Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate AO356_30130 AO356_30130 pyridine nucleotide-disulfide oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30130 Length = 410 Score = 237 bits (605), Expect = 4e-67 Identities = 162/416 (38%), Positives = 220/416 (52%), Gaps = 25/416 (6%) Query: 5 PFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDAL---LNDDGEQRA 61 P +IVGAGHA R A LR + +++IG E LPY+RP LSK L +N D Sbjct: 4 PLIIVGAGHAGGRAALTLREQGYTGRLILIGDELHLPYERPPLSKGLLQGMMNLDD---- 59 Query: 62 FVRDAAWYDAQRIALRL----GTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFG 117 + W D++ L + G V +++ + R++L DG LPY++L+LATG R R Sbjct: 60 ---CSLWSDSRLTELSIEHLAGNPVKSLDPQHHRLQLTDGRWLPYSRLLLATGGRARRLS 116 Query: 118 GPIDAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPA 177 + Y+RT +A ALR+ L+ G R+ ++GGGFIGLEVAA AR LGC VT+++ Sbjct: 117 LVPEPLANVLYLRTHDEALALRSALMPGTRLVIIGGGFIGLEVAATARTLGCQVTLLEAG 176 Query: 178 ARLLQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVV 237 RL R LPE V LH ++GV ++ ++ + D + D VVV Sbjct: 177 PRLAGRVLPEAVSQALLELHRQQGVDVRLNVALERVQGIERAEVVQLVDGQVLPCDWVVV 236 Query: 238 GIGVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEV---TMHFNPLLGRHVRIES 294 GIG+ PN+ELA AAGL+V GIRVDA RT+ IFAAG+V +H + L R E+ Sbjct: 237 GIGMQPNIELAAAAGLEVGQGIRVDAQLRTSAPDIFAAGDVCEFRLHADALFQRQ---ET 293 Query: 295 WQVAENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPF 354 W+ AE Q AA NLLG + + +P WSDQYD LQ +G+ + VR A G Sbjct: 294 WRNAETQGRHAALNLLGGELPFEGVPGFWSDQYDWGLQTVGVISPAPPSAVR-TLASGGL 352 Query: 355 TVFGLGGDGRIVAAAAVNLG----RDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 +F L + R+ A G +DI RLIA LAD V LK L Sbjct: 353 LLFYLDTEQRLQGACGWGQGNSVAKDIKLCERLIANLTPLSVDALADADVPLKHLL 408 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: 333 Number of extensions: 16 Number of successful extensions: 4 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: 410 Length adjustment: 31 Effective length of query: 375 Effective length of database: 379 Effective search space: 142125 Effective search space used: 142125 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