Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate H281DRAFT_05961 H281DRAFT_05961 D-3-phosphoglycerate dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >FitnessBrowser__Burk376:H281DRAFT_05961 Length = 315 Score = 204 bits (520), Expect = 3e-57 Identities = 125/312 (40%), Positives = 188/312 (60%), Gaps = 9/312 (2%) Query: 4 PVVLI-ADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEAD--ALLVRSATTVDAEVL 60 PVVL+ A LAP + L V P D ++A E A++VR V+A ++ Sbjct: 8 PVVLVTAADLAPQALDMLTQFDVVFAGKQPTEDDIVALCAEHKPVAIIVRYGK-VNARIM 66 Query: 61 AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAA 120 AA L+++++ G G+D +D AA ARG+ V A +N + AEHA AL+LA ++ +P Sbjct: 67 DAAENLQVISKHGSGIDVIDQAAAAARGIAVRAAVGANAAAVAEHAWALILACAKSVPHL 126 Query: 121 DASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAA 180 DA +R+ W +S+ E+ G+T+G+VGLG IG+ VA AAFG V+A+DPY A+ A Sbjct: 127 DARMRQGHWDKSTHKSVELDGRTLGLVGLGAIGRRVAAIGAAFGMNVLAFDPY---AKEA 183 Query: 181 QLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAA 240 G++L+SLD+L A +D +S+H P T E +++++ LA+ K G I+VN ARGGL+DEAA Sbjct: 184 PAGVKLVSLDELYAASDVVSLHCPLTAENRQMLNRDTLARFKRGAILVNTARGGLIDEAA 243 Query: 241 LADAITGGHVRAAGLDVFATEPCT-DSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESV 299 LA+A+ G +R AGLD F EP T P ++ +++PH+G + A G A +V Sbjct: 244 LAEALASGQLRFAGLDSFDVEPMTYPHPFQQIPNAILSPHIGGVSDAAYVNMGKGAAANV 303 Query: 300 RLALAGEFVPDA 311 LA+ E +A Sbjct: 304 -LAVVEEHARNA 314 Lambda K H 0.317 0.133 0.370 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: 358 Number of extensions: 22 Number of successful extensions: 2 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: 528 Length of database: 315 Length adjustment: 31 Effective length of query: 497 Effective length of database: 284 Effective search space: 141148 Effective search space used: 141148 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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