Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate WP_011602148.1 FRAAL_RS03920 shikimate dehydrogenase
Query= curated2:Q8PFE9 (283 letters) >NCBI__GCF_000058485.1:WP_011602148.1 Length = 268 Score = 103 bits (256), Expect = 5e-27 Identities = 84/213 (39%), Positives = 108/213 (50%), Gaps = 10/213 (4%) Query: 6 YAVFGHPVAHSLSPAIHADFGKQTGIALDYTAIDASLEDFSAALQRFADEGG-KGANVTL 64 YAV G PVA +P++ + I + A F+ L+ A G G VT+ Sbjct: 8 YAVIGDPVAQVQAPSLLNPLFARLAIDAVLVPVHARPASFATVLRGLAATGNLDGVLVTI 67 Query: 65 PLKEAAYALASSLSDRARLAGAVNTL-VRNDGQWQGDNTDGAGLVRDLTERQGLDLRGRR 123 P K AA ALA+ S AR++G+ N L G W+ DN DGAG VR LT G +RGRR Sbjct: 68 PHKVAACALATEHSAAARISGSANVLRPIPGGGWRADNFDGAGFVRGLT-AAGHPVRGRR 126 Query: 124 VLLLGAGGAARGVAPALLEAGITAMVVVNRSPERADALCDALGE--PARVTSRYIEDLRE 181 V L+GAGGA +A ALL+AG + V + + AL L E P R + + + Sbjct: 127 VALMGAGGAGSAIAVALLDAGCGPLSVHDPDRAKCAALLARLDEHWPGRAAAVAVAE-PA 185 Query: 182 LGDFELIVNATAAG-RDRDAGAF---ALPLGLV 210 LGD +L VNAT G R D F ALP G V Sbjct: 186 LGDADLAVNATPLGLRPEDPLPFPPAALPAGCV 218 Lambda K H 0.319 0.135 0.391 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: 182 Number of extensions: 9 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: 283 Length of database: 268 Length adjustment: 25 Effective length of query: 258 Effective length of database: 243 Effective search space: 62694 Effective search space used: 62694 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: 47 (22.7 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