Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_067074469.1 MCUHO_RS03740 class I fructose-bisphosphate aldolase family protein
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_001602375.1:WP_067074469.1 Length = 261 Score = 273 bits (699), Expect = 2e-78 Identities = 129/258 (50%), Positives = 183/258 (70%), Gaps = 2/258 (0%) Query: 10 LGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIV 69 +GK +RLERI +R + + V++PMDHG + G I+GL ++ +TVN V+EGGANA++LHKG+V Sbjct: 2 IGKEIRLERIMDRNTGRAVVIPMDHGFTMGQIEGLCNMTETVNAVSEGGANAIVLHKGMV 61 Query: 70 RHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDWE 129 + GHR +GKD+GLI+HLS T+++P+P KVIV TVEEA+ +GADAVSIH+N+G+ + Sbjct: 62 KGGHRKHGKDIGLIVHLSASTSMNPDPNDKVIVCTVEEAVALGADAVSIHINLGAPNESR 121 Query: 130 AYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYTG 189 G + C WG+PL+ M+YPRGK I + P+ + H R+ ELGAD++KT+YTG Sbjct: 122 MLESAGEVVRDCNRWGIPLLIMIYPRGKGI-DPTSPQSIGHCVRVAEELGADLIKTNYTG 180 Query: 190 DIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVGI 249 D ++FR + C PV++AGG K+ D E L I+DA++AGAAGV +GRN FQ DD Sbjct: 181 DPETFRRITAACSVPVMIAGGEKSG-DVETLTTIRDAIDAGAAGVCMGRNAFQRDDPARF 239 Query: 250 TRAVCKIVHENADVEEAL 267 A+ ++VHE EAL Sbjct: 240 IAAISRVVHEGKSAAEAL 257 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: 273 Number of extensions: 13 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: 273 Length of database: 261 Length adjustment: 25 Effective length of query: 248 Effective length of database: 236 Effective search space: 58528 Effective search space used: 58528 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