Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_059153651.1 V474_RS23770 Gfo/Idh/MocA family oxidoreductase
Query= reanno::Smeli:SMc00588 (308 letters) >NCBI__GCF_001046635.1:WP_059153651.1 Length = 308 Score = 369 bits (948), Expect = e-107 Identities = 185/309 (59%), Positives = 223/309 (72%), Gaps = 2/309 (0%) Query: 1 MSPINIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGT-VDGIDNFKSIEAMIDAVPA 59 M PI IA+VGVGKI RDQHLPA+A N + L A S H V+G+ + KS++ +I+ PA Sbjct: 1 MDPIRIAVVGVGKIARDQHLPAIAGNKAFSLAATVSPHDAGVEGVSHHKSLDELIENGPA 60 Query: 60 VEAVSLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFASWHS 119 V+AV+LC PPQ RY+ A AL G HVFLEKPPGATLSE L + AE+ G +LFA+WHS Sbjct: 61 VDAVALCTPPQVRYDLAVQALNKGMHVFLEKPPGATLSECVALSSRAEKVGTTLFAAWHS 120 Query: 120 RYAPAVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALSIMTH 179 R+A V A+ +LA I +V+I+W+EDVR WHP Q WIW GGLGVFDPGINALSI+TH Sbjct: 121 RFAAGVAPARAWLAERRIESVKIVWREDVRVWHPGQAWIWEPGGLGVFDPGINALSILTH 180 Query: 180 ILPRPVFITSATLEFPENRDAPIAATIAFSDAEKLDVAAEFDWRQTGKQSWDIVAETDAG 239 ILPRPVF+ +ATLE P NR APIAA I F D + + DWRQTG QSWDIV ETDAG Sbjct: 181 ILPRPVFLKTATLEIPANRAAPIAADIQFRDTAGAPIHMDLDWRQTGPQSWDIVVETDAG 240 Query: 240 GMVLSEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVADAFMLGR 299 + LS GGA L + H E + EYP LY RFA +I+ GRSDVD+APLR VADAF+ G Sbjct: 241 TLKLSNGGAVLTLPTGAEHSE-DLEYPGLYARFANLIRGGRSDVDIAPLRLVADAFLRGN 299 Query: 300 RKFVEAFHD 308 R+ V+AFHD Sbjct: 300 RQTVDAFHD 308 Lambda K H 0.320 0.134 0.405 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: 338 Number of extensions: 16 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: 308 Length of database: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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 (21.8 bits) S2: 48 (23.1 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