Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_050462532.1 AKL27_RS09330 D-glycerate dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_001189915.1:WP_050462532.1 Length = 327 Score = 183 bits (465), Expect = 7e-51 Identities = 103/317 (32%), Positives = 170/317 (53%), Gaps = 8/317 (2%) Query: 3 KILITDPLHESAVEILKQAGEVEVATG---LTVEELKLKIKDVDALVIRSGTTATREIIE 59 KI + + +E L Q +VE T +EL +K K D L T + Sbjct: 4 KIFVARAVFPEVLERLSQHFDVESNQDDRIFTADELLVKAKGKDGLFATPSEPVTAALFA 63 Query: 60 ASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQAT 119 A+ LK + VG +N+DL AAT+ G++ N PD + + A+ + +++A AR + ++ Sbjct: 64 ANPQLKAVCNMAVGYNNIDLAAATKAGVMATNTPDVLNETTADFGWALLMATARRVTESE 123 Query: 120 ASIKSG---KWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDP--YIPE 174 +++G KW SF G +++G TLGI+G+GRIGQ +A+R+ F M ++ Y+ PE Sbjct: 124 HWLRAGHWKKWSYDSFVGPDVHGSTLGIIGMGRIGQAIARRSMGFDMNVLYYNRSRLSPE 183 Query: 175 DVASELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLI 234 + + +EL +D + L +P + + H IG ++ALMK ++N ARGG++ Sbjct: 184 LEVRANNARHVGKEELLRTADHVILVLPYSAASHHTIGAAELALMKPQATLINLARGGIV 243 Query: 235 DEAALYDALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVA 294 D+AAL L +G I AA LDVFE EP L L+N++ TPH +++ +L+ A Sbjct: 244 DDAALIATLRAGGIAAAGLDVFENEPAFNPDFLGLSNVVLTPHIASASTPTRLAMANCAA 303 Query: 295 EQTVKILKGESAENVVN 311 + + L G + N++N Sbjct: 304 DNLIAALSGNTPPNLLN 320 Lambda K H 0.316 0.134 0.364 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: 356 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: 523 Length of database: 327 Length adjustment: 31 Effective length of query: 492 Effective length of database: 296 Effective search space: 145632 Effective search space used: 145632 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