Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_013835838.1 THICY_RS06585 phosphoglycerate dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >NCBI__GCF_000214825.1:WP_013835838.1 Length = 416 Score = 515 bits (1326), Expect = e-150 Identities = 264/407 (64%), Positives = 320/407 (78%), Gaps = 3/407 (0%) Query: 5 SLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTH 64 SL K+KI LL+EG+H A R GY+NI H GAL +LK +++D HFIG+RSRT Sbjct: 12 SLAKEKINILLLEGIHPGAEAYFREQGYSNIISHAGALSPSELKTALQDCHFIGIRSRTQ 71 Query: 65 LTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLL 124 LT +++ A KL AIGCFCIGTNQVDL AA + GIPVFNAPFSNTRSVAELV+GE+LLLL Sbjct: 72 LTAELLAQAPKLNAIGCFCIGTNQVDLTAAMRLGIPVFNAPFSNTRSVAELVLGEILLLL 131 Query: 125 RGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIEN 184 R VPE NA AHR +W K A G+FEARGK LGIIGYG IG+QL ILAE+LGM V FYDI Sbjct: 132 RRVPEKNALAHRSIWQKSAQGAFEARGKTLGIIGYGRIGSQLSILAENLGMRVIFYDIAK 191 Query: 185 KLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVV 244 +LPL NA QV L++LL+ +DVVSLHVPE P T+ M+G +++++MKPGSLLINA+RG VV Sbjct: 192 QLPLNNAQQVASLAELLSKADVVSLHVPETPETEWMIGHQQLAMMKPGSLLINAARGRVV 251 Query: 245 DIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENI 304 DIPAL DAL S LAGAAIDVFPTEP TN PF S L DNV+LTPHIGGST+EAQ +I Sbjct: 252 DIPALADALQSGQLAGAAIDVFPTEPETNKQPFESVLRGLDNVILTPHIGGSTEEAQASI 311 Query: 305 GLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGR-RLMHIHENRPGVLTALNKIFAEQGV 363 G EVA KL+ YSD GS++SAVNFPEV+LP H GR RL+HIH N+PG+LT +N+ FA Q + Sbjct: 312 GAEVAAKLVAYSDIGSSISAVNFPEVALPEHIGRSRLLHIHHNQPGILTQINQAFAAQNI 371 Query: 364 NIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410 NIAAQYLQT++++GYVVID++A + + L +K IPGT+R RLL+ Sbjct: 372 NIAAQYLQTNSEIGYVVIDLDAKD--RDAGLAQLKQIPGTLRTRLLH 416 Lambda K H 0.318 0.135 0.383 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: 485 Number of extensions: 14 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: 410 Length of database: 416 Length adjustment: 31 Effective length of query: 379 Effective length of database: 385 Effective search space: 145915 Effective search space used: 145915 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 (21.7 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