Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF3765 Psest_3834 NAD(P)H-nitrite reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__psRCH2:GFF3765 Length = 394 Score = 102 bits (254), Expect = 2e-26 Identities = 83/278 (29%), Positives = 125/278 (44%), Gaps = 4/278 (1%) Query: 1 MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60 MSA P VI+G G A A R D P+++I A+ Y +P LS N + E Sbjct: 1 MSA-PVVIIGTGLAGYNLAREFRKLDTQTPLLLITADDGRSYSKPLLSTGFAANKNAENL 59 Query: 61 AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120 A + +R+ TRV ++ +RV + + +PY LVLA G++ Sbjct: 60 GMATAGAMAEQLNAEIRIHTRVTRLDPANRRVWIGN-EPVPYRDLVLAWGAQTIQVPVAG 118 Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180 DA + + D R + RRV +LG G IG E A G V ++ P+ ++ Sbjct: 119 DAADAVFPINDLHDYGRFRDAVAGKRRVLILGAGLIGCEFANDLLLGGHEVDLVAPSEQV 178 Query: 181 LQRALPEVVGAYAHRLHDERGVGFQM-ATLPRAIRAAAGGGAIVETDRGDVHADVVVVGI 239 + LP + G F + ATL R R+ G A + +D D+VV + Sbjct: 179 MPGLLPLQAAEAVRNGLEGIGARFHLGATLERLQRSTDGLQATL-SDGSQRSCDLVVSAV 237 Query: 240 GVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGE 277 G+ P ELA AGL+V GI VD +T+ ++A G+ Sbjct: 238 GLRPRTELAAEAGLEVKRGIVVDRLLQTSAEHVYAVGD 275 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: 310 Number of extensions: 18 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: 394 Length adjustment: 31 Effective length of query: 375 Effective length of database: 363 Effective search space: 136125 Effective search space used: 136125 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 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