Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate RR42_RS21755 RR42_RS21755 shikimate dehydrogenase
Query= curated2:Q1AWA3 (284 letters) >FitnessBrowser__Cup4G11:RR42_RS21755 Length = 278 Score = 165 bits (418), Expect = 9e-46 Identities = 108/262 (41%), Positives = 143/262 (54%), Gaps = 6/262 (2%) Query: 5 RIDGETSLVGLIGHPVSHSLSPQMHNASFAALGLNYVYVPLDVPPEELEAGVRGL-RALG 63 +IDG T LVG+I P++H +PQ+ NAS A GLN V VP V +L+ + G A Sbjct: 2 QIDGNTQLVGIIAAPIAHVRTPQLFNASVARQGLNAVCVPFHVDAAQLQTFLAGAPAAQN 61 Query: 64 FRGFNVTMPHKERVCALVDRLDEAARISGAVNTVAVE-EDGSLLGMNTDGSGFLLACREA 122 +G VTMPHKE V A+ L +AAR+ G+VN + + + G +G N DG GF+ RE Sbjct: 62 LQGLVVTMPHKEAVVAICGELTDAARLLGSVNAMRFDRQKGFWVGGNFDGDGFVAGLRER 121 Query: 123 GVEPSGRVALVAGAGGAAAAVAVALLRAGLSELRIANRTPGRALGLRERLGGLGGRVEVF 182 G SG+ L GAGGA ++A A+ R +EL I NR+ +A E L + Sbjct: 122 GHSLSGKRVLQLGAGGAGKSMAYAMAREQPAELVIYNRSADKA---EELAASLKAVLPTV 178 Query: 183 PLSGLAEAAGGADILVNATYLGMRAGDPLPFPEELLRPGVAVCDAVYRPGKSTALVRAAR 242 + G D++VNAT LG+R D P P E L G VC+AV R G T L++AAR Sbjct: 179 SIRAGDNNPAGFDVVVNATALGLRDTDATPLPAEQLGAGTLVCEAVIRDG-DTPLLKAAR 237 Query: 243 RRGLAAVPGELMLLYQGVEAQR 264 RG A G+ ML Q VE R Sbjct: 238 ERGCAVHHGQWMLYGQIVEIAR 259 Lambda K H 0.319 0.138 0.402 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: 193 Number of extensions: 9 Number of successful extensions: 4 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: 284 Length of database: 278 Length adjustment: 26 Effective length of query: 258 Effective length of database: 252 Effective search space: 65016 Effective search space used: 65016 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 (21.7 bits) S2: 47 (22.7 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