Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF2881 PS417_14730 nitrite reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__WCS417:GFF2881 Length = 846 Score = 91.3 bits (225), Expect = 1e-22 Identities = 103/348 (29%), Positives = 146/348 (41%), Gaps = 34/348 (9%) Query: 7 VIVGAGHAARRTAEALRARDA--DAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64 ++VG G L R A + + E YDR LS + D E A + Sbjct: 8 IVVGNGMVGHHCVAQLIERGALDHYRLHVFSEEPMRAYDRVHLS-EYFSGRDAESLA-LS 65 Query: 65 DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDA-- 122 DA+ Y + L LG V I+R V DG + Y KLVLATGS F PID Sbjct: 66 DASLYQTPGVTLHLGVPVLEIDRARCEVITADGC-VAYDKLVLATGSY--PFVPPIDGAE 122 Query: 123 GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182 G RT+ D A+R RR V+GGG +GLE A A + LG V++ A RL+ Sbjct: 123 GDSRLVYRTLEDLDAIRKAAANARRGVVVGGGLLGLEAANALKSLGLEAHVVEFAPRLMP 182 Query: 183 RALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGD-VHADVVVVGIGV 241 L + G + GVG ++ ++I A + + + D++V G+ Sbjct: 183 VQLDDFGGLALKAQIERLGVGVHLSRATQSISAGEHYRYRMNFANDEFLETDLIVFSAGI 242 Query: 242 LPNVELAQAAGLDVD--NGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAE 299 LA+ AGLD+ G+ ++ C + D I+A GE L G + +Q+A Sbjct: 243 RAQDALARQAGLDIGPRGGVVINDECLSCDPNIYAIGECASWNGSLFG--LVAPGYQMAR 300 Query: 300 N----------QPAVAA-----ANLLGAD-----DAYAELPWLWSDQY 327 +P V A LLG D DA+A P S Q+ Sbjct: 301 GVAALLCKQTAEPFVGADMSTKLKLLGVDVGSIGDAHAHTPGARSYQF 348 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: 650 Number of extensions: 27 Number of successful extensions: 3 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: 846 Length adjustment: 36 Effective length of query: 370 Effective length of database: 810 Effective search space: 299700 Effective search space used: 299700 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: 53 (25.0 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