Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_057508152.1 ABB28_RS08120 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_001431535.1:WP_057508152.1 Length = 638 Score = 248 bits (632), Expect = 7e-70 Identities = 176/512 (34%), Positives = 266/512 (51%), Gaps = 37/512 (7%) Query: 32 PLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYS 90 P +G+ S+N+++ H + E ++ R G T G + A+CDG+ G GM S Sbjct: 68 PNLGIITSYNDMLSAHQPFETYPEQIREIAREWGATAQVAGGVPAMCDGVTQGRGGMELS 127 Query: 91 LPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGV 149 L SR+VIA + I + DA + + CDKI PG L+ A +P + + GPM PG+ Sbjct: 128 LFSRDVIAQSTAIGLSHDMFDAAIYLGVCDKIVPGLLIGALAFGHLPSVFVPAGPMTPGI 187 Query: 150 YGKERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLM 209 K++ + ++ E EEL + E ++ G G+C TAN+ +L EAMG+ Sbjct: 188 PNKQKAEVRE-----RYAAGEATREELLEAEAASYHGAGTCTFYGTANSNQVLLEAMGVQ 242 Query: 210 LPGASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAVDMALGGS 266 LPGAS V + R + +R ++M G +I+ +A+ NAI MA GGS Sbjct: 243 LPGASFVNPEQTLRGALTREATVRALEMTALGDDYRPIGRIIDERAIVNAIVALMATGGS 302 Query: 267 TNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKEL 326 TN +H A+A GI + + D++S+ +P + + P+G V AGG V EL Sbjct: 303 TNHTIHWIAVARAAGIVVTWDDMDQLSQLIPLLTRVYPNGEADVNRFAAAGGPAFVFGEL 362 Query: 327 GEAGLIHKDALTVT---------------GKTVWEN--VKDAAVLDREVIRPLDNPYSPF 369 AGL+H D +TV G+ W + ++ A D +V R +DNP+ Sbjct: 363 IRAGLMHGDIVTVARGGMADYAREPRLQDGQVTWVDGIIRSA---DEDVARGVDNPFESQ 419 Query: 370 GGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIR 429 GGL +L+G+L +++K SAVK + + A V D + K G + V V+R Sbjct: 420 GGLRLLRGNL--GRSLIKLSAVKPQYRSIEAPAVVVDAPQVLNKLHAAGLLPQDFVAVVR 477 Query: 430 YEGPRGGPGMREMLTATAAVMAL--GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGG 486 Y+GPR GM E L + A ++ L G +VALVTDGR SGA+ + PA H++PEAA GG Sbjct: 478 YQGPRAN-GMPE-LHSLAPLLGLLQNQGRRVALVTDGRLSGASGKIPAAIHMTPEAARGG 535 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518 P+ +++GD I +D E L++LVDE E R Sbjct: 536 PLGKLREGDIIRLDGEAGTLEVLVDEAEWAAR 567 Lambda K H 0.319 0.138 0.401 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: 970 Number of extensions: 65 Number of successful extensions: 9 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: 552 Length of database: 638 Length adjustment: 37 Effective length of query: 515 Effective length of database: 601 Effective search space: 309515 Effective search space used: 309515 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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