3NUQ,4G9B,1CQZ,2B0C


Conserved Protein Domain Family
HAD-SF-IA-v3

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TIGR01509: HAD-SF-IA-v3 
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haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 3 (this model) is found in the enzymes beta-phosphoglucomutase (TIGR01990) and deoxyglucose-6-phosphatase, while many other enzymes of subfamily IA exhibit this variant as well as variant 1 (TIGR01549). These three variant models were created with the knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly related HAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity]
Statistics
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PSSM-Id: 273662
View PSSM: TIGR01509
Aligned: 34 rows
Threshold Bit Score: 104.424
Threshold Setting Gi: 499187302
Created: 8-Oct-2014
Updated: 11-Oct-2014
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:

3NUQ_A        61 FFDIDNCLYKS.[11].ILRFFQTHLKLS     P.[ 3].HVLNNSY     Y.[1].E.[2].LAI.[10].ALE 126
gi 485656287  14 LLDMDGTLLDL.[ 6].WQKLVPETWGAK.[2].V.[ 1].PQEAMEY     M.[2].Q.[2].DVQ.[ 6].CLD 71
gi 499209680  15 ILDLDGTLIDL.[ 6].WKTVVPQAYAKK     C.[ 1].LDLATSR.[3].K.[1].R.[2].AIE.[ 6].CLD 72
gi 505258464  34 VFDIGKVLIHY.[ 5].YSRLVPDEAERS.[6].C.[ 1].SDWNIEQ     D.[2].R.[2].EEA.[ 6].NHP 94
gi 499189933  18 AFDWGGVFTVG.[11].ERSGVPVEKVRE     S.[ 8].EVGAWTL     P     Q.[2].ETV.[ 6].TLP 83
gi 499272446   8 MIDVEGVLVCG.[ 7].WASTIEDDLGLS     V.[ 4].QEFFSPY     W.[2].I.[2].GRA.[ 6].KPV 67
gi 392891716  11 VYDFGGVLLSY.[11].RSLGLPDDAVHS     E.[16].FLGTLTV     D.[8].Q.[2].KHK.[ 3].KLT 89
gi 563510      7 AFDLDGVLALP.[10].EALALPRDFLLG     A.[13].MKGKITF     S.[7].E.[2].RKS.[ 6].NLP 83
gi 499176709   8 VFDLDGVLIDS.[15].GLPRPDRQTVVS     L.[ 2].LKASLML     E.[2].G.[2].RQE.[ 3].IFK 70
1CQZ_A         7 AFDLDGVLALP.[10].EALALPRDFLLG     A.[13].MKGKITF     S.[7].E.[2].RKS.[ 6].NLP 83

3NUQ_A       127 .[1].N.[1].L.[1].DDSLPL.[4].K     PDIPLRNMLLRLRQS     G.[4].L     WLFTNAY     K 171
gi 485656287  72 .[6].G.[1].D.[1].CAMTTE.[5].V     LREDTIPFLEALKAS     G     K.[2].ILLTNAH     P 120
gi 499209680  73 .[6].D.[1].P.[1].RELYQA.[5].K     VRSDVAPFLQAVRKM     N.[2].M     ILLTDSN     P 121
gi 505258464  95 .[1].R.[6].F.[1].RHWHEM.[2].H     AYVETVAIMGGLIAD     G     W.[2].TMLTNFA.[6].A 146
gi 499189933  84 .[1].A.[1].F     EALYLG.[2].H     DNAPMYTTLAALPRS.[1].R     V     GLLSNNY     P 122
gi 499272446  68 .[6].H.[1].P.[1].DDFIAY.[6].R     LNIKLLEELRQQRKA     G.[2].V     YLATDQE     H 117
gi 392891716  90 .[6].P     F.[1].ECLRGE.[2].K     IHKNMQKTVEILHKK     G.[2].T     AMLTNNM     F 134
gi 563510     84 .[6].Q.[1].F.[1].QAMAAR     S     INRPMLQAAIALKKK     G.[2].T     CIVTNNW     L 127
gi 499176709  71 .[1].F.[1].Q.[1].FYIENL.[4].A     PMPNAVTVLTTLKQR     D.[2].I     LACTSGD     R 113
1CQZ_A        84 .[1].N.[1].S.[1].SQIFSQ.[3].A.[2].INRPMLQAAIALKKK     G.[2].T     CIVTNNW.[5].K 132

3NUQ_A       172 .[6].LRL     LGI     A.[1].LFDGLTY.[8].LVCKPHVKAFEKAMKESGLA.[4].AYFIDDSGKNIETGIK 240
gi 485656287 121      HNL.[6].TGL     D.[1].HLDLLLS.[4].GYPKEDQRLWHAVAEATGLK.[3].TLFIDDSEAILDAAAQ 184
gi 499209680 122      FSL.[6].CDF     V.[1].TFDLLLS.[4].GAPKIEQPLWHNLQQKHYFN.[3].TLFIDDTENVLDSAKQ 185
gi 505258464 147      QKL     YPF     L.[1].LPRGVTV.[4].RLIKPDLAIYRTHAEAFDLD.[3].TLFIDDSAANVEGARA 204
gi 499189933 123      VVS     EHL.[5].F.[1].RFDALVF.[4].GHKKPAPEAFAALEQKMGLP.[3].VAFVDDVQENIDAAGA 185
gi 499272446 118 .[5].LVE.[1].LGL     G.[1].HCDGIYY.[4].GSRKPDQAFFKQVAALSGLR.[3].LLLVDDPPANIDAARL 181
gi 392891716 135 .[5].KET.[3].CDL     T     HFDEVVE.[4].HLMKPDARFYHLVEKRLGVK.[3].IVFLDDLHENIEAAEK 199
gi 563510    128 .[5].RDS.[5].CEL     S.[1].HFDFLIE.[4].GMIKPEPQIYNFLLDTLKAK.[3].VVFLDDFGSNLKPARD 195
gi 499176709 114 .[3].TAA.[3].VGL     W.[1].AIETMLA.[4].PFAKPDPRYLQQLLAPYDYQ.[1].LLHVEDAEVGIRMGQA 175
1CQZ_A       133 .[3].LAQ.[2].CEL     S.[1].HFDFLIE.[4].GMIKPEPQIYNFLLDTLKAK.[3].VVFLDDFGSNLKPARD 195

3NUQ_A       241 LGM     KTC.[2]. 248
gi 485656287 185 FGI     RYC.[2]. 192
gi 499209680 186 FGI.[1].YTV.[2]. 194
gi 505258464 205 AGW     HAV.[2]. 212
gi 499189933 186 FGF     HGI.[2]. 193
gi 499272446 182 CGW     NAI.[2]. 189
gi 392891716 200 LGW     NTI.[2]. 207
gi 563510    196 MGM     VTI.[2]. 203
gi 499176709 176 CGA     VSI.[2]. 183
1CQZ_A       196 MGM     VTI.[2]. 203
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