Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate WP_041457111.1 AVA_RS25130 low specificity L-threonine aldolase
Query= BRENDA::Q88R13 (346 letters) >NCBI__GCF_000204075.1:WP_041457111.1 Length = 345 Score = 482 bits (1241), Expect = e-141 Identities = 228/345 (66%), Positives = 273/345 (79%) Query: 1 MTDKSQQFASDNYSGICPEAWVAMEKANRGHDRAYGDDQWTERASEYFRNLFETDCEVFF 60 M +QFASDNY+GICPEA M KAN+G AYG+D+WT++A++YFR LFE DCEVFF Sbjct: 1 MNSNLEQFASDNYAGICPEAMDYMIKANQGSAPAYGNDEWTQKAADYFRELFEIDCEVFF 60 Query: 61 AFNGTAANSLALASLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLTAASVNGKLTPQ 120 FNGTAANSL+LA+LCQSYHSVIC ETAH+ETDECGAPEF SNGSKLL A NGKLTPQ Sbjct: 61 TFNGTAANSLSLAALCQSYHSVICHETAHIETDECGAPEFASNGSKLLLAKGENGKLTPQ 120 Query: 121 SIREVALKRQDIHYPKPRVVTITQATEVGTVYRPDELKAISATCKELGLNLHMDGARFTN 180 I V KR DIHYPKP+V++ITQATE+GT+Y +EL AI + L +HMDGARF N Sbjct: 121 EIESVITKRADIHYPKPKVISITQATELGTLYSIEELLAIKEVAHKYQLKIHMDGARFAN 180 Query: 181 ACAFLGCSPAELTWKAGVDVLCFGGTKNGMAVGEAILFFNRQLAEDFDYRCKQAGQLASK 240 + A + SPAE++WK+GVDVLCF GTKNGMA+GEAI+FFNR LAEDFDYRCKQAGQLASK Sbjct: 181 SVAAMNKSPAEMSWKSGVDVLCFCGTKNGMALGEAIIFFNRALAEDFDYRCKQAGQLASK 240 Query: 241 MRFLSAPWVGLLEDGAWLRHGNHANHCAQLLASLVSDLPGVELMFPVEANGVFLQMPEHA 300 MRF+SAPW+GLLE GAWL++ +AN CA L + + + GVE+MFP EAN VF+++PE Sbjct: 241 MRFISAPWLGLLETGAWLKNARYANQCAAYLENELLKIEGVEIMFPREANAVFVKLPEQV 300 Query: 301 IEALRGKGWRFYTFIGSGGARFMCSWDTEEARVRELAADIRTIIG 345 I L+ K W FYTFIG GG RFMCSW+T + R+ EL DI+T +G Sbjct: 301 INDLKAKNWLFYTFIGVGGVRFMCSWNTTKGRIDELIGDIKTGLG 345 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: 421 Number of extensions: 5 Number of successful extensions: 1 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: 345 Length adjustment: 29 Effective length of query: 317 Effective length of database: 316 Effective search space: 100172 Effective search space used: 100172 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 Jul 25 2024. The underlying query database was built on Jul 25 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