Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate WP_211218710.1 G579_RS0109880 glycerate kinase
Query= metacyc::MONOMER-20837 (380 letters) >NCBI__GCF_000423825.1:WP_211218710.1 Length = 387 Score = 343 bits (879), Expect = 6e-99 Identities = 182/381 (47%), Positives = 245/381 (64%), Gaps = 2/381 (0%) Query: 1 MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60 ++++IAPD+FK SL A VA+AIAAG P A + P+ADGGEGTV ++LAA G L Sbjct: 8 LQLVIAPDAFKGSLEARAVAEAIAAGCRRALPDAVIRCFPLADGGEGTVASLLAARGGRL 67 Query: 61 RRQQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRA 120 R +V GPLG VEA + L D A+IE+A ASGL L+P +RD ++++GTGEL+R Sbjct: 68 RGVRVHGPLGEPVEAGYAILPDG-AAVIELAAASGLPLLPAARRDPLRASSFGTGELVRD 126 Query: 121 ALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLD 180 ALD G R+I+ +GGSA ND G G +QALG + DA+ Q++ PGG AL +A I + D Sbjct: 127 ALDQGCRRLIVGLGGSAVNDGGLGLLQALGFRFLDAKGQSVGPGGGALGAIARIDVSQAD 186 Query: 181 PRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKD 240 PRL + A DV+ PL GP GA+ FGPQKGA+P ++ L+A + H+AD A L Sbjct: 187 PRLRDAQLIAATDVDTPLLGPEGATHTFGPQKGATPAMLETLEAGMRHYADKIAETLAVR 246 Query: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTL 300 V D PG+GAAGG G A AFLGA+ R+GV +V E +G+ A+ GADL+ITGEGR D QT Sbjct: 247 VHDLPGAGAAGGCGAALHAFLGAEIRSGVALVMEALGVAAALAGADLLITGEGRIDGQTR 306 Query: 301 RGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVA-AAFALPAGPMSLEQACSEAP 359 RGK P+GVAR+A +H VPV+++AG + + G+ +P PMSLE A + Sbjct: 307 RGKAPYGVARLAKRHGVPVLMLAGAVAPEARMLLEDGICDVLLGIPPAPMSLEIALAHTA 366 Query: 360 RLLRERASDIARVWRLASSKG 380 + L + A + R +RL G Sbjct: 367 QHLADGAEQLLRAYRLGRRSG 387 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: 453 Number of extensions: 17 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 Apr 09 2024. 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