Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_090447867.1 BLS63_RS21615 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_900100495.1:WP_090447867.1 Length = 321 Score = 168 bits (426), Expect = 2e-46 Identities = 101/311 (32%), Positives = 177/311 (56%), Gaps = 17/311 (5%) Query: 12 INEKGISELEE-VAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIA 70 + + +S LE+ AE+ ++ TP ++++ ++ + + + ++ + A P LK++ Sbjct: 17 LGDLDMSPLEQSFAELQLHGQSTPAQVIERLRGAE-VAISNKVPLDAATFAACPALKLVL 75 Query: 71 RAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWE 130 A G +N+D++AA + G+ V N + +VA+H++ L+LALA ++ +V+ G+W+ Sbjct: 76 VAATGTNNIDLEAAREHGVTVCNCQGYGTPSVAQHTLMLLLALATRLPDYQTAVRAGRWQ 135 Query: 131 KNR------FMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGV 184 + + F +EL GKTLG++G G +G V +AFGM +++ + + Sbjct: 136 QAQQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLLGQLPGRPPRQDRL-- 193 Query: 185 TVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRA 244 L+ LL + D +++H PL +T +LI E E LMK TAF++N ARGG+++E AL Sbjct: 194 ---PLDELLPQVDALSLHCPLNADTLNLIGEYELSLMKPTAFLINTARGGLVNEQALADC 250 Query: 245 LKDGEIAGAALDVFEEEPP-EGSPLL--ELENVVLTPHIGASTSEAQRDAAIIVANEIKT 301 L+ G + GAA DV +EPP +G+PLL ++ +++TPH + EA R +I E Sbjct: 251 LRRGHLGGAATDVLTQEPPRDGNPLLAADIPRLIVTPHSAWGSREA-RQRIVIQLMENAQ 309 Query: 302 VFQGGAPRNVL 312 F GAPR V+ Sbjct: 310 AFFSGAPRRVV 320 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: 314 Number of extensions: 16 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: 321 Length adjustment: 31 Effective length of query: 494 Effective length of database: 290 Effective search space: 143260 Effective search space used: 143260 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