Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_954 Length = 567 Score = 277 bits (709), Expect = 7e-79 Identities = 182/531 (34%), Positives = 277/531 (52%), Gaps = 26/531 (4%) Query: 30 RYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHP 89 R M Y M EE +P++G+A S +TPCN +LA AGI +AGG F Sbjct: 28 RSMYYAMGYEEGDFVKPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFGTPT 87 Query: 90 IAEQSRRPTAALDRNLAYLGLVE-----ILHGYPLDGVVLTTGCDKTTPACLMAAATTDL 144 I++ T + +L ++ + G +DGV++ GCDK P LM ++ Sbjct: 88 ISDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGLMGMLRANV 147 Query: 145 PAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTM 204 PAI + GG +L GH++G+ + +V + A AAG++ E+ A P G C M Sbjct: 148 PAIYVYGGTILPGHYQGKDLNIVSV-FEAVGENAAGKLSDFDLKEIEKRAIPGTGSCGGM 206 Query: 205 GTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAF 264 TA +M++ EALG+SLP +++ P+ E+ A + K + E + +DI+P I+T+++ Sbjct: 207 YTANTMSSAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAIKKDIKPRDIVTKKSI 266 Query: 265 ENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGF 324 ENA+AV A G S+N H +AIA GVE S+DD++R+ P+L + P+GKYL Sbjct: 267 ENAVAVIMATGGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPSGKYLAVDL 326 Query: 325 HRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEI---VSSSLTSNADVIHPFDTPLKHRA 381 HRAGG+P VM L AG LH DC T+ G+T+ E+ V ++ DVI P + P+ + Sbjct: 327 HRAGGIPQVMKVLLNAGLLHGDCLTIEGKTVAEVLKDVPDQPRADQDVIRPINNPMYAQG 386 Query: 382 GFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPAL 441 +L GN +S G + T L P A VFE + I A Sbjct: 387 HLAILKGN--------LSPEGAVAKITGLKNP----VITGPARVFEDEQSALEAI--LAG 432 Query: 442 DIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSIL 500 I ++V+R +G G PG E+ +AP ALI G+ +S+ + DGR SG + + Sbjct: 433 KIKAGDVMVLRYLGPKGGPGMPEM--LAPTGALIGAGLGESVGLITDGRFSGGTWGMVVG 490 Query: 501 NMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWTPNIP 551 +++PEAA GG +A + D + +D + L + +EE+ARRR WT P Sbjct: 491 HVAPEAAAGGTIAFVHEGDSITIDARQLLLELNVSEEEIARRRAAWTAPAP 541 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: 834 Number of extensions: 43 Number of successful extensions: 5 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: 567 Length adjustment: 36 Effective length of query: 558 Effective length of database: 531 Effective search space: 296298 Effective search space used: 296298 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