Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate AZOBR_RS06795 AZOBR_RS06795 serine/threonine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__azobra:AZOBR_RS06795 Length = 331 Score = 205 bits (521), Expect = 2e-57 Identities = 123/313 (39%), Positives = 175/313 (55%), Gaps = 9/313 (2%) Query: 7 IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66 I EA RL RT L+ + +E++G + K E LQR+G+FK RGA N ++ E Sbjct: 14 IVEAAARLDGFAVRTPLLENALLNERVGGRVLLKPEVLQRSGSFKFRGAFNRLSQLTPEE 73 Query: 67 LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126 GV+ S+GNHAQGVA +A LLG+P+ + MP P K+ TR YGAEVVL R + Sbjct: 74 RRGGVVAWSSGNHAQGVAAAAALLGMPAVIVMPSDAPALKIANTRGYGAEVVLYDRWTES 133 Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQE------LPDVANILVPIGGGG 180 A A EERGA V P+D P +MAGQGT+GLE+ + +PD +++ P GGG Sbjct: 134 REAIATAIAEERGAATVPPYDHPQIMAGQGTVGLEIAAQAQAIGAVPD--DVIAPCSGGG 191 Query: 181 LIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQ-VPVTVTLADGIAVKKPGVN 239 L++G+ATA+R + P R+ E A SL G+ V+ ++ D + PG Sbjct: 192 LMSGVATAVRHSFPDARLWAAEPAGFDDVARSLAAGERVENAAGQRSICDALLTPTPGAL 251 Query: 240 TFPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVC 299 TFP+++DL+ + V + E+ A+ KL+VE GAV LAA+L ++ Sbjct: 252 TFPVMKDLLSGSLAVTDAEVKAAMAYAFTVLKLVVEPGGAVGLAAVLTGKLPAAGRTVAV 311 Query: 300 VLSGGNIDVKTIS 312 VLSGGN+D T + Sbjct: 312 VLSGGNVDAATFT 324 Lambda K H 0.319 0.137 0.383 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: 289 Number of extensions: 12 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: 402 Length of database: 331 Length adjustment: 30 Effective length of query: 372 Effective length of database: 301 Effective search space: 111972 Effective search space used: 111972 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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