Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate HSERO_RS14545 HSERO_RS14545 nitrite reductase
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS14545 Length = 407 Score = 124 bits (311), Expect = 5e-33 Identities = 122/401 (30%), Positives = 171/401 (42%), Gaps = 30/401 (7%) Query: 7 VIVGAGHAARRTAEALRARDADA-PIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRD 65 V+VG G A RT E L D I + GAE Y+R LS L D + Sbjct: 15 VVVGNGMAGMRTVEELLKLAPDLYDITVFGAEPHGNYNRIMLSP-VLAGDKSIDDIMLNP 73 Query: 66 AAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSR--VRTFGGPIDAG 123 AWYD I L G V I+R + V G T+ Y +L+LATGS + G G Sbjct: 74 RAWYDDNGITLHAGDPVVHIDRRQRTVHAKSGLTVQYDRLLLATGSTPFIIPVPGHQLPG 133 Query: 124 VVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQR 183 V+A R + D A+ R V+GGG +GLE A + G +VTV+ L+ + Sbjct: 134 VIAF--RDIQDVDAMLQAARTHRHAVVIGGGLLGLEAANGLMRQGMDVTVVHVTDALMNQ 191 Query: 184 ALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGVLP 243 L + A + +++G+ F + I A+ D + AD+VV+ GV P Sbjct: 192 QLDKPAAALLKKALEDKGLRFLLNAHTEEIVGPDRVTAVRFKDGSSIPADLVVMTAGVRP 251 Query: 244 NVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQPA 303 N+ LA+AAGL + I VD +T D ++A GE H G I W +Q Sbjct: 252 NIALAKAAGLHCERAIIVDDTLQTYDPRVYAVGECVQHRKATFGLVAPI--W----DQAR 305 Query: 304 VAAANLLGADD-AYAELPWLWSDQY-DCNLQMLGLFGAGQTT--VVRGDPARGPFTVFGL 359 V A+L GA Y + + +L G F G T ++ DP RG + L Sbjct: 306 VCGAHLAGAGHRRYVQQATATKLKVTGVDLYSAGDFIGGDDTEDLIVRDPRRGVYKRLVL 365 Query: 360 GGDGRIVAAA-------------AVNLGRDIGAARRLIAAG 387 G R+V A + GRDI + RR + G Sbjct: 366 RGT-RLVGAVLYGDVKDGPWYFDLIQSGRDISSFRRELPFG 405 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: 360 Number of extensions: 19 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: 407 Length adjustment: 31 Effective length of query: 375 Effective length of database: 376 Effective search space: 141000 Effective search space used: 141000 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