Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_012102401.1 CKL_RS10125 C-terminal binding protein
Query= curated2:O27051 (525 letters) >NCBI__GCF_000016505.1:WP_012102401.1 Length = 329 Score = 199 bits (505), Expect = 2e-55 Identities = 112/270 (41%), Positives = 163/270 (60%), Gaps = 6/270 (2%) Query: 12 INEKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIAR 71 + E GI LE V + + ++ DFD +VV + ++T+E+IE+ P LKII Sbjct: 22 LKEWGIDSLELVE---IKDREGKKPFIEYAYDFDGVVVEYQ-QMTKEIIESLPNLKIITL 77 Query: 72 AGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEK 131 +G +NVD+ AAT+ + V N P + VA H+IG+++ L RKI DR V++GKW+ Sbjct: 78 QSIGYNNVDISAATENNVCVTNIPGFCTEEVALHTIGMIIDLVRKITFLDRLVRKGKWDP 137 Query: 132 N-RFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVT-VTDL 189 + L KT+G+ G I ++ KA G++++VY P +KE EE G V Sbjct: 138 LCGYKTYRLTDKTIGLYFFGSIPKAMMPMLKAMGLNVLVYAPTKTKEYLEEFGAEKVETF 197 Query: 190 ETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGE 249 + LL +SD V++H PL T HLISE E KLMK++A+++N ARG ++DE AL +ALK+G Sbjct: 198 DELLIKSDFVSLHCPLMASTTHLISERELKLMKESAYLINTARGKVVDETALIKALKEGR 257 Query: 250 IAGAALDVFEEEPPEGSPLLELENVVLTPH 279 I AA+DV E+E E S L LEN V+TPH Sbjct: 258 IKAAAVDVIEDEDNEQSELFSLENTVITPH 287 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: 365 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: 329 Length adjustment: 31 Effective length of query: 494 Effective length of database: 298 Effective search space: 147212 Effective search space used: 147212 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