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 SMa1846 SMa1846 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__Smeli:SMa1846 Length = 347 Score = 181 bits (458), Expect = 3e-50 Identities = 117/324 (36%), Positives = 184/324 (56%), Gaps = 26/324 (8%) Query: 4 VCVIEGDGIGKEVIPEAIKILNELGE---FEIIKGEAGLECL--KKYGNALPEDTIEKAK 58 + +I GDGIG++V A ++L+ + F + C K+ G +P D IE + Sbjct: 6 IALIPGDGIGQDVTDAAWQVLSTVARHSGFTLTGTSFPWSCAFYKETGAMMPADGIEALR 65 Query: 59 EADIILFGAITSPK--PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIGKIADYEF 116 D IL G++ P P + + ++ +RK F YAN+RP +L+ + Sbjct: 66 PFDAILLGSVGWPAEVPDSISLH-GLLLPIRKAFVQYANIRP------HRLLSGVEGP-- 116 Query: 117 LNAKNIDIVIIRENTEDLYVG-----RERLENDTAIAERVITRKGSERIIRFAFEYAIKN 171 L A + DI+ +RENTE Y G + ++ A+ + TR G ERI+RFAFE A + Sbjct: 117 LKASDFDILCVRENTEGEYSGAGGRVHQGTADEVAVETSIFTRAGVERILRFAFEQA-RQ 175 Query: 172 NRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFDVIV 230 R K++ + K+N + + + EV ++ Y ++E Y +D+ A ++ PE DV+V Sbjct: 176 RRGKLASVTKSNAQKHSMVFWDEVTRQLADEYPDVEVTSYHIDAMAARVVMAPESLDVVV 235 Query: 231 TTNMFGDILSDEASALIGGLGLAPSANIGDDK---ALFEPVHGSAPDIAGKGIANPMASI 287 +N+FGDIL+D +A+ GGLG A SANI D+ ++FEPVHGSAPDIA GIANP+A+I Sbjct: 236 ASNLFGDILTDLGAAIQGGLGFAASANINPDRSAPSMFEPVHGSAPDIAHLGIANPIAAI 295 Query: 288 LSIAMLFDYIGEKEKGDLIREAVK 311 S AM+ +++GE+E +I A++ Sbjct: 296 WSGAMMLEHLGEREAAGMIMAALE 319 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: 264 Number of extensions: 11 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: 347 Length adjustment: 29 Effective length of query: 318 Effective length of database: 318 Effective search space: 101124 Effective search space used: 101124 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