Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_011305942.1 MBAR_RS04965 fructose-bisphosphate aldolase
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_000195895.1:WP_011305942.1 Length = 265 Score = 360 bits (923), Expect = e-104 Identities = 168/262 (64%), Positives = 211/262 (80%) Query: 10 LGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIV 69 +GK +R+ER+ NRES VI+PMDHG+S+GPI GLI+I TVN VAEGGANAVL+ KG+V Sbjct: 4 IGKKIRIERLMNRESRNMVIIPMDHGISDGPIDGLINITDTVNKVAEGGANAVLMQKGMV 63 Query: 70 RHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDWE 129 ++GHRGYG D+GLI+H+SG +++SP+P KV V TVEE I+MGADAVS+H+N+GS+ + + Sbjct: 64 KYGHRGYGHDIGLIVHISGSSSLSPDPNAKVQVCTVEEVIKMGADAVSMHINIGSETEAD 123 Query: 130 AYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYTG 189 LG I+ C WGMPL+ MMYPRGK I N DP VAHAAR+GAELGAD+VKT YTG Sbjct: 124 QLEQLGKISRDCTEWGMPLLTMMYPRGKKITNPHDPVNVAHAARIGAELGADVVKTVYTG 183 Query: 190 DIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVGI 249 D DSFRDVV+GCP PVV+AGGPKT+TD E L+MI AMEAGA G A+GRN+FQH D V + Sbjct: 184 DPDSFRDVVRGCPVPVVIAGGPKTSTDLELLEMIDGAMEAGARGAAIGRNVFQHKDPVRL 243 Query: 250 TRAVCKIVHENADVEEALKEIR 271 TRA+C+IVH VEEAL++++ Sbjct: 244 TRAICEIVHHRRPVEEALEQLK 265 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: 300 Number of extensions: 8 Number of successful extensions: 1 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: 265 Length adjustment: 25 Effective length of query: 248 Effective length of database: 240 Effective search space: 59520 Effective search space used: 59520 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