Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate CA265_RS02210 CA265_RS02210 threonine aldolase
Query= BRENDA::Q9X266 (343 letters) >FitnessBrowser__Pedo557:CA265_RS02210 Length = 341 Score = 284 bits (727), Expect = 2e-81 Identities = 154/333 (46%), Positives = 203/333 (60%), Gaps = 2/333 (0%) Query: 2 IDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMG 61 +D RSDTVTKPT M AM A+VGDDV+GED T++ LE A F EA LF PSGTM Sbjct: 6 LDFRSDTVTKPTAGMLDAMMNAKVGDDVFGEDETVHALETKLASIFNMEAGLFCPSGTMT 65 Query: 62 NQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRP 121 NQ++I TQ DEVI + +H++ YE+G +A SG + G G + P+ + I Sbjct: 66 NQIAIKCFTQPMDEVICDQTAHVYRYEIGGIAYHSGASVRLLYGDRGILTPELIEPEINE 125 Query: 122 RNIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNASIASGV 181 NIH+P +SL+ +ENT N+ GG L I I + G+ +H+DGARIFNA +A+G Sbjct: 126 DNIHYPNSSLVVLENTVNKGGGSCYTLSQIAPIHHLCNIKGLKLHLDGARIFNALVATGD 185 Query: 182 PVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVLAAAGI 241 EY Y D + CLSKGL APVGSV++G + I +ARK RK GGGMRQAG LAAAGI Sbjct: 186 QASEYGKYFDGISVCLSKGLGAPVGSVLLGSKQMIHKARKIRKAFGGGMRQAGFLAAAGI 245 Query: 242 IALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVKTNMVILRTDNLKVNAHGFIEALR 301 AL V RLK+DH +A+ LA L Y + V+TN+VI + K +A + + Sbjct: 246 YALDHHVTRLKDDHAHAQALANALASTKYVKSVMPVETNIVIFEVE--KGSAEKIVHQFK 303 Query: 302 NSGVLANAVSDTEIRLVTHKDVSRNDIEEALNI 334 G+ N S + IRLVTH D+S I++A+ I Sbjct: 304 EKGLHCNTTSASTIRLVTHLDLSTEMIDQAIEI 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: 301 Number of extensions: 9 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: 341 Length adjustment: 29 Effective length of query: 314 Effective length of database: 312 Effective search space: 97968 Effective search space used: 97968 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 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