Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate SMc01990 SMc01990 ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Smeli:SMc01990 Length = 409 Score = 246 bits (627), Expect = 1e-69 Identities = 152/411 (36%), Positives = 221/411 (53%), Gaps = 12/411 (2%) Query: 1 MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60 M + VIVG G A R A+ L A+ I +IG E PY+RP LSK LL + Sbjct: 1 MMPERIVIVGGGQAGGRVAQILAGSPANLDIALIGLEPHPPYNRPPLSKGVLLGKSELKD 60 Query: 61 AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120 + A R+ G R ++++ A+ V DDG L Y KLVLATGSRVR P Sbjct: 61 CVIWPQGDATAGRVRFYPGRRAESLDIHARHVITDDGARLDYDKLVLATGSRVRRLSVPG 120 Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180 +RT DA A+ + R +R+ V+GGGF+GLE+AAAAR G V++ RL Sbjct: 121 AECDGVFTLRTFDDAVAIARRFHRSKRLLVVGGGFVGLEIAAAARSRGLETVVVEATNRL 180 Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGG--AIVETDRGDVHADVVVVG 238 L R +P+ +GA R H+ GV F++ ++ + A G + V ++ V D+ V+G Sbjct: 181 LSRIVPQEIGAALARYHEAAGVSFRVGSMVEKLVANRSGKLKSAVLSNGETVPCDLAVIG 240 Query: 239 IGVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVA 298 +GV N ELA+ AGL+V GIR D+ R + ++A G+ ++PL R+VR+E+WQ A Sbjct: 241 VGVTANTELAKEAGLEVQVGIRTDSALRASADGVYACGDAVSFWHPLFERYVRVEAWQNA 300 Query: 299 ENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGL--FGAGQTTVVRGDPARGPFTV 356 E+ V A+ LLG D +P+ WSDQY+ ++Q+ G+ FG+ T + + Sbjct: 301 EDHARVVASQLLGQDMVCDTVPFFWSDQYEWSMQIAGIPYFGSQLVT----NTVEEAKIL 356 Query: 357 FGLGGDGRIVAAAAVN----LGRDIGAARRLIAAGAMPDPQQLADPTVGLK 403 + L GR+VAA + +GR I ARRLI A P+PQ L + L+ Sbjct: 357 YHLDARGRLVAATGLGHDRLIGRKIAEARRLIKRRARPNPQMLKTGQIQLE 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: 362 Number of extensions: 19 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: 409 Length adjustment: 31 Effective length of query: 375 Effective length of database: 378 Effective search space: 141750 Effective search space used: 141750 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