Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_013644226.1 METBO_RS03180 shikimate dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >NCBI__GCF_000191585.1:WP_013644226.1 Length = 286 Score = 157 bits (398), Expect = 4e-43 Identities = 105/286 (36%), Positives = 152/286 (53%), Gaps = 24/286 (8%) Query: 260 TKVFGIIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLV--DDVASFLQTYSSTDFAGFSC 317 T VFGIIG PV HS SP ++N AFK G D +++ V + + + S GF+ Sbjct: 6 TNVFGIIGDPVEHSLSPGMHNAAFKELGMDNIYVPFQVKAEHLEDAILGAQSLGVKGFNV 65 Query: 318 TIPHKEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQN 377 TIPHK + D +D A IGAVN I ++ A G+NTD +GA+ AIE+ Sbjct: 66 TIPHKTEVINYLDYLDIAAGLIGAVNTIEFGKNGA--VGHNTDGIGAVMAIEE------- 116 Query: 378 GNSAGASPLNGKLFVVIGAGGAGKALGYGAKEKGA-RVVIANRTYDRAREL----AETIG 432 +P+ K V++GAGGA +A+ + G +VIANRT ++A EL E + Sbjct: 117 -----VTPVKNKKVVILGAGGASRAIAFQLLLSGVDNLVIANRTVEKAGELKTDLVEKLD 171 Query: 433 GDALSLADLENFHPE--DGMILANTTSIGMQPKVDETPIPKHALKHYSLVF-DAVYTPKI 489 + EN E D IL NTT +GM P VDE P+ + H +V D VY P Sbjct: 172 HEVRVSGLDENLTQELSDTAILINTTPVGMYPNVDEKPVVTAEMMHPDMVVNDIVYNPLK 231 Query: 490 TRLLKEAEECGATIVSGLEMFIGQAYGQYERYTGLPAPKELFRKIM 535 T LL EA++ GA +SG++M + Q ++ +TG+ P E+F++ + Sbjct: 232 TGLLNEADKAGAKSISGIKMLMYQGVEAFKIWTGIEPPVEIFQRAL 277 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: 333 Number of extensions: 19 Number of successful extensions: 6 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