Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate CCNA_03190 CCNA_03190 low-specificity L-threonine aldolase
Query= BRENDA::O50584 (346 letters) >FitnessBrowser__Caulo:CCNA_03190 Length = 344 Score = 254 bits (649), Expect = 2e-72 Identities = 149/341 (43%), Positives = 198/341 (58%), Gaps = 13/341 (3%) Query: 8 FASDNYSGICPEAWAAMEKANHGHERAYGDDQWTARAADHFRKLFETDCEVFFAFNGTAA 67 FASDN +G PE A+ AN G YG D + AAD R + D +V F +GTAA Sbjct: 11 FASDNVAGAMPEVMEALIAANAGTASGYGTDHVSRAAADRIRAALDADAQVRFTASGTAA 70 Query: 68 NSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLTARSEGGKLTPASIREVAL 127 N+ AL+ L Q + +V+ E AH+ TDE GAP FF G L+ GK+ A++ E AL Sbjct: 71 NAFALTLLAQPHEAVLAHEHAHICTDETGAPGFFGQGVGLIGLPGASGKMELAAL-EAAL 129 Query: 128 KRQDIHYPKP-RVVTITQATEVGSVYRPDELKAISATCKELGLNLHMDGARFSNACAFLG 186 + D+ Y +P +++T ATE G+VY D L+A+ A K G +H+DGAR +NA A G Sbjct: 130 AQPDVSYRQPAAALSLTTATEYGTVYSEDHLRALIAPVKAKGYGVHLDGARLANAVA--G 187 Query: 187 CTPAELTWKAGIDVLCFGGTKNGMAVGEAILFFNRKLAEDFDYRCKQAGQLASKMRFLSA 246 + K G+D+L GGTK G EA++F N A+ D R K AGQL SK RFL+A Sbjct: 188 GFDLKSIAKMGVDILVMGGTKAGSTPTEAVVFLNPDHAKRLDARLKHAGQLISKGRFLAA 247 Query: 247 PWVGLL----EDGAWLRHAAHANHCAQLLSSLVADIPGVELMFPVEANGVFLQMSEPALE 302 PW+GLL + W AAHAN AQ L++L+ V + PVEANG+F++M E ALE Sbjct: 248 PWLGLLGENGQTAPWAARAAHANAMAQKLAALMP----VPIKHPVEANGIFVEMDELALE 303 Query: 303 ALRNKGWRFYTFIGSGGARFMCSWDTEEARVRELAADIRAV 343 LR +GW Y F+ G RFMCSW T V +L A ++ V Sbjct: 304 RLRGEGWFVYRFL-DGTVRFMCSWATTPEMVEDLGAALKRV 343 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: 332 Number of extensions: 11 Number of successful extensions: 3 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: 344 Length adjustment: 29 Effective length of query: 317 Effective length of database: 315 Effective search space: 99855 Effective search space used: 99855 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 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