Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_092482325.1 BM299_RS04760 hydroxyacid dehydrogenase
Query= uniprot:Q5JGC4 (304 letters) >NCBI__GCF_900115975.1:WP_092482325.1 Length = 330 Score = 224 bits (572), Expect = 2e-63 Identities = 133/315 (42%), Positives = 198/315 (62%), Gaps = 14/315 (4%) Query: 2 KVLVAAPLHEKAIEVLKNAGFEVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEAA 61 KVL+ +HE+ + +++ A E+ P E+ +++ + D DA+IVRS KVT +IEA Sbjct: 4 KVLLTEAIHEEGMNIIREAA-ELEIAADPGEETVIKAIADADALIVRSS-KVTSAIIEAG 61 Query: 62 PKLKVIGRAGVGLDNIDLKAAEERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRK 121 KLKVIGR G+GLDNIDLKAA++ G+ VVN+P A+ SVAE + + + +++ D Sbjct: 62 KKLKVIGRHGMGLDNIDLKAADQYGVAVVNTPDANVLSVAEHVLATMLYLCKRLKEVDNA 121 Query: 122 MREGVWAKKQCM-GI---------ELEGKTIGVVGFGRIGYQVAKIAN-ALGMKVLFYDP 170 +R G + + + G+ EL GKT+G+VG G+I ++A+I M+V YD Sbjct: 122 LRTGEFDRPGSLPGLVTKLGYTTQELYGKTLGLVGVGKIARRIAEICTKGFDMQVCGYDA 181 Query: 171 YPNEERAKEVGGK-FADLETLLKESDVVTLHVPLVDATYHLINEERLKLMKPTAILINAA 229 Y + ++ G + LE + +++D +++HVPL T LI +++L LMKPTA LIN+A Sbjct: 182 YLAPDVIQQAGVEPCGSLEEVFEKADFISVHVPLTPGTRGLIGKKQLDLMKPTAFLINSA 241 Query: 230 RGAVVDTDALVKALQEGWIAGAGLDVFEEEPLPADHPLTKLDNVVLTPHIGASTVEAQMR 289 RG VV+ D L +AL+E IAGA +DVF +EP +HPL LDNVV+TPHI A T A +R Sbjct: 242 RGGVVNEDDLYQALKEKSIAGAAVDVFAQEPPGKNHPLFTLDNVVVTPHIAAMTDGALVR 301 Query: 290 AGVEVAEKIVEALKG 304 +VAE +V L+G Sbjct: 302 MARDVAEGVVSVLRG 316 Lambda K H 0.317 0.136 0.378 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: 292 Number of extensions: 14 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: 304 Length of database: 330 Length adjustment: 27 Effective length of query: 277 Effective length of database: 303 Effective search space: 83931 Effective search space used: 83931 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: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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