Align oxygen-insensitive NAD(P)H nitroreductase; EC 1.-.-.-; EC 1.5.1.34 (characterized)
to candidate 5208176 Shew_0688 dihydropteridine reductase (RefSeq)
Query= CharProtDB::CH_002389 (217 letters) >FitnessBrowser__PV4:5208176 Length = 217 Score = 237 bits (604), Expect = 1e-67 Identities = 118/209 (56%), Positives = 151/209 (72%), Gaps = 1/209 (0%) Query: 9 KRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNY 68 KR++TKAFD S+K+ ++ E+IK LL+ SPSSTNSQPWHF++ASTEEGKA++A+ A ++ Sbjct: 10 KRYTTKAFDPSRKIADDKIEEIKQLLRMSPSSTNSQPWHFVLASTEEGKAQIAE-ATSDF 68 Query: 69 VFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMH 128 FN K+L+ASHV+V C KT MD+ L V++QEDADGRFA AK GR FFA+MH Sbjct: 69 AFNTAKILNASHVLVLCTKTNMDEAHLLKVLEQEDADGRFADEAAKQGQHNGRSFFANMH 128 Query: 129 RKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVV 188 R +L D WM KQVYL +GN LLG + L +DA PIEGF+A L+ L KGY + VV Sbjct: 129 RIELKDSQHWMEKQVYLALGNLLLGASLLDIDATPIEGFNATKLNQVLELPAKGYAASVV 188 Query: 189 VPVGHHSVEDFNATLPKSRLPQNITLTEV 217 V +G+HS +DFNA LPKSRLP TE+ Sbjct: 189 VALGYHSEDDFNAKLPKSRLPIETLFTEI 217 Lambda K H 0.317 0.131 0.379 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: 150 Number of extensions: 6 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: 217 Length of database: 217 Length adjustment: 22 Effective length of query: 195 Effective length of database: 195 Effective search space: 38025 Effective search space used: 38025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 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