Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011371670.1 SUDEN_RS00165 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000012965.1:WP_011371670.1 Length = 311 Score = 150 bits (380), Expect = 5e-41 Identities = 99/313 (31%), Positives = 165/313 (52%), Gaps = 17/313 (5%) Query: 4 MKVLIADSIN--EKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIE 61 MK++I D++ + +S + + + T +L + IKD D ++V ++ +T E ++ Sbjct: 1 MKIVILDALTFGDSDLSTFYSLGDTQIFQTTLSSQLQERIKDAD-VIVTNKVVITDEHMQ 59 Query: 62 AAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIAD 121 P LK+I A G++NVD++ A R I V N +S +V +H+ ++ L D Sbjct: 60 NTPSLKLICVAATGMNNVDLEGAKKRAIEVKNVSGYSSDSVIQHTFSMLFYLIGHSKYYD 119 Query: 122 RSVKEGKWEKNRFMG------IELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYIS 175 VK G + K+ E+ GK GIIG+G IG V K FG +I+ Y + Sbjct: 120 NYVKNGSYAKSEIFTDVSRPFFEIKGKKWGIIGLGEIGRGVANIAKTFGAEILYYS---T 176 Query: 176 KEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGI 235 + + T L+ LL+ DI++IH PL T +L+ E ++ KD A I+N RGGI Sbjct: 177 SKKNQNNQYTSVSLDELLKSCDIISIHAPLNENTLNLLDYKELQMCKDGAVILNLGRGGI 236 Query: 236 IDEDALYRALKDGEIAGAALDVFEEEPPE-GSPLLEL---ENVVLTPHIGASTSEAQRDA 291 I+E+A+ R + + +I LDV EP E +PLL + +N+ +TPHI ++ EA++ Sbjct: 237 INEEAVSRIVDERDIL-FGLDVLSREPIESNNPLLHVKNRDNLYITPHIAWTSIEARKTL 295 Query: 292 AIIVANEIKTVFQ 304 V + IK+ ++ Sbjct: 296 IDGVTSNIKSFYE 308 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: 338 Number of extensions: 13 Number of successful extensions: 4 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: 311 Length adjustment: 31 Effective length of query: 494 Effective length of database: 280 Effective search space: 138320 Effective search space used: 138320 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 10 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