Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate SMc00884 SMc00884 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Smeli:SMc00884 Length = 574 Score = 431 bits (1108), Expect = e-125 Identities = 247/577 (42%), Positives = 343/577 (59%), Gaps = 20/577 (3%) Query: 1 MSDTPERRLRSEQWFNDPAHADMTALYVER-YMNYGMTREELQSGRPIIGIAQTGSDLTP 59 MSD ++ LRS W+ H D ++ R +M + + GRPIIGI T S+LTP Sbjct: 1 MSDK-KKELRSRHWYGG-THKDG---FIHRSWMKNQGFPDHVFDGRPIIGICNTWSELTP 55 Query: 60 CNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPL 119 CN H LA+ VK G+ +AGG P+EFPV + E RPTA L RNL + + E + Y + Sbjct: 56 CNSHLRILAEGVKRGVWEAGGFPVEFPVSSLGETQMRPTAMLFRNLLAMDVEEAIRAYGI 115 Query: 120 DGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAA 179 DGVVL GCDKTTP LM AA+ DLP IV+S GPML+G KG+ IGSGT +W + A Sbjct: 116 DGVVLLGGCDKTTPGQLMGAASVDLPTIVVSSGPMLNGKWKGKDIGSGTDVWKFSEAVRA 175 Query: 180 GEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAY 239 GE+ + FM + S S G C TMGTA +M ++ EA+G+SLP A++PA R +++ Sbjct: 176 GEMSLQEFMAAESGMSRSPGVCMTMGTATTMASIVEAMGLSLPTNAALPAVDARRMALSH 235 Query: 240 ATGKRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDD 299 TGKRI E+V +D+R S+I+T++ FEN I +A+G S+N H++AIA G++L L+D Sbjct: 236 MTGKRIVEMVHEDLRLSKILTKENFENGIIANAAVGGSTNAVVHMLAIAGRAGIDLCLED 295 Query: 300 WQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIV 359 + R+G VP +VNCMP+GKYL E AGG+P+VM+ +Q LH D TV G I + Sbjct: 296 FDRVGGQVPCIVNCMPSGKYLIEDLAYAGGLPAVMNRIQHL--LHPDAPTVFGVPISKYW 353 Query: 360 SSSLTSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENS 418 ++ N DVI P D PL+ AG VL GN + A++K S E + Sbjct: 354 EAAEVYNDDVIRPLDNPLRAAAGIRVLKGNLAPNGAVIKPSAASEHLL-----------A 402 Query: 419 FEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQG 478 E A VF+ ED A+IDDP L + E ILV++G G GYPG AEV NM P L+++G Sbjct: 403 HEGPAYVFDTIEDLRAKIDDPDLPVTEDTILVLKGCGPKGYPGMAEVGNMPIPRRLVEKG 462 Query: 479 IDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEE 538 + + + D R SGT+ +L++SPEA GG LA+++T DR+++D +NLL+ +EE Sbjct: 463 VRDMVRISDARMSGTAFGTVVLHVSPEANAGGPLAIVRTGDRIRLDALKGELNLLVSEEE 522 Query: 539 MARRRLEWTPNIPPSQTPWQELYRQLVGQLSTGGCLE 575 +A R W P + +LY V Q G L+ Sbjct: 523 LAARMAAWQPPEQKWHRGYYKLYHDTVLQADKGADLD 559 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: 976 Number of extensions: 53 Number of successful extensions: 4 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: 574 Length adjustment: 36 Effective length of query: 558 Effective length of database: 538 Effective search space: 300204 Effective search space used: 300204 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