Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_043745705.1 AMB_RS23010 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000009985.1:WP_043745705.1 Length = 278 Score = 119 bits (299), Expect = 1e-31 Identities = 91/264 (34%), Positives = 132/264 (50%), Gaps = 17/264 (6%) Query: 241 KVFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFV--DDLKEFFRVYSSPDFAGFSVG 298 ++ G++ PV HS+ P LH +G +G Y+P+ V + L+ R FAG +V Sbjct: 8 RLAGVLGWPVSHSRSPRLHGFWLEQMGIDGAYLPLAVAPEHLETVIRALPRMGFAGANVT 67 Query: 299 IPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNGLT 358 +P+KEAV+ D +DPLA+ IGAVNT++ R DG L G NTD + + T Sbjct: 68 VPHKEAVMRLVDHLDPLARRIGAVNTLVVRQ-DGTLEGRNTDAYGFFENLRQGCPLWEPT 126 Query: 359 NGAAFLPSPLAGKLFVLVGAGGAGRA-LAFGAKSRRAEIVIFDIDFDRAKALAAAVSGEA 417 +G A ++GAGGA RA +A A + EI + + +RA LAA + G Sbjct: 127 SGPA-----------AVIGAGGAARAVVAALADAGVPEIRLANRSRERAATLAADLGGPV 175 Query: 418 LPFENLASFQPEKG-AILANATPIGMHPNKDRIPVSEASLKDYVVVFDAVYTPRKTTLLK 476 + + +G A+L N T +GM + + + A+L VV D VY P T LL Sbjct: 176 TVVDWAERAESLEGCALLVNTTTLGM-TGQSSLDLDLAALPTTSVVNDIVYVPLVTDLLA 234 Query: 477 DAEAAGAITVSGVEMFLRQAIGQF 500 A A G V G+ M L QA+ F Sbjct: 235 RATARGNPIVDGLGMLLHQAVPGF 258 Lambda K H 0.320 0.138 0.405 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: 289 Number of extensions: 20 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: 521 Length of database: 278 Length adjustment: 30 Effective length of query: 491 Effective length of database: 248 Effective search space: 121768 Effective search space used: 121768 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: 50 (23.9 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