Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate GFF2473 Psest_2521 aconitate hydratase 1
Query= curated2:Q97EE0 (422 letters) >FitnessBrowser__psRCH2:GFF2473 Length = 891 Score = 135 bits (341), Expect = 4e-36 Identities = 107/358 (29%), Positives = 170/358 (47%), Gaps = 66/358 (18%) Query: 119 DVIIGADSHTCTYGALGVFSTGVGSTDMAVGMATGKAWFKVPEAIKFVLKGKPAKWVSGK 178 D ++G DSHT LGV GVG + M +PE I F L GK + V+ Sbjct: 206 DTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFRLTGKLNEGVTAT 265 Query: 179 DIILHIIGMIGVDGALYKSMEYTGDGLEYLSMDDRFTIANMAIEAGAKNGIFPVDEKTIE 238 D++L + M+ G + K +E+ G GL++L + DR TI NMA E GA G FPVD+ TI+ Sbjct: 266 DLVLTVTQMLRKHGVVGKFVEFYGPGLDHLPLADRATIGNMAPEYGATCGFFPVDQVTID 325 Query: 239 YMK--GRSDRELKKFDADEDA------------EYSRVIEIDLSTLKPTVAFPHLPENTK 284 Y++ GR++ + +A A E++ +E+DLS ++P+VA P P++ Sbjct: 326 YLRLTGRNEERIALVEAYSKAQGMWRDSNSPAPEFTATLELDLSQVRPSVAGPKRPQDRV 385 Query: 285 TIDQVG--------------EVNVDQVV----------------IGSCTNGRMEDLRIAA 314 T+ +G + + D V I SCTN ++ +AA Sbjct: 386 TLGDIGANFDLLLETSGRQQQADTDFAVAAEQFQLKHGAVVIAAITSCTNTSNPNVLMAA 445 Query: 315 SILKGKKIKKG------IRLIVFPGTQNI--YLEAMEEGLVRTFIEAGGIVSTPTCGPCL 366 ++ K I++G ++ + PG++ + YLE GL R E G + C C+ Sbjct: 446 GLVAKKAIERGLQRKPWVKTSLAPGSKVVTDYLE--RAGLTRYLDELGFNLVGYGCTTCI 503 Query: 367 GGHMGI-------LAEGERAISTT---NRNFVGRMGHPKSEV-YLASPAVAAASAIAG 413 G + + + + +S+ NRNF GR+ HP + +LASP + A A+AG Sbjct: 504 GNSGPLPDAIGQAITDNDLIVSSVLSGNRNFEGRV-HPLVKANWLASPPLVVAFALAG 560 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: 813 Number of extensions: 44 Number of successful extensions: 4 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: 891 Length adjustment: 37 Effective length of query: 385 Effective length of database: 854 Effective search space: 328790 Effective search space used: 328790 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