Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SM_b20299 SM_b20299 N-acetylneuraminate lyase
Query= BRENDA::Q9I4W3 (292 letters) >FitnessBrowser__Smeli:SM_b20299 Length = 299 Score = 123 bits (308), Expect = 6e-33 Identities = 78/229 (34%), Positives = 121/229 (52%), Gaps = 7/229 (3%) Query: 2 IAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIR 61 + G AL+TPF +D ++ LVDF ++ G + + G++GE+ ++E + Sbjct: 3 LEGIYSALLTPFSEDESIDRQAIGALVDFQVRLGIDGVYVGGSSGEAMLQSLDERADYLS 62 Query: 62 RVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRH 121 V GR+ +IA G +TR+A+ L++ A G A + P+Y ++ + H+R Sbjct: 63 DVAAAASGRLTLIAHVGTIATRDALRLSQHAAKSGYQAISAIPPFYYDFSRPEVMAHYRE 122 Query: 122 IAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDF 181 +A+ A+P I+YN P RTS LPE VE LS PNIIGIK + D+ + + + V D Sbjct: 123 LADVSALPLIVYNFPARTSGFTLPELVELLSH-PNIIGIKHTSSDMFQLERIRHAV-PDA 180 Query: 182 LVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAAR 230 +VY+G D + +G +G I T N M DL A+R AAA R Sbjct: 181 IVYNGYDEMCLAGFAMGAQGAIGTTYNF----MGDL-FVALRDCAAAGR 224 Lambda K H 0.319 0.134 0.393 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: 202 Number of extensions: 10 Number of successful extensions: 2 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: 292 Length of database: 299 Length adjustment: 26 Effective length of query: 266 Effective length of database: 273 Effective search space: 72618 Effective search space used: 72618 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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