Align 3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_074201835.1 BUQ81_RS07110 DUF3410 domain-containing protein
Query= uniprot:A0A1X9ZCD3 (315 letters) >NCBI__GCF_900141795.1:WP_074201835.1 Length = 380 Score = 100 bits (248), Expect = 7e-26 Identities = 85/274 (31%), Positives = 131/274 (47%), Gaps = 49/274 (17%) Query: 35 AEALKNYDAITVRSATKVRKELIDAVPNIKLIGRGGVGMDNIDVEYARSQGINVVNTPAA 94 AEA+K DA+ VRS T+V L+ A ++ +G VG+D++D + R GI+ + Sbjct: 39 AEAVKEADALIVRSRTQVNASLL-AGSRVRFVGSTVVGLDHVDQPWLRQAGIHFFSAQGC 97 Query: 95 SSLSVAELVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELSGKTIGIIGFGR 154 +S++VAE V F L A+ GT L G+T+GIIG G Sbjct: 98 NSVAVAEYVI------------------------FALLDWAHRHGTTLRGRTLGIIGVGH 133 Query: 155 IGRATAKVALGLGMNVLAYDLYPSESEITLEFQGGKSVSIPIKTVSLDEVITGSDFFSLH 214 +GR K A LG+ L D P +E +F P++T+ L +V D ++H Sbjct: 134 VGREVLKRAEALGLRCLLND--PPRAEREADFP-----HTPLETL-LPQV----DLLTVH 181 Query: 215 TPF------ADKPILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKVSFAGLDVF 268 TP +L AE A++ I+N +RGG IDE A ++ V D + Sbjct: 182 TPLITTGTHPTHHLLNAERLARVPPQTLIINAARGGIIDETAWLEHPGDKVV-----DCW 236 Query: 269 DNEPTPLAEILTHPKISLTPHIGASTNEAQERIG 302 +NEP A +L+ +++ TPHI + +A+ R G Sbjct: 237 ENEPQINAALLSAAQLA-TPHIAGHSLDAKLRGG 269 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: 246 Number of extensions: 15 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: 315 Length of database: 380 Length adjustment: 29 Effective length of query: 286 Effective length of database: 351 Effective search space: 100386 Effective search space used: 100386 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: 49 (23.5 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