Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_012673927.1 SULAZ_RS01815 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000021545.1:WP_012673927.1 Length = 262 Score = 110 bits (274), Expect = 5e-29 Identities = 84/258 (32%), Positives = 127/258 (49%), Gaps = 26/258 (10%) Query: 122 IVGPCAVESYEQVAEVAAAAKK-----QGIKILRGGAFKP--RTSPYDFQGLGVE-GLQI 173 I GPC +ES E EVA ++ I+ + +F R+S F+G G+E GL + Sbjct: 7 IAGPCVIESREICFEVAEVLRQLQEKYSDIRFVFKSSFDKANRSSLESFRGRGLEWGLSV 66 Query: 174 LKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRG 233 LK V D+F L V+++I + + +D+IQI A + +LL AA K V +K+G Sbjct: 67 LKDVKDKFGLEVLTDIHESYQAKPVSEVVDIIQIPAFLCRQTDLLLAAAETGKEVNVKKG 126 Query: 234 LAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVD 293 + N + + G D+I L ERG T +D + I++Q + PV D Sbjct: 127 QFLAPWDTKNIVDKLKFGGADKIYLTERG--TTFGYNNLVVDFRGLKIMRQ--YAPVIFD 182 Query: 294 VTHST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPE 342 THS G+R+ P AKAA+ +G DG+ E HPDP ALSD Q+ + + Sbjct: 183 ATHSVQIPGGLGKASGGQREFAYPLAKAAVVVGVDGLFFETHPDPDKALSDGPNQIPLKD 242 Query: 343 FE---KWLNELKPMVKVN 357 F + L L+ V++N Sbjct: 243 FPTIVENLLRLREFVEIN 260 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: 215 Number of extensions: 14 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: 358 Length of database: 262 Length adjustment: 27 Effective length of query: 331 Effective length of database: 235 Effective search space: 77785 Effective search space used: 77785 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: 48 (23.1 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