Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011021352.1 MA_RS06920 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000007345.1:WP_011021352.1 Length = 319 Score = 242 bits (617), Expect = 2e-68 Identities = 138/319 (43%), Positives = 201/319 (63%), Gaps = 7/319 (2%) Query: 4 MKVLIADSI--NEKGISELEEVAEVVV--NTTITPEELLDAIKDFDAIVVRSRTKVTREV 59 MK+++ADSI ++ LE + E+ + + ++ +E +D IKD D +VV R V+ E Sbjct: 1 MKIVVADSIFLTDEYRKRLEALGELEIYDSVPVSLDEFIDRIKDADIVVV-GRYGVSAEA 59 Query: 60 IEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAI 119 + +APRLK+I+ G DNVD++ ATD G++V N P +VAE L L L R++ + Sbjct: 60 LRSAPRLKMISLWQTGFDNVDLEEATDHGVIVSNVPSYAFESVAEFVFALTLNLLRRVHL 119 Query: 120 ADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAA 179 AD +++EG ++ ++G +L KT+G++G G IG +V+ F M+++ + S E A Sbjct: 120 ADMNLREGLFDWKYYVGNQLMSKTIGVLGTGEIGKRVIQIAHGFNMNVLSVTAHPSPERA 179 Query: 180 EEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDED 239 + +GV DL+TLL ESDIVT+HVPLTPET H+I E MK TA ++N ARG +++E Sbjct: 180 KALGVKFVDLDTLLSESDIVTLHVPLTPETEHMIGARELAKMKPTAILINTARGKVVEEA 239 Query: 240 ALYRALKDGEIAGAALDVFEEEP-PEGSPLLELENVVLTPHIGASTSEAQRDAAIIVANE 298 AL ALK+ +IAGA LDVFE EP SPLLE+ NVVLTPHI A SE D ++ E Sbjct: 240 ALMEALKEKKIAGAGLDVFEREPLSMDSPLLEMHNVVLTPHI-AFLSEESLDECTYISIE 298 Query: 299 IKTVFQGGAPRNVLNMPVM 317 +F G P+NV+N V+ Sbjct: 299 NVEMFAKGKPQNVVNPSVL 317 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: 393 Number of extensions: 19 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: 319 Length adjustment: 31 Effective length of query: 494 Effective length of database: 288 Effective search space: 142272 Effective search space used: 142272 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