215 +A+ R ++ + KANVL +T L+ + ++ +A ++P V + + VDN AMQLV P+ Sbjct: 177 ELAQKRGKRLCSV-DKANVLEVTI-LWREVMERLAPEYPDVELSHMYVDNAAMQLVRAPK 234 Query: 216 RFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDT-TAVFEPVHGSAPDIAGKGIANP 274 +FDV+VT N+ GDILSD AA L G +G+ PS ++ ++ ++EP HGSAPDIAGKGIANP Sbjct: 235 QFDVMVTGNMFGDILSDAAAMLTGSIGMLPSASLNESGQGMYEPCHGSAPDIAGKGIANP 294 Query: 275 TAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 A ILS AMML Y LGE E A R+E AV VL+ G RT D+ + T T + +A+ Sbjct: 295 LATILSVAMMLRYSLGEPEFAGRIEAAVGKVLDDGLRTADIASEGTRTVSTREMGDAV 352 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: 297 Number of extensions: 18 Number of successful extensions: 7 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: 359 Length adjustment: 29 Effective length of query: 305 Effective length of database: 330 Effective search space: 100650 Effective search space used: 100650 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