Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate 208018 DVU2521 shikimate kinase
Query= metacyc::MONOMER-21144 (185 letters) >MicrobesOnline__882:208018 Length = 180 Score = 252 bits (644), Expect = 2e-72 Identities = 129/173 (74%), Positives = 144/173 (83%) Query: 13 ARIAPDGCVSIIGMAGAGKTTVGRELALQLGWAHVDTDNLIEATYGTRLQAVADSMDKES 72 AR+ CV+IIGMAGAGKTTVGRELA Q+ WAHVDTD+LIEATYGT LQ VADSM KE+ Sbjct: 8 ARLFEGCCVTIIGMAGAGKTTVGRELARQMDWAHVDTDSLIEATYGTVLQNVADSMSKEA 67 Query: 73 FLDVEAGVIRRIGARRTVLSTGGSVVYRHEAMAHLAALGPLVYLDVSLPLILKRIAMNPD 132 FLDVEAG+I RIGA+R VLSTGGSVVYR EAM HLA+LGP+VYLDVSLPLIL+RIA NPD Sbjct: 68 FLDVEAGIICRIGAKRAVLSTGGSVVYRAEAMRHLASLGPVVYLDVSLPLILERIARNPD 127 Query: 133 RGLAIAPGQTIEDLYNERIALYRRYATFTVAADALSPGGCATRIVAWLTGGEA 185 RGLAIAPGQTIEDLYNER ALY Y FT+ AD L+P C I++WL +A Sbjct: 128 RGLAIAPGQTIEDLYNERKALYETYQDFTLTADTLTPEECGRAILSWLETADA 180 Lambda K H 0.321 0.137 0.403 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: 170 Number of extensions: 1 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: 185 Length of database: 180 Length adjustment: 19 Effective length of query: 166 Effective length of database: 161 Effective search space: 26726 Effective search space used: 26726 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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