Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate BWI76_RS23920 BWI76_RS23920 D-3-phosphoglycerate dehydrogenase
Query= BRENDA::P0A9T0 (410 letters) >FitnessBrowser__Koxy:BWI76_RS23920 Length = 410 Score = 749 bits (1935), Expect = 0.0 Identities = 375/410 (91%), Positives = 398/410 (97%) Query: 1 MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60 MAKVSLEKDKIKFLLVEGVHQKA++SLRAAGYTNIEFHKGALD E+LK SIRDAHFIGLR Sbjct: 1 MAKVSLEKDKIKFLLVEGVHQKAVDSLRAAGYTNIEFHKGALDSEELKASIRDAHFIGLR 60 Query: 61 SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120 SRTHLTE++ AAEKLVA+GCFCIGTNQVDL+AAAKRGIPVFNAPFSNTRSVAELVIGEL Sbjct: 61 SRTHLTEEIFAAAEKLVAVGCFCIGTNQVDLNAAAKRGIPVFNAPFSNTRSVAELVIGEL 120 Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180 LL+LRGVP ANAKAHRGVWNKLA GSFEARGKKLGIIGYGHIGTQLGILAESLGM+VYFY Sbjct: 121 LLMLRGVPAANAKAHRGVWNKLAVGSFEARGKKLGIIGYGHIGTQLGILAESLGMHVYFY 180 Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240 DIE+KLPLGNATQVQHLSDLLNMSDVVSLHVPEN STKNM+GA+E++LMKPG+LLINASR Sbjct: 181 DIESKLPLGNATQVQHLSDLLNMSDVVSLHVPENASTKNMIGAEELALMKPGALLINASR 240 Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPF SPLCEFDNV+LTPHIGGSTQEA Sbjct: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFNSPLCEFDNVILTPHIGGSTQEA 300 Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNKIFAE 360 QENIGLEVAGKL KYSDNGSTLSAVNFPEVSLPLHGGRRL+HIHENRPGVLTALN+IFA Sbjct: 301 QENIGLEVAGKLAKYSDNGSTLSAVNFPEVSLPLHGGRRLLHIHENRPGVLTALNQIFAA 360 Query: 361 QGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410 QG+NIAAQYLQT+ QMGYVVIDIEA+EDVA+ ALQAMKAIPGTIRARLL+ Sbjct: 361 QGINIAAQYLQTTPQMGYVVIDIEAEEDVAQAALQAMKAIPGTIRARLLF 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: 647 Number of extensions: 10 Number of successful extensions: 1 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: 410 Length adjustment: 31 Effective length of query: 379 Effective length of database: 379 Effective search space: 143641 Effective search space used: 143641 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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