Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate PP_1986 PP_1986 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__Putida:PP_1986 Length = 214 Score = 66.6 bits (161), Expect = 3e-16 Identities = 44/122 (36%), Positives = 64/122 (52%), Gaps = 24/122 (19%) Query: 13 DVDTDAIIP------------GP-------YLRTTDPYELASHCMAGIDENFP---KKVK 50 +VDTD IIP GP YL PY+ + ++E F + + Sbjct: 18 NVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPYQ--DNSKRPLNEEFVLNHARYQ 75 Query: 51 EGDVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEI 110 V++A ENFGCGSSRE A A+ G +++IA SFA IF+ N+ GL+PII + +E+ Sbjct: 76 GASVLLARENFGCGSSREHAPWALDEYGFRSIIAPSFADIFFNNSFKNGLLPIILSDEEV 135 Query: 111 KD 112 + Sbjct: 136 DE 137 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: 109 Number of extensions: 5 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: 214 Length adjustment: 20 Effective length of query: 150 Effective length of database: 194 Effective search space: 29100 Effective search space used: 29100 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: 44 (21.6 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