Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate Echvi_4068 Echvi_4068 isocitrate dehydrogenase
Query= BRENDA::P33197 (496 letters) >FitnessBrowser__Cola:Echvi_4068 Length = 487 Score = 365 bits (937), Expect = e-105 Identities = 213/495 (43%), Positives = 303/495 (61%), Gaps = 29/495 (5%) Query: 19 RKLITVIPGDGIGPECVEATLKVLEAAKAPLAYEVREAGASVFRRGIASGVPQETIESIR 78 ++ ITV GDGIGPE ++ATL++LEAA A + EV E G V+ +GI+SG+ + +S+R Sbjct: 4 KRKITVAYGDGIGPEIMKATLEILEAAGAQIEPEVIEIGEQVYLKGISSGIEPKAWDSLR 63 Query: 79 KTRVVLKGPLETPVGYGEKSANVTLRKLFETYANVRPVREF-PNVPTPYAGRGIDLVVVR 137 +T++ LK P+ TP G G KS NVT RK YANVRP + + P + T + D+V+VR Sbjct: 64 ETKIFLKSPITTPQGGGFKSLNVTTRKTLGLYANVRPCKAYSPYIRTHFPET--DMVIVR 121 Query: 138 ENVEDLYAGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELARAEGRKKVHCATKSNIMKL 197 EN EDLYAGIEH QT V Q LKLIS GSEKI+R+AFE A+ RKKV C TK NIMKL Sbjct: 122 ENEEDLYAGIEHRQTDDVYQCLKLISRPGSEKIIRYAFEYAKKYNRKKVTCMTKDNIMKL 181 Query: 198 AEGTLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVTTNMNGDILSDLTSGL 257 A+G + F VA+EYP+IEA H I+D + +PE F+VIVT N+ GDI+SD+ + + Sbjct: 182 ADGLFHKVFNDVAKEYPEIEADHKIIDIGTALIADKPEMFDVIVTLNLYGDIISDVAAQI 241 Query: 258 IGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAVMMLRYLEEFATADLI 317 G +G S+N+G +VA+FEA+HGSAP AG+N+ NP+ +L A+MML ++ + A+ + Sbjct: 242 TGSVGLGGSSNVGEDVAMFEAIHGSAPDIAGQNIANPSGLLNGAIMMLVHIGQPEVAEKV 301 Query: 318 ENALLYTLEEGRVLTGDVVGYDRGAK-----TTEYTEAIIQNLGKTPRKTQVRGYKPFRL 372 NA + TLE+G + TGD+ Y G T E+ +A+I LG+ P K P Sbjct: 302 SNAWMKTLEDG-IHTGDI--YQEGVSSQLVGTKEFAQAVIDRLGQKPEK-----MVPAEF 353 Query: 373 PQVDGA--------IAPIVPRSRRVVGVDVFV---ETNLLPEALGKALEDLAAGTPFRLK 421 + DGA +A P + ++G+DVF+ E + +G L + A +++ Sbjct: 354 KKGDGADDNMGAIKLADRKPCKKDLIGLDVFIDWKENDRDANVIGDKLRAVDA-DGLKMQ 412 Query: 422 MISNRGTQVYPPTGGLTDLVDHYRCRFLYTGEGEAKDPEILDLVSRVAS-RFRWMHLEKL 480 +I+NRG +VYP T DH+R RF + ++LD++ +V F ++ E L Sbjct: 413 LITNRGVKVYPDGMKETFCSDHWRVRFFNADQSTITHGQVLDVLKQVEDLGFDFIKTENL 472 Query: 481 QEFDGEPGFTKAQGE 495 FDGE GF+ AQGE Sbjct: 473 YTFDGERGFSLAQGE 487 Lambda K H 0.317 0.136 0.390 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: 639 Number of extensions: 39 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: 496 Length of database: 487 Length adjustment: 34 Effective length of query: 462 Effective length of database: 453 Effective search space: 209286 Effective search space used: 209286 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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