Align dihydromonapterin reductase (EC 1.5.1.50) (characterized)
to candidate GFF4590 PS417_23490 dihydrofolate reductase
Query= BRENDA::P0AFS3 (240 letters) >FitnessBrowser__WCS417:GFF4590 Length = 236 Score = 198 bits (503), Expect = 9e-56 Identities = 104/233 (44%), Positives = 149/233 (63%), Gaps = 3/233 (1%) Query: 8 PILITGGGRRIGLALAWHFINQKQPVIVSYRTHYPAIDGLINAGAQCIQADFSTNDGVMA 67 PILITG G+R+GL A +++ PVI SYR+ P + L GA + ADFS+ G++A Sbjct: 7 PILITGAGQRVGLHCAQRLLDEGHPVIFSYRSERPGVQALRARGAVGLFADFSSEAGILA 66 Query: 68 FADEVLKSTHGLRAILHNASAWMAEKPGAPLADVLACMMQIHVNTPYLLNHALERLLRGH 127 F E+ T LRAI+HNASAW+AE P + M +H+ PYL+N LL+ Sbjct: 67 FIAELNTHTQSLRAIIHNASAWIAETPDDE-SRAFTDMFSVHMLAPYLINLHCSPLLQRS 125 Query: 128 GHAASDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNSIAPSLILFN 187 A DI+H +D VV +GS +HIAY A+KA LD++T SFA + AP +KVN IAP++++FN Sbjct: 126 SPA--DIVHISDDVVRKGSRQHIAYCATKAGLDSLTLSFAAQFAPLIKVNGIAPAMVMFN 183 Query: 188 EHDDAEYRQQALNKSLMKTAPGEKEVIDLVDYLLTSCFVTGRSFPLDGGRHLR 240 + DDA+YR + L KS + PG + + V YLL + +VTG + ++GGRH++ Sbjct: 184 DGDDADYRAKVLAKSALGIEPGPEVIYQSVRYLLDNPYVTGTTLTVNGGRHIK 236 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: 182 Number of extensions: 7 Number of successful extensions: 3 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: 236 Length adjustment: 23 Effective length of query: 217 Effective length of database: 213 Effective search space: 46221 Effective search space used: 46221 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 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