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_086508286.1 BZY95_RS01750 aconitate hydratase
Query= curated2:Q8TVF2 (418 letters) >NCBI__GCF_002151265.1:WP_086508286.1 Length = 656 Score = 250 bits (639), Expect = 8e-71 Identities = 153/397 (38%), Positives = 211/397 (53%), Gaps = 7/397 (1%) Query: 21 GDIVVANIDVAMVHDITGPITVQRLEEMGVERVWDPSKIVVLFDHQVPADSVEAAENHKI 80 G + ID A++ D+ G + + LE MG++RV + + V AD++ A E + Sbjct: 22 GSEIALRIDQALLQDVLGTLVMLELEAMGLDRVKTQPSVQYIDHGLVQADNLNA-ETYLF 80 Query: 81 MREFVEEQGIEHFYDVREGVCHQVLPEKGHVRPGDVIVGADSHTCTHGALGAFATGIGST 140 ++ E G+ + G+ H V E + PG IVG DSHT G+LG A G G Sbjct: 81 LKSACERFGV-WYSGPGNGISHPVHMEHFGI-PGQSIVGCDSHTTAAGSLGMLAIGAGGI 138 Query: 141 DMAAVFATGKLWFRVPETYRVEITGELPEGVYAKDVVLKVTGEIGADGATYMAIEYHGEV 200 ++A A L+ +PE + + + G LP+ V AKD VL++ G GA IEYHG Sbjct: 139 EVAMAMAGEPLYLSMPEIWGIRLAGSLPDWVSAKDAVLELLRRHGVAGAKNTIIEYHGPG 198 Query: 201 VREMSVSDRMCLCNMAIEMGAKTGMVPPDEKTLEYVKKRA-GTEGRPVEPDPDARYEAEL 259 + +S DR L NM EMGA + P DE+ ++ R + +P+ +P Y+ E Sbjct: 199 LANLSAMDRHVLANMGTEMGATATVFPSDEEARRFLAARGREADWKPLAAEPGCTYDREE 258 Query: 260 TLDVSDLEPQVAKPFSPDNVVPVGEVEGIAIDQVFIGSCTNGRYEDLKVAAEVLEGEEVH 319 LD+S LEP +A P SPD VVPV EV G + Q +IGS N Y D V AE++ G V Sbjct: 259 VLDLSSLEPLIALPSSPDKVVPVREVVGEPLHQAYIGSSGNPGYRDFAVVAEMVRGRTVA 318 Query: 320 DDVRLIVIPASREVYHRTLKDGVLEVLHEAGALICPPNCGPCLGGHMG-VLAEGERCVAT 378 D V L + P+SR+V ++DG L L +GA + C C+G MG A G + T Sbjct: 319 DGVSLDINPSSRQVLATLIRDGYLADLVASGARLHQTGCNGCIG--MGQAPAVGRNSLRT 376 Query: 379 SNRNFPGRMGHRESEVYLASPATAAASAIEGEITDPR 415 RNFPGR G RE V+L SP TAAASA+ G I DPR Sbjct: 377 VPRNFPGRSGTREDSVFLCSPETAAASALAGSIADPR 413 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: 636 Number of extensions: 50 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: 418 Length of database: 656 Length adjustment: 35 Effective length of query: 383 Effective length of database: 621 Effective search space: 237843 Effective search space used: 237843 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: 52 (24.6 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