Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate 5210317 Shew_2760 isocitrate dehydrogenase (RefSeq)
Query= BRENDA::Q945K7 (374 letters) >FitnessBrowser__PV4:5210317 Length = 335 Score = 333 bits (853), Expect = 5e-96 Identities = 164/332 (49%), Positives = 230/332 (69%), Gaps = 3/332 (0%) Query: 45 TATLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPRTQSFLTWESLESVRRNK 104 T T+ PGDGIGP I +S K+ AG E+E G + L +L+ + +N+ Sbjct: 5 TITVIPGDGIGPSIIDSAIKILDKAGCDFEYEFADAGLAALEKQGELLPQRTLDMIEKNR 64 Query: 105 VGLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSLPGYKTRYDDVDLITIRENTEGE 164 + LKGP+ TP+G+G S+N+TLRK+ LYANVRP S G + RYD++D+IT+RENTEG Sbjct: 65 ITLKGPLTTPVGEGFTSINVTLRKKFGLYANVRPVLSFKGTQARYDNIDIITVRENTEGM 124 Query: 165 YSGLEHQVVR--GVVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIMQKTDGL 222 YSGL V E+ IITRQ + ++ +A+ A+ GR++V+ +HKANIM+ T GL Sbjct: 125 YSGLGQTVSEDGATAEATSIITRQGAEQITTFAYELARKEGRKKVTIVHKANIMKSTSGL 184 Query: 223 FLKCCREVAEKYPEITYEEVVIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLVGGL 282 FLK REV+++YP+IT EE+++D CM LV NP FDV+V NL+GDI+SDLCAGLVGGL Sbjct: 185 FLKVAREVSQRYPDITTEEMIVDATCMKLVMNPENFDVIVTTNLFGDILSDLCAGLVGGL 244 Query: 283 GLTPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMMLRHLKFNEQAEQIHSA 342 G+ P NIG++ A+ EAVHGSAPDIAGKNLANPT+++L+ + ML +L +++A+ I +A Sbjct: 245 GMAPGANIGKN-AAIFEAVHGSAPDIAGKNLANPTSVILASIQMLEYLGMSDKAQAIRAA 303 Query: 343 IINTIAEGKYRTADLGGSSTTTEFTKAICDHL 374 + I EG T DLGG+ T++FT+A+ + L Sbjct: 304 VSAVIEEGDRTTRDLGGTHGTSDFTQAVLERL 335 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: 320 Number of extensions: 11 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: 335 Length adjustment: 29 Effective length of query: 345 Effective length of database: 306 Effective search space: 105570 Effective search space used: 105570 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 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