Align L-fuconate dehydratase; FucD; EC 4.2.1.68 (characterized)
to candidate WP_009153233.1 SACMADRAFT_RS07685 fuconate dehydratase
Query= SwissProt::Q8P3K2 (441 letters) >NCBI__GCF_000244955.1:WP_009153233.1 Length = 425 Score = 596 bits (1536), Expect = e-175 Identities = 283/424 (66%), Positives = 341/424 (80%) Query: 1 MRTIIALETHDVRFPTSRELDGSDAMNPDPDYSAAYVVLRTDGAEDLAGYGLVFTIGRGN 60 M IIAL+THD+RFPTS+ LDGSDAMNPDPDYSA+YV LRTD A+ L G+G VFTIGRGN Sbjct: 1 MARIIALQTHDIRFPTSKTLDGSDAMNPDPDYSASYVRLRTDAADGLEGHGFVFTIGRGN 60 Query: 61 DVQTAAVAALAEHVVGLSVDKVIADLGAFARRLTNDSQLRWLGPEKGVMHMAIGAVINAA 120 DVQ AA+ AL H+VG V + + DLG R L +DSQLRWLGPEKG+MHMAIGA +NA Sbjct: 61 DVQVAALRALEGHLVGRDVAETLDDLGGVWRELVHDSQLRWLGPEKGIMHMAIGAAVNAL 120 Query: 121 WDLAARAANKPLWRFIAELTPEQLVDTIDFRYLSDALTRDEALAILRDAQPQRAARTATL 180 WDL A+ A PLWR ++ L+PE++VD IDFRYL+DALTR++ALA+LR A+P RA R L Sbjct: 121 WDLKAKRAGVPLWRLLSSLSPEEIVDLIDFRYLTDALTREDALALLRSAEPGRAERETRL 180 Query: 181 IEQGYPAYTTSPGWLGYSDEKLVRLAKEAVADGFRTIKLKVGANVQDDIRRCRLARAAIG 240 + QGYPAYTT+PGWLGY D+KL +L +EA+ GF IKLKVGA++ DD+RR R+AR G Sbjct: 181 LAQGYPAYTTTPGWLGYDDDKLAKLCREAIEQGFTHIKLKVGADLDDDLRRLRIARDICG 240 Query: 241 PDIAMAVDANQRWDVGPAIDWMRQLAEFDIAWIEEPTSPDDVLGHAAIRQGITPVPVSTG 300 PDI +AVDANQRWDV AI W + LA FDIAW+EEPTSPDDVL HAAI + + PVPV+TG Sbjct: 241 PDIKIAVDANQRWDVAEAIRWTKALARFDIAWVEEPTSPDDVLAHAAIAKAVAPVPVATG 300 Query: 301 EHTQNRVVFKQLLQAGAVDLIQIDAARVGGVNENLAILLLAAKFGVRVFPHAGGVGLCEL 360 EH NRVVFKQLLQ+G + ++Q+DA RV GVNEN+AILLLAAKFGV V PHAGGVGLCE Sbjct: 301 EHIANRVVFKQLLQSGGLSVLQLDATRVAGVNENIAILLLAAKFGVPVCPHAGGVGLCEA 360 Query: 361 VQHLAMADFVAITGKMEDRAIEFVDHLHQHFLDPVRIQHGRYLAPEVPGFSAEMHPASIA 420 VQHLAM DFVA++G ++ R IEFVDHLH+HF+ PV ++ GRYLAP PG EM+P SIA Sbjct: 361 VQHLAMFDFVAVSGSLDGRVIEFVDHLHEHFVTPVDVRGGRYLAPAAPGAGTEMYPTSIA 420 Query: 421 EFSY 424 E+++ Sbjct: 421 EYTH 424 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: 674 Number of extensions: 22 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: 441 Length of database: 425 Length adjustment: 32 Effective length of query: 409 Effective length of database: 393 Effective search space: 160737 Effective search space used: 160737 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 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