Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate 3608263 Dshi_1667 nitrite reductase (NAD(P)H), large subunit (RefSeq)
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Dino:3608263 Length = 810 Score = 144 bits (362), Expect = 1e-38 Identities = 130/391 (33%), Positives = 178/391 (45%), Gaps = 25/391 (6%) Query: 7 VIVGAGHAARRTAEALRARDADA-PIVMIGAERELPYDRPALSKDALLNDDGEQRAFVRD 65 VI+GAG A+ R E L D DA I + AE Y+R LS L D Sbjct: 6 VIIGAGMASGRVIEHLLKEDPDAFEITLFNAEPRGNYNRIMLSP-VLSGDKSYADIITHT 64 Query: 66 AAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDA--- 122 WY+ I R G V I+RE V G LPY KL++ATGS F P++ Sbjct: 65 DDWYEQNGITCRFGEHVVRIDRETGTVVGQRGA-LPYDKLLIATGSA--PFIIPVEGKDL 121 Query: 123 -GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLL 181 GV+ + R + D A+ G + V+GGG +GLE AA ++ G +VTV+ L+ Sbjct: 122 PGVITY--RDLDDTNAMIEAAASGGKAVVIGGGLLGLEAAAGLKERGMDVTVLHLMGHLM 179 Query: 182 QRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDVHADVVVVGIGV 241 +R L E G R ++RG+ + AI ++ D + AD+VV+ +G+ Sbjct: 180 ERQLDESAGFLLRRDLEKRGIKVKCRASTAAILGETRVEGVLLEDNEGLEADLVVMAVGI 239 Query: 242 LPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQ 301 P LA AGLDV GI VDA RT+D I A GE L G + +Q Sbjct: 240 RPETRLATDAGLDVARGITVDAELRTSDPDIHAVGECVEFDGQLFGLVAPL------YDQ 293 Query: 302 PAVAAANLLGADDAYAELPWLWSDQY---DCNLQMLGLF--GAGQTTVVRGDPARGPFTV 356 V A +LLG A+ P S + C+L G F GAG+ +V DP+RG + Sbjct: 294 ARVVADSLLGRSAAFT--PKELSTKLKVTGCDLFSAGDFADGAGREDIVFRDPSRGVYKR 351 Query: 357 FGLGGDGRIVAAAAVNLGRDIGAARRLIAAG 387 L + R+V A RD LI +G Sbjct: 352 LVL-EENRLVGAVFYGDTRDSNWFFGLIQSG 381 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: 694 Number of extensions: 43 Number of successful extensions: 5 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: 810 Length adjustment: 36 Effective length of query: 370 Effective length of database: 774 Effective search space: 286380 Effective search space used: 286380 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: 53 (25.0 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