Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase
Query= curated2:Q5LZF5 (196 letters) >FitnessBrowser__BFirm:BPHYT_RS33980 Length = 905 Score = 48.5 bits (114), Expect = 4e-10 Identities = 41/123 (33%), Positives = 59/123 (47%), Gaps = 9/123 (7%) Query: 70 TILITGDNFGAGSSREHAAWALADYGFKVVIAGSFGDIHYNNELNNGMLPIVQPIEVRRK 129 T++ G+ +G GSSR+ AA G KVV+A SF IH +N + G+LP+ + Sbjct: 776 TVVFAGEEYGTGSSRDWAAKGTQLLGVKVVVARSFERIHRSNLVGMGVLPL--QFKGSDS 833 Query: 130 LEQLKPTDEVTVDLEQQKI-ISPVGEFTFEI-DGEWKHKLLNGLDDIGITMQYEDLITEY 187 ++ L T E T D+E P E T I D E K K + L I ++ +Y Sbjct: 834 VQSLGITGEETYDIEGLGADFKPQQEVTLVIRDKEGKEKRVQVLLRIDTPIE-----VDY 888 Query: 188 EKH 190 KH Sbjct: 889 YKH 891 Lambda K H 0.318 0.139 0.423 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: 445 Number of extensions: 27 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: 196 Length of database: 905 Length adjustment: 31 Effective length of query: 165 Effective length of database: 874 Effective search space: 144210 Effective search space used: 144210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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