Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate 7026694 Shewana3_3827 aconitate hydratase (RefSeq)
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__ANA3:7026694 Length = 863 Score = 50.4 bits (119), Expect = 8e-11 Identities = 35/123 (28%), Positives = 60/123 (48%), Gaps = 22/123 (17%) Query: 50 KEGDVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDE 109 K+ +I+AG ++G GSSR+ A ++ G++A++A+ F RI N + +G++P+ E Sbjct: 731 KQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGE 790 Query: 110 IKD-------------GDIV-EIDLDKEEIVITNKN-----KTIKCETPKGLEREILAAG 150 + GDI DL ++IT KN + C E I +AG Sbjct: 791 NRATYGIDGTEVFDVYGDIAPRADL---TVIITRKNGERVEVPVTCRLDTAEEVSIYSAG 847 Query: 151 GLV 153 G++ Sbjct: 848 GVL 850 Score = 26.6 bits (57), Expect = 0.001 Identities = 15/42 (35%), Positives = 24/42 (57%) Query: 32 ELASHCMAGIDENFPKKVKEGDVIVAGENFGCGSSREQAVIA 73 ELA+ ++G+ EN P + +G VI+A +S + VIA Sbjct: 376 ELAARGISGVVENEPGLMPDGAVIIAAITSCTNTSNPRNVIA 417 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: 354 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 170 Length of database: 863 Length adjustment: 30 Effective length of query: 140 Effective length of database: 833 Effective search space: 116620 Effective search space used: 116620 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: 49 (23.5 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