Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_073038589.1 BUB04_RS08490 hypothetical protein
Query= curated2:Q58424 (524 letters) >NCBI__GCF_900129305.1:WP_073038589.1 Length = 297 Score = 225 bits (573), Expect = 2e-63 Identities = 131/297 (44%), Positives = 180/297 (60%), Gaps = 12/297 (4%) Query: 8 DPLHEDAIKILEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVI 67 +PL + I E G LT+EE+ AD ++V V+R VIE A +LK + Sbjct: 2 EPLLKGCRVIYNETGRT-----LTEEEMCRLASGADGILV-GVDPVSRKVIEGAPRLKAV 55 Query: 68 GRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEW 127 + GVGVDNID EA E+GI + P A+++SVAELT+GL+ ARN+ A A +K G W Sbjct: 56 SKYGVGVDNIDREALEERGIPLATTPGANNVSVAELTVGLLFVLARNLYAAAAEVKAGGW 115 Query: 128 DRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKE--VAESMGVELV 185 R R G EL GKTLG++G G IG++V +RA+ M + YDPY E + E L Sbjct: 116 SRVR--GTELTGKTLGLVGCGGIGREVARRARGLLMKVCFYDPYFQDERFIREHELERL- 172 Query: 186 DDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALK 245 + EL +DF++LHVPLT +TR ++ RE++ LMK A ++N ARG L+DE+AL+ AL Sbjct: 173 -SLEELLAVSDFVSLHVPLTGETRKLMNRERLGLMKPGAYLINTARGELVDEEALHWALS 231 Query: 246 EGKIRAAALDVFEEEPPKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVL 302 G++ AA DVF +EPP D+PLL LDN + TPH GA T EA E + ++L Sbjct: 232 SGRLAGAACDVFSKEPPGDHPLLRLDNFLLTPHVGAHTHEAVTRMAKAATENLLRLL 288 Lambda K H 0.316 0.137 0.372 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: 370 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: 524 Length of database: 297 Length adjustment: 31 Effective length of query: 493 Effective length of database: 266 Effective search space: 131138 Effective search space used: 131138 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 (21.5 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