Align BadI (characterized)
to candidate N515DRAFT_0930 N515DRAFT_0930 methylglutaconyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__Dyella79:N515DRAFT_0930 Length = 264 Score = 95.1 bits (235), Expect = 1e-24 Identities = 76/249 (30%), Positives = 114/249 (45%), Gaps = 10/249 (4%) Query: 11 RNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQST 70 R GV + +NRP NAF + EL AL AG D++V A+VL GAG +F G D + Sbjct: 10 RAGVRTVTMNRPQVHNAFDDSLIAELTDALAAAGRDENVRAVVLTGAG-ASFSAGADLNW 68 Query: 71 HDGNYDGRGTVG----LPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEK 126 G L + L ++ +PKP +ARV G A GGG L CD+ I + Sbjct: 69 MRGMAKASEAENREDSLRLAALMRTLQFLPKPTVARVNGAAYGGGVGLIACCDIAIGVDS 128 Query: 127 AIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDE 186 A FG K+G V P + ++ +G +++R ++ + + A+ +GL + CV +E Sbjct: 129 AKFGLTEVKLGLV-PAVISPYVIAAIGLRQSRRLFLTGELFDASTAQRIGLLHQCVRAEE 187 Query: 187 LDAEVQKWGEELCERSPTALAIAK----RSFNMDTAHQAGIAGMGMYALKLYYDTDESRE 242 LD + + P A A AK R D A I + + E +E Sbjct: 188 LDDALAGVLAAFAKAGPVAQAQAKRLALRVAGQDQAQAERIDRENAELIARLRVSAEGQE 247 Query: 243 GVKALQEKR 251 G+ A +KR Sbjct: 248 GLGAFLDKR 256 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: 143 Number of extensions: 6 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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: 47 (22.7 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