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: 499337380
Created: 8-Oct-2014
Updated: 2-Oct-2020
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:
XP_961344     16 ALTFDVFGTCVAWRekVASALASATES-KLSSAsasnstssDGMPPSDQVLSRARSLtredwarfaQE-WRRAYG----- 88  Neurospora cras...
WP_021703071   6 GIVFDLYGTLYDVHsvVQACESAYPGQ-GEAIS--------RLWRQKQLEYTWLSSL---------MG-RYASFEqr--- 63  Pseudomonas alc...
WP_003537251   5 AYVFDAYGTLFDVHaaVRRHAEAIGPD-GQAFS--------ELWRAKQLEYSWVRSL---------MG-AYVDFW----- 60  Sinorhizobium m...
WP_010967980  59 YMTFDVVGTLIDFEggLKDCLAGIAAE-AGAT-----------IDGEEALSLYRAAR---------YSkDADLFP----- 112 Sinorhizobium m...
WP_011027089  26 VVVFDVLGTLVDEPggLRAGIREAVPAaDDAFV--------DELLALWQGHVEREQRr-------vVR-GRRAYAdsgii 89  Streptomyces co...
XP_961344     89 --DwtrsfvpddTPWMDTDTFHL------DslvdllanwqldglftmpeieKLSLTWHDLPPWPDTIQGLNllgsryhT- 159 Neurospora cras...
WP_021703071  64 teE---------ALRYTCKHLGL------Atdet--------------tlrQLGQAYLHLAPHPDTTAALR-------Rl 107 Pseudomonas alc...
WP_003537251  61 --Elt-----eqSLDYAFQRFPS------Adpk---------------lkkPLLDAYWALDCYPEVPAVLKglkelgaR- 111 Sinorhizobium m...
WP_010967980 113 --Ddl-----vrVYLEIAPKLGL------Paepk--------------ygeRFRDSTKNWKGFADSAEALA-------R- 157 Sinorhizobium m...
WP_011027089  90 daE---------AARLVADRAGVgdpaavD---------------------RLAGAGRRLPPWSDSAAGLD-------Rl 132 Streptomyces co...
XP_961344    160 ------VA------LtNANQAtlKDLNSQKGVDDSLPLGFQRLLSCD-MyRAYKPNPKVYQGGLRDLDLQ---PGEVAMV 223 Neurospora cras...
WP_021703071 108 kasglpMA------I-ASNGS--HHSIEQVVSHSDMGWAFDHLISVE-TvKVFKPDNRVYSLAEQTMAIP---RDRLLFV 174 Pseudomonas alc...
WP_003537251 112 ------IA------I-LSNGS--PAMLASAVKNAALDIIIDDVFSVD-AvKAFKTAPAVYDLVTTSYRLY---PQAVSFQ 172 Sinorhizobium m...
WP_010967980 158 ------LAkscrlvA-MTNAR--RWAFDLFAQQLGNPFYA--AFTADdT-GTEKPDPVFFEKVFDFVGSEgnsKDDILHV 225 Sinorhizobium m...
WP_011027089 133 tr-rlvVL------G-LSNAS--HTAVPRIAAYAGLRWHG--ALSGE-TvRAYKPAPEVYRLAVDTAGCP---PDRVLMV 196 Streptomyces co...
XP_961344    224 AAHLGDLGAAKKE 236 Neurospora crassa OR74A
WP_021703071 175 SSNSWDATGARHF 187 Pseudomonas alcaligenes
WP_003537251 173 SSNRWDIAGATKF 185 Sinorhizobium meliloti
WP_010967980 226 AQSQYHDIGISRK 238 Sinorhizobium meliloti
WP_011027089 197 AAHAWDLRGARAG 209 Streptomyces coelicolor
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