Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_048192322.1 PYRFU_RS03400 3-phosphoglycerate dehydrogenase
Query= BRENDA::Q972A9 (313 letters) >NCBI__GCF_000223395.1:WP_048192322.1 Length = 308 Score = 316 bits (810), Expect = 4e-91 Identities = 162/305 (53%), Positives = 225/305 (73%), Gaps = 3/305 (0%) Query: 6 VKALITDPIDEILIKTLREKGIQVDYMPEISKEELLNIIGNYDIIVVRSRTKVTKDVIEK 65 +K L+TDP+D++L+ L + G+QVDY P + +EELL IIG+YDI+VVRSRTKV ++VI++ Sbjct: 1 MKVLVTDPVDKLLLGILEKHGLQVDYRPGVPREELLKIIGDYDILVVRSRTKVDREVIDR 60 Query: 66 GKKLKIIARAGIGLDNIDTEEAEKRNIKVVYAPGASTDSAVELTIGLMIAAARKMYTSMA 125 G+KLK+IARAG+GLDNID + A ++ IKVV APGA+ S ELTIGL+IAAAR + Sbjct: 61 GEKLKVIARAGVGLDNIDVQHAIEKGIKVVNAPGAAAQSVAELTIGLLIAAARFFKAHIV 120 Query: 126 LAKSGIFKK--IEGLELAGKTIGIVGFGRIGTKVGIIANAMGMKVLAYDILDIREKAEKI 183 + + K G+EL+GKT+G++GFGRIG +V IA +GM+VLAYD++D ++A +I Sbjct: 121 SLERREWSKGRWTGVELSGKTLGVIGFGRIGYRVAKIARGLGMRVLAYDVVDASDRAREI 180 Query: 184 NAKAV-SLEELLKNSDVISLHVTVSKDAKPIIDYPQFELMKDNVIIVNTSRAVAVNGKAL 242 A+ L+ +L+ SD I+LHV ++K+ +ID E MKD VIIVNTSR ++ KAL Sbjct: 181 GAEFTRDLDVVLRESDAITLHVPLTKETYHLIDRDALEKMKDGVIIVNTSRGPVIDTKAL 240 Query: 243 LDYIKKGKVYAYATDVFWNEPPKEEWELELLKHERVIVTTHIGAQTKEAQKRVAEMTTQN 302 L+Y++ GKV+A A DV +EPPKEEWE L+ H RVIVT HIGA+T+EA++RVAE T Sbjct: 241 LEYLESGKVFAAALDVLEHEPPKEEWEWRLVHHPRVIVTPHIGAETREAKRRVAEETAYA 300 Query: 303 LLNAM 307 +L A+ Sbjct: 301 ILEAL 305 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: 300 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: 313 Length of database: 308 Length adjustment: 27 Effective length of query: 286 Effective length of database: 281 Effective search space: 80366 Effective search space used: 80366 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