Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_011868824.1 MMARC5_RS05395 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_000016125.1:WP_011868824.1 Length = 330 Score = 306 bits (783), Expect = 6e-88 Identities = 171/333 (51%), Positives = 219/333 (65%), Gaps = 12/333 (3%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSC 62 ++IC+IEGDGIG EV+PAA VL+ATG+ EF A AG E FE+ G ++PEET+ + Sbjct: 2 HKICVIEGDGIGKEVVPAAVEVLKATGIEFEFNYALAGDEVFEKTGVALPEETINAAKTA 61 Query: 63 HATLFGAATSPTRKVPGFFGAIRYLRRRLDLYANVRPAKS-RPVPGSRPGVDLVIVRENT 121 A LFGAA V I LR+ LD YAN+RP KS + + G+D +IVRENT Sbjct: 62 DAVLFGAAGETAADV------IVKLRKILDTYANIRPVKSYNGINCLKTGIDYIIVRENT 115 Query: 122 EGLYVEQERRYLD-VAIADAVISKKASERIGRAALRIAEGRPRKTLHI----AHKANVLP 176 EGLY E + V +A VI+K+ASERI + A +A+ R + AHKANVL Sbjct: 116 EGLYKGIESEITEGVTVATRVITKEASERIFKHAFEMAKDRKSTGKEVKVTCAHKANVLK 175 Query: 177 LTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAAG 236 +T GLF T EV+KD+ + +D VD M ++ RPE FD++VT+NL GDILSD A G Sbjct: 176 ITDGLFKKTFYEVSKDYEDIKTEDFYVDAMNMYIISRPETFDIVVTSNLFGDILSDGAVG 235 Query: 237 LVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKR 296 +VGGLG+APSGN+GD +FEP+HGSAPDIAGKG+ANPTA IL+A MML YL E AA + Sbjct: 236 MVGGLGMAPSGNVGDDYGLFEPIHGSAPDIAGKGLANPTATILTAVMMLRYLKENGAADK 295 Query: 297 VEKAVDLVLERGPRTPDLGGDATTEAFTEAVVE 329 VEKA++ VL G TPDLGG +T + V + Sbjct: 296 VEKALEEVLSLGLTTPDLGGTLSTSEMGQEVAK 328 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: 301 Number of extensions: 9 Number of successful extensions: 4 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: 330 Length adjustment: 28 Effective length of query: 306 Effective length of database: 302 Effective search space: 92412 Effective search space used: 92412 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