Align Homoisocitrate dehydrogenase; HICDH; EC 1.1.1.87 (characterized)
to candidate WP_086510509.1 BZY95_RS13880 isocitrate/isopropylmalate dehydrogenase family protein
Query= SwissProt::O14104 (362 letters) >NCBI__GCF_002151265.1:WP_086510509.1 Length = 363 Score = 192 bits (488), Expect = 1e-53 Identities = 125/368 (33%), Positives = 190/368 (51%), Gaps = 31/368 (8%) Query: 7 IVLGLIPADGIGKEVVPAARRLMENLPAKHKLKFDFIDLDAGWGTFERTGKALPERTVER 66 + LG++ D IG E+VPAA + + + L D+ + G + G +P+ T+E Sbjct: 6 LTLGVLNGDDIGHEIVPAAVEVAQAAAERCGLVIDWRHMPLGRKALDEFGTTMPDGTLET 65 Query: 67 LKTECNAALFGAVQSPTHKVAGYSSPIVALRKKMGLYANVRPVKSLD--GAKGKPVDLVI 124 L T L KV G +P LRK L+ANVRP +S G +DLVI Sbjct: 66 LSTFDGFILGPIGHREYPKVEGAINPHPILRKHFDLFANVRPTRSYPDIGCIYDDIDLVI 125 Query: 125 VRENTECLYVKEERMVQNT----PGKRVAEAIRRISEEASTKIGKMAFEIAKSRQKIRES 180 VREN E + + +V + P + V ++R I+ E S K+ A E+A++R K Sbjct: 126 VRENNEG-FQPDRNVVAGSGEFRPTEDVTISVRVITREGSRKVATAALELARARNK---- 180 Query: 181 GTYSIHKKPLVTIIHKSNVMSVTDGLFRESCRHAQSLDPSYASINVDEQIVDSMVYRLFR 240 +T++HK+ V + G+F E C A +Y + VDE IVD+ L R Sbjct: 181 ---------RLTVVHKNTVYKLGCGMFVEECYKAAE---AYPDVKVDEAIVDTFAMHLIR 228 Query: 241 EPECFDVVVAPNLYGDILSDGAASLIGSLGLVPSANVG-DNFVMSEPVHGSAPDIAGRGI 299 P+ +DVVV N++GDIL+D AA L+G LG+ P +G N M++ HGSAPDIAG G+ Sbjct: 229 NPQQYDVVVTTNMFGDILTDEAAGLVGGLGMAPGLCIGRGNMAMAQATHGSAPDIAGTGL 288 Query: 300 ANPVATFRSVALMLEFMGH-------QDAAADIYTAVDKVLTEGKVLTPDLGGKSGTNEI 352 ANP A S +++E++G Q AAA + + L + + TPD+ G+ +++ Sbjct: 289 ANPYAMIESTRMLIEWLGRRHELPGAQAAAALMAKGIQAALADPRTRTPDIRGQGRLSDM 348 Query: 353 TDAVLANI 360 + +LA I Sbjct: 349 VNGMLAAI 356 Lambda K H 0.317 0.134 0.380 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: 315 Number of extensions: 16 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: 362 Length of database: 363 Length adjustment: 29 Effective length of query: 333 Effective length of database: 334 Effective search space: 111222 Effective search space used: 111222 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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