Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate WP_029134469.1 A3GO_RS0117290 glycerate kinase
Query= BRENDA::Q9X1S1 (417 letters) >NCBI__GCF_000428045.1:WP_029134469.1 Length = 410 Score = 202 bits (513), Expect = 2e-56 Identities = 139/421 (33%), Positives = 217/421 (51%), Gaps = 19/421 (4%) Query: 1 MFDPESLKKLAIEIVKKSIEAVFPDRAVKETLPKLNLDRVILVAVGKAAWRMAKAAYEVL 60 M D ++ + I + ++ V V+E+L + + V L+A+GKAA M + A +VL Sbjct: 1 MPDMAGARRDLLTIFQAALTRVEGRACVRESL-RGDQGTVSLIALGKAAQSMTQGALDVL 59 Query: 61 GKKIRKGVVVTKYGHSEGPI---DDFEIYEAGHPVPDENTIKTTRRVLELVDQLNENDTV 117 G ++ G+V++K GH + + E GHPVPDE +++ R ++E + ++ + Sbjct: 60 GDRVLDGLVISKAGHMDESLLRARGLGCLEGGHPVPDERSLRAGRELVEFIRTRPKDRRL 119 Query: 118 LFLLSGGGSSLFELPLEGVSLEEIQKLTSALLKSGASIEEINTVRKHLSQVKGGRFAERV 177 LFL+SGG S L EL +G+ L +Q++ LL SG SI+ +N VRK LS++KGG + Sbjct: 120 LFLISGGTSGLVELLRDGIDLASLQRVNQWLLGSGLSIDAMNRVRKSLSRIKGGGLIPLL 179 Query: 178 FPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDALKVLEKYGI-ETSESVKRAILQET 236 L++SDV GD VI SG D E L+ + + ++ + Sbjct: 180 QGRPAQVLLISDVPGDEPGVIGSGLLVAD----EHPACGLDDLALPDWLRALVPPVPPPV 235 Query: 237 PKHLSNVEIHLIGNVQKVCDEAKSLAKEKGFNAEIITTSLDCEAREAGRFIASIMKEVKF 296 P N+ + ++ ++ + A A+E G+ + L + GR +A +++ Sbjct: 236 PTKADNIRVSIVASLADAREAAADKARELGYAVTLSRAHLGGDVNVVGRRLAYELRDA-- 293 Query: 297 KDRPLKKPAALIFGGETVVHVKGN-GIGGRNQELALSAAIALEGIEGVILCSAGTDGTDG 355 ++GGE +H+ + G GGRNQ LAL A + G V +AGTDG DG Sbjct: 294 ------WSGLYVWGGEPTIHLPEHPGQGGRNQHLALVVACQIAGRRDVCFLAAGTDGGDG 347 Query: 356 PTDAAGGIVD-GSTAKTLKAMGEDPYQYLKNNDSYNALKKSGALLITGPTGTNVNDLIIG 414 P + AG IVD GS + + +G DP L DS L+ SG L+ TGPTGTNV DL+IG Sbjct: 348 PGEDAGAIVDGGSVGRGCRVLGVDPEVCLTQADSGRFLEASGDLIQTGPTGTNVMDLMIG 407 Query: 415 L 415 L Sbjct: 408 L 408 Lambda K H 0.314 0.134 0.371 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: 363 Number of extensions: 26 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: 417 Length of database: 410 Length adjustment: 31 Effective length of query: 386 Effective length of database: 379 Effective search space: 146294 Effective search space used: 146294 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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