Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate BWI76_RS19755 BWI76_RS19755 fructuronate reductase
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__Koxy:BWI76_RS19755 Length = 488 Score = 560 bits (1444), Expect = e-164 Identities = 284/486 (58%), Positives = 350/486 (72%), Gaps = 5/486 (1%) Query: 1 MTTIVDSNLP--VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEV 58 MTTI + LP V P +D S+L SRIVH G GAFHRAHQAL T +L + DWGICE+ Sbjct: 1 MTTIATATLPEGVQLPQYDRSQLRSRIVHFGFGAFHRAHQALLTDRVLNAGGGDWGICEI 60 Query: 59 NLMPGNDRVLIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARP 118 +L G DR L+ L++Q L+TV EKGAE + ++G++ E L+ ++D I+ P Sbjct: 61 SLFSG-DR-LMSQLRQQDHLFTVLEKGAEGNQPIVVGAVHECLNAKLDSLAAIIEKFCEP 118 Query: 119 QTAIVSLTVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLK 178 Q AIVSLT+TEKGYC D ASG LD+ P I HDL+NPT P+S G +VEAL RR++ L Sbjct: 119 QVAIVSLTITEKGYCIDPASGLLDMTQPRIIHDLQNPTLPQSVPGILVEALSRRRQRELP 178 Query: 179 AFTVMSCDNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQ 238 FTV+SCDN+ NGHV K AVLG+A+ R P+LA WI E V+FP TMVDRIVPAAT E+L Sbjct: 179 PFTVLSCDNIPNNGHVVKNAVLGMAEKRSPELAQWIAERVSFPGTMVDRIVPAATDESLA 238 Query: 239 EIADQLGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGS 298 EI+ LGV DPCAI+CEPF QWVIEDNFV GRP W+ G Q DV+P+E MKLRMLNGS Sbjct: 239 EISAALGVEDPCAISCEPFIQWVIEDNFVAGRPAWETAGVQMTDDVLPWEQMKLRMLNGS 298 Query: 299 HSFLAYLGYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERF 358 HSFLA+LGYL G+ I+D + +P +R AA+ LM+ EQAPTLS+ +G DL AYA LIERF Sbjct: 299 HSFLAWLGYLAGHAHISDCMQDPIFRSAAYRLMLDEQAPTLSI-QGVDLTAYADSLIERF 357 Query: 359 SNPSLRHRTWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGN 418 SNP+L+HRTWQIAMDGSQKLPQR+LD +R+HL G W LALGVAGWMRY G+D+ GN Sbjct: 358 SNPALKHRTWQIAMDGSQKLPQRMLDGIRVHLAQGSHWPLLALGVAGWMRYVSGIDDGGN 417 Query: 419 AIDVVDPMLAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478 AID+ DP+ + QK+ + RV ALL L IF DLPQ+ FV +TAA+ QL G Sbjct: 418 AIDIRDPLADKIQKLVSASDEHQRVAALLTLEEIFGRDLPQDPQFVAYITAAWHQLAAFG 477 Query: 479 ARECVA 484 AR+ +A Sbjct: 478 ARQAIA 483 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: 773 Number of extensions: 34 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