Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate CCNA_01885 CCNA_01885 short chain dehydrogenase
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__Caulo:CCNA_01885 Length = 258 Score = 122 bits (307), Expect = 5e-33 Identities = 80/242 (33%), Positives = 119/242 (49%), Gaps = 4/242 (1%) Query: 9 LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRCD 68 L+G+ +TG G+G A A +GA V LD+ ++A E+ + V CD Sbjct: 11 LEGRVAAVTGASRGLGRATAALLAAEGAMVALLDLKAHWAQAAADEIIAAGGKAVGLGCD 70 Query: 69 LMNLEAIKAVFAEIGDV----DVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQ 124 + + EA+ A + D DVLVNNA + LA + D ++V +++ Q Sbjct: 71 VSDREALTATLGAVNDAHGRFDVLVNNAMWNVYEPLAAIRPESLDRMVSVGFSGVIWGMQ 130 Query: 125 AVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCV 184 A AP M GGG+++N S+S LG+ + + Y KAG+ GMTRA A ELG +IRV V Sbjct: 131 AAAPLMAASGGGSIVNIASVSAQLGIPNGIAYCGVKAGVAGMTRAAAAELGAMNIRVNAV 190 Query: 185 VPGNVKTKRQEKWYTPEGEAQIVAAQCLKGRIVPENVAALVLFLASDDASLCTGHEYWID 244 P V T+ + + E A + L E++A V +LA DD+ TG +D Sbjct: 191 APSTVDTEGVRRVVSEERIAMRIGQTPLGRLGTTEDIAKAVRYLACDDSDFVTGQMLTVD 250 Query: 245 AG 246 G Sbjct: 251 GG 252 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: 144 Number of extensions: 4 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: 248 Length of database: 258 Length adjustment: 24 Effective length of query: 224 Effective length of database: 234 Effective search space: 52416 Effective search space used: 52416 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