Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate GFF368 Psest_0369 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__psRCH2:GFF368 Length = 380 Score = 453 bits (1165), Expect = e-132 Identities = 218/373 (58%), Positives = 276/373 (73%) Query: 26 DRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAG 85 DRI W+ L LPL PVSDAKVLTGRQ PL V+++ E++S+ G +G+GFSYS R+G Sbjct: 8 DRISWIGLRAVELPLQRPVSDAKVLTGRQLPLASVSLLFVELQSQQGHKGLGFSYSLRSG 67 Query: 86 GQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAK 145 G YAHA+E+A LLGEDPNDI +++++L WA AS+GR G+AVQ+I+ D ALWD+KA+ Sbjct: 68 GPAQYAHARELAPLLLGEDPNDIARLWSRLSWASASIGRGGLAVQSIAAFDTALWDLKAR 127 Query: 146 RAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAE 205 RAGLPLAKLLGAHRD+V CYNTSGG+L P+++V++ SR GIGGIKLKVGQP+ Sbjct: 128 RAGLPLAKLLGAHRDAVPCYNTSGGYLQAPIEEVIEKAEASRARGIGGIKLKVGQPDRHA 187 Query: 206 DIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQ 265 D+RR+ A+R+ GD LMVD NQQWDR TA RMGR +E+F L WIEEPLDA+D+EGHA Sbjct: 188 DLRRVEALRKHFGDGVALMVDVNQQWDRTTAARMGRALEEFELTWIEEPLDAHDLEGHAA 247 Query: 266 LAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKL 325 LAA L TP+ TGEML S E I A D + DAPR+GGI+PFL++ + A + G + Sbjct: 248 LAAQLITPVGTGEMLGSAAEACAFIERGAVDVIMHDAPRIGGITPFLQVAEAARRRGIVM 307 Query: 326 APHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQAR 385 APHF ME+H+HL+AAY W+EHFEWL PLF E+LE+RDG M + R GLG +LSEQ Sbjct: 308 APHFVMELHIHLAAAYEHATWVEHFEWLEPLFRERLEIRDGCMQVPTRAGLGLSLSEQVA 367 Query: 386 RWTQLTCEFGKRP 398 WT + FG +P Sbjct: 368 GWTLASETFGTKP 380 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: 540 Number of extensions: 12 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: 380 Length adjustment: 30 Effective length of query: 368 Effective length of database: 350 Effective search space: 128800 Effective search space used: 128800 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 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