Align Dihydromonapterin reductase; H(2)-MPt reductase; EC 1.5.1.50; Dihydrofolate reductase; DHFR; EC 1.5.1.3 (uncharacterized)
to candidate Dsui_0694 Dsui_0694 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein
Query= curated2:A8AGY5 (240 letters) >FitnessBrowser__PS:Dsui_0694 Length = 251 Score = 92.4 bits (228), Expect = 7e-24 Identities = 74/246 (30%), Positives = 114/246 (46%), Gaps = 13/246 (5%) Query: 2 GKNQPLPILITGGGRRIGLAIAWHFLNQKQPVIVSYRTHYPAIDGLT-------QAGALC 54 G Q IL+TGG +R+G AIA +++ YR+ L A+C Sbjct: 5 GNLQGKAILVTGGAKRVGAAIARRLHAAGASLVLHYRSAAAEARSLAAELNAQRDGSAVC 64 Query: 55 IQADFSTDDGVLAFAEKIKTHTPGLRAILHNASAWMAEAPGTPLSDVLACMMQIHVNTPY 114 IQAD + E+ T L +++NAS++ G+ ++ + P Sbjct: 65 IQADLLQTSALPGLVEQSVTAFGRLDGLVNNASSFFRTPLGSIDEAAWDDLVGSNFKAPL 124 Query: 115 LLNHALERLLRGHGHAATDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEV 174 L A LR G A +++ TD ER + Y A+K AL +TR+ A +LAP V Sbjct: 125 FLTQAAAPHLRASGGA---VVNITDVHAERPLVGYPLYCAAKGALLTLTRALAAELAPVV 181 Query: 175 KVNAIAPSLILFNEND--DAEYRQQALNKSLMKTAPGEKEVIDLVDYLLT-SCFVTGRSF 231 +VNA+AP IL+ E D+ RQ + +L+ ++ V +LL S ++TG+ Sbjct: 182 RVNAVAPGPILWPEGSDFDSAARQAIVADTLLGREGSPADIARAVHFLLVDSPYITGQVI 241 Query: 232 AVDGGR 237 VDGGR Sbjct: 242 NVDGGR 247 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: 150 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: 251 Length adjustment: 24 Effective length of query: 216 Effective length of database: 227 Effective search space: 49032 Effective search space used: 49032 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