Align Glycerate 3-kinase; D-Glycerate-3-kinase; Glycerate kinase 2; GK2; EC 2.7.1.31 (characterized)
to candidate 200934 SO1770 glycerate kinase, putative (NCBI ptt file)
Query= SwissProt::P77364 (381 letters) >FitnessBrowser__MR1:200934 Length = 384 Score = 414 bits (1063), Expect = e-120 Identities = 215/383 (56%), Positives = 269/383 (70%), Gaps = 6/383 (1%) Query: 1 MKIVIAPDSFKESLSAEKCCQAIKAGFSTLFPDANYICLPIADGGEGTVDAMVAATGGNI 60 MKIVIAPDSFKESLSA AI+ G + PD + +P+ADGGEGTV +MV ATGG+I Sbjct: 1 MKIVIAPDSFKESLSALDVANAIEQGLMQVIPDCEIVKIPVADGGEGTVQSMVDATGGSI 60 Query: 61 VTLEVCGPMGEKVNAFYGLTGDGKT------AVIEMAAASGLMLVAPEKRNPLLASSFGT 114 V+LEV GP+G KVNA YG+ G AVIEMA+ASGL V E+RNPLL +S+GT Sbjct: 61 VSLEVMGPLGHKVNAHYGILGQQTAQQTQPIAVIEMASASGLHHVPREQRNPLLTTSYGT 120 Query: 115 GELIRHALDNDIRHIILGIGGSATVDGGMGMAQALGVRFLDADGQALAANGGNLARVASI 174 GELI AL+ I+HII+G+GGSAT DGG GMAQALG+ LD G++L+A G LA++A+I Sbjct: 121 GELICDALNRGIKHIIVGLGGSATNDGGAGMAQALGILLLDKHGKSLSAGGAALAKLANI 180 Query: 175 EMDECDPRLANCHIEVACDVDNPLVGARGAAAVFGPQKGATPEMVEELEQGLQNYARVLQ 234 +M P L C EVACDVDNPL G RGA+A+FGPQKGAT EMV L+ L +YA V+ Sbjct: 181 DMSNAHPLLKECTFEVACDVDNPLCGERGASAIFGPQKGATAEMVNTLDSALSHYADVIA 240 Query: 235 QQTEINVCQMAGGGAAGGMGIAAAVFLNADIKPGIEIVLNAVNLAQAVQGAALVITGEGR 294 Q + AG GAAGGMG+ FL A+++PG+EIV+ V LA ++GA LVITGEGR Sbjct: 241 QSGVTDHRHQAGAGAAGGMGLGVMAFLGAELRPGVEIVMQTVGLADKIRGADLVITGEGR 300 Query: 295 IDSQTAGGKAPLGVASVAKQFNVPVIGIAGVLGDGVEVVHQYGIDAVFSILPRLAPLAEV 354 ID QT GK P+GV A+ N+P IGIAG LGD V + G+ A+F I+P L+PL +V Sbjct: 301 IDGQTIFGKTPMGVLKQAQLQNIPTIGIAGCLGDNANAVLEQGMAAIFPIIPHLSPLDDV 360 Query: 355 LASGETNLFNSARNIACAIKIGQ 377 LA+ +TNL N+ARNI + +GQ Sbjct: 361 LANAKTNLINTARNIGAVLMLGQ 383 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: 496 Number of extensions: 29 Number of successful extensions: 2 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 17 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