Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_086508280.1 BZY95_RS01720 3-phosphoglycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_002151265.1:WP_086508280.1 Length = 315 Score = 160 bits (406), Expect = 5e-44 Identities = 99/286 (34%), Positives = 161/286 (56%), Gaps = 11/286 (3%) Query: 4 MKVLIADSINE-----KGISELEEVAEVVVNTTITPEE-LLDAIKDFDAIV-VRSRTKVT 56 MK++I D + ++LE + + T+T E+ L++ +D DA+V +R RT +T Sbjct: 1 MKIVIPDDYQDCVRHLDAFAKLEGHEVTIYDDTVTDEDALVERFRDADALVLIRERTPIT 60 Query: 57 REVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARK 116 ++ P LK I++ G G +VD+ A G+ V+ A + AE + GL+LA R Sbjct: 61 ESLLARLPNLKAISQTGGGAAHVDMAACKRHGVTVM-AGTGSPYAAAELTWGLVLAAMRH 119 Query: 117 IAIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISK 176 I ++K G+W+ R +G L G+TLGI G G+IG + +AF M+++V+ ++ Sbjct: 120 IPEEFENLKAGRWQ--RTLGTGLKGRTLGIFGYGKIGKLIARYGQAFEMNVLVWGREGTR 177 Query: 177 EAAEEMGVTVTDLET-LLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGI 235 A E G+ V + L SD++++H+ L +TR ++S ++ MK TA +VN +R + Sbjct: 178 TRAAEAGLEVAASQAELFERSDVLSLHLRLNADTRGIVSAEDLARMKPTALLVNTSRAPL 237 Query: 236 IDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIG 281 I AL AL++G AA+DVF+EEP PLL L N + TPH+G Sbjct: 238 IAPGALETALREGRPGRAAVDVFDEEPVTSHPLLALPNFLATPHLG 283 Lambda K H 0.316 0.135 0.366 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: 331 Number of extensions: 15 Number of successful extensions: 4 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: 525 Length of database: 315 Length adjustment: 31 Effective length of query: 494 Effective length of database: 284 Effective search space: 140296 Effective search space used: 140296 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