Align L-arabinose 1-dehydrogenase (NAD(P)(+)); D-galactose 1-dehydrogenase; EC 1.1.1.376; EC 1.1.1.120; EC 1.1.1.48 (characterized)
to candidate Pf6N2E2_1441 Uncharacterized oxidoreductase ydgJ (EC 1.-.-.-)
Query= SwissProt::Q53TZ2 (309 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1441 Length = 308 Score = 315 bits (806), Expect = 1e-90 Identities = 156/303 (51%), Positives = 201/303 (66%) Query: 5 VSLGVVGIGKIARDQHLPAIDAEPGFKLTACASRHAEVTGVRNYRDLRALLAAERELDAV 64 + LG+VG GKIA+DQH+PAI A P F+L A A++ GV N+R L LL ++DA+ Sbjct: 4 IRLGLVGYGKIAQDQHVPAIHANPAFQLVAVATQGQPCAGVENFRSLGELLENGPQVDAI 63 Query: 65 SLCAPPQVRYAQARAALEAGKHVMLEKPPGATLGEVAVLEALARERGLTLFATWHSRCAS 124 + C PPQ R+A + AL AGKHV++EKPP ATLGE L RE+G++ WHSR A Sbjct: 64 AFCTPPQGRFALVQQALAAGKHVLVEKPPCATLGEAMALVEQVREQGVSGLFAWHSRYAP 123 Query: 125 AVEPAREWLATRAIRAVQVRWKEDVRRWHPGQQWIWEPGGLGVFDPGINALSIVTRILPR 184 + AR+WLA+R + +VQ+ WKEDVR+WHPGQ WIW+PGGLGVFDPGINALSI T +L Sbjct: 124 GIAAARDWLASRTLHSVQIDWKEDVRKWHPGQAWIWQPGGLGVFDPGINALSIATHLLAL 183 Query: 185 ELVLREATLIVPSDVQTPIAAELDCADTDGVPVRAEFDWRHGPVEQWEIAVDTADGVLAI 244 L + A L VP + Q+PIAA + AD + +RAEFD+ HG E W I + A+GVL + Sbjct: 184 PLFVEAAELRVPDNCQSPIAASIKMADARHLDIRAEFDFDHGHDELWSIEIRCAEGVLRL 243 Query: 245 SRGGAQLSIAGEPVELGPEREYPALYAHFHALIARGESDVDVRPLRLVADAFLFGRRVQT 304 GGA LSI G + E EY A+Y HF LI SD+D++PLRLVAD+F G R Sbjct: 244 DNGGALLSIDGVRQAVSEEGEYAAVYRHFQQLINDKASDMDLQPLRLVADSFFVGSRTAV 303 Query: 305 DAF 307 + F Sbjct: 304 EPF 306 Lambda K H 0.321 0.136 0.421 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: 334 Number of extensions: 10 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: 309 Length of database: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 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: 48 (23.1 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