Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_059153417.1 V474_RS22305 Gfo/Idh/MocA family oxidoreductase
Query= reanno::Smeli:SMc00588 (308 letters) >NCBI__GCF_001046635.1:WP_059153417.1 Length = 306 Score = 318 bits (814), Expect = 1e-91 Identities = 160/306 (52%), Positives = 205/306 (66%), Gaps = 2/306 (0%) Query: 1 MSPINIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGTVDGIDNFKSIEAMIDAVPAV 60 M P+ + +VG+GKI RDQH PA+A N L+A ASRHG +DG+D + I M+ A A+ Sbjct: 1 MEPVRLGLVGIGKIARDQHFPAIAGNDRLNLVATASRHGRLDGVDGYHDIAEMVSAT-AL 59 Query: 61 EAVSLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFASWHSR 120 +AVSLC PP RYE A A+ AG HV LEKPP TLS V L A A + GVSLFA+WHSR Sbjct: 60 DAVSLCTPPDGRYEQALIAIEAGVHVMLEKPPAVTLSHVEALVAAARKAGVSLFATWHSR 119 Query: 121 YAPAVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALSIMTHI 180 A V A+ +LA I VRI WKED+R WHP QEWI GG GVFDPGINALSI T I Sbjct: 120 EAAGVAPARAWLADKRIDAVRIDWKEDIRRWHPGQEWILGPGGFGVFDPGINALSIATEI 179 Query: 181 LPRPVFITSATLEFPENRDAPIAATIAFSDAEKLDVAAEFDWRQTGKQSWDIVAETDAGG 240 LPR +F+ SA+++ PE R +P+AA+I +V AEFD+ QTG Q+W I +TDAG Sbjct: 180 LPRELFVESASMDVPEGRASPLAASILMR-CGSAEVRAEFDFLQTGPQTWSIEVDTDAGT 238 Query: 241 MVLSEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVADAFMLGRR 300 + L++GG+ + + G+ P++EY LY RFA+++ DVDL PLR VADAF++ R Sbjct: 239 LRLTQGGSVIQLPGEAEQTAPDEEYARLYDRFADLVAERAIDVDLRPLRLVADAFLIADR 298 Query: 301 KFVEAF 306 + EAF Sbjct: 299 RVTEAF 304 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: 308 Number of extensions: 19 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: 306 Length adjustment: 27 Effective length of query: 281 Effective length of database: 279 Effective search space: 78399 Effective search space used: 78399 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