Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate PfGW456L13_1889 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= curated2:B7JJG8 (557 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 Length = 608 Score = 251 bits (642), Expect = 4e-71 Identities = 174/509 (34%), Positives = 267/509 (52%), Gaps = 34/509 (6%) Query: 34 IAICNSFIEIIPGHKHLNEFGKLVKEAVRAAGMV-PFEFNTIGVDDGIAMGHIGMRYSLP 92 IAI +S+ +++ H+ F +L+K+A+R G V F T + DG+ G GM SLP Sbjct: 68 IAIVSSYNDMLSAHQPYEVFPELIKKALREIGSVGQFAGGTPAMCDGVTQGEPGMELSLP 127 Query: 93 SREIIADSVETVVNAHWFDGMICIPNCDKITPGMMMAALRI-NIPTVFVSGGPMAAGKTS 151 SRE+IA S ++ + FDG + + CDKI PG+MM ALR ++P +FV GGPM +G ++ Sbjct: 128 SREVIALSTAVALSHNMFDGALLLGICDKIVPGLMMGALRFGHLPMIFVPGGPMVSGISN 187 Query: 152 KGDVVDLSSVFEGVGAYQSGKISEEELKDIEDHGCPSCGSCSGMFTANSMNCLCEVLGLA 211 K D+ Y GK + EEL + E S G+C+ TAN+ L EV+GL Sbjct: 188 K-QKADVRQ------KYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 Query: 212 LPGNGSILAIDPRREELIKQAAEKLKILIER--DIKP-RDIVTEEAIDDAFALDMAMGGS 268 LPG + P R+ L ++AA ++ L ++ D P +IV E ++ ++ A GGS Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQVTRLTKQNGDFMPIGEIVDERSLVNSIVALHATGGS 300 Query: 269 TNTVLHTLALAQEAGLDYDMNRIDAVSRRVPHLCKVSPASNWHMEDIDRAGGISAILKEM 328 TN LH A+A AG+ + +S VP L V P + AGG+S +++E+ Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360 Query: 329 SRKEGVLHLDRITATGQTL----------------RENIAHAEIKDKEVIHSLENPHSEE 372 + G+LH + T G L RE + + D+ ++ + S E Sbjct: 361 -LEAGLLHENVNTVMGHGLSRYTQEPFLDNGQLVWREGV--TDSLDESILRPVARAFSAE 417 Query: 373 GGLRILKGNLAKDGAVIKSGATEVIRFEGPCVIFNSQDEALAGIMLGKVKKGDVVIIRYE 432 GGLR+++GNL + + + A E E P ++F Q + G ++K V ++R++ Sbjct: 418 GGLRVMEGNLGRGVMKVSAVAVENQIVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQ 477 Query: 433 GPRGGPGMPEMLAPTSAIAGM-GLGADVALLTDGRFSGASRGISVG-HISPEAAAGGTIA 490 GPR GMPE+ T + + G VAL+TDGR SGAS I H+SPEA GG +A Sbjct: 478 GPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALA 536 Query: 491 LLEQGDIVCIDVEERLLEVRVSDEELDKR 519 +++GDI+ +D + LE++V EE R Sbjct: 537 RVQEGDIIRVDGVKGTLELKVDAEEFAAR 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: 54 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: 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