Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate HSERO_RS10055 HSERO_RS10055 glycerate kinase
Query= metacyc::MONOMER-20837 (380 letters) >FitnessBrowser__HerbieS:HSERO_RS10055 Length = 387 Score = 283 bits (723), Expect = 7e-81 Identities = 160/376 (42%), Positives = 221/376 (58%), Gaps = 3/376 (0%) Query: 3 IIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGELRR 62 ++IAPDSFK SLSAE VA+AI AG+ P A++ P+ADGGEGT+DA++ A GE Sbjct: 13 VVIAPDSFKGSLSAEDVARAIGAGIQAAIPDAEIRLRPIADGGEGTLDALMHA-GGERFA 71 Query: 63 QQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRAAL 122 R G EA G L D +A++E A GL +T G G+ I+A L Sbjct: 72 VACRNAAGQMTEALVGILKDG-SAVVESAAIVGLTDTAGTAVAVERRSTLGVGDAIKALL 130 Query: 123 DLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLDPR 182 D GA ++A+GGS+TND GAG + ALG +DA + P L R+ + LD R Sbjct: 131 DRGARSFLVALGGSSTNDGGAGLLAALGVVFYDAAGVEVAPAPAELHRVVRVDASGLDAR 190 Query: 183 LAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKDVR 242 + + F +DV+NPLCG GA+A+FGPQKG P V LD L HFA L + Sbjct: 191 VKEAHFVAMSDVDNPLCGAEGATAVFGPQKGVQPDQVAPLDQTLAHFAQVLEEALGRQAA 250 Query: 243 DEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTLRG 302 PG+GAAGGLG+A LGAQFR+G + VA+ +GL+ A+ GAD +ITGEGR DAQTL G Sbjct: 251 TLPGAGAAGGLGYAL-LMLGAQFRSGAQTVADHIGLDQALTGADWLITGEGRSDAQTLHG 309 Query: 303 KTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPRLL 362 K PF ++ A Q VP +++G + + F++ GP +L+ A ++AP+LL Sbjct: 310 KAPFIASQRARQLGVPATLLSGGIDRHSLAQLQTSFSGCFSIVFGPGALQDAIAQAPQLL 369 Query: 363 RERASDIARVWRLASS 378 + A +AR+W+ A++ Sbjct: 370 QASAEQLARLWQSAAA 385 Lambda K H 0.318 0.135 0.398 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: 360 Number of extensions: 19 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: 380 Length of database: 387 Length adjustment: 30 Effective length of query: 350 Effective length of database: 357 Effective search space: 124950 Effective search space used: 124950 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