Align L-fuconate dehydratase; FucD; EC 4.2.1.68 (characterized)
to candidate CA265_RS12250 CA265_RS12250 enolase
Query= SwissProt::Q8P3K2 (441 letters) >FitnessBrowser__Pedo557:CA265_RS12250 Length = 388 Score = 103 bits (257), Expect = 9e-27 Identities = 70/227 (30%), Positives = 116/227 (51%), Gaps = 9/227 (3%) Query: 186 PAYTTSPGWLGYSDEKLVRLAKEAVADGFRTIKLKVGA---NVQDDIRRCRLARAAIGPD 242 PAY S GW ++ + V GF+ +K++VG VQ I R + ARAA+GPD Sbjct: 151 PAYA-SGGWA--DEQNIGEQLMGYVNKGFKGVKMRVGVMDDTVQKSINRVKAARAALGPD 207 Query: 243 IAMAVDANQRWDVGPAIDWMRQLAEFDIAWIEEPTSPDDVLGHAAIRQGITPVPVSTGEH 302 I + VDA+ + V A + R + + ++ W EEP SPD+ G A +R T +P++ GE Sbjct: 208 IKLMVDAHGTFSVPEAKQFCRGVEDCNVYWFEEPISPDNRKGTAEVR-AATDIPIAAGES 266 Query: 303 TQNRVVFKQLLQAGAVDLIQIDAARVGGVNENLAILLLAAKFGVRVFPHAGGVGLCELVQ 362 LLQ A+D++Q DAA +GG++E + + LA+ V + PH G + Sbjct: 267 EFTSFDIHDLLQIRAIDVVQPDAAIIGGISEAMRVSHLASVHQVELAPHCWGSAF-SFMA 325 Query: 363 HLAMADFVAITGKMEDRAIEFVDHLHQHFLDPVRIQHGRYLAPEVPG 409 L +A F + + + + ++ ++ + + + +G AP PG Sbjct: 326 GLTVA-FASASATIIEFSLGGNPMMYDLVNEQIAVVNGEISAPTAPG 371 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: 368 Number of extensions: 18 Number of successful extensions: 2 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: 388 Length adjustment: 31 Effective length of query: 410 Effective length of database: 357 Effective search space: 146370 Effective search space used: 146370 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