Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate Ac3H11_2427 Threonine dehydratase, catabolic (EC 4.3.1.19)
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2427 Length = 334 Score = 237 bits (604), Expect = 3e-67 Identities = 130/315 (41%), Positives = 192/315 (60%), Gaps = 4/315 (1%) Query: 12 DDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTD 71 DD+ A +RLAG + T + R N ER ++F K EN+QRTG+FK RGA+N L+ +D Sbjct: 16 DDVAAAARRLAGVAHHTPVMRCNTIDERLGAKLFFKCENLQRTGAFKFRGAYNALAQFSD 75 Query: 72 AEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNF 131 A++ GV+ SAGNHAQ ++LS +L + VVMP+ A SK+AAT +Y A+VV + Sbjct: 76 AQREHGVLTFSAGNHAQAIALSARLLDMPALVVMPEDAAASKMAATREYGAQVVTYNRYT 135 Query: 132 NDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAG 191 D A ++ G IPP+D P VIAGQGT LE+++++ D+D + V +GGGGL++G Sbjct: 136 EDREAISRQLAHERGMTLIPPFDHPHVIAGQGTAALELLQEVPDLDYLFVCLGGGGLLSG 195 Query: 192 IAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNLTYEIV 251 +A +++ P +VIGV+ E + S +G I T+ADG G LTY I+ Sbjct: 196 SLLAAQALAPRCKVIGVEPETANDAQQSLRAGHIVRIPNPHTIADGAQAPSLGELTYPII 255 Query: 252 RELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAAL--LSGKLD--QYIQNRKTV 307 RE V+DIV VS+ ++ ++ +R KVV E GALA A + SG+ D + +Q Sbjct: 256 REHVEDIVTVSDQQLIQALRFFAERMKVVVEPTGALAFAGVQAFSGEDDGAKLLQGEHVG 315 Query: 308 SIISGGNIDLSRVSQ 322 I+SGGN+DL R+++ Sbjct: 316 VIVSGGNVDLPRLAR 330 Lambda K H 0.318 0.136 0.386 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: 236 Number of extensions: 6 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: 329 Length of database: 334 Length adjustment: 28 Effective length of query: 301 Effective length of database: 306 Effective search space: 92106 Effective search space used: 92106 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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