Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate SMc02045 SMc02045 oxidoreductase
Query= uniprot:Q6LWW6 (523 letters) >FitnessBrowser__Smeli:SMc02045 Length = 310 Score = 162 bits (409), Expect = 2e-44 Identities = 89/250 (35%), Positives = 149/250 (59%), Gaps = 3/250 (1%) Query: 57 IIEASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIP 116 +I A+++L+ I+R G G+DN+ L +GI V+ A A+++ VAEL G++LAA R+IP Sbjct: 64 VIAAADSLRAISRNGTGIDNLPLSLLKGRGIRVLKAEGANAVGVAELAVGLILAALRHIP 123 Query: 117 QATASIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDV 176 TA I++G W R +G EI +T+GI+G G IG++VA+ A +++A+DP+ P +V Sbjct: 124 AETAGIRAGGWPRS--RGKEIAERTVGIIGCGAIGKRVARAVSAMRASVIAHDPFRP-NV 180 Query: 177 ASELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDE 236 K ++DE+ +D ++LH P + ++ ++A + + +++N AR L+DE Sbjct: 181 EVYGPFKWGSLDEVFAEADIVSLHCPAPADGRPIVDAARLAAVPPHAILINTARATLVDE 240 Query: 237 AALYDALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQ 296 A+ AL+ G+++A A DVF +EPP L + +I T H G T+E+ A I Sbjct: 241 VAVRAALDEGRLQAYATDVFVEEPPAPGSLASHPRVIATSHIGGLTDESVSKATAIAVTN 300 Query: 297 TVKILKGESA 306 + L+ ESA Sbjct: 301 LLSALEEESA 310 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: 350 Number of extensions: 17 Number of successful extensions: 3 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: 310 Length adjustment: 31 Effective length of query: 492 Effective length of database: 279 Effective search space: 137268 Effective search space used: 137268 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 09 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