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_074201047.1 BUQ81_RS03680 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >NCBI__GCF_900141795.1:WP_074201047.1 Length = 357 Score = 204 bits (518), Expect = 4e-57 Identities = 136/341 (39%), Positives = 199/341 (58%), Gaps = 28/341 (8%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57 KV V+ GDGIG E+ +A+K+L L + E+ + G G+ LPE T++ A Sbjct: 4 KVLVLPGDGIGPEITEQAVKVLKRLSDEGAIDIEMEEALVGGAAYDAEGSPLPESTMQLA 63 Query: 58 KEADIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADY 114 +EAD IL GA+ P+ ++ K P ++ LR L+AN+RP L ++A Sbjct: 64 READAILLGAVGGPQYDDLPRDKRPEKGLLGLRSGLGLFANLRP------AMLYPQLAHA 117 Query: 115 EFLNAK---NIDIVIIRENTEDLYVGRER----LENDTAIAERVITRKGSE--RIIRFAF 165 L + +DI+I+RE T +Y G+ R LEN SE RI AF Sbjct: 118 SSLKPEVVSGLDILIVRELTGGIYFGQPRGIRTLENGEREGFNTYVYSESEIKRIAHVAF 177 Query: 166 EYAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPE 224 + A K N KKV+ I K+NVL +T+ L+ EV E+ K Y ++ + LVD+ AM L++ P+ Sbjct: 178 QAAQKRN-KKVTSIDKSNVLEVTE-LWKEVVTEVAKDYPDVTLEHMLVDNAAMQLVRWPK 235 Query: 225 KFDVIVTTNMFGDILSDEASALIGGLGLAPSANIGDD-KALFEPVHGSAPDIAGKGIANP 283 +FDV++T NMFGDILSDEAS L G +G+ PSA++ ++ K ++EP HGSAPDIAG+ IANP Sbjct: 236 QFDVMLTGNMFGDILSDEASMLTGSIGMLPSASLNEENKGMYEPSHGSAPDIAGQDIANP 295 Query: 284 MASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL 323 +A+ILS AM+ Y +G +++ I +AV L T D+ Sbjct: 296 LATILSAAMMLRYSLGAEDQAARIEQAVSKVLDQGLRTADI 336 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: 288 Number of extensions: 18 Number of successful extensions: 5 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 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