Align dihydromonapterin reductase (EC 1.5.1.50) (characterized)
to candidate WP_086509327.1 BZY95_RS07490 dihydromonapterin reductase
Query= BRENDA::P0AFS3 (240 letters) >NCBI__GCF_002151265.1:WP_086509327.1 Length = 237 Score = 200 bits (509), Expect = 2e-56 Identities = 102/233 (43%), Positives = 139/233 (59%) Query: 8 PILITGGGRRIGLALAWHFINQKQPVIVSYRTHYPAIDGLINAGAQCIQADFSTNDGVMA 67 PILITGG +R+G A ++ PVIVSYR P ++ L G ++ADF+T G++ Sbjct: 5 PILITGGAQRLGRHCAERLVDDGHPVIVSYRRERPELEALRRRGIVTLRADFATEAGILD 64 Query: 68 FADEVLKSTHGLRAILHNASAWMAEKPGAPLADVLACMMQIHVNTPYLLNHALERLLRGH 127 F + T LRAI+HNAS W + + ++H+ PYL+N LL Sbjct: 65 FIARLKGETRSLRAIVHNASDWAPDSRDEQAGATFERLFRVHMLAPYLINLHCRELLEAC 124 Query: 128 GHAASDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNSIAPSLILFN 187 G DI+H TDYV ++GS KH AYAA+KA L+N+T SFA APE++VN+IAP+LI+ Sbjct: 125 GEPQRDIVHMTDYVAQKGSKKHAAYAATKAGLENLTLSFAAMYAPEIQVNAIAPALIMLG 184 Query: 188 EHDDAEYRQQALNKSLMKTAPGEKEVIDLVDYLLTSCFVTGRSFPLDGGRHLR 240 E DD Y +QA KS M PG + + YLL + +VTG + P+DGGRHLR Sbjct: 185 EDDDEAYAEQARAKSAMAMVPGPGVIYQSLRYLLDNRYVTGITLPVDGGRHLR 237 Lambda K H 0.322 0.136 0.407 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: 175 Number of extensions: 4 Number of successful extensions: 1 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: 240 Length of database: 237 Length adjustment: 23 Effective length of query: 217 Effective length of database: 214 Effective search space: 46438 Effective search space used: 46438 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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