Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate WP_058857692.1 AS188_RS03580 pyridine nucleotide-disulfide oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >NCBI__GCF_001482365.1:WP_058857692.1 Length = 399 Score = 190 bits (483), Expect = 6e-53 Identities = 136/365 (37%), Positives = 178/365 (48%), Gaps = 21/365 (5%) Query: 4 DPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDG-EQRAF 62 + VIVGA A A A R + ++G + + PYDRP LSKD L G E A Sbjct: 2 ESLVIVGASLAGLAAARAARNHGYTGRLTVVGEDPQRPYDRPPLSKDFLAGRIGAEDLAL 61 Query: 63 VRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDA 122 +A DA+ + LG R + + + V LDDG L LV+ATG+ R+ PI Sbjct: 62 ETEADDLDAEWV---LGVRAVSFDAVTRTVVLDDGRLLHAEGLVVATGASPRSLP-PIAG 117 Query: 123 GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182 +RTVADA LR L GRR+ V+G GFIG EVA+ A +LG VTV++ + L Sbjct: 118 LDNVVTLRTVADAHRLRELLAPGRRLVVVGAGFIGAEVASTAHELGLEVTVVEKSPTPLC 177 Query: 183 RALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRG-DVHADVVVVGIGV 241 L +GA LH+ GV T A G V G + ADVVVVGIG Sbjct: 178 GPLGAELGAVVAGLHERAGVELLCGTDIERFEVAGGAVRAVHLAGGRQLPADVVVVGIGA 237 Query: 242 LPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQ 301 PN + +G+++ NG+ DA RT + A G+ ++P G H R+E W A + Sbjct: 238 APNTAWLEGSGVELGNGVLCDAVGRTGVPGVVAVGDCAAWYDPATGTHRRVEHWTGAAER 297 Query: 302 PAVAAANLLGADDA---YAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFG 358 PA+A LLGAD A + P+ WSDQY LQ GD ARG V+ Sbjct: 298 PAIAVGALLGADPAELPAVKPPYFWSDQYGTRLQF------------AGDAARGDRIVYE 345 Query: 359 LGGDG 363 GG G Sbjct: 346 QGGPG 350 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: 433 Number of extensions: 32 Number of successful extensions: 6 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: 399 Length adjustment: 31 Effective length of query: 375 Effective length of database: 368 Effective search space: 138000 Effective search space used: 138000 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