Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_028950293.1 Q385_RS0103255 hydroxyacid dehydrogenase
Query= uniprot:Q5JGC4 (304 letters) >NCBI__GCF_000619805.1:WP_028950293.1 Length = 342 Score = 190 bits (482), Expect = 5e-53 Identities = 114/288 (39%), Positives = 166/288 (57%), Gaps = 21/288 (7%) Query: 23 EVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEAAPKLKVIGRAGVGLDNIDLKAA 82 EV + + P +D VEL K++D IV K+ + V+ LK+I G D+ID++ Sbjct: 28 EVEFTKEPLDDTNVELYKNIDVAIVFIYSKLNKDVLSKMANLKLIITRSTGYDHIDVEYT 87 Query: 83 EERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKKQCMGIELEGKTI 142 + I V N PG + +VAE LI A+ARK + +G++++ GI+L GKTI Sbjct: 88 SKNSITVCNVPGYGNNTVAEYTFALILALARKFKPMIERTSKGIFSRDGLTGIDLMGKTI 147 Query: 143 GVVGFGRIGYQVAKIANALGMKVLFYDPYPNEERAKEVGGKFADLETLLKESDVVTLHVP 202 GV+G GRIG V +IA GMK+L YD Y ++E + G ++ LE LL+ SD+VTLHVP Sbjct: 148 GVIGAGRIGKHVIRIAYGFGMKILVYDRYKDKELIDKYGVEYVGLEDLLRMSDIVTLHVP 207 Query: 203 LVDATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIA-GAGLDVFEEEPL 261 +T+HLIN +KLMK A+L+N +RG VV+ +A+V+AL+EG +A G GLD FE E + Sbjct: 208 YNKSTHHLINRFNIKLMKLDAMLVNTSRGPVVEMEAIVQALKEGRLAGGVGLDTFEAEEV 267 Query: 262 --------PADHPLTKL------------DNVVLTPHIGASTVEAQMR 289 D P KL +NV+++PH +T +A R Sbjct: 268 LIEEEYLKRDDIPAIKLKKALESFYVLHSENVIVSPHNAYNTKDALYR 315 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: 258 Number of extensions: 10 Number of successful extensions: 2 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: 342 Length adjustment: 28 Effective length of query: 276 Effective length of database: 314 Effective search space: 86664 Effective search space used: 86664 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