Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate 6938304 Sama_2423 isocitrate dehydrogenase (RefSeq)
Query= BRENDA::Q945K7 (374 letters) >FitnessBrowser__SB2B:6938304 Length = 336 Score = 329 bits (844), Expect = 6e-95 Identities = 165/332 (49%), Positives = 227/332 (68%), Gaps = 3/332 (0%) Query: 45 TATLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPRTQSFLTWESLESVRRNK 104 T T+ PGDGIGP I +S K+ AG E+E G + L +L+ + +N+ Sbjct: 5 TITVIPGDGIGPSIIDSALKILDKAGCDFEYEFADAGLTALEKHGELLPQRTLDLIEKNR 64 Query: 105 VGLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSLPGYKTRYDDVDLITIRENTEGE 164 + LKGP+ TP+G+G S+N+TLRK+ +LYANVRP S G + RY+++D+IT+RENTEG Sbjct: 65 ITLKGPLTTPVGEGFTSINVTLRKKFSLYANVRPVNSFKGTQARYENIDIITVRENTEGM 124 Query: 165 YSGLEHQVVR--GVVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIMQKTDGL 222 YSG +V E+ IITRQ + ++ +A+ A+ GR++V+ +HKANIM+ T GL Sbjct: 125 YSGYGQKVSDDGSTAEATSIITRQGAEQITTFAYELARKEGRKKVTIVHKANIMKSTSGL 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+ V ML +L ++A I +A Sbjct: 245 GMAPGANIGA-SAAIFEAVHGSAPDIAGKNLANPTSVILASVQMLEYLGMADKAAAIRNA 303 Query: 343 IINTIAEGKYRTADLGGSSTTTEFTKAICDHL 374 + I EG T DLGG+ TT+FT+A+ D L Sbjct: 304 VAAVIEEGDRTTRDLGGTHGTTDFTQAVLDRL 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: 319 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: 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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