Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate BPHYT_RS09440 BPHYT_RS09440 glycerate kinase
Query= metacyc::MONOMER-20837 (380 letters) >FitnessBrowser__BFirm:BPHYT_RS09440 Length = 381 Score = 301 bits (770), Expect = 3e-86 Identities = 179/371 (48%), Positives = 224/371 (60%), Gaps = 5/371 (1%) Query: 3 IIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGELRR 62 ++IAPDSFK SLSAE VAQAIAAG+ P A++ CPMADGGEGT+DA+L GE R Sbjct: 10 VVIAPDSFKGSLSAEQVAQAIAAGIKRARPAAEVRICPMADGGEGTLDAMLTR-GGERRT 68 Query: 63 QQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTS-TTYGTGELIRAA 121 VRG G EA G LAD +AIIE AE G+ P G + +T G GE IRA Sbjct: 69 LSVRGAAGPVREALTGLLADG-SAIIETAEVVGIT-DPVGMGVPVEARSTRGMGEAIRAL 126 Query: 122 LDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLDP 181 +D G R +A+GGS+TND GAG + LG +LFDA+ L L+RLA + + LD Sbjct: 127 MDAGVRRFFVALGGSSTNDGGAGLLAGLGLKLFDAQDNELDATPEQLARLARVDVSQLDA 186 Query: 182 RLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKDV 241 RL+ +F +DV+NPL G HGA+A+FGPQKG P V LDAAL FAD L + Sbjct: 187 RLSSTQFVGMSDVDNPLTGEHGATAVFGPQKGVKPEQVATLDAALARFADLLEPALGRTA 246 Query: 242 RDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTLR 301 R PG+GAAGGLGFA LGAQF G E VA +GL+ A+ GAD +ITGEGR D QTL Sbjct: 247 RQLPGAGAAGGLGFALH-MLGAQFEPGAETVARQIGLDAALEGADWLITGEGRSDVQTLH 305 Query: 302 GKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPRL 361 GK PF R A VP +++G + A + F+ GP++LE A +A RL Sbjct: 306 GKAPFIACRHAQAAGVPATLLSGGVDSAALPRLAEYFSGCFSPAPGPITLEVAIRDAARL 365 Query: 362 LRERASDIARV 372 L + A + R+ Sbjct: 366 LADEAEQLTRL 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: 389 Number of extensions: 22 Number of successful extensions: 5 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: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 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