Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_011320553.1 AVA_RS19555 sedoheptulose 7-phosphate cyclase
Query= curated2:A1AQL5 (359 letters) >NCBI__GCF_000204075.1:WP_011320553.1 Length = 410 Score = 154 bits (389), Expect = 4e-42 Identities = 103/327 (31%), Positives = 162/327 (49%), Gaps = 12/327 (3%) Query: 36 GRVAVISNPAVAELYAEQVRASLVESGNQVTLILIPEGEEHKNAATLNLVYDQLIQAGLD 95 GR I + V+ LY Q++A G ++ L I E K T V D L Sbjct: 49 GRCLAIVDANVSRLYGNQIQAYFQYYGIELRLFPITITEPDKTIQTFERVIDVFADFKLV 108 Query: 96 RNSYIVALGGGVVGDLAGFAAATFLRGIPFVQVPTTLLAQVDSSVGGKTAIDHPRGKNLI 155 R ++ +GGG++ D+ GFA +T+ R ++++PTTL+ +D+SV K A++H + KN + Sbjct: 109 RKEPVLVVGGGLITDVVGFACSTYRRSSNYIRIPTTLIGLIDASVAIKVAVNHRKLKNRL 168 Query: 156 GAFYQPRLVLIDVETLTTLPQREFRAGLAEVIKYGVAMDLAFYELLERDSGRIL-----E 210 GA++ R V +D L TLP + R G+AE++K V +ELLE+ +L Sbjct: 169 GAYHASRKVFLDFSLLRTLPTDQVRNGMAELVKIAVVAHQEVFELLEKYGEELLRTHFGN 228 Query: 211 MDA-----DCLERIVLRCCELKARVVEQDEKESGLRAILNYGHTLGHAIETLAGYGTLVH 265 +DA + R+ + + + E L ++ YGHT +E LA + H Sbjct: 229 IDATPEIKEIAHRLTYKAIHKMLELEVPNLHELDLDRVIAYGHTWSPTLE-LAPRLPMFH 287 Query: 266 GEAVAIGMVLAARISLAGGYCSEGDVSRIVALLGRFGLPCIPPRIDQGRLAETLLTDKKS 325 G AV + M +A I+ GY + + RI+ L+ R GL P +D L + + Sbjct: 288 GHAVNVDMAFSATIAARRGYITIAERDRILGLMSRVGLSLDHPMLDIDILWRGTESITLT 347 Query: 326 RSGIIRFICNRGIGDCVVVN-LTAEQL 351 R G++R + IGDCV VN LT E+L Sbjct: 348 RDGLLRAAMPKPIGDCVFVNDLTREEL 374 Lambda K H 0.321 0.140 0.401 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: 291 Number of extensions: 18 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: 359 Length of database: 410 Length adjustment: 30 Effective length of query: 329 Effective length of database: 380 Effective search space: 125020 Effective search space used: 125020 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 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