Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_013419585.1 RVAN_RS09860 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000166055.1:WP_013419585.1 Length = 347 Score = 116 bits (291), Expect = 7e-31 Identities = 84/254 (33%), Positives = 136/254 (53%), Gaps = 22/254 (8%) Query: 66 KVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRR 125 K+I+ SAG++N+DL A + G+ V +V A+AE V L++ L R+I++A +R Sbjct: 70 KLIALRSAGFNNLDLAAAERLGLCVMRVPAYAPTAIAEHAVALMLALNRRINHAYNRVRE 129 Query: 126 GEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWSRHRKVNVEK 185 G + + GF ++ G+ VGI+G G IG+++AR + FG + + ++ Sbjct: 130 GNFSLDHLV--GF----NMEGRTVGIVGTGKIGESLARIMHGFGCHILGYDIYQNPAC-I 182 Query: 186 ELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-GKYLVNIGRGALVDEKA 244 L +Y+D+ LL +SDIV L PLT +T H+INEE +K ++ G L+N RG LV+ +A Sbjct: 183 ALGMKYVDLPTLLSESDIVSLHCPLTPETKHLINEETLKLMKPGSMLINTARGGLVNAEA 242 Query: 245 VTEAIKQGKLKGY-ATDVFEKEP---VREH----------ELFKYEWETVLTPHYAGLAL 290 V EA+K+ Y DV+E+E +H EL ++T H A L Sbjct: 243 VIEALKRKDGLAYVGMDVYEREEGLFFSDHSSSIIQDDVFELLTTMRNVIVTGHQAFLTR 302 Query: 291 EAQEDVGFRAVENL 304 EA ++ + N+ Sbjct: 303 EALAEIAHTTLGNV 316 Lambda K H 0.319 0.139 0.393 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: 240 Number of extensions: 10 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: 333 Length of database: 347 Length adjustment: 28 Effective length of query: 305 Effective length of database: 319 Effective search space: 97295 Effective search space used: 97295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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