Align Protein DJ-1 homolog D; AtDJ1D; Lactoylglutathione lyase DJ1D; EC 4.4.1.5 (characterized)
to candidate H281DRAFT_05074 H281DRAFT_05074 protease I
Query= SwissProt::Q9M8R4 (388 letters) >FitnessBrowser__Burk376:H281DRAFT_05074 Length = 193 Score = 233 bits (595), Expect = 3e-66 Identities = 111/191 (58%), Positives = 140/191 (73%), Gaps = 1/191 (0%) Query: 196 ANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSE 255 A K+ILFL GD+ EDYE VPFQ+LQA+G VDAVCP+KKAGDR TAIHDFEGDQTY+E Sbjct: 2 AAKKILFLTGDFAEDYETMVPFQALQAVGHVVDAVCPDKKAGDRIKTAIHDFEGDQTYTE 61 Query: 256 KPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHG 315 KPGH FAL +F+D YDAL I GGRAPEYL LN V+ +V++F + KP+A+ICH Sbjct: 62 KPGHLFALNASFEDADPRQYDALAIAGGRAPEYLRLNPKVIELVRQFAEAGKPIAAICHA 121 Query: 316 QQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFV 375 Q+LAAA V++G++ +AYPA V L GG + + P+D TDGN VT AWP HPE++ Sbjct: 122 AQLLAAADVIRGKRISAYPACAPEVKLAGGEFAD-IPVDAAITDGNFVTAPAWPAHPEWL 180 Query: 376 SQLMALLGIQV 386 Q + LLG ++ Sbjct: 181 RQFLVLLGTRI 191 Score = 199 bits (507), Expect = 4e-56 Identities = 95/190 (50%), Positives = 128/190 (67%), Gaps = 1/190 (0%) Query: 4 SRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFES 63 ++ +L L GD+ EDYE MVPFQALQA G V VCP KKAGD TA+HDF G QTY E Sbjct: 3 AKKILFLTGDFAEDYETMVPFQALQAVGHVVDAVCPDKKAGDRIKTAIHDFEGDQTYTEK 62 Query: 64 RGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQ 123 GH F LNA+F++ D +YD L I GGRAPEYL L V+ELV++F+ +GKPIA+ICH Sbjct: 63 PGHLFALNASFEDADPRQYDALAIAGGRAPEYLRLNPKVIELVRQFAEAGKPIAAICHAA 122 Query: 124 LILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQ 183 +LAAAD + G++ +AY P + AG ++ + I D + DG+ +TA + HPE+++ Sbjct: 123 QLLAAADVIRGKRISAYPACAPEVKLAGGEFAD-IPVDAAITDGNFVTAPAWPAHPEWLR 181 Query: 184 LFVKALGGKI 193 F+ LG +I Sbjct: 182 QFLVLLGTRI 191 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: 305 Number of extensions: 7 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: 193 Length adjustment: 25 Effective length of query: 363 Effective length of database: 168 Effective search space: 60984 Effective search space used: 60984 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)
Align Protein DJ-1 homolog D; AtDJ1D; Lactoylglutathione lyase DJ1D; EC 4.4.1.5 (characterized)
to candidate H281DRAFT_00047 H281DRAFT_00047 protease I
Query= SwissProt::Q9M8R4 (388 letters) >FitnessBrowser__Burk376:H281DRAFT_00047 Length = 193 Score = 211 bits (538), Expect = 1e-59 Identities = 101/191 (52%), Positives = 137/191 (71%), Gaps = 1/191 (0%) Query: 196 ANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSE 255 A KRI+FL GD+ EDYE+ VPFQ+L+ +G +VD VCP KK GD+ TAIHDFEGDQTY+E Sbjct: 2 AAKRIVFLTGDFAEDYEMMVPFQALEMIGHKVDTVCPGKKRGDKIKTAIHDFEGDQTYTE 61 Query: 256 KPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHG 315 KPGH F L NFDD+ YDAL+I GGRAPEYL LNE V+ IV+EF + K +A++CHG Sbjct: 62 KPGHLFILNANFDDVEVDDYDALMIVGGRAPEYLRLNERVVEIVQEFAGAGKLIAAVCHG 121 Query: 316 QQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFV 375 Q+LAAA V++G++ + YPA ++ L GG + + +D TDGN VT + HP ++ Sbjct: 122 AQLLAAADVIRGKRISGYPACAPDIRLAGGEYAD-IRMDDAITDGNFVTCPVYLAHPRWL 180 Query: 376 SQLMALLGIQV 386 +Q++ LG ++ Sbjct: 181 AQVLLQLGTEI 191 Score = 189 bits (481), Expect = 4e-53 Identities = 91/190 (47%), Positives = 125/190 (65%), Gaps = 1/190 (0%) Query: 4 SRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFES 63 ++ ++ L GD+ EDYE+MVPFQAL+ G V TVCPGKK GD TA+HDF G QTY E Sbjct: 3 AKRIVFLTGDFAEDYEMMVPFQALEMIGHKVDTVCPGKKRGDKIKTAIHDFEGDQTYTEK 62 Query: 64 RGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQ 123 GH F LNA FD+V++ YD L+I GGRAPEYL L VVE+V+EF+ +GK IA++CHG Sbjct: 63 PGHLFILNANFDDVEVDDYDALMIVGGRAPEYLRLNERVVEIVQEFAGAGKLIAAVCHGA 122 Query: 124 LILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQ 183 +LAAAD + G++ + Y P + AG ++ + I D + DG+ +T Y HP ++ Sbjct: 123 QLLAAADVIRGKRISGYPACAPDIRLAGGEYAD-IRMDDAITDGNFVTCPVYLAHPRWLA 181 Query: 184 LFVKALGGKI 193 + LG +I Sbjct: 182 QVLLQLGTEI 191 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: 317 Number of extensions: 9 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: 193 Length adjustment: 25 Effective length of query: 363 Effective length of database: 168 Effective search space: 60984 Effective search space used: 60984 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 Apr 09 2024. 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