Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate GFF2932 PGA1_c29790 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__Phaeo:GFF2932 Length = 201 Score = 69.7 bits (169), Expect = 3e-17 Identities = 46/146 (31%), Positives = 79/146 (54%), Gaps = 23/146 (15%) Query: 13 DVDTDAIIPGPYLRTTDP------------YELASHCMAGIDENFPKKVKEGDVIVAGEN 60 ++DTD IIP +L++ Y +A N P+ ++ ++++AG+N Sbjct: 18 NIDTDMIIPKVFLKSIQRTGFGKNLFDEMRYNRDGSEIADFVLNKPQ-YRDAEILIAGDN 76 Query: 61 FGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEI----KDGD-- 114 FGCGSSRE A AI GI+ +++ SFA IF+ N+ G++PI+ +++ KD + Sbjct: 77 FGCGSSREHAPWAIADFGIRCIVSTSFADIFFNNSFKNGILPIVLPQEQVDLLMKDAEKG 136 Query: 115 ---IVEIDLDKEEIVITNKNKTIKCE 137 + +DL+ +EI T+ + IK E Sbjct: 137 ANARMTVDLEAQEI-STSDGEVIKFE 161 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: 105 Number of extensions: 11 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: 201 Length adjustment: 19 Effective length of query: 151 Effective length of database: 182 Effective search space: 27482 Effective search space used: 27482 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