Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_011649349.1 RL_RS35850 hydroxyacid dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000009265.1:WP_011649349.1 Length = 324 Score = 182 bits (462), Expect = 2e-50 Identities = 111/320 (34%), Positives = 179/320 (55%), Gaps = 10/320 (3%) Query: 1 MSKILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60 MS I T PLH +A +L+ AG++ VA+ E L + + +V+R+ E Sbjct: 1 MSFIFSTHPLHPAAKSMLEAAGDLRVASAPDPETLLREGRGAGIVVVRAPIPPA--FFED 58 Query: 61 SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120 + L+ R G G+D V LDAAT G++V N P A++ +VAE +F + LA R Sbjct: 59 APALRAAIRHGAGLDMVPLDAATRAGVLVANVPGANASTVAEHVFLVTLALLRRFRAMDR 118 Query: 121 SIKSGKWDR---KSFKGMEIYGKTLGIVGLGRIGQQVAKRAQ-AFGMTIVAYDPYIPEDV 176 ++ W +S +++ G+T+GI+G+G +G+ + K A+ FG+ +VA PE V Sbjct: 119 DLRQSGWAAGRAQSDTAVDLAGRTMGIIGMGNVGKAILKIAKFGFGLEVVATSRS-PESV 177 Query: 177 ASELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDE 236 G++ L +DEL +D + L PLTP+T ++ +I MK +++N +RG +ID+ Sbjct: 178 PD--GVRFLKIDELVATADIVLLCCPLTPETTGLLNAGRIGRMKPTAILVNVSRGPVIDD 235 Query: 237 AALYDALNSGKIKAAALDVFEQEP-PKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAE 295 AAL +AL G+I AALDVF +P P + P +N+I TPH TEE+ + GT A Sbjct: 236 AALIEALRDGRIGGAALDVFATQPLPLDHPYFGFDNVIVTPHLAGLTEESMMRMGTGAAS 295 Query: 296 QTVKILKGESAENVVNLPMV 315 + ++++KG+ N+ N +V Sbjct: 296 EALRVIKGDLPVNLRNPEVV 315 Lambda K H 0.316 0.134 0.364 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: 377 Number of extensions: 20 Number of successful extensions: 5 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: 523 Length of database: 324 Length adjustment: 31 Effective length of query: 492 Effective length of database: 293 Effective search space: 144156 Effective search space used: 144156 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: 50 (23.9 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