Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate RR42_RS05695 RR42_RS05695 pyridoxal-5'-phosphate-dependent protein subunit beta
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__Cup4G11:RR42_RS05695 Length = 339 Score = 200 bits (508), Expect = 5e-56 Identities = 116/317 (36%), Positives = 178/317 (56%), Gaps = 5/317 (1%) Query: 10 AIDDIIEAKQRLAGRIYKTGMPR---SNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKL 66 ++ +I +RL G++ +T + R +++LK E Q TG+FK+RGA N + Sbjct: 15 SLPEIQSTARRLQGKVLETPVWRWQTGAALQLDAGTQVWLKLELFQITGTFKVRGALNSI 74 Query: 67 SSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVL 126 + + + +GVVA SAGNHA V+ + + G+ K+ MP A ++VAA + AEV+L Sbjct: 75 EHMDASARARGVVAASAGNHAMAVAYAAKVAGVGAKLAMPATASPARVAACREAGAEVLL 134 Query: 127 HGDNFNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGG 186 D + A ++V EGR + PYD P + G T+GLE+M + +D V+VP+GGG Sbjct: 135 LPD-VHAAFAHALQLVADEGRTMVHPYDGPLIAQGTATVGLELMRQVAGLDAVVVPVGGG 193 Query: 187 GLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNL 246 GL GIA A+K INP RV GV+ E M SF +G T T+AD + Sbjct: 194 GLCGGIAAAVKQINPACRVYGVEPEGADAMNRSFEAGRPQTLERVATVADSLGAPYALDY 253 Query: 247 TYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQYIQNRKT 306 +Y + R+ VD +V VS++ IR +M L + K+ TE A A++ AALL G L Q + +K Sbjct: 254 SYGVCRQFVDGMVRVSDEAIRAAMRILYRDMKLATEPATAVSTAALL-GPLRQTLAGKKV 312 Query: 307 VSIISGGNIDLSRVSQI 323 I+ G N+D +R +++ Sbjct: 313 ALIVCGSNLDAARFAEL 329 Lambda K H 0.318 0.136 0.386 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: 187 Number of extensions: 4 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: 339 Length adjustment: 28 Effective length of query: 301 Effective length of database: 311 Effective search space: 93611 Effective search space used: 93611 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: 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