Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate YP_002827149.1 NGR_c26400 dihydroxy-acid dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000018545.1:YP_002827149.1 Length = 578 Score = 343 bits (881), Expect = 8e-99 Identities = 201/537 (37%), Positives = 311/537 (57%), Gaps = 19/537 (3%) Query: 15 HRSLFYAMGYTPEDLK-KPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPS 73 HRS MGY P D + KP+I I+N+ ++ P H H + V+ VK GV AGG P+E+P+ Sbjct: 26 HRSRTMQMGYDPADWEGKPIIAIINTWSDAQPCHMHFKDRVEWVKRGVLQAGGFPMELPA 85 Query: 74 IGICDGISMNHSGMKYPLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARL 133 + + + + + M Y R ++A E + +H D VL+G CDK PG++MGA + Sbjct: 86 LSLSENF-VKPTTMLY----RNMLAMETEELLRSHPIDGAVLMGGCDKTTPGLVMGAVSM 140 Query: 134 NVPAIYVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCA 193 VP IY+ GPML G GK + F+ G +S ++ IE + G C Sbjct: 141 GVPFIYLPAGPMLRGNYAGKYLGSGTDGFKYWDERRAGTISKEEWQGIEGGIARSYGHCM 200 Query: 194 GLFTANSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKE 253 + TA++M ++AEA+G+ LPG +IPA ++++ G +I+++V + + I+T Sbjct: 201 TMGTASTMTAIAEAMGLTLPGASSIPAADANHQRMSTQCGRRIVDMVWEDLTPDRIITPA 260 Query: 254 AFKNAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHH-M 312 A +NA+ + MA G S+N +HL+A+A A V L L+D D R P I + P+GT + M Sbjct: 261 AVQNAVTVAMATGCSTNAIIHLIAMARRAGVPLQLDDLDRTGRTTPVIANIRPSGTAYLM 320 Query: 313 VDLDEAGGISAVLKELMDANLIFKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYSNEG 372 D AGG+ A++K+L D + +TVTGK L E + + + N+ VIRPL+NP +EG Sbjct: 321 EDFYYAGGLRALMKQLGDK--LDSSAITVTGKPLTEGLGDVKIWNEDVIRPLSNPVYHEG 378 Query: 373 GIAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVFDGEELAFDAI--MNKKIHPGDVVVI 430 +A+L+GNLAPDGAV+K +A +P+ H+G A V D I + + P V+V+ Sbjct: 379 SLAVLKGNLAPDGAVIKPAACDPKFHRHRGPALVADSYPELKKIIDDPDYPLTPDTVLVL 438 Query: 431 RYEGPKGCPGMRE--MLSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISPEASEGG 488 R GP+G PGM E M+ A++ LGL + I+D R SG + G C+ H+SPE+ GG Sbjct: 439 RNAGPQGGPGMPEWGMIPMPKALLKLGL-RDMVRISDARMSGTSFGACVLHVSPESFVGG 497 Query: 489 PIALIEEGDLIEIDISNRRISLLVSPEELSKRKENWIQPPCKAPDGTYLKRYSKLVT 545 P+AL+ GD++E+DI R +++L+S E+L+ R+ W +AP+ Y + Y L T Sbjct: 498 PLALLRTGDMVELDIPARSLNMLISEEDLAARRAAW-----RAPEPPYERGYGFLFT 549 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: 805 Number of extensions: 33 Number of successful extensions: 6 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: 578 Length adjustment: 36 Effective length of query: 518 Effective length of database: 542 Effective search space: 280756 Effective search space used: 280756 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 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