Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_052667738.1 NITAL_RS19105 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000969705.1:WP_052667738.1 Length = 355 Score = 266 bits (679), Expect = 8e-76 Identities = 134/244 (54%), Positives = 167/244 (68%) Query: 95 LVSRKKKPEDTIVDIKGEKIGDGQQRFIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAF 154 LVS P + V + IG I GPCAVE+ EQ AK+ G ILRGGA+ Sbjct: 71 LVSNDAHPRPSTVWVGDVPIGRDTVTLIAGPCAVETEEQTDAACRMAKESGAAILRGGAY 130 Query: 155 KPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQN 214 KPRTSPY FQGLG GL IL V+ + DL ++E+VTPA ++ D++Q+GARNMQN Sbjct: 131 KPRTSPYAFQGLGEAGLDILHGVSRDLDLPFVTEVVTPADVDTVAAKADMLQVGARNMQN 190 Query: 215 FELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTL 274 F+LLK G KPVLLKRGL ATI E+I AAEYI GN Q++LCERGIRTYE TRNTL Sbjct: 191 FQLLKEVGMAGKPVLLKRGLTATIDEWIMAAEYIAHTGNLQVVLCERGIRTYEPMTRNTL 250 Query: 275 DISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDS 334 D+SAVP+ + THLPV +D +HS G+RDL+LP +AA+A+GADG++ +VHP P AL D Sbjct: 251 DVSAVPVAQSLTHLPVIIDPSHSGGKRDLVLPLTRAAIAVGADGIIIDVHPRPEAALCDG 310 Query: 335 AQQM 338 Q + Sbjct: 311 PQAL 314 Lambda K H 0.316 0.134 0.369 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: 325 Number of extensions: 12 Number of successful extensions: 1 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: 358 Length of database: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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: 49 (23.5 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