Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate BWI76_RS09550 BWI76_RS09550 low-specificity L-threonine aldolase
Query= BRENDA::P75823 (333 letters) >FitnessBrowser__Koxy:BWI76_RS09550 Length = 333 Score = 587 bits (1514), Expect = e-172 Identities = 288/333 (86%), Positives = 311/333 (93%) Query: 1 MIDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQ 60 MIDLRSDTVTRP RAMLEAMMAAPVGDDVYGDDPTVN LQ +AAEL+GKEAAIFLPTGTQ Sbjct: 1 MIDLRSDTVTRPGRAMLEAMMAAPVGDDVYGDDPTVNELQRFAAELAGKEAAIFLPTGTQ 60 Query: 61 ANLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKI 120 ANLVALLSHC+RGEEYIVGQ AHNYL+EAGGAAVLGSIQPQPIDAAADGTLPLDKVA KI Sbjct: 61 ANLVALLSHCQRGEEYIVGQGAHNYLYEAGGAAVLGSIQPQPIDAAADGTLPLDKVAAKI 120 Query: 121 KPDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCE 180 KPDDIHFA T+LLSLENTHNGKVLPREYLKEAWEFTR+R L LHVDGARIFNAVV YGCE Sbjct: 121 KPDDIHFAPTRLLSLENTHNGKVLPREYLKEAWEFTRQRGLGLHVDGARIFNAVVDYGCE 180 Query: 181 LKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIY 240 L++IT+YCDSFTICLSKGLG PVGSLLVG+ +YI+RAIRWRKM GGGMRQ+GILAAAG+Y Sbjct: 181 LRDITRYCDSFTICLSKGLGAPVGSLLVGSEEYIRRAIRWRKMVGGGMRQAGILAAAGLY 240 Query: 241 ALKNNVARLQEDHDNAAWMAEQLREAGADVMRQDTNMLFVRVGEENAAALGEYMKARNVL 300 AL+NNVARL+EDHDNAAWMAEQLR GADVMR DTNMLFVRVGE A ALGEY++ R VL Sbjct: 241 ALQNNVARLKEDHDNAAWMAEQLRAVGADVMRHDTNMLFVRVGEARATALGEYLRERGVL 300 Query: 301 INASPIVRLVTHLDVSREQLAEVAAHWRAFLAR 333 INASPIVRLVTH+DV+R+QLAEV +HW+AFL R Sbjct: 301 INASPIVRLVTHIDVNRQQLAEVVSHWQAFLNR 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: 488 Number of extensions: 7 Number of successful extensions: 1 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: 333 Length adjustment: 28 Effective length of query: 305 Effective length of database: 305 Effective search space: 93025 Effective search space used: 93025 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