Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate RR42_RS26430 RR42_RS26430 ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS26430 Length = 428 Score = 267 bits (683), Expect = 4e-76 Identities = 165/415 (39%), Positives = 228/415 (54%), Gaps = 15/415 (3%) Query: 1 MSAD-PFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQ 59 MS D P +I+GAG A A ALRA D IVM+G E PY+RP LSK L ++ ++ Sbjct: 1 MSQDAPILIIGAGQAGATAAAALRALGHDGGIVMVGGEAHAPYERPPLSKAVLADEQQDE 60 Query: 60 RAFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGP 119 R V +Y Q I LRL T V +++ + DG + +++ +LATG R R Sbjct: 61 RIGVHAPGFYAEQGIDLRLATTVASLDPASATAHCADGQAISFSRCLLATGGRARALPAL 120 Query: 120 IDAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAAR 179 + HY+R++ADAR LRA L R R V V+GGGF+GLE A+ AR +G VTV++ A Sbjct: 121 PEGQPRVHYLRSLADARGLRAALRRERAVLVIGGGFLGLETASTARAMGLAVTVVEAAPL 180 Query: 180 LLQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGI 239 LLQRA+P V + + G+ ++ +I AA A++ D + A + VV I Sbjct: 181 LLQRAVPSVFSDWLAQRVRGLGIDLRLGCGIASIPPAADEVAVMLADGTALRAPLAVVAI 240 Query: 240 GVLPNVELAQAAGLDV---DNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQ 296 G+ PNV LA+AAGL + + GI+VDA CRT+ +FAAG+ + PL G+ +R+ESWQ Sbjct: 241 GLHPNVGLAEAAGLALHPGNGGIQVDAHCRTSAPGVFAAGDCASQYQPLFGQEMRLESWQ 300 Query: 297 VAENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGD-------- 348 A Q +AAA +LG A + LPW W+DQ CN+QMLG +RG Sbjct: 301 NANEQARIAAAAMLGVPTAPSALPWFWTDQLGCNIQMLGAMDPALRYTLRGSMEAPGADT 360 Query: 349 PARGPFTVFGLGGDGRIVAAAAVNLGRDIGAARRLIAAGAMPDPQQLADPTVGLK 403 P R F + G+ G ++ A AVN G D+ R LI G D L D + LK Sbjct: 361 PPR--FLLLGMAG-AQLRHAIAVNAGGDLRPLRNLIEQGTACDIGLLCDTALPLK 412 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: 424 Number of extensions: 22 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: 428 Length adjustment: 31 Effective length of query: 375 Effective length of database: 397 Effective search space: 148875 Effective search space used: 148875 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