Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate PfGW456L13_2941 Glycerate kinase (EC 2.7.1.31)
Query= metacyc::MONOMER-20837 (380 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2941 Length = 378 Score = 623 bits (1607), Expect = 0.0 Identities = 307/377 (81%), Positives = 339/377 (89%) Query: 1 MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60 MKI+IAPDSFKDSLSA+GVA AIA GL++VWP AQLI+CPMADGGEGTV+++LAAC+G+ Sbjct: 1 MKIVIAPDSFKDSLSAQGVADAIALGLAQVWPDAQLIKCPMADGGEGTVESILAACEGQQ 60 Query: 61 RRQQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRA 120 RR VRGPLG TVEA WGWL SHTAIIEMAEASGLQLVP QRDAC S+T+GTG+LIRA Sbjct: 61 RRTLVRGPLGATVEAAWGWLPQSHTAIIEMAEASGLQLVPVAQRDACISSTFGTGQLIRA 120 Query: 121 ALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLD 180 ALD GA+R+ILAIGGSATND GAGAMQALG +L DA+ QTL PGGLAL +LA + L +D Sbjct: 121 ALDAGAQRVILAIGGSATNDGGAGAMQALGVKLLDAQGQTLSPGGLALGQLARVDLSEID 180 Query: 181 PRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKD 240 PRLAQVRF+IAADVNNPLCGPHGASAIFGPQKGASPV V+QLD ALGHFADHCAR L D Sbjct: 181 PRLAQVRFDIAADVNNPLCGPHGASAIFGPQKGASPVQVEQLDRALGHFADHCARALNND 240 Query: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTL 300 VRDEPGSGAAGGLGFAAKAFLGAQF AGVEVVAELVGL DAV GADLVITGEGRFDAQTL Sbjct: 241 VRDEPGSGAAGGLGFAAKAFLGAQFTAGVEVVAELVGLADAVAGADLVITGEGRFDAQTL 300 Query: 301 RGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPR 360 RGKTPFGVAR+A +H VPVIVIAGTLGEGY+ +Y HG+ AAFAL +GPM+LEQAC+EAPR Sbjct: 301 RGKTPFGVARVAREHGVPVIVIAGTLGEGYQALYEHGIDAAFALASGPMTLEQACAEAPR 360 Query: 361 LLRERASDIARVWRLAS 377 LLRERA+D+ARVWRLAS Sbjct: 361 LLRERATDVARVWRLAS 377 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: 549 Number of extensions: 12 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: 378 Length adjustment: 30 Effective length of query: 350 Effective length of database: 348 Effective search space: 121800 Effective search space used: 121800 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