Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate HSERO_RS11425 HSERO_RS11425 aconitate hydratase
Query= curated2:Q97EE0 (422 letters) >FitnessBrowser__HerbieS:HSERO_RS11425 Length = 873 Score = 130 bits (326), Expect = 2e-34 Identities = 111/367 (30%), Positives = 166/367 (45%), Gaps = 55/367 (14%) Query: 103 GIEHALIPEK---------GLAVPGDVIIGADSHTCTYGALGVFSTGVGSTDMAVGMATG 153 GI H + EK G+A P D ++G DSHT ALGV + GVG + M Sbjct: 170 GIMHQINLEKMSPVIHAKDGVAFP-DTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGR 228 Query: 154 KAWFKVPEAIKFVLKGKPAKWVSGKDIILHIIGMIGVDGALYKSMEYTGDGLEYLSMDDR 213 +W ++P+ I L G+ ++ DI+L + + + +E+ GDG L++ DR Sbjct: 229 ASWMRLPDIIGVELTGRRQPGITATDIVLSLTEFLRKQKVVGAYLEFYGDGAASLTLGDR 288 Query: 214 FTIANMAIEAGAKNGIFPVDEKTIEYMK--GRSDRELKKF-----------DADEDAEYS 260 TI+NMA E GA +F +D++TI+Y+K GR D ++K D EY Sbjct: 289 ATISNMAPEYGATAAMFSIDQQTIDYLKLTGREDEQVKLVETYAKEAGLWSDTLAKVEYE 348 Query: 261 RVIEIDLSTLKPTVAFPHLPENT-------------KTIDQVGEVNVDQVVIG---SCTN 304 RV+ DLST+ T+A P P K ++ G++ V+I SCTN Sbjct: 349 RVLRFDLSTVVRTLAGPSNPHKRLPVSELAAQGIAGKVENEPGKMPDGAVIIAAITSCTN 408 Query: 305 GRMEDLRIAASILK------GKKIKKGIRLIVFPGTQNIYLEAMEEGLVRTFIEAGGIVS 358 IAA +L G K ++ + PG++ + L E GL + G + Sbjct: 409 TSNPRNVIAAGLLARNANRLGLARKPWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIV 468 Query: 359 TPTCGPCLG--GHMGILAEGE--------RAISTTNRNFVGRMGHPKSEVYLASPAVAAA 408 C C G G + + E A+ + NRNF GR+ + +LASP + A Sbjct: 469 AFACTTCNGMSGALDPKIQQEIIDRDLYSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVA 528 Query: 409 SAIAGKI 415 AIAG I Sbjct: 529 YAIAGTI 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: 816 Number of extensions: 42 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: 873 Length adjustment: 37 Effective length of query: 385 Effective length of database: 836 Effective search space: 321860 Effective search space used: 321860 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