Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_092350711.1 BLU87_RS16075 threonine ammonia-lyase
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_900107645.1:WP_092350711.1 Length = 403 Score = 384 bits (986), Expect = e-111 Identities = 209/402 (51%), Positives = 274/402 (68%), Gaps = 1/402 (0%) Query: 1 MLPYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMT 60 ML +I EA L+ VR TE+IHS +S+ LG P+YFKCEN Q TG+FKIRGA NF++ Sbjct: 1 MLTPQMIDEAALGLKGVVRPTEIIHSPFYSKMLGAPLYFKCENHQYTGSFKIRGAYNFLS 60 Query: 61 SQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLT 120 +P E LA G+ITAS GNH +GVA +A L P V MP+ TP K AT YGA V L Sbjct: 61 KRPVEQLANGIITASGGNHGKGVASAALSLKCPCRVIMPDGTPLSKELATLQYGAAVELY 120 Query: 121 GRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGG 180 G +EA + A Q E+ L+V FD LVMAGQGTIGLE+LQELP + ++ VP+GGGG Sbjct: 121 GDTHEEAESYARQLAEKDNLLYVPAFDHELVMAGQGTIGLEILQELPTIESLFVPVGGGG 180 Query: 181 LIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPV-TVTLADGIAVKKPGVN 239 LIAGIATAI+ P VRIIGVE A SA + + G + T + A+ +AVKK G Sbjct: 181 LIAGIATAIKAVKPGVRIIGVEAAGVASASLARRNGYPKSISTRTHSFAEEVAVKKIGEL 240 Query: 240 TFPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVC 299 TFPII VDE++ V+EE I AIV+L+E++ L+VEGAGAV LAAL+ T+C Sbjct: 241 TFPIIEHYVDEIITVDEESITRAIVSLMEKSNLVVEGAGAVSLAALIYGFRKVRKENTLC 300 Query: 300 VLSGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHD 359 +LSGGN+D+ ++ VVE+GL+ GRYL+L++E+ D+PGALA L ++E KANI ++HD Sbjct: 301 LLSGGNLDIHNLARVVEKGLLTEGRYLQLRLEIADIPGALAHLTHILSELKANIFQVSHD 360 Query: 360 RRSKSLPIGKTEVLIELETRGFEHIQEVISHLQGVGYLVDVL 401 R SLP+G+ EVL++LETRG EHIQE++ L+ Y +V+ Sbjct: 361 RHKSSLPLGEAEVLLDLETRGAEHIQEILMRLEDERYRPEVI 402 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: 382 Number of extensions: 12 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: 403 Length adjustment: 31 Effective length of query: 371 Effective length of database: 372 Effective search space: 138012 Effective search space used: 138012 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: 50 (23.9 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