Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF2358 Psest_2406 nitrite reductase [NAD(P)H], large subunit
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__psRCH2:GFF2358 Length = 852 Score = 109 bits (272), Expect = 4e-28 Identities = 95/284 (33%), Positives = 134/284 (47%), Gaps = 12/284 (4%) Query: 1 MSADPFVIVGAGHAARRTAEALRARDADA--PIVMIGAERELPYDRPALSKDALLNDDGE 58 ++ + VIVG G E L R A + + G ER+ YDR LS + D E Sbjct: 8 LTLEKLVIVGNGMVGHHCIEQLIERGALTRYELHVFGEERQRAYDRVHLS-EYFGGRDAE 66 Query: 59 QRAFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGG 118 A +A +Y + + LG +V I+RE + V G PY +L+LATGS F Sbjct: 67 SLAMC-EADYYASHGVYTHLGVQVLGIDRERKEVITSAGRQ-PYDQLILATGSY--PFVP 122 Query: 119 PIDA--GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDP 176 PI G RT+ D A+RA RR V+GGG +GLE A A + LG V++ Sbjct: 123 PITGAEGSARLVYRTLDDLDAIRAAATNARRGVVVGGGLLGLEAANALKSLGLEAHVVEF 182 Query: 177 AARLLQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAG-GGAIVETDRGDVHADVV 235 A RL+ L GA + GVG ++ + I A + TD + D++ Sbjct: 183 APRLMPVQLDGEGGAALKARIESLGVGVHLSRATQEIVAGEDYAWRMNFTDGEFLETDLI 242 Query: 236 VVGIGVLPNVELAQAAGLDV--DNGIRVDAGCRTADRAIFAAGE 277 V G+ P L + A L++ GI +D+ CRT+D AIFA GE Sbjct: 243 VFSAGIRPQDALGRVAELEIAQRGGIVIDSECRTSDPAIFAIGE 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: 700 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: 852 Length adjustment: 37 Effective length of query: 369 Effective length of database: 815 Effective search space: 300735 Effective search space used: 300735 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