Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_041102223.1 SUTH_RS11140 phosphonate dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000828635.1:WP_041102223.1 Length = 335 Score = 176 bits (446), Expect = 7e-49 Identities = 120/339 (35%), Positives = 181/339 (53%), Gaps = 21/339 (6%) Query: 1 MRPKVGVLLKMKREALEELKKYADVEIILYPSGEEL--KGVIGRF---DGIIVSPTTKIT 55 M+PKV + + E ++ L ++ V I + E L + ++ R D I+ T + Sbjct: 1 MKPKVVLTSWVHPEVIDRLAQHCTV--IPNTTRERLAREEILSRAKDADAIMTFMTDSVD 58 Query: 56 REVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRK 115 L RL+V+ C GYDN D++ T+RGI++T V LL+ AE T+GL+I L RK Sbjct: 59 DAFLAACPRLRVVGCALKGYDNYDVDACTRRGIWITNVPDLLTIPTAELTIGLLIGLTRK 118 Query: 116 IHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYW 175 I D+ +R G ++ + G L G+ +GI+GMGA+G+AIA RL + ++L Y Sbjct: 119 ILQGDQLVRSGSFDGWRPVLYG----AGLTGRTLGIIGMGAVGQAIAARLQGYELELLYA 174 Query: 176 -SRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-GKYLVN 233 S V +E L R + +D LL SD V+ +P DT H+I+ + ++ G +LVN Sbjct: 175 DSLPLPVAMEARLGLRRVAMDRLLADSDYVVPMVPYGEDTLHLIDARAIAAMKHGAFLVN 234 Query: 234 IGRGALVDEKAVTEAIKQGKLKGYATDVFEKE----PVR----EHELFKYEWETVLTPHY 285 RG++VDEKAV +A++ GKL GYA DVFE E P R L T+ TPH Sbjct: 235 ACRGSVVDEKAVADALEAGKLAGYAADVFELEEWARPDRPTKISARLLADSERTLFTPHI 294 Query: 286 AGLALEAQEDVGFRAVENLLKVLRGEVPEDLVNKEVLEV 324 + + A N+L+VL G+ P+ VN+ V +V Sbjct: 295 GSAVDSVRIAIEMEATTNILQVLAGQEPQGAVNRPVTKV 333 Lambda K H 0.319 0.139 0.393 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: 248 Number of extensions: 11 Number of successful extensions: 5 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: 333 Length of database: 335 Length adjustment: 28 Effective length of query: 305 Effective length of database: 307 Effective search space: 93635 Effective search space used: 93635 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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