Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate WP_011155770.1 TX73_RS01035 aconitate hydratase AcnA
Query= curated2:Q8TVF2 (418 letters) >NCBI__GCF_000195775.1:WP_011155770.1 Length = 905 Score = 112 bits (279), Expect = 6e-29 Identities = 101/359 (28%), Positives = 147/359 (40%), Gaps = 62/359 (17%) Query: 115 DVIVGADSHTCTHGALGAFATGIGSTDMAAVFATGKLWFRVPETYRVEITGELPEGVYAK 174 D +VG DSHT L G+G + A L +PE ++ G L EGV A Sbjct: 215 DTLVGTDSHTTMVNGLAVLGWGVGGIEAEAAMLGQPLSMLLPEVVGFKLKGALKEGVTAT 274 Query: 175 DVVLKVTGEIGADGATYMAIEYHGEVVREMSVSDRMCLCNMAIEMGAKTGMVPPDEKTLE 234 D+VL VT + G +E+ G + +SV+D+ + NMA E GA G P D +T++ Sbjct: 275 DLVLTVTQMLRKQGVVGKFVEFFGPGLDNLSVADKATIANMAPEYGATCGFFPVDGETID 334 Query: 235 YVKK--RAGTEGRPVE------------PDPDARYEAELTLDVSDLEPQVAKPFSPDNVV 280 Y+K RA VE PD + LTLD++D+ P +A P P+ V Sbjct: 335 YLKTSGRASARVALVEKYAKAQGLFRTAKSPDPVFTVTLTLDLADVVPSLAGPKRPEGRV 394 Query: 281 PVGEV-EGI--AIDQVF---------------------------IGSCTNGRYEDLKVAA 310 + V EG A+D + I SCTN + + A Sbjct: 395 ALPAVAEGFTTAMDAEYKKALDGARYKVEGRNFDIGHGDVVIAAITSCTNTSNPSVLIGA 454 Query: 311 EVL------EGEEVHDDVRLIVIPASREVYHRTLKDGVLEVLHEAGALICPPNCGPCLGG 364 +L +G + V+ + P S+ V G+ + L + G + C C+ G Sbjct: 455 GLLARNAAAKGLKAAPWVKTSLAPGSQVVAEYLANSGLQKDLDKVGFNLVGFGCTTCI-G 513 Query: 365 HMGVLAEG-----------ERCVATSNRNFPGRMGHRESEVYLASPATAAASAIEGEIT 412 + G L E V + NRNF GR+ YLASP A A+ G +T Sbjct: 514 NSGPLPEEISKSINDNGIVAAAVLSGNRNFEGRVSPDVQANYLASPPLVVAYALAGSVT 572 Lambda K H 0.317 0.136 0.401 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: 842 Number of extensions: 46 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 418 Length of database: 905 Length adjustment: 37 Effective length of query: 381 Effective length of database: 868 Effective search space: 330708 Effective search space used: 330708 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 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