Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Ac3H11_2082 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= curated2:Q9YG88 (553 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Length = 589 Score = 244 bits (623), Expect = 7e-69 Identities = 192/542 (35%), Positives = 276/542 (50%), Gaps = 44/542 (8%) Query: 35 PLIAVVAAWSEAGPCN--FNVLPGSLR---VKEG--VRSAGGVPLAVPTIVVNDGINMGT 87 P I VV A+++ + + P LR K+G V+ AGGVP + DG+ GT Sbjct: 66 PNIGVVTAYNDMLSAHQPYQSYPAVLRDEAAKQGATVQVAGGVP------AMCDGVTQGT 119 Query: 88 PGMRYSLISRELIADTIEAQVASHGFDGWVGIGGCDKTQPGIMM-AMARLDLPSIYIYGG 146 PGM SL SR+ IA ++ FDG + +G CDK PG+++ A+ LP +++ G Sbjct: 120 PGMELSLFSRDAIAMATAVALSHDVFDGALLLGVCDKIVPGLLIGALHYGHLPCVFVPAG 179 Query: 147 TAEHGVLDGETVTVQSAFEAVGAYLKGLIDEERLYEIEKAAMPTPGTCQGLFTANTMAIL 206 G+ + + V+ Y +GL+ + L + E AA +PGTC TAN+ +L Sbjct: 180 PMGTGLSNKDKAKVREQ------YAQGLVGRDELLQAESAAYHSPGTCTFYGTANSNQML 233 Query: 207 AEALGLSPLGSA--SPPATSSERARELARAGALAVGLVETGLTP-RRILTYEAFYNAIVT 263 EA+GL G+A SP + E A L +G TP +++ NA+ Sbjct: 234 LEAMGLHVPGAAFESPGTEAREAFTRQALRTVLDIGKRSKRFTPIGKLVDERCIVNAMAA 293 Query: 264 LMAISGSTNAVLHLLAIAREAGVKLALDDFDEASRKVPVIAALAPAGKYTMVDLHNVGGA 323 L+A GSTN ++H +AIAR AG+ + DFDE S VP++A + P G + GG Sbjct: 294 LLATGGSTNHLIHWVAIARSAGILIDWTDFDELSSVVPLLARVYPNGDADVNQFQAAGGP 353 Query: 324 PVILRKLLDRGLLYGE--AVTVEGVEIGKLLSKWEPRT--DYNILYDFDKPYKPHAGLRI 379 P ILR+LL G ++ + +V V G+ G K P D ++L P+ P GLR+ Sbjct: 354 PWILRELLAGGFMHPDVMSVNVGGIADG---GKSAPAVSGDTSVLRPVSAPFSPTGGLRL 410 Query: 380 LRGSLAPRGAVMKIGASGILK--FKGAAKVFDSEEEAFKAIERGYVEEGDVVVVRYVGPK 437 L+G L AV+K+ A + + A+VFDS+E A G V + V VVR+ GP+ Sbjct: 411 LQGRLG--RAVIKVSAVPEDRHIIEAPARVFDSQEALLAAFSAGDVNQDMVAVVRFQGPQ 468 Query: 438 GAPGMPEMLKITAAI-VGAGLGEKVALITDGRFSGATRGVMVG-HAAPEAAVGGPIALVE 495 A GMPE+ K+T + V G KVAL+TDGR SGA+ V H PEA GGP+A V Sbjct: 469 -ANGMPELHKLTPPLAVLQNQGFKVALVTDGRMSGASGKVPAAIHVTPEALAGGPLAKVR 527 Query: 496 NGDEIVIDGEKGTLDVLLGGDELARRRDKWSPPPLPKQ-----GLLRKYAKLVTQADEGA 550 +GD + +D GTLDVL+ DE SP P Q L + + A++GA Sbjct: 528 DGDIVRVDAVAGTLDVLV--DEATWAARTPSPYSAPAQTGFGRELFTNFRRHAGGAEQGA 585 Query: 551 VT 552 T Sbjct: 586 CT 587 Lambda K H 0.318 0.138 0.402 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: 843 Number of extensions: 54 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: 553 Length of database: 589 Length adjustment: 36 Effective length of query: 517 Effective length of database: 553 Effective search space: 285901 Effective search space used: 285901 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 (21.7 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