Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_106712703.1 CU102_RS19205 aconitate hydratase AcnA
Query= curated2:B4UAN1 (191 letters) >NCBI__GCF_003010955.1:WP_106712703.1 Length = 895 Score = 52.4 bits (124), Expect = 2e-11 Identities = 40/118 (33%), Positives = 58/118 (49%), Gaps = 17/118 (14%) Query: 70 ILVAGDNFGCGSSREHAPWALVDAGVRAVISTRIADIFRNNALKNGLVPVVLDAASHAKL 129 ++ AG +G GSSR+ A GVRAVI+ I R+N + G+VP VL+ + + Sbjct: 769 VIFAGVEYGNGSSRDWAAKGTNLLGVRAVIAQSFERIHRSNLVGMGIVPFVLEEGTSWQS 828 Query: 130 LAAPGASVRVDVEA-----------QTVTLPDGSTARFPLDGFARYCLLNGVDELGFL 176 L G V V +E TVT DGS+ + PL C ++ +DEL +L Sbjct: 829 LGLKGDEV-VSIEGLASIQPRQKTFATVTYADGSSKQVPL-----ICRIDTIDELEYL 880 Lambda K H 0.321 0.138 0.411 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: 404 Number of extensions: 21 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: 191 Length of database: 895 Length adjustment: 31 Effective length of query: 160 Effective length of database: 864 Effective search space: 138240 Effective search space used: 138240 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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