Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate AZOBR_RS11025 AZOBR_RS11025 isocitrate dehydrogenase
Query= BRENDA::P33197 (496 letters) >FitnessBrowser__azobra:AZOBR_RS11025 Length = 481 Score = 343 bits (880), Expect = 8e-99 Identities = 212/481 (44%), Positives = 291/481 (60%), Gaps = 20/481 (4%) Query: 22 ITVIPGDGIGPECVEATLKVLEAAKAPLAYEVREAGASVFRRGIASGVPQETIESIRKTR 81 ITV GDGIGPE +A L V+EAA A L E AG V+RRG G+ SIR+TR Sbjct: 7 ITVARGDGIGPEITDAVLHVMEAAGARLKVEEVPAGEQVYRRGHLGGLDAAGWGSIRRTR 66 Query: 82 VVLKGPLETPVGYGEKSANVTLRKLFETYANVRP-VREFPNVPTPYAGRGIDLVVVRENV 140 V LKGP+ TP GYG KS NVT R +ANVRP V P V T + +D+V++REN Sbjct: 67 VFLKGPITTPQGYGNKSLNVTARTTLGLFANVRPCVSHHPYVRTRHPR--MDVVIIRENE 124 Query: 141 EDLYAGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELARAEGRKKVHCATKSNIMKLAEG 200 EDLYAGIEH QT V Q++KLIS GSE+IVR+AF+ ARA R+KV K N+MK+ +G Sbjct: 125 EDLYAGIEHRQTDDVIQSVKLISRPGSERIVRYAFDYARANHRRKVTAFVKDNVMKMTDG 184 Query: 201 TLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVTTNMNGDILSDLTSGLIGG 260 + F ++A EYP+I+A H+IVD A +L +PE+F+VIVT N+ GDI+SD+ + + G Sbjct: 185 LFLKIFNEIAAEYPEIKADHLIVDIGAARLADQPERFDVIVTLNLYGDIVSDIAAQITGS 244 Query: 261 LGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAVMMLRYLEEFATADLIENA 320 +G A SANIG+ A+FEA+HGSAP AG+ + NP+ +L++AVMML ++ + A I NA Sbjct: 245 VGLAGSANIGDACAMFEAIHGSAPMIAGQGIANPSGLLMAAVMMLVHIGQGDVAARIHNA 304 Query: 321 LLYTLEEGRVLTGDVVGYDRGAK-----TTEYTEAIIQNLGKTPRKTQVRGYKPFRLPQV 375 L T+E+G V T D+ ++RG T + +A+++ LG+ P GY P Sbjct: 305 WLKTIEDG-VHTVDI--FNRGVSRQRVGTHAFADAVVERLGQMPVTLPTVGYAVTARPAY 361 Query: 376 DGAIAPIVPRSRRV---VGVDVFVE-TNLLPEALGKALEDLAAGTP-FRLKMISNRGTQV 430 + + + PR + V VGVDVF+ P+ L + L TP RL ISNR +V Sbjct: 362 ESGVR-LSPRRKAVKELVGVDVFLHWPGGNPDELAGLV--LPVATPALRLSSISNRSQKV 418 Query: 431 YPPTGGLTDLVDHYRCRFLYTGEGEAKDPEILDLVSRVA-SRFRWMHLEKLQEFDGEPGF 489 +P DH+RCRFL P+I++L+S +A + + E L FDG+ GF Sbjct: 419 WPEGNIGVFCTDHWRCRFLAPEGVAVGHPDIVELLSGLARAGLDFTQTENLCNFDGKSGF 478 Query: 490 T 490 + Sbjct: 479 S 479 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: 618 Number of extensions: 32 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: 496 Length of database: 481 Length adjustment: 34 Effective length of query: 462 Effective length of database: 447 Effective search space: 206514 Effective search space used: 206514 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 Apr 09 2024. 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