Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate CCNA_00651 CCNA_00651 nitrite reductase (NAD(P)H) catalytic subunit
Query= SwissProt::Q84BZ0 (406 letters) >FitnessBrowser__Caulo:CCNA_00651 Length = 822 Score = 128 bits (321), Expect = 7e-34 Identities = 127/397 (31%), Positives = 178/397 (44%), Gaps = 32/397 (8%) Query: 7 VIVGAGHAARRTAEALRARDADAPIVMI-GAERELPYDRPALSKDALLNDDGEQRAFVRD 65 V++G G A R E + RD D V I GAE + Y+R LS L + + + D Sbjct: 11 VVIGNGMAGCRAVEEVLKRDPDRYAVTIFGAEPRVNYNRIMLSP-VLAGEKAFEDIVIND 69 Query: 66 AAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGS---RVRTFGGPIDA 122 AWY I L G V AI+ A++V + G + Y KL+LATGS R+ GG + Sbjct: 70 EAWYRDNGITLHAGRAVTAIDLAARKVFAEGGLEIGYDKLILATGSDPFRLPLPGGDLK- 128 Query: 123 GVVAHYVRTVADARA-LRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLL 181 GVV R + D A L A R V+GGG +GLE A + G TV+ L+ Sbjct: 129 GVVTF--RDLDDVNAMLAASAEPDARAVVIGGGLLGLEAAYGLARRGMAATVVHLMDVLM 186 Query: 182 QRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDV-HADVVVVGIG 240 +R L E G +RGV + I A G ++ G V D++V+ +G Sbjct: 187 ERQLDESAGYLLREALADRGVETVLGAHSEEIVGADGQVTGLKLKDGRVLPCDLLVMAVG 246 Query: 241 VLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAEN 300 + PN LA+AAGL V+ G+ VD RT+D +FA GE H G I W++ Sbjct: 247 IRPNTTLAKAAGLTVNRGVAVDDAMRTSDPDVFAVGECVEHRGQCYGLVAPI--WEMCR- 303 Query: 301 QPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLG--LFGAGQ-------TTVVRGDPAR 351 A+A A L + AY L++ G +F AG+ +V D AR Sbjct: 304 --ALAQA-LTDGEGAYQ------GSVLSTRLKVSGVDVFSAGKFAGGEGCEDIVFRDAAR 354 Query: 352 GPFTVFGLGGDGRIVAAAAVNLGRDIGAARRLIAAGA 388 G + + DG++ A D G L+ AGA Sbjct: 355 GVYKRVVI-EDGKVAGAVLFGDAADGGWYFDLMKAGA 390 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: 713 Number of extensions: 33 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: 822 Length adjustment: 36 Effective length of query: 370 Effective length of database: 786 Effective search space: 290820 Effective search space used: 290820 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