Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate SM_b20820 SM_b20820 ferredoxin reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Smeli:SM_b20820 Length = 409 Score = 296 bits (759), Expect = 6e-85 Identities = 178/410 (43%), Positives = 238/410 (58%), Gaps = 17/410 (4%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 VI+GAG R A ALR + I + GAE LPY+RP LSKD L F+ A Sbjct: 5 VIIGAGECGARAAFALREKGFGGEITLTGAEPHLPYERPPLSKDGLAQ--ASLPKFIAGA 62 Query: 67 AWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGG-PIDAGVV 125 A Y+ RI + G ++I+R + V L DG +L Y +L+LATG+R R F P +AG + Sbjct: 63 ARYEEARITVLTGVTAESIDRVHKAVTLSDGVSLDYDRLLLATGARPRAFPRVPENAGRI 122 Query: 126 AHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRAL 185 +RT ADA A+R L G R+AV+GGGFIGLE+AA AR+LG V +++ R+L R + Sbjct: 123 -RTLRTHADALAIRGALTPGARLAVIGGGFIGLELAATARKLGAEVVLVEGLPRVLSRGV 181 Query: 186 PEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLPNV 245 PE + H GV AI A G ++ D D+ AD++VVGIG +PN Sbjct: 182 PEEIAVLVAERHRREGVEIICGAQIAAIDGAGDGARLLLADGVDIEADLIVVGIGAVPNT 241 Query: 246 ELAQAAGLDVDNGIRVDAGCRTAD-----RAIFAAGEVTMHFNPLLGRHVRIESWQVAEN 300 ELA+AAGL ++NGI VD T+D R AA + H+ GR VR+E+W+ A++ Sbjct: 242 ELAEAAGLAIENGIAVDERLCTSDPRHLCRPATAAPSLCPHYG---GRRVRLEAWRNAQD 298 Query: 301 QPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFGLG 360 Q A+AAANL+GA + +PW WSDQY+ LQ+ GL +TT VR D G F +F L Sbjct: 299 QGALAAANLMGAGETMVSVPWFWSDQYEFTLQIAGLADGAETT-VRRDMEEGAFILFHLD 357 Query: 361 GDGRIVAAAAVNLG----RDIGAARRLIAAGAMPDPQQLADPTVGLKTFL 406 G+GR++AA+ + G RDI A LIAAGA P+P LA P LK L Sbjct: 358 GEGRLIAASGIGPGNAVARDIRLAEMLIAAGAKPEPLALASPETRLKKLL 407 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: 370 Number of extensions: 19 Number of successful extensions: 6 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: 409 Length adjustment: 31 Effective length of query: 375 Effective length of database: 378 Effective search space: 141750 Effective search space used: 141750 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