Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_073040668.1 BUB04_RS14270 hypothetical protein
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_900129305.1:WP_073040668.1 Length = 325 Score = 197 bits (501), Expect = 4e-55 Identities = 115/300 (38%), Positives = 173/300 (57%), Gaps = 1/300 (0%) Query: 13 RLRKRV-RRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGV 71 R+ +RV +T L SE+LG +Y K EN T +FK+RGA+NFM + P E + GV Sbjct: 22 RIVERVLEKTHLTSYRRLSEELGAEVYVKHENHLPTNSFKVRGAVNFMANVPPEVVRNGV 81 Query: 72 ITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAA 131 + A+ GNH VA++A G+ V +PE P+ YGA+++ G +F EA Sbjct: 82 VVATKGNHGLAVAWAAQEKGIFCNVVVPEGNNPELNANILAYGAQLIEQGSDFYEAQDYC 141 Query: 132 VQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIATAIRE 191 + E G ++ ++PL+++G T+GLE+ +ELPDV IL+PIGGG A +AT I+ Sbjct: 142 EELAENAGYYYLRQGNEPLLISGIATMGLEIFEELPDVDVILMPIGGGTGCAALATVIQG 201 Query: 192 THPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEV 251 +P V +IGV+ A PS + S ++GK V VP T+ADG+A + + +++D + +V Sbjct: 202 INPQVELIGVQAANMPSFYESWRQGKKVVVPAAETVADGLAARSAFEVPWAVLKDRIRDV 261 Query: 252 VLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGNIDVKTI 311 VL+ EEE+ + L T+ L E AGA LAA R K V V++GGNI V+ + Sbjct: 262 VLLTEEELLEGVRLALRYTQNLAEVAGAASLAAAFKIRERLRGKKVVSVMTGGNITVERL 321 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: 275 Number of extensions: 9 Number of successful extensions: 1 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: 325 Length adjustment: 29 Effective length of query: 373 Effective length of database: 296 Effective search space: 110408 Effective search space used: 110408 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 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