Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_011382582.1 AMB_RS00680 3-dehydroquinate synthase
Query= curated2:Q6MF52 (352 letters) >NCBI__GCF_000009985.1:WP_011382582.1 Length = 352 Score = 169 bits (429), Expect = 8e-47 Identities = 104/287 (36%), Positives = 159/287 (55%), Gaps = 4/287 (1%) Query: 47 EQLFKLSWNFSVLLIPEGETSKSLKQTTRCWRHFIKHQLDRYSLVVALGGGVICDLAGFV 106 E++ + + SVLLI E +KSL+ +H + L R L++A+GGG+I D+ F+ Sbjct: 44 ERMGAILAHHSVLLIEAVEPNKSLECFPAYVQHLVAKGLRRDHLLIAIGGGIIQDITCFL 103 Query: 107 ASCYMRGIDTIYLPTTLLAMVDASIGGKTGINTSKSKNIIGSFHLPKKILIDPFTLKTLS 166 A+ +RG+ + PTTLLA D+ IG K+ IN +KNI+G+F P +++I L TL Sbjct: 104 AATMLRGVKWRFYPTTLLAQCDSCIGSKSSINCGDAKNILGTFTPPNEVVIATTFLDTLD 163 Query: 167 KKHYQAGFAEIIKYGMIASPSLFEFLENSWS-LIEQRDEGLLEIIIQQSCAIKKKYVEAD 225 + ++G E++K I+ P F L + + L +RD + I++S IKK Y+E D Sbjct: 164 PREVRSGIGEMLKVHAISGPEDFTALASRYDRLFTERD--AMIATIRRSLEIKKSYIEVD 221 Query: 226 FKDLGIRAQLNYGHTFGHVIEMMSRYQYLHGEAVSIGMSCAAYLSCQMGLTTQETMQRQD 285 D G R N GH+FGH IE + + HG AVS+GM A + S +G+ T+ + Sbjct: 222 EFDQGPRLVFNLGHSFGHAIEAATDFAVPHGIAVSMGMDMANWTSWHLGIGTEAHFRTGH 281 Query: 286 ALCQQAQLPIHLPHFPLTRFTYLMAKDKKGR-NGSINLILPEKVGKV 331 + + PL RF +AKDKK +GS+ LILP+K G+V Sbjct: 282 GVLAKNYAGYQATPVPLDRFLAALAKDKKNTGSGSVTLILPDKEGRV 328 Lambda K H 0.322 0.137 0.407 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: 285 Number of extensions: 17 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: 352 Length of database: 352 Length adjustment: 29 Effective length of query: 323 Effective length of database: 323 Effective search space: 104329 Effective search space used: 104329 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 (21.9 bits) S2: 49 (23.5 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