Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate BPHYT_RS21090 BPHYT_RS21090 FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS21090 Length = 409 Score = 179 bits (455), Expect = 1e-49 Identities = 130/388 (33%), Positives = 192/388 (49%), Gaps = 21/388 (5%) Query: 8 IVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDAA 67 IVG G AA R E LR D I ++ AE LPYDRP LSKD LL RD A Sbjct: 14 IVGGGLAALRCTEELRRGGHDGRIAIVTAEPHLPYDRPPLSKDVLLGAKEFDEVQYRDDA 73 Query: 68 WYDAQRIALRLG---TRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGV 124 +Y ++ + L T + +ERE + +G+ + + L++ TG+ R+F P+ + Sbjct: 74 FYRDHQVDMYLSHPATELRILEREV----VANGSAIAFDDLLICTGASPRSF--PLKSNC 127 Query: 125 VAHY-VRTVADARALRAQLVRGR-RVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182 Y + + D LRA L G RV +LG GFIG EVA+ AR LG T+++ AA L+ Sbjct: 128 DGIYTLGRIEDTLRLRAALRSGAPRVVILGAGFIGAEVASCARSLGLETTIVNLAATPLE 187 Query: 183 RALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVE---TDRGDVHADVVVVGI 239 RA+ +G LH + GV + +I G G + E T+ + D++V+GI Sbjct: 188 RAVGPEMGGMLSALHADHGVRLLCSV---SIAEIFGDGRVEELLLTNGERIACDILVIGI 244 Query: 240 GVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAE 299 G PN+ + +GL++ NGI DA I+AAG+V N L GR +R E W A Sbjct: 245 GSTPNIGWLEGSGLELANGIVCDAALSAGPPGIYAAGDVAWWPNGLFGRGMRCEQWTNAA 304 Query: 300 NQPAVAAANLLGADDA---YAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTV 356 Q A N+L + + + WSDQY +Q G A + +V+G G F Sbjct: 305 EQGRHVARNILAGHEGRTPFVGSNYFWSDQYGKRIQFAGSEVADEVKIVKGSYGEGHFLA 364 Query: 357 FGLGGDGRIVAAAAVNLGRDIGAARRLI 384 + GD ++ A A+N + + A++ I Sbjct: 365 YYRKGD-QLCGALALNEPKSLMLAKQQI 391 Lambda K H 0.322 0.138 0.410 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: 322 Number of extensions: 17 Number of successful extensions: 4 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: 406 Length of database: 409 Length adjustment: 31 Effective length of query: 375 Effective length of database: 378 Effective search space: 141750 Effective search space used: 141750 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 (21.9 bits) S2: 50 (23.9 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