Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate Echvi_1691 Echvi_1691 Predicted dehydrogenases and related proteins
Query= reanno::Smeli:SM_b21109 (360 letters) >FitnessBrowser__Cola:Echvi_1691 Length = 345 Score = 258 bits (659), Expect = 2e-73 Identities = 144/331 (43%), Positives = 201/331 (60%), Gaps = 7/331 (2%) Query: 23 IVIFGAGSIVGDAHLPAYRNAGFPVAGIFDPDAGKAAALARASDV-MAFTSEEE--ALSA 79 I+ GAG IV DAHLPAY+ AGF V G++D D A +LA A + F S +E A + Sbjct: 3 ILQIGAGGIVKDAHLPAYKIAGFEVEGVYDLDEENAISLATAFGIPRVFGSLDELTAHAT 62 Query: 80 ENAIFDLATPPAAHASILSKLPKGSFALIQKPLGSDLAAATGILEICRERNIRAAANFQL 139 E+ +FD+A P +A +L KLP G+ LIQKP+G DL AA IL +CR++ ++A NFQ+ Sbjct: 63 EDTVFDVAVPGSAVLEVLEKLPDGAVVLIQKPMGEDLEAAKAILALCRKKKLKAGVNFQM 122 Query: 140 RFAPMMLALKDAIATGYLGEVVDFDAWLALATPWGLWPFLKGLPRIEIAMHSIHYLDLVR 199 R+AP + ++ I G++GEV D + + + TPW LW FL R+EI HSIHY+DLVR Sbjct: 123 RYAPYIQKAREIIQAGHIGEVCDIEVKINVYTPWHLWDFLFTASRVEILYHSIHYVDLVR 182 Query: 200 SLLGDPRGVHAKTIGHPN-HDVAQTRTAAILDYGDAVRCVLSVNHDHDFGRRFQACEFRI 258 S G+P V+AKTI HP +A +T I+DYG + NH H FG + Q +I Sbjct: 183 SFFGNPEKVYAKTIKHPKMTQLASVKTNIIMDYGALKGANILTNHAHAFGLKHQQSYVKI 242 Query: 259 CGTRGAAYVKLGVNLDYPRGEPDEL-WIRPAGG--ADWIQVPLEGSWFPDAFANRMANLQ 315 GT+GA +++G+ +YP+G D+ +I A G A+W +V + G+WFP AF M ++ Sbjct: 243 EGTKGAIMIEMGLLKNYPQGTADKFEYIIAAEGKEAEWKEVEIAGTWFPHAFIGSMTEMK 302 Query: 316 RHAGGEDDELIGSVEDAWRTMALVEAAYQSS 346 + SVED TMA VEAA+QSS Sbjct: 303 KALENPAYLPDNSVEDCIYTMACVEAAHQSS 333 Lambda K H 0.321 0.137 0.430 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: 317 Number of extensions: 16 Number of successful extensions: 5 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: 360 Length of database: 345 Length adjustment: 29 Effective length of query: 331 Effective length of database: 316 Effective search space: 104596 Effective search space used: 104596 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: 49 (23.5 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