Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012976399.1 AZL_RS20625 phosphogluconate dehydratase
Query= curated2:B8DMM1 (555 letters) >NCBI__GCF_000010725.1:WP_012976399.1 Length = 612 Score = 261 bits (666), Expect = 7e-74 Identities = 176/514 (34%), Positives = 270/514 (52%), Gaps = 34/514 (6%) Query: 31 RPLVGVVNAANEVVPGHVHLHTIAEAVKAGVRAAGGTPMEFPAI-AVCDGLAMNHEGMHF 89 +P +G+V A N+++ H ++ VRAAGG + A+CDG+ +EGM Sbjct: 70 QPSIGIVTAYNDMLSAHQPYEHYPALIRQSVRAAGGVAQVAGGVPAMCDGVTQGYEGMEL 129 Query: 90 SLPSREIIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRMD-IPSIMVSGGPMLAG 148 SL SR++IA + + + FD ++ + CDK VPG+++ L +P+I V GPM +G Sbjct: 130 SLFSRDVIALATGVALSHATFDGVLCLGICDKIVPGLVIGSLAFGHLPTIFVPAGPMPSG 189 Query: 149 GTLAGRTDLISVFEAVGRVQRGDMTMAELDEMTETACPGCGSCAGMFTANTMNCMAETMG 208 + A + + ++ A G++ R ++ AE A G+C TANT + E MG Sbjct: 190 LSNADKAKVRQLY-AQGKIGRDELLEAE-----SQAYHAPGTCTFYGTANTNQMLMEIMG 243 Query: 209 LALPGNGTIPAVTAARVRLAKHAGMKVMELLEKNITPR--SIVTPRAVANAVAVDMALGG 266 L LPG + T R L A +V+ + I RA+ N + +A GG Sbjct: 244 LHLPGASFVNPDTPLRDALTDAAARRVVAMAAPGAGSPIGRIADERALVNGIVGLLATGG 303 Query: 267 STNTVLHLPAVFGEAGLDLTLDIFDEVSRKTPNLCKLSPAGHHHIQDLHAAGGIPAVMAE 326 STN LH+PA+ AG++LT + F ++S P L ++ P G + H AGG+P ++ + Sbjct: 304 STNHTLHIPAIAAAAGIELTWEDFSDLSAVVPLLARVYPNGSADVNRFHQAGGMPFIIGQ 363 Query: 327 LTRKGLVDTSVMTVTGKTLAE---NLAELNA------------RVLNPDVIRSADAPYSA 371 L GLV T + TV G+ E ++ EL+ + +P V+ + AP++A Sbjct: 364 LIDAGLVHTDIATVWGEGGLEPYRSMPELDEGGALSWTRSATDQSGDPTVVATTAAPFAA 423 Query: 372 QGGIAILKGSLAPQGAVVKQSAVAPEMMVREAVARVFDSEGEAHAAIMGGKINKGDAIII 431 +GG+ +L G+L V+K SAV PE V EA ARVFD++ AA G +++ +++ Sbjct: 424 EGGLRVLTGNLG--RGVIKISAVKPEHRVIEAPARVFDNQEAVQAAFRAGDLDRDVVVVV 481 Query: 432 RYEGP--RGGPGMREMLSPTAAIAGMGLGADVALITDGRFSG--GTRGAAIGHVSPEAAD 487 RY+GP G P + ++ P + G VAL+TDGR SG G AAI HV+PE Sbjct: 482 RYQGPAANGMPELHKLTPPLGVLQDKGF--KVALVTDGRMSGASGKVPAAI-HVTPEVKG 538 Query: 488 GGNIGLVREGDHILIDIPARRLDLLVDEAELAAR 521 GG +G VR+GD + +D A LD LVD AE +R Sbjct: 539 GGPLGRVRDGDILRLDAEAGTLDALVDSAEWQSR 572 Lambda K H 0.319 0.134 0.387 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: 997 Number of extensions: 66 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: 555 Length of database: 612 Length adjustment: 36 Effective length of query: 519 Effective length of database: 576 Effective search space: 298944 Effective search space used: 298944 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 (21.8 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