Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Phaeo:GFF723 Length = 571 Score = 419 bits (1076), Expect = e-121 Identities = 244/533 (45%), Positives = 324/533 (60%), Gaps = 14/533 (2%) Query: 44 GRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDR 103 GRPIIGI T S+LTPCN +LA+ VK G+ +AGG P+EFPV + E +PTA L R Sbjct: 37 GRPIIGICNTWSELTPCNSGLRDLAEGVKRGVWEAGGFPVEFPVMSLGETQMKPTAMLFR 96 Query: 104 NLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGEL 163 NL + + E + Y +DGVVL GCDKTTP LM AA+ DLPAIV+S GPML+G +G+ Sbjct: 97 NLLAMDVEESIRAYGIDGVVLLGGCDKTTPGQLMGAASVDLPAIVVSSGPMLNGKWQGKD 156 Query: 164 IGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPG 223 IGSGT +W + AGE+ + FM + S S G C TMGTA +M +L EA+GMSLP Sbjct: 157 IGSGTDVWKFSEAVRAGEMTLQDFMAAESGMSRSKGVCMTMGTASTMASLVEAMGMSLPT 216 Query: 224 CASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPH 283 A++PA R +A+ TGKRI E+V +DI+PS ++TR+AF NAI +A+G S+N H Sbjct: 217 NAALPAVDARRMALAHLTGKRIVEMVEEDIKPSDVLTREAFVNAIMANAAVGGSTNAVVH 276 Query: 284 LIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRL 343 L+A+A +G ELSLDD+ +G D+PLLVNCMP+GKYL E F AGG+P V+ +L G L Sbjct: 277 LLALAGRVGAELSLDDFD-LGSDIPLLVNCMPSGKYLMEDFCYAGGMPVVLKQLADNGHL 335 Query: 344 HEDCATVSGRTIGEIVSSSLTSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVG 402 + TV G I + N DVI FD P+K AG VL GN + AI+K S Sbjct: 336 RSN-TTVLGGDILAYAEGAECFNDDVIKSFDEPVKPAAGLRVLRGNLAPNGAIVKPSAAT 394 Query: 403 EAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGS 462 + +L E E A VFE ED A ID L + + ILV++GVG GYPG Sbjct: 395 D-----HLLE------HEGVAHVFETIEDMKANIDRDDLPVTKDSILVLKGVGPKGYPGM 443 Query: 463 AEVVNMAPPAALIKQGIDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLK 522 EV NM P L+++G+ + + DGR SGT+ IL++SPE+ GG L L+QT DR++ Sbjct: 444 PEVGNMPIPRKLVREGVRDMIRISDGRMSGTAFGTVILHVSPESQAGGPLGLVQTGDRIR 503 Query: 523 VDLNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQLVGQLSTGGCLE 575 V T++LL+ +EE+ RR W P + +LY V Q G L+ Sbjct: 504 VSAKNGTLDLLVSEEELTARREAWQPEPLHYTRGYAKLYVDSVLQAEKGADLD 556 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: 933 Number of extensions: 53 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: 594 Length of database: 571 Length adjustment: 36 Effective length of query: 558 Effective length of database: 535 Effective search space: 298530 Effective search space used: 298530 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