Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate GFF2469 PGA1_c25010 low specificity L-threonine aldolase LtaE
Query= BRENDA::A0T1V9 (348 letters) >FitnessBrowser__Phaeo:GFF2469 Length = 344 Score = 289 bits (740), Expect = 6e-83 Identities = 162/347 (46%), Positives = 214/347 (61%), Gaps = 6/347 (1%) Query: 1 MIFSSDNWAGAHPAIAESLVTHAKGYASAYGTSELDRKVEERFSEVFER-DVAVFFVGTG 59 M F+SDN A+P I +L GYA YG E KV E+FE AV+ V TG Sbjct: 1 MHFASDNSGPANPEILTALSAANTGYAMGYGADEEMAKVTSCIREIFEAPQAAVYLVATG 60 Query: 60 TAANSLALSIANRAGGIAFCHREAHVNVDECGAPQFFSHGARLSAVGGARGKMDPAKLEA 119 TAAN LALS ++ FC R+AH+NVDEC P+F++ GA+L+ V A KM PA L Sbjct: 61 TAANVLALSTLSQPWQTLFCTRQAHINVDECNGPEFYTGGAKLTLVSDA-DKMTPADLRQ 119 Query: 120 EIRRFPKENVHGGQPMAVTLTQATESGTVYSLGEIEAIASIARSQTLPLHMDGARFANAL 179 + VHG Q V++TQ TE GTVY+L E+ A+ +++S LP+H+DGARF NAL Sbjct: 120 ALEGEENRGVHGPQRGPVSITQVTEFGTVYTLDELRALCDVSKSYGLPVHLDGARFTNAL 179 Query: 180 VSLGTTPAEMTWKRGIDLLSFGGTKNGCWCAEALVLFDPSRAQEMHFLRKRSAQLFSKSR 239 VSLG TPAEMTWK G+D++SFGGTKNGC EA++ FDP+ AQE + RKR A LFSK R Sbjct: 180 VSLGCTPAEMTWKAGVDVVSFGGTKNGCMGVEAVIFFDPAEAQEFEYRRKRGAHLFSKHR 239 Query: 240 FVAAQFDAYLAGDLWLDLARHANAMARRLADGITASAESRLAWAPDANEVFVVLKREAAS 299 +++AQ AYL DLWL A ANA A RLA G+ +A + + P AN +F L R Sbjct: 240 YLSAQMLAYLTDDLWLRNASAANAKAARLAAGL-RNAGAHFSHDPQANMIFAALPRATHQ 298 Query: 300 RLRQQGALFYDWEVPHDLEGSLAEDEGLFRLVTSFATRAEDVDRFVA 346 RL GA+++ W+ L+G+ AE+ R V ++ + +D F+A Sbjct: 299 RLFDAGAVYHLWD--GTLDGA-AEEAVTARFVCDWSVGDDQIDAFLA 342 Lambda K H 0.320 0.132 0.394 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: 342 Number of extensions: 13 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: 348 Length of database: 344 Length adjustment: 29 Effective length of query: 319 Effective length of database: 315 Effective search space: 100485 Effective search space used: 100485 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 Aug 03 2021. The underlying query database was built on Aug 03 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