Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate 3610012 Dshi_3393 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::P33197 (496 letters) >FitnessBrowser__Dino:3610012 Length = 357 Score = 190 bits (483), Expect = 6e-53 Identities = 138/360 (38%), Positives = 196/360 (54%), Gaps = 34/360 (9%) Query: 22 ITVIPGDGIGPECVEATLKVLE-----AAKAPLAYEVREAGASVFRRGIASGVPQETIES 76 ITV GDGIGPE + TL +L AA L ++ GA + + +P+ ++++ Sbjct: 6 ITVFDGDGIGPEIMAPTLGLLRKLAGTAATYDLNFDSHPMGAGHYAQ-TGQALPRASLDA 64 Query: 77 IRKTRVVLKGPLETP-VGYG---EKSANVTLRKLFETYANVRPVREFPNVPTPYAGRG-I 131 R + +L + P + Y E + + +R + YA VRPVR P PTP G + Sbjct: 65 ARASDAILLSAMGLPDIRYPDGTEITPQIDIRIALDLYAGVRPVRIVPGHPTPLHAPGPV 124 Query: 132 DLVVVRENVEDLY--AGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELA-------RAEG 182 D V++RE+ E L+ G + +TL+ I+ SEK+ RFAF LA R EG Sbjct: 125 DFVLIRESTEGLFHTKGKGTVTKDHATETLQ-ITRDTSEKLFRFAFALAAQRKASGRGEG 183 Query: 183 RKKVHCATKSNIMKLAEGTLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVT 242 R V C K+N+ + A + F+ A +PD+ A H VD A +V RP+ F+V+VT Sbjct: 184 R--VTCVDKANVFR-AFAFFREIFDAEAARHPDLIADHAYVDAMALWMVTRPQTFDVMVT 240 Query: 243 TNMNGDILSDLTSGLIGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAV 302 NM GDILSDL +GL+GGLG APSA+IG++ A+F+ HG+AP AG+ + NP A++LSA Sbjct: 241 ENMFGDILSDLGAGLMGGLGLAPSADIGDDNAVFQPCHGTAPDIAGRGIANPLAMILSAA 300 Query: 303 MMLRYL------EEFAT-ADLIENALLYTLEEGRVLTGDVVGYDRGAKTTEYTEAIIQNL 355 MML +L E AT + A+ L EGRVLT D+ G A T E A+ L Sbjct: 301 MMLDWLALRGQNAELATDGQRLREAVEAVLTEGRVLTRDLGG---NASTEEAAAAVAAKL 357 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: 414 Number of extensions: 28 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: 357 Length adjustment: 32 Effective length of query: 464 Effective length of database: 325 Effective search space: 150800 Effective search space used: 150800 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: 50 (23.9 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