Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Dyella79:N515DRAFT_0569 Length = 568 Score = 258 bits (659), Expect = 5e-73 Identities = 180/557 (32%), Positives = 272/557 (48%), Gaps = 35/557 (6%) Query: 45 RPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRN 104 +P++ + T S+++PCN + ELA++V GIR AGG P+EF + + T + + Sbjct: 31 KPLVAVVHTWSNVSPCNLNLRELAEQVAEGIRAAGGTPIEFNTIAVTDGIAMGTPGMRAS 90 Query: 105 LAYLGLVE-----ILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHH 159 L ++ + G+ LD +V+ GCDKT PA MA A D+PA+ L GG + G H Sbjct: 91 LISREVITDSIELAVDGHCLDAMVVLCGCDKTIPAAAMAMARLDIPAVALYGGTIAHGTH 150 Query: 160 KGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGM 219 I V + A AG+ID + A P G C TA +M + LG+ Sbjct: 151 DAHPITIQQV-FEAVGAHGAGKIDDAELAAVERDACPGAGACGGQFTANTMAMVLTTLGL 209 Query: 220 SLPGCASIPAPYRERGQMAYATGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSN 279 S G IPA + + A G+ + D +R+ P ++ R + NA + +A S+N Sbjct: 210 SPMGFNDIPATHPAKAAAARRCGELVMDCLREQRTPRALINRTSLRNAARMVAATAGSTN 269 Query: 280 CPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQK 339 HL+AIAR G +LED++ + P++ + +P G+Y AGG V EL Sbjct: 270 AVLHLLAIAREAGAPWTLEDFEPASKHTPVIADLLPGGRYTAVEMFGAGGAARVAQELIA 329 Query: 340 AGRLHEDCATVSGKTI-GEIVSNSLTSNTDVIHPFDTPLKHRAGFIVLSGNFF-DSAIMK 397 AG L +D TV+G+++ E + DVI P PLK R G+ +L GN + I+K Sbjct: 330 AGML-DDVPTVTGRSLFEEAAAAPRAEQQDVILPVGQPLKPRGGYSILYGNLAPEGCILK 388 Query: 398 MSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTV 457 ++ G FE A VFE E A + I + ++VIR G Sbjct: 389 LAGKG-------------ATHFEGTARVFESEEQAFAAVQQGR--IAKGDVIVIRNEGPA 433 Query: 458 GYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLK 516 G PG E++ + AALI +G+ D + + DGR SG + + +M+PEA GG +ALL+ Sbjct: 434 GGPGMREMLGVT--AALIGRGLGDDVALITDGRFSGATHGFMVGHMAPEAVRGGPIALLR 491 Query: 517 TNDRLKVDLNTRTVNLLIDDAEMAQRRREWIPNIPPSQTPWQELYRQLVGQLSTGGCLEP 576 DR+++D R + DA++A+RR+ W P P T Y +LVG S G P Sbjct: 492 DGDRIRIDAGLREI---ATDADLAERRQHWTPPAPKVTTGALAKYARLVGSASDGANTHP 548 Query: 577 AT-----LHLRVIARSG 588 T H++V A G Sbjct: 549 ETSVATPKHVQVTATEG 565 Lambda K H 0.319 0.135 0.407 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: 881 Number of extensions: 51 Number of successful extensions: 8 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: 594 Length of database: 568 Length adjustment: 36 Effective length of query: 558 Effective length of database: 532 Effective search space: 296856 Effective search space used: 296856 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 (21.7 bits) S2: 53 (25.0 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