Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate GFF1478 PS417_07515 aconitate hydratase
Query= uniprot:A0A1X9Z766 (195 letters) >FitnessBrowser__WCS417:GFF1478 Length = 913 Score = 44.7 bits (104), Expect = 5e-09 Identities = 37/121 (30%), Positives = 61/121 (50%), Gaps = 18/121 (14%) Query: 69 VLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQVSDEFLAQI 128 V+VAG+ +G GSSR+ AA G AVI+ F I + N + G+LP+Q L Q Sbjct: 784 VVVAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFK---LDQN 840 Query: 129 FKAVDNNPKSALEV----DLE-----NQTVTIV-ETGAQESFEINPYKKSCLINGYDDID 178 K++ K +++ D+E N T+ I E G+ E E+ C I+ ++++ Sbjct: 841 RKSLKLTGKEKIDILGLTDVEIVPRMNLTLVITREDGSSEKVEV-----LCRIDTLNEVE 895 Query: 179 F 179 + Sbjct: 896 Y 896 Lambda K H 0.318 0.135 0.393 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: 371 Number of extensions: 16 Number of successful extensions: 1 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: 195 Length of database: 913 Length adjustment: 31 Effective length of query: 164 Effective length of database: 882 Effective search space: 144648 Effective search space used: 144648 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: 50 (23.9 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