Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate WP_090448703.1 BLS63_RS26060 low specificity L-threonine aldolase
Query= BRENDA::O50584 (346 letters) >NCBI__GCF_900100495.1:WP_090448703.1 Length = 347 Score = 629 bits (1622), Expect = 0.0 Identities = 296/345 (85%), Positives = 326/345 (94%) Query: 1 MTDQSQQFASDNYSGICPEAWAAMEKANHGHERAYGDDQWTARAADHFRKLFETDCEVFF 60 M+D SQQFASDNYSGICPEAWAAM +ANHGH+RAYGDDQWTARAAD FR+LFETDCEVFF Sbjct: 1 MSDSSQQFASDNYSGICPEAWAAMAEANHGHDRAYGDDQWTARAADQFRQLFETDCEVFF 60 Query: 61 AFNGTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLTARSEGGKLTPA 120 AFNGTAANSLAL++LCQSYHSVICSETAHVETDECGAPEFFSNGSKLL A +E GKLTPA Sbjct: 61 AFNGTAANSLALAALCQSYHSVICSETAHVETDECGAPEFFSNGSKLLLAHTENGKLTPA 120 Query: 121 SIREVALKRQDIHYPKPRVVTITQATEVGSVYRPDELKAISATCKELGLNLHMDGARFSN 180 +IRE+ALKRQDIHYPKP+VV++TQATEVG+VYRP E++AISATC+ELGLNLHMDGARFSN Sbjct: 121 AIREIALKRQDIHYPKPKVVSLTQATEVGTVYRPAEVRAISATCRELGLNLHMDGARFSN 180 Query: 181 ACAFLGCTPAELTWKAGIDVLCFGGTKNGMAVGEAILFFNRKLAEDFDYRCKQAGQLASK 240 ACAFLGCTPAELTW+AG+DVLCFGGTKNGMAVGEAILFFN+ LAEDFDYRCKQAGQLASK Sbjct: 181 ACAFLGCTPAELTWEAGVDVLCFGGTKNGMAVGEAILFFNKALAEDFDYRCKQAGQLASK 240 Query: 241 MRFLSAPWVGLLEDGAWLRHAAHANHCAQLLSSLVADIPGVELMFPVEANGVFLQMSEPA 300 MR+LSAPWVGLL++ AWL +A HAN CA+LL+ LV+D+PGV LMFPVEANGVFLQMSEPA Sbjct: 241 MRYLSAPWVGLLQNDAWLYYAGHANRCARLLAELVSDVPGVSLMFPVEANGVFLQMSEPA 300 Query: 301 LEALRNKGWRFYTFIGSGGARFMCSWDTEEARVRELAADIRAVMS 345 LEALR +GWRFYTFIG+GGARFMCSWDT E RVRELAADIR M+ Sbjct: 301 LEALRARGWRFYTFIGAGGARFMCSWDTAEERVRELAADIRTAMA 345 Lambda K H 0.321 0.133 0.413 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: 502 Number of extensions: 10 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: 347 Length adjustment: 29 Effective length of query: 317 Effective length of database: 318 Effective search space: 100806 Effective search space used: 100806 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 Sep 24 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