Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate 16795 b2711 nitric oxide reductase (NCBI)
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Keio:16795 Length = 377 Score = 111 bits (277), Expect = 4e-29 Identities = 96/311 (30%), Positives = 148/311 (47%), Gaps = 21/311 (6%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRDA 66 VI+G+G AAR+ + +R +DA P+ +I A+ Y++P LS +++ R Sbjct: 6 VIIGSGFAARQLVKNIRKQDATIPLTLIAADSMDEYNKPDLSH--VISQGQRADDLTRQT 63 Query: 67 AWYDAQRIALRL--GTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDAGV 124 A A++ L L T V I+ EA+ V+ Y KLVLATG+ F P+ Sbjct: 64 AGEFAEQFNLHLFPQTWVTDIDAEARVVK-SQNNQWQYDKLVLATGASA--FVPPVPGRE 120 Query: 125 VAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQRA 184 + + + + RA QL RRV ++GGG IG E+A + G VT+ID AA +L Sbjct: 121 LMLTLNSQQEYRACETQLRDARRVLIVGGGLIGSELAMDFCRAGKAVTLIDNAASILASL 180 Query: 185 L-PEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLP 243 + PEV HRL E GV + + + + G + ++ D V+ G+ P Sbjct: 181 MPPEVSSRLQHRL-TEMGVHLLLKSQLQGLEKTDSGIQATLDRQRNIEVDAVIAATGLRP 239 Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAG---EVTMHFNPLLGRHVRIESWQVAEN 300 LA+ AGL ++ G+ VD+ +T++ I+A G E+ P L Q + Sbjct: 240 ETALARRAGLTINRGVCVDSYLQTSNTDIYALGDCAEINGQVLPFL---------QPIQL 290 Query: 301 QPAVAAANLLG 311 V A NLLG Sbjct: 291 SAMVLAKNLLG 301 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: 235 Number of extensions: 15 Number of successful extensions: 2 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: 377 Length adjustment: 31 Effective length of query: 375 Effective length of database: 346 Effective search space: 129750 Effective search space used: 129750 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