Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_011650505.1 RL_RS03935 phosphogluconate dehydratase
Query= SwissProt::P55186 (617 letters) >NCBI__GCF_000009265.1:WP_011650505.1 Length = 607 Score = 187 bits (476), Expect = 9e-52 Identities = 165/565 (29%), Positives = 257/565 (45%), Gaps = 54/565 (9%) Query: 35 PIIAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTI-AVDDGIAMGHGGMLYS 93 P + + ++ + H + ++ AGGVA+ + A+ DG+ G GM S Sbjct: 68 PNLGIITAYNDMLSAHQPFETYPAIIREAAAEAGGVAQVAGGVPAMCDGVTQGQPGMELS 127 Query: 94 LPSRDLIADSVEYMVNAHCADAIVCISNCDKITPGMLMAAMRL-NIPVVFVSGGPMEAGK 152 L SRDLIA S ++ + DA + + CDKI PG+++AA+ ++P +FV GPM G Sbjct: 128 LFSRDLIAMSAGVGLSHNMFDAALFLGVCDKIVPGLVIAALSFGHLPSIFVPAGPMTTGL 187 Query: 153 VT-VKGKIRALDLVDAMVVAADDSYSDEEVEAIEKAACPTCGSCSGMFTANSMNCLTEAL 211 K ++R L A+ E+ E + G+C+ TANS L E + Sbjct: 188 PNDEKSRVRQL--------FAEGKVGRAELLEAESKSYHGPGTCTFYGTANSNQMLMEIM 239 Query: 212 GLSLPGNGSVLATHADREALFKEAGRVVVDLCQRWYEQEDATALPRGIATRAAFENAMSL 271 G +PG+ + REAL +EA + + + E A + I R+ + L Sbjct: 240 GFHMPGSSFINPGTPLREALTREAAKRALAITALGNEFTPAGEM---IDERSVVNGVVGL 296 Query: 272 DIAMGGSTNTVLHLLAAAHEGGIDFSMADIDRLSRHVPCLSKVAP-AKSDVHMEDVHRAG 330 A GGSTN LHL+A A GI + DI LS VP L++V P +DV+ AG Sbjct: 297 H-ATGGSTNHTLHLVAMARAAGIQLTWQDIAELSEIVPLLARVYPNGLADVN--HFQAAG 353 Query: 331 GVMAILGELERGGLIDASQPTVHAPTMGEALARWDIGRTNSQIAHEFFKAAPGGKPTQVA 390 G+ ++ EL + GL+ TV G+ LA + + A GG Sbjct: 354 GMGFLIKELLKHGLVHDDVRTV----FGQGLAAYTV------------DARLGGN----- 392 Query: 391 FSQAARWEELDLDRENGVIRSVEHPFSKDGGLAVLFGNLAPEGCIVKTAGVDESILTFRG 450 R + + V+ S+E PF +GGL +L GNL ++K + V Sbjct: 393 -GAVLREPSPEKSVDPKVLSSIETPFQANGGLKMLRGNLGK--AVIKISAVKPERHIIEA 449 Query: 451 TARVFESQDAAVSGILGGQVKAGEVVVIRYEGPK--GGPGMQEMLYPTTYLKSKGLGAAC 508 A +F SQ A G++ + V+R++GPK G P + ++ P L+ +G Sbjct: 450 PAIIFHSQQALQDAFKEGKLNRDFIAVVRFQGPKANGMPELHKLTPPLGVLQDRGF--RV 507 Query: 509 ALVTDGRFSGGTSGLSIG-HVSPEAGEGGLIALVETGDPILIDIPTRGITLEVSDAVLAA 567 AL+TDGR SG + + HV+PEA +GG IA + GD I +D + + V A +A Sbjct: 508 ALLTDGRMSGASGKVPAAIHVTPEAVDGGPIARIREGDIIRLDAIKGTLEVLVDAADMAE 567 Query: 568 RR-------EAQLARGKDAWTPLNR 585 R + + G++ + P R Sbjct: 568 REPVVVDLSDNEFGMGRELFAPFRR 592 Lambda K H 0.318 0.134 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: 981 Number of extensions: 61 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: 617 Length of database: 607 Length adjustment: 37 Effective length of query: 580 Effective length of database: 570 Effective search space: 330600 Effective search space used: 330600 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