Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate WP_089323376.1 CHB58_RS06895 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q58667 (170 letters) >NCBI__GCF_900188395.1:WP_089323376.1 Length = 169 Score = 165 bits (417), Expect = 4e-46 Identities = 88/161 (54%), Positives = 110/161 (68%), Gaps = 4/161 (2%) Query: 2 IIKGRAHKFGDDVDTDAIIPGPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGENF 61 + +G+A KFGDD++TD IIP YL T+DP ELA HCM D FP KV++GD+IVAG+NF Sbjct: 5 VYRGKAFKFGDDINTDEIIPARYLNTSDPAELAKHCMEDADPEFPSKVQKGDIIVAGKNF 64 Query: 62 GCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIAN---TDEIKDGDIVEI 118 GCGSSRE A IAIK G+ AVIAKSFARIFYRN IN+GL PI + + I++GDIVE+ Sbjct: 65 GCGSSREHAPIAIKAAGVSAVIAKSFARIFYRNCINIGL-PIFESPEAVEGIEEGDIVEV 123 Query: 119 DLDKEEIVITNKNKTIKCETPKGLEREILAAGGLVNYLKKR 159 + I KN + REI+ AGGL+ Y KK+ Sbjct: 124 NPVTGIIRNITKNTEFQATPIPPEIREIMDAGGLMEYAKKK 164 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: 139 Number of extensions: 8 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: 169 Length adjustment: 18 Effective length of query: 152 Effective length of database: 151 Effective search space: 22952 Effective search space used: 22952 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: 43 (21.2 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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