Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate AO356_10780 AO356_10780 pyridine nucleotide-disulfide oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10780 Length = 510 Score = 174 bits (440), Expect = 7e-48 Identities = 130/379 (34%), Positives = 188/379 (49%), Gaps = 8/379 (2%) Query: 3 ADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLND-DGEQRA 61 A FVI+GAG A A ALR + I++I E E YDR LSK L D + A Sbjct: 115 ARTFVIIGAGAAGTACAAALREKGFGGRILLIDREAEAGYDRTVLSKYVLAGDMPVNETA 174 Query: 62 FVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGP-I 120 +RD ++ QRI RL V ++ A++++L DG L Y ++ATG +T P I Sbjct: 175 PLRDETYFTQQRIE-RLHGEVTHLDPGARQIQLADGRRLDYDAALIATGGEPKTPALPGI 233 Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180 D V +R++A AR + + G+R ++G FI +EVA++ R+ +VTV+ Sbjct: 234 DLPQV-FVLRSIAHARQILDTVRPGQRAVIIGDSFIAMEVASSLRKRELSVTVLARHPVP 292 Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIG 240 L E VG H GV +Q I A+V + + AD+V+VGIG Sbjct: 293 FAAQLSESVGQAILARHRANGVVYQSDGEAARIEGTHKVEAVVLDNGQRLAADLVIVGIG 352 Query: 241 VLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAEN 300 V P E + D + VDAG R AD ++A G++ PL G VRIE W++A+ Sbjct: 353 VHPATEPFAQLPREQDQSLSVDAGMRVAD-GLWAVGDIATF--PLHGTPVRIEHWRLAQQ 409 Query: 301 QPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLG 360 Q +AAAN+LG D+ Y ++P+ W+ + LG +G P PF LG Sbjct: 410 QARIAAANMLGGDERYLDVPFFWTYHFGKRYDYLGHAEHWDEVEFKGTPEHPPFIAL-LG 468 Query: 361 GDGRIVAAAAVNLGRDIGA 379 DG + AA A + GR + A Sbjct: 469 KDGLVAAAVACDEGRAMAA 487 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: 455 Number of extensions: 22 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: 510 Length adjustment: 33 Effective length of query: 373 Effective length of database: 477 Effective search space: 177921 Effective search space used: 177921 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