Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate Pf6N2E2_4027 Ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4027 Length = 510 Score = 173 bits (438), Expect = 1e-47 Identities = 124/378 (32%), Positives = 186/378 (49%), Gaps = 6/378 (1%) Query: 3 ADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDG-EQRA 61 A FVI+GAG A A ALR + I+MI E E YDR LSK L D + A Sbjct: 115 ARTFVIIGAGAAGTACAAALREKGFGGRILMIDREAEAGYDRTVLSKYVLAGDMAVNETA 174 Query: 62 FVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPID 121 +RD ++ QRI RL V ++ +A++++L DG L Y ++ATG + P Sbjct: 175 PLRDETYFTRQRIE-RLHGEVTHLDPDARQIQLADGRQLDYDAALIATGGEPKMPALPGI 233 Query: 122 AGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLL 181 +R++A AR + + G++ ++G FI +EVA++ R+ G +VTV+ Sbjct: 234 ELPQVFVLRSIAHARQILDTVRPGQQAVIIGDSFIAMEVASSLRKRGLDVTVLARHPVPF 293 Query: 182 QRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGV 241 + E VG H GV + I A A+V + + AD+V++GIGV Sbjct: 294 AAQMGESVGQAILARHRANGVVYHTDGEAARIEGAHKVEAVVLDNGQRLAADLVIIGIGV 353 Query: 242 LPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQ 301 P E + D + VDAG R A+ ++A G++ PL G VRIE W++A+ Q Sbjct: 354 HPATEPFAGLPREQDQSLSVDAGMRVAE-GVWAVGDIATF--PLNGAPVRIEHWRLAQQQ 410 Query: 302 PAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGG 361 +AAAN+LG D+ Y ++P+ W+ + LG +G P PF LG Sbjct: 411 ARIAAANMLGGDERYLDVPFFWTYHFGKRYDYLGHAEHWDEVEFKGTPEHPPFIAL-LGK 469 Query: 362 DGRIVAAAAVNLGRDIGA 379 DG + AA A + GR + A Sbjct: 470 DGLVAAAVACDEGRAMAA 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: 448 Number of extensions: 23 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