Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate Pf1N1B4_4393 Ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4393 Length = 413 Score = 240 bits (613), Expect = 5e-68 Identities = 162/406 (39%), Positives = 210/406 (51%), Gaps = 5/406 (1%) Query: 5 PFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64 P VIVGAGHA R A LR +++IG E PY+RP LSK L + Sbjct: 7 PLVIVGAGHAGGRAALTLRGEGYSGRLILIGDESHAPYERPPLSKGLLQGTVELAGYSLC 66 Query: 65 DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGV 124 D A I G V ++ + R++L DG+ L YA+L+LATG R R + + Sbjct: 67 DTAQLAELGIEHLAGNPVKCLDPQQHRLQLADGSWLHYARLLLATGGRSRRLASVPEHLL 126 Query: 125 VAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRA 184 Y+RT +A ALRA L RV ++GGGFIGLEVAA AR LGC VT+++ RL R Sbjct: 127 NVLYLRTHDEALALRASLQPDTRVVIIGGGFIGLEVAATARALGCTVTLLEAGPRLAGRV 186 Query: 185 LPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPN 244 LPE + + LH RGV ++ A++ ++ D + D+VVVGIG+ PN Sbjct: 187 LPEQLSSVLLELHRSRGVDVRLNVAIEAVQGTTHVESVQLVDGELLPCDLVVVGIGMQPN 246 Query: 245 VELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPAV 304 ELA AAGL+V GIRVDA RT+ IFAAG+V G R E+W+ AE Q Sbjct: 247 TELAAAAGLEVGQGIRVDAQLRTSAPDIFAAGDVCEFRLHPQGVFQRQETWRNAETQGRH 306 Query: 305 AAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLGGDGR 364 AA NLLG + + +P WSDQYD LQ +G+ Q T R P G F +F L + Sbjct: 307 AALNLLGGELPFEVIPGFWSDQYDWGLQTVGVIANTQPTASRTTPG-GGFLLFYLDAEQC 365 Query: 365 IVAAAAVNLG----RDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 + A G +DI RLIA + LAD V LK L Sbjct: 366 LQGACGWGQGNSIAKDIKLCERLIAHRNLLSVDALADADVPLKQLL 411 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: 342 Number of extensions: 18 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: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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