Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_013842411.1 DESRU_RS12195 C-terminal binding protein
Query= curated2:O27051 (525 letters) >NCBI__GCF_000215085.1:WP_013842411.1 Length = 331 Score = 248 bits (634), Expect = 2e-70 Identities = 134/322 (41%), Positives = 200/322 (62%), Gaps = 7/322 (2%) Query: 1 MSRMKVLIADSINEKGISELEEVAEVVVNTTI----TPEELLDAIKDFDAIVVRSRTKVT 56 MS +KV++ D E E +A++ V+ T EEL++A KD D ++ ++T Sbjct: 1 MSNLKVVVTDYEYSTLKYEEEVLAQIGVSLVPAQCKTEEELIEACKDADGLL-NQYAQLT 59 Query: 57 REVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARK 116 VI+A R K+I R GVG++ VD+ AAT++GI V+N P+ V++H++ L+LA RK Sbjct: 60 PRVIQALDRCKVIGRYGVGINTVDLAAATEKGICVVNVPDYCMDEVSDHAMALLLACVRK 119 Query: 117 IAIADRSVKEGKWEKNRFMGI-ELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYIS 175 + + VK+G W+ + + L GK LG+I GRI + + +AFG++++V+DPYI Sbjct: 120 TVLMNNEVKKGNWDYKVSVPVYRLRGKNLGLISFGRIAQTLAKKAQAFGLNLLVFDPYIP 179 Query: 176 KEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGI 235 AE+ GV LE LL+ SD +++H PL ET HL+ E EFK+MK +AFI+N RG + Sbjct: 180 DAVAEQFGVKKVSLEELLQTSDFISVHAPLNAETEHLLGEKEFKMMKKSAFIINTGRGPV 239 Query: 236 IDEDALYRALKDGEIAGAALDVFEEEPPEG-SPLLELENVVLTPHIGASTSEAQRDAAII 294 IDE+AL +AL++G IAGA LDV E EP SPLL+++NV+L PH+ + EA D I Sbjct: 240 IDEEALVKALQEGWIAGAGLDVLEIEPVRSESPLLKMDNVILNPHVAWYSEEAGTDLQIK 299 Query: 295 VANEIKTVFQGGAPRNVLNMPV 316 A + V QG PRN++N + Sbjct: 300 AAQGVAEVLQGYYPRNLVNKEI 321 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: 370 Number of extensions: 13 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: 331 Length adjustment: 31 Effective length of query: 494 Effective length of database: 300 Effective search space: 148200 Effective search space used: 148200 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