Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate CA265_RS08565 CA265_RS08565 oxidoreductase
Query= reanno::Smeli:SM_b21109 (360 letters) >FitnessBrowser__Pedo557:CA265_RS08565 Length = 360 Score = 292 bits (748), Expect = 8e-84 Identities = 155/336 (46%), Positives = 208/336 (61%), Gaps = 6/336 (1%) Query: 17 PVAPRPIVIFGAGSIVGDAHLPAYRNAGFPVAGIFDPDAGKAAALARASDVM-AFTSEEE 75 P +PI+I GAG IVGDAHLPAY+ AGF V GI + +A LA ++ + S E Sbjct: 12 PETKQPIIIIGAGGIVGDAHLPAYKIAGFEVHGIVNRTKERAQKLADTFGILNVYNSVAE 71 Query: 76 A--LSAENAIFDLATPPAAHASILSKLPKGSFALIQKPLGSDLAAATGILEICRERNIRA 133 A L+ NA++DL P + L +LP GS LIQKP+G D A ILE+CR +N++A Sbjct: 72 AVKLAPANAVYDLTIMPEQYIETLKQLPDGSAVLIQKPMGDDFTQAKEILELCRAKNLKA 131 Query: 134 AANFQLRFAPMMLALKDAIATGYLGEVVDFDAWLALATPWGLWPFLKGLPRIEIAMHSIH 193 A NFQLRFAP + A K I G +GE+ D + + + TPW ++P + PR+EI HSIH Sbjct: 132 AINFQLRFAPFVSAAKYLIDKGLIGELYDMEVRVTVKTPWEIFPHVIIHPRLEIQYHSIH 191 Query: 194 YLDLVRSLLGDPRGVHAKTIGHPNHDVAQTRTAAILDYGDAVRCVLSVNHDHDFGRRFQA 253 Y+DL+RS LG+P + AKT+ HP +++ +R+ + DYGD + V++ NHDHDFG Q Sbjct: 192 YVDLIRSFLGNPESILAKTLKHPAKNLSSSRSTILFDYGDTMHAVINTNHDHDFGPNHQE 251 Query: 254 CEFRICGTRGAAYVKLGVNLDYPRGEPDEL---WIRPAGGADWIQVPLEGSWFPDAFANR 310 + GT+GA K+G+ +DYP G PD + A W V LEGSWFP+AF Sbjct: 252 SYIKWEGTKGAIVAKIGLLMDYPHGVPDVFEYCIVEDGKQAAWQTVKLEGSWFPEAFIGT 311 Query: 311 MANLQRHAGGEDDELIGSVEDAWRTMALVEAAYQSS 346 MANL R+ G L SVED +TMA+VE+AYQSS Sbjct: 312 MANLMRYNEGSAAILHTSVEDVIQTMAVVESAYQSS 347 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: 346 Number of extensions: 12 Number of successful extensions: 3 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: 360 Length adjustment: 29 Effective length of query: 331 Effective length of database: 331 Effective search space: 109561 Effective search space used: 109561 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