Align Protein DJ-1 homolog D; AtDJ1D; Lactoylglutathione lyase DJ1D; EC 4.4.1.5 (characterized)
to candidate PP_0893 PP_0893 ThiJ/PfpI family protein
Query= SwissProt::Q9M8R4 (388 letters) >FitnessBrowser__Putida:PP_0893 Length = 195 Score = 226 bits (576), Expect = 4e-64 Identities = 109/189 (57%), Positives = 140/189 (74%), Gaps = 1/189 (0%) Query: 198 KRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSEKP 257 K+IL L GDY+EDYE VPFQ+L +G V AVCPEK AG TAIHDFEG+QTYSEKP Sbjct: 7 KKILMLVGDYVEDYEAMVPFQALSMVGHTVHAVCPEKLAGQTVRTAIHDFEGEQTYSEKP 66 Query: 258 GHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHGQQ 317 GH FAL +F + SYDAL+IPGGRAPEYL LNE VL++V+ F + KP+A++CHG Q Sbjct: 67 GHNFALNYDFVRVRPESYDALLIPGGRAPEYLRLNEKVLDLVRAFDQAGKPIAAVCHGAQ 126 Query: 318 ILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQ 377 +LAAAGVL+GR+C+AYPA V L GGT+++ +D+ DGNLVT AWP HP +++ Sbjct: 127 LLAAAGVLEGRECSAYPACAPEVRLAGGTFID-IAVDQAHVDGNLVTAPAWPAHPAWLAA 185 Query: 378 LMALLGIQV 386 + +LG ++ Sbjct: 186 FLKVLGTRI 194 Score = 199 bits (507), Expect = 4e-56 Identities = 97/190 (51%), Positives = 127/190 (66%), Gaps = 1/190 (0%) Query: 4 SRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFES 63 ++ +L+L GDY+EDYE MVPFQAL G TVH VCP K AG + TA+HDF G QTY E Sbjct: 6 AKKILMLVGDYVEDYEAMVPFQALSMVGHTVHAVCPEKLAGQTVRTAIHDFEGEQTYSEK 65 Query: 64 RGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQ 123 GHNF LN F V YD L+IPGGRAPEYL L V++LV+ F ++GKPIA++CHG Sbjct: 66 PGHNFALNYDFVRVRPESYDALLIPGGRAPEYLRLNEKVLDLVRAFDQAGKPIAAVCHGA 125 Query: 124 LILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQ 183 +LAAA + GR+C+AY P + AG +++ I D VDG+L+TA + HP ++ Sbjct: 126 QLLAAAGVLEGRECSAYPACAPEVRLAGGTFID-IAVDQAHVDGNLVTAPAWPAHPAWLA 184 Query: 184 LFVKALGGKI 193 F+K LG +I Sbjct: 185 AFLKVLGTRI 194 Lambda K H 0.321 0.138 0.425 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: 332 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 388 Length of database: 195 Length adjustment: 25 Effective length of query: 363 Effective length of database: 170 Effective search space: 61710 Effective search space used: 61710 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 (21.8 bits) S2: 47 (22.7 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