Align L-fuconate dehydratase; FucD; EC 4.2.1.68 (characterized)
to candidate RR42_RS22655 RR42_RS22655 mandelate racemase
Query= SwissProt::Q8P3K2 (441 letters) >FitnessBrowser__Cup4G11:RR42_RS22655 Length = 385 Score = 114 bits (284), Expect = 7e-30 Identities = 110/391 (28%), Positives = 158/391 (40%), Gaps = 70/391 (17%) Query: 28 PDPDYSAAYVVLRTDGAEDLAGYGLVFTIGRGNDVQTAAVAALAEHVVGLSVDKVIADLG 87 P + + + + T+G + G G + G Q A +A ++G + + Sbjct: 43 PMTEIAILFAEIETEGGDK--GLGFSYAKRAGGPGQFAHAREIAPALIGEDANDIA---- 96 Query: 88 AFARRLTNDSQLRWLGPE---KGVMHMAIGAVINAAWDLAARAANKPLWRFIAELTPEQL 144 RL N +L W G G+ AIGA A WDL AR AN PL + Sbjct: 97 ----RLWN--KLIWAGASVGRSGLATQAIGAFDVALWDLKARRANLPLAKL--------- 141 Query: 145 VDTIDFRYLSDALTRDEALAILRDAQPQRAARTATLIEQGYPAYTTSPGWLGYSDEKLVR 204 L RD+ Y TS G+L ++L+ Sbjct: 142 ------------------LGAHRDS---------------VKCYNTSGGFLHTPLDQLLM 168 Query: 205 LAKEAVADGFRTIKLKVGA-NVQDDIRRCRLARAAIGPDIAMAVDANQRWDVGPAIDWMR 263 A ++V G IKLKVG + DI+R R +G A+ VDANQ+WD A R Sbjct: 169 NASKSVEKGIGGIKLKVGQPDCAADIQRVETVRKHLGDGFALMVDANQQWDRPTAQRMCR 228 Query: 264 QLAEFDIAWIEEPTSPDDVLGHAAIRQGITPVPVSTGEHTQNRVVFKQLLQAGAVDLIQI 323 L +F++ WIEEP D GHAA+ P++TGE + L++ A D + Sbjct: 229 ILEQFNLIWIEEPLDAYDSEGHAALAAQF-DTPIATGEMLTSVAEHWDLIRHRAADYLMP 287 Query: 324 DAARVGGVNENLAILLLAAKFGVRVFPHAGGVGLCELVQHLAMADFVAITGKMEDRAIEF 383 D RVGG+ L + LA G+ + PH EL HLA A + +E Sbjct: 288 DGPRVGGITPFLTVATLADHAGLMIAPHFA----MELHVHLAAA-------YPREPWVEH 336 Query: 384 VDHLHQHFLDPVRIQHGRYLAPEVPGFSAEM 414 + L F + + I+ GR L P PG + Sbjct: 337 FEWLEPLFNERLEIKDGRMLVPTRPGIGVSL 367 Lambda K H 0.321 0.136 0.409 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: 433 Number of extensions: 19 Number of successful extensions: 5 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: 441 Length of database: 385 Length adjustment: 31 Effective length of query: 410 Effective length of database: 354 Effective search space: 145140 Effective search space used: 145140 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: 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