Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate RR42_RS34965 RR42_RS34965 dioxygenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__Cup4G11:RR42_RS34965 Length = 511 Score = 353 bits (906), Expect = e-102 Identities = 205/491 (41%), Positives = 278/491 (56%), Gaps = 20/491 (4%) Query: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSD-----WGICEVNLMPGND 65 V RP + RL IVHLG GAFHRAHQA T L + +D WGI V+L + Sbjct: 18 VLRPRYARERLRGGIVHLGIGAFHRAHQAAVTQAALHADAADAHSLDWGIVGVSLRRPDT 77 Query: 66 RVLIENLKKQQLLYTVA-----EKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQT 120 R + L QQ LYT+A + G+ +L++IG++ L D + +L +A Sbjct: 78 R---DALAPQQGLYTLALRGVRDDGSRFVQLQVIGAVMAVL-VAADDPDAVLERIAHEDA 133 Query: 121 AIVSLTVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAF 180 IVSLTVTEKGYC D A+G L+ ++P I HDL + AP +AIGY+ L+ R +GL Sbjct: 134 RIVSLTVTEKGYCHDPATGTLNFSDPGIAHDLLHAGAPVTAIGYLARGLQRRMARGLPPL 193 Query: 181 TVMSCDNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEI 240 T++SCDN+ NG + +L D L W+ E FP MVDRIVP T + I Sbjct: 194 TLLSCDNIAANGDTLRGLLLAFCARVDGALHDWVAERCGFPNAMVDRIVPKTTVDDAARI 253 Query: 241 ADQLGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHS 300 + LGV D + EPF QWV+ED FV GRP W+ GAQFV PFE +K R++NGSHS Sbjct: 254 SAALGVEDAWPVVGEPFLQWVMEDRFVAGRPRWEAGGAQFVEHAHPFETLKHRLVNGSHS 313 Query: 301 FLAYLGYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSN 360 +AYLG + G+ T + PA R +M QE PTL G D AY L+ RF+N Sbjct: 314 TMAYLGMVAGWATTDRAIAVPAMRALVAGMMEQEMQPTLPALPGLDTAAYRRDLLARFAN 373 Query: 361 PSLRHRTWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAI 420 P+L+H+T QIAMDGSQK+PQRLL P+R L+ G + LALGVAGW+ + +G DE G Sbjct: 374 PALQHKTSQIAMDGSQKIPQRLLAPIRERLRAGAPFPRLALGVAGWLHFLRGRDEHGAEY 433 Query: 421 DVVDPMLAEFQKINAQYQG-----ADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLC 475 + DP+ + + + A+ + ADR+ A+ + +F DL + FV + + L Sbjct: 434 RIEDPLASSLRALLAEAEARHAREADRIAAIASFTPVFG-DLAASRVFVETLATQTRMLR 492 Query: 476 ERGARECVAAL 486 ERG +AA+ Sbjct: 493 ERGVLATIAAV 503 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: 676 Number of extensions: 37 Number of successful extensions: 2 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: 511 Length adjustment: 34 Effective length of query: 452 Effective length of database: 477 Effective search space: 215604 Effective search space used: 215604 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