Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Echvi_2131 Echvi_2131 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9YEJ7 (270 letters) >FitnessBrowser__Cola:Echvi_2131 Length = 282 Score = 114 bits (285), Expect = 2e-30 Identities = 80/258 (31%), Positives = 123/258 (47%), Gaps = 22/258 (8%) Query: 26 VRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKP------RTSPYSFQG 79 V +G + +GPC+VES++ E VKE A FK RTS SF+G Sbjct: 14 VVLGKEKPVLFSGPCAVESFDICMEIGSTVKEQAAKNGFSYVFKASFDKANRTSSGSFRG 73 Query: 80 LGLE-GLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRS 138 +G++ L++L+R G E G+P+VT++ + V+ AD+LQI A + LL G + Sbjct: 74 IGMDKSLEVLQRVGKELGVPLVTDIHESYQAAEVAEVADVLQIPAFLCRQTDLLLAAGNT 133 Query: 139 GKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKE 198 GK + +KRG E++ A + GN V L ERG +D+ ++ +++ Sbjct: 134 GKAIKIKRGQFMAPEDMQYAVNKVRSTGNQNVCLTERGFSL--GYHNLVVDMRSLPTMRQ 191 Query: 199 ATHLPVIVDPSH-----------PAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSD 247 PV+ D +H G+R P LA+A A G DG +E HP P +ALSD Sbjct: 192 --FAPVVFDITHSVQQPGGQGGSSGGQRQFAPFLARAAAATGVDGFFIETHPEPAKALSD 249 Query: 248 AKQQLTPGEFARLMGELR 265 + A + L+ Sbjct: 250 GPNMVPLDRMAGFLEMLK 267 Lambda K H 0.318 0.136 0.392 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: 169 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 270 Length of database: 282 Length adjustment: 25 Effective length of query: 245 Effective length of database: 257 Effective search space: 62965 Effective search space used: 62965 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 09 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