Align BadI (characterized)
to candidate GFF4202 HP15_4142 naphthoate synthase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__Marino:GFF4202 Length = 260 Score = 370 bits (950), Expect = e-107 Identities = 174/260 (66%), Positives = 212/260 (81%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M +ED++Y+ NGVA I INRPD+ NAFRG TC EL+ A +AG++KD+G IV GAG++ Sbjct: 1 MTYEDILYDENNGVATITINRPDRYNAFRGQTCMELLDAFNRAGWNKDIGVIVFTGAGEK 60 Query: 61 AFCTGGDQSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDL 120 AFCTGGDQ H+G YDGRG +GLP+EEL IR+VPKPVIARV G+AIGGG+VL ICDL Sbjct: 61 AFCTGGDQGAHEGQYDGRGLIGLPVEELQRTIREVPKPVIARVNGFAIGGGHVLHVICDL 120 Query: 121 TICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANL 180 +I SE AIFGQVGPK+GSVDPG+GTA+LARVVGEK+AREIWY+C++YS ++A GL N Sbjct: 121 SIASETAIFGQVGPKVGSVDPGFGTAYLARVVGEKRAREIWYLCRKYSAQQALEWGLVNA 180 Query: 181 CVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYDTDES 240 VP ++LD EVQKW EE+ E+SPTA++IAKRSFN D+ + AGI +GM AL LYYDTDES Sbjct: 181 VVPPEQLDEEVQKWCEEILEKSPTAISIAKRSFNADSDNIAGIGALGMQALSLYYDTDES 240 Query: 241 REGVKALQEKRKPEFRKYIK 260 +EGV A EKRKPEFRKY K Sbjct: 241 KEGVNAFLEKRKPEFRKYYK 260 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: 307 Number of extensions: 8 Number of successful extensions: 1 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: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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