Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_035217304.1 G491_RS29065 hypothetical protein
Query= BRENDA::A0A482F152 (272 letters) >NCBI__GCF_000429905.1:WP_035217304.1 Length = 305 Score = 159 bits (401), Expect = 9e-44 Identities = 103/293 (35%), Positives = 155/293 (52%), Gaps = 31/293 (10%) Query: 4 PLVTQTNSQTRPIDIGSGLTVGGSSVVMMAGPCSVESYEQTRQTAQAIAALGGRVLRGGA 63 PL T N Q R I G+ + VGG + +MAGPC+VES Q + A+A++ G +++RGG Sbjct: 14 PLSTAKNYQ-RKIMAGN-VPVGGKDLTIMAGPCTVESKTQIFEAAKAVSEAGAKMIRGGV 71 Query: 64 FKPRT--------APDSFQGLGI-EGLRI----------------LREVADEFNMLVITE 98 +KP T PD+ GL E +R+ ++E A+++ + VI+E Sbjct: 72 YKPLTFPYGDPLGQPDADSGLPANERMRVVPRSEQDQAAEKRLGYMKEAAEKYGLAVISE 131 Query: 99 ALGVDNLDAVVEYADIIQIGSRNMQHFPLLWEVGGTSIPVLLKRGYMSTVEEWLAAAEHI 158 + D +D + +Y D+ Q+G R+M + L+ + + P+LLKR Y ++ L EH Sbjct: 132 IMYADTMDMMSKYVDMFQVGYRHMFNMDLVEALATSDKPILLKRHYGESLRSLLGVCEHF 191 Query: 159 ASRGNEDIILCERGI---RGFDNATRNVLDIGSI-ALVKAETSYPVIADPSHATGRVDLV 214 +RG D +CERG+ + +R +LDI +I A+ + S PVI DPSHAT + V Sbjct: 192 DARGKHDYAICERGVTVPHTHNVNSRAILDIQAIPAMAEYAPSVPVIIDPSHATFKRSYV 251 Query: 215 VAAARAGVAAGADGLLVEAHPTPAEALSDSTQQLPLDHLPDLWIQVGRTAAAI 267 A +RA +AAGA GLL+E HP P A D Q L L ++ A I Sbjct: 252 AAMSRAAIAAGAHGLLIEVHPDPENAWIDPLQALGFSDFEKLMREIEAIAKII 304 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: 151 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: 305 Length adjustment: 26 Effective length of query: 246 Effective length of database: 279 Effective search space: 68634 Effective search space used: 68634 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