Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate BPHYT_RS29600 BPHYT_RS29600 threonine aldolase
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__BFirm:BPHYT_RS29600 Length = 335 Score = 349 bits (896), Expect = e-101 Identities = 183/333 (54%), Positives = 234/333 (70%), Gaps = 1/333 (0%) Query: 1 MIDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQ 60 MIDLRSDTVTRP+ AML AM AA VGDDV+GDDPTV LQ AE +GKEA +F P+GTQ Sbjct: 1 MIDLRSDTVTRPTPAMLAAMSAAQVGDDVWGDDPTVLRLQATLAERTGKEAGLFFPSGTQ 60 Query: 61 ANLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKI 120 +NL AL++HC RG+EYIVGQ AH Y +E GGAAVLGSIQPQP++ AADG++PL+K+A I Sbjct: 61 SNLAALMAHCARGDEYIVGQLAHTYKYEGGGAAVLGSIQPQPLENAADGSIPLEKIAAAI 120 Query: 121 KPDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCE 180 KP D HFART+LL+LENT GKVLP Y+ EA + R+ L+ H+DGAR++NA VA G Sbjct: 121 KPIDNHFARTRLLALENTIGGKVLPAGYVAEAVQLARQHGLSAHLDGARVYNAAVASGKP 180 Query: 181 LKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIY 240 + + + DS ++C SKGLG PVGS+LVG+R I A RWRK+ GGGMRQ+G+LAAA +Y Sbjct: 181 VAALCEPFDSVSVCFSKGLGAPVGSVLVGSRALIDVAHRWRKVLGGGMRQAGVLAAACLY 240 Query: 241 ALKNNVARLQEDHDNAAWMAEQLREAG-ADVMRQDTNMLFVRVGEENAAALGEYMKARNV 299 AL +NV RL +DH +AA +A L V TNM+F + +++ A L ++K R + Sbjct: 241 ALDHNVERLADDHAHAAHLAAGLEAIDQVKVQSVATNMVFAQFPQQHCAPLEAWLKERGI 300 Query: 300 LINASPIVRLVTHLDVSREQLAEVAAHWRAFLA 332 L R VTH DVSR + A + + A Sbjct: 301 LTQMLYASRFVTHKDVSRGDIDTFIATVKGYFA 333 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: 374 Number of extensions: 14 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: 335 Length adjustment: 28 Effective length of query: 305 Effective length of database: 307 Effective search space: 93635 Effective search space used: 93635 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 09 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