Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate Echvi_2941 Echvi_2941 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Cola:Echvi_2941 Length = 448 Score = 105 bits (263), Expect = 2e-27 Identities = 97/347 (27%), Positives = 152/347 (43%), Gaps = 67/347 (19%) Query: 44 VSDAKVLTGRQK---------PLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAK 94 V D + T R+K P A II + D EG G +++ G + A + Sbjct: 21 VKDIRFPTSREKHGSDAMNPDPDYSAAYIILKTNQPD-LEGHGLTFTIGRGNEICCAALE 79 Query: 95 EIADNLLGED----PNDIDKIY------TKLLWAGASVGRSGMAVQAISPIDIALWDMKA 144 IA +++G+D D+ + +++ W G G +A A+ A+WD+ A Sbjct: 80 AIAHHVIGKDLAALTADMGAFWRTVNSDSQIRWLGPEKGVVHLATGALVN---AVWDLYA 136 Query: 145 KRAGLPLAKLLGA------------------------------------------HRDSV 162 K PL KLLG + Sbjct: 137 KVEQKPLWKLLGEMTPEQLLSCIDFSYITDVLTKEEALDILKESEKGKKERIRYLEENGY 196 Query: 163 QCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFP 222 Y TS G+L +++ + +++ G IK+KVG N +DIRR +RE +G++ Sbjct: 197 PGYTTSAGWLGYTDEKIRRLCREAKQEGWKHIKMKVGA-NLQDDIRRAGIIREEIGEDMY 255 Query: 223 LMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALD-TPIATGEMLT 281 LM+DANQ+W+ AI +++ +FN +WIEEP DI GH +A A+ +ATGE Sbjct: 256 LMMDANQRWEVAEAIENMKELAKFNPLWIEEPTSPDDILGHKAIADAVQPILVATGEHCQ 315 Query: 282 SFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPH 328 + +QL+ A Q D+ RVGG++ L IM +A K + PH Sbjct: 316 NRVIFKQLMQAGALQICQIDSCRVGGVNENLAIMLIAKKFDIPVCPH 362 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: 424 Number of extensions: 23 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: 398 Length of database: 448 Length adjustment: 32 Effective length of query: 366 Effective length of database: 416 Effective search space: 152256 Effective search space used: 152256 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