Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate GFF2535 PS417_12925 serine dehydratase
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__WCS417:GFF2535 Length = 321 Score = 221 bits (564), Expect = 1e-62 Identities = 121/312 (38%), Positives = 188/312 (60%), Gaps = 4/312 (1%) Query: 13 DIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTDA 72 D+I+A QRL G + T + S ++F+K E++QR GSFK RGAFN LS Sbjct: 8 DVIDAAQRLEGVAHATPVFTSRTLDALTGAQVFIKCEHLQRAGSFKFRGAFNALSQFNPQ 67 Query: 73 EKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNFN 132 +++ GVVA S+GNHAQG++L+ +LGI +VMP AP +KVAAT +Y A VVL+ D F Sbjct: 68 QRKAGVVAFSSGNHAQGIALAAQLLGIPATIVMPTDAPAAKVAATREYGASVVLY-DRFT 126 Query: 133 DTIAKVS-EIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAG 191 + ++ + +G IPPYD P ++AGQGT E++E +D + V +GGGG+++G Sbjct: 127 EDREQIGRNLATEQGLTLIPPYDHPHILAGQGTAAKELLESTGPLDALFVGLGGGGMLSG 186 Query: 192 IAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNLTYEIV 251 A++ ++++P + GV+ E + SF SG I T T+ADG GN T+ I+ Sbjct: 187 TALSTRALSPDCLLYGVEPEAGNDGQRSFRSGSIVHIDTPKTIADGAQTQHLGNYTFPII 246 Query: 252 RELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQYIQNRKTVSIIS 311 R+ V+DI+ VS+ E+ +M +QR K+V E G L AALL+ + ++ I++ Sbjct: 247 RDNVNDILTVSDAELVAAMKFFMQRMKMVVEPTGCLGLAALLNEA--GRFKGQRVGIIVT 304 Query: 312 GGNIDLSRVSQI 323 GGN+D+ + + + Sbjct: 305 GGNVDIEKYAAL 316 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: 247 Number of extensions: 9 Number of successful extensions: 1 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: 321 Length adjustment: 28 Effective length of query: 301 Effective length of database: 293 Effective search space: 88193 Effective search space used: 88193 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: 48 (23.1 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