Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate 7026694 Shewana3_3827 aconitate hydratase (RefSeq)
Query= curated2:Q97EE0 (422 letters) >FitnessBrowser__ANA3:7026694 Length = 863 Score = 129 bits (323), Expect = 5e-34 Identities = 103/348 (29%), Positives = 161/348 (46%), Gaps = 46/348 (13%) Query: 113 GLAVPGDVIIGADSHTCTYGALGVFSTGVGSTDMAVGMATGKAWFKVPEAIKFVLKGKPA 172 G+A P D ++G DSHT ALGV + GVG + M ++ ++P+ I L GKP Sbjct: 189 GVAFP-DTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQ 247 Query: 173 KWVSGKDIILHIIGMIGVDGALYKSMEYTGDGLEYLSMDDRFTIANMAIEAGAKNGIFPV 232 ++ DI+L + + + + +E+ G+G E L++ DR TI+NM E GA +F + Sbjct: 248 PGITATDIVLALTEFLRKEKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYI 307 Query: 233 DEKTIEY--MKGRSDRELKKF-----------DADEDAEYSRVIEIDLSTLKPTVAFPHL 279 D++T++Y + GRSD ++K D + AEY R + DLS++ T+A P Sbjct: 308 DQQTLDYLTLTGRSDEQVKLVETYAKTTGLWSDDLKHAEYPRTLHFDLSSVVRTIAGPSN 367 Query: 280 PENTKTIDQVGEVNVDQVV----------------IGSCTNGRMEDLRIAASIL------ 317 P ++ + VV I SCTN IAA +L Sbjct: 368 PHARVPTTELAARGISGVVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANA 427 Query: 318 KGKKIKKGIRLIVFPGTQNIYLEAMEEGLVRTFIEAGGIVSTPTCGPCLG--GHMGILAE 375 KG K ++ + PG++ + L E L+ G + C C G G + + + Sbjct: 428 KGLSRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQ 487 Query: 376 GE--------RAISTTNRNFVGRMGHPKSEVYLASPAVAAASAIAGKI 415 E A+ + NRNF GR+ + +LASP + A AIAG I Sbjct: 488 QEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535 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: 840 Number of extensions: 36 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: 863 Length adjustment: 37 Effective length of query: 385 Effective length of database: 826 Effective search space: 318010 Effective search space used: 318010 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 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