Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 3606698 Dshi_0129 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Dino:3606698 Length = 577 Score = 278 bits (710), Expect = 6e-79 Identities = 190/557 (34%), Positives = 281/557 (50%), Gaps = 31/557 (5%) Query: 31 YMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPV--- 87 Y GMT EE+ +P++G+A ++ PCN AQ VK G++ A G P EF Sbjct: 29 YYAMGMTEEEIH--QPLVGVATCWNEAAPCNIALSRQAQAVKMGVKQASGTPREFTTITV 86 Query: 88 -HPIAEQSRRPTAALDRNLAYLGLVEI-LHGYPLDGVVLTTGCDKTTPACLMAAATTDLP 145 IA ++L A VE+ + G+ D +V GCDK+ P +MA ++P Sbjct: 87 TDGIAMGHEGMRSSLASREAIADTVELTMRGHCYDAIVGLAGCDKSLPGMMMAMVRLNVP 146 Query: 146 AIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMG 205 ++ + GG +L G GE + V A D E + A PS G C Sbjct: 147 SVFIYGGSILPGRLNGEDVTVQDVFEAVGKHQAGNYTDAE-LEVLERVACPSAGACGGQF 205 Query: 206 TALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVRQDIRPSQIMTRQAFE 265 TA +M ++EA+G++LP A PAPY R Q A+G+ + DL+ + IR I+TR++ E Sbjct: 206 TANTMACVSEAIGLALPNSAGAPAPYESRDQYGEASGRAVMDLIEKGIRARDIVTRKSLE 265 Query: 266 NAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPAGKYLGEGFH 325 NA + + G S+N HL AIA G+E +L+D I D P V+ P GKY+ + + Sbjct: 266 NAARIVACTGGSTNAGLHLPAIAHEAGIEFTLQDVCDIFRDTPYFVDLKPGGKYVAKDMY 325 Query: 326 RAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSN-SLTSNTDVIHPFDTPLKHRAGFI 384 AGGVP VM EL++AG +HEDC TV+G +IGE + +L ++ VI+P DTPL G + Sbjct: 326 EAGGVPVVMRELRRAGLIHEDCMTVTGYSIGEELDKVTLEADGRVIYPVDTPLSTTGGVV 385 Query: 385 VLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDI 443 L GN + AI+K++ + + + F A VFE ED + + A Sbjct: 386 GLEGNLAPEGAIVKIAGMSD-----------DQLVFTGPARVFECEEDAFEAVQNRA--Y 432 Query: 444 DERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNM 502 E + VIR G G PG E+ +A AAL QG+ + + DGR SG + + ++ Sbjct: 433 AEGDVFVIRNEGPAGGPGMREM--LATTAALSGQGMGKKVALITDGRFSGATRGFCVGHV 490 Query: 503 SPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQRRREWI---PNIPPSQTPWQE 559 PEAA GG +A+LK D + +D +++ + + E+A R+ W I S W+ Sbjct: 491 GPEAAHGGPIAMLKDGDMITIDALKGELSVALSEDELAARKDAWSGPRETIYASGALWK- 549 Query: 560 LYRQLVGQLSTGGCLEP 576 Y QLVG G P Sbjct: 550 -YAQLVGGARLGAVTHP 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: 825 Number of extensions: 45 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: 577 Length adjustment: 37 Effective length of query: 557 Effective length of database: 540 Effective search space: 300780 Effective search space used: 300780 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