Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF27 HP15_27 FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Marino:GFF27 Length = 432 Score = 196 bits (497), Expect = 1e-54 Identities = 140/387 (36%), Positives = 195/387 (50%), Gaps = 5/387 (1%) Query: 1 MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60 MS IVGAG A + A +LR I +IG E +LPY RP LSK +L + Sbjct: 23 MSLSSVAIVGAGQAGFQVAASLRQGGFKGKISLIGDEPDLPYQRPPLSKAYMLGKIKRES 82 Query: 61 AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120 R ++ Q I L T ++ I+R+ +RV L GT Y LVLATG+ R P Sbjct: 83 LAFRPETFFQEQDIDLIHDTAIE-IDRQNRRVVLQSGTVCHYDHLVLATGAHNRPLALPG 141 Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180 + ++T+ DA AL ++ R V V+G GFIGLE AA A Q NV VID R Sbjct: 142 EDLQGVFGIKTLKDADALSPEVKSARDVVVIGAGFIGLEFAAIAVQ-NANVQVIDMGQRA 200 Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDV-HADVVVVGI 239 + RA+ + + H E GV F + + + G VE + G++ AD+VV GI Sbjct: 201 MARAISQEMSEVFEETHQEWGVTFHFNQGVKRLIGSNGKVTGVEKEDGEILKADLVVYGI 260 Query: 240 GVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVT-MHFNPLLGRHVRIESWQVA 298 GV+PN+ +A AGL ++NGI+VD+ T D I A G+V G+ RIES A Sbjct: 261 GVVPNIAIASEAGLTIENGIKVDSNLLTNDPHISAIGDVACFPCTHNEGQFTRIESVPNA 320 Query: 299 ENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFG 358 +Q AA LLG+ ++ +PW W+DQ + LQ+ GL TTV G F+V Sbjct: 321 MDQARAVAARLLGSPSPFSSVPWFWTDQGNLKLQIAGLSTGFDTTVTLGSKDSRQFSVLC 380 Query: 359 LGGDGRIVAAAAVNLGRDIGAARRLIA 385 G VA A N D A +++++ Sbjct: 381 F-RKGHFVAVEACNRPGDHLAGKKILS 406 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: 331 Number of extensions: 17 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: 432 Length adjustment: 32 Effective length of query: 374 Effective length of database: 400 Effective search space: 149600 Effective search space used: 149600 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