Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate H281DRAFT_03422 H281DRAFT_03422 dihydroxyacid dehydratase (EC 4.2.1.9)
Query= curated2:A0Q0E8 (554 letters) >FitnessBrowser__Burk376:H281DRAFT_03422 Length = 592 Score = 348 bits (894), Expect = e-100 Identities = 209/519 (40%), Positives = 304/519 (58%), Gaps = 14/519 (2%) Query: 15 HRSLFYAMGYTPED-LKKPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPS 73 HRS MGY D + KP+I +VN+ +EI H H + V+ VK G+ AGG P+E+P Sbjct: 26 HRSRTAQMGYHASDYMGKPVIAVVNTWSEINSCHTHFKQRVEEVKRGIWQAGGFPVEMPV 85 Query: 74 IGICDGISMNHSGMKYPLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARL 133 + + + + M Y R +A E + ++ FD VL+G CDK PG+LMGA + Sbjct: 86 MTLAEPFQ-KPTTMLY----RNFLAMETEEILKSYPFDGCVLMGGCDKTTPGLLMGAISM 140 Query: 134 NVPAIYVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCA 193 N+P+I++ GPML G G+ + ++ G +++D+ IE + G C Sbjct: 141 NLPSIFLPAGPMLRGNWNGRTLGSGSDTWKYWAELRAGKITEDEWKGIESGIARSPGHCM 200 Query: 194 GLFTANSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKE 253 + TA++M S AEALG+ LPG +IPA R Q A G +I+E+V +K DILT + Sbjct: 201 TMGTASTMTSAAEALGLTLPGFSSIPAVDSRHAQFASLTGQRIVEMVWTDVKPSDILTAK 260 Query: 254 AFKNAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMV 313 +F NA+ +A+ GS+N +HL+A+A A + LT FDE+SR P I L P+G + M Sbjct: 261 SFDNAVTTVLAMSGSTNAIVHLVAVARRAGIDLTTARFDELSRITPVIGNLRPSGQYLME 320 Query: 314 DLDEAGGISAVLKELMDANLIFKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYSNEGG 373 D AGG+ A+L EL D LI Q+TV G TL ENI + + ND VIR NP G Sbjct: 321 DFFYAGGLRALLLELGD--LIDGSQMTVNGSTLGENIAGAEIFNDDVIRKRGNPVVASDG 378 Query: 374 IAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVF-DGEELAFDAIM-NKKIHPGDVVVIR 431 +A+L GNLAPDGAV+K +A+E +L H+G A VF D ++A M + I V+V++ Sbjct: 379 LAVLTGNLAPDGAVIKPAAMEAHLLNHRGRAVVFKDYADMAARIDMEDLDITADSVIVLQ 438 Query: 432 YEGPKGCPGMRE--MLSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISPEASEGGP 489 + GP G PGM E L ++ G+ + I+D R SG + G C+ H++PE+ GGP Sbjct: 439 HAGPVGAPGMPEWGQLPIPQKLLKQGV-RDMVRISDARMSGTSYGACVLHVAPESFVGGP 497 Query: 490 IALIEEGDLIEIDISNRRISLLVSPEELSKRKENWIQPP 528 +AL+++GD+I++D++ RR+ L VS EELS RK W QPP Sbjct: 498 LALVKDGDMIQLDVAARRLHLEVSDEELSARKAAW-QPP 535 Lambda K H 0.317 0.136 0.392 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: 731 Number of extensions: 27 Number of successful extensions: 5 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: 554 Length of database: 592 Length adjustment: 36 Effective length of query: 518 Effective length of database: 556 Effective search space: 288008 Effective search space used: 288008 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 (21.6 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