Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_068176041.1 HTA01S_RS23390 hypothetical protein
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_001592305.1:WP_068176041.1 Length = 323 Score = 147 bits (370), Expect = 6e-40 Identities = 106/314 (33%), Positives = 160/314 (50%), Gaps = 11/314 (3%) Query: 2 LPYTLIQEADDRLRKRVRRTELIHSHHF-----SEKLGIPIYFKCENLQRTGAFKIRGAL 56 +P+TL AD RV E + + S++LG + K EN GAFKIRG L Sbjct: 1 MPHTLPTLADIEAATRVVYREFPATPQYRWATLSQRLGADCWIKHENHTPVGAFKIRGGL 60 Query: 57 NFMTS-QPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGA 115 + + R L + V++A+ GNH Q + ++A GV ++ +P +K A R G Sbjct: 61 TYFDQLRQRGELPREVVSATRGNHGQSIGWAARTHGVACSIVVPRGNSLEKNAAMRALGV 120 Query: 116 EVVLTGRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVP 175 ++ G +F E+ A++ ERGA V F L + G T E + +P + + VP Sbjct: 121 NLIEHGADFQESREHAMRLAAERGAHMVPSFHKDL-LRGVSTYWWEFFKAVPQLDVVYVP 179 Query: 176 IG-GGGLIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVK 234 IG G G + IA + H RI+GV +A A + S+ G++V+ PVT LADG+A + Sbjct: 180 IGQGSGACSAIAAKLALGH-QARIVGVVSAHATTYADSIAAGRVVEAPVTTELADGMACR 238 Query: 235 KPGVNTFPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLS 294 + ++ +D +V V ++E+A A+ L T L EGAGA AA + T L Sbjct: 239 VADADALAVLAPHLDHIVRVTDDEVAAAMRTLFADTHNLAEGAGAAAFAAAWQEKET-LQ 297 Query: 295 GKTVCV-LSGGNID 307 G +V V LSGGN+D Sbjct: 298 GLSVGVSLSGGNVD 311 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: 246 Number of extensions: 14 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: 402 Length of database: 323 Length adjustment: 29 Effective length of query: 373 Effective length of database: 294 Effective search space: 109662 Effective search space used: 109662 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 Apr 10 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