Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_012536129.1 AFE_RS01995 aconitate hydratase
Query= curated2:O27440 (162 letters) >NCBI__GCF_000021485.1:WP_012536129.1 Length = 645 Score = 75.9 bits (185), Expect = 1e-18 Identities = 54/168 (32%), Positives = 88/168 (52%), Gaps = 17/168 (10%) Query: 7 KFPDDVDTDIIIPGRYLVM---RDPEKLREHVMEGLDPEFPSKVKP--GDFIVAGKNFGC 61 + DD+ TD I+P V+ + + E V +D FP++ K G FIVAG N+G Sbjct: 473 RLEDDITTDHIMPAGAKVLPLRSNLPAISEFVFHMVDETFPARAKAAGGGFIVAGHNYGQ 532 Query: 62 GSSREHAPLALKGAGIAAVIAESFARIFYRNAINVGIPLLEAPGITE--KLNEGDEIEVD 119 GSSREHA LA + G+ AV+ +SFARI N +N GI L + K+ GD + ++ Sbjct: 533 GSSREHAALAPRYLGVRAVLVKSFARIHLANLVNFGILPLTFVDAADYAKVQAGDRLSLE 592 Query: 120 -----LDRGVIIRGD-DEFPFKKLPDFM----VEILEKGGLIPYLKKK 157 L++ + +R + F +P +E++ KGG + + +++ Sbjct: 593 LGGLALNKALTLRDETGGFEISVMPQLASARDLELILKGGALSWAREQ 640 Lambda K H 0.320 0.146 0.436 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: 284 Number of extensions: 14 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: 162 Length of database: 645 Length adjustment: 27 Effective length of query: 135 Effective length of database: 618 Effective search space: 83430 Effective search space used: 83430 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 (21.7 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