Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_038207982.1 Q392_RS13275 shikimate dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >NCBI__GCF_000745855.1:WP_038207982.1 Length = 278 Score = 124 bits (311), Expect = 4e-33 Identities = 103/287 (35%), Positives = 142/287 (49%), Gaps = 21/287 (7%) Query: 259 DTKVF---GIIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLV--DDVASFLQTYSSTDFA 313 DT F GI+G PV HS+SP L+ G G ++ L V + + ++ + FA Sbjct: 3 DTATFRLAGIMGWPVAHSRSPRLHGHWLAEHGLAGAYVPLPVPPERLGEAVRGLRALGFA 62 Query: 314 GFSCTIPHKEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLR 373 G + TIPHK A + DEV+P+A+ IGAVN I+ D +L G NTD G + GLR Sbjct: 63 GCNVTIPHKVAVMAHLDEVEPMARLIGAVNTIV-VLPDGRLLGRNTDGEGWL----QGLR 117 Query: 374 GSQNGNSAGASPLNGKLFVVIGAGGAGKALGYGAKEKGARVV-IANRTYDRARELAETIG 432 + G A P V++GAGGA +A+G +G + IANRT RA LA ++G Sbjct: 118 DAHPGWRADTGPA-----VMLGAGGAARAVGAALVAQGVPALRIANRTRARAEALAASLG 172 Query: 433 GDALSLADLENFHP--EDGMILANTTSIGMQPKVDETPIPKHALKHYSLVFDAVYTPKIT 490 A ++ D ED +L NTTS GMQ K + L ++V D VYTP T Sbjct: 173 PVA-TVHDWSEREALLEDAALLVNTTSQGMQGK-PSLELSLARLPRTAMVSDVVYTPLET 230 Query: 491 RLLKEAEECGATIVSGLEMFIGQAYGQYERYTGL-PAPKELFRKIMS 536 LL A G GL M + QA + + G+ P R +M+ Sbjct: 231 PLLAAARSRGNPAADGLGMLLSQARPGFAAWFGVTPEVTPALRALMA 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: 273 Number of extensions: 10 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: 538 Length of database: 278 Length adjustment: 30 Effective length of query: 508 Effective length of database: 248 Effective search space: 125984 Effective search space used: 125984 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