Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate N515DRAFT_0108 N515DRAFT_0108 gluconate 2-dehydrogenase
Query= curated2:O27051 (525 letters) >FitnessBrowser__Dyella79:N515DRAFT_0108 Length = 334 Score = 193 bits (490), Expect = 9e-54 Identities = 115/328 (35%), Positives = 183/328 (55%), Gaps = 12/328 (3%) Query: 2 SRMKVLIADSINEKGISELEEVAEV---VVNTTITPEELLDAIKDFDAIVVRSRTKVTRE 58 +R KV ++ + + ++ L E +V V +PE L + + DA ++ V Sbjct: 3 ARQKVWVSRPLFPEVLARLSEYVDVQAEAVERRHSPEALREHLAGVDAALIGLADPVGAA 62 Query: 59 VIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 +E RL++IA VG +N+D+ A T GI+ N P+ + TVA+++ LML AR++ Sbjct: 63 AVEGNRRLRVIANLAVGYNNLDLPALTRAGILACNTPDVLNETVADYAWALMLGAARRMG 122 Query: 119 IADRSVKEGKWEKNR----FMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYI 174 A+R ++ G+W ++G +++GKTLGI+GMGRIG + R F M ++ ++ Sbjct: 123 AAERWLRAGQWRGGMRFDDWLGFDVHGKTLGILGMGRIGQAIARRAAGFDMHVLYHNRSR 182 Query: 175 SKEAAE-EMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARG 233 E E E T+ D LLR +D + + +P + E+ H I E LMK TA +VN ARG Sbjct: 183 LPEPVERECRATLVDKAELLRRADHLILVLPYSRESHHAIGAAELALMKPTAVLVNVARG 242 Query: 234 GIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAI 293 GI+D+ AL AL++G + A LDVFE EP + LL LENV+L+PHI +++++ +R A Sbjct: 243 GIVDDAALAAALREGRLGAAGLDVFEGEPALHADLLRLENVLLSPHIASASADTRRAMAT 302 Query: 294 IVANEIKTVF----QGGAPRNVLNMPVM 317 + A+ + + G P LN VM Sbjct: 303 LAADNVLAALGHGPRAGRPPAPLNPEVM 330 Lambda K H 0.316 0.135 0.366 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: 383 Number of extensions: 15 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: 525 Length of database: 334 Length adjustment: 32 Effective length of query: 493 Effective length of database: 302 Effective search space: 148886 Effective search space used: 148886 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