Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_059151689.1 V474_RS11785 phosphogluconate dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_001046635.1:WP_059151689.1 Length = 608 Score = 197 bits (502), Expect = 8e-55 Identities = 162/544 (29%), Positives = 260/544 (47%), Gaps = 53/544 (9%) Query: 33 GKPI-IAVVNSFTQFVPGHV---HLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHD 88 GK I + ++ ++ + H D +L ARE+ A VA A+ DG+ G D Sbjct: 70 GKSINLGIITAYNDMLSAHQPYGRYPDQMKLFAREVGATAQVAG--GVPAMCDGVTQGFD 127 Query: 89 GMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRL-NIPTVFVSGGP 147 GM SL SR+ IA S ++ D + CDKI PG+ + ++R ++P +FV GP Sbjct: 128 GMELSLFSRDTIALSTAIGLSHAMFDGTALLGICDKIVPGLFIGAMRFGHLPAIFVPAGP 187 Query: 148 MEAGKVVMHGKTHALDLVDAMVAAADDKISDEDVQTIERSACPTCGSCSGMFTANSMNCL 207 M +G + K L A+ K+ E++ E ++ + G+C+ TANS + Sbjct: 188 MPSG-ISNKEKQKTRQLY------AEGKVGREELLASESASYHSAGTCTFYGTANSNQMM 240 Query: 208 TEALGLSLPGNGSTLATHLDRKRLFVEAGHLIVDLARRYYEQDDVKALPRTIASKQAFEN 267 E +GL +P + R+ L EA H + + R+ +D + + + + K A N Sbjct: 241 MELMGLHVPASAFVQPNTPLRQALTREATHRLAAMTRK---GEDYRPMAKVVDEK-AIIN 296 Query: 268 AMTLDIAMGGSTNTVLHILAAAHEGEIDFTMADIDALSRRVPCLSKVAPAKSDVHMEDVH 327 AM +A GGSTN +H+ A A G I D D LS VP +++V P S + Sbjct: 297 AMAGLLATGGSTNHAIHLPAMARAGGILIDWEDFDELSSVVPLITRVYPNGSG-DVNHFQ 355 Query: 328 RAGGIMSILGELDKGGLLNRDCPTVHAETLGDAIDRWDITRTNSETVRKFYRAAPGGIPT 387 AGGI ++ EL GL + D TV T G A Y + P Sbjct: 356 AAGGIGWVIRELLGAGLAHGDVLTV--ATGGMAA----------------YASEP----- 392 Query: 388 QVAFSQEARWDELDTDRENGVIRSVEHPFSKDGGLAVLKGNLAIDGCIVKTAGVDESILK 447 V + W + ++ ++R V +PF DGG+ +++GNL KT+ VDE Sbjct: 393 -VMRDDKLSWIPIPETTDDTMVRPVSNPFLPDGGMRLVQGNLGRG--TFKTSAVDEQRWT 449 Query: 448 FSGPARVFESQDASVKAILANEVKAGDVVVIRYEGPK--GGPGMQEMLYPTSYLKSKGLG 505 P RVF++Q+ +A A E+ +VV+R++GP+ G P + ++ P L+ KG Sbjct: 450 IEAPCRVFDTQEGVSQAFKAGELDRDVIVVVRFQGPRANGMPELHKLTPPLGVLQDKGF- 508 Query: 506 KACALITDGRFSGGTSGLSIG-HASPEAANGGTIGLVREGDMIDIDIPNRTISLRVSETE 564 AL+TDGR SG + + H +PEA GG + +++GD++ + + T+S + + Sbjct: 509 -KVALVTDGRMSGASGKVPAAIHVTPEALGGGPLAYLQDGDIVRLCAEDGTLS---TTAD 564 Query: 565 LAAR 568 L+AR Sbjct: 565 LSAR 568 Lambda K H 0.318 0.134 0.391 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: 911 Number of extensions: 53 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 612 Length of database: 608 Length adjustment: 37 Effective length of query: 575 Effective length of database: 571 Effective search space: 328325 Effective search space used: 328325 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 Jul 26 2024. The underlying query database was built on Jul 25 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