Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate AZOBR_RS28130 AZOBR_RS28130 pyridine nucleotide-disulfide oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__azobra:AZOBR_RS28130 Length = 417 Score = 268 bits (684), Expect = 3e-76 Identities = 171/404 (42%), Positives = 227/404 (56%), Gaps = 9/404 (2%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 VIVGAG + AE+LRA D PI +IG E PY RP LSK L E + +R A Sbjct: 15 VIVGAGQGGLQVAESLRAEGYDGPITLIGEEASAPYHRPPLSKAILAGTMEEAQLAIRGA 74 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTF---GGPIDAG 123 +++ QRIAL GTRV AI+R A+ VRL+DG L Y L LATG+RVR G +D G Sbjct: 75 EFFERQRIALLTGTRVAAIDRSARHVRLEDGRRLEYRGLALATGARVRRLPVAGDELD-G 133 Query: 124 VVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQR 183 V+ +R++ DAR +R L R RV V+GGG+IGLEVAAAAR+ G VT+++ A RLL R Sbjct: 134 VLG--LRSLDDARRIRVALDRAARVVVIGGGYIGLEVAAAARKRGLEVTILEAADRLLAR 191 Query: 184 ALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVH-ADVVVVGIGVL 242 + + A+ LH +G ++ A+ G V T G H AD+VVVG+G++ Sbjct: 192 SATPFLAAFYADLHRSQGALVELGAKVVALDGQGGRVTAVRTADGRSHPADLVVVGVGIV 251 Query: 243 PNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQP 302 P+ LA+ GL D GI VD RT D AI A G+ T G +R+ES Q A Q Sbjct: 252 PDTALAEGCGLACDGGILVDDSARTDDPAIVAVGDCTAR-RTGTGTPLRLESVQNAVEQG 310 Query: 303 AVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGD 362 AAA LLG + + PW WSDQYD LQ++GL V+RG P F+ F D Sbjct: 311 RSAAAALLGRERPFTAAPWFWSDQYDVKLQIVGLSADHDRMVLRGSPEDRRFSAFYFRRD 370 Query: 363 GRIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 +VA ++N D A R+L+ M P+Q AD ++ L + + Sbjct: 371 A-LVAIDSINRPADHMAGRKLLDHKTMITPEQAADESLPLASLM 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: 417 Number of extensions: 21 Number of successful extensions: 3 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: 417 Length adjustment: 31 Effective length of query: 375 Effective length of database: 386 Effective search space: 144750 Effective search space used: 144750 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