Align dihydromonapterin reductase (EC 1.5.1.50) (characterized)
to candidate 7026365 Shewana3_3507 short chain dehydrogenase (RefSeq)
Query= BRENDA::P0AFS3 (240 letters) >FitnessBrowser__ANA3:7026365 Length = 239 Score = 237 bits (605), Expect = 1e-67 Identities = 128/237 (54%), Positives = 163/237 (68%), Gaps = 5/237 (2%) Query: 8 PILITGGGRRIGLALAWHFINQKQPVIVSYRTHYPAIDGLINAGAQCIQADFSTNDGVMA 67 PI+ITG G+RIG ALA H + Q VI +YR+HYP+ID L + GA IQ DF N + Sbjct: 4 PIIITGVGKRIGYALAKHLLAQGHKVIGTYRSHYPSIDELQSLGATLIQCDFYDNAQLQT 63 Query: 68 FADEVLKSTHGLRAILHNASAWMAEK-PGAPLADVLACMMQIHVNTPYLLNHALERLLRG 126 ++ L +RAI+HNAS W+ + P +V+ MMQ+HV+ PY +N AL LR Sbjct: 64 LIEQ-LSQYPKIRAIIHNASDWLPDNSPSLAAHEVMQRMMQVHVSVPYQMNLALASQLRA 122 Query: 127 HGHA---ASDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNSIAPSL 183 G ASDIIHFTDYV E+GS KH+AYAASKAALDN+T SFA +LAPEVKVN+IAP++ Sbjct: 123 GGEGEIGASDIIHFTDYVAEKGSAKHMAYAASKAALDNLTLSFAAQLAPEVKVNAIAPAM 182 Query: 184 ILFNEHDDAEYRQQALNKSLMKTAPGEKEVIDLVDYLLTSCFVTGRSFPLDGGRHLR 240 ILFN DD YRQ+ L K+++ G +E+I LVDYLL S +VTGR +DGGRHL+ Sbjct: 183 ILFNPSDDEAYRQKTLAKAILPKEAGNQEIIALVDYLLASRYVTGRCHNVDGGRHLK 239 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: 174 Number of extensions: 6 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: 240 Length of database: 239 Length adjustment: 23 Effective length of query: 217 Effective length of database: 216 Effective search space: 46872 Effective search space used: 46872 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