Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate YP_002827151.1 NGR_c26420 dihydroxy-acid dehydratase
Query= curated2:B2UYT6 (552 letters) >NCBI__GCF_000018545.1:YP_002827151.1 Length = 580 Score = 338 bits (867), Expect = 3e-97 Identities = 194/540 (35%), Positives = 311/540 (57%), Gaps = 15/540 (2%) Query: 16 RSLLKALGLT-NEEISRPIIGIVSSQNEIIPGHMNLDKITEAVRKGVLMSGGTPLVVPTI 74 RS + +G + + I +PIIGI+++ +++ P H + V++G+ +GG + +P+I Sbjct: 29 RSRMMQMGYSAGDYIGKPIIGILNTWSDLNPCHAHFKDRVHDVKRGIAQAGGFAVELPSI 88 Query: 75 GVCDGIAMGHEGMKYSLVTRELIADSIECMVKAHAFDALVLIPNCDKIVPGMVMAALRVN 134 V + S++ R L+A E ++ H D +VL+ CDK P +VM AL Sbjct: 89 SVDETFTK-----PTSMLYRNLLAMEAEEQIRCHPLDGVVLMGGCDKSTPALVMGALSAG 143 Query: 135 VPAVVISGGPMLAGKHKGKDI-SLTTMFEAVGSYENGTMDEKELCDLEECACPTCGSCSG 193 VP + + GPML G H GK + S + ++ G + + E +E + G+C Sbjct: 144 VPMIYLPAGPMLRGHHAGKILGSGSDAWKYWDERRAGNISDSEWLGIEGGIARSFGTCMT 203 Query: 194 MFTANSMNCLCEVLGIALPGNGTIPAVFSERIRLAKKAGMAVMDMLKNDIKPRDIINERS 253 M TA++M + + +G+ LPG +IPA S IR++ + G +++M+ D++P I+ E S Sbjct: 204 MGTASTMTAIVDAMGLTLPGASSIPAADSGHIRMSSECGRRIVEMVWEDLRPDRIVTEAS 263 Query: 254 IMNALKADMALGCSTNSVLHITAIANEAKVNMNLDIINDLSSKTPDLCKLAPASNIHI-E 312 I NA MA GCSTN+V+H+ AIA A + ++LD ++ L TP + + P+ ++ E Sbjct: 264 IRNAAIVAMATGCSTNAVIHLLAIARRANIPLSLDDLDALGRTTPLIANIRPSGKDYLME 323 Query: 313 NLYAAGGITAIMNELSKKDILDLNCITVTGKTQGENIKGVTVKDYEVIRPIDNPYSENGG 372 + + AGG+ A+M +L +D L+ + +TVTG++ GE ++G V + +VIRP+ NP G Sbjct: 324 DFFYAGGLRALMLQL--EDRLNRSALTVTGRSLGETLEGAAVYNDDVIRPLSNPVYPEGS 381 Query: 373 IAILRGNLAPDGAVVKRAAVLPKMLVHEGPARVFNSEEEANTAIFDKT--INPGDVIVIR 430 +A+LRGNL PDGAV+K AA PK HEGPA VF+S E AI D+ + P V+V+R Sbjct: 382 LAVLRGNLCPDGAVIKPAACDPKFWQHEGPALVFDSYPEMKAAIDDEALDVTPDTVLVLR 441 Query: 431 YEGPKGGPGMRE--MLQATAAIAGMGLDDSVALITDGRFSGATRGASIGHVSPEAASGGM 488 GPKGGPGM E ML A+ G D + I+D R SG + GA + HV PE+ GG Sbjct: 442 NAGPKGGPGMPEWGMLPIPKALIKQGHRDMLR-ISDARMSGTSYGACVLHVVPESYVGGP 500 Query: 489 IGLLENGDIISIDINNAKLEVKLSDEEIKRRKLNFKPLEPKVKEGYLSRYAKLVSSASEG 548 + LL GDI+ +D+ +L++ +++EE+ R+ + P PK G+ +++ V A +G Sbjct: 501 LALLRTGDIVRMDLPRRRLDMLVAEEELAARRASLAPPAPKFGRGFGWMFSQHVMQADKG 560 Lambda K H 0.316 0.135 0.382 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: 784 Number of extensions: 46 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: 552 Length of database: 580 Length adjustment: 36 Effective length of query: 516 Effective length of database: 544 Effective search space: 280704 Effective search space used: 280704 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