Align L-threonine dehydratase catabolic TdcB; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate WP_011513321.1 PCRYO_RS05055 pyridoxal-phosphate dependent enzyme
Query= curated2:Q99U50 (346 letters) >NCBI__GCF_000013905.1:WP_011513321.1 Length = 326 Score = 184 bits (467), Expect = 3e-51 Identities = 114/320 (35%), Positives = 171/320 (53%), Gaps = 11/320 (3%) Query: 13 IVSLGDIEEAKASIKPFIRRTPLIKSMYLSQNITKGNVYLKLENMQFTGSFKFRGASNKI 72 I +L D+ EA IKP+I RTP++ S +L++ + ++ K EN Q G+FK RGASN + Sbjct: 10 IPTLDDMLEAHERIKPYIHRTPVLTSRFLNE-LAGCEMFFKCENFQKAGAFKVRGASNAV 68 Query: 73 NHLSDEQKAKGIIGASAGNHAQGVALTAKLLGIDATIVMPETAPIAKQNATKGYGAKVIL 132 LSDE G+ S+GNHA ++ A GI +VMP +AP AK+ A +GYG + Sbjct: 69 FGLSDEDAKNGVCTHSSGNHALSLSYAAGQRGIPCNVVMPHSAPEAKKAAVRGYGGIITE 128 Query: 133 KGKNFNETRLYMEELAKENGMTIVHPYDDKFVMAGQGTIGLEILDDIWNV----NTVIVP 188 + ++ E G VHPY+D V+AGQ T E L+ + + + V+ P Sbjct: 129 CEPSTTSREEVFAKVQAETGGDFVHPYNDPRVIAGQATCSREFLEQMEEIGEKPDMVVAP 188 Query: 189 VGGGGLIAGIATALKSFNPSIHIIGVQAENVHGMAESFYKRALTEHREDSTIADGCDVKV 248 +GGGG+I+G L + P + I + N A SF + +T+ADG +KV Sbjct: 189 IGGGGMISGTCLTLSNLAPDVKIYAAEPLNADDAARSFKAGHIIADDAPNTVADG--LKV 246 Query: 249 P-GEKTYEVVKHLVDEFILVSEEEIEHAMQDLMQRAKIITEGAGALPTAAILSGKIDKKW 307 P + T+ V + V + + +EEEI AM+ KII E + A+P A IL +K Sbjct: 247 PLKDLTWHFVSNYVTDILTATEEEIVEAMKLTWTHMKIIIEPSCAVPLAVILK---NKDV 303 Query: 308 LEGKNVVALVSGGNVDLTRV 327 GK V +++GGNVDL ++ Sbjct: 304 FAGKKVGVIITGGNVDLDKL 323 Lambda K H 0.315 0.133 0.373 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: 236 Number of extensions: 13 Number of successful extensions: 6 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: 346 Length of database: 326 Length adjustment: 28 Effective length of query: 318 Effective length of database: 298 Effective search space: 94764 Effective search space used: 94764 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 (21.6 bits) S2: 49 (23.5 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