Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate WP_004511698.1 GMET_RS13850 aconitate hydratase
Query= SwissProt::Q58667 (170 letters) >NCBI__GCF_000012925.1:WP_004511698.1 Length = 648 Score = 83.2 bits (204), Expect = 8e-21 Identities = 59/167 (35%), Positives = 91/167 (54%), Gaps = 21/167 (12%) Query: 11 GDDVDTDAIIPG-----PYLRTTDPYELASHCMAGIDENFPKKVKE--GDVIVAGENFGC 63 GD++ TD I+P PY R+ P ++ +D +F K+ KE V++ GEN+G Sbjct: 479 GDNISTDTIMPAGNKVLPY-RSNIP-AISQFVFEHLDPDFHKRAKEKGNGVVIGGENYGQ 536 Query: 64 GSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPII----ANTDEIKDGD-IVEI 118 GSSRE A +A +Y GI+A I KSFARI N +N G++P+ A+ D +K GD +V Sbjct: 537 GSSREHAALAPRYLGIRAKIVKSFARIHKANLVNFGILPLTFRNPADYDLVKQGDRLVFP 596 Query: 119 DLDK-------EEIVITNKNKTIKCETPKGLEREILAAGGLVNYLKK 158 D+ + E V + + + +R+ L AGG +N++KK Sbjct: 597 DVRRLVASGAAEIPVRVDGREIVTILEVSDRQRQELLAGGTLNFVKK 643 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: 268 Number of extensions: 13 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: 648 Length adjustment: 28 Effective length of query: 142 Effective length of database: 620 Effective search space: 88040 Effective search space used: 88040 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: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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