Align L-threonine dehydratase catabolic TdcB; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate WP_011802704.1 PNAP_RS16665 threonine/serine dehydratase
Query= curated2:Q99U50 (346 letters) >NCBI__GCF_000015505.1:WP_011802704.1 Length = 314 Score = 129 bits (324), Expect = 1e-34 Identities = 96/299 (32%), Positives = 146/299 (48%), Gaps = 15/299 (5%) Query: 29 FIRRTPLIKSMYLSQNITKGNVYLKLENMQFTGSFKFRGASNKINHLSDEQKAKGIIGAS 88 FIRRTPL K + + V+LKLE++Q GSFK RG N++ LS+ G+I AS Sbjct: 22 FIRRTPLWKLPGGALGVDCAEVWLKLEHLQTGGSFKARGMLNRL--LSNPIPPSGVIVAS 79 Query: 89 AGNHAQGVALTAKLLGIDATIVMPETAPIAKQNATKGYGAKVILKGKNFNETRLYMEELA 148 GN A AK LG+ + +PE + AK+ GA+V++ G + + Sbjct: 80 GGNAGIATAAAAKELGVPCEVFVPEISSPAKRARLAALGARVMVGGAAYADALRACLARQ 139 Query: 149 KENGMTIVHPYDDKFVMAGQGTIGLEILDDIWNVNTVIVPVGGGGLIAGIATALKSFNPS 208 +E G + H YD V+ G GT+ LEI ++V+V VGGGGLI G+A F Sbjct: 140 QETGALLTHAYDQPEVLVGAGTMALEIEQQGGLPDSVLVSVGGGGLIGGVA---NWFGHR 196 Query: 209 IHIIGVQAENVHGMAESFYKRALTEHREDSTI----ADGCDVKVPGEKTYEVVKHLVDEF 264 ++ ++ E +A S ++ D + AD + G ++V + V + Sbjct: 197 SRVVALEPE----LAPSLFRARQAGRPVDVEVGGIAADSLGARRIGSLAWDVTQAQVRDA 252 Query: 265 ILVSEEEIEHAMQDLMQRAKIITEGAGALPTAAILSGKIDKKWLEGKNVVALVSGGNVD 323 +L+S+E I A L Q K+ E A ALP AA+ S + + + V ++ G NVD Sbjct: 253 LLLSDESIRTAQLWLWQELKLAVEPAAALPLAALHSRRYVPR--ADETVCLIICGANVD 309 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: 196 Number of extensions: 6 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: 346 Length of database: 314 Length adjustment: 28 Effective length of query: 318 Effective length of database: 286 Effective search space: 90948 Effective search space used: 90948 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 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