Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_028990713.1 G579_RS0114300 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::A0A482F152 (272 letters) >NCBI__GCF_000423825.1:WP_028990713.1 Length = 280 Score = 102 bits (255), Expect = 7e-27 Identities = 80/258 (31%), Positives = 126/258 (48%), Gaps = 27/258 (10%) Query: 31 MMAGPCSVESYEQTRQTA----QAIAALGGRVLRGGAFKP--RTAPDSFQGLGIE-GLRI 83 ++AGPC +ES TA + A LG + +F R++ SF+G G++ GL+I Sbjct: 16 LIAGPCVIESEALALDTAGQLKEITARLGIPFIYKSSFDKANRSSERSFRGPGLDAGLKI 75 Query: 84 LREVADEFNMLVITEALGVDNLDAVVEYADIIQIGSRNMQHFPLLWEVGGTSIPVLLKRG 143 L +V E + V+T+ +D + D++Q + + + V PV +K+G Sbjct: 76 LDKVRREIGVPVLTDVHEIDEIAPTAAVVDVLQTPAFLCRQTNFIHAVAAAGKPVNIKKG 135 Query: 144 YMSTVEEWLAAAEHIASRGNEDIILCERGIR-GFDNATRNVLDIGSIALVKAETSYPVIA 202 + E + GN+ I++CERG+ G++N V D+ S+A+++ +T PV+ Sbjct: 136 QFLAPWDMKNVVEKARTTGNQQIMVCERGVSFGYNNL---VSDMRSLAVMR-DTGCPVVF 191 Query: 203 DPSHAT-----------GRVDLVVAAARAGVAAGADGLLVEAHPTPAEALSDSTQQLPLD 251 D +H+ G+ + V ARA VAAG GL +E HP PA ALSD PL Sbjct: 192 DATHSVQLPGGQGDKSGGQREFVPVLARAAVAAGVAGLFMETHPDPACALSDGPNAWPLG 251 Query: 252 HLPDLWIQVGRTAAAIDR 269 + DL T IDR Sbjct: 252 MMADLL----ETLQVIDR 265 Lambda K H 0.318 0.134 0.387 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: 147 Number of extensions: 5 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: 272 Length of database: 280 Length adjustment: 25 Effective length of query: 247 Effective length of database: 255 Effective search space: 62985 Effective search space used: 62985 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 (21.7 bits) S2: 47 (22.7 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