Align L-threonine dehydratase catabolic TdcB; L-serine dehydratase; Threonine deaminase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate RR42_RS11110 RR42_RS11110 serine dehydratase
Query= SwissProt::P11954 (329 letters) >FitnessBrowser__Cup4G11:RR42_RS11110 Length = 320 Score = 235 bits (599), Expect = 1e-66 Identities = 126/312 (40%), Positives = 189/312 (60%), Gaps = 2/312 (0%) Query: 12 EDILEAKKRLAGKIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTE 71 +D+ A R+ G ++T + RS + E+F K EN+QR G+FK RGAFN +S E Sbjct: 8 DDVSAAAARIEGYAHRTPVMRSRTADKDVGAELFFKCENLQRMGAFKFRGAFNAVSKFDE 67 Query: 72 AEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNF 131 ++R GVVA S+GNHAQG++L+ ++LGI +VMP AP +KVAAT Y A+VV++ Sbjct: 68 RQRRAGVVAYSSGNHAQGIALAASILGIPATIVMPHDAPAAKVAATRGYGAKVVIYDRYT 127 Query: 132 NDTIAKVSEIVETEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAG 191 D A ++ E G IPPYD P VIAGQGT E+ E+ ++D + V +GGGGL++G Sbjct: 128 EDREAIGRKLAEEHGLTLIPPYDHPDVIAGQGTAAKELFEETGELDALFVCLGGGGLLSG 187 Query: 192 IAIAIKSINPTIKVIGVQAENVHGMAASYYTGEITTHRTTGTLADGCDVSRPGNLTYEIV 251 A++ ++++P K+ GV+ + S+ TG I T T+ADG GN T+EI+ Sbjct: 188 SALSARALSPQCKIYGVEPAAGNDGQQSFRTGSIVHIETPKTIADGAQTQHLGNYTFEII 247 Query: 252 RELVDDIVLVSEDEIRNSMIALIQRNKVITEGAGALACAALLSGKLDSHIQNRKTVSIIS 311 R VDDIV ++DE+ + M R K++ E G L AA+ + K + +Q ++ +IS Sbjct: 248 RRDVDDIVTATDDELVDCMRFFASRMKLVVEPTGCLGFAAVRAMK--AELQGKRVGVLIS 305 Query: 312 GGNIDLSRVSQI 323 GGNID+ R + + Sbjct: 306 GGNIDIDRFAAL 317 Lambda K H 0.317 0.136 0.382 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: 245 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: 329 Length of database: 320 Length adjustment: 28 Effective length of query: 301 Effective length of database: 292 Effective search space: 87892 Effective search space used: 87892 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: 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