Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate WP_068174994.1 HTA01S_RS21310 low-specificity L-threonine aldolase
Query= BRENDA::P75823 (333 letters) >NCBI__GCF_001592305.1:WP_068174994.1 Length = 357 Score = 340 bits (873), Expect = 2e-98 Identities = 179/340 (52%), Positives = 230/340 (67%), Gaps = 8/340 (2%) Query: 1 MIDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQ 60 ++DLRSDTVT+P+ AM AMMAAP+GDDV+GDDPTVNALQD A ++GKEAA+F+P+GTQ Sbjct: 3 IVDLRSDTVTQPTAAMRAAMMAAPLGDDVFGDDPTVNALQDRIAAITGKEAALFMPSGTQ 62 Query: 61 ANLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKI 120 +NL +L+HC RG+EYIVGQ AH Y +E GGAAV GS+QPQP+ A G + L +A I Sbjct: 63 SNLCGILAHCGRGDEYIVGQLAHTYRYEGGGAAVFGSVQPQPLVQDAAGCMALSDIAAAI 122 Query: 121 KPDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGC- 179 KPDD HFART+LL LENT NG V+P +YL++A E R LA H+DGAR+FNA VA Sbjct: 123 KPDDPHFARTRLLCLENTWNGHVMPDDYLRDATELARAHGLATHLDGARVFNAAVASAAM 182 Query: 180 ------ELKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGI 233 L+EI + DS ++C SKGLG PVGS L G+R+ I+ A R RKM GGG+RQ+G+ Sbjct: 183 GQGATDRLREIADHFDSLSVCFSKGLGAPVGSALCGSRELIQSARRIRKMAGGGLRQAGL 242 Query: 234 LAAAGIYALKNNVARLQEDHDNAAWMAEQLRE-AGADVMRQDTNMLFVRVGEENAAALGE 292 LAA ++AL ++V RL +DH NA +AE L G V TN++FV V + L + Sbjct: 243 LAACALHALDHHVDRLADDHANARRLAEGLSGIEGLTVKSAQTNIVFVDVADGRGPGLLD 302 Query: 293 YMKARNVLINASPIVRLVTHLDVSREQLAEVAAHWRAFLA 332 ++KA VL +R VTHLDV + A F A Sbjct: 303 FLKANGVLATGLIGLRFVTHLDVDAAGIDHALACVHRFFA 342 Lambda K H 0.319 0.134 0.391 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: 371 Number of extensions: 10 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: 333 Length of database: 357 Length adjustment: 29 Effective length of query: 304 Effective length of database: 328 Effective search space: 99712 Effective search space used: 99712 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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