Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate 3606652 Dshi_0083 3-isopropylmalate dehydratase, small subunit (RefSeq)
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__Dino:3606652 Length = 201 Score = 68.2 bits (165), Expect = 8e-17 Identities = 41/109 (37%), Positives = 59/109 (54%), Gaps = 11/109 (10%) Query: 13 DVDTDAIIPGPYLRTTDPYELASHCMAGI------DEN-----FPKKVKEGDVIVAGENF 61 ++DTD IIP +L+T L + + +EN + ++ ++V GENF Sbjct: 18 NIDTDMIIPKQFLKTIKRSGLGVNLFDEMRYDRQGNENPDFVLNKPQYRDAQILVTGENF 77 Query: 62 GCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEI 110 GCGSSRE A A+ GI+ VIA SFA IFY N G++PI +E+ Sbjct: 78 GCGSSREHAPWALLDFGIRCVIAPSFADIFYNNCFKNGILPIALPQEEV 126 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: 104 Number of extensions: 6 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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