Align Glycerate 3-kinase; D-Glycerate-3-kinase; Glycerate kinase 2; GK2; EC 2.7.1.31 (characterized)
to candidate WP_012277881.1 SHAL_RS14520 glycerate kinase
Query= SwissProt::P77364 (381 letters) >NCBI__GCF_000019185.1:WP_012277881.1 Length = 384 Score = 411 bits (1057), Expect = e-119 Identities = 212/375 (56%), Positives = 273/375 (72%), Gaps = 5/375 (1%) Query: 1 MKIVIAPDSFKESLSAEKCCQAIKAGFSTLFPDANYICLPIADGGEGTVDAMVAATGGNI 60 MKIVIAPDSFKESL+A + I+ GF T+ P+A YI +P+ADGGEGTV +MV AT G I Sbjct: 1 MKIVIAPDSFKESLTAMEVANEIERGFRTVLPNAEYIKIPVADGGEGTVQSMVDATDGTI 60 Query: 61 VTLEVCGPMGEKVNAFYGLTG-----DGKTAVIEMAAASGLMLVAPEKRNPLLASSFGTG 115 + L V GP+G KV AFYG+ G D KTAVIEMAAASGL LVA +KRNPL+ +S+GTG Sbjct: 61 IKLNVTGPLGHKVQAFYGILGVGYQGDKKTAVIEMAAASGLHLVAEDKRNPLMTTSYGTG 120 Query: 116 ELIRHALDNDIRHIILGIGGSATVDGGMGMAQALGVRFLDADGQALAANGGNLARVASIE 175 ELI AL+ I HII+G+GGSAT DGG GMAQA+G L++ G+A++ G L + SI+ Sbjct: 121 ELIVDALNRGIEHIIIGLGGSATNDGGAGMAQAIGAHLLNSAGKAISPGGAALTELVSID 180 Query: 176 MDECDPRLANCHIEVACDVDNPLVGARGAAAVFGPQKGATPEMVEELEQGLQNYARVLQQ 235 + + P + C EVACDV+NPL G +GA+A+FGPQKGATPEMVE+L+ L++YA ++ Sbjct: 181 LTDLHPLIKACSFEVACDVNNPLCGNKGASAIFGPQKGATPEMVEQLDNALKHYADIIAC 240 Query: 236 QTEINVCQMAGGGAAGGMGIAAAVFLNADIKPGIEIVLNAVNLAQAVQGAALVITGEGRI 295 + AG GAAGGMG+ FL A++KPGI+IV+ VNLA +GA LVITGEGR+ Sbjct: 241 CAIQDNRDYAGAGAAGGMGLGVMAFLGAELKPGIDIVMETVNLAGLAKGADLVITGEGRL 300 Query: 296 DSQTAGGKAPLGVASVAKQFNVPVIGIAGVLGDGVEVVHQYGIDAVFSILPRLAPLAEVL 355 DSQT GK P+GVA VAK + VI IAG + D V+ ++GIDA+FSI PR PLAEVL Sbjct: 301 DSQTLHGKTPMGVAGVAKAQGISVIAIAGCVSDDANVLLEHGIDALFSITPRALPLAEVL 360 Query: 356 ASGETNLFNSARNIA 370 ++ + NL+++A+NIA Sbjct: 361 SNAKHNLYSTAKNIA 375 Lambda K H 0.318 0.136 0.391 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: 485 Number of extensions: 21 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: 381 Length of database: 384 Length adjustment: 30 Effective length of query: 351 Effective length of database: 354 Effective search space: 124254 Effective search space used: 124254 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 (21.7 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