Align Shikimate kinase; Short=SK; EC 2.7.1.71 (characterized, see rationale)
to candidate YP_004140715.1 Mesci_1507 shikimate kinase
Query= uniprot:AROK_RHIME (192 letters) >NCBI__GCF_000185905.1:YP_004140715.1 Length = 203 Score = 197 bits (501), Expect = 1e-55 Identities = 96/170 (56%), Positives = 129/170 (75%) Query: 20 LGKRNLVFIGLMGAGKSAIGRLTAQALGVPFVDSDHEIERVSRMTVSDLFATYGEEEFRA 79 LG R++VF+GLMGAGK+AIGR A L +PF+DSD EIE VSRMTV +LF YGE EFRA Sbjct: 20 LGSRSVVFVGLMGAGKTAIGRKVATMLALPFIDSDQEIESVSRMTVPELFERYGETEFRA 79 Query: 80 LEARVLKRLLRSGPRVVSTGGGAYINERSRRHIKKGGLTIWLNAELDVLWERVNKRDTRP 139 LE RV+ R+L +GP+V+STGGGA++N ++R I G+++WL AELD+L +RV K+ RP Sbjct: 80 LEQRVILRVLENGPQVLSTGGGAFMNAQTREAIAAHGVSVWLKAELDLLMDRVAKKQNRP 139 Query: 140 LLKTENPKQTLENLMRARYPIYAEADLTVLSRDVKKEAMVEEVLAAVADH 189 LLK+ +P+ LE LM RYP+YA +D+TV +RD +KE + EV+ A+ H Sbjct: 140 LLKSADPRAVLERLMGERYPVYATSDVTVPTRDDRKEVIATEVVDALCRH 189 Lambda K H 0.317 0.133 0.370 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: 110 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: 192 Length of database: 203 Length adjustment: 20 Effective length of query: 172 Effective length of database: 183 Effective search space: 31476 Effective search space used: 31476 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: 45 (21.9 bits)
This GapMind analysis is from Apr 10 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