Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PP_3191 PP_3191 putative threonine ammonia-lyase / dehydratase
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__Putida:PP_3191 Length = 350 Score = 202 bits (514), Expect = 1e-56 Identities = 123/302 (40%), Positives = 171/302 (56%), Gaps = 3/302 (0%) Query: 7 IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66 IQ+A LR V T L+HS S G + KCE+LQ TG+FK RGA N M P EA Sbjct: 40 IQDAHAALRPAVSITPLLHSPRLSALTGCEVLLKCEHLQHTGSFKFRGASNKMRLLPAEA 99 Query: 67 LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126 +GVI AS+GNH Q +A + + GVP V+ K A R GAEVV + Sbjct: 100 RKQGVIAASSGNHGQALALAGKMAGVPVKVYTTTGASAYKTEAMRALGAEVVCLPTDPLS 159 Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIA 186 A A + + +G FV P++D V+AGQGTIG+E+L++ PD+ + V +GGGG+I+GI Sbjct: 160 AELEAARQAKAQGVPFVSPYNDLQVIAGQGTIGMELLEQAPDLDAVFVAVGGGGMISGIG 219 Query: 187 TAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIA-VKKPGVNTFPIIR 245 A+R P IIG A P+ SL+ G+I+++ TL+DG A +PG TFP+ + Sbjct: 220 AALRVLKPGTEIIGCWPANDPTLQQSLKAGEIIELDACETLSDGTAGGVEPGSITFPLCQ 279 Query: 246 DLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCV-LSGG 304 L+ + VLV E+EI A+ + + ++EGA AV +A + R GK V V L G Sbjct: 280 ALLTDTVLVSEDEIRCAMRDIASSERWIIEGAAAVAVAG-MQRLAERYQGKRVAVILCGR 338 Query: 305 NI 306 NI Sbjct: 339 NI 340 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: 273 Number of extensions: 16 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: 350 Length adjustment: 30 Effective length of query: 372 Effective length of database: 320 Effective search space: 119040 Effective search space used: 119040 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 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