Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate H281DRAFT_02952 H281DRAFT_02952 fructuronate reductase
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__Burk376:H281DRAFT_02952 Length = 497 Score = 293 bits (749), Expect = 1e-83 Identities = 168/419 (40%), Positives = 230/419 (54%), Gaps = 9/419 (2%) Query: 14 VQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAPD-WAIVGVGLTGSDRSKKKA 72 + P YD + PGIVH G+G F RAH+A Y E L W IVGV L +D S Sbjct: 19 IVVPTYDRASLAPGIVHLGLGAFHRAHQAVYTEHTLRAGDHRWGIVGVSLRRADTS---- 74 Query: 73 EEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDPAIRIVSMTITE 132 E AQD LY++ + + +V+GAL L+AP P AVL + DP IVS+TITE Sbjct: 75 EALTAQDHLYTV-DVRDGAADSFQVVGALIASLVAPQSPAAVLDAMTDPRGHIVSLTITE 133 Query: 133 GGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFTVMSCDNLR 192 GY N +GA + ++ + DL+ P + G+VV AL R AG + TVMSCDNL Sbjct: 134 KGYCRNPASGALEFDHPDIDHDLREGSAPRSAIGFVVRALALRRAAGLRPLTVMSCDNLP 193 Query: 193 HNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLNAASGLDDD 252 NG+ R L +A+ DP LA WIE FPN MVDRI P + ++ G D Sbjct: 194 SNGDTMRALTLAFAREADPALADWIEREGAFPNTMVDRIVPLTTDADRTRVAEELGAYDA 253 Query: 253 LPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVMLCFPGILV 312 P++ E F QWV+ED+FA RP E+AG +V D +E K+RMLN H L + G L+ Sbjct: 254 WPVITEPFSQWVIEDRFAGPRPAWERAGATLVRDARPYEQAKLRMLNGAHSALAYLGSLI 313 Query: 313 GYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNKAMSDQTLR 372 GY+ VD AI LL +++ L +V PTL P+ L YR + +RF N A+ + + Sbjct: 314 GYDTVDQAIGAPALLNFVESMLRDEVEPTLSRPA---LARYRADLFTRFRNTALDHRLQQ 370 Query: 373 IASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKGGTYESSEPTYG 431 IA+DG K+ W E+VR ++ +AF +A ++ L G+DE G TY ++P G Sbjct: 371 IATDGSQKLPQRWLESVRANLKSGAPTECLAFALAGWIAYLGGQDETGRTYVIADPLAG 429 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: 565 Number of extensions: 24 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: 497 Length adjustment: 34 Effective length of query: 451 Effective length of database: 463 Effective search space: 208813 Effective search space used: 208813 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