Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_013133956.1 ARNIT_RS00710 2-hydroxyacid dehydrogenase
Query= BRENDA::Q972A9 (313 letters) >NCBI__GCF_000092245.1:WP_013133956.1 Length = 309 Score = 136 bits (342), Expect = 7e-37 Identities = 87/263 (33%), Positives = 149/263 (56%), Gaps = 14/263 (5%) Query: 50 IVVRSRTKVTKDVIEKGKKLKIIARAGIGLDNIDTEEAEKRNIKVVYAPGASTDSAVELT 109 IV+ ++ +TK+VI+ +LK+I + G++N+D E A+ + I+V G ST S +LT Sbjct: 46 IVITNKVLITKEVID-ATELKLICISATGMNNVDIEYAKHKGIEVKNVAGYSTSSVAQLT 104 Query: 110 IGLMIAAARKM--YTSMALA----KSGIFKKIEG--LELAGKTIGIVGFGRIGTKVGIIA 161 I + +KM Y++ KS IF I+ +EL GKT GI+G G IG KV IA Sbjct: 105 ISFALHFIQKMDYYSNYVKEGNWQKSKIFTHIDEPFMELDGKTWGIIGLGSIGEKVAQIA 164 Query: 162 NAMGMKVLAYDILDIREKAEKINAKAVSLEELLKNSDVISLHVTVSKDAKPIIDYPQFEL 221 +A G + Y + A N A L L+ SD+IS+H +++ K +++Y +L Sbjct: 165 SAFGCNIKYYSTSGMNYNA---NYDATDLASLISESDIISIHSPLNEKTKDLLNYENMKL 221 Query: 222 MKDNVIIVNTSRAVAVNGKALLDYIKKGKVYAYATDVFWNEPPKEEWEL-ELLKHERVIV 280 +K++ I++N +R +N +++ +K+ +Y +A D EP +E+ L ++L++E VI+ Sbjct: 222 LKNDSIVINVARGGIINEYDIVEILKEKNIY-FALDTVTTEPIEEDSPLNDILENENVII 280 Query: 281 TTHIGAQTKEAQKRVAEMTTQNL 303 T HI + EA+K++ E N+ Sbjct: 281 TPHIAWSSIEARKKLIEGVYNNI 303 Lambda K H 0.317 0.134 0.361 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: 238 Number of extensions: 19 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: 313 Length of database: 309 Length adjustment: 27 Effective length of query: 286 Effective length of database: 282 Effective search space: 80652 Effective search space used: 80652 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: 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