Align Homoisocitrate dehydrogenase; HICDH; Homo(2)-isocitrate/homo(3)-isocitrate dehydrogenase; Isohomocitrate dehydrogenase; IHDH; NAD-dependent threo-isohomocitrate dehydrogenase; EC 1.1.1.87; EC 1.1.1.- (characterized)
to candidate 3610012 Dshi_3393 3-isopropylmalate dehydrogenase (RefSeq)
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__Dino:3610012 Length = 357 Score = 199 bits (505), Expect = 1e-55 Identities = 134/352 (38%), Positives = 196/352 (55%), Gaps = 33/352 (9%) Query: 4 VCVIEGDGIGKEVIPEAIKILNELG------EFEIIKGEAGLECLKKYGNALPEDTIEKA 57 + V +GDGIG E++ + +L +L + G + G ALP +++ A Sbjct: 6 ITVFDGDGIGPEIMAPTLGLLRKLAGTAATYDLNFDSHPMGAGHYAQTGQALPRASLDAA 65 Query: 58 KEADIILFGAITSPKPGEVKNYK-SPIITLRKMFHLYANVRPINNFGIGQLIGKIADYEF 116 + +D IL A+ P + +P I +R LYA VRP+ Sbjct: 66 RASDAILLSAMGLPDIRYPDGTEITPQIDIRIALDLYAGVRPVRIVP--------GHPTP 117 Query: 117 LNAKN-IDIVIIRENTEDLY--VGRERLENDTAIAERVITRKGSERIIRFAFEYAIKNNR 173 L+A +D V+IRE+TE L+ G+ + D A ITR SE++ RFAF A + Sbjct: 118 LHAPGPVDFVLIRESTEGLFHTKGKGTVTKDHATETLQITRDTSEKLFRFAFALAAQRKA 177 Query: 174 K-----KVSCIHKANVLRITDGLFLEVFN-EIKKHYNIEADDYLVDSTAMNLIKHPEKFD 227 +V+C+ KANV R F E+F+ E +H ++ AD VD+ A+ ++ P+ FD Sbjct: 178 SGRGEGRVTCVDKANVFRAF-AFFREIFDAEAARHPDLIADHAYVDAMALWMVTRPQTFD 236 Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGDDKALFEPVHGSAPDIAGKGIANPMASI 287 V+VT NMFGDILSD + L+GGLGLAPSA+IGDD A+F+P HG+APDIAG+GIANP+A I Sbjct: 237 VMVTENMFGDILSDLGAGLMGGLGLAPSADIGDDNAVFQPCHGTAPDIAGRGIANPLAMI 296 Query: 288 LSIAMLFDYIGEKEK-------GDLIREAVKYCLINKKV-TPDLGGDLKTKD 331 LS AM+ D++ + + G +REAV+ L +V T DLGG+ T++ Sbjct: 297 LSAAMMLDWLALRGQNAELATDGQRLREAVEAVLTEGRVLTRDLGGNASTEE 348 Lambda K H 0.319 0.140 0.397 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: 310 Number of extensions: 16 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: 347 Length of database: 357 Length adjustment: 29 Effective length of query: 318 Effective length of database: 328 Effective search space: 104304 Effective search space used: 104304 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