Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate WP_090439679.1 BLS63_RS03200 mandelate racemase/muconate lactonizing enzyme family protein
Query= BRENDA::Q8ZL58 (398 letters) >NCBI__GCF_900100495.1:WP_090439679.1 Length = 385 Score = 456 bits (1174), Expect = e-133 Identities = 220/372 (59%), Positives = 278/372 (74%) Query: 26 DRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAG 85 DRI WV L LPL VSDAKVL+GRQ PL V+++ AEI S G G+GF Y+ R+G Sbjct: 13 DRIVWVALRSVHLPLQQAVSDAKVLSGRQPPLAAVSLLFAEIESAQGHSGLGFGYTLRSG 72 Query: 86 GQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAK 145 G YAHA+E+A L+GEDPNDI ++++KL WAGASVGRSG+AVQAI+ +D ALWD+KA+ Sbjct: 73 GPAQYAHAQELAPLLIGEDPNDIARLWSKLAWAGASVGRSGVAVQAIAALDTALWDLKAR 132 Query: 146 RAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAE 205 RAGLPLAKLLGA RD+V CYNTSGG+L P+++++ + GIGG+K+KVGQ + AE Sbjct: 133 RAGLPLAKLLGAQRDAVPCYNTSGGYLQAPIEELIDKAQQALGRGIGGVKIKVGQADQAE 192 Query: 206 DIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQ 265 D+RR+ A+R+ LG++ PLMVDANQQWDR TA+RMGR +EQ+ L WIEEPLDA+D+ GHA Sbjct: 193 DLRRVAALRKRLGEQVPLMVDANQQWDRTTALRMGRALEQYQLEWIEEPLDAHDLAGHAA 252 Query: 266 LAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKL 325 LAA LDTPI +GEMLTS E + A D + DAPR+GGI+PFLK+ LA G + Sbjct: 253 LAAQLDTPIGSGEMLTSAAEVTAYVESGAVDVIMHDAPRIGGITPFLKVASLAESRGLVM 312 Query: 326 APHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQAR 385 APHF ME+HLHL+AAY + W+EHFEWL PLF E+LE+RDG M + R GLG +LSE+ Sbjct: 313 APHFVMEIHLHLAAAYEHQTWVEHFEWLEPLFEERLEIRDGCMRVPTRPGLGLSLSERVA 372 Query: 386 RWTQLTCEFGKR 397 WT E G+R Sbjct: 373 SWTVARWECGRR 384 Lambda K H 0.319 0.136 0.410 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: 541 Number of extensions: 18 Number of successful extensions: 1 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: 398 Length of database: 385 Length adjustment: 31 Effective length of query: 367 Effective length of database: 354 Effective search space: 129918 Effective search space used: 129918 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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