Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PfGW456L13_3031 Threonine dehydratase biosynthetic (EC 4.3.1.19)
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031 Length = 337 Score = 214 bits (544), Expect = 4e-60 Identities = 131/306 (42%), Positives = 181/306 (59%), Gaps = 5/306 (1%) Query: 20 RTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNH 79 RT L + SE LG I K E+LQ T +FKIRGA N + A+GV+TASAGNH Sbjct: 29 RTPLQPAPALSEALGNQILLKREDLQPTFSFKIRGAYNKLVQLSEVQKARGVVTASAGNH 88 Query: 80 AQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERG 139 AQGVA +A LG+ +T+ MP +TP KV R GA+ VL G +F A A A+ E G Sbjct: 89 AQGVALAARELGINATIVMPCTTPQLKVIGVRSRGADAVLHGESFPFALACALDLARETG 148 Query: 140 ALFVHPFDDPLVMAGQGTIGLEVL-QELPDVANILVPIGGGGLIAGIATAIRETHPHVRI 198 FV PFDDP V+AGQGT+ +E+L Q + I VP+GGGGLIAGIA ++ P VR+ Sbjct: 149 RTFVSPFDDPEVIAGQGTVAMEILRQHQGPLDAIFVPVGGGGLIAGIAAYVKYLRPEVRV 208 Query: 199 IGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEE 258 IGVE+ + ++ G+ V +P T ADG+AV + G F + R VD+VV V +E Sbjct: 209 IGVESEHSACLQAAMHAGERVVLPSVGTFADGVAVAQIGAYGFEVCRFCVDDVVTVSNDE 268 Query: 259 IALAIVALLERTKLLVEGAGAVPLAALLNRRV--TDLSGKT-VCVLSGGNIDVKTISVVV 315 + AI + + T+ + E +GA+ +A + R V T G+T V + SG NI+ ++ V Sbjct: 269 LCAAIKNIYDDTRSITEPSGALAVAG-IKRYVAQTGALGQTLVAIDSGANINFDSLGHVA 327 Query: 316 ERGLVA 321 ER ++ Sbjct: 328 ERAALS 333 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: 289 Number of extensions: 13 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: 337 Length adjustment: 30 Effective length of query: 372 Effective length of database: 307 Effective search space: 114204 Effective search space used: 114204 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