Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate 3607557 Dshi_0969 Mannitol dehydrogenase domain (RefSeq)
Query= curated2:P39160 (486 letters) >FitnessBrowser__Dino:3607557 Length = 499 Score = 297 bits (760), Expect = 6e-85 Identities = 187/480 (38%), Positives = 261/480 (54%), Gaps = 12/480 (2%) Query: 9 LPVARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDS-DWGICEVNLMPGNDRV 67 L + RP +D SRL IVH+G G FHRAHQA Y H L+++ + DW I + P D Sbjct: 15 LAIERPRYDRSRLTPGIVHIGVGNFHRAHQAWYLHRLMQAGQALDWAIIGAGVRP-YDAA 73 Query: 68 LIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTV 127 + + L Q L T+ E ++ +++GSM + L P +DG ++ MA P IV++TV Sbjct: 74 MRDKLLAQDCLTTLIELAPDNVSAEVVGSMIDYL-PIVDGNGPLIAQMADPAIRIVAMTV 132 Query: 128 TEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDN 187 TE GY D + D ++P + HD P P++A G IV ALR RR G FT +SCDN Sbjct: 133 TESGYYIDPVTKGFDASHPDLVHDAAQPDRPRTAFGAIVAALRARRAAGHGPFTCLSCDN 192 Query: 188 VRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVY 247 ++ NG + + V+ LA+ DP LA WI+ + +FP +MVD I PA P+ L +A Q G+ Sbjct: 193 LQGNGDILRQTVVSLARLTDPALADWIDTHASFPNSMVDCIAPATGPKELA-LAAQFGIR 251 Query: 248 DPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGY 307 D + E FRQWVIED F GRP+WD VGA F DV +E MK+R+LN H LA G Sbjct: 252 DVAVVTHEAFRQWVIEDEFCAGRPNWDAVGATFSDDVHAYETMKIRILNAGHQVLANAGE 311 Query: 308 LGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRT 367 G ETI+ + +P + +E APT++ G +Y L+ RF+NP + T Sbjct: 312 NLGIETISGCMAHPGIAAFFGKVQREEIAPTVAPVPGKTPASYVNLIETRFANPRIVDTT 371 Query: 368 WQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPML 427 ++A DGS + P +L VR L G S LAL A W R GV E G I DP+ Sbjct: 372 RRVAFDGSARHPGFVLPIVRDQLAAGRSVEGLALVEALWARMCAGVREDGTEIAPNDPL- 430 Query: 428 AEFQKINAQYQGADRVKAL-LGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486 + ++ + A AL LG +G++ DL Q+ F A A + ++G C AAL Sbjct: 431 --WDRLAPVARAARTDPALWLGQTGLYG-DLKQSEPFADAFCAWLVLIWDKG---CEAAL 484 Lambda K H 0.320 0.135 0.408 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: 655 Number of extensions: 32 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: 486 Length of database: 499 Length adjustment: 34 Effective length of query: 452 Effective length of database: 465 Effective search space: 210180 Effective search space used: 210180 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: 52 (24.6 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