Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate AO356_28535 AO356_28535 mannitol dehydrogenase
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28535 Length = 485 Score = 389 bits (998), Expect = e-112 Identities = 223/458 (48%), Positives = 281/458 (61%), Gaps = 7/458 (1%) Query: 25 IVHLGCGAFHRAHQALYTH-HLLESTDSDWGICEVNLMPGNDRVLIENLKKQQLLYTVAE 83 IVHLG GAFHRAHQA+Y HL +SDWG+C NL ++R L+E L++Q Y VAE Sbjct: 18 IVHLGLGAFHRAHQAVYLQRHLNRHGESDWGVCSANLR--SNRTLVEQLREQDGRYHVAE 75 Query: 84 -KGAESTELKIIGSMKEALHPEIDG--CEGILNAMARPQTAIVSLTVTEKGYCADAASGQ 140 + E L+ IG +++AL+ G E +L MA PQT IV+LTVTEKGYC +SGQ Sbjct: 76 YRDCEQVTLREIGVLRQALYVGEGGPDLEQLLMRMAAPQTRIVTLTVTEKGYCLSPSSGQ 135 Query: 141 LDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGHVAKVAVL 200 L +P I HDL +P AP+SA G ++EALR RR G+ AFTV+ CDN+ +NG + AV Sbjct: 136 LRSEDPAIAHDLAHPQAPRSAPGIVLEALRRRRAAGVPAFTVLCCDNMPDNGQRTRQAVS 195 Query: 201 GLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACEPFRQW 260 LA +D LA W+E+ V FP MVDRIVPA E+ + + +QL +DP A+ CE F QW Sbjct: 196 ALAALQDEALAQWVEQQVAFPSCMVDRIVPAMDGESFRRL-EQLDCHDPAAVVCESFSQW 254 Query: 261 VIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIADTVTN 320 VIED+F GRPDW+ G Q V DV PFE MKLRMLNGSHS LAY+G L G++T+ + V++ Sbjct: 255 VIEDHFPLGRPDWEVEGVQMVDDVGPFETMKLRMLNGSHSLLAYVGLLVGHDTVFEAVSD 314 Query: 321 PAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGSQKLPQ 380 M E APTL MP G DL+ YA L RF+N SL+HR QIAMDGSQKLPQ Sbjct: 315 ANLLHLIGRYMADEAAPTLDMPAGIDLSVYAHDLKARFANDSLQHRLRQIAMDGSQKLPQ 374 Query: 381 RLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQKINAQYQGA 440 R L + L G ALG+A W+ Y A V DP+ A F + +++GA Sbjct: 375 RWLLGAQQLLDQGRGIDCTALGIAAWIHYCTQPLPGRPAHVVDDPLSATFADLAGRFEGA 434 Query: 441 DRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478 RV A+L L +F L A F AV AY L G Sbjct: 435 SRVDAVLDLHEVFPPRLSARAVFRDAVHHAYSALTRDG 472 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: 681 Number of extensions: 40 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 485 Length adjustment: 34 Effective length of query: 452 Effective length of database: 451 Effective search space: 203852 Effective search space used: 203852 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