Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate YP_002827955.1 NGR_c34780 2-hydroxyacid dehydrogenase protein
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000018545.1:YP_002827955.1 Length = 319 Score = 95.1 bits (235), Expect = 2e-24 Identities = 83/281 (29%), Positives = 123/281 (43%), Gaps = 13/281 (4%) Query: 35 ANIRLADIWLAEPGLAAPLVNHASGLRWMQSTFAGVDLLVKPRQRRDYLLTN-VRGIFGP 93 + I A +W + P L + A L+ + S AGVD ++K D L V Sbjct: 45 SGIDYAVVWKSAPDL----FSRAPDLKVVFSGGAGVDHVLKLPGLPDVPLVRFVDRTLTT 100 Query: 94 LMSEYLFGYLLARQREHDLYKSQQQQKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKH 153 MSE++ L R+H Y++ ++ W S + ++G G + + A+ Sbjct: 101 RMSEWVVMQCLLHLRQHRAYEALVKKHEWRDLSQPEAADITVGIMGMGVLGQDAARKLAV 160 Query: 154 FGMKVAGINRSAKATEGFDEVATLEALPTLMARADAIASILPSTEATRGILNENILARMK 213 G KV G +RS +A EG E L +AR D + +LP T T+GI N + ++ Sbjct: 161 MGFKVIGWSRSKRAVEGI-ETFDAAGLDAFLARTDFLVGLLPLTADTKGIFNATLFKKLS 219 Query: 214 PDA-----VLFNLGRG-DVLDLDALERQLRQHPQQQAVLDVFNQEPLPEDHPIWGLGNVI 267 V N GRG ++ D LE L A LDVF +EPL + W + NV Sbjct: 220 RKGPFGAPVFINAGRGGSQVEADILEC-LDSGVLGGASLDVFEKEPLSRESRFWDIPNVY 278 Query: 268 VTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSHRVNFERGY 308 VTPH+AA S + + +F G L H V+ GY Sbjct: 279 VTPHVAASSDVKALFAHVEEQIERFESGLALEHVVDKVAGY 319 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: 216 Number of extensions: 10 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: 319 Length adjustment: 27 Effective length of query: 281 Effective length of database: 292 Effective search space: 82052 Effective search space used: 82052 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