Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Ga0059261_2649 Ga0059261_2649 Dihydroxyacid dehydratase/phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Korea:Ga0059261_2649 Length = 618 Score = 300 bits (768), Expect = 1e-85 Identities = 188/515 (36%), Positives = 285/515 (55%), Gaps = 24/515 (4%) Query: 23 GLIDEELR--RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGI 80 GL +ELR RP+IG+A + +++ P + H +AE V+ GIR AGG +EF + + Sbjct: 55 GLSLKELRSGRPIIGIAQTGSDLSPCNRHHLVLAERVREGIRDAGGIAIEFPVHPIQETG 114 Query: 81 AMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILI 140 G+ +L ++ + + LD VV+ CDK TP L+AAA + +P I + Sbjct: 115 KRPTAGLDRNLAYLGLVE-----ALYGYPLDGVVLTIGCDKTTPACLMAAATVNIPAIAL 169 Query: 141 NGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSCAGLFTANT 198 + GPM+ G + ER ++ + ++ G + E +L S+ P G C + TA T Sbjct: 170 SVGPMLNGWHKGERTGSGTIVWKARQMLAAGEIDDDEFIRLVASSAPSTGYCNTMGTATT 229 Query: 199 MNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIA 258 MN L+EA+G+ LPG++ +PA R A TG+R V++V + P ILTR+A ENAI Sbjct: 230 MNSLAEALGMSLPGSAAIPAPHRDRQEVAYQTGLRAVELVRADVKPSDILTREAFENAIV 289 Query: 259 VDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGG 318 V+ A+GGSTN+ +HL A+A +G+DLP++ + E VP + ++ P+G + D RAGG Sbjct: 290 VNSAIGGSTNAPIHLAAIARHIGVDLPIDAWQEKGHAVPLLVNLQPAGEYLGEDYYRAGG 349 Query: 319 IPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGS 378 +PAV+ +L +AGLIH+DA TV GK++ N + A+ D +VIRP P G +L+G+ Sbjct: 350 VPAVVSQLIDAGLIHEDAGTVNGKSIGANCRGVAIEDEKVIRPFAQPLKDAAGFIVLRGN 409 Query: 379 LAPNGAVVKASAVKRELW-----------KFKGVARVFDREEDAVKAIRGGE--IEPGTV 425 L A++K S + E F+G A VFD ED I I P T+ Sbjct: 410 LF-ESAIMKTSVISDEFRDRYLSNPDDPDAFEGPAVVFDGPEDYHARIDDPALGITPETL 468 Query: 426 IVIRYEGPRGGPGMREMLTATAAVMALGLG-DKVALVTDGRFSGATRGPAIGHVSPEAAA 484 + +R GP G PG E++ + G + + DGR SG + P+I + SPEAAA Sbjct: 469 LFMRGAGPVGYPGAAEVVNMRPPAYLIREGIHALPCIGDGRQSGTSGSPSILNASPEAAA 528 Query: 485 GGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERR 519 G +AL++ GD + ID+ K D+L+ EL ERR Sbjct: 529 MGGLALIRTGDRVRIDLGKGTADVLIPSAELAERR 563 Lambda K H 0.319 0.138 0.401 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: 905 Number of extensions: 51 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: 552 Length of database: 618 Length adjustment: 36 Effective length of query: 516 Effective length of database: 582 Effective search space: 300312 Effective search space used: 300312 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 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