Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ga0059261_1621 Ga0059261_1621 Predicted dehydrogenases and related proteins
Query= reanno::Smeli:SMc00588 (308 letters) >FitnessBrowser__Korea:Ga0059261_1621 Length = 307 Score = 335 bits (858), Expect = 1e-96 Identities = 165/303 (54%), Positives = 218/303 (71%), Gaps = 1/303 (0%) Query: 4 INIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGTVDGIDNFKSIEAMIDAVPAVEAV 63 I + +VG+GKI RDQHLPA+A + D+ L A ASRHG VDG++ SI +I A P ++A+ Sbjct: 4 IKLGLVGIGKIARDQHLPAIAASVDFELAATASRHGRVDGVEGHGSIVELIAARPEIDAL 63 Query: 64 SLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFASWHSRYAP 123 SLC PP+ R+E A A+AAGKHV LEKPP AT+SE LE A GVSL+A+WHSR A Sbjct: 64 SLCTPPEGRFEQAMAAIAAGKHVMLEKPPAATVSEARTLEQAAYAAGVSLYATWHSREAG 123 Query: 124 AVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALSIMTHILPR 183 V+AA+ +LA+ I VRI W ED+R WHP Q+WI AAGG GVFDPGINALSI T ILP+ Sbjct: 124 EVDAARDWLAARRIDAVRIRWMEDIRQWHPGQDWILAAGGFGVFDPGINALSIATRILPQ 183 Query: 184 PVFITSATLEFPENRDAPIAATIAFSDAEKLDVAAEFDWRQTGKQSWDIVAETDAGGMVL 243 P+ + +AT++ P NR PIAA++ F +V A+FD+ QTG+Q+W I ETDAG + L Sbjct: 184 PLTVLAATMDIPANRACPIAASVRFRTG-SAEVDAKFDFLQTGEQTWQIEVETDAGLLRL 242 Query: 244 SEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVADAFMLGRRKFV 303 +EGG +L G+ P++EYP LYR FAE+I++G+SDVDL P++ VADAF++ R+ V Sbjct: 243 TEGGGRLERPGQPSLSGPDREYPRLYRAFAELIRSGQSDVDLQPIQLVADAFLVAERRIV 302 Query: 304 EAF 306 + F Sbjct: 303 DPF 305 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: 300 Number of extensions: 15 Number of successful extensions: 2 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: 307 Length adjustment: 27 Effective length of query: 281 Effective length of database: 280 Effective search space: 78680 Effective search space used: 78680 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 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