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 CA265_RS15850 CA265_RS15850 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__Pedo557:CA265_RS15850 Length = 363 Score = 196 bits (497), Expect = 1e-54 Identities = 136/372 (36%), Positives = 200/372 (53%), Gaps = 47/372 (12%) Query: 4 VCVIEGDGIGKEVIPEAIKILNELGEF--------EIIKGEAGLECLKKYGNALPEDTIE 55 + VI GDGIG EV L ++ E E + G A +E G LP++T+E Sbjct: 5 ILVIPGDGIGPEVTTWGKAALEKIAEIFGHEFAFEEALMGHAAIEVT---GEPLPDETLE 61 Query: 56 KAKEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIGKI 111 KA+++D ILFGAI K P + ++ +RK L+AN+RPI F Sbjct: 62 KARQSDAILFGAIGHAKYDNDPSLKVRPEQGLLKIRKELGLFANLRPILLFD-------- 113 Query: 112 ADYEFLNAKNI--------DIVIIRENTEDLYVGRERLEND--TAIAERVITRKGSERII 161 E L A +I DI+ RE T D+Y G + D TA + R ERI Sbjct: 114 ---ELLQASSIKPEILRGTDILFFRELTGDVYFGEKTRSEDRNTASDLMIYHRYEVERIA 170 Query: 162 RFAFEYAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLI 220 A++ A + N K++ + KANVL + L+ E EI K Y ++E + +D+ AM LI Sbjct: 171 HKAYQAAQQRN-KRLCSVDKANVLE-SSRLWRETVQEIAKQYPDVETEHMFIDNAAMQLI 228 Query: 221 KHPEKFDVIVTTNMFGDILSDEASALIGGLGLAPSANIGDDKALFEPVHGSAPDIAGKGI 280 K+P+KFDV++T N+FGDIL+DEAS + G +G+ SA++G+ FEP+HGSA DIAGK + Sbjct: 229 KNPKKFDVVLTANLFGDILTDEASQIAGSMGMLASASVGESTGFFEPIHGSAHDIAGKDL 288 Query: 281 ANPMASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDLGGD-------LKTKDV 332 ANP+ASILS A++ + G KE+ L+ + + L T D+ L T ++ Sbjct: 289 ANPLASILSAALMLEIGFGLKEEAKLLVDTIDQVLKEGFRTHDIADQSTNRFKVLGTAEM 348 Query: 333 GDEILNYIRKKL 344 G +L ++ +KL Sbjct: 349 GKLVLKFLSQKL 360 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: 317 Number of extensions: 20 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: 363 Length adjustment: 29 Effective length of query: 318 Effective length of database: 334 Effective search space: 106212 Effective search space used: 106212 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 Jul 25 2024. The underlying query database was built on Jul 25 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