Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_092994374.1 BLP65_RS06220 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::A0A482F152 (272 letters) >NCBI__GCF_900102855.1:WP_092994374.1 Length = 278 Score = 102 bits (253), Expect = 1e-26 Identities = 76/245 (31%), Positives = 114/245 (46%), Gaps = 23/245 (9%) Query: 31 MMAGPCSVESYEQTRQTAQAIAALGGRVLRGGAFKP------RTAPDSFQGLGIE-GLRI 83 ++AGPC +ES ++A + A+ R+ FK RT+ DS +G G+E GLRI Sbjct: 16 LIAGPCMIESEALVLESATELKAITERLGIPLIFKSSFDKANRTSADSPRGPGLEEGLRI 75 Query: 84 LREVADEFNMLVITEALGVDNLDAVVEYADIIQIGSRNMQHFPLLWEVGGTSIPVLLKRG 143 L V E + V+T+ LD V E D++Q + + + V PV +K+G Sbjct: 76 LERVQRELQLPVLTDVHEFTPLDEVAEVVDVLQTPAFLCRQTDFIQAVARQGRPVNIKKG 135 Query: 144 YMSTVEEWLAAAEHIASRGNEDIILCERGIR-GFDNATRNVLDIGSIALVKAETSYPVIA 202 + E GN+ I++CERG+ G++ ++ + S+ ET PV+ Sbjct: 136 QFLAPGDMAHVVEKARVTGNDRIMICERGVSFGYNTLISDMRGLASM----RETGAPVVF 191 Query: 203 DPSHAT-----------GRVDLVVAAARAGVAAGADGLLVEAHPTPAEALSDSTQQLPLD 251 D +H+ G+ V ARA VAAG GL +E HP P ALSD PL Sbjct: 192 DATHSVQQPGGQGGRSGGQRQFVPVLARAAVAAGVSGLFMETHPHPDSALSDGPNMWPLG 251 Query: 252 HLPDL 256 + L Sbjct: 252 EIERL 256 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: 146 Number of extensions: 8 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: 278 Length adjustment: 25 Effective length of query: 247 Effective length of database: 253 Effective search space: 62491 Effective search space used: 62491 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