Align 3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate 3607169 Dshi_0590 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= uniprot:A0A1X9ZCD3 (315 letters) >FitnessBrowser__Dino:3607169 Length = 311 Score = 77.0 bits (188), Expect = 5e-19 Identities = 52/165 (31%), Positives = 81/165 (49%), Gaps = 16/165 (9%) Query: 145 KTIGIIGFGRIGRATAKVALGLGMNVLAYDLYPSESEITLEFQGGKSVSIPIKTVSLDEV 204 + + ++G G +G A ++ + L V Y P + F G +L Sbjct: 137 RKVTVVGLGALGAAVSEALVALNFQVRGYARRPKDIPGVESFSGD----------ALHAA 186 Query: 205 ITGSDFFSL---HTPFADKPILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKVS 261 + G++ L HTP A + IL A A + G ++N RGG +D+ AL+ AL+SG+V Sbjct: 187 LVGAEVVILLVPHTP-ATEGILDAGALACLAEGAVVLNPGRGGLVDDAALLAALDSGQVG 245 Query: 262 FAGLDVFDNEPTPLAE-ILTHPKISLTPHIGASTN-EAQERIGTE 304 A LD F EP P + +HPK+++TPHI + T E R+ E Sbjct: 246 HATLDTFRTEPLPPDDPYWSHPKVTVTPHIASETRPETAARVVVE 290 Lambda K H 0.316 0.135 0.374 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: 222 Number of extensions: 11 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: 315 Length of database: 311 Length adjustment: 27 Effective length of query: 288 Effective length of database: 284 Effective search space: 81792 Effective search space used: 81792 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