Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate YP_427543.1 Rru_A2456 D-3-phosphoglycerate dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >NCBI__GCF_000013085.1:YP_427543.1 Length = 411 Score = 473 bits (1218), Expect = e-138 Identities = 238/410 (58%), Positives = 301/410 (73%), Gaps = 1/410 (0%) Query: 1 MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60 M+ +SL KDKI+ +L E +H A+E + GY NIE GALD E LK+ IRDAH +G+R Sbjct: 1 MSNLSLPKDKIRVVLFENIHDSAVEYFHSRGYHNIERLTGALDGEALKDKIRDAHMVGIR 60 Query: 61 SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120 SRT LT DV+ +AEKL+A+GCFCIGTNQVDLDAA GIPVFNAP+SNTRSVAELV+ E Sbjct: 61 SRTRLTRDVLESAEKLMAVGCFCIGTNQVDLDAAELLGIPVFNAPYSNTRSVAELVVAEA 120 Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180 ++++R +P N H G WNK A G E RGK LGI+GYGHIGTQ+ +LAES+GM V ++ Sbjct: 121 VMMMRDIPRRNWDTHEGGWNKAATGCHEVRGKTLGIVGYGHIGTQVSVLAESMGMSVRYF 180 Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240 DI KL +GNA L++L+ ++DVV+LHVP+ T++M+ A +I+ MK G+ LINASR Sbjct: 181 DIVEKLAIGNAQPCATLNELMAVADVVTLHVPDTADTRDMIRAPQIAAMKDGAYLINASR 240 Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300 G VVDI AL +AL + L GAA+DVFP EPA+ DPF SPL NVLLTPHIGGST+EA Sbjct: 241 GKVVDIDALAEALTAGKLRGAAVDVFPKEPASLGDPFESPLRGMRNVLLTPHIGGSTEEA 300 Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGG-RRLMHIHENRPGVLTALNKIFA 359 Q IG EVA KL+KYSD+GSTL AVNFPEV+LP R +HIH N PGV++ALN++F+ Sbjct: 301 QMGIGREVAEKLVKYSDDGSTLGAVNFPEVALPQQASVTRFLHIHRNVPGVMSALNEVFS 360 Query: 360 EQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLL 409 +NI QYL T+ ++GYVV+D+E D E QA+ AI GT+R R L Sbjct: 361 SHHINIRGQYLMTNPRVGYVVVDVEKDLKAGEGFRQALAAINGTLRFRFL 410 Lambda K H 0.318 0.135 0.383 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: 452 Number of extensions: 13 Number of successful extensions: 2 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: 410 Length of database: 411 Length adjustment: 31 Effective length of query: 379 Effective length of database: 380 Effective search space: 144020 Effective search space used: 144020 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 (21.7 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