Align BadI (characterized)
to candidate BWI76_RS20065 BWI76_RS20065 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__Koxy:BWI76_RS20065 Length = 285 Score = 238 bits (608), Expect = 8e-68 Identities = 121/260 (46%), Positives = 167/260 (64%), Gaps = 4/260 (1%) Query: 3 FEDLIYE-IRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRA 61 + D+ Y+ +G+A I INRP NAFR T E+I+AL A YD ++G IVL G GD+A Sbjct: 22 YTDIRYQKSADGIAKITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIVLTGEGDKA 81 Query: 62 FCTGGDQST---HDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATIC 118 FC GGDQ + G D G L + + IR PKPV+A V GY+IGGG+VL +C Sbjct: 82 FCAGGDQKVRGDYGGYQDDSGVHHLNVLDFQRQIRTCPKPVLAMVAGYSIGGGHVLHMMC 141 Query: 119 DLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLA 178 DLTI +E AIFGQ GPK+GS D G+G +++AR+VG+KKAREIW++C++Y ++A MGL Sbjct: 142 DLTIAAENAIFGQTGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAQQALDMGLV 201 Query: 179 NLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYDTD 238 N VP +L+ E +W E+ + SP AL K + N D QAG+ + A L+Y T+ Sbjct: 202 NTVVPLADLEKETVRWCREMLQNSPMALRCLKAALNADCDGQAGLQELAGNATMLFYMTE 261 Query: 239 ESREGVKALQEKRKPEFRKY 258 E +EG A +KR+P+F K+ Sbjct: 262 EGQEGRNAFNQKRQPDFSKF 281 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: 257 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: 285 Length adjustment: 25 Effective length of query: 235 Effective length of database: 260 Effective search space: 61100 Effective search space used: 61100 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