Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_073036508.1 BUB04_RS01900 threonine ammonia-lyase
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_900129305.1:WP_073036508.1 Length = 399 Score = 344 bits (883), Expect = 2e-99 Identities = 184/391 (47%), Positives = 257/391 (65%), Gaps = 2/391 (0%) Query: 7 IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66 I++A L+ R+ RT L++S S+ G +Y K ENLQ+TG+FK+RGA + + Sbjct: 6 IRDAARVLKARIIRTPLVYSPTLSDLFGADVYLKLENLQKTGSFKVRGATYKILKNRDKL 65 Query: 67 LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126 +GV+ ASAGNHAQGVA +A GVP+ + MP K ATR+YG +V+L G + E Sbjct: 66 GPRGVVAASAGNHAQGVALAARQAGVPAVIVMPVWASITKQIATRNYGGDVILHGTSLSE 125 Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIA 186 + A++ E G F+HPFDD +MAGQGT+GLE+L++LPD +LVP+GGGGLI GI Sbjct: 126 SLDKALELSRE-GRTFIHPFDDEDIMAGQGTVGLEILEDLPDPDLVLVPVGGGGLIGGIG 184 Query: 187 TAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRD 246 TAI+ P +++GVE A PSA+ +L+ G++V V ++ADGIAVK+ G TF +IR Sbjct: 185 TAIKALRPRTQVVGVEAAVCPSANEALRTGRLVAVGSAQSIADGIAVKRLGEKTFEVIRR 244 Query: 247 LVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSG-KTVCVLSGGN 305 VD VV V+EE IA A++ LLER K+L EGAGAVPL ALL V G K V V+SGGN Sbjct: 245 RVDRVVTVDEEHIAEALLLLLERKKVLAEGAGAVPLGALLTGAVRCEKGRKVVLVVSGGN 304 Query: 306 IDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHDRRSKSL 365 +D + V+ +GL+ +GR ++ V++DD+PG+LARL +A AN+ I HDR L Sbjct: 305 VDSPLLGRVLTKGLLKSGRLMRFTVQVDDVPGSLARLLGVVAAHGANVLHIYHDRNVPDL 364 Query: 366 PIGKTEVLIELETRGFEHIQEVISHLQGVGY 396 P+ T V +E+ETRGF+H++ + L+ GY Sbjct: 365 PLHVTRVELEVETRGFDHMEALTEALKTAGY 395 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: 397 Number of extensions: 11 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: 399 Length adjustment: 31 Effective length of query: 371 Effective length of database: 368 Effective search space: 136528 Effective search space used: 136528 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