Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate H281DRAFT_03846 H281DRAFT_03846 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin reductase subunit
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Burk376:H281DRAFT_03846 Length = 419 Score = 254 bits (650), Expect = 3e-72 Identities = 159/402 (39%), Positives = 210/402 (52%), Gaps = 4/402 (0%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 VIVGA +A + A + R D IV+IG E PY RP LSK L E+R +R Sbjct: 6 VIVGASYAGLQLAASARESGHDGDIVLIGDEPHAPYQRPPLSKGFLTGSFAEERLPLRSP 65 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVVA 126 A+Y R+ TR I+RE +++ L DG L Y L L TG+RVR + Sbjct: 66 AFYGEMRMQWMPSTRALRIDRERKQIELHDGARLAYDHLALTTGARVRKLDCKGASHDAV 125 Query: 127 HYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRALP 186 HY+R + DAR L + RR V+GGG+IGLE AA+ RQ G +VTV++ AR+L R Sbjct: 126 HYLRDLRDARRLVERTQTARRAVVVGGGYIGLEAAASLRQKGLDVTVVETEARVLARVAS 185 Query: 187 EVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPNVE 246 + R H GV + AI A G A+ D + D+VVVGIGVLPN E Sbjct: 186 PSISVIMQRAHTRHGVSLALGRKVVAIHDVADGVAVELDDGARLSCDLVVVGIGVLPNTE 245 Query: 247 LAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTM---HFNPLLGRHVRIESWQVAENQPA 303 LA GLDV GI VDA RT+D +I AAG+ ++ P RIES Q A + Sbjct: 246 LAAGCGLDVAGGIVVDACARTSDPSIVAAGDCAAFVPYWAPTGSAACRIESVQNANDMAR 305 Query: 304 VAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDG 363 AAA++LG + Y +PW WSDQYD LQM G+ VRG G F++F D Sbjct: 306 TAAASVLGRSEPYRAVPWFWSDQYDLKLQMAGVNTGFTDFAVRGSVDEGKFSLFYF-RDD 364 Query: 364 RIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTF 405 R+VA ++N +D AR+L++ G + + P LK F Sbjct: 365 RLVAVDSINRPQDHMLARKLLSTGTRLSVEDVNGPGFDLKAF 406 Score = 25.8 bits (55), Expect = 0.003 Identities = 9/22 (40%), Positives = 17/22 (77%) Query: 147 RVAVLGGGFIGLEVAAAARQLG 168 R+ ++G + GL++AA+AR+ G Sbjct: 4 RLVIVGASYAGLQLAASARESG 25 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: 376 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 406 Length of database: 419 Length adjustment: 31 Effective length of query: 375 Effective length of database: 388 Effective search space: 145500 Effective search space used: 145500 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