Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate WP_005456797.1 SACCYDRAFT_RS13140 isocitrate dehydrogenase
Query= BRENDA::Q945K7 (374 letters) >NCBI__GCF_000244975.1:WP_005456797.1 Length = 481 Score = 258 bits (659), Expect = 2e-73 Identities = 150/344 (43%), Positives = 210/344 (61%), Gaps = 12/344 (3%) Query: 39 SSTTPITATLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEI-DPRTQSFLTWESL 97 S++ PIT GDGIGPEI E+ V AG ++ + +G + + +T E+L Sbjct: 5 STSAPITVA--HGDGIGPEIMEATLSVLNAAGAALDIDTITIGESVYQAGNPAGVTPEAL 62 Query: 98 ESVRRNKVGLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSL-PGYKTRYDDVDLIT 156 ES+RR V LK P+ TP G G +SLN+T+RK LYANVRPC + P T++ +D++ Sbjct: 63 ESIRRTGVFLKAPITTPQGGGFKSLNVTVRKTFGLYANVRPCVAYAPFVATKHPGMDVVI 122 Query: 157 IRENTEGEYSGLEHQVVRGVVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIM 216 +REN E Y+G+EH+ VV+ LK+I+RQ RV YAF YA + R +V+A K NIM Sbjct: 123 VRENEEDLYAGIEHRQTDEVVQCLKLISRQGCERVIRYAFEYATAYRRTKVTAFTKDNIM 182 Query: 217 QKTDGLFLKCCREVAEKYPEITYEEVVIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCA 276 + TDGLF + EVA YP+I E ++D L P FDV+V+PNLYGDI+SD+ A Sbjct: 183 KMTDGLFHRVFDEVAADYPDIQAEHWIVDIGAAKLADTPEAFDVVVLPNLYGDILSDVAA 242 Query: 277 GLVGGLGLTPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMMLRHLKFNEQA 336 + G +GL S NIGE VA+ EA+HGSAP AG+++ANP+ LLL+ V ML H+ + A Sbjct: 243 QIAGSVGLAGSANIGE-RVAMFEAIHGSAPRRAGQDVANPSGLLLAAVQMLVHIGQADVA 301 Query: 337 EQIHSAIINTIAEGKYRTADLGGSST------TTEFTKAICDHL 374 ++H+A + TI +G T D+ T TT F ++ D L Sbjct: 302 SRVHNAWLRTIEDG-IHTYDIYEPDTSTSKVGTTAFAASVIDRL 344 Lambda K H 0.318 0.134 0.389 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: 437 Number of extensions: 22 Number of successful extensions: 4 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: 374 Length of database: 481 Length adjustment: 32 Effective length of query: 342 Effective length of database: 449 Effective search space: 153558 Effective search space used: 153558 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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