Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate SMc00880 SMc00880 oxidoreductase
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__Smeli:SMc00880 Length = 256 Score = 218 bits (555), Expect = 9e-62 Identities = 118/252 (46%), Positives = 166/252 (65%), Gaps = 6/252 (2%) Query: 1 MSSAIYPSLKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRAL-EAELAGSP 59 + S+ +P L+ + V++TGGGSGIGA L FARQGA V F+DIA E S AL E A + Sbjct: 3 LPSSQFPDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTG 62 Query: 60 IPPVYKRCDLMNLEAIKAV----FAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVN 115 P + + DL N+EA++A A++G V VLVNNA DDR L VT WDE ++VN Sbjct: 63 QAPHFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVN 122 Query: 116 LRHMLFCTQAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELG 175 LRH+ F QAVAP M+++GGG+++NF SI++ L + ++ Y TAKAGI G+T++LA +LG Sbjct: 123 LRHLFFMCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLG 182 Query: 176 PDDIRVTCVVPGNVKTKRQEK-WYTPEGEAQIVAAQCLKGRIVPENVAALVLFLASDDAS 234 PD+IRV ++PG + T+RQ + W T E A++ QCLK +V +++ LFLASD ++ Sbjct: 183 PDNIRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSA 242 Query: 235 LCTGHEYWIDAG 246 T ID G Sbjct: 243 AMTAQAMIIDGG 254 Lambda K H 0.319 0.137 0.416 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: 170 Number of extensions: 4 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: 248 Length of database: 256 Length adjustment: 24 Effective length of query: 224 Effective length of database: 232 Effective search space: 51968 Effective search space used: 51968 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 (21.7 bits) S2: 46 (22.3 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