Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate GFF2771 HP15_2715 low specificity L-threonine aldolase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1114 (346 letters) >FitnessBrowser__Marino:GFF2771 Length = 343 Score = 469 bits (1207), Expect = e-137 Identities = 216/342 (63%), Positives = 271/342 (79%), Gaps = 1/342 (0%) Query: 4 KSQQFASDNYSGICPEAWAAMEQANHGHQRAYGDDEWTARASDGFRKLFETDCEVFFAFN 63 +S+QFASDNYSG+CP+AW AME AN + AYG+D WT +A+DG R LF+TDC+V+F FN Sbjct: 3 QSEQFASDNYSGVCPQAWKAMEAANRMDEPAYGEDSWTQKAADGLRTLFDTDCDVYFVFN 62 Query: 64 GTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPDSIR 123 GTAANSLAL+S+ QS+HSVIC E AH+ETDECG PE+ SNG+KLL+ + ENGKLTP+SI Sbjct: 63 GTAANSLALASIGQSFHSVICHELAHIETDECGGPEYASNGAKLLLGQGENGKLTPESIE 122 Query: 124 EVALKRQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSNACA 183 + KR DIHYPKP+ ++LTQATEVG+VYTP+E++ I + LN+HMDGARF+NA A Sbjct: 123 HLVTKRTDIHYPKPKALSLTQATEVGTVYTPEELKVIRSVADRHKLNIHMDGARFANAVA 182 Query: 184 FLGCTPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASKMRF 243 L PA++TWKAGVDVLCF GTKNG+A+GEA++FFN LAEDF++RCKQAGQLASKMR+ Sbjct: 183 ALDVHPAEITWKAGVDVLCFSGTKNGLALGEAVVFFNRSLAEDFEWRCKQAGQLASKMRY 242 Query: 244 LSAPWVGILENDAWLKYANHANHCAQLLAELVSDIPGVELMFPVQANGVFLQLSEPAIAA 303 +SAPW G+LE D WL+ A HAN CAQ LA + +PG++L +P Q NGVF+++ EP AA Sbjct: 243 ISAPWCGLLEGDVWLQNARHANACAQRLAAGLEGLPGIQLRYPRQVNGVFVEMPEPLQAA 302 Query: 304 LTAKGWRFYTFIGNGGARFMCSWDTEQERVRELAKDIREVMS 345 L AKGWRFY FIG G AR MCSW T E+V D+R ++S Sbjct: 303 LRAKGWRFYNFIG-GSARLMCSWATTNEQVDRFLSDVRALVS 343 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: 438 Number of extensions: 10 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: 346 Length of database: 343 Length adjustment: 29 Effective length of query: 317 Effective length of database: 314 Effective search space: 99538 Effective search space used: 99538 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