Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_052669763.1 NITAL_RS17280 aconitate hydratase
Query= curated2:Q726X3 (167 letters) >NCBI__GCF_000969705.1:WP_052669763.1 Length = 670 Score = 74.7 bits (182), Expect = 3e-18 Identities = 56/176 (31%), Positives = 88/176 (50%), Gaps = 22/176 (12%) Query: 9 KVGDHIDTDAIIPARFLVTTDAQKLGE------NCMEGLEHGWVARVK----SGDIMVGG 58 + GD + TD I+ A V + E + ++ H ++ +G ++VGG Sbjct: 481 ETGDDVSTDEILRAGAAVLPYRSNIPEIARFAFDVIDPTYHDRAVAIQEAGGAGHVVVGG 540 Query: 59 RNFGCGSSREHAPIAILGAGMPVVVAHSFARIFYRNGFNMGLLLLEVGD--DVDKIADGD 116 RN+G GSSREHA +A G+ + S+ARI ++N N G+L L D D D +A GD Sbjct: 541 RNYGQGSSREHAALAPRHVGLRATLVVSYARIHWQNLANFGVLPLRFADERDRDALAQGD 600 Query: 117 DIE-------VDAASGVIT--NRTTGATITCA-PVPQSMRELLDTGGLVPYVRARL 162 + +D+ SG +T N T G TIT + E + +GG++ Y++ RL Sbjct: 601 RLRLTGLHAALDSGSGEVTVENLTQGTTITAVHDLSPRQVERIRSGGVIRYMKERL 656 Lambda K H 0.321 0.139 0.417 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: 266 Number of extensions: 11 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: 167 Length of database: 670 Length adjustment: 28 Effective length of query: 139 Effective length of database: 642 Effective search space: 89238 Effective search space used: 89238 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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