Align L-allo-threonine aldolase (EC 4.1.2.49) (characterized)
to candidate Ac3H11_4475 Low-specificity L-threonine aldolase (EC 4.1.2.48)
Query= BRENDA::O07051 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4475 Length = 355 Score = 330 bits (846), Expect = 3e-95 Identities = 177/352 (50%), Positives = 233/352 (66%), Gaps = 19/352 (5%) Query: 5 DLRSDTVTQPTDAMRQCMLHAEVGDDVYGEDPGVNALEAYGADLLGKEAALFVPSGTMSN 64 D RSDTVTQPT AMR+ M A +GDDV+ +DP VNAL+ + A+LLG EAALF PSGT +N Sbjct: 3 DFRSDTVTQPTPAMREAMFKAPLGDDVFADDPSVNALQDHAAELLGFEAALFAPSGTQTN 62 Query: 65 LLAVMSHCQRGEGAVLGSAAHIYRYEAQGSAVLGSVALQPVPMQADGSLALADVRAAIAP 124 L+A+ HCQRG+ A++G + H YR+EA G AVLGS+ QPV Q DG+L +AD+ AAI P Sbjct: 63 LIALWGHCQRGDEAIVGQSWHTYRWEAGGMAVLGSIQPQPVETQPDGTLRVADIAAAIKP 122 Query: 125 DDVHFTPTRLVCLENTHNGKVLPLPYLREMRELVDEHGLQLHLDGARLFNAVVASG---- 180 DD HF TRLV LENT G+VLP Y+ ++ +L GL +HLDGAR+FNA A+ Sbjct: 123 DDPHFARTRLVVLENTTGGQVLPPAYIADVAQLARSRGLAMHLDGARMFNAATANAARNG 182 Query: 181 ----HTVRELVAPFDSVSICLSKGLGAPVGSLLVGSHAFIARARRLRKMVGGGMRQAGIL 236 R L + FDS S+CLSKGLGAPVGSL++GS FI +ARR RK++GGGMRQAG+L Sbjct: 183 TDVYAEARALCSHFDSASLCLSKGLGAPVGSLVLGSRDFIRQARRTRKILGGGMRQAGVL 242 Query: 237 AQAGLFALQQHVVRLADDHRRARQLAEGLA----ALPGI--RLDLAQVQTNMVFLQLTSG 290 A AG +ALQ HV RLADDH +LA+GLA + P + ++ + QTN++F L + Sbjct: 243 AAAGSYALQHHVRRLADDHANLDRLAQGLAEANRSHPVLKDKITVLPWQTNILFTDLHAE 302 Query: 291 ESAPLLAFMKARGI-----LFSGYGELRLVTHLQIHDDDIEEVIDAFTEYLG 337 + A++ G+ L+ G LR VTHL + + D+ +D + G Sbjct: 303 VAPAFTAWLAQHGVRVTSSLYGGATRLRWVTHLDVSEADVTAALDCVARFTG 354 Lambda K H 0.322 0.137 0.396 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: 398 Number of extensions: 16 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: 338 Length of database: 355 Length adjustment: 29 Effective length of query: 309 Effective length of database: 326 Effective search space: 100734 Effective search space used: 100734 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