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Conserved domains on  [gi|1999643143|ref|WP_206732588|]
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dynamin family protein, partial [Lelliottia nimipressuralis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1-121 1.77e-71

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member PRK09866:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 741  Bit Score: 226.65  E-value: 1.77e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1999643143   1 MHTQTIFELSQEAERLLQLALQNLDALKSMPIAVldsttaamTGETNNVLPLHFSTRGVETQLSMLNNELRKITRLEMVL 80
Cdd:PRK09866    1 MYTQTLYELSQEAERLLQLSRQQLQLLEKMPLSV--------PGDDAPQLALPWSQPNIAERHAMLNNELRKISRLEMVL 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1999643143  81 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTP 121
Cdd:PRK09866   73 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTP 113
 
Name Accession Description Interval E-value
PRK09866 PRK09866
clamp-binding protein CrfC;
1-121 1.77e-71

clamp-binding protein CrfC;


Pssm-ID: 182123 [Multi-domain]  Cd Length: 741  Bit Score: 226.65  E-value: 1.77e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1999643143   1 MHTQTIFELSQEAERLLQLALQNLDALKSMPIAVldsttaamTGETNNVLPLHFSTRGVETQLSMLNNELRKITRLEMVL 80
Cdd:PRK09866    1 MYTQTLYELSQEAERLLQLSRQQLQLLEKMPLSV--------PGDDAPQLALPWSQPNIAERHAMLNNELRKISRLEMVL 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1999643143  81 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTP 121
Cdd:PRK09866   73 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTP 113
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 78-119 7.25e-10

Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.


Pssm-ID: 206739 [Multi-domain]  Cd Length: 180  Bit Score: 53.70  E-value: 7.25e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1999643143  78 MVLAIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRH 119
Cdd:cd09912     1 FLLAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVITVLRY 42
Dynamin_N pfam00350
Dynamin family;
80-119 9.30e-09

Dynamin family;


Pssm-ID: 459775 [Multi-domain]  Cd Length: 168  Bit Score: 50.31  E-value: 9.30e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1999643143  80 LAIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRH 119
Cdd:pfam00350   1 IAVVGDQSSGKSSVLNALLGRDILPRGPGPTTRRPTVLRL 40
YeeP COG3596
Predicted GTPase [General function prediction only];
71-118 5.00e-03

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 35.13  E-value: 5.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1999643143  71 RKITRLEMVLAIVGTMKAGKSTTINAIVGTEVLP-NRNRPMTALPTLIR 118
Cdd:COG3596    33 LLVELPPPVIALVGKTGAGKSSLINALFGAEVAEvGVGRPCTREIQRYR 81
 
Name Accession Description Interval E-value
PRK09866 PRK09866
clamp-binding protein CrfC;
1-121 1.77e-71

clamp-binding protein CrfC;


Pssm-ID: 182123 [Multi-domain]  Cd Length: 741  Bit Score: 226.65  E-value: 1.77e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1999643143   1 MHTQTIFELSQEAERLLQLALQNLDALKSMPIAVldsttaamTGETNNVLPLHFSTRGVETQLSMLNNELRKITRLEMVL 80
Cdd:PRK09866    1 MYTQTLYELSQEAERLLQLSRQQLQLLEKMPLSV--------PGDDAPQLALPWSQPNIAERHAMLNNELRKISRLEMVL 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1999643143  81 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTP 121
Cdd:PRK09866   73 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTP 113
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 78-119 7.25e-10

Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.


Pssm-ID: 206739 [Multi-domain]  Cd Length: 180  Bit Score: 53.70  E-value: 7.25e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1999643143  78 MVLAIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRH 119
Cdd:cd09912     1 FLLAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVITVLRY 42
Dynamin_N pfam00350
Dynamin family;
80-119 9.30e-09

Dynamin family;


Pssm-ID: 459775 [Multi-domain]  Cd Length: 168  Bit Score: 50.31  E-value: 9.30e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1999643143  80 LAIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRH 119
Cdd:pfam00350   1 IAVVGDQSSGKSSVLNALLGRDILPRGPGPTTRRPTVLRL 40
YeeP COG3596
Predicted GTPase [General function prediction only];
71-118 5.00e-03

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 35.13  E-value: 5.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1999643143  71 RKITRLEMVLAIVGTMKAGKSTTINAIVGTEVLP-NRNRPMTALPTLIR 118
Cdd:COG3596    33 LLVELPPPVIALVGKTGAGKSSLINALFGAEVAEvGVGRPCTREIQRYR 81
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 81-111 8.44e-03

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 33.97  E-value: 8.44e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1999643143  81 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMT 111
Cdd:cd00882     1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGT 31
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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