Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate RR42_RS23230 RR42_RS23230 glycerate kinase
Query= metacyc::MONOMER-20837 (380 letters) >FitnessBrowser__Cup4G11:RR42_RS23230 Length = 396 Score = 272 bits (696), Expect = 1e-77 Identities = 167/375 (44%), Positives = 215/375 (57%), Gaps = 13/375 (3%) Query: 3 IIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGELRR 62 I+IAPDSFK SL+A VA AIAAG+ P A + Q PMADGGEGT+DA+LAA G+ Sbjct: 9 IVIAPDSFKGSLAAGQVAAAIAAGIQRALPGATIRQRPMADGGEGTIDAMLAA-GGQRTG 67 Query: 63 QQVRGPLGGTVEARWGWLADSHTAIIEMAEASGL-----QLVPPGQRDACTSTTYGTGEL 117 +VRG G A LA A+IE AE G+ P QR +T G G+ Sbjct: 68 IEVRGAHGAARIATVALLAGDR-AVIESAEIVGITDPAGMACPVAQR-----STTGLGDA 121 Query: 118 IRAALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLE 177 I+A LDLG I + +GGS+TND GAG + LG +L DA+ + +PP AL +LA I Sbjct: 122 IKALLDLGVREIFVGLGGSSTNDGGAGLLHGLGLRLLDAQGRDIPPTPAALPQLAAIDAS 181 Query: 178 NLDPRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVL 237 LDPRLA R DV NPL GP GA+A+FGPQKG V +DAAL + A L Sbjct: 182 QLDPRLASTRLVAMCDVTNPLTGPLGATAVFGPQKGVQAQDVDAIDAALAGYDRLLAPAL 241 Query: 238 PKDVRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDA 297 + D G+GAAGGLG+A LGAQ R G ++VA+ V L+ A+ GAD +ITGEGR D Sbjct: 242 GRHAVDAAGAGAAGGLGYAL-LMLGAQMRPGADIVADCVDLDGALAGADWLITGEGRSDV 300 Query: 298 QTLRGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSE 357 QTL GK P + A VP +++G + F+L GP+++EQA + Sbjct: 301 QTLSGKAPLIACQRAHACGVPASLLSGAIDPAALPALGTHFTGCFSLAPGPITVEQAMAN 360 Query: 358 APRLLRERASDIARV 372 A LL + A +AR+ Sbjct: 361 ASALLSDAAEQMARL 375 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: 448 Number of extensions: 30 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: 396 Length adjustment: 30 Effective length of query: 350 Effective length of database: 366 Effective search space: 128100 Effective search space used: 128100 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