Align 3-isopropylmalate dehydratase small subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase
Query= curated2:Q9V1I9 (163 letters) >FitnessBrowser__azobra:AZOBR_RS02985 Length = 896 Score = 52.0 bits (123), Expect = 3e-11 Identities = 42/125 (33%), Positives = 57/125 (45%), Gaps = 23/125 (18%) Query: 54 VVVGGKNFGIGSSRESAALALKAAGVSGIIAKSFGRIFYRNAVNLGIPLLIGDTDELEDG 113 VV+ GK +G GSSR+ AA K G+ +IA+SF RI N V +GI L + D L Sbjct: 769 VVIAGKEYGTGSSRDWAAKGTKLLGIRAVIAESFERIHRSNLVGMGI-LPLQFKDGLTRN 827 Query: 114 DVITVNWETGEV------------------RKNGQTLQFEPLPGF----LLEIVREGGIL 151 D+ ET ++ R +GQT Q L +E R GG+L Sbjct: 828 DLALDGTETFDIDGIEQDLRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVL 887 Query: 152 EFIRR 156 F+ R Sbjct: 888 NFVLR 892 Lambda K H 0.321 0.142 0.425 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: 316 Number of extensions: 15 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: 163 Length of database: 896 Length adjustment: 30 Effective length of query: 133 Effective length of database: 866 Effective search space: 115178 Effective search space used: 115178 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: 49 (23.5 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