Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF2177 PS417_11105 pyridine nucleotide-disulfide oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__WCS417:GFF2177 Length = 399 Score = 236 bits (603), Expect = 7e-67 Identities = 164/406 (40%), Positives = 217/406 (53%), Gaps = 16/406 (3%) Query: 5 PFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64 P +IVGAGHA R A LR +++IG E LPY+RP LSK L + Sbjct: 4 PLIIVGAGHAGGRAALTLREEGYTGRLILIGDEPHLPYERPPLSKGLLQGTADLAGYSLC 63 Query: 65 DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGV 124 D A I G V ++ + R++L DG LPYA L+LATG R R P + Sbjct: 64 DRARLAELGIEHIAGNPVTHLQPQQHRLQLADGQWLPYAGLLLATGGRARRL--PQEQAH 121 Query: 125 VAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRA 184 V Y+RT +A ALR+ L G R+ V+GGGFIGLEVAA AR LGC VT+++ RL R Sbjct: 122 VL-YLRTHDEALALRSALKAGTRLVVVGGGFIGLEVAATARGLGCEVTLLEAGPRLAGRV 180 Query: 185 LPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPN 244 LP V+ LH + GV ++ +I+A A+ D + D+VVVGIG+ PN Sbjct: 181 LPPVISEALLTLHRQHGVDVRLNMALESIQA----DAVWLVDGQRLPCDLVVVGIGMQPN 236 Query: 245 VELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPAV 304 +ELA AAGL+V GIRVD+ RT+ I+AAG+V L G + R E+W+ AE Q Sbjct: 237 IELAAAAGLEVGQGIRVDSHLRTSAPGIYAAGDVCEF--RLGGEYQRQETWRNAEAQGRH 294 Query: 305 AAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDGR 364 AA NLLG + + LP WSDQYD +Q +G+ +V A G +F L D R Sbjct: 295 AALNLLGRELPFEALPGFWSDQYDWGVQTVGVI---TPLMVSRPLASGGMLLFYLDADQR 351 Query: 365 IVAAA----AVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 + A ++ +DI RLI+A P LADP + LK L Sbjct: 352 LQGACGWAPGNSVAKDIKLCERLISAHLSLAPASLADPELSLKHLL 397 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: 341 Number of extensions: 25 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: 399 Length adjustment: 31 Effective length of query: 375 Effective length of database: 368 Effective search space: 138000 Effective search space used: 138000 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