Align L-allo-threonine aldolase (EC 4.1.2.49) (characterized)
to candidate WP_011840167.1 RSPH17029_RS00510 low-specificity L-threonine aldolase
Query= BRENDA::O07051 (338 letters) >NCBI__GCF_000015985.1:WP_011840167.1 Length = 339 Score = 329 bits (844), Expect = 5e-95 Identities = 179/328 (54%), Positives = 219/328 (66%), Gaps = 3/328 (0%) Query: 5 DLRSDTVTQPTDAMRQCMLHAEVGDDVYGEDPGVNALEAYGADLLGKEAALFVPSGTMSN 64 D RSDTVT+P MR M A+VGD VY + P LEA A+ LGKEA+LF PSGT SN Sbjct: 6 DFRSDTVTRPGPEMRAAMAAADVGDAVYDDCPTTLRLEAVAAERLGKEASLFFPSGTQSN 65 Query: 65 LLAVMSHCQRGEGAVLGSAAHIYRYEAQGSAVLGSVALQPVPMQADGSLALADVRAAIAP 124 L A+M+HC+RG+ ++G AH YR+E G+AVLGSV QP+P DG + L +R AI P Sbjct: 66 LAAIMAHCERGDEFLVGQQAHAYRHEGGGAAVLGSVQPQPLPNGPDGCIPLDAIREAIKP 125 Query: 125 DDVHFTPTRLVCLENTHNGKVLPLPYLREMRELVDEHGLQLHLDGARLFNAVVASGHTVR 184 DD HF TRL+ LENT NG+VL Y++ L +HGL HLDGARL NA VASG Sbjct: 126 DDFHFARTRLLALENTFNGRVLDPAYVQAATALARDHGLAAHLDGARLMNAAVASGQAAA 185 Query: 185 ELVAPFDSVSICLSKGLGAPVGSLLVGSHAFIARARRLRKMVGGGMRQAGILAQAGLFAL 244 L APFD+VS+CLSKGLGAPVGS+L G I RARR+RKM+GGGMRQ G+LA A L AL Sbjct: 186 TLAAPFDTVSLCLSKGLGAPVGSVLAGPRPVIERARRIRKMLGGGMRQTGVLAAAALHAL 245 Query: 245 QQHVVRLADDHRRARQLAEGLAALPGIRLDLAQVQTNMVFLQLTSGESAPLLAFMKARGI 304 +++V RLA+DH RA +LAE L+ P L QTNMVF+ + A AF+ ARGI Sbjct: 246 ERNVDRLAEDHARAARLAEVLSRFPA--LGSGPAQTNMVFMAPDGIDVASFKAFLSARGI 303 Query: 305 -LFSGYGELRLVTHLQIHDDDIEEVIDA 331 + GYG LR VTHL + D + V +A Sbjct: 304 AMGGGYGVLRWVTHLDLDDAALTRVAEA 331 Lambda K H 0.322 0.137 0.396 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: 14 Number of successful extensions: 3 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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 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