Conserved Protein Domain Family
HAD-SF-IA-v2

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TIGR01493: HAD-SF-IA-v2 
Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid dehalogenase
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 2 (this model) is distinctive of the type II haloacid dehalogenases, and nearly all of the sequences are also part of the HAD, type II equivalog model (TIGR01428). 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.
Statistics
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PSSM-Id: 130557
View PSSM: TIGR01493
Aligned: 5 rows
Threshold Bit Score: 183.88
Threshold Setting Gi: 21218946
Created: 8-Oct-2014
Updated: 11-Oct-2014
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102516   16 ALTFDVFGTCVAWRekVASALASATES-KLSSAsasnstssDGMPPSDQVLSRARSLtredwarfaQE-WRRAYG----- 88
gi 545466506   6 GIVFDLYGTLYDVHsvVQACESAYPGQ-GEAIS--------RLWRQKQLEYTWLSSL---------MG-RYASFEqr--- 63
gi 489632811   5 AYVFDAYGTLFDVHaaVRRHAEAIGPD-GQAFS--------ELWRAKQLEYSWVRSL---------MG-AYVDFW----- 60
gi 499270587  59 YMTFDVVGTLIDFEggLKDCLAGIAAE-AGAT-----------IDGEEALSLYRAAR---------YSkDADLFP----- 112
gi 499337380  26 VVVFDVLGTLVDEPggLRAGIREAVPAaDDAFV--------DELLALWQGHVEREQRr-------vVR-GRRAYAdsgii 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102516   89 --DwtrsfvpddTPWMDTDTFHL------DslvdllanwqldglftmpeieKLSLTWHDLPPWPDTIQGLNllgsryhT- 159
gi 545466506  64 teE---------ALRYTCKHLGL------Atdet--------------tlrQLGQAYLHLAPHPDTTAALR-------Rl 107
gi 489632811  61 --Elt-----eqSLDYAFQRFPS------Adpk---------------lkkPLLDAYWALDCYPEVPAVLKglkelgaR- 111
gi 499270587 113 --Ddl-----vrVYLEIAPKLGL------Paepk--------------ygeRFRDSTKNWKGFADSAEALA-------R- 157
gi 499337380  90 daE---------AARLVADRAGVgdpaavD---------------------RLAGAGRRLPPWSDSAAGLD-------Rl 132
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102516  160 ------VA------LtNANQAtlKDLNSQKGVDDSLPLGFQRLLSCD-MyRAYKPNPKVYQGGLRDLDLQ---PGEVAMV 223
gi 545466506 108 kasglpMA------I-ASNGS--HHSIEQVVSHSDMGWAFDHLISVE-TvKVFKPDNRVYSLAEQTMAIP---RDRLLFV 174
gi 489632811 112 ------IA------I-LSNGS--PAMLASAVKNAALDIIIDDVFSVD-AvKAFKTAPAVYDLVTTSYRLY---PQAVSFQ 172
gi 499270587 158 ------LAkscrlvA-MTNAR--RWAFDLFAQQLGNPFYA--AFTADdT-GTEKPDPVFFEKVFDFVGSEgnsKDDILHV 225
gi 499337380 133 tr-rlvVL------G-LSNAS--HTAVPRIAAYAGLRWHG--ALSGE-TvRAYKPAPEVYRLAVDTAGCP---PDRVLMV 196
                        250
                 ....*....|...
gi 85102516  224 AAHLGDLGAAKKE 236
gi 545466506 175 SSNSWDATGARHF 187
gi 489632811 173 SSNRWDIAGATKF 185
gi 499270587 226 AQSQYHDIGISRK 238
gi 499337380 197 AAHAWDLRGARAG 209
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