Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_012403640.1 BPHY_RS21890 aconitate hydratase AcnA
Query= curated2:Q97EE0 (422 letters) >NCBI__GCF_000020045.1:WP_012403640.1 Length = 905 Score = 142 bits (358), Expect = 4e-38 Identities = 109/364 (29%), Positives = 165/364 (45%), Gaps = 68/364 (18%) Query: 119 DVIIGADSHTCTYGALGVFSTGVGSTDMAVGMATGKAWFKVPEAIKFVLKGKPAKWVSGK 178 D ++G DSHT +GV GVG + GM +F P+ + LKGK + V+ Sbjct: 206 DTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVHLKGKLREGVTAT 265 Query: 179 DIILHIIGMIGVDGALYKSMEYTGDGLEYLSMDDRFTIANMAIEAGAKNGIFPVDEKTIE 238 D++L I ++ + + K +E+ G+G LS+ DR TI NMA E GA G FPVDEKTI+ Sbjct: 266 DLVLTITELLRKEKVVGKFVEFFGEGTRSLSLPDRATIGNMAPEYGATMGFFPVDEKTID 325 Query: 239 YMK--GRSDRELKKFD----ADE--------DAEYSRVIEIDLSTLKPTVAFPHLPENTK 284 Y K GR+D E+ F+ A + D +Y++V+ +DL T+ P++A P P++ Sbjct: 326 YFKGTGRTDAEISAFENYFKAQDLFGIPDAGDIDYTKVVTLDLGTVAPSLAGPKRPQDRI 385 Query: 285 TIDQVGEVNVDQ------------------------------------VVIGSCTNGRME 308 I V VD I SCTN Sbjct: 386 EITHVKSTFVDLFSKPVNENGFAKKAADLDTQYTTSNGVNVKNGDILIAAITSCTNTSNP 445 Query: 309 DLRIAASILKGKKIKKG------IRLIVFPGTQNIYLEAMEEGLVRTFIEAGGIVSTPTC 362 + +AA +L K ++ G I+ + PG++ + + GL+ + G ++ C Sbjct: 446 SVLLAAGLLAKKAVEAGLEVAPHIKTSLAPGSRIVTEYLTKTGLLPYLDKLGFTLAAYGC 505 Query: 363 GPCLGGHMGILAEGERAIS----------TTNRNFVGRMGHPKSEV-YLASPAVAAASAI 411 C+G + E AI+ + NRNF R+ HP +LASP + A AI Sbjct: 506 TTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNFEARI-HPNIRANFLASPPLVVAYAI 564 Query: 412 AGKI 415 AG I Sbjct: 565 AGTI 568 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: 870 Number of extensions: 33 Number of successful extensions: 2 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: 422 Length of database: 905 Length adjustment: 37 Effective length of query: 385 Effective length of database: 868 Effective search space: 334180 Effective search space used: 334180 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