Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate N515DRAFT_3206 N515DRAFT_3206 threonine dehydratase
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__Dyella79:N515DRAFT_3206 Length = 316 Score = 133 bits (334), Expect = 1e-35 Identities = 87/289 (30%), Positives = 144/289 (49%), Gaps = 5/289 (1%) Query: 32 TPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHA 91 TPL++ L L +L K E P+ SFK RG +A T +++ASAGN Sbjct: 24 TPLRRAAALDDALGCRLLGKDETDNPIGSFKGRGTEWFVA--TALNSGEAIVSASAGNFG 81 Query: 92 QGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGF 151 QG+A ++ R G + K++A+R G EV L G +FD AK+ A + +++ Sbjct: 82 QGLARAATRRGHACTVFAAQTANPAKLEAMRALGAEVRLAGVDFDAAKSAARQYAEEHRL 141 Query: 152 TWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIA 211 +V P + G T+ALELL + A + V VP+G G L G+ +++ P ++++A Sbjct: 142 RFVEDGAEPAIAQGAATIALELLAEAAP-EVVLVPLGNGALLEGIGSVLRARAPSVEIVA 200 Query: 212 VEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAIC 271 V A + +K +L+AG ++ A+G+AV+ + D I+ V + Sbjct: 201 VVAAGAPSMKLSLEAGRAIETAHADTIADGIAVRVPIASRLPQLRRCCDRIVAVSEAQLL 260 Query: 272 AAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILSGANVN 320 AM+ + + V EP+GA +AG+ A H G +A +L G N++ Sbjct: 261 DAMRLIQRHLGMVVEPAGAAGVAGILAEPARH--AGRLVATVLCGKNIH 307 Lambda K H 0.321 0.138 0.403 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: 322 Number of extensions: 17 Number of successful extensions: 4 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: 514 Length of database: 316 Length adjustment: 31 Effective length of query: 483 Effective length of database: 285 Effective search space: 137655 Effective search space used: 137655 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