Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF834 HP15_813 D-isomer specific 2-hydroxyacid dehydrogenase family protein
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__Marino:GFF834 Length = 389 Score = 126 bits (316), Expect = 9e-34 Identities = 81/256 (31%), Positives = 127/256 (49%), Gaps = 4/256 (1%) Query: 57 ASGLRWMQSTFAGVDLLVKPRQ-RRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKS 115 A L+W+ +T AGVD L+ P R D +TN RGIF ++EY+ +L ++ Sbjct: 130 ADKLQWIHATSAGVDALMFPDLIRGDVTVTNARGIFDRTIAEYVLCTILMFAKDFPNSIR 189 Query: 116 QQQQKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATE-GFDEV 174 Q + W + +G ++L++G GSI + + + G+K GI R + + F V Sbjct: 190 LQMKHQWKHRDTERAEGKQVLVVGAGSIGRQIGRLVGAAGLKAHGIARKPRKEDPDFVAV 249 Query: 175 ATLEALPTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALER 234 + L + AD + P T T G+ +E MK A L N+GRG ++ D L Sbjct: 250 HGNDDLYEQLGHADFVVIAAPLTPQTEGLFDEKAFKAMKNSARLINIGRGPIVKTDDLIT 309 Query: 235 QLRQHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAP--SFPEQVAEIFSSNYHKF 292 L A LDVF +EPL EDHP+W + NV +T H+A + + + F N+ ++ Sbjct: 310 ALENGEIAGAGLDVFEEEPLAEDHPLWDMENVTMTAHMAGDFIGWKRALTDQFLENFDRW 369 Query: 293 LLGETLSHRVNFERGY 308 G+ L + V+ E GY Sbjct: 370 HKGDELFNLVDKELGY 385 Lambda K H 0.320 0.137 0.404 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: 274 Number of extensions: 11 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: 308 Length of database: 389 Length adjustment: 29 Effective length of query: 279 Effective length of database: 360 Effective search space: 100440 Effective search space used: 100440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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