Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate GFF2850 HP15_2794 L-allo-threonine aldolase
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__Marino:GFF2850 Length = 336 Score = 359 bits (922), Expect = e-104 Identities = 186/333 (55%), Positives = 235/333 (70%), Gaps = 3/333 (0%) Query: 1 MIDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQ 60 MID RSDTVTRP+ M EAM +A VGDDVYGDDPTVN+LQ YAAE G EAA+F TGTQ Sbjct: 1 MIDFRSDTVTRPTPEMREAMASAEVGDDVYGDDPTVNSLQAYAAERLGFEAALFTATGTQ 60 Query: 61 ANLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKI 120 ANL+A++SHC RG+EY+ GQ+AHNY +E GGAAVLGS+QPQPI+ DG++ L+K I Sbjct: 61 ANLLAIMSHCGRGDEYLCGQSAHNYKYEGGGAAVLGSVQPQPIENEPDGSIDLEKARAAI 120 Query: 121 KPDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCE 180 K DD HFA T+LLSLENT GKVLP +Y +A F E L LH+DGARIFNA V C+ Sbjct: 121 KADDFHFAVTRLLSLENTIGGKVLPLDYQAQARAFCDEHGLLLHLDGARIFNAAVKSNCD 180 Query: 181 LKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIY 240 + EIT++ DS ++CLSKGLG PVGSLL+G+ +IKRA R RKM GGGMRQ+GILAAAG Sbjct: 181 VTEITRHYDSVSVCLSKGLGAPVGSLLLGSESFIKRATRLRKMVGGGMRQAGILAAAGRI 240 Query: 241 ALKNNVARLQEDHDNAAWMAE---QLREAGADVMRQDTNMLFVRVGEENAAALGEYMKAR 297 AL+ RL EDH+NA +++ ++ E + TN+++ R A+ L +Y+ + Sbjct: 241 ALEKGPLRLLEDHENAEYLSNGLAKIPELEVNPASTQTNIVYARCKAGQASQLKDYLAEQ 300 Query: 298 NVLINASPIVRLVTHLDVSREQLAEVAAHWRAF 330 +LI A +R VTH DVSRE + + R F Sbjct: 301 GILITAGDPIRFVTHQDVSREDVDTLLTAIRQF 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: 365 Number of extensions: 8 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: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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