Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate 16641 b2542 phenylpropionate dioxygenase, ferredoxin reductase subunit (NCBI)
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Keio:16641 Length = 400 Score = 212 bits (540), Expect = 1e-59 Identities = 146/406 (35%), Positives = 202/406 (49%), Gaps = 9/406 (2%) Query: 1 MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60 M +IVG G AA A +LR + + + ER LPY+RP LSK LL +D Q Sbjct: 1 MKEKTIIIVGGGQAAAMAAASLRQQGFTGELHLFSDERHLPYERPPLSKSMLL-EDSPQL 59 Query: 61 AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120 V A W+ + L G + + R+ + + L +G + + +L +ATG+ R Sbjct: 60 QQVLPANWWQENNVHLHSGVTIKTLGRDTRELVLTNGESWHWDQLFIATGAAARPLPLLD 119 Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180 G +R DA LR L R V ++G G IGLE+AA+A Q C VTVI+ AA + Sbjct: 120 ALGERCFTLRHAGDAARLREVLQPERSVVIIGAGTIGLELAASATQRRCKVTVIELAATV 179 Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGD--VHADVVVVG 238 + R P V Y + H + GV L AI G + T + + ADVV+ G Sbjct: 180 MGRNAPPPVQRYLLQRHQQAGVRI---LLNNAIEHVVDGEKVELTLQSGETLQADVVIYG 236 Query: 239 IGVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVA 298 IG+ N +LA+ A LD NGI +D CRT D AIFA G+V + H R ESW+ A Sbjct: 237 IGISANEQLAREANLDTANGIVIDEACRTCDPAIFAGGDVAITRLDNGALH-RCESWENA 295 Query: 299 ENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFG 358 NQ +AAA +LG PW WSDQY NLQ +G G + RG+P F Sbjct: 296 NNQAQIAAAAMLGLPLPLLPPPWFWSDQYSDNLQFIGDM-RGDDWLCRGNPETQKAIWFN 354 Query: 359 LGGDGRIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLKT 404 L +G ++ A +N GR+I R+ I +G D + L D + LK+ Sbjct: 355 L-QNGVLIGAVTLNQGREIRPIRKWIQSGKTFDAKLLIDENIALKS 399 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: 340 Number of extensions: 14 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: 400 Length adjustment: 31 Effective length of query: 375 Effective length of database: 369 Effective search space: 138375 Effective search space used: 138375 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