Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate BWI76_RS19345 BWI76_RS19345 D-arabinitol 4-dehydrogenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__Koxy:BWI76_RS19345 Length = 455 Score = 192 bits (489), Expect = 2e-53 Identities = 138/443 (31%), Positives = 219/443 (49%), Gaps = 14/443 (3%) Query: 26 VHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLKKQ---QLLYTVA 82 +H+G G+FHRAHQA Y H L+ S D W I N+ ++V ++ L Q +L TV+ Sbjct: 8 LHIGLGSFHRAHQAWYLHRLIASGDKRWHIAAGNIRNDAEQV-VQALAAQGGRYVLETVS 66 Query: 83 EKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAASGQLD 142 +G E + I S+++ L P G + ++N A PQT +++ TVTE GY + QL+ Sbjct: 67 PEGER--EYEEITSIQKLL-PWQAGLQPLINEGANPQTKVIAFTVTEGGYYLNTRH-QLE 122 Query: 143 LNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGHVAKVAVLGL 202 +NP ++ DL K+ G + L R T+++CDNVR NG ++ Sbjct: 123 TSNPDLQADLAGEC--KTIYGTLARILEKRMADNAGPLTLLNCDNVRHNGERFHDGMVEF 180 Query: 203 AQARDPQLAA-WIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACEPFRQWV 261 Q Q W+ N T P TMVDRI P + I Q G+ D + E F QWV Sbjct: 181 LQLTGKQAVIDWMAVNTTCPNTMVDRITPRPAADLPARIKAQTGIDDKAPVMGETFIQWV 240 Query: 262 IEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIADTVTNP 321 +E+NF + RP + VG + VA V+P+E K+R+LN SHS +A+ G L G + I ++ Sbjct: 241 VENNFRDERPKLEAVGVEMVASVIPYEEAKIRILNASHSCIAWAGTLIGQQYIHESTLTD 300 Query: 322 AYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGSQKLPQR 381 A + ++ P L G DL Y ++++RF+NP ++ ++A DG K+P Sbjct: 301 FIYAIADRYVTEDVIPCLG-DNGIDLPTYRDVVLKRFTNPYIQDTNQRVAADGFSKIPAM 359 Query: 382 LLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQKINAQYQGAD 441 + ++ Q G A+ A + + + + D +L + Q ++ ++ D Sbjct: 360 IAPTLQECYQRGVRPEATAMLPALFFVFMEQWHKGTLPYQYQDGIL-DAQAVHEMFEAQD 418 Query: 442 RVKALLGLSGIFADDLPQNADFV 464 V AL + L NADF+ Sbjct: 419 PV-ALYARNTALFGTLADNADFL 440 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: 563 Number of extensions: 22 Number of successful extensions: 5 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: 455 Length adjustment: 33 Effective length of query: 453 Effective length of database: 422 Effective search space: 191166 Effective search space used: 191166 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: 51 (24.3 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