Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate AO353_26900 AO353_26900 glycerate kinase
Query= metacyc::MONOMER-20837 (380 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26900 Length = 380 Score = 605 bits (1559), Expect = e-178 Identities = 305/379 (80%), Positives = 335/379 (88%) Query: 1 MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60 MKI+IAPDSFKDSLSAE VA AIA GL+EVWP A L++CPMADGGEGTV+++LAAC+GEL Sbjct: 1 MKIVIAPDSFKDSLSAEAVATAIALGLAEVWPDATLVKCPMADGGEGTVESILAACEGEL 60 Query: 61 RRQQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRA 120 R V+GPLG V+A WGWL +HTAIIEMAEASGLQLVP GQRDAC S+T+GTGELIRA Sbjct: 61 RSASVQGPLGIQVDAHWGWLPHNHTAIIEMAEASGLQLVPVGQRDACISSTFGTGELIRA 120 Query: 121 ALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLD 180 ALD GA+RIILAIGGSATNDAGAGA+QALG +L DA+ QTL PGGLAL++LA I L +D Sbjct: 121 ALDAGAQRIILAIGGSATNDAGAGALQALGVRLLDAQGQTLQPGGLALAQLARIDLSEMD 180 Query: 181 PRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKD 240 PRLA VRFEIAADVNNPLCGPHGASAIFGPQKGAS VQQLD ALGHFA CA+ L KD Sbjct: 181 PRLASVRFEIAADVNNPLCGPHGASAIFGPQKGASVEQVQQLDQALGHFAGICAQTLGKD 240 Query: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTL 300 +RDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVA+LVGLE+AVR ADLVITGEGRFDAQTL Sbjct: 241 LRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVADLVGLEEAVRDADLVITGEGRFDAQTL 300 Query: 301 RGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPR 360 RGKTPFGVARIA Q VPVIVIAGTLGEGY+QMY HGV AAFAL +GPM+LEQAC++APR Sbjct: 301 RGKTPFGVARIARQQGVPVIVIAGTLGEGYQQMYEHGVDAAFALASGPMTLEQACTDAPR 360 Query: 361 LLRERASDIARVWRLASSK 379 LL +RA DIARVWRLA K Sbjct: 361 LLHDRARDIARVWRLAVHK 379 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: 531 Number of extensions: 7 Number of successful extensions: 1 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: 380 Length adjustment: 30 Effective length of query: 350 Effective length of database: 350 Effective search space: 122500 Effective search space used: 122500 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