Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate PfGW456L13_3417 Ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3417 Length = 411 Score = 213 bits (542), Expect = 8e-60 Identities = 154/389 (39%), Positives = 197/389 (50%), Gaps = 8/389 (2%) Query: 1 MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60 M+ VIVGAG A + A +LR D I +IG E LPY RP LSK LL Sbjct: 1 MTLASVVIVGAGQAGFQVAASLRQEGYDGRITLIGDEPGLPYQRPPLSKAYLLGKIQGTN 60 Query: 61 AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120 R A +Y QRI L L + AI+R+ RV L G + Y LVLATG+ R P Sbjct: 61 LLFRPAEFYATQRIEL-LHDQATAIDRQNGRVVLASGEAISYDHLVLATGAHNRPLPVPG 119 Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180 ++T ADA AL R V V+G GFIGLE AA A G NV V++ A R Sbjct: 120 AELPQVFGIKTKADADALAPLAKEARNVVVIGAGFIGLEFAAVAAAQGANVHVLELAERP 179 Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGD-VHADVVVVGI 239 + RA+ + + H+ GV F I G V+T G + AD+VV GI Sbjct: 180 MARAVSREMSELFRQAHEAWGVHFDFRQGLSRIDGDNGKVCAVQTADGRALPADLVVFGI 239 Query: 240 GVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLG---RHVRIESWQ 296 GV+PN +LA AGL ++NGI+VDA T+D I A G+V P L +H R+ES Q Sbjct: 240 GVIPNAQLATEAGLAIENGIKVDANLLTSDPRISALGDVASF--PCLQNDEQHTRLESVQ 297 Query: 297 VAENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTV 356 A +Q AA L+G Y LPW W+DQ D LQ+ GL +TVV G P +V Sbjct: 298 NAIDQARAVAARLMGKPAPYGALPWFWTDQGDLKLQIAGLSNGYDSTVVLGSPQDKQLSV 357 Query: 357 FGLGGDGRIVAAAAVNLGRDIGAARRLIA 385 D R+VA + N D AAR+++A Sbjct: 358 LCFRND-RLVAVESCNRMGDHMAARKILA 385 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: 361 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: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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