Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 200048 SO0862 D-3-phosphoglycerate dehydrogenase (NCBI ptt file)
Query= BRENDA::C3SVM7 (410 letters) >FitnessBrowser__MR1:200048 Length = 409 Score = 566 bits (1458), Expect = e-166 Identities = 282/411 (68%), Positives = 337/411 (81%), Gaps = 3/411 (0%) Query: 1 MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60 MAK SL+KDKIK LL+EGVHQ A++ AGYTNIE+HK +L DE L ESI+DAHFIG+R Sbjct: 1 MAKHSLDKDKIKILLLEGVHQSAVDVFERAGYTNIEYHKASLGDEALHESIKDAHFIGIR 60 Query: 61 SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120 SRT L+ DV+ AEKL+AIGCFCIGTNQVDL A GIPVFNAPFSNTRSVAELV+GE+ Sbjct: 61 SRTQLSADVLKRAEKLIAIGCFCIGTNQVDLATAESLGIPVFNAPFSNTRSVAELVLGEI 120 Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180 ++L+RG+PE NA AHRG W K AAGS+E RGK LG+IGYGHIGTQLGILAE+LGM V F+ Sbjct: 121 IMLMRGIPERNAIAHRGGWMKTAAGSYEVRGKTLGVIGYGHIGTQLGILAETLGMRVVFF 180 Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240 DIE+KLPLGNA Q+ + LL +DVVSLHVPE P TK+M+ E + M+ GS+ INASR Sbjct: 181 DIEDKLPLGNAQQIHSMEQLLAQADVVSLHVPETPQTKDMISTAEFAAMRKGSIFINASR 240 Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300 GTVVDI AL AL +HLAGAAIDVFP EP +N D F SPL DNVLLTPH+GGST EA Sbjct: 241 GTVVDIDALTVALKERHLAGAAIDVFPVEPQSNDDEFISPLRGLDNVLLTPHVGGSTAEA 300 Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLH-GGRRLMHIHENRPGVLTALNKIFA 359 QENIG+EVAGKL KYSDNGST+SAVNFPEVSLP+H G RL+HIH+NRPGVL +NK F+ Sbjct: 301 QENIGIEVAGKLAKYSDNGSTVSAVNFPEVSLPMHKGTSRLLHIHQNRPGVLIKINKAFS 360 Query: 360 EQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410 E+G+NIAAQYLQT+A++GYVV++++ + AE+AL +KAI GT+R R+L+ Sbjct: 361 EKGINIAAQYLQTTAEIGYVVMEVDTHQ--AEEALVELKAIDGTLRTRVLF 409 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: 508 Number of extensions: 18 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: 409 Length adjustment: 31 Effective length of query: 379 Effective length of database: 378 Effective search space: 143262 Effective search space used: 143262 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 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