Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate 3606683 Dshi_0114 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Dino:3606683 Length = 401 Score = 237 bits (605), Expect = 4e-67 Identities = 157/405 (38%), Positives = 218/405 (53%), Gaps = 15/405 (3%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 V++GAG A LR + ++G E PY RP LSK LL D E+R ++R A Sbjct: 5 VVIGAGQAGASLVAKLRVLGHQGAVTLVGEEPVPPYQRPPLSKGYLLGDMAEERLYLRPA 64 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVR----TFGGPIDA 122 +Y I L+LGT V A++ A V L D L Y +L TGS R + GG +D Sbjct: 65 RYYAENGITLKLGTPVKAVDTGACEVFLGD-ERLSYDQLAFTTGSVPRRLPASIGGTLD- 122 Query: 123 GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182 GV VRT+AD A+ Q+ G+ V ++GGG+IGLE AA A +LG VT+++ A R+LQ Sbjct: 123 GVFT--VRTLADVDAMAPQMSAGKHVLIVGGGYIGLEAAAVASKLGLRVTLVEMADRILQ 180 Query: 183 RALPEVVGAYAHRLHDERGVGFQMAT-LPRAIRAAAGGGAIVETDRGDVHADVVVVGIGV 241 R A+ +LH + GV + L R A GA + +D ++ D+V+VG+G+ Sbjct: 181 RVAAPETSAFFRKLHADHGVDLREGVGLDRLTGEGAVTGARL-SDGSELALDLVIVGVGI 239 Query: 242 LPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQ 301 P +LA AAG+ +DNGI VDA RT+ ++AAG+ P G +R+ES Q A +Q Sbjct: 240 APATDLAAAAGVALDNGIAVDALGRTSAPGVWAAGDCAS--LPHRGARIRLESVQNAIDQ 297 Query: 302 PAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGG 361 AAN+LGA+ Y PW WSDQYD LQ+ GL VVR D G + + G Sbjct: 298 AEAVAANMLGAETPYVPKPWFWSDQYDVKLQIAGLNTGYDRVVVRDD--AGAISHWYYAG 355 Query: 362 DGRIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 + ++A A+N R +RLI G PD +ADP LK + Sbjct: 356 N-TLLAVDAMNAPRAYMVGKRLIDGGKSPDATLVADPATELKDLM 399 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: 392 Number of extensions: 20 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: 401 Length adjustment: 31 Effective length of query: 375 Effective length of database: 370 Effective search space: 138750 Effective search space used: 138750 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