Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_029133702.1 A3GO_RS0112635 D-glycerate dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000428045.1:WP_029133702.1 Length = 321 Score = 165 bits (418), Expect = 2e-45 Identities = 108/315 (34%), Positives = 169/315 (53%), Gaps = 11/315 (3%) Query: 5 VVLIADKLAPSTVAALGDQVEVRWVDGPDR----DKLLAAVPEADALLVRSATTVDAEVL 60 VVL+ KL + A L + R+ + DR D+L+ ADA++ + A V+ Sbjct: 6 VVLVTRKLPDAVEARLERDYDARF-NSADRVYTSDELVEFSAGADAIIPCHTEKLTAAVI 64 Query: 61 AAAP-KLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPA 119 P ++ + VG D++D+DAA ARG++V N P + AE A+ L+L A+R+ Sbjct: 65 ERLPDSVRAICSFSVGFDHIDLDAAKARGIIVTNTPDVLSDATAEIAMLLILGAARRAHE 124 Query: 120 ADASLREHTWKRSSFSG---TEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYD-PYVS 175 + +R TW S G ++ GK +G++G+GR+GQ++A+R F + ++ +S Sbjct: 125 GEQQIRTATWSDWSAIGGLGIQVTGKRLGILGMGRVGQILAKRARGFDMQIHYHNRSRLS 184 Query: 176 PARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGL 235 P A I S++ LL + DF+S+H P TPET L++ E L G I+VN ARG + Sbjct: 185 PDIEAG-AIYHGSVEQLLPQCDFLSLHCPATPETERLMNAERLGLLPDGAILVNTARGAI 243 Query: 236 VDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDV 295 VD+ AL +A+ G + AAGLDVF EP D L + PH+G++T E +D G Sbjct: 244 VDDDALIEALRSGKLFAAGLDVFNNEPDIDPRYKALDNTFLLPHIGSATRETRDAMGFRA 303 Query: 296 AESVRLALAGEFVPD 310 +++ AG PD Sbjct: 304 LDNLDAITAGREPPD 318 Lambda K H 0.317 0.133 0.370 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: 376 Number of extensions: 22 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: 528 Length of database: 321 Length adjustment: 31 Effective length of query: 497 Effective length of database: 290 Effective search space: 144130 Effective search space used: 144130 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