Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate Ac3H11_2599 Glyoxylate reductase (EC 1.1.1.79) / Glyoxylate reductase (EC 1.1.1.26) / Hydroxypyruvate reductase (EC 1.1.1.81); 2-ketoaldonate reductase, broad specificity (EC 1.1.1.215) (EC 1.1.1.-)
Query= curated2:O27051 (525 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2599 Length = 329 Score = 199 bits (506), Expect = 1e-55 Identities = 120/324 (37%), Positives = 178/324 (54%), Gaps = 8/324 (2%) Query: 1 MSRMKVLIADSINEKGISELEEVAEVVVN---TTITPEELLDAIKDFDAIVVRSRTKVTR 57 MS+ ++L+A +I + L E +V N TP+EL + D D ++ ++ Sbjct: 1 MSKPRILVARAIFPDIVDRLREHFDVEANPDDVIWTPQELAARLADKDGVLTTGSQRIDA 60 Query: 58 EVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKI 117 ++ AAPRLKI A VG +N DV A T G+ N P+ + T A+ L++A AR++ Sbjct: 61 ALLAAAPRLKICANMAVGYNNFDVDAMTAAGVQGTNTPDVLTETTADFGFALLMATARRM 120 Query: 118 AIADRSVKEGKWEK---NRFMGIELNGKTLGIIGMGRIGSQVVVR-TKAFGMDIMVYD-P 172 ++ ++ G+W K + F G +++G TLGIIGMGRIG + R FGM ++ ++ Sbjct: 121 TESEHYLRAGQWTKWSYDMFAGSDIHGSTLGIIGMGRIGQGIAKRGAHGFGMKVIYHNRS 180 Query: 173 YISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCAR 232 +S E E + + LLR +D V + VP T + H I E LMK TA ++N AR Sbjct: 181 RLSAELEAECKASYVGKDELLRTADHVMLVVPYTAASHHTIGAAELALMKPTATLINIAR 240 Query: 233 GGIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAA 292 GGI+D+ AL AL++G IA A LDVFE EP LL + NVVLTPHI ++T +R A Sbjct: 241 GGIVDDAALAVALREGRIAAAGLDVFEGEPSVHPDLLTVPNVVLTPHIASATVPTRRAMA 300 Query: 293 IIVANEIKTVFQGGAPRNVLNMPV 316 + A+ + G P +N PV Sbjct: 301 NLAADNLIAFLGGRGPLTPVNQPV 324 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: 16 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: 329 Length adjustment: 31 Effective length of query: 494 Effective length of database: 298 Effective search space: 147212 Effective search space used: 147212 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