Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_057508923.1 ABB28_RS12365 phosphoglycerate dehydrogenase
Query= BRENDA::A4VGK3 (468 letters) >NCBI__GCF_001431535.1:WP_057508923.1 Length = 414 Score = 506 bits (1304), Expect = e-148 Identities = 258/413 (62%), Positives = 318/413 (76%), Gaps = 2/413 (0%) Query: 58 MQMSQTSLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEDLKTALSGDELKEKIADAHFIG 117 M +TS K I+ LLLEGV Q AVD AAGY+ IE AL DELK +IADAH +G Sbjct: 1 MSPKKTSYPKQDIRVLLLEGVSQTAVDVFTAAGYSQIELHSKALPEDELKARIADAHIVG 60 Query: 118 IRSRTQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLA 177 IRSR+QL+ EV AK++IAVGCFCIGTNQVDL+AA GI VFNAPYSNTRSVAELV+A Sbjct: 61 IRSRSQLSAEVLAEAKRVIAVGCFCIGTNQVDLDAAELAGIPVFNAPYSNTRSVAELVIA 120 Query: 178 EAILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIIGYGSIGTQLSVLAEALGMQVF 237 EAI+L RGIP+KNA CHRGGW KSAA S E+RGK LGIIGYG IGTQ+ VLAE+LG+QV Sbjct: 121 EAIMLTRGIPQKNAECHRGGWSKSAAGSHEVRGKTLGIIGYGHIGTQVGVLAESLGLQVI 180 Query: 238 FYDVVTKLPLGNATQIGSLYELLGMCDIVSLHVPELPSTQWMIGEKEIRAMKKGAILINA 297 F+DV KL LGNA SL +LL DI++LHVPE P+TQWMIG E+ M++GA +INA Sbjct: 181 FHDVEAKLALGNARAAVSLDDLLERSDIITLHVPETPATQWMIGATELAKMRRGAHVINA 240 Query: 298 ARGTVVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFESPLRGLDRVILTPHIGGSTA 357 ARGT+V++ L AA+ H+ GAA+DVFPVEPK N + FESPL D VILTPH+GGST Sbjct: 241 ARGTIVDIAALDAALGSGHIGGAALDVFPVEPKGNGDVFESPLTAHDNVILTPHVGGSTL 300 Query: 358 EAQANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHQNIPGVMSEINKV 417 EAQ NIG+EVA KLV+YSDNG+++++VNFPEV LP H G RLLHIH+N+PGV+S++N++ Sbjct: 301 EAQDNIGIEVAAKLVRYSDNGSTLTAVNFPEVTLPEHDGSLRLLHIHRNVPGVLSKVNEI 360 Query: 418 FADNGINICGQFLQTNEKVGYVVIDVDKEYSDLAL--EKLQHVNGTIRSRVLF 468 F+ + +NI GQFL+T+ KVGYVVID+ A ++L + GT+R+RVL+ Sbjct: 361 FSRHNVNIDGQFLRTDAKVGYVVIDITASVEQAAAVRDELAAIPGTLRTRVLY 413 Lambda K H 0.318 0.135 0.385 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: 545 Number of extensions: 22 Number of successful extensions: 2 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: 468 Length of database: 414 Length adjustment: 32 Effective length of query: 436 Effective length of database: 382 Effective search space: 166552 Effective search space used: 166552 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: 51 (24.3 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