Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate YP_001328870.1 Smed_3211 shikimate 5-dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >NCBI__GCF_000017145.1:YP_001328870.1 Length = 286 Score = 121 bits (303), Expect = 4e-32 Identities = 92/283 (32%), Positives = 146/283 (51%), Gaps = 30/283 (10%) Query: 265 IIGKPVGHSKSPLLYNQAFKSAGFDGVF-LHLLVDDV-ASFLQTYS--STDFAGFSCTIP 320 + G PV HS+SPL++ K G G + H + D F++ + F G + TIP Sbjct: 14 VAGYPVKHSRSPLIHGYWLKRFGIQGSYRAHEVTSDAFPDFMRQIKEGTAGFCGGNVTIP 73 Query: 321 HKEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQNGNS 380 HKEAA + D D ++ +GA N + + NTD G ++ +++ +G ++ Sbjct: 74 HKEAAFRLSDRPDELSAELGAANTLWLENGTIR--ATNTDGRGFVANLDERAKGWDRISA 131 Query: 381 AGASPLNGKLFVVIGAGGAGKALGYGAKEKGARVV-IANRTYDRARELAETIGG--DALS 437 A V++GAGGA +A+ +++G + + + NRT +RARELA+ G A S Sbjct: 132 A----------VILGAGGASRAVIQAIRDRGVKAIHVVNRTPERARELADRFGSAVHAHS 181 Query: 438 LADLENFHPEDGMILANTTSIGMQ----PKVDETPIPKHALKHYSLVFDAVYTPKITRLL 493 +A L G+ + NTTS+GM P +D + + + A+ V D VY P T LL Sbjct: 182 MAALPEVLSGAGLFV-NTTSLGMDGEPAPAIDFSKLARDAV-----VTDIVYVPLKTPLL 235 Query: 494 KEAEECGATIVSGLEMFIGQAYGQYERYTGL-PAPKELFRKIM 535 ++AEE G +V GL M + QA +E++ GL P E R+I+ Sbjct: 236 RQAEEQGFRVVDGLGMLLHQAAPGFEKWFGLRPVVDEALREII 278 Lambda K H 0.317 0.135 0.385 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: 332 Number of extensions: 16 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: 538 Length of database: 286 Length adjustment: 31 Effective length of query: 507 Effective length of database: 255 Effective search space: 129285 Effective search space used: 129285 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 (21.6 bits) S2: 50 (23.9 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