Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate SMc00914 SMc00914 oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Smeli:SMc00914 Length = 405 Score = 243 bits (621), Expect = 6e-69 Identities = 161/403 (39%), Positives = 209/403 (51%), Gaps = 7/403 (1%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 V+VG G AA LRA PI ++ AE LPY RP LSK LL + R R Sbjct: 6 VVVGGGQAAFALVAKLRALKDMRPITVVAAEASLPYQRPPLSKKYLLREMTLDRLLYRPE 65 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVVA 126 AWY I +RL T V ++R A++V L DG+ L Y L ATG+ R + + Sbjct: 66 AWYAEHEIDIRLSTTVTRVDRLAKQVALSDGSMLTYETLAFATGATPRRLPAAVGGDLAG 125 Query: 127 HY-VRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRAL 185 + VR DA L ++ GRRV V+GGG+IGLE AA AR G VTVI+ A R+LQR Sbjct: 126 VFVVRDFRDADRLAEEMQPGRRVLVVGGGYIGLEAAAVARTSGLEVTVIEMADRILQRVA 185 Query: 186 PEVVGAYAHRLHDERGVGFQMAT-LPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPN 244 A +H GV + T L R I A +D + D+V+VGIGV N Sbjct: 186 SAATSAIVREIHRSHGVDIRERTGLHRLIGDNGRVTAAELSDGSVIPVDIVIVGIGVAAN 245 Query: 245 VELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPAV 304 LA AG++ NGI VD+ RT+D I A G+ + P G +R+ES Q A +Q Sbjct: 246 DALAHEAGIETANGIVVDSHGRTSDPTIVAMGDCAV--LPWDGMRIRLESVQNAVDQAEA 303 Query: 305 AAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAG-QTTVVRGDPARGPFTVFGLGGDG 363 AA L G D Y PW WSDQYD LQ+ G FG G T+VR +G +V+ G Sbjct: 304 VAAVLAGGTDPYDPKPWFWSDQYDVKLQIAG-FGLGHDETLVRQGQRQGSVSVWYF-RQG 361 Query: 364 RIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 +++A A+N + ++L+ AGA PD LADP V LK L Sbjct: 362 KLIAVDAINDAKAYVTGKKLLEAGATPDRLLLADPQVDLKALL 404 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: 379 Number of extensions: 19 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: 405 Length adjustment: 31 Effective length of query: 375 Effective length of database: 374 Effective search space: 140250 Effective search space used: 140250 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