Align xylitol 2-dehydrogenase (EC 1.1.1.9) (characterized)
to candidate 3607669 Dshi_1078 Alcohol dehydrogenase zinc-binding domain protein (RefSeq)
Query= reanno::BFirm:BPHYT_RS16050 (365 letters) >FitnessBrowser__Dino:3607669 Length = 345 Score = 135 bits (341), Expect = 1e-36 Identities = 106/341 (31%), Positives = 162/341 (47%), Gaps = 31/341 (9%) Query: 22 KDYRVEQVSKPRAGAHELVIRIAACGICASDCKCHSGAKMFWGGPSPWVKAPVIPGHEFF 81 +D +E V +P +V+++ ACG+C SD H W G P VK I GHE+ Sbjct: 11 EDLVLEDVPEPVCPEDGVVLKVLACGVCRSDW--HG-----WVGEHPRVKPGQIGGHEYC 63 Query: 82 GFVEEIGEGAADHFGVKMGDRVIAEQIVPCGKCRYCKSGQYWMCEVHNIFGFQREVADGG 141 G V E G AA K GDRV+A I+ CG C C++G C + GF V G Sbjct: 64 GEVIEAGPRAA----FKPGDRVVAPFILACGSCPSCQAGAQNTCPNQRLPGF---VEPGA 116 Query: 142 MAEYMRIPPTAIVHKIPDGISLEDAAIIEPLACAIHTV-----NRGEVQLDDVVVIAGAG 196 AEY+ +P + ++PD +S AA L C + T R VQ + V + G G Sbjct: 117 FAEYVAVPFDHNLSRLPDSLSPTVAA---GLGCRVTTAWHALTGRAAVQGAEWVAVHGTG 173 Query: 197 PLGLMMTQIAHLKTPKKLVVIDLVEERLALAREYGADVTINPKQDDALAIIHSLTDGYGC 256 +GL +A+ +++ +D+V+E+L A ++GA+VT+N ++ D A I +T G G Sbjct: 174 GIGLSSVILANA-LGARVIAVDVVDEKLTHAAQHGAEVTLNAREGDVAARIKQITGG-GA 231 Query: 257 DVYIETTGAPIGVNQGMDLIRKLGRFVEFSVFGADTT---LDWSVI--GDRKELDVRGAH 311 V IE G P VN ++ +R LGR V+ + T ++ S I G+ RG Sbjct: 232 HVAIEALGIPETVNASLECLRPLGRHVQVGLPTGHTARMEINMSAIYQGNLAVYGTRG-- 289 Query: 312 LGPYCYPIAIDLLARGLVTSKGIVTHGFSLEEWDEAIKIAN 352 + + YP + L+ G V ++ L ++ N Sbjct: 290 MPSWRYPSLLSLIETGRVDMSPLIAREIGLSGTSAELRAFN 330 Lambda K H 0.322 0.140 0.435 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: 333 Number of extensions: 27 Number of successful extensions: 6 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: 365 Length of database: 345 Length adjustment: 29 Effective length of query: 336 Effective length of database: 316 Effective search space: 106176 Effective search space used: 106176 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 (21.9 bits) S2: 49 (23.5 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