Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF2881 PGA1_c29270 rhodocoxin reductase ThcD
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Phaeo:GFF2881 Length = 403 Score = 233 bits (595), Expect = 6e-66 Identities = 154/403 (38%), Positives = 213/403 (52%), Gaps = 7/403 (1%) Query: 6 FVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRD 65 FV++GAG A LR + + I +IG+E +PY RP LSK LL + +R ++R Sbjct: 4 FVVIGAGQAGASLVAQLRKQGFEGEITLIGSEPVVPYQRPPLSKAYLLGELELERLYLRP 63 Query: 66 AAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGVV 125 ++Y I L+LG +V AI+ A+ V L+D L Y +L L TGS R I + Sbjct: 64 ESFYADSNITLKLGQQVQAIDPAAKTVTLED-EVLHYDQLALTTGSSPRRLPAAIGGDLN 122 Query: 126 AHYV-RTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRA 184 YV R +AD A+ + G R ++GGG+IGLE AA + G VT+++ A R+LQR Sbjct: 123 GVYVLRDLADVDAMAPVVKDGARTLIVGGGYIGLEAAAVCAKRGVAVTLVEMAGRILQRV 182 Query: 185 LPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGG-GAIVETDRGDVHADVVVVGIGVLP 243 Y LH GV + + G V +D V D VVVG+G+ P Sbjct: 183 AAPETSDYFRALHTGHGVDIREGIGLERLEGENGTVSRAVLSDGSTVEVDFVVVGVGITP 242 Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPA 303 +LA+AAGL ++NGI+VDA RT+D +I+AAG+ P G +R+ES A +Q Sbjct: 243 ASDLAEAAGLTLENGIKVDAQGRTSDPSIWAAGDCASF--PYCGSRIRLESVPNAIDQAE 300 Query: 304 VAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDG 363 VAA N+LGA++ Y PW WSDQYD LQ+ GL G VV G + + GD Sbjct: 301 VAARNMLGANETYVAKPWFWSDQYDVKLQIAGL-NTGYDNVVTRAGQDGTMSFWYYTGD- 358 Query: 364 RIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 ++VA A+N R A+RLI AG D +AD LK L Sbjct: 359 QLVAVDAMNDPRAYMVAKRLIEAGRTADKAVVADVEADLKPLL 401 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: 378 Number of extensions: 22 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: 403 Length adjustment: 31 Effective length of query: 375 Effective length of database: 372 Effective search space: 139500 Effective search space used: 139500 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