Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Pf6N2E2_2898 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= curated2:B7JJG8 (557 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2898 Length = 608 Score = 249 bits (637), Expect = 2e-70 Identities = 170/507 (33%), Positives = 265/507 (52%), Gaps = 30/507 (5%) Query: 34 IAICNSFIEIIPGHKHLNEFGKLVKEAVRAAGMV-PFEFNTIGVDDGIAMGHIGMRYSLP 92 IAI +S+ +++ H+ F + +K+A+R G V F T + DG+ G GM SLP Sbjct: 68 IAIVSSYNDMLSAHQPYETFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 Query: 93 SREIIADSVETVVNAHWFDGMICIPNCDKITPGMMMAALRI-NIPTVFVSGGPMAAGKTS 151 SRE+IA S ++ + FDG + + CDKI PG+MM ALR ++PT+FV GGPM +G ++ Sbjct: 128 SREVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISN 187 Query: 152 KGDVVDLSSVFEGVGAYQSGKISEEELKDIEDHGCPSCGSCSGMFTANSMNCLCEVLGLA 211 K + D+ Y GK + EEL + E S G+C+ TAN+ L EV+GL Sbjct: 188 K-EKADVRQ------RYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 Query: 212 LPGNGSILAIDPRREELIKQAAEKLKILIERD---IKPRDIVTEEAIDDAFALDMAMGGS 268 LPG + P R+ L ++AA ++ + ++ + +IV E ++ ++ A GGS Sbjct: 241 LPGASFVNPNTPLRDALTREAAFQVTRMTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300 Query: 269 TNTVLHTLALAQEAGLDYDMNRIDAVSRRVPHLCKVSPASNWHMEDIDRAGGISAILKEM 328 TN LH A+A AG+ + +S VP L V P + AGG+S +++E+ Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360 Query: 329 SRKEGVLHLDRITATGQTLRENIAHAEIKDKE--------------VIHSLENPHSEEGG 374 + G+LH + T G L ++D E ++ + S EGG Sbjct: 361 -LEAGLLHENVNTVLGHGLSRYTQEPFLEDGELVWRDGPIESLDENILRPVARAFSPEGG 419 Query: 375 LRILKGNLAKDGAVIKSGATEVIRFEGPCVIFNSQDEALAGIMLGKVKKGDVVIIRYEGP 434 LR+++GNL + + + A E E P ++F Q + G ++K V ++R++GP Sbjct: 420 LRVMEGNLGRGVMKVSAVALENQVVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGP 479 Query: 435 RGGPGMPEMLAPTSAIAGM-GLGADVALLTDGRFSGASRGISVG-HISPEAAAGGTIALL 492 R GMPE+ T + + G VAL+TDGR SGAS I H+SPEA GG +A + Sbjct: 480 RSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARV 538 Query: 493 EQGDIVCIDVEERLLEVRVSDEELDKR 519 ++GDI+ +D + LE++V EE R Sbjct: 539 QEGDIIRVDGVKGTLELKVDAEEFAAR 565 Lambda K H 0.318 0.137 0.400 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: 801 Number of extensions: 51 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: 557 Length of database: 608 Length adjustment: 36 Effective length of query: 521 Effective length of database: 572 Effective search space: 298012 Effective search space used: 298012 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 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