Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Ga0059261_3694 Ga0059261_3694 threonine ammonia-lyase, medium form
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__Korea:Ga0059261_3694 Length = 420 Score = 301 bits (772), Expect = 2e-86 Identities = 176/405 (43%), Positives = 243/405 (60%), Gaps = 8/405 (1%) Query: 2 LPYTL--IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFM 59 LP TL +Q A R+ V T +HS S+ G +Y K ENLQ T A+K RGALN + Sbjct: 18 LPVTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALNTL 77 Query: 60 TSQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVL 119 A AKGVI ASAGNHAQG+A+ + LG+P T+ MP+STP KV T +GA ++L Sbjct: 78 LQLDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKSTPTVKVMQTESHGATIIL 137 Query: 120 TGRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGG 179 G FDEAYA A Q + G FVHPFDDP ++AGQGT+ LE+L + P + ++VPIGGG Sbjct: 138 EGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEMLADAPAIDTLIVPIGGG 197 Query: 180 GLIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPV-TVTLADGIAVKKPGV 238 GLI+G T + + ++GV+ PS + P+ TLA+GIAVK+PG Sbjct: 198 GLISGALTVAKAADKPIEVVGVQAELFPS---MFNRFTGAHEPIGGDTLAEGIAVKEPGG 254 Query: 239 NTFPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTV 298 T I+ LVDE++LV E + A+ LL+ K +VEGAGA LAAL+ + GKTV Sbjct: 255 LTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMT-QPERFRGKTV 313 Query: 299 -CVLSGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIIT 357 +L+GGNID + ++ V+ R L +GR +L++ L D PGAL ++A E NI ++ Sbjct: 314 GVILTGGNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVARIFQEQTVNILELS 373 Query: 358 HDRRSKSLPIGKTEVLIELETRGFEHIQEVISHLQGVGYLVDVLK 402 H R +LP + +E ETR H++ +IS LQ GY V +++ Sbjct: 374 HQRIFTNLPAKGLSLDVECETRDRAHLERLISALQEAGYEVRLIE 418 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: 385 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: 420 Length adjustment: 31 Effective length of query: 371 Effective length of database: 389 Effective search space: 144319 Effective search space used: 144319 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