Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate SMc02016 SMc02016 ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Smeli:SMc02016 Length = 420 Score = 224 bits (571), Expect = 4e-63 Identities = 143/405 (35%), Positives = 209/405 (51%), Gaps = 12/405 (2%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 VIVG GHA R A+ALR I ++ E PY+RP LSK L + + A + A Sbjct: 14 VIVGCGHAGARAAQALRTNGWHGGITLVDGEGRTPYERPPLSKAVLKGESEAEDAPLFPA 73 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVVA 126 + I + G AI+R +++RL DG ++ Y +L+LATG+ R P + Sbjct: 74 DFLAKNDIHVLKGVAAAAIDRPTRQLRLSDGGSIAYHRLLLATGAEPRNLIVPGADLPGS 133 Query: 127 HYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRALP 186 H +R+ DA + L G + ++GGG IGLE AA+A GC VTV++ R + RA+P Sbjct: 134 HTLRSADDAARIFPYLRPGAEIVIVGGGLIGLEAAASATVRGCKVTVVEAGPRPMMRAVP 193 Query: 187 EVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAI--VETDRGDV-HADVVVVGIGVLP 243 + H+ + V F L R + G G + V D G V VV+ +GV P Sbjct: 194 AELSHEVRLFHESKDVRF---VLGRQVSELEGDGRVRCVRLDDGTVLPCTAVVISVGVSP 250 Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPA 303 LA+AAGL++DNGI VD RT+D I+AAG+ F + G +R+E W+ AE+Q Sbjct: 251 RTALAEAAGLEIDNGIAVDRFLRTSDPFIYAAGDACA-FEQVSGPRMRLECWKNAEDQGT 309 Query: 304 VAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDG 363 +A N+LG+D+AY LPW+WSDQ+D +Q+ G G V R P ++ L D Sbjct: 310 LAGRNMLGSDEAYVPLPWMWSDQFDRTMQIAGQAGGSAEDVRRRCP-DSTLLIYHLDKDQ 368 Query: 364 RIVAAAAVNLGRDIGAARR----LIAAGAMPDPQQLADPTVGLKT 404 I+ + R++ R L+ G P + LADP L++ Sbjct: 369 MILGISGFGSIREVSRGVRMGQLLMERGIRPGRKALADPEFDLRS 413 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: 385 Number of extensions: 23 Number of successful extensions: 5 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: 420 Length adjustment: 31 Effective length of query: 375 Effective length of database: 389 Effective search space: 145875 Effective search space used: 145875 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