Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate AZOBR_RS18565 AZOBR_RS18565 nitrite reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__azobra:AZOBR_RS18565 Length = 821 Score = 132 bits (333), Expect = 3e-35 Identities = 104/312 (33%), Positives = 150/312 (48%), Gaps = 12/312 (3%) Query: 7 VIVGAGHAARRTAEALRARDADA-PIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRD 65 V+VG G A RT E L A+ D I + GAE Y+R LS L + ++ + Sbjct: 15 VVVGNGMAGIRTLEELLAKAPDRYDITVFGAEPHPNYNRIMLSP-VLAGEKTFEQIVLNG 73 Query: 66 AAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSR--VRTFGGPIDAG 123 WY+A I L G RV+ I+R V G T+PY KL++ATGS + G G Sbjct: 74 RDWYEANGIRLLTGDRVEVIDRANCTVTAISGLTVPYDKLLIATGSTPVIIPVPGSTLTG 133 Query: 124 VVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQR 183 VV R +AD + RG R V+GGG +GLE A + G +VTV+ L++R Sbjct: 134 VVG--FRDLADVDTMLEAAARGGRAVVIGGGLLGLEAANGLKVKGMDVTVLHLMDTLMER 191 Query: 184 ALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLP 243 L GA + RG+ I + A+ + ++ AD+VV+ +G+ P Sbjct: 192 QLDRSAGALLRHELERRGITVLTGADTAEIVGSEKVSAVRLKNGQELPADLVVMAVGIRP 251 Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPA 303 N L +AAGL GI+VD T+D AI + GE H G + +++A+ Sbjct: 252 NTTLGKAAGLACGRGIQVDDAMTTSDPAILSVGECVEHRGQTYGLVAPL--FEMAK---- 305 Query: 304 VAAANLLGADDA 315 VAAA L G+ +A Sbjct: 306 VAAARLAGSAEA 317 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: 673 Number of extensions: 33 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: 821 Length adjustment: 36 Effective length of query: 370 Effective length of database: 785 Effective search space: 290450 Effective search space used: 290450 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