Align L-fuconate dehydratase; EC 4.2.1.68 (characterized, see rationale)
to candidate Echvi_2941 Echvi_2941 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= uniprot:D8J108 (425 letters) >FitnessBrowser__Cola:Echvi_2941 Length = 448 Score = 562 bits (1449), Expect = e-165 Identities = 264/421 (62%), Positives = 328/421 (77%) Query: 3 KITALRVLDVRFPTSQSLDGSDAMNPDPDYSAAYVILDTDNAALKGHGLTFTIGRGNEIC 62 KIT +V D+RFPTS+ GSDAMNPDPDYSAAY+IL T+ L+GHGLTFTIGRGNEIC Sbjct: 15 KITDYQVKDIRFPTSREKHGSDAMNPDPDYSAAYIILKTNQPDLEGHGLTFTIGRGNEIC 74 Query: 63 CAAIRAMEHLVVGLELEWIAADMGRFWRHVTSDSQLRWIGPDKGAIHLATGAVVNAAWDL 122 CAA+ A+ H V+G +L + ADMG FWR V SDSQ+RW+GP+KG +HLATGA+VNA WDL Sbjct: 75 CAALEAIAHHVIGKDLAALTADMGAFWRTVNSDSQIRWLGPEKGVVHLATGALVNAVWDL 134 Query: 123 WAKAEGKPVWKLVADMSPEELVRTIDFRYITDCITPDEALALLREKEAGKAERLRVLEQE 182 +AK E KP+WKL+ +M+PE+L+ IDF YITD +T +EAL +L+E E GK ER+R LE+ Sbjct: 135 YAKVEQKPLWKLLGEMTPEQLLSCIDFSYITDVLTKEEALDILKESEKGKKERIRYLEEN 194 Query: 183 GYPCYTTSAGWLGYEDAKLRRLCQEAIDQGFNHVKLKVGRDLADDKRRVTIAREVLGPER 242 GYP YTTSAGWLGY D K+RRLC+EA +G+ H+K+KVG +L DD RR I RE +G + Sbjct: 195 GYPGYTTSAGWLGYTDEKIRRLCREAKQEGWKHIKMKVGANLQDDIRRAGIIREEIGEDM 254 Query: 243 KLMIDANQVWEVHQAIDWVNQLAFAQPWFIEEPTSPDDVEGHRKIREGIGAVKVATGEMC 302 LM+DANQ WEV +AI+ + +LA P +IEEPTSPDD+ GH+ I + + + VATGE C Sbjct: 255 YLMMDANQRWEVAEAIENMKELAKFNPLWIEEPTSPDDILGHKAIADAVQPILVATGEHC 314 Query: 303 QNRVLFKQFIMRDAIDVVQIDSCRLGGVNEILAVMLMAAKYGKVVCPHAGGVGLCEYVQH 362 QNRV+FKQ + A+ + QIDSCR+GGVNE LA+ML+A K+ VCPHAGGVGLCEYVQH Sbjct: 315 QNRVIFKQLMQAGALQICQIDSCRVGGVNENLAIMLIAKKFDIPVCPHAGGVGLCEYVQH 374 Query: 363 LSMIDYLCISGSKEGRVTEYVDHLHEHFVDPCVVKNAAYMPPSRPGFSIEMKPQSLEQYR 422 LSM+DY+ ISGS EGRV EYVDHLHEHF+DP V+K Y P PG+SI+MK SLE+Y Sbjct: 375 LSMVDYISISGSMEGRVIEYVDHLHEHFIDPVVIKKGRYQVPKLPGYSIQMKAASLEEYD 434 Query: 423 F 423 F Sbjct: 435 F 435 Lambda K H 0.322 0.137 0.429 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: 637 Number of extensions: 21 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: 425 Length of database: 448 Length adjustment: 32 Effective length of query: 393 Effective length of database: 416 Effective search space: 163488 Effective search space used: 163488 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 (21.9 bits) S2: 51 (24.3 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