Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_013136522.1 ARNIT_RS13720 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= curated2:Q97EE0 (422 letters) >NCBI__GCF_000092245.1:WP_013136522.1 Length = 864 Score = 143 bits (361), Expect = 2e-38 Identities = 123/406 (30%), Positives = 188/406 (46%), Gaps = 57/406 (14%) Query: 66 PDHFTPNKDIKSAEHCKMIRQFAKSKEIENYFEI--GEMGIEHALIPEK---------GL 114 PD F N+DI+ + +KE N ++ GI H + EK G+ Sbjct: 132 PDAFQKNRDIEDRRNADRFHFINWTKEAFNNVDVIPPGNGIMHQINLEKMSPVVHNIDGI 191 Query: 115 AVPGDVIIGADSHTCTYGALGVFSTGVGSTDMAVGMATGKAWFKVPEAIKFVLKGKPAKW 174 A P D ++G DSHT ALGV + GVG + M ++ +VPE I + G A+ Sbjct: 192 ASP-DTLVGTDSHTPHVDALGVIAVGVGGLEAENVMLGNPSYMRVPEIIGVEITGVRAEG 250 Query: 175 VSGKDIILHIIGMIGVDGALYKSMEYTGDGLEYLSMDDRFTIANMAIEAGAKNGIFPVDE 234 ++ DI L + + + + +E+ G G++YL++ DR TIANM E GA GIF +DE Sbjct: 251 ITATDIALAMTSFLRENNVISAYLEFFGSGVQYLNLGDRATIANMTPEYGASAGIFAIDE 310 Query: 235 KTIEYM--KGRSDRELKKFDA-----------DEDAEYSRVIEIDLSTLKPTVAFPHLPE 281 +TI+Y+ GR ++K +A ++A Y+R IE DLS + ++A P P Sbjct: 311 QTIDYLTVTGRDAAQVKLVEAYAKANGLWADQFDNATYARTIEFDLSKVTRSLAGPSKPH 370 Query: 282 N---TKTI-------------DQVGEVNVDQVVIGSCTNGRMEDLRIAASILKGKKIKKG 325 T T+ D++ + + I SCTN IAA +L K + G Sbjct: 371 KLVPTSTLRAEGIVKEWKQDGDKIPDGGILIAAITSCTNTSNPRNVIAAGLLAKKANELG 430 Query: 326 ------IRLIVFPGTQNIYLEAMEEGLVRTFIEAGGIVSTPTCGPCLG--GHMGILAEGE 377 ++ + PG++ I + E GL+ + G V C C G G + + E Sbjct: 431 LTRKPWVKSSLAPGSKVIEVYLKEAGLLSEMEKLGFGVVGFACTTCNGMSGALDPAIQKE 490 Query: 378 --------RAISTTNRNFVGRMGHPKSEVYLASPAVAAASAIAGKI 415 A+ + NRNF GR+ E +LASPA+ A A+AG I Sbjct: 491 VVDNDIYTTAVLSGNRNFDGRIHPYVKEAFLASPALVIAYALAGTI 536 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: 823 Number of extensions: 43 Number of successful extensions: 3 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: 422 Length of database: 864 Length adjustment: 37 Effective length of query: 385 Effective length of database: 827 Effective search space: 318395 Effective search space used: 318395 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: 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