Align BadI (characterized)
to candidate RR42_RS23695 RR42_RS23695 dihydroxynaphthoic acid synthetase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS23695 Length = 260 Score = 449 bits (1155), Expect = e-131 Identities = 209/260 (80%), Positives = 236/260 (90%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M +ED++Y++RNG AWI INRP+KMNAFRG TCDELI A+ +AGYD+++GAIVLAGAG++ Sbjct: 1 MNYEDILYDVRNGAAWITINRPEKMNAFRGRTCDELIHAINRAGYDREIGAIVLAGAGEK 60 Query: 61 AFCTGGDQSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDL 120 AFCTGGDQS H+G YDGRGT+GLPMEELH AIRDVPKPVIARVQGYAIGGGNV+ TICD Sbjct: 61 AFCTGGDQSAHEGQYDGRGTIGLPMEELHNAIRDVPKPVIARVQGYAIGGGNVICTICDF 120 Query: 121 TICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANL 180 TI SEKA+FGQVGPK+GSVDPGYGTAFLARVVGEKKAREIWYMC+RY EA AMGL N Sbjct: 121 TIASEKAVFGQVGPKVGSVDPGYGTAFLARVVGEKKAREIWYMCRRYPAAEALAMGLVNA 180 Query: 181 CVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYDTDES 240 VPH++LDAEVQKW +E+ E+SPTALAIAKRSFNMDTAHQ+GIAGMGMYALKLYYDT+ES Sbjct: 181 VVPHEQLDAEVQKWCDEIMEKSPTALAIAKRSFNMDTAHQSGIAGMGMYALKLYYDTEES 240 Query: 241 REGVKALQEKRKPEFRKYIK 260 REGV A QEKRKP+FRKY K Sbjct: 241 REGVTAFQEKRKPDFRKYAK 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: 372 Number of extensions: 9 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