Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Miya:8501301 Length = 555 Score = 282 bits (721), Expect = 3e-80 Identities = 184/548 (33%), Positives = 292/548 (53%), Gaps = 31/548 (5%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 G+TREE++ RP++G+ +++ P + H +A+ VKAG+R AGG PMEFP + + Sbjct: 23 GLTREEIE--RPLVGVVNAANEVVPGHVHLHTIAEAVKAGVRAAGGTPMEFPAIAVCDGL 80 Query: 95 RRPTAALDRNLAYLGLV----EILH-GYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 + +L ++ EI+ +P D +V CDK+ P LMA D+P+I++ Sbjct: 81 AMNHEGMHFSLPSREIIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRMDIPSIMV 140 Query: 150 SGGPMLDGHHKGELIGSGTVL--WHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTA 207 SGGPML G G L G ++ + A + G++ EMT A P G C M TA Sbjct: 141 SGGPMLAG---GTLAGRTDLISVFEAVGRVQRGDMTMAELDEMTETACPGCGSCAGMFTA 197 Query: 208 LSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVRQDIRPSQIMTRQAFENA 267 +MN +AE +G++LPG +IPA R ++A G ++ +L+ ++I P I+T +A NA Sbjct: 198 NTMNCMAETMGLALPGNGTIPAVTAARVRLAKHAGMKVMELLEKNITPRSIVTPRAVANA 257 Query: 268 IAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPAGKYLGEGFHRA 327 +AV ALG S+N HL A+ G++L+L+ + + P L PAG + + H A Sbjct: 258 VAVDMALGGSTNTVLHLPAVFGEAGLDLTLDIFDEVSRKTPNLCKLSPAGHHHIQDLHAA 317 Query: 328 GGVPSVMHELQKAGRLHEDCATVSGKTIGEIVS--NSLTSNTDVIHPFDTPLKHRAGFIV 385 GG+P+VM EL + G + TV+GKT+ E ++ N+ N DVI D P + G + Sbjct: 318 GGIPAVMAELTRKGLVDTSVMTVTGKTLAENLAELNARVLNPDVIRSADAPYSAQGGIAI 377 Query: 386 LSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDID 444 L G+ A++K S V EA A VF+ + HA I I+ Sbjct: 378 LKGSLAPQGAVVKQSAVAPEMMVR-----------EAVARVFDSEGEAHAAI--MGGKIN 424 Query: 445 ERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDS-LPCLGDGRQSGTSASPSILNMS 503 + ++IR G G PG E+ ++P AA+ G+ + + + DGR SG + +I ++S Sbjct: 425 KGDAIIIRYEGPRGGPGMREM--LSPTAAIAGMGLGADVALITDGRFSGGTRGAAIGHVS 482 Query: 504 PEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQRRREWIPNIPPSQTPWQELYRQ 563 PEAA GG + L++ D + +D+ R ++LL+D+AE+A RR ++P P +P Y + Sbjct: 483 PEAADGGNIGLVREGDHILIDIPARRLDLLVDEAELAARRETFVPLEKPVTSPLLRRYAR 542 Query: 564 LVGQLSTG 571 V +TG Sbjct: 543 QVTSAATG 550 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: 926 Number of extensions: 52 Number of successful extensions: 6 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: 555 Length adjustment: 36 Effective length of query: 558 Effective length of database: 519 Effective search space: 289602 Effective search space used: 289602 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