Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate H281DRAFT_06137 H281DRAFT_06137 dihydroxyacid dehydratase (EC 4.2.1.9)
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Burk376:H281DRAFT_06137 Length = 583 Score = 340 bits (873), Expect = 7e-98 Identities = 196/529 (37%), Positives = 298/529 (56%), Gaps = 15/529 (2%) Query: 45 RPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRN 104 RP+IGI TGS C+ + +L + VK G+ AGG+P++FP + E PT+ RN Sbjct: 50 RPVIGIVNTGSGFNACHGNMPQLVEAVKRGVMLAGGLPVDFPTISVHESFSSPTSMYLRN 109 Query: 105 LAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELI 164 L + E++ P+D VVL GCDKT PA LM AA+ ++PAI L G ML G H+ E + Sbjct: 110 LMSMDTEEMIRAQPMDAVVLIGGCDKTVPAQLMGAASAEIPAIQLVTGSMLTGSHRSERV 169 Query: 165 GSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGC 224 G+ T A EID E ++ SVG C+ MGTA +M +AEALGM++PG Sbjct: 170 GACTDCRRYWGKFRASEIDQEEINDVNNQLVASVGTCSVMGTASTMACIAEALGMTVPGG 229 Query: 225 ASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHL 284 A+ PA +R ++A TG +L + + +I+T +AFENA+ V A+G S+N HL Sbjct: 230 ATPPAVTADRIRVAEQTGTTAVKLASERLTIDKILTPKAFENAMRVLLAIGGSTNAIVHL 289 Query: 285 IAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLH 344 A+A +G ++ LD R+G++ P+L++ P G++ E FH+AGGV +++ EL+ LH Sbjct: 290 SAVAGRLGHKIGLDSLDRMGKETPVLLDLKPTGQHYMEDFHKAGGVATLLRELKPL--LH 347 Query: 345 EDCATVSGRTIGE-IVSSSLTSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVG 402 D TVSG T+GE I +S + DV+ F P+ + G V+ GN AI+K S Sbjct: 348 LDAMTVSGHTLGEQIEASGPGFSQDVVRSFSQPIYPQGGLAVVRGNLAPGGAIIKQSAAD 407 Query: 403 EAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGS 462 + E RA+VFE ED R+DD +LD+ +LV++ +G VG PG Sbjct: 408 PKLME-----------HEGRAVVFENLEDLINRVDDESLDVKADDVLVLKNIGPVGAPGM 456 Query: 463 AEVVNMAPPAALIKQGIDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLK 522 E + P L + G+ + + DGR SGT+ +L+++PEAA GG A +Q DR++ Sbjct: 457 PEAGYIPIPRKLARAGVKDMVRISDGRMSGTAFGTIVLHVTPEAAAGGPFAYVQNGDRIR 516 Query: 523 VDLNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQLVGQLSTG 571 + ++ R V+LL+ DE++ +R + P + +++L+ Q V Q G Sbjct: 517 LSVSNREVSLLVSDEKLKQRAADKPIKRPTADRGYRKLFLQTVTQADEG 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: 895 Number of extensions: 55 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: 583 Length adjustment: 37 Effective length of query: 557 Effective length of database: 546 Effective search space: 304122 Effective search space used: 304122 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