Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_034999263.1 DL88_RS17860 phosphogluconate dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000745425.1:WP_034999263.1 Length = 612 Score = 241 bits (614), Expect = 8e-68 Identities = 168/522 (32%), Positives = 276/522 (52%), Gaps = 54/522 (10%) Query: 32 PLIGIVNSHNEIIPGHF---HLNEIVQAVKLGVAS----AGGTPIEIPSIGICDGISMNH 84 P + I+ ++N+++ H H E++++ A AGG P +CDGI+ Sbjct: 71 PNLAIITAYNDMLSAHRPYEHYPELIRSAAREAACTAQVAGGVP------AMCDGITQGE 124 Query: 85 SGMKYPLASRELIADSIEAMTIAHK-FDALVLVGNCDKIVPGMLMGAARL-NVPAIYVSG 142 +GM L SR++IA S A+ ++H+ FDA V +G CDKIVPG+++GA ++PA+++ Sbjct: 125 AGMDLSLFSRDVIALST-AVALSHQTFDAAVYLGICDKIVPGLVIGALSFGHLPAVFIPS 183 Query: 143 GPM---LPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCAGLFTAN 199 GPM +P K K L + EG + + L +E S G+C TAN Sbjct: 184 GPMPSGIPNPEKAKVRQL----------FVEGKVGREALLDVEARSYHAPGTCTFYGTAN 233 Query: 200 SMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELV---KKKIKLRDILTKEAFK 256 + L E +G+ LPG + R+ L + A + + L + + +L + AF Sbjct: 234 TNQMLMEIMGLHLPGASFVTPDTPLREALTRAAATRALALTALGNEYTPIGRLLDERAFV 293 Query: 257 NAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMVDLD 316 N I A GGS+N TLHL+A+A A + + +DF +++ P +T++ P G+ + Sbjct: 294 NGIVGLNATGGSTNHTLHLVAMAAAAGILIDWQDFADLAEVTPLLTRIYPNGSADVNHFH 353 Query: 317 EAGGISAVLKELMDANLIFKDQLTVTGKTLEENIK-------NSLVLND--------SVI 361 AGG+ +++EL+D L+ +D TV G+TLE + +LV D +V+ Sbjct: 354 AAGGMGFLIRELLDVGLLHRDAGTVFGQTLEAYTQEPGLDGDGALVWRDAPAQSGDPAVL 413 Query: 362 RPLNNPYSNEGGIAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVFDGEELAFDAIMNKK 421 RP+ +P+ GG+ +L G+L AV+K SAV PE + AR+F +E A + Sbjct: 414 RPVADPFQATGGLKLLNGSLG--RAVIKTSAVAPERHVIEAPARIFHSQEALQAAFKAGE 471 Query: 422 IHPGDVVVIRYEGPK--GCPGMREMLSPTAAIIGLGLEKSTALITDGRFSGGT-RGPCIG 478 + V V+R++GPK G P + +++ P ++ G + AL+TDGR SG + + P Sbjct: 472 LERDVVAVVRFQGPKAIGMPELHKLMPPLGSLQDRGFK--VALVTDGRLSGASGKVPAAI 529 Query: 479 HISPEASEGGPIALIEEGDLIEIDISNRRISLLVSPEELSKR 520 H++PEA EGGPIA + +GDL+ +D +S+LV +E + R Sbjct: 530 HVTPEAVEGGPIARLRDGDLVRLDAVAGTLSVLVDAQEWAAR 571 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: 853 Number of extensions: 56 Number of successful extensions: 8 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: 612 Length adjustment: 36 Effective length of query: 518 Effective length of database: 576 Effective search space: 298368 Effective search space used: 298368 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 10 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