Align oxygen-insensitive NAD(P)H nitroreductase; EC 1.-.-.-; EC 1.5.1.34 (characterized)
to candidate 202809 SO3715 oxygen-insensitive NAD(P)H nitroreductase (NCBI ptt file)
Query= CharProtDB::CH_002389 (217 letters) >FitnessBrowser__MR1:202809 Length = 217 Score = 233 bits (595), Expect = 2e-66 Identities = 117/216 (54%), Positives = 152/216 (70%), Gaps = 1/216 (0%) Query: 2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVA 61 D+ +A KR++TKAFD +K + ++ IKTLLQ+SPSSTNSQPWHF++A T EGKA +A Sbjct: 3 DLSFLAKKRYTTKAFDPTKIIPTDKIADIKTLLQFSPSSTNSQPWHFVLAGTAEGKALIA 62 Query: 62 KSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGR 121 + A +Y FN +K+LDASHVVV C +T +D+ L V++QE DGRFA EAK GR Sbjct: 63 Q-ATEHYAFNTQKILDASHVVVLCTRTQLDEAHLLQVLEQEAKDGRFANEEAKQGQHNGR 121 Query: 122 KFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEK 181 FFA+MH+ +L D WM KQVYL +G +LG + L +DA PIEGFDA L+ GL+EK Sbjct: 122 SFFANMHKFELKDAQHWMEKQVYLALGTLMLGASVLDIDACPIEGFDATKLNQVLGLREK 181 Query: 182 GYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217 G + VVV +G+ S EDFNA LPKSRL Q + TE+ Sbjct: 182 GLCASVVVALGYRSEEDFNAKLPKSRLAQEVIFTEI 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: 152 Number of extensions: 3 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