Align BadI (characterized)
to candidate AO353_25665 AO353_25665 crotonase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25665 Length = 368 Score = 76.6 bits (187), Expect = 7e-19 Identities = 50/154 (32%), Positives = 78/154 (50%), Gaps = 4/154 (2%) Query: 5 DLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCT 64 D++ E+RN + + +NRP +NA L + L D + A+VL GAG++AFC Sbjct: 19 DVLAEVRNHIGHLTLNRPAGLNAITLDMVRSLHRQLDAWSKDPHIHAVVLRGAGEKAFCA 78 Query: 65 GGDQSTHDGNYDGRGTV--GLPMEE--LHTAIRDVPKPVIARVQGYAIGGGNVLATICDL 120 GGD + ++ GT+ +EE L AI KPV+A + G+ +GGG L DL Sbjct: 79 GGDIRSLYDSFKSGGTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADL 138 Query: 121 TICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGE 154 + +E++ +G G+ FL R+ GE Sbjct: 139 RVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGE 172 Lambda K H 0.319 0.138 0.418 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: 230 Number of extensions: 11 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: 260 Length of database: 368 Length adjustment: 27 Effective length of query: 233 Effective length of database: 341 Effective search space: 79453 Effective search space used: 79453 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Sep 17 2021. The underlying query database was built on Sep 17 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