Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate RR42_RS31785 RR42_RS31785 nitrite reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS31785 Length = 849 Score = 108 bits (271), Expect = 5e-28 Identities = 91/309 (29%), Positives = 141/309 (45%), Gaps = 12/309 (3%) Query: 7 VIVGAGHAARRTAEAL-RARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRD 65 +I+G G + E L A D + ++ E YDR LS + E + V + Sbjct: 4 IIIGHGMVGHKFLECLAEAGSQDLEVTVLCEEPRPAYDRVHLS-EFFAGKSAEDLSLV-E 61 Query: 66 AAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVV 125 A +++ + LRL R I+R A+ V + G TL Y KL++ATGS P Sbjct: 62 AGFFERSNMLLRLNARATGIDRAAKTVTVSTGETLSYDKLIMATGSYPFVPPLPGKDRKD 121 Query: 126 AHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRAL 185 RT+ D A++ R R V+GGG +GLE A A R +G V++ A RL+ + Sbjct: 122 CFVYRTIEDLEAMQECGARSRTGVVIGGGLLGLECAKALRDMGLQTHVVEFAPRLMAVQV 181 Query: 186 PEVVGAYAHRLHDERGV-GFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPN 244 + GA R +E GV + G + D + D++V G+ P Sbjct: 182 DDGGGAMLRRKIEELGVTAHTRKNTVEIVDGEDGTHRMNFADGSHLDTDMIVFSAGIRPR 241 Query: 245 VELAQAAGLDVD--NGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQP 302 ELA+A+GL + GI VD C ++D ++A GE + + G + +++A Sbjct: 242 DELARASGLAIGERGGIAVDNQCLSSDPDVYAIGECALWDGKIYG--LVAPGYEMAR--- 296 Query: 303 AVAAANLLG 311 VAA +LLG Sbjct: 297 -VAAKHLLG 304 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: 630 Number of extensions: 24 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: 849 Length adjustment: 37 Effective length of query: 369 Effective length of database: 812 Effective search space: 299628 Effective search space used: 299628 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