Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate PP_3175 PP_3175 putative Dioxygenase, ferredoxin reductase component
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Putida:PP_3175 Length = 506 Score = 151 bits (382), Expect = 4e-41 Identities = 113/351 (32%), Positives = 166/351 (47%), Gaps = 7/351 (1%) Query: 6 FVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLND--DGEQRAFV 63 FV+VGAG A L A +V I ER+ YDR ALSK + E A + Sbjct: 118 FVVVGAGAAGSAAVATLLAHGFAGRLVWIDQERQPAYDRTALSKFVIAGQMPPDEVPALL 177 Query: 64 RDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAG 123 A Q + + G +V + + ++V L DG + Y +LATG + P Sbjct: 178 EADALRKGQ-LERKYG-KVRTLNSQKRQVTLADGQQIDYDACLLATGGKALRPDIPGADL 235 Query: 124 VVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQR 183 +R++ DA L G+ V ++G GFIGLE A+A R+ G V V+ L R Sbjct: 236 PGVFTLRSLEDAARLLDAAEPGQPVVIVGDGFIGLEAASALRKYGVQVHVVSRHEVPLAR 295 Query: 184 ALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLP 243 L E +G LH+ +G+ F T I A+ T+ + +V++G GV P Sbjct: 296 QLGERIGRCIRALHERKGITFHGPTEVERIEGLDKVEAVQLTNGERLQTPLVLLGTGVRP 355 Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPA 303 Q L D +RVDA R AD ++AAG++ PL GR VRIE W++A+ Sbjct: 356 ATAFLQGVPLGEDKSVRVDAEMRAAD-GLWAAGDIATF--PLTGRPVRIEHWRLAQQHGV 412 Query: 304 VAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPF 354 +AAAN+LG YA++P+ W+ Q+ ++LG G+P +G F Sbjct: 413 IAAANMLGEQRRYADVPFFWTYQHGRTYEVLGHARDWNRIEFVGEPEKGDF 463 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: 413 Number of extensions: 28 Number of successful extensions: 4 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: 506 Length adjustment: 33 Effective length of query: 373 Effective length of database: 473 Effective search space: 176429 Effective search space used: 176429 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: 51 (24.3 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