Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF2610 HP15_2554 D-3-phosphoglycerate dehydrogenase-like protein
Query= BRENDA::A4VGK3 (468 letters) >FitnessBrowser__Marino:GFF2610 Length = 409 Score = 615 bits (1587), Expect = 0.0 Identities = 305/409 (74%), Positives = 355/409 (86%) Query: 60 MSQTSLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEDLKTALSGDELKEKIADAHFIGIR 119 MS TSL+KSKI+ LLLEGVHQ+A+DTL AAGYTNIE L +L+ +EL EKIADAHF+GIR Sbjct: 1 MSNTSLEKSKIRILLLEGVHQSAIDTLNAAGYTNIEYLSHSLAEEELIEKIADAHFVGIR 60 Query: 120 SRTQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEA 179 SRTQLTE+VF+ AKKL+AVGCFCIGTNQVDL AA RGIAVFNAP+SNTRSVAELVLA+A Sbjct: 61 SRTQLTEKVFEAAKKLVAVGCFCIGTNQVDLQAATRRGIAVFNAPFSNTRSVAELVLAQA 120 Query: 180 ILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIIGYGSIGTQLSVLAEALGMQVFFY 239 ILLLRG+PEKNA HRG W+KSA +S+EIRGKKLGIIGYG+IGTQ SVLAE LGM V+FY Sbjct: 121 ILLLRGVPEKNAKAHRGEWLKSAKDSYEIRGKKLGIIGYGNIGTQFSVLAEGLGMDVYFY 180 Query: 240 DVVTKLPLGNATQIGSLYELLGMCDIVSLHVPELPSTQWMIGEKEIRAMKKGAILINAAR 299 DVV+KL +GNATQ+G+L ELL + D+VSLHVPE P+T++M ++ MK G+IL+NA+R Sbjct: 181 DVVSKLSIGNATQVGTLQELLNIADVVSLHVPETPATKYMFKAEQFAQMKPGSILMNASR 240 Query: 300 GTVVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFESPLRGLDRVILTPHIGGSTAEA 359 GTVV++D LA A+ L+GAAIDVFPVEPKSNDEEF SPLR D VILTPH+GGST EA Sbjct: 241 GTVVDIDALADALGSGKLLGAAIDVFPVEPKSNDEEFVSPLREFDNVILTPHVGGSTIEA 300 Query: 360 QANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHQNIPGVMSEINKVFA 419 QANIG EVAEKL YSDNGTSVSSVNFPEVALPSHP +HRLLHIH+N+PGVMSEIN+VF+ Sbjct: 301 QANIGREVAEKLAMYSDNGTSVSSVNFPEVALPSHPNQHRLLHIHENVPGVMSEINQVFS 360 Query: 420 DNGINICGQFLQTNEKVGYVVIDVDKEYSDLALEKLQHVNGTIRSRVLF 468 +NGIN+CGQ+LQT E +GYVV+DV+KEY +LA EKL V GTIR RVLF Sbjct: 361 ENGINVCGQYLQTKEDIGYVVVDVNKEYGELAQEKLLKVKGTIRCRVLF 409 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: 567 Number of extensions: 11 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: 468 Length of database: 409 Length adjustment: 32 Effective length of query: 436 Effective length of database: 377 Effective search space: 164372 Effective search space used: 164372 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 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