Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate HSERO_RS09030 HSERO_RS09030 hypothetical protein
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__HerbieS:HSERO_RS09030 Length = 351 Score = 142 bits (359), Expect = 1e-38 Identities = 97/300 (32%), Positives = 153/300 (51%), Gaps = 6/300 (2%) Query: 30 SEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA-LAKGVITASAGNHAQGVAFSAD 88 ++ LG ++ K EN TGAFK+RG + ++ R+ GV++A+ GNH Q V +A Sbjct: 38 NQALGAEVWVKHENHAPTGAFKVRGGMVYLHHLARQQPQLSGVVSATRGNHGQSVGLAAR 97 Query: 89 LLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEA--YAAAVQAQEERGALFVHPF 146 LG+ +T+ +P+ +K A R G E++ G F E+ YA + AQ++ L + P Sbjct: 98 RLGISATIVVPQGNSREKNAAMRALGVELIEHGSEFQESREYAQQLAAQQQ---LHMIPS 154 Query: 147 DDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIATAIRETHPHVRIIGVETAAA 206 ++AG + +E+ P + +LVPIG G + G A RIIGV +A A Sbjct: 155 LHRDLVAGVASYWMELFAAQPGLDVVLVPIGQGSGMCGAVAARNALGLSTRIIGVVSAHA 214 Query: 207 PSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEEIALAIVAL 266 + S + G+ ++ PV+ +ADG+A + P + ++ VDEVV V ++E+ A+ Sbjct: 215 LAYKLSFEAGRKIESPVSTCIADGVACRVPDQASLEVLFSEVDEVVAVTDDEVMDAMKLA 274 Query: 267 LERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGNIDVKTISVVVERGLVAAGRYL 326 T + EGAGA LAA R K LSGGN+D ++ V+ R A L Sbjct: 275 YIATHNVAEGAGACALAAAWQLRARLRGLKVGVTLSGGNVDHDVLARVLARAAAPADMLL 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: 290 Number of extensions: 13 Number of successful extensions: 3 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: 351 Length adjustment: 30 Effective length of query: 372 Effective length of database: 321 Effective search space: 119412 Effective search space used: 119412 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