Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011989005.1 CKL_RS02155 3-phosphoglycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000016505.1:WP_011989005.1 Length = 320 Score = 233 bits (593), Expect = 1e-65 Identities = 127/314 (40%), Positives = 204/314 (64%), Gaps = 5/314 (1%) Query: 5 KVLIADSINEKGISELEEVA-EVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEAA 63 K+LI +SI E+G+ L++ E+ + + + L++ +KD DAI+VR +T +VI A Sbjct: 4 KILITESIEEEGVEYLKKFGYEIKMPRDTSEDVLIEEVKDCDAILVRM-ANITEKVIRAG 62 Query: 64 PRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRS 123 +LK+I+R GVGV+NVD+K A++ I + NAPES TVAE+++GL++ALA+K + DR Sbjct: 63 KKLKVISRFGVGVNNVDIKTASELSIQITNAPESNKNTVAEYTMGLIIALAKKFFLYDRG 122 Query: 124 VKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVR-TKAFGMDIMVYDPYISKEAAEEM 182 +++G ++ +GI+L GK LGI+G+G IG + ++ +K FGM ++ + +I +E+ Sbjct: 123 LRKGNFKVRDILGIDLEGKVLGIVGLGSIGKLLALKASKGFGMKVIGFKRHIDEESKSLD 182 Query: 183 GVTVTD-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDAL 241 V +TD L+ +L SD V+++VPLT T +I + E MK AF++N ARG ++D DAL Sbjct: 183 YVELTDSLDYVLENSDFVSLNVPLTKATTKIIGKRELSFMKKDAFLINTARGEVVDNDAL 242 Query: 242 YRALKDGEIAGAALDVFEEE-PPEGSPLLELENVVLTPHIGASTSEAQRDAAIIVANEIK 300 AL + +IAGAA DVF+ E P + +P+ ++ENV++TPH A T EA + ++ A I Sbjct: 243 CNALLNKQIAGAATDVFDGEIPSKDNPIFKMENVIVTPHSAAHTIEAMKRMSVHAAIGIH 302 Query: 301 TVFQGGAPRNVLNM 314 V G P +N+ Sbjct: 303 EVLSGNKPSWPVNI 316 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: 402 Number of extensions: 23 Number of successful extensions: 6 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: 320 Length adjustment: 31 Effective length of query: 494 Effective length of database: 289 Effective search space: 142766 Effective search space used: 142766 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