Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_051294939.1 G496_RS19260 hypothetical protein
Query= curated2:O27051 (525 letters) >NCBI__GCF_000429985.1:WP_051294939.1 Length = 322 Score = 190 bits (483), Expect = 6e-53 Identities = 109/301 (36%), Positives = 173/301 (57%), Gaps = 15/301 (4%) Query: 4 MKVLIA--DSINEKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIE 61 +K+L A D + K L+++A+V ++ +LL A +D ++VR R+ ++++ Sbjct: 2 LKILNAEPDRYSRKAFETLKQIAQVD-EINLSGSDLLKASSQYDILIVRLRSYISKDFFT 60 Query: 62 AAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSI-----TVAEHSIGLMLALARK 116 R+K + A G+D+VD +AA + G ++N T +EH+IGL+LAL R Sbjct: 61 PESRMKYLVTATTGIDHVDTRAAEENGTTILNLRGETDFLRTITATSEHTIGLILALLRH 120 Query: 117 IAIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISK 176 I A +SV E W ++ F+G +L +TLG+IG+GR+GS+V KAF M I YDP+I Sbjct: 121 IPFAHKSVLENNWNRDLFIGRDLCSQTLGLIGLGRLGSKVAEFAKAFDMKIKAYDPFIPD 180 Query: 177 EAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGII 236 + E + L +L S I+++HV L T+ +I E E K M + A I+N +RG +I Sbjct: 181 KEWPEYVERCSSLSEILSSSSIISLHVHLDDSTKGMIGETEVKKMANGAVIINTSRGALI 240 Query: 237 DEDALYRALKDGEIAGAALDVFEEEPPEG---SPLLEL----ENVVLTPHIGASTSEAQR 289 +E AL L G++ GAALDV EE +G SPLL +N+++TPHIG +T ++ Sbjct: 241 NEQALLDGLNSGKLGGAALDVLAEEIHDGSKNSPLLSYAIKHDNLIITPHIGGATLDSMH 300 Query: 290 D 290 + Sbjct: 301 N 301 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: 355 Number of extensions: 18 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: 525 Length of database: 322 Length adjustment: 31 Effective length of query: 494 Effective length of database: 291 Effective search space: 143754 Effective search space used: 143754 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