Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate WP_009780581.1 MED217_RS10920 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >NCBI__GCF_000152985.1:WP_009780581.1 Length = 560 Score = 267 bits (682), Expect = 1e-75 Identities = 174/523 (33%), Positives = 273/523 (52%), Gaps = 29/523 (5%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 G+T E+L+ +P+IGIA TG + PCN H +LA VK G +A + + F +++ Sbjct: 27 GLTDEDLK--KPLIGIASTGYEGNPCNMHLNDLATYVKKGASNADLVGLIFNTIGVSDGI 84 Query: 95 RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 T + R++ + ++ DG+V GCDK P L+A + P+I++ Sbjct: 85 SNGTPGMRFSLPSRDIIADSMETVVQAMSYDGLVTVVGCDKNMPGALIAQLRLNRPSILV 144 Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209 GG + G H G+ + + + A AG ID F E+ A P G C M TA + Sbjct: 145 YGGTIASGCHNGKKLDIISA-FEAYGQKVAGTIDDNEFKEVVHKACPGAGACGGMYTANT 203 Query: 210 MNALAEALGMSLPGCASIPA--PYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENA 267 M + EALGMSLP +S PA + Q G+ + L+ QDI+PS I+T+++ ENA Sbjct: 204 MASAIEALGMSLPFNSSNPAVTDANIKEQECIKAGEALKYLLEQDIKPSDIVTKESLENA 263 Query: 268 IAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRA 327 I + + LG S+N H +AIA+ V+ +L+D+QR+ ++ PLL + P+GKY E H Sbjct: 264 IRLVTVLGGSTNAVLHFLAIAKAAQVDFTLEDFQRLSDNTPLLADLKPSGKYSMEDLHGV 323 Query: 328 GGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSS--SLTSNADVIHPFDTPLKHRAGFIV 385 GG+P V+ + G LH DC TV+G+T+ E + +L D+I P + P+K + Sbjct: 324 GGIPGVLKYMLDNGMLHGDCLTVTGKTLAENLKDVPNLIDGQDIIRPLNKPIKDSGHIRI 383 Query: 386 LSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDE 445 L GN + V + K LS G N F + V EG + + D Sbjct: 384 LFGN-----LATEGAVAKITGKEGLSFTGTANVFNSELEVNEGIKSGKVKKGD------- 431 Query: 446 RCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSP 504 +++IR G G PG E+ + P ++++ G+ + + DGR SG S + ++SP Sbjct: 432 --VVIIRYEGPKGGPGMPEM--LKPTSSIMGAGLGKDVALITDGRFSGGSHGFVVGHVSP 487 Query: 505 EAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWT 547 EA VGG +AL++ D + +D T+N+ I DEE+A+RR +WT Sbjct: 488 EAQVGGNIALVENGDVISIDAVKNTINIDITDEELAKRREKWT 530 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: 816 Number of extensions: 54 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 594 Length of database: 560 Length adjustment: 36 Effective length of query: 558 Effective length of database: 524 Effective search space: 292392 Effective search space used: 292392 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 24 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