Align 3-isopropylmalate dehydrogenase; EC 1.1.1.85; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH (uncharacterized)
to candidate GFF838 HP15_817 3-isopropylmalate dehydrogenase
Query= curated2:B0RIP4 (355 letters) >FitnessBrowser__Marino:GFF838 Length = 384 Score = 240 bits (613), Expect = 4e-68 Identities = 159/384 (41%), Positives = 212/384 (55%), Gaps = 33/384 (8%) Query: 1 MPRTISLAVVPGDGIGPEVVHEALRVLREAVPADVSLDT--TQYPFGAGHFLET-GQILT 57 M +T +AV PGDGIGPEVV EA+R L E + A LD T++P+ + + E G+ + Sbjct: 1 MAQTTRIAVTPGDGIGPEVVAEAVRCL-ETLRAKHGLDLEWTRFPWPSHAWHEEHGESMP 59 Query: 58 DSDLAALAQHDAILLGAVGG----DPRDARLAGGIIERGLLLKLRFAFDHYINLRPTALL 113 LA L ++DAILLGA+G D D L I LL +R FD ++ RP LL Sbjct: 60 ADALAQLQKYDAILLGALGDPGPMDDPDRYLLPDSISLAPLLDMRKGFDQWVCERPARLL 119 Query: 114 PGVASPLA--APGQVDFVVVREGTEGPYAGNGGVLRRGTEHEIATEVSVNTAHGVERTVR 171 PG LA +D +V+RE +EG Y GG LR+GT E+AT++ V T +R +R Sbjct: 120 PGARQYLADERAKDIDMLVIRENSEGEYVSQGGRLRKGTPDEVATQMEVFTRKATDRIIR 179 Query: 172 FAFELAEKRDRKRVT--------------------LVHKTNVLTFAGSLWQRTVDRVAAE 211 + FE A R RV+ LV K N L + G ++ D ++ E Sbjct: 180 YGFEQARNRAADRVSEGRTRTFRTLDGRTCESQVCLVTKRNALRYWGDMYTEAFDEISKE 239 Query: 212 HPDVTVDYLHVDATMIFLVTDPSRFDVIVSDNLFGDIITDLAAAISGGIGLAASGNVNPT 271 +PDV + VDA + V P FDV+V+ NL GDI+TDLAA +SGG+G+A S N+NPT Sbjct: 240 YPDVATHHELVDAACMKFVQSPWAFDVVVASNLQGDILTDLAAVLSGGMGVAPSCNLNPT 299 Query: 272 GA-FPSMFEPVHGSAPDIAGQQKADPTAAILSVALLLDHLGLSE-AAARVSAAVSDDLAA 329 PSMFEP HGSAPDIAGQ ADPTA + + A +L+ LG + A A + D +AA Sbjct: 300 DPDMPSMFEPTHGSAPDIAGQGLADPTAMLFTAARMLEWLGRKDPAIAAAGKELFDAVAA 359 Query: 330 -RATGDAAPRSTAEVGDAILRALS 352 A + R T E+G AI LS Sbjct: 360 DLAENSGSRRGTHEIGSAICERLS 383 Lambda K H 0.319 0.136 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: 377 Number of extensions: 23 Number of successful extensions: 6 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: 355 Length of database: 384 Length adjustment: 30 Effective length of query: 325 Effective length of database: 354 Effective search space: 115050 Effective search space used: 115050 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 (21.7 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