Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate HSERO_RS01420 HSERO_RS01420 serine/threonine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__HerbieS:HSERO_RS01420 Length = 326 Score = 226 bits (577), Expect = 6e-64 Identities = 127/301 (42%), Positives = 177/301 (58%), Gaps = 4/301 (1%) Query: 10 ADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAK 69 A +R++ RT ++ S +LG ++FKCEN QR GAFK RGA+N +T Sbjct: 19 AAERIKPWAHRTPVLRSRTADTELGAQLFFKCENFQRMGAFKFRGAMNALTQFDATQRKH 78 Query: 70 GVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYA 129 GVIT S+GNHAQG A +A LLG+P+ + MP+ P KV ATR YGAEVV R ++ A Sbjct: 79 GVITFSSGNHAQGTALAAQLLGIPAVIVMPQDAPAAKVAATRGYGAEVVTYDRYTEDREA 138 Query: 130 AAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIATAI 189 + ER + P+D P VMAGQGT LE+LQE + + V +GGGGL++G A A Sbjct: 139 IGARLAAERKMTLIPPYDHPHVMAGQGTATLELLQETGPLDALFVCLGGGGLLSGAALAA 198 Query: 190 RETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVD 249 R P +I GVE A SL+ G++V + T+ADG + G TF +IR+LVD Sbjct: 199 RALSPACKIYGVEPQAGNDGQQSLRAGQVVHIDTPKTIADGAQTQHLGKYTFGVIRELVD 258 Query: 250 EVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTD-LSGKTV-CVLSGGNID 307 ++ V +EE+ + ER K++VE G + AA R++ D L GK V ++SGGN+D Sbjct: 259 DIHTVSDEELVAGMRFFAERMKMVVEPTGCLGFAAA--RKLKDQLQGKRVGVIISGGNVD 316 Query: 308 V 308 + Sbjct: 317 L 317 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: 277 Number of extensions: 12 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: 402 Length of database: 326 Length adjustment: 29 Effective length of query: 373 Effective length of database: 297 Effective search space: 110781 Effective search space used: 110781 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