Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate WP_036258293.1 DL86_RS03570 low specificity L-threonine aldolase
Query= BRENDA::A0T1V9 (348 letters) >NCBI__GCF_000746085.1:WP_036258293.1 Length = 354 Score = 313 bits (802), Expect = 4e-90 Identities = 165/349 (47%), Positives = 221/349 (63%), Gaps = 4/349 (1%) Query: 1 MIFSSDNWAGAHPAIAESLVTHAKGYASAYGTSELDRKVEERFSEVFERDVAVFFVGTGT 60 M F+SDN GA I ++++ KG + AYG + E EVFE+++A F V TGT Sbjct: 1 MDFTSDNTTGASQPILDAILAANKGPSPAYGADPFSARAAELLGEVFEKEIACFLVATGT 60 Query: 61 AANSLALSIANRAGGIAFCHREAHVNVDECGAPQFFSHGARLSAVGGARGKMDPAKLEAE 120 A+N+LAL G FCH++AHV DECGAP+ F+ GA+L + G GK+ P A Sbjct: 61 ASNALALGALCPPWGAVFCHQDAHVLDDECGAPEMFTAGAKLVGIPGHAGKIAPRDFAAA 120 Query: 121 IRRFPKENVHGGQPMAVTLTQATESGTVYSLGEIEAIASIARSQTLPLHMDGARFANALV 180 + FP+ V QP A++L+QATE G +Y+ E+ +A+IA L +HMDGARFANALV Sbjct: 121 LANFPRGVVKTVQPAALSLSQATECGALYTCAELSELAAIAHDAKLQVHMDGARFANALV 180 Query: 181 SLGTTPAEMTWKRGIDLLSFGGTKNGCWCAEALVLFDPSRAQEMHFLRKRSAQLFSKSRF 240 +LGTTPAEM+WK GID+LSFG TKNG EAL+ FDP RA + + RKR SK RF Sbjct: 181 ALGTTPAEMSWKAGIDVLSFGATKNGALACEALIFFDPRRALNLPYQRKRGGHTLSKGRF 240 Query: 241 VAAQFDAYLAGDLWLDLARHANAMARRLADGITASAESRLAWAPDANEVFVVLKREAASR 300 + AQ AYL L+LA+ ANA A RLA+G+ + RL W +ANEVF +L R+ + Sbjct: 241 LGAQMVAYLEKGHGLELAKTANARAVRLAEGLAKAPGVRLPWTREANEVFAILPRKTDAA 300 Query: 301 LRQQGALFYDWEVPHDLEGSL---AEDEGLFRLVTSFATRAEDVDRFVA 346 L+ GAL+Y+W + + +EDE RLVTSFAT+A D++RF+A Sbjct: 301 LKAAGALYYEWSF-RSFDPKIVLPSEDEVFVRLVTSFATQASDIERFLA 348 Lambda K H 0.320 0.132 0.394 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: 328 Number of extensions: 13 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: 348 Length of database: 354 Length adjustment: 29 Effective length of query: 319 Effective length of database: 325 Effective search space: 103675 Effective search space used: 103675 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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