Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate WP_012281279.1 HM1_RS00460 aconitate hydratase
Query= SwissProt::Q58667 (170 letters) >NCBI__GCF_000019165.1:WP_012281279.1 Length = 641 Score = 84.3 bits (207), Expect = 4e-21 Identities = 60/172 (34%), Positives = 94/172 (54%), Gaps = 24/172 (13%) Query: 9 KFGDDVDTDAIIPGPY----LRTTDPYELASHCMAGIDENFPKKVKEGD--VIVAGENFG 62 K GD++ TD I+P LR+ P ++ + AG+D F ++ K IV G+N+G Sbjct: 472 KVGDNITTDHIMPAGAKILPLRSNIP-AISQYVFAGVDATFAERAKAAGQGFIVGGQNYG 530 Query: 63 CGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPII----ANTDEIKDGDIVEI 118 GSSRE A +A Y GIKAVI +SFARI N IN G++P+ + ++ GD++EI Sbjct: 531 QGSSREHAALAPMYLGIKAVITQSFARIHRANLINFGILPLTFADEGDIAKVNRGDVLEI 590 Query: 119 ----------DLDKEEIVITNKNKTIKCE-TPKGLEREILAAGGLVNYLKKR 159 + + V T + ++ + TP+ + I+ AGGL+NY K++ Sbjct: 591 ADVAAKLGTCETLEVRNVTTGETFLVRPDLTPR--QVAIIKAGGLLNYTKEQ 640 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: 270 Number of extensions: 17 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: 641 Length adjustment: 28 Effective length of query: 142 Effective length of database: 613 Effective search space: 87046 Effective search space used: 87046 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