Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF835 Psest_0849 6-phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__psRCH2:GFF835 Length = 608 Score = 259 bits (661), Expect = 3e-73 Identities = 176/507 (34%), Positives = 267/507 (52%), Gaps = 31/507 (6%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 + + ++N+++ H + E ++ +R G G + A+CDG+ G GM ++ Sbjct: 68 VAIVTAYNDMLSAHQPYEGYPERLRQALRDVGSVGQVAGGVPAMCDGVTQGEPGMELAIA 127 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SREVIA + + + + DA +++ CDKI PG L+ A R +P + + GPM G+ Sbjct: 128 SREVIAMSTAVALSHNLFDAALLLGICDKIVPGLLIGALRFGHLPAVFVPAGPMPSGLAN 187 Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211 K++ R + +EL E A PG+C TANT ML E MGL LP Sbjct: 188 KDKAAV-----RQRYAEGKASRDELLAAEMQAYHSPGTCTFYGTANTNQMLMEVMGLHLP 242 Query: 212 GASTV-PAVEARRLWYAKLTGMRIVKMVEEG--LTP-DKILTRKALENAIAVDMALGGST 267 G+S V P R A+ ++ ++ +G TP +++ + L NAI A GGST Sbjct: 243 GSSFVNPGTPLRDALTAE-AARQVTRLTPQGGCFTPLGELVDERVLVNAIVALHATGGST 301 Query: 268 NSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELG 327 N LH+ A+A GI L + ++S VP +A + P+G + AGG+ +++EL Sbjct: 302 NHTLHMPAIAQAAGIQLTWQDMADLSAVVPTLARVYPNGPADINHFHAAGGVAVLVRELL 361 Query: 328 EAGLIHKDALTVTGKTVWENVKD--------------AAVLDREVIRPLDNPYSPFGGLA 373 AGL+H+D TV G+ + ++ AA LD ++RP+ P+S GGL Sbjct: 362 AAGLLHEDVHTVMGRGLSRYTQEPFLEGGRLTWREGAAASLDESLLRPVARPFSAEGGLR 421 Query: 374 ILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGP 433 ++ G+L V+K SAV E + ARVF + + V+A + GE+E V V+R++GP Sbjct: 422 VMSGNL--GRGVMKVSAVAPEHRVVEAPARVFADQLELVEAFKAGELERDVVAVVRFQGP 479 Query: 434 RGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALV 491 R GM E+ T + L G KVALVTDGR SGA+ + PA HV PEA GGP+A V Sbjct: 480 RAN-GMPELHKLTPYLGLLQDRGFKVALVTDGRMSGASGKVPAAIHVCPEAIDGGPLARV 538 Query: 492 QDGDEIVIDIEKRRLDLLVDEKELEER 518 +DGD + +D + L++LVD EL R Sbjct: 539 RDGDLLRVDGQAGVLEVLVDAAELAGR 565 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: 924 Number of extensions: 53 Number of successful extensions: 7 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