Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_013076962.1 BTUS_RS15260 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein
Query= BRENDA::O08651 (533 letters) >NCBI__GCF_000092905.1:WP_013076962.1 Length = 328 Score = 124 bits (312), Expect = 4e-33 Identities = 91/280 (32%), Positives = 137/280 (48%), Gaps = 17/280 (6%) Query: 20 RKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTG 79 R L + G+ VVE+ L + EL+ +++ V D++ +++++ +AG G Sbjct: 21 RAKLPEVGVDVVERDQLIRHP---ELK----VLIPGVEPVNRDLLEGLREVRLIHQAGVG 73 Query: 80 VDNVDLEAATRKGVLVMNTPN---GNSLSAAELTCGMLMCLARQIPQATASMKDGKWDRK 136 VD+VD+EAAT GV V N P+ GN+ S AE+ ++ L+R+I QA G W Sbjct: 74 VDSVDVEAATELGVWVANVPSYGSGNAESVAEIALWHMLTLSRRIRQARERFLSGDWGNP 133 Query: 137 KFMGTELNGKTLGILGLGRIGREVAARMQAFGMKTVGYDPIISPEVAASFGVQQLPLEE- 195 +G L +T+GI G+G IG+ +A R+ FG++ +G P ++ F P E Sbjct: 134 --LGVSLRNRTVGIYGVGGIGKALAERLVPFGVRLIGIKRSPDPSLSGLFDWLAGPEERD 191 Query: 196 -IWPLCDFITVHTPL-LPSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQ 253 + DF+ V PS F K +N +RG VDE ALL AL G Sbjct: 192 RLLQESDFVVVTASANSPSEVIPFTVRDFLLMKPSAYFINVSRGIWVDEEALLAALDMGA 251 Query: 254 CAGAALDVFTEEPP--RDRALVDHENVISCPHLGASTKEA 291 AGA LDV EEPP N++ PH+G T ++ Sbjct: 252 IAGAGLDVVREEPPPIPSAWTAGGRNLLITPHIGGCTDQS 291 Lambda K H 0.318 0.134 0.394 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: 371 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: 533 Length of database: 328 Length adjustment: 32 Effective length of query: 501 Effective length of database: 296 Effective search space: 148296 Effective search space used: 148296 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