Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate Pf6N2E2_1861 Ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1861 Length = 411 Score = 278 bits (710), Expect = 3e-79 Identities = 160/400 (40%), Positives = 222/400 (55%), Gaps = 1/400 (0%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 VIVGAGHA LR I++IG E ELPY RP LSK L + + +R A Sbjct: 9 VIVGAGHAGAELVATLRQNGYPGRIILIGDEPELPYRRPPLSKTYLSGEASRESLLIRSA 68 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVVA 126 A YD ++A G +V AI+RE + V L DG T Y KLVLATG R R P Sbjct: 69 AAYDKLQVACWTGVQVCAIDRERRTVTLSDGRTQAYDKLVLATGGRPRRLEEPAAQKPNV 128 Query: 127 HYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRALP 186 HY+R +AD L+ V G+R+ V+GGG+IGLE A+ + G VTV++ A R+L R Sbjct: 129 HYIRNLADIERLQPDFVAGKRLLVIGGGYIGLEAASVGIKNGLQVTVLEAAPRVLARVAA 188 Query: 187 EVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPNVE 246 + A+ +H RGV + T + + A ++ +D ++ D+++VGIG+LPN + Sbjct: 189 PEISAFYEGVHRRRGVDVRTETSVQVFQGAERVESVQLSDGSELPVDLIIVGIGILPNDQ 248 Query: 247 LAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPAVAA 306 LA+ AGL++DNGI VD+ +T D I A G+ H N LG +RIES A+ Q AA Sbjct: 249 LARDAGLEIDNGIVVDSYAQTLDPDILAVGDCARHVNGFLGCLIRIESVPSAQEQARTAA 308 Query: 307 ANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDGRIV 366 + G + + +PW WSDQ+D LQM+GL V+RGD A F F L G ++ Sbjct: 309 HTICGKNLPHIAVPWFWSDQFDLKLQMVGLSQGYDQLVLRGDMAAESFCAFYL-RKGVVL 367 Query: 367 AAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 + AVN +D +RL+A DPQ LAD ++ LK+ L Sbjct: 368 SVDAVNRPQDFMVGKRLVAERVQVDPQVLADESIDLKSLL 407 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: 355 Number of extensions: 12 Number of successful extensions: 2 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: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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: 50 (23.9 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