Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate WP_089302170.1 CHB84_RS14645 low specificity L-threonine aldolase
Query= BRENDA::Q9X266 (343 letters) >NCBI__GCF_900188115.1:WP_089302170.1 Length = 360 Score = 251 bits (641), Expect = 2e-71 Identities = 145/337 (43%), Positives = 207/337 (61%), Gaps = 13/337 (3%) Query: 1 MIDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTM 60 +IDLRSDT+T P E MR AMA AEVGD+V DPT+ LE+ A+ GK AAL+ PSGTM Sbjct: 8 LIDLRSDTLTVPDEPMRAAMAGAEVGDNVLDGDPTVRALEQRTAQLLGKPAALWTPSGTM 67 Query: 61 GNQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPV-----PGKNGAMDPDDV 115 N +++ H QRGD + D+H+ E+G+ A L+G MP + PG+ + + Sbjct: 68 ANVIALCLHLQRGDRFLAPRDAHVLLNELGSAAWLAGGMPEAIGTDLGPGRPSPHTLERI 127 Query: 116 RKAIRPRNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNA 175 A R + RTSL+ +ENTHN +GG V+P + ++ A++ G++VH+DGAR++NA Sbjct: 128 ISAGRNAPYYALRTSLLCLENTHNAAGGAVIPADEHAQLVATARDGGLSVHLDGARLWNA 187 Query: 176 SIASGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGV 235 ++A VP ADSV C SKGL APVGS + G +FIE AR+ R+MLGGG+RQ GV Sbjct: 188 AVALNVPPAALTVGADSVSVCFSKGLGAPVGSALAGSAEFIEHARRTRQMLGGGVRQGGV 247 Query: 236 LAAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHG 295 LAA+ + AL +M D L DH NA LA L ++G+ V +TN+V+ +++ H Sbjct: 248 LAASCLKALDRM-DELATDHANAARLASGLSDLGWDV--PTPQTNIVLGAVADVERTLH- 303 Query: 296 FIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEAL 332 +LR +LA ++ +R V H+ ++ IEEAL Sbjct: 304 ---SLRELDILAMPMAG-RVRFVVHRAITSAVIEEAL 336 Lambda K H 0.319 0.135 0.384 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: 314 Number of extensions: 14 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: 343 Length of database: 360 Length adjustment: 29 Effective length of query: 314 Effective length of database: 331 Effective search space: 103934 Effective search space used: 103934 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 (21.7 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