Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF2757 PGA1_c28000 phosphogluconate dehydratase Edd
Query= curated2:A4YEN4 (557 letters) >FitnessBrowser__Phaeo:GFF2757 Length = 607 Score = 250 bits (638), Expect = 1e-70 Identities = 178/532 (33%), Positives = 270/532 (50%), Gaps = 40/532 (7%) Query: 16 KAPNRAFLKAMG------LTDDDISKPL-------VGVAVAWNEAGPCNIHLLGLSQVVK 62 K P RA L G T +D PL +G+ A+N+ + Q ++ Sbjct: 35 KGPARAHLSCSGQAHAYAATGED-QMPLAEGTAGHLGIVTAYNDMLSAHQPFETYPQRIR 93 Query: 63 EGIRELGGTPRTFTA-PVLIDGIAMGSESMKYSLVSREVIANTVELTVNGHGYDGFVALG 121 + +R +GGT + P + DG+ G M+ SL SR+ IA + ++ + +D V LG Sbjct: 94 DAVRRVGGTAQVAGGVPAMCDGVTQGEAGMELSLFSRDTIAMATGIALSHNVFDATVYLG 153 Query: 122 GCDKTQPGLMMSMARL-NIPSVYMYGGTTLPGNFRGRDIAIGDVYEAVGAFSAGKITAED 180 CDK PGL++ ++P+V++ G G I+ D + F+AG+I ++ Sbjct: 154 VCDKIVPGLVIGAQVFGHLPAVFLPAGPMTSG------ISNDDKAKVRQKFAAGEIGRDE 207 Query: 181 LRIMEDNAIPGPGACGGLYTANTMAMLSEALGLSLPGSSAPPAVSSDRTKFAKETGRTLM 240 L E A GPG C TANT ML E +GL LPGSS + R +E R + Sbjct: 208 LLKSEMAAYHGPGTCTFYGTANTNQMLMEFMGLHLPGSSFVNPGTDMRAALTEEGARRAL 267 Query: 241 KVMEIG---LKPRDILTFEAFENGIALLMASGGSTNGVLHLLAIAHEAGVSLTLDDFDRI 297 + +G DIL A+ NGI LM +GGSTN ++HL+A+A G+ L DF + Sbjct: 268 ALSALGNDYTPVCDILDERAYVNGIVGLMTTGGSTNLLIHLIAMARAGGIILDWQDFSEL 327 Query: 298 SKKVPEIVNMKPGGDYVMADLYRVGGTPVILKKLLDRGLLHGDTITVTGKTMAQNLSEYK 357 S VP + + P G + + GG ++ +LL+ G LH DT TV G + +E Sbjct: 328 SDVVPLLARVYPNGLADVNHFHAAGGLGYVIGQLLNSGHLHSDTRTVAGSGLESYTAEPF 387 Query: 358 I-----------PEFKHDHIVRDLSNPFLPSGGIRILKGSLAPEGSVVKLSASKIKYHRG 406 + E +D I+R S PF P+GG+ L G+L + A + + Sbjct: 388 LSDDGLVWKPGAAESLNDKIIRPASAPFQPTGGLARLSGNLGTGVMKISAVAPEHRMVEA 447 Query: 407 PARVFNSEEEAFETVLKKKINEGD-VVVIRYEGPKGGPGMREMLAVTSAI-VGQGLGEKV 464 PARVF+ +EE ++++GD ++V+R++GPK GM E+ ++T + + QG G+KV Sbjct: 448 PARVFHDQEEVKAAFKAGELDKGDMIIVVRFQGPKAN-GMPELHSMTPFLGIMQGRGQKV 506 Query: 465 ALVTDGRFSGATRGLMVG-HVAPEAAVGGPIALIRDGDTIVIDGEKGRLDVE 515 ALVTDGR SGA+ + HV PEA GGPI+ +RDGD + +D G L+V+ Sbjct: 507 ALVTDGRMSGASGKIPSAIHVVPEALDGGPISKLRDGDMVRVDALTGTLEVK 558 Lambda K H 0.316 0.137 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: 932 Number of extensions: 47 Number of successful extensions: 7 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: 557 Length of database: 607 Length adjustment: 36 Effective length of query: 521 Effective length of database: 571 Effective search space: 297491 Effective search space used: 297491 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