Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate PP_3178 PP_3178 glycerate kinase
Query= metacyc::MONOMER-20837 (380 letters) >FitnessBrowser__Putida:PP_3178 Length = 379 Score = 551 bits (1419), Expect = e-161 Identities = 271/376 (72%), Positives = 315/376 (83%) Query: 1 MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60 MKI+IAPDSFKDSL A GVA+AIAAGLSE WP+A+L++CPMADGGEGT++ +LAA +GEL Sbjct: 1 MKIVIAPDSFKDSLDAAGVARAIAAGLSEAWPEAELVECPMADGGEGTMEVILAASRGEL 60 Query: 61 RRQQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRA 120 RRQ VRGPLG VEA WGWL S TAIIEMA+ASGLQ VP GQRDAC S+T+GTGELI A Sbjct: 61 RRQTVRGPLGQYVEAGWGWLPQSRTAIIEMAQASGLQQVPTGQRDACRSSTWGTGELIAA 120 Query: 121 ALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLD 180 ALD GA R++LAIGGSATNDAG+G ++ALG +L DA+ Q L GGLAL++LAHI LD Sbjct: 121 ALDAGARRVVLAIGGSATNDAGSGMLRALGLRLLDADGQALEEGGLALAKLAHIDASGLD 180 Query: 181 PRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKD 240 PRLA V+FE+AADV+NPLCG +GASAIFGPQKGA+P V+ LD AL HFADHCA +L D Sbjct: 181 PRLAGVQFEVAADVDNPLCGANGASAIFGPQKGANPQQVEALDHALNHFADHCALLLGAD 240 Query: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTL 300 VRD PG GAAGG+GFAA+AF+ AQFR GVEVVAEL GL+ +GADLV+TGEGRFDAQTL Sbjct: 241 VRDYPGCGAAGGMGFAARAFMDAQFRPGVEVVAELAGLDALAQGADLVVTGEGRFDAQTL 300 Query: 301 RGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPR 360 RGKTP GVAR+A +H VPV+V+AGTLGEGY+Q+YAHGV A FAL GPMSLEQAC+ A Sbjct: 301 RGKTPMGVARVAKRHGVPVVVLAGTLGEGYQQLYAHGVDAVFALANGPMSLEQACANAAE 360 Query: 361 LLRERASDIARVWRLA 376 LL+ RA DI R+WR A Sbjct: 361 LLQARACDIGRLWRCA 376 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: 534 Number of extensions: 19 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: 379 Length adjustment: 30 Effective length of query: 350 Effective length of database: 349 Effective search space: 122150 Effective search space used: 122150 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