Align Dihydromonapterin reductase; H(2)-MPt reductase; EC 1.5.1.50; Dihydrofolate reductase; DHFR; EC 1.5.1.3 (uncharacterized)
to candidate WP_057509340.1 ABB28_RS14570 pteridine reductase
Query= curated2:A8AGY5 (240 letters) >NCBI__GCF_001431535.1:WP_057509340.1 Length = 245 Score = 104 bits (259), Expect = 2e-27 Identities = 83/243 (34%), Positives = 123/243 (50%), Gaps = 20/243 (8%) Query: 10 LITGGGRRIGLAIAWHFLNQKQPVIVSYRTHYPAIDGLTQAG----------ALCIQADF 59 LITG RRIG AIA H L+Q IV + + D L QA L +QAD Sbjct: 9 LITGSARRIGAAIAGH-LHQAGYNIVLHANR--SSDELQQAAFAFELARPGSVLALQADL 65 Query: 60 STDDGVLAFAEKIKTHTPGLRAILHNASAWMAEAPGTPLSDVLACMMQIHVNTPYLLNHA 119 D + E+ H L A+++NAS + A G ++ + + ++ P LL A Sbjct: 66 RDSDALADLVEQAVAHFGRLDALVNNASNFFATPLGQITAEAVDDLYAVNARAPLLLAQA 125 Query: 120 LE-RLLRGHGHAATDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNA 178 L R HG II+ TD + H AY +KAAL+ +TRS A +LAP+V+VNA Sbjct: 126 AAPHLRRSHG----SIINLTDLHGSQPMRDHPAYCMAKAALEMVTRSLALELAPKVRVNA 181 Query: 179 IAPSLILFNENDDAEYRQQA-LNKSLMKTAPGEKEVIDLVDYLLTSC-FVTGRSFAVDGG 236 +AP IL+ E ++ ++A L ++ + +E+ + V +L+ FVTG + +DGG Sbjct: 182 VAPGAILWPETGKDDFAREALLARTPLARIGTVEEIAEAVRWLIADAGFVTGHTLRLDGG 241 Query: 237 RHL 239 R L Sbjct: 242 RTL 244 Lambda K H 0.321 0.136 0.406 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: 156 Number of extensions: 10 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: 245 Length adjustment: 23 Effective length of query: 217 Effective length of database: 222 Effective search space: 48174 Effective search space used: 48174 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