Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate BPHYT_RS28510 BPHYT_RS28510 dioxygenase
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__BFirm:BPHYT_RS28510 Length = 492 Score = 300 bits (769), Expect = 6e-86 Identities = 175/432 (40%), Positives = 238/432 (55%), Gaps = 13/432 (3%) Query: 2 ITRETLKSLPAN----VQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAPD-WA 56 ++ L SL A V P YD + PGIVH G+G F RAH+A Y E L W Sbjct: 3 LSNAALASLAARAAGKVVVPAYDRASLAPGIVHLGLGAFHRAHQALYTEHALRAGDHRWG 62 Query: 57 IVGVGLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLK 116 IVGV L +D S E AQD LY++ + +++V+GAL L+AP P AVL Sbjct: 63 IVGVSLRRADTS----EALTAQDHLYAV-DVRDGTADSLQVIGALIASLVAPQSPAAVLD 117 Query: 117 HLVDPAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRW 176 + DP IVS+TITE GY N +GA ++ + DL+ P + G+VV AL R Sbjct: 118 AMTDPRCHIVSLTITEKGYCRNPASGALQFDHPDIAHDLRAAAAPRSAIGFVVRALALRR 177 Query: 177 DAGGKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVS 236 AG FTV+SCDNL NG+ R L +A+ DP LA WIE A FPN MVDRI P + Sbjct: 178 AAGLGPFTVLSCDNLPSNGDTMRALTLAFARETDPALADWIELEAAFPNTMVDRIVPLTT 237 Query: 237 AEIAKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIR 296 ++ G DD P++ E F QWV+ED+FA RP E+AG +VGD +E K+R Sbjct: 238 DADRLRVAKQLGADDAWPVITEPFSQWVIEDRFAGPRPAWERAGATLVGDARPYEQAKLR 297 Query: 297 MLNAGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDS 356 MLN H L + G L+GY+ VD AI +L +++ L +V PTL P+ L YR Sbjct: 298 MLNGAHSALAYLGSLIGYDTVDQAIGAPAVLNFVESMLRDEVEPTLSRPA---LATYRAE 354 Query: 357 VISRFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGR 416 + +RF N A+ + +IA+DG K+ W E+VR ++ R+AF +A ++ L G Sbjct: 355 LFARFRNTALDHRLQQIATDGSQKLPQRWLESVRANLKSGAPTERLAFALAGWIAYLGGH 414 Query: 417 DEKGGTYESSEP 428 DE G TY ++P Sbjct: 415 DETGRTYAIADP 426 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: 553 Number of extensions: 20 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: 492 Length adjustment: 34 Effective length of query: 451 Effective length of database: 458 Effective search space: 206558 Effective search space used: 206558 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