Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Pf6N2E2_802 Threonine dehydratase biosynthetic (EC 4.3.1.19)
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 Length = 335 Score = 219 bits (559), Expect = 7e-62 Identities = 133/306 (43%), Positives = 186/306 (60%), Gaps = 3/306 (0%) Query: 20 RTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNH 79 RT L + SE LG I K E+LQ T +FKIRGA N + E A+GVITASAGNH Sbjct: 29 RTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVQLTPEQRARGVITASAGNH 88 Query: 80 AQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERG 139 AQGVA +A LG+ +++ MP +TP KV R+ GAE +L G +F A A A++ E+ G Sbjct: 89 AQGVALAARELGISASIVMPVTTPQLKVLGVRNRGAEAILHGESFPFALAHALELAEQSG 148 Query: 140 ALFVHPFDDPLVMAGQGTIGLEVLQELP-DVANILVPIGGGGLIAGIATAIRETHPHVRI 198 FV PFDDP V+AGQGT+ +E+L++ P + I VP+GGGGLIAGIA ++ P VRI Sbjct: 149 WEFVSPFDDPDVIAGQGTVAMEILRQHPGQLDAIFVPVGGGGLIAGIAAYVKYLRPEVRI 208 Query: 199 IGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEE 258 IGVE+ + +L G+ V +P T ADG+AV + G + I R VDEV+ V ++ Sbjct: 209 IGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVDEVMTVSNDQ 268 Query: 259 IALAIVALLERTKLLVEGAGAVPLAALLNRRV-TDLSGKT-VCVLSGGNIDVKTISVVVE 316 + AI + + T+ + E +GA+ +A + T G+T V + SG NI+ ++ V E Sbjct: 269 LCAAIKDIYDDTRSITEPSGALAVAGIKQYVAGTGARGQTLVAIDSGANINFDSLRHVAE 328 Query: 317 RGLVAA 322 R V+A Sbjct: 329 RAAVSA 334 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: 288 Number of extensions: 11 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: 335 Length adjustment: 30 Effective length of query: 372 Effective length of database: 305 Effective search space: 113460 Effective search space used: 113460 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