Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate GFF1856 PGA1_c18830 aconitate hydratase AcnA
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__Phaeo:GFF1856 Length = 895 Score = 57.0 bits (136), Expect = 8e-13 Identities = 47/155 (30%), Positives = 67/155 (43%), Gaps = 31/155 (20%) Query: 22 GPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGENFGCGSSREQAVIAIKYCGIKA 81 GP T YE + MA ++ P V+ GE +G GSSR+ A G+KA Sbjct: 745 GPDGEQTSVYEAS---MAYQEQGIPL------VVFGGEQYGAGSSRDWAAKGTALLGVKA 795 Query: 82 VIAKSFARIFYRNAINVGLIPI--------------------IANTDEIKDGDIVEIDLD 121 VIA+SF RI N + +G+IP I D IK + V D+ Sbjct: 796 VIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLTGDETVSIHGLDTIKPQEEVSCDIT 855 Query: 122 KEEIVITNKNKTIKCETPKGLEREILAAGGLVNYL 156 + T K T+KC E E + GG+++Y+ Sbjct: 856 YGD--GTTKTITLKCRIDTAPEIEYIEHGGVLHYV 888 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: 367 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 170 Length of database: 895 Length adjustment: 30 Effective length of query: 140 Effective length of database: 865 Effective search space: 121100 Effective search space used: 121100 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: 50 (23.9 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