Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate N515DRAFT_4398 N515DRAFT_4398 L-threonine aldolase
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__Dyella79:N515DRAFT_4398 Length = 340 Score = 357 bits (917), Expect = e-103 Identities = 188/332 (56%), Positives = 238/332 (71%), Gaps = 3/332 (0%) Query: 2 IDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQA 61 +DLRSDTVT+P+RAM EAM+ A VGDDVYG+DPTVNALQ A+ G EA +F+PTGTQ+ Sbjct: 4 VDLRSDTVTKPTRAMREAMLLAVVGDDVYGEDPTVNALQAKLADELGFEAGLFVPTGTQS 63 Query: 62 NLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKIK 121 NL+AL++HCERG+EY+VG AH Y FE GGAAVLGSIQPQPI ADGTLPLDK+A IK Sbjct: 64 NLLALMAHCERGDEYLVGADAHTYKFEGGGAAVLGSIQPQPIPHDADGTLPLDKLAAAIK 123 Query: 122 PDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCEL 181 P D HFART+LL+LENT +G+ LP +YL A +F RER L H+DGAR+FNA VA G Sbjct: 124 PVDPHFARTRLLALENTWHGRALPLDYLHAAQKFARERGLGFHLDGARLFNAAVASGVHA 183 Query: 182 KEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIYA 241 +EI D+ ++CLSKGLG PVGS+L+G +++A RWRK+ GGG RQ+G+LAAA I+A Sbjct: 184 REIAGLFDTVSVCLSKGLGAPVGSVLLGPGALVEKARRWRKVAGGGWRQAGMLAAAAIHA 243 Query: 242 LKNNVARLQEDHDNAAWMAEQLRE-AGADVMRQDTNMLFVRVGEENAAALGEYMKARNVL 300 L ++VARL EDH AA +A +L G ++ TNM+FV V L +++ V Sbjct: 244 LDHHVARLAEDHARAATLATRLGHLPGVKLLGHHTNMVFVDVPAARLRELDAHLREAQVR 303 Query: 301 INAS--PIVRLVTHLDVSREQLAEVAAHWRAF 330 I+ P +RLVTHLDV + L V + AF Sbjct: 304 ISIGYLPTLRLVTHLDVDDDGLERVVDAFEAF 335 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: 376 Number of extensions: 12 Number of successful extensions: 2 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: 340 Length adjustment: 28 Effective length of query: 305 Effective length of database: 312 Effective search space: 95160 Effective search space used: 95160 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