Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_017895597.1 PN53_RS02430 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000816635.1:WP_017895597.1 Length = 343 Score = 284 bits (727), Expect = 2e-81 Identities = 138/261 (52%), Positives = 189/261 (72%) Query: 95 LVSRKKKPEDTIVDIKGEKIGDGQQRFIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAF 154 L +R P++++V+I G K+G + I GPC+VES EQ+ E+A KK G K LRGGAF Sbjct: 71 LANRLFHPDNSVVNIDGRKVGGNELAIIAGPCSVESEEQIVEIAKDVKKSGAKFLRGGAF 130 Query: 155 KPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQN 214 KPRTSPY FQGL EGL++LK E L +++EI++ IE+ ++ +DVIQ+GARNMQN Sbjct: 131 KPRTSPYSFQGLRTEGLELLKIARQETGLPIVTEIMSANMIEKFVEDVDVIQVGARNMQN 190 Query: 215 FELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTL 274 FELLK G KKP+LLKRGL+ATI E + +AEYIMS+GN+ +ILCERGIRT+E TRNTL Sbjct: 191 FELLKELGKTKKPILLKRGLSATIEELLMSAEYIMSEGNENVILCERGIRTFENYTRNTL 250 Query: 275 DISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDS 334 D+SA+P +K+ +HLP+ VD +H+ G ++ P AKAA+A+GADG++ EVH DP AL D Sbjct: 251 DLSAIPAIKKLSHLPIIVDPSHAAGLWWMVEPLAKAAVAVGADGLIIEVHNDPQNALCDG 310 Query: 335 AQQMAIPEFEKWLNELKPMVK 355 Q + F+ + +L +V+ Sbjct: 311 QQSITPNRFDNLMGDLNKLVE 331 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: 318 Number of extensions: 9 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: 343 Length adjustment: 29 Effective length of query: 329 Effective length of database: 314 Effective search space: 103306 Effective search space used: 103306 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 Jul 25 2024. The underlying query database was built on Jul 25 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