Align L-allo-threonine aldolase (EC 4.1.2.49) (characterized)
to candidate 3608752 Dshi_2144 Threonine aldolase (RefSeq)
Query= BRENDA::O07051 (338 letters) >FitnessBrowser__Dino:3608752 Length = 344 Score = 296 bits (758), Expect = 5e-85 Identities = 165/334 (49%), Positives = 211/334 (63%), Gaps = 7/334 (2%) Query: 5 DLRSDTVTQPTDAMRQCMLHAEVGDDVYGEDPGVNALEAYGADLLGKEAALFVPSGTMSN 64 DLRSDTVT+P MR M AEVGDD YGEDP V LEA A+ K A LF P+G MSN Sbjct: 16 DLRSDTVTRPCAGMRAAMADAEVGDDCYGEDPTVLRLEAVLAERTDKAAGLFFPTGCMSN 75 Query: 65 LLAVMSHCQRGEGAVLGSAAHIYRYEAQGSAVLGSVALQPVPMQADGSLALADVRAAIAP 124 L A+M+ C RGE ++G H+Y EA ++VLG+++L P+P+ DG L A++RAA+ P Sbjct: 76 LAALMAQCARGEEVIVGRDYHVYADEAASASVLGALSLVPIPVAEDGGLEPAEIRAALKP 135 Query: 125 DDVHFTPTRLVCLENTHNGKVLPLPYLREMRELVDEHGLQLHLDGARLFNAVVASGHTVR 184 +DVH+ +RL+CLENT G+ +PL + E GL +HLDGAR FNAV A G + Sbjct: 136 EDVHYARSRLLCLENTVGGRAVPLARMAAAVRTGREAGLSVHLDGARFFNAVTALGSSEA 195 Query: 185 ELVAPFDSVSICLSKGLGAPVGSLLVGSHAFIARARRLRKMVGGGMRQAGILAQAGLFAL 244 EL D+VS+CLSKGLGAP G++LVG IA ARRLRK++GGGMRQ+G+LA AGL+AL Sbjct: 196 ELAGLADTVSLCLSKGLGAPAGTVLVGPTPVIAEARRLRKLLGGGMRQSGVLAAAGLWAL 255 Query: 245 QQHVVRLADDHRRARQLAEGLAALPGIRLDLAQVQTNMVFLQLTSGESAPLLAFMKARGI 304 + + RLA+DH RA +LA L L +R TNMVF A L A M +G+ Sbjct: 256 EHQLPRLAEDHARAARLARALIPLGTVRQG-----TNMVFFTPPVQNRAALAARMAGQGV 310 Query: 305 LFS--GYGELRLVTHLQIHDDDIEEVIDAFTEYL 336 S G G +RLV H + D + I AF L Sbjct: 311 RISDPGEGAIRLVVHRDVDDAALTAAIAAFESCL 344 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: 379 Number of extensions: 12 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: 344 Length adjustment: 29 Effective length of query: 309 Effective length of database: 315 Effective search space: 97335 Effective search space used: 97335 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