Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Ga0059261_1479 Ga0059261_1479 Lactate dehydrogenase and related dehydrogenases
Query= BRENDA::Q9Z564 (529 letters) >FitnessBrowser__Korea:Ga0059261_1479 Length = 332 Score = 186 bits (473), Expect = 9e-52 Identities = 113/320 (35%), Positives = 176/320 (55%), Gaps = 9/320 (2%) Query: 3 SKPVVLIAEELSPATVDALGPDFEI---RHCNGADRAELLPAIADVDAILVRSATKVDAE 59 ++P V + EL A +G F+ + DRA LL A+AD D ++ +DA+ Sbjct: 8 ARPRVAVTRELPDAIAARMGELFDTSFNQSDEAMDRAALLAAVADCDVLVPTVTDTIDAD 67 Query: 60 AVAAA-KKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNI 118 +AAA ++LK++A G G++++D+ AA G++V N P A++ LIV+ R + Sbjct: 68 LIAAAGERLKLIANFGSGVNHIDLKAARARGIVVTNTPGVLTEDTADMTMALIVSVPRRL 127 Query: 119 PQANAALKNGEWKRSKYTGV---ELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYV 175 + +++G+WK G+ + K LG+VG+GRIG VA+R AFG+ + ++ + Sbjct: 128 AEGEKLVRSGQWKGWSPGGMLGHRIGGKKLGIVGMGRIGQAVARRARAFGLSIHYHNRHR 187 Query: 176 QPARA-AQMGVKVLS-LDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAAR 233 P A++G LD +L D +T+H P E+ LI + + P V ++NA+R Sbjct: 188 LPEVVEAELGAAWHGDLDAMLREIDILTIHTPLNEESRDLIDARRIGLLGPQVYLINASR 247 Query: 234 GGIVDEEALYSALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAG 293 GGIVDEEA+ AL+ GR+AGAGLDV+ EP D L VV TPH+G++T E + G Sbjct: 248 GGIVDEEAMVDALEAGRLAGAGLDVWRFEPQIDPRLLALPNVVMTPHMGSATYEGRHATG 307 Query: 294 IAVAKSVRLALAGELVPDAV 313 V ++R G PD V Sbjct: 308 EKVIANIRFWADGHRPPDQV 327 Lambda K H 0.315 0.133 0.362 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: 399 Number of extensions: 22 Number of successful extensions: 4 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: 529 Length of database: 332 Length adjustment: 32 Effective length of query: 497 Effective length of database: 300 Effective search space: 149100 Effective search space used: 149100 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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