Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 3607592 Dshi_1001 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::P9WNX3 (528 letters) >FitnessBrowser__Dino:3607592 Length = 316 Score = 186 bits (472), Expect = 1e-51 Identities = 109/304 (35%), Positives = 164/304 (53%), Gaps = 6/304 (1%) Query: 6 VLIADKLAPSTVAALGDQVEVRWVDG--PDRDKLLAAVPEADALLVRSATTVDAEVLAAA 63 V+I + + ++ G +V+V + DR L AV AD ++VR+ T VD L AA Sbjct: 5 VVITETIDTRALSRFGPEVDVIYAPELVEDRAACLVAVARADGVIVRNRTQVDRPFLDAA 64 Query: 64 PKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADAS 123 +L+++ G GLDN+D+ A ARG+ V A +N S AE+ + L +R+ + Sbjct: 65 SRLRVIGLLGTGLDNIDMAACAARGISVHPATGANTRSVAEYVITAALMLTRRAFMSTPE 124 Query: 124 LREHTWKRSSFS-GTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQL 182 ++E W R G EI G+ +G+ G G + Q VA+ ++ +DP++ P Sbjct: 125 MQEGAWPRGPLGEGGEIAGRKLGLYGCGAVAQAVARLAKPLSMTILGHDPHLGPGHPLWT 184 Query: 183 GIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALA 242 + +S +LLARAD +S+HLP TPET G ID AL KPG I++N A G +VD A+ Sbjct: 185 EVTRVSDAELLARADVLSLHLPLTPETRGRIDATALTAMKPGAILINTAHGEIVDARAVC 244 Query: 243 DAITGGHVRAAGLDVFATEP--CTDSPLFE-LAQVVVTPHLGASTAEAQDRAGTDVAESV 299 DA+ GH+ A LDVF EP D+ F + +++TPH+ T EA R ++V Sbjct: 245 DALRRGHLGGAALDVFEPEPLGTQDAARFRGVPNLILTPHVAGVTVEADRRVSALTVDNV 304 Query: 300 RLAL 303 R AL Sbjct: 305 RAAL 308 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: 388 Number of extensions: 29 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: 316 Length adjustment: 31 Effective length of query: 497 Effective length of database: 285 Effective search space: 141645 Effective search space used: 141645 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 Aug 03 2021. The underlying query database was built on Aug 03 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