Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate PP_1705 PP_1705 nitrite reductase [NAD(P)H] large subunit
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Putida:PP_1705 Length = 850 Score = 103 bits (258), Expect = 1e-26 Identities = 89/278 (32%), Positives = 131/278 (47%), Gaps = 12/278 (4%) Query: 7 VIVGAGHAARRTAEALRARDA--DAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64 VIVG G E L +R A + + G ER+ YDR LS+ + + Sbjct: 14 VIVGNGMVGHHCVEQLVSRGALQRFEVRVFGEERQRAYDRVHLSE--YFGGSCAETLALC 71 Query: 65 DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPID--A 122 + +Y+A + L LG V I+RE + V G Y +LVLATGS F PI+ + Sbjct: 72 EHDFYEANGVHLHLGEAVLEIDRERREVVTAAGR-YGYDQLVLATGSY--PFVPPIEGSS 128 Query: 123 GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182 G RT+ D +RA RR V+GGG +GLE A A + LG V++ A RL+ Sbjct: 129 GNARLVYRTLDDLDGIRAAAAGARRGVVVGGGLLGLEAANALKSLGLEAHVVEFAPRLMP 188 Query: 183 RALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGD-VHADVVVVGIGV 241 L GA + GVG ++ +++ A + D G+ + D++V G+ Sbjct: 189 VQLDGEGGAALKAQIEALGVGVHLSRATQSVSAGETYRYRMNFDGGEHLETDLIVFSAGI 248 Query: 242 LPNVELAQAAGLDV--DNGIRVDAGCRTADRAIFAAGE 277 P L + GLD+ G+ +D CR++D IFA GE Sbjct: 249 RPQDALGRGCGLDIAARGGVVIDNHCRSSDPRIFAIGE 286 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: 708 Number of extensions: 36 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: 850 Length adjustment: 37 Effective length of query: 369 Effective length of database: 813 Effective search space: 299997 Effective search space used: 299997 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