Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_110805915.1 C8J30_RS10520 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_003217355.1:WP_110805915.1 Length = 291 Score = 130 bits (326), Expect = 4e-35 Identities = 88/253 (34%), Positives = 137/253 (54%), Gaps = 10/253 (3%) Query: 15 RLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIVRHG-H 73 RL RIFN ++ +TV++ DHG GP GL + + +A+ A+ ++ +G +R Sbjct: 39 RLSRIFNPKTGRTVMLAFDHGYFQGPATGLERMDLNILPLADH-ADVLMCTRGALRSTVP 97 Query: 74 RGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDWEAYRD 133 K V L SGG +I + + +E+AIR+G A++ V +GS+ + ++ + Sbjct: 98 PSNTKPVAL--RCSGGNSILTELSNETVAVEIEDAIRLGVCAMAAQVYIGSEYEHKSITN 155 Query: 134 LGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYTGDIDS 193 + + +T +G+P +A+ G RD A R+ AELGA VKT + + Sbjct: 156 VLKLIDTGTRYGIPTLAVT---GVGKDMARDARYFGLATRIAAELGAHYVKTYFVEE--G 210 Query: 194 FRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVGITRAV 253 F V GCP P+V+AGG K + E L M A++ GAAGV +GRNIFQ + V + +AV Sbjct: 211 FEKVAAGCPVPLVIAGGKKL-PELEALDMAWKAIDQGAAGVDMGRNIFQSEAPVAMIQAV 269 Query: 254 CKIVHENADVEEA 266 K+VHEN +EA Sbjct: 270 AKVVHENYTAKEA 282 Lambda K H 0.318 0.138 0.401 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: 193 Number of extensions: 11 Number of successful extensions: 5 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: 273 Length of database: 291 Length adjustment: 26 Effective length of query: 247 Effective length of database: 265 Effective search space: 65455 Effective search space used: 65455 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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