Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012333340.1 M446_RS17025 glyoxylate/hydroxypyruvate reductase A
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000019365.1:WP_012333340.1 Length = 317 Score = 135 bits (340), Expect = 1e-36 Identities = 91/276 (32%), Positives = 132/276 (47%), Gaps = 8/276 (2%) Query: 37 IRLADIWLAEPGLAAPLVNHASGLRWMQSTFAGVDLLVKPRQRRDYLLTN-VRGIFGPLM 95 +R+A + +P A L L W+QS +AGV+ LV+ + V M Sbjct: 46 VRVAVVANPDPAEVARLPR----LAWIQSLWAGVERLVRDLGAAGVPIVRLVDPELARTM 101 Query: 96 SEYLFGYLLARQREHDLYKSQQQQKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFG 155 +E + + QR+ Y+ QQ+ +W P Y+ + LLG G + A G Sbjct: 102 AEAVLAWTFFLQRDMPAYRRQQEAGIWRPLPYRAPAEMTVGLLGFGLLGAAAAGRLDEAG 161 Query: 156 MKVAGINRSAKATEGFDEVATL---EALPTLMARADAIASILPSTEATRGILNENILARM 212 +VA +R+ +A G + ATL + L L+A +D + +LP T ATRG+L A M Sbjct: 162 FRVAAWSRTPRARPGAEAGATLAGPDGLARLLAGSDVVVCLLPMTPATRGLLGAAQFAAM 221 Query: 213 KPDAVLFNLGRGDVLDLDALERQLRQHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHI 272 KP A L N GRG ++ DAL L AVLDVF+ EPLP + P+W V V PH+ Sbjct: 222 KPGAALMNFGRGPIVATDALLAALESGQLSHAVLDVFDTEPLPPESPLWRHPGVTVLPHV 281 Query: 273 AAPSFPEQVAEIFSSNYHKFLLGETLSHRVNFERGY 308 AP+ P A I + N + + V+ RGY Sbjct: 282 TAPTNPRSAAAIVAENLRGYRRTGRIPAAVDAARGY 317 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: 270 Number of extensions: 12 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: 317 Length adjustment: 27 Effective length of query: 281 Effective length of database: 290 Effective search space: 81490 Effective search space used: 81490 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