Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_013258997.1 DEBA_RS10935 aconitate hydratase
Query= curated2:O27440 (162 letters) >NCBI__GCF_000143965.1:WP_013258997.1 Length = 639 Score = 71.6 bits (174), Expect = 2e-17 Identities = 50/125 (40%), Positives = 74/125 (59%), Gaps = 10/125 (8%) Query: 7 KFPDDVDTDIIIPG--RYLVMR-DPEKLREHVMEGLDPEFPSKVKP--GDFIVAGKNFGC 61 K D++ TD I+P + L +R + + + V +DP+FP+K + +V G N+G Sbjct: 471 KVGDNITTDHIMPAGSKILPLRSNVPAISQFVFNAVDPDFPAKAQACAPAAVVGGDNYGQ 530 Query: 62 GSSREHAPLALKGAGIAAVIAESFARIFYRNAINVGI-PLLEA-PGITEKLNEGDEIEVD 119 GSSREHA LA + G+ +A+SFARI N IN G+ PL+ A P ++L+EG IE+ Sbjct: 531 GSSREHAALAPRYLGVQVKLAKSFARIHKANLINFGVLPLVFADPADYDRLDEGQRIEL- 589 Query: 120 LDRGV 124 RGV Sbjct: 590 --RGV 592 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: 300 Number of extensions: 18 Number of successful extensions: 2 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: 639 Length adjustment: 27 Effective length of query: 135 Effective length of database: 612 Effective search space: 82620 Effective search space used: 82620 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 Jul 25 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