Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate AO356_10300 AO356_10300 3-phosphoglycerate dehydrogenase
Query= BRENDA::Q9I6H5 (409 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10300 Length = 409 Score = 723 bits (1865), Expect = 0.0 Identities = 365/409 (89%), Positives = 388/409 (94%) Query: 1 MSKTSLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEYLKTALSGDELKERIADAHFIGIR 60 MSKTSLDKSKIKFLLLEGVHQ+AVD LK+AGYT+IEY+ ++L +LKE+IADAHFIGIR Sbjct: 1 MSKTSLDKSKIKFLLLEGVHQSAVDVLKSAGYTSIEYITSSLPEAQLKEKIADAHFIGIR 60 Query: 61 SRTQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEA 120 SRTQLTEE+FD AKKL+AVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEA Sbjct: 61 SRTQLTEEIFDHAKKLVAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEA 120 Query: 121 ILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEALGMQVFFY 180 ILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAE LGMQVFFY Sbjct: 121 ILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEGLGMQVFFY 180 Query: 181 DTVTKLPLGNAVQIGSLHELLGMSDIVSLHVPELPSTQWMIGEKEIRAMKKGGILINAAR 240 DTVTKLPLGNA Q+ LHELLGMSDIV+LHVPE +TQWMIGEKEIRA+KKGGILINAAR Sbjct: 181 DTVTKLPLGNATQVNDLHELLGMSDIVTLHVPETAATQWMIGEKEIRAIKKGGILINAAR 240 Query: 241 GTVVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFASPLRGLDRVILTPHIGGSTAEA 300 GTVV+LD LA AIKD+HLIGAAIDVFPVEP+SND+ F SPLRGLD VILTPHIGGSTAEA Sbjct: 241 GTVVKLDALAEAIKDKHLIGAAIDVFPVEPRSNDDIFESPLRGLDNVILTPHIGGSTAEA 300 Query: 301 QANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHANIPGVMSEINKVFA 360 QANIGLEVAEKLVKYSDNGTSVSSVNFPEVALP+HPGKHRLLHIH NIPGVMSEINKVFA Sbjct: 301 QANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPAHPGKHRLLHIHENIPGVMSEINKVFA 360 Query: 361 DNGINVSGQYLQTNEKVGYVVIDVDAEYSDLALEKLQQVNGTIRSRVLF 409 +NGIN+SGQ+LQTNEKVGYVVIDVDAEYSDLA EKLQ +NGTIR RVLF Sbjct: 361 ENGINISGQFLQTNEKVGYVVIDVDAEYSDLAQEKLQHINGTIRCRVLF 409 Lambda K H 0.317 0.135 0.381 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: 627 Number of extensions: 18 Number of successful extensions: 1 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: 409 Length of database: 409 Length adjustment: 31 Effective length of query: 378 Effective length of database: 378 Effective search space: 142884 Effective search space used: 142884 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