Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate WP_019868382.1 METMI_RS0121605 isocitrate/isopropylmalate dehydrogenase family protein
Query= BRENDA::Q945K7 (374 letters) >NCBI__GCF_000384075.1:WP_019868382.1 Length = 336 Score = 323 bits (827), Expect = 6e-93 Identities = 167/330 (50%), Positives = 222/330 (67%), Gaps = 5/330 (1%) Query: 45 TATLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPRTQSFLTWESLESVRRNK 104 T TL GDGIGP I + KV GV I WEE Y G + + L E++ S + + Sbjct: 3 TITLIKGDGIGPSIMDEAVKVIDATGVKITWEETYAGMSAFEKFGTPLPDETMASFDKTR 62 Query: 105 VGLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSLPGYKTRYDDVDLITIRENTEGE 164 V KGP+ T +G G RS+N+ LR++ +LYANVRP S G KTR++DVD++ +RENTEG Sbjct: 63 VAFKGPLTTVVGTGFRSINVALRQKYDLYANVRPAKSWAGIKTRFEDVDIVIVRENTEGL 122 Query: 165 YSGLEHQVV--RGVVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIMQKTDGL 222 Y+GLEH + + + ESL ++TR AS R+ +YAF YA+ + R++V+ HKANI++ T GL Sbjct: 123 YAGLEHYLTPKKDIAESLAVVTRAASERIIDYAFQYARDNHRQKVTVCHKANILKYTQGL 182 Query: 223 FLKCCREVAEKYPEITYEEVVIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLVGGL 282 FL RE+A +YP+I ++E +ID CM +V NP FDV+V N++GDI+SDL AGLVGGL Sbjct: 183 FLDVAREIAPRYPDIQFDEKIIDAACMHMVMNPKQFDVVVTTNMFGDILSDLTAGLVGGL 242 Query: 283 GLTPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMMLRHLKFNEQAEQIHSA 342 GL P NIG D AL EAVHGSAPDIAGKNLANP A++++G MML H+ E AE++ A Sbjct: 243 GLIPGANIGSD-AALFEAVHGSAPDIAGKNLANPIAVIMAGAMMLSHIGEVEAAERVVKA 301 Query: 343 IINTIAEGKYRTADLGGSST--TTEFTKAI 370 + + EG Y T DL +S TTE AI Sbjct: 302 VEKVVNEGVYVTPDLNPNSKVGTTEMGSAI 331 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: 345 Number of extensions: 12 Number of successful extensions: 3 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: 336 Length adjustment: 29 Effective length of query: 345 Effective length of database: 307 Effective search space: 105915 Effective search space used: 105915 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: 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