Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate Pf6N2E2_1114 Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1114 Length = 853 Score = 90.5 bits (223), Expect = 2e-22 Identities = 95/314 (30%), Positives = 142/314 (45%), Gaps = 22/314 (7%) Query: 7 VIVGAGHAARRTAEALRARDA--DAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64 +++G G E L R A + + E YDR LS + D E A + Sbjct: 15 IVIGNGMVGHHCVEQLIERGALNHYRVHVFSEEPMRAYDRVHLS-EYFSGRDAESLA-LG 72 Query: 65 DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDA-- 122 +A+ Y I L LG V I+R+A +V + L Y KLVLATGS F PI+ Sbjct: 73 EASLYQTPGITLHLGVPVLEIDRDAHQV-VTAHDRLHYDKLVLATGSY--PFVPPIEGAE 129 Query: 123 GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182 G RT+ D A+RA RR V+GGG +GLE A A + LG V++ A RL+ Sbjct: 130 GDSCLVYRTLEDLDAIRAAASNARRGVVVGGGLLGLEAANALKTLGLEAHVVEFAPRLMP 189 Query: 183 RALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGD---VHADVVVVGI 239 L G ++ GVG ++ ++I +AG + GD + D++V Sbjct: 190 VQLDPQGGLALKARIEKLGVGVHLSKGTQSI--SAGEQYRYRMNFGDDDFLETDLIVFSA 247 Query: 240 GVLPNVELAQAAGLDVD--NGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQV 297 G+ LA+ + L + G+ +D C+++D I+A GE + G + +Q+ Sbjct: 248 GIRAQDALARQSDLQIGPRGGVVIDDHCQSSDPDIYAIGECAAWNGSIFG--LVAPGYQM 305 Query: 298 AENQPAVAAANLLG 311 A N AA L G Sbjct: 306 ARN----VAARLCG 315 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: 666 Number of extensions: 37 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: 853 Length adjustment: 37 Effective length of query: 369 Effective length of database: 816 Effective search space: 301104 Effective search space used: 301104 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