Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Ac3H11_3523 Xylonate dehydratase (EC 4.2.1.82)
Query= curated2:A0Q0E8 (554 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3523 Length = 593 Score = 279 bits (714), Expect = 2e-79 Identities = 180/553 (32%), Positives = 294/553 (53%), Gaps = 24/553 (4%) Query: 19 FYAMGYTPEDLK--KPLIGIVNSHNEIIP-GHFHLNEIVQAVKLGVASAGGTPIEIPSIG 75 F G TPE+L+ +P+IGI + +++ P HL ++ + V+ G+ AGG P+E P Sbjct: 31 FMNYGLTPEELRSGRPIIGIAQTGSDLSPCNRIHL-DLARRVRDGIRDAGGIPMEFPVHP 89 Query: 76 ICDGISMNHSGMKYPLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARLNV 135 I + + + LA L+ + + DA+VL CDK P +M A+ +++ Sbjct: 90 IFENCRRPTAALDRNLAYLGLVE-----ILYGYPIDAVVLTTGCDKTTPAGVMAASTVDI 144 Query: 136 PAIYVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCAGL 195 PAI +SGGPML G G+ + + + A G + +++ + +S P+ G C + Sbjct: 145 PAIVLSGGPMLDGWHDGQLVGSGTVIWRSRRQLAAGEIDEEEFLQRACNSAPSAGHCNTM 204 Query: 196 FTANSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKEAF 255 TA++MN++AEALG++LPG IPAPY R Q+A G +I+E+ + ++ ILT+E+F Sbjct: 205 GTASTMNAVAEALGLSLPGCAAIPAPYRERGQMAYETGRRIVEMAYEDLRPSRILTRESF 264 Query: 256 KNAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMVDL 315 NA+++ GGSSN +H+MA+A A V LT +D+ + + +P + + PAG Sbjct: 265 LNALSVVSVAGGSSNAQVHIMAMARHAGVQLTAQDWTDHAYDLPLLLNMQPAGQFLGERF 324 Query: 316 DEAGGISAVLKELMDANLIFKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYSNEGGIA 375 AGG+ A++ EL A + D +VTGKT+ EN++ + VIRP +NP ++ G Sbjct: 325 FRAGGVPALMWELQQAGKLHADCASVTGKTVGENLQGRETHDREVIRPFSNPLMHKAGFM 384 Query: 376 ILRGNLAPDGAV---VKQSAVEPEMLYHKGVARVFDGEELAFD------AIMNK---KIH 423 +L GNL G + V A L G +F+ + F+ A +N I Sbjct: 385 VLSGNLFDFGIMKTSVISEAFRQRYLSRPGQEGIFEARAVVFEGADDYHARINDPALNID 444 Query: 424 PGDVVVIRYEGPKGCPGMREM--LSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHIS 481 G ++V+R GP G PG E+ + P A+I G+ + + DGR SG P I + S Sbjct: 445 EGCILVMRGAGPIGWPGSAEVVNMQPPDALIKRGI-NTLPTLGDGRQSGTADSPSILNAS 503 Query: 482 PEASEGGPIALIEEGDLIEIDISNRRISLLVSPEELSKRKENWIQPPCKAPDGTYLKRYS 541 PE++ GG ++ ++ GD + ID++ R LV+PEE+++RK + PP A + Y Sbjct: 504 PESAVGGGLSWLQSGDTVRIDLNTGRCDALVTPEEIARRKRDLPAPPVPASQSPWEALYR 563 Query: 542 KLVTSASTGAVLE 554 + + GA L+ Sbjct: 564 EKTGQLADGATLD 576 Lambda K H 0.317 0.136 0.392 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: 780 Number of extensions: 36 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: 554 Length of database: 593 Length adjustment: 36 Effective length of query: 518 Effective length of database: 557 Effective search space: 288526 Effective search space used: 288526 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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