Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate 351343 BT1815 low-specificity L-threonine aldolase (NCBI ptt file)
Query= BRENDA::Q88R13 (346 letters) >FitnessBrowser__Btheta:351343 Length = 337 Score = 254 bits (649), Expect = 2e-72 Identities = 134/336 (39%), Positives = 195/336 (58%), Gaps = 1/336 (0%) Query: 6 QQFASDNYSGICPEAWVAMEKANRGHDRAYGDDQWTERASEYFRNLFETDCEVFFAFNGT 65 + FASDN SG+ P A+ +AN H YGDD+WTE A + F DC F FNGT Sbjct: 2 RSFASDNNSGVHPLVMEALSRANADHALGYGDDRWTEEAVAKIKETFTQDCVPLFVFNGT 61 Query: 66 AANSLALASLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLTAASVNGKLTPQSIREV 125 +N +AL + + YHS+ C+ETAH+ DECG+P + G ++ A+ +GKLTP+ ++ Sbjct: 62 GSNVVALQVMTRPYHSIFCAETAHIYVDECGSPVKMT-GCQIRPIATTDGKLTPELMQPY 120 Query: 126 ALKRQDIHYPKPRVVTITQATEVGTVYRPDELKAISATCKELGLNLHMDGARFTNACAFL 185 D H+ +PR + I+Q TE+GT+Y P+ELK ++ G+ +HMDGAR NACA L Sbjct: 121 LHGFGDQHHSQPRALYISQCTELGTIYTPEELKRLTDFAHLNGMYVHMDGARIANACAAL 180 Query: 186 GCSPAELTWKAGVDVLCFGGTKNGMAVGEAILFFNRQLAEDFDYRCKQAGQLASKMRFLS 245 S ELT G+D+L FGGTKNG+ +GE ++ FN+ L + + KQ+ QLASKMR+LS Sbjct: 181 HLSLKELTVDCGIDILSFGGTKNGLMMGECVIIFNKDLQREARFVRKQSAQLASKMRYLS 240 Query: 246 APWVGLLEDGAWLRHGNHANHCAQLLASLVSDLPGVELMFPVEANGVFLQMPEHAIEALR 305 + L D WL++ HAN A L + +LP V E+N +FL MP I+ + Sbjct: 241 CQFTTYLTDDLWLKNAAHANAMAGKLYRALKELPEVTFTQKPESNQLFLTMPRPTIDRML 300 Query: 306 GKGWRFYTFIGSGGARFMCSWDTEEARVRELAADIR 341 + ++ + R + S+DT E V + +R Sbjct: 301 ESYFFYFWNEANHEIRLVTSFDTTEEDVNQFIRLLR 336 Lambda K H 0.321 0.134 0.420 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: 323 Number of extensions: 8 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: 346 Length of database: 337 Length adjustment: 29 Effective length of query: 317 Effective length of database: 308 Effective search space: 97636 Effective search space used: 97636 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 09 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