Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate Dsui_3199 Dsui_3199 3-isopropylmalate dehydratase, small subunit
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__PS:Dsui_3199 Length = 212 Score = 66.6 bits (161), Expect = 3e-16 Identities = 46/144 (31%), Positives = 72/144 (50%), Gaps = 29/144 (20%) Query: 12 DDVDTDAIIPGPYLRTT----------DPYELASHCMAGIDE-------NF---PKKVKE 51 ++VDTDAIIP +L++ D + H G+D NF ++ + Sbjct: 17 NNVDTDAIIPKQFLKSIKRSGFGPNAFDEWRYMDHGEPGMDNSKRPLNPNFVLNQQRYQG 76 Query: 52 GDVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEI- 110 V++ NFGCGSSRE A A+ G + VIA+SFA IF+ N G++PI+ EI Sbjct: 77 ASVLLTRSNFGCGSSREHAPWALLDYGFRVVIAESFADIFFNNCFKNGILPIVLPKTEID 136 Query: 111 --------KDGDIVEIDLDKEEIV 126 G + +DL+++++V Sbjct: 137 ALFGLTEYTPGFKLVVDLEQQKVV 160 Lambda K H 0.318 0.139 0.399 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: 100 Number of extensions: 4 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: 170 Length of database: 212 Length adjustment: 20 Effective length of query: 150 Effective length of database: 192 Effective search space: 28800 Effective search space used: 28800 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: 44 (21.6 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