Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate AO353_27690 AO353_27690 isocitrate dehydrogenase
Query= curated2:O29627 (326 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27690 Length = 418 Score = 139 bits (349), Expect = 2e-37 Identities = 108/364 (29%), Positives = 169/364 (46%), Gaps = 60/364 (16%) Query: 4 IVVIPGDGIGKEVMEAAMLILEKL-------DLPFEYSYYDAGDEALEKYGKA--LPDET 54 I I GDGIG ++ + +++ + + AG++A + Y + LP ET Sbjct: 31 IPFIEGDGIGVDISPVMIKVVDAAVKKAYGGERKISWMEVYAGEKATQVYDQDTWLPQET 90 Query: 55 LEACRKSDAVLFGA----AGETAADVIVRLRRELGTFANVRPAKAIEGIECLY--PG-LD 107 L+A + + G G + V LR++L + +RP + EG+ PG +D Sbjct: 91 LDAVKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVRWFEGVPSPVKKPGDVD 150 Query: 108 IVVVRENTECLYMGFEFGFGD---------------VTE---------AIRVITREASER 143 + + REN+E +Y G E+ G VT+ I+ ++ E ++R Sbjct: 151 MTIFRENSEDIYAGIEWKAGSPEATKVIKFLKEEMGVTKIRFDQNCGIGIKPVSLEGTKR 210 Query: 144 IARYAFELAKREGRKKVTALHKANVMKKTCGLFRDVCREVAKDY---------PEIQYN- 193 +AR A + R +T +HK N+MK T G F++ EVA + P +Q+ Sbjct: 211 LARKALQYVVDNDRDSLTIVHKGNIMKFTEGAFKEWAYEVAAEEFGATLLDGGPWMQFKN 270 Query: 194 ----------DYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLVGGLGLAPSANV 243 D DA +++ P +DVI T N+ GD +SD A VGG+G+AP AN+ Sbjct: 271 PKTGKNVIVKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGANL 330 Query: 244 GERTAIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKKVEEAVEKTIKEGK 303 + A+FE HG A AGK NP ++IL+A MMLRH G+ E A + + I Sbjct: 331 SDTVAMFEATHGTAPKYAGKDQVNPGSLILSAEMMLRHMGWTEAADLIIKGTNGAISAKT 390 Query: 304 KTPD 307 T D Sbjct: 391 VTYD 394 Lambda K H 0.321 0.139 0.399 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: 281 Number of extensions: 14 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: 326 Length of database: 418 Length adjustment: 30 Effective length of query: 296 Effective length of database: 388 Effective search space: 114848 Effective search space used: 114848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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