Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate 16281 b2172 predicted dehydrogenase, NAD-dependent (NCBI)
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__Keio:16281 Length = 488 Score = 541 bits (1393), Expect = e-158 Identities = 272/485 (56%), Positives = 343/485 (70%), Gaps = 5/485 (1%) Query: 1 MTTIVDSNLP--VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEV 58 M TI LP V P +D +L+SRIVH G GAFHRAHQAL T +L + DWGICE+ Sbjct: 1 MNTIASVTLPHHVHAPRYDRQQLQSRIVHFGFGAFHRAHQALLTDRVLNAQGGDWGICEI 60 Query: 59 NLMPGNDRVLIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARP 118 +L G+ L+ L+ Q LYTV EKGA+ ++ I+G++ E L+ ++D I+ P Sbjct: 61 SLFSGDQ--LMSQLRAQNHLYTVLEKGADGNQVIIVGAVHECLNAKLDSLAAIIEKFCEP 118 Query: 119 QTAIVSLTVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLK 178 Q AIVSLT+TEKGYC D A+G LD +NP I HDL+ P P SA G +VEAL+ RRE+GL Sbjct: 119 QVAIVSLTITEKGYCIDPATGALDTSNPRIIHDLQTPEEPHSAPGILVEALKRRRERGLT 178 Query: 179 AFTVMSCDNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQ 238 FTV+SCDN+ +NGHV K AVLG+A+ R P+LA WI+E+V+FP TMVDRIVPAAT E+L Sbjct: 179 PFTVLSCDNIPDNGHVVKNAVLGMAEKRSPELAGWIKEHVSFPGTMVDRIVPAATDESLV 238 Query: 239 EIADQLGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGS 298 EI+ LGV DPCAI+CEPF QWV+EDNFV GRP W+ G Q V DV+P+E MKLRMLNGS Sbjct: 239 EISQHLGVNDPCAISCEPFIQWVVEDNFVAGRPAWEVAGVQMVNDVLPWEEMKLRMLNGS 298 Query: 299 HSFLAYLGYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERF 358 HSFLAYLGYL G+ I+D + + A+R AA LM+ EQAPTL + + DL YA LI RF Sbjct: 299 HSFLAYLGYLSGFAHISDCMQDRAFRHAARTLMLDEQAPTLQIKD-VDLTQYADKLIARF 357 Query: 359 SNPSLRHRTWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGN 418 +NP+L+H+TWQIAMDGSQKLPQR+L +R+H W LALGVAGWMRY GVD+ GN Sbjct: 358 ANPALKHKTWQIAMDGSQKLPQRMLAGIRIHQGRETDWSLLALGVAGWMRYVSGVDDAGN 417 Query: 419 AIDVVDPMLAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478 AIDV DP+ + +++ A RV ALL L +F DDLP N FV A+ A+QQ+ + G Sbjct: 418 AIDVRDPLSDKIRELVAGSSSEQRVTALLSLREVFGDDLPDNPHFVQAIEQAWQQIVQFG 477 Query: 479 ARECV 483 A + + Sbjct: 478 AHQAL 482 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: 744 Number of extensions: 31 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: 488 Length adjustment: 34 Effective length of query: 452 Effective length of database: 454 Effective search space: 205208 Effective search space used: 205208 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