Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011913559.1 PST_RS12285 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000013785.1:WP_011913559.1 Length = 609 Score = 270 bits (689), Expect = 2e-76 Identities = 179/521 (34%), Positives = 272/521 (52%), Gaps = 33/521 (6%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 + + +++N+++ H + E ++ +R G G + A+CDG+ G GM SL Sbjct: 69 VAIVSAYNDMLSAHQPYEHFPEMIRQALREIGSVGQFAGGVPAMCDGVTQGEAGMEMSLA 128 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SREVIA + + + + DA +M+ CDKI PG ++ A R +P I + GGPM G+ Sbjct: 129 SREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMIGALRFGHLPTIFVPGGPMPSGIPN 188 Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211 KE+ R + EEL + E + PG+C TANT ++ E MGL LP Sbjct: 189 KEKAAV-----RQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQVVMEIMGLHLP 243 Query: 212 GASTVPAVEARRLWYAKLTGMRIVKMVEEG--LTP-DKILTRKALENAIAVDMALGGSTN 268 G+S V R + ++ ++ + TP +++ K++ N++ A GGSTN Sbjct: 244 GSSFVNPYTPLRDALTREAAQQVTRLTHQAGNYTPLCQVVDEKSIVNSVVALNATGGSTN 303 Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328 LH+ A A GI L + ++S VP +A + P+G+ V GG+P +++ L + Sbjct: 304 HTLHIPAFARAAGIQLTWQDMADLSEVVPTLAKVYPNGQADVNHFHACGGVPFMVRTLLD 363 Query: 329 AGLIHKDALTVTGKTVWENVKD--------------AAVLDREVIRPLDNPYSPFGGLAI 374 AGL+H+D TV GK + +++ A LD ++RP + P+SP GGL + Sbjct: 364 AGLLHEDVHTVVGKGLRRYIQEPFLDGDKLVWRDGPAQSLDETILRPAERPFSPEGGLRV 423 Query: 375 LKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGPR 434 L+G+L V K SAV E + ARVF + + A + GE+E + V+R++GP+ Sbjct: 424 LEGNL--GRGVTKISAVAPEHRVVEAPARVFIDQSELAAAFKAGELERDFIAVVRFQGPK 481 Query: 435 GGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALVQ 492 GM E+ T + L G KVALVTDGR SGA+ + PA HV PEA GGP+ALV+ Sbjct: 482 AN-GMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVCPEALDGGPLALVR 540 Query: 493 DGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGI 533 DGD I +D E L LVD E R +P ++P GI Sbjct: 541 DGDIIRVDGETGELRALVDPAEWATR----QPAIRPEDMGI 577 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: 844 Number of extensions: 51 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: 552 Length of database: 609 Length adjustment: 36 Effective length of query: 516 Effective length of database: 573 Effective search space: 295668 Effective search space used: 295668 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