Align BadI (characterized)
to candidate 203808 SO4739 naphthoate synthase (NCBI ptt file)
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__MR1:203808 Length = 300 Score = 179 bits (454), Expect = 6e-50 Identities = 112/275 (40%), Positives = 154/275 (56%), Gaps = 19/275 (6%) Query: 3 FEDLIYEIR--NGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 F D+ Y +G I INRPD +NAFR T DEL AL A DVG +L G G Sbjct: 22 FTDITYHRAKAHGTVRIAINRPDCLNAFRPKTVDELYIALDHARQWSDVGCALLTGNGPS 81 Query: 61 A-----FCTGGDQST-------HDGNYDGRGTVG----LPMEELHTAIRDVPKPVIARVQ 104 A F +GGDQ ++G +G+ + L + E+ IR +PK VIA V Sbjct: 82 AKGQYSFSSGGDQRIRGKDGYKYEGAEEGKADLARMGRLHILEVQRLIRFMPKVVIAVVP 141 Query: 105 GYAIGGGNVLATICDLTICS-EKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYM 163 G+A+GGG+ L +CDLT+ S E AIF Q P + S D GYG+A+LA+++G+K+AREI++ Sbjct: 142 GWAVGGGHSLHVVCDLTLASKEHAIFKQTDPDVASFDSGYGSAYLAKMIGQKRAREIFFC 201 Query: 164 CKRYSGKEAEAMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGI 223 YS EA AMG+ N VPH EL+ E +W +E+ +SPTA+ + K FNM G Sbjct: 202 GFNYSADEAFAMGMVNKSVPHAELEVEALRWAKEINSKSPTAMRMLKYGFNMTDDGMVGQ 261 Query: 224 AGMGMYALKLYYDTDESREGVKALQEKRKPEFRKY 258 A +L Y + E++EG A EKR +F + Sbjct: 262 QLFAGEATRLAYASAEAQEGRDAFLEKRDQDFSAF 296 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: 220 Number of extensions: 11 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: 300 Length adjustment: 26 Effective length of query: 234 Effective length of database: 274 Effective search space: 64116 Effective search space used: 64116 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