Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012475790.1 CPHAMN1_RS12050 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000020545.1:WP_012475790.1 Length = 294 Score = 140 bits (354), Expect = 3e-38 Identities = 91/265 (34%), Positives = 149/265 (56%), Gaps = 24/265 (9%) Query: 85 LGDVKI--GNGYFTIIAGPCSVEGREMLMETAHFLSEL----GVKVLRGGAYKP--RTSP 136 +G+VK+ G F IAGPC +EGREM ++ A L + G+ + G+++ R+S Sbjct: 19 VGNVKVPLDRGLF-FIAGPCVIEGREMALDVASVLHAIRESEGIACIFKGSFRKANRSSA 77 Query: 137 YSFQGLGEKG-LEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLS 195 SF G+G+ LE L E ++ M V+T+ ++ +V+ Y D++QI A ++ LL+ Sbjct: 78 ASFTGIGDSAALEILGEIRGRFDMPVLTDVHETQEVERVSPYVDVLQIPAFLSRQTDLLT 137 Query: 196 KAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAV 255 AG V +K+G E+ +A+ +A +GNT+I+L ERG TF +D + Sbjct: 138 AAGRSGLCVNIKKGQFMAPEDMAFAAQKVAETGNTRIMLTERGT-TFGYHNL-VVDFRGI 195 Query: 256 PIIRKESHLPILVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHPEPE 304 P + K + P++ D +HS GG R+ ++P++RAA+A G HG+ EVHPEP+ Sbjct: 196 PEMSKTGY-PVVYDATHSLQLPSSAQGTSGGVREYLLPMARAAVAAGVHGLFFEVHPEPQ 254 Query: 305 KALSDGKQSLDFELFKELVQEMKKL 329 A+SD + + F E+V +M+KL Sbjct: 255 HAMSDAATQVSLKEFPEIVHQMQKL 279 Lambda K H 0.318 0.138 0.388 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: 201 Number of extensions: 15 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: 338 Length of database: 294 Length adjustment: 27 Effective length of query: 311 Effective length of database: 267 Effective search space: 83037 Effective search space used: 83037 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: 48 (23.1 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