Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate RR42_RS34965 RR42_RS34965 dioxygenase
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__Cup4G11:RR42_RS34965 Length = 511 Score = 268 bits (685), Expect = 3e-76 Identities = 164/498 (32%), Positives = 253/498 (50%), Gaps = 21/498 (4%) Query: 5 ETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILE------HAPDWAIV 58 +TL LP +V P Y + ++ GIVH G+G F RAH+A + L H+ DW IV Sbjct: 9 DTLAQLPHDVLRPRYARERLRGGIVHLGIGAFHRAHQAAVTQAALHADAADAHSLDWGIV 68 Query: 59 GVGLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKST----VRVMGALRDYLLAPADPEAV 114 GV L D A Q LY+L + ++V+GA+ L+A DP+AV Sbjct: 69 GVSLRRPDTRDALAP----QQGLYTLALRGVRDDGSRFVQLQVIGAVMAVLVAADDPDAV 124 Query: 115 LKHLVDPAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRR 174 L+ + RIVS+T+TE GY + TG + + + DL + P T GY+ L+R Sbjct: 125 LERIAHEDARIVSLTVTEKGYCHDPATGTLNFSDPGIAHDLLHAGAPVTAIGYLARGLQR 184 Query: 175 RWDAGGKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPT 234 R G T++SCDN+ NG+ R L + D L W+ E FPN MVDRI P Sbjct: 185 RMARGLPPLTLLSCDNIAANGDTLRGLLLAFCARVDGALHDWVAERCGFPNAMVDRIVPK 244 Query: 235 VSAEIAKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVK 294 + + A +++AA G++D P+V E F QWV+ED+F GRP E G Q V +E +K Sbjct: 245 TTVDDAARISAALGVEDAWPVVGEPFLQWVMEDRFVAGRPRWEAGGAQFVEHAHPFETLK 304 Query: 295 IRMLNAGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYR 354 R++N H + + G++ G+ D AI + + + +++ PTL A G+ YR Sbjct: 305 HRLVNGSHSTMAYLGMVAGWATTDRAIAVPAMRALVAGMMEQEMQPTLPALPGLDTAAYR 364 Query: 355 DSVISRFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLR 414 +++RF+N A+ +T +IA DG K+ +R + R+A G+A +L LR Sbjct: 365 RDLLARFANPALQHKTSQIAMDGSQKIPQRLLAPIRERLRAGAPFPRLALGVAGWLHFLR 424 Query: 415 GRDEKGGTYESSEPTYGDAEWKLAKAD-----DFESSLKLPAFDG-WRDLDTSELDQKVI 468 GRDE G Y +P LA+A+ + + + +F + DL S + + + Sbjct: 425 GRDEHGAEYRIEDPLASSLRALLAEAEARHAREADRIAAIASFTPVFGDLAASRVFVETL 484 Query: 469 VLR-KIIREKGVKAAIPA 485 + +++RE+GV A I A Sbjct: 485 ATQTRMLRERGVLATIAA 502 Lambda K H 0.317 0.135 0.398 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: 567 Number of extensions: 28 Number of successful extensions: 4 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: 485 Length of database: 511 Length adjustment: 34 Effective length of query: 451 Effective length of database: 477 Effective search space: 215127 Effective search space used: 215127 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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