Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate SMa1872 SMa1872 threonine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__Smeli:SMa1872 Length = 323 Score = 252 bits (643), Expect = 1e-71 Identities = 135/309 (43%), Positives = 193/309 (62%), Gaps = 1/309 (0%) Query: 7 IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66 I+EA +RL+ VR T L+ + + G +Y K E LQ TGAFKIRGALN S RE Sbjct: 10 IREARERLKPHVRHTPLLRAEKIEKAAGCQLYLKPETLQITGAFKIRGALNKALSLSREE 69 Query: 67 LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126 +A G+I S+GNHAQG++++A +LGV + +P +TP K+ T+ GAEV+L + Sbjct: 70 IANGIIATSSGNHAQGLSYAAKMLGVKVILVLPVTTPKIKIENTKALGAEVILFDGDNAA 129 Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIA 186 + + E +H F+DP+VMAGQGTIG E+L++L DV ++VP+GGGGLI+GIA Sbjct: 130 RWKKVYEIAEGNKYAVIHGFEDPVVMAGQGTIGCEILEDLDDVDTVIVPLGGGGLISGIA 189 Query: 187 TAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRD 246 TAI+ET P VR+IG E A P +S + +P+ T+ADG+ + PG N +PII Sbjct: 190 TAIKETKPSVRVIGAEPALTPKYFHSRVNKERTSLPLKNTIADGLRISVPGQNPYPIIEK 249 Query: 247 LVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRV-TDLSGKTVCVLSGGN 305 VDE+VLVE+E I + AL + KL+ E A ++ + ALL + L K VLSGGN Sbjct: 250 YVDEIVLVEDEHIIAGMRALAKDAKLIAEPAASIGVGALLAGIIDVKLDEKVCAVLSGGN 309 Query: 306 IDVKTISVV 314 D++ ++ + Sbjct: 310 WDLRDLAAI 318 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: 284 Number of extensions: 14 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: 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 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