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 WP_072905195.1 BUB13_RS02510 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >NCBI__GCF_900142125.1:WP_072905195.1 Length = 362 Score = 196 bits (499), Expect = 6e-55 Identities = 139/358 (38%), Positives = 199/358 (55%), Gaps = 27/358 (7%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57 KV V+ GDGIG EV+ EA+K+L+ + + FE G + G ALP+ T+E Sbjct: 6 KVAVLPGDGIGPEVMAEALKVLDAIEKKYDVSFERTTANVGGAGIDNEGKALPDSTVEIC 65 Query: 58 KEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIGKIAD 113 K +D ILFG++ PK P + + + ++ LRK+F L+ N+RP F L G + Sbjct: 66 KASDAILFGSVGGPKWESLPPDEQPERGALLPLRKIFGLFCNLRPAIIFPA--LTGASSL 123 Query: 114 YEFLNAKNIDIVIIRENTEDLYVGRER-LENDTAIAERVITRKGS----ERIIRFAFEYA 168 E + D++++RE T +Y + +E + A T K S ERI AFE A Sbjct: 124 KEEVIEGGFDLLVVRELTGGIYFAEPKGIEGEGAARTGFDTMKYSDAEVERITHVAFEAA 183 Query: 169 IKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFD 227 K KKV I KANVL T L+ EV + K Y ++E VD+ AM L+K P++FD Sbjct: 184 RKRG-KKVCSIDKANVLS-TSVLWREVVERVAKEYPDVELSHMYVDNAAMQLVKWPKQFD 241 Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGDDK-ALFEPVHGSAPDIAGKGIANPMAS 286 V++ NMFGDI+SDEA+ L G LG+ PSA++ + ++EP GSAPDIAG+GIANP+A Sbjct: 242 VMLCGNMFGDIISDEAAMLTGSLGMLPSASLAEGSFGMYEPSGGSAPDIAGQGIANPIAQ 301 Query: 287 ILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL------GGDLKTKDVGDEIL 337 ILS +M+ Y G E D I AV+ L + T D+ + T ++GD I+ Sbjct: 302 ILSASMMLRYSFGMIEAADAIDAAVEKTLNDGYRTGDIYQGTASEKKVNTAEIGDAII 359 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: 315 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: 362 Length adjustment: 29 Effective length of query: 318 Effective length of database: 333 Effective search space: 105894 Effective search space used: 105894 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