Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate AZOBR_RS31255 AZOBR_RS31255 galactose 1-dehydrogenase
Query= reanno::Smeli:SMc00588 (308 letters) >FitnessBrowser__azobra:AZOBR_RS31255 Length = 325 Score = 301 bits (771), Expect = 1e-86 Identities = 155/315 (49%), Positives = 203/315 (64%), Gaps = 9/315 (2%) Query: 2 SPINIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGTVD------GIDNFKSIEAMID 55 +P+ + IVG GKI RDQH+PA+A +RL A S HG + + F+S M+ Sbjct: 10 APLTLGIVGFGKIARDQHVPAIAATGLFRLAAVVSPHGAIPEETGLGDVAVFRSQTEMLA 69 Query: 56 AVPAVEAVSLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFA 115 A+P ++AV++C PP R+ AL AGKHV +EKPP ATL+E+ L AE +LFA Sbjct: 70 ALPGLDAVAICTPPAVRHPLTVEALRAGKHVLIEKPPAATLTELRLLLDAAEGAKRTLFA 129 Query: 116 SWHSRYAPAVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALS 175 +WHSR+ AVE + LA A +RNV I WKEDVR WHP Q+WI+AAGG GVFDPGINALS Sbjct: 130 AWHSRFNAAVEETRRRLAGATVRNVAITWKEDVRRWHPGQDWIFAAGGFGVFDPGINALS 189 Query: 176 IMTHILPRPVFITSATLEFPENRDAPIAATIAFSDAEKL---DVAAEFDWRQTGKQSWDI 232 I+T ILP PV + A L P NRD PIAAT+ A V A FD+ Q G+Q+W I Sbjct: 190 ILTEILPAPVVVRDAELRVPANRDTPIAATLRMEGAAGSAVGTVTAAFDFLQEGEQTWAI 249 Query: 233 VAETDAGGMVLSEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVA 292 ETD+GG+ L+ GG +L++DG +V +P+ EY +YRRF +I DVD PL+ VA Sbjct: 250 AIETDSGGLDLTHGGTRLSVDGVLVLAKPDAEYQGIYRRFHHLIADAAGDVDARPLQLVA 309 Query: 293 DAFMLGRRKFVEAFH 307 DA ++GR + +AFH Sbjct: 310 DACLVGRWRTTDAFH 324 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: 342 Number of extensions: 6 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: 325 Length adjustment: 27 Effective length of query: 281 Effective length of database: 298 Effective search space: 83738 Effective search space used: 83738 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