Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate PP_1010 PP_1010 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Putida:PP_1010 Length = 608 Score = 268 bits (685), Expect = 4e-76 Identities = 183/539 (33%), Positives = 279/539 (51%), Gaps = 32/539 (5%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 + + +++N+++ H E +K +R G G + A+CDG+ G GM ++ Sbjct: 68 VAIVSAYNDMLSAHQPYLHFPEQIKQALREVGSVGQFAGGVPAMCDGVTQGEPGMELAIA 127 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SREVIA + + + + DA +M+ CDKI PG ++ A R +P I + GGPM+ G+ Sbjct: 128 SREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISN 187 Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211 K++ D R + EEL + E ++ PG+C TANT ++ E MGL LP Sbjct: 188 KQKADV-----RQRYAEGKASREELLESEMNSYHSPGTCTFYGTANTNQLVMEVMGLHLP 242 Query: 212 GASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAVDMALGGSTN 268 GAS V R ++ +M + + +I+ KAL N+I A GGSTN Sbjct: 243 GASFVNPYTPLRDALTAEAAQQVTRMTKASGSFMPLGEIVDEKALVNSIVALHATGGSTN 302 Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328 LH+ A+A GI L + ++S VP ++ + P+G+ + AGG+ +++EL + Sbjct: 303 HTLHIPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLD 362 Query: 329 AGLIHKDALTV---------------TGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLA 373 AGL+H+D TV GK VW + LD ++RP+ P+S GGL Sbjct: 363 AGLLHEDVNTVAGHGLRRYTQEPFLDNGKLVWREGPQHS-LDESILRPVSRPFSAEGGLR 421 Query: 374 ILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGP 433 +++G+L V+K SAV E + ARVF ++ A + GE+E V V+R++GP Sbjct: 422 VMEGNL--GRGVMKVSAVAPEHQVVEAPARVFQDQQSLADAFKAGELERDFVAVVRFQGP 479 Query: 434 RGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALV 491 R GM E+ T + L G KVALVTDGR SGA+ + PA HV PEA GGP+A V Sbjct: 480 RCN-GMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKIPAAIHVCPEAYDGGPLARV 538 Query: 492 QDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRG-ILRRYAKMALSADKGGA 549 +DGD + +D + L ++V +EL R P+ L G L + +MA S + GA Sbjct: 539 RDGDIVRVDGVEGTLRIMVSAEELASRELPPAPQGNDLGCGRELFGFMRMAFSPAEQGA 597 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: 852 Number of extensions: 59 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: 608 Length adjustment: 36 Effective length of query: 516 Effective length of database: 572 Effective search space: 295152 Effective search space used: 295152 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 09 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