Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate WP_068863709.1 I603_RS07595 FAD-dependent oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >NCBI__GCF_001677335.1:WP_068863709.1 Length = 415 Score = 237 bits (604), Expect = 5e-67 Identities = 158/407 (38%), Positives = 215/407 (52%), Gaps = 10/407 (2%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 VIVG GH + A ALR + + I+MIG + PY+RP LSK+ L D G QR +R Sbjct: 12 VIVGTGHGGAQAAIALRQQGHEGSILMIGRDNAPPYERPPLSKEYLAGDKGFQRIMIRPE 71 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVV- 125 ++ + IAL+LG V AI+ A R+ + DG+ + Y KL+ + G R P+ V+ Sbjct: 72 KFWAEKGIALKLGAAVTAIDAAAHRITISDGSMVTYRKLIWSGGGDPRRL--PVPGAVLP 129 Query: 126 -AHYVRTVADARALRAQLVRG-RRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQR 183 YVR +DA + L RG R V+GGG+IGLE AA R+LGC V +++ RLL R Sbjct: 130 GVFYVRDKSDADTMMLALERGASRAVVIGGGYIGLEAAAVLRKLGCEVVLVEMLPRLLAR 189 Query: 184 ALPEVVGAYAHRLHDERGVGFQMATLPRAIRAA-AGGGAIVETDRG-DVHADVVVVGIGV 241 E + + H +GV ++ T +A+ AG V D G +V D+VVVGIG+ Sbjct: 190 VAGEELSRFYAEEHRRQGVDVRLETGVQAVLGEDAGKVTGVRLDNGEEVACDMVVVGIGI 249 Query: 242 LPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHV-RIESWQVAEN 300 +P V AAG NG+ VD CRT I+A G+ H N V R+ES Q A + Sbjct: 250 VPAVGPLIAAGAAGSNGVDVDEYCRTTLDDIYAIGDCAAHANRYADNAVIRLESVQNAHD 309 Query: 301 QPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLG 360 A ++G +AY LPW WS+QYD LQ GL TV+RGDP FTV L Sbjct: 310 MANTVARAIMGEKEAYEALPWFWSNQYDLKLQTAGLNLGYDQTVLRGDPEARKFTVVYL- 368 Query: 361 GDGRIVAAAAVNLGRDIGAARRLIAAG-AMPDPQQLADPTVGLKTFL 406 +G +A V +D R+L+ +G DP LADP V LK + Sbjct: 369 KNGVPIAFDCVGTMKDYVQGRKLLESGVGRIDPALLADPEVALKDLI 415 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: 391 Number of extensions: 15 Number of successful extensions: 5 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: 415 Length adjustment: 31 Effective length of query: 375 Effective length of database: 384 Effective search space: 144000 Effective search space used: 144000 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 24 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