Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_005458834.1 SACCYDRAFT_RS19615 D-2-hydroxyacid dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000244975.1:WP_005458834.1 Length = 325 Score = 144 bits (363), Expect = 3e-39 Identities = 93/285 (32%), Positives = 148/285 (51%), Gaps = 7/285 (2%) Query: 31 DDNPANIRLADIWLAEPGL--AAPLVNHASG-LRWMQSTFAGVDLLVKPRQR-RDYLLTN 86 D+ P +R AD L A P HA+ LRW+ AGVD ++ P R D +LTN Sbjct: 36 DELPDALRGADALFVYDFLSRAVPGAWHAADRLRWLHIASAGVDPVMFPELRDSDVVLTN 95 Query: 87 VRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQKLWLPGSYKTLQGSELLLLGTGSIAKH 146 RG+F ++EY+ G ++A ++ QQQ+ W + + G+ L++GTG I + Sbjct: 96 SRGVFDSAIAEYVLGVVIAFAKDFAGSLRLQQQRAWRHRETERVAGTSALVVGTGPIGRA 155 Query: 147 LAQTAKHFGMKVAGINRSAKATE-GFDEVATLEALPTLMARADAIASILPSTEATRGILN 205 +A+ GM+V G R A+ + F V E L + D + ++ P TE TRG+ + Sbjct: 156 IARLLGAVGMRVTGAGRRARDGDPDFGRVVASEDLTRHLPDFDVVVAVAPLTEQTRGMFD 215 Query: 206 ENILARMKPDAVLFNLGRGDVLDLDALERQLRQHPQQQAVLDVFNQEPLPEDHPIWGLGN 265 A M+P A N+GRG+++ + L LR A LDVF QEPLP + P+W + N Sbjct: 216 ARAFAAMRPGARFVNVGRGELVVTEDLVSALRGGHLSGAALDVFEQEPLPPESPLWAMEN 275 Query: 266 VIVTPHIAAP--SFPEQVAEIFSSNYHKFLLGETLSHRVNFERGY 308 V+V+ H++ + + E+F+ N+ ++ G L + V+ GY Sbjct: 276 VLVSAHMSGDFVGWRNALVEVFADNFARWCGGRPLRNVVDKRLGY 320 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: 241 Number of extensions: 13 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: 325 Length adjustment: 27 Effective length of query: 281 Effective length of database: 298 Effective search space: 83738 Effective search space used: 83738 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: 48 (23.1 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