Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_068166822.1 HTA01S_RS01680 phosphogluconate dehydratase
Query= curated2:Q03UL2 (580 letters) >NCBI__GCF_001592305.1:WP_068166822.1 Length = 612 Score = 234 bits (598), Expect = 6e-66 Identities = 171/525 (32%), Positives = 262/525 (49%), Gaps = 48/525 (9%) Query: 47 KKPFIAICNSYVEIIPGHV-------HLRELADVAKQAIRDAGGIPFEFNTIGVDDGIAM 99 + P + I +Y +++ H LRE A + AGG+P + DG+ Sbjct: 69 RAPHVGIVTAYNDMLSAHQPYEHYPERLREYAHALGVTAQVAGGVP------AMCDGVTQ 122 Query: 100 GHLGMRYSLPSRELIADSAETVITAHWFDGVFFLPNCDKITPGMIMASLRC-NVPSVFVS 158 G GM SL SR++IA + ++ + FD FL CDKI PG+ M + + ++ +VFV Sbjct: 123 GAAGMELSLFSRDVIALATSVALSHNVFDAALFLGICDKIVPGLFMGAAQFGHLSAVFVP 182 Query: 159 GGPMKAGLDPQGKATTLSSMFEAVGAFKSGLMTEEEFLEMEQNACPTCGSCAGMFTANSM 218 GPM +GL KA + GL+ E LE E A + G+C TANS Sbjct: 183 AGPMTSGLSNDAKAKVRQQ-------YAQGLVGREALLESEAQAYHSPGTCTFYGTANSN 235 Query: 219 NTLMEVMGIALPFNGTALAISDERRDLIRDGAKQLM-----RMVKENVKPRDLITKEALD 273 LME+MG+ LP + + RD + A Q R + V D+++ + Sbjct: 236 QMLMEIMGLHLP-GASFVNPGTPLRDALTQAAMQRAVANTGRTGEPAVCLADILSVNTIV 294 Query: 274 DAMALDMAMGGSTNTVLHVLSIAHEAGIDYDQADINEIAKKVPYLSKIAPSSKWAMEDVH 333 + + +A GGSTN +H++++A AG+ D D E++ VP L+++ P+ + H Sbjct: 295 NGIIGLLATGGSTNHTIHLVAMARAAGVLIDWDDFAELSAVVPLLARVYPNGSADVNHFH 354 Query: 334 NAGGVPAIINELIRMGDVLHPDRMTVTGKTLRENVADHEI-------------INDEIIR 380 AGG+ +++EL+ G +LH + MTV G L V + + D + Sbjct: 355 AAGGMGFLMHELLTHG-LLHANVMTVMGAGLTAYVNEPWLDDGALAWRPVPTTSGDTSVL 413 Query: 381 KFDVNPYSKQGGLSILYGNLAPKGSVIKAGGVDPSIKDFTGEAIVFNSEQEAVEAIDSGQ 440 + P+S GGL +L GNL SV+K V P + +A+V + +Q+ + ++GQ Sbjct: 414 RPVAEPFSADGGLRLLKGNLG--RSVVKVSAVKPEHRVVRAQAVVVSDQQDLLALFNNGQ 471 Query: 441 IHAGHVLIIRYEGPKGGPGMPEM--LGPTSAITGMGLGKEVALVTDGRFSGASRGISVG- 497 I+ + ++RY+GP+ GMPE+ L P A+ G +VALVTDGR SGAS + Sbjct: 472 INKDLIAVVRYQGPRAN-GMPELHKLTPPLAVL-QDKGFKVALVTDGRMSGASGKVPAAI 529 Query: 498 HVSPEAADDGPIALVENGDKITIDLVNRTMHLHVDDTELAERHEH 542 H+SPEA DGPIA V +GD IT+D + L VD LA R+ H Sbjct: 530 HLSPEALADGPIARVMDGDWITLDCERGVLELEVDAATLAARNIH 574 Lambda K H 0.318 0.135 0.395 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: 812 Number of extensions: 45 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: 580 Length of database: 612 Length adjustment: 37 Effective length of query: 543 Effective length of database: 575 Effective search space: 312225 Effective search space used: 312225 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 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