Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate Ga0059261_2028 Ga0059261_2028 L-threonine aldolase (EC 4.1.2.5)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1114 (346 letters) >FitnessBrowser__Korea:Ga0059261_2028 Length = 333 Score = 273 bits (698), Expect = 5e-78 Identities = 154/335 (45%), Positives = 202/335 (60%), Gaps = 7/335 (2%) Query: 7 QFASDNYSGICPEAWAAMEQANHGHQRAYGDDEWTARASDGFRKLFETDCEVFFAFNGTA 66 +F SDN + CPE AA+ AN AY D + F +LFETD V + GTA Sbjct: 2 RFFSDNAAPACPEVLAALTAANV-QDTAYDGDALSQSLDARFSELFETDAAVLWLPTGTA 60 Query: 67 ANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPDSIREVA 126 AN LAL+SLC Y V+C AH++ DE GAPEFF++G+KLL+A KLTPD+IR V Sbjct: 61 ANCLALASLCPPYGGVVCHREAHIQADEAGAPEFFTHGAKLLLAEGAGAKLTPDAIRAVI 120 Query: 127 LK-RQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSNACAFL 185 + + +H+ +P +++T ATE G YTP E AI A KE GL H+DGARF+NA L Sbjct: 121 DRIKPGVHWTQPHAISITNATEYGLAYTPQETAAIGALAKERGLGFHVDGARFANALVHL 180 Query: 186 GCTPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASKMRFLS 245 GCTPADL+W+AGVD L FG KNG EA++FF LA+ R K+AG L SK RFL+ Sbjct: 181 GCTPADLSWRAGVDALSFGFIKNGGMGAEALVFFRPDLAQAARVRRKRAGHLQSKGRFLA 240 Query: 246 APWVGILENDAWLKYANHANHCAQLLAELVSDIPGVELMFPVQANGVFLQLSEPAIAALT 305 A +L+ + WL+ A AN A LLA+ G L+ PVQ+N +FL+ + A+L Sbjct: 241 AQLHAMLDGELWLRNARAANAGAALLAQAA----GPRLLHPVQSNALFLKATAEEAASLR 296 Query: 306 AKGWRFYTFIGNGGARFMCSWDTEQERVRELAKDI 340 A+G+ FY + G R + SWD + VR LA I Sbjct: 297 AQGFGFYDW-APGEIRVVVSWDQDAAAVRPLADAI 330 Lambda K H 0.320 0.133 0.416 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: 287 Number of extensions: 14 Number of successful extensions: 4 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: 333 Length adjustment: 28 Effective length of query: 318 Effective length of database: 305 Effective search space: 96990 Effective search space used: 96990 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