Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate 5208646 Shew_1155 threonine aldolase (RefSeq)
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__PV4:5208646 Length = 335 Score = 347 bits (891), Expect = e-100 Identities = 184/324 (56%), Positives = 227/324 (70%), Gaps = 4/324 (1%) Query: 1 MIDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQ 60 MID RSDTVT+P+ AM AM A VGDDVYGDDP+VN L+ AAE G ++A+F +GTQ Sbjct: 1 MIDFRSDTVTQPTAAMRRAMADAQVGDDVYGDDPSVNRLEAMAAERFGFDSALFTSSGTQ 60 Query: 61 ANLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKI 120 ANL+AL+SHC+RG+EY+ GQ AHNY FE GGAAVLGSIQPQP+ DG++ L + I Sbjct: 61 ANLLALMSHCDRGDEYLCGQQAHNYKFEGGGAAVLGSIQPQPLTNQPDGSILLSDIEAAI 120 Query: 121 KPDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCE 180 KPDD HFART+LLSLENT GKVLP+ YL EA + L +H+DGARI NA VA+ + Sbjct: 121 KPDDFHFARTRLLSLENTIGGKVLPQSYLAEAQALAFNKRLKIHLDGARIANAAVAHNLD 180 Query: 181 LKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIY 240 + +ITQY DS +ICLSKGL PVGSLL+G+ I +A RWRKM GGGMRQ+GILA AG Sbjct: 181 IADITQYFDSVSICLSKGLCAPVGSLLLGDERLINKARRWRKMLGGGMRQAGILAVAGEI 240 Query: 241 ALKNNVARLQEDHDNAAWMAEQLR---EAGADVMRQDTNMLFVRVGEENAA-ALGEYMKA 296 AL V+RL DH+NA ++AEQL E D+ TNMLF RV E A L +KA Sbjct: 241 ALNEQVSRLAVDHENARYLAEQLSCLDEFEVDLGEVQTNMLFARVVEGVAIDKLATSLKA 300 Query: 297 RNVLINASPIVRLVTHLDVSREQL 320 +LI+ +R+VTH D+ E + Sbjct: 301 SGILISPGKTLRMVTHADIRLEDI 324 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: 349 Number of extensions: 12 Number of successful extensions: 4 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