Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_025764552.1 X939_RS0117325 pyridoxal-phosphate dependent enzyme
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_000566685.1:WP_025764552.1 Length = 323 Score = 211 bits (538), Expect = 2e-59 Identities = 119/303 (39%), Positives = 176/303 (58%), Gaps = 2/303 (0%) Query: 7 IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66 ++EA R+ + RT L+ S +E G ++FK ENLQ+ GAFKIRGALN M S Sbjct: 17 LREAHQRITPFIHRTPLMTSQMLNELTGAHLFFKPENLQKIGAFKIRGALNAMLSLDSAV 76 Query: 67 LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126 LA G+ T S+GNHAQ +A +A L G+ + + MP + P KV A R YGA + ++ Sbjct: 77 LANGLATHSSGNHAQAIACAAALRGIKAYIVMPHNAPKVKVSAVRGYGASITFCENTPED 136 Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVAN-ILVPIGGGGLIAGI 185 A + E GA F+HPF+ VM GQ T+ E++++ + + +L P+GGGGL++G Sbjct: 137 REAVVARIVAETGATFIHPFNHYGVMEGQATVAKEMIEDSTEPFDYLLAPVGGGGLLSGT 196 Query: 186 ATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIR 245 A + + +IG E A A SLQ G I + P T+ADG+ + G TFP+I Sbjct: 197 ALSAHYFSKNTLVIGAEPEGAADAVLSLQSGSIQKAPYVDTIADGL-LTYLGDKTFPVIH 255 Query: 246 DLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGN 305 V E+VLV ++EI A+ + ER KL+VE +GAV LAA++ + + ++SGGN Sbjct: 256 KFVSEIVLVSDQEIVEAMRLIWERMKLVVEPSGAVTLAAIIRHKKLFEGKRVGVIVSGGN 315 Query: 306 IDV 308 +D+ Sbjct: 316 VDL 318 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: 270 Number of extensions: 12 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: 323 Length adjustment: 29 Effective length of query: 373 Effective length of database: 294 Effective search space: 109662 Effective search space used: 109662 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 24 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