Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_004512090.1 GMET_RS06430 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::A0A482F152 (272 letters) >NCBI__GCF_000012925.1:WP_004512090.1 Length = 272 Score = 108 bits (269), Expect = 2e-28 Identities = 82/263 (31%), Positives = 130/263 (49%), Gaps = 23/263 (8%) Query: 13 TRPIDIGSGLTVGGSSVVMMAGPCSVESYEQTRQTAQAIAALGGRVLRGGAFKP------ 66 TR I IG+ G +V++AGPC +E+ T + A+ + + + FK Sbjct: 2 TREIAIGNVKMGGSRPLVLIAGPCVIENETATLRCAERLMTIVNGLSIPLIFKASYDKAN 61 Query: 67 RTAPDSFQGLGI-EGLRILREVADEFNMLVITEALGVDNLDAVVEYADIIQIGSRNMQHF 125 RT+ +F+G G+ EGLRIL +V + + VI++ ++ + E DI+QI + + Sbjct: 62 RTSVTAFRGPGLKEGLRILAKVKESLGLPVISDIHSIEQVQPAAEVLDILQIPAFLCRQT 121 Query: 126 PLLWEVGGTSIPVLLKRGYMSTVEEWLAAAEHIASRGNEDIILCERGIR-GFDNATRNVL 184 LL E T V +K+G + I + GNE IIL ERG G++N V Sbjct: 122 DLLVEAARTGCVVNVKKGQFLAPWDMENVVGKIVASGNERIILTERGASFGYNNL---VS 178 Query: 185 DIGSIALVKAETSYPVIADPSHAT-----------GRVDLVVAAARAGVAAGADGLLVEA 233 D+ S+ +++ +PV+ D +H+ G+ + V +RA VA G DG+ +E Sbjct: 179 DMRSLPIMR-RFGFPVVFDATHSVQLPGGQGGSSGGQREFVEYLSRAAVATGIDGVFLEV 237 Query: 234 HPTPAEALSDSTQQLPLDHLPDL 256 H P +AL D +PLD LP L Sbjct: 238 HEEPDKALCDGPNSVPLDDLPVL 260 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: 158 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: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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