NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2085572653|gb|QZI84292|]
View 

hypothetical protein PM129_002 [Escherichia phage vB_EcoP-PM129]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Peptidase_S74_CIMCD cd10144
Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F ...
 716-829 3.39e-49

Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F endosialidase and related proteins; This peptidase S74 family includes C-terminal intramolecular chaperone domain (CIMCD) of Escherichia coli phage K1F endosialidase, Bacillus phage GA-1 neck appendage protein, and Bacteriophage T5 L-shaped tail fibre. This domain acts as a molecular chaperone; during virus particle assembly, the CIMCD of phage tailspike proteins induces the homo-trimerization of phage tailspike proteins by chaperoning the formation of a triple beta-helix. Homo-trimeric phage tailspike proteins are then auto-cleaved by the CIMCD domain. This family also includes the peptidase S74 Intramolecular Chaperone Auto-processing (ICA) domain of mammalian Myrf. The ICA domain drives the homo-oligomerization of Myrf in the endoplasmic reticulum (ER) membrane. The homo-oligomeric Myrf is proteolyzed by the ICA domain, releasing its N-terminal fragments from the ER membrane.


:

Pssm-ID: 381748 [Multi-domain]  Cd Length: 113  Bit Score: 169.04  E-value: 3.39e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653 716 SDARDKTEPLNISDALLDAWSEVDFVQFQYLDRIEEKGaDSARWHFGIIAQRAKEAFERHGIDAHRYGFLCFDSWDDVYE 795
Cdd:cd10144     1 SDARLKTEIREIDDAELDAWKKVRFVQYKWKEAVAEKG-DDARLHFGVIAQEVIAAFEDAGLDAGKYGILCYDEWDAVTD 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2085572653 796 EDANgYRKLITPAGSRYGIRYEEVLILEAALMRR 829
Cdd:cd10144    80 EVIT-MENVGIEAGERYGTRYDELLIFEAAAQRR 112
PHA00430 super family cl28018
tail fiber protein
 11-113 3.05e-16

tail fiber protein


The actual alignment was detected with superfamily member PHA00430:

Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 83.02  E-value: 3.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653  11 NTQYRIEFDYLARTFVVVTLVNSSNptlnRVLEVGRDYRFLNPTMIEM---LVDQSGFDIVRIHRQT-GTDLVVDFRNGS 86
Cdd:PHA00430   17 NVDFNIPFEYLARKFVVVTLIGVDR----KELILNQDYRFATKTTISTtkaWGPADGYTLIEIRRFTsATDRLVDFTDGS 92

                          90       100
                  ....*....|....*....|....*..
gi 2085572653  87 VLTASDLTNSELQAIHIAEEGRDQTVD 113
Cdd:PHA00430   93 ILRAYDLNISQIQTLHVAEEARDLTAD 119
Tail_spike_N super family cl39985
Tail spike TSP1/Gp66 receptor binding N-terminal domain; Bacteriophages recognize and bind to ...
 156-211 9.59e-16

Tail spike TSP1/Gp66 receptor binding N-terminal domain; Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs of podovirus G7C tailspikes gp63.1 and gp66 are essential for infection of its natural host bacterium E. coli 4s. Gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The two N-terminal domains show 70% sequence identity to the N-terminal region of the CBA120 phage tailspike 1 (orf210, TSP1). The N-terminal domain of TSP1 is the virion head binding domain that interfaces with the phage baseplate. The N-terminal domain can be further divided into two subdomains, each beginning with a alpha-helix followed by an anti-parallel beta-sandwich. Subdomain two folds similarly to the chitin binding domain of Chitinase from Bacillus circulans.


The actual alignment was detected with superfamily member pfam18668:

Pssm-ID: 408449  Cd Length: 70  Bit Score: 72.60  E-value: 9.59e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2085572653 156 SFEKGYNVTTWSEVLLWEEDGDYYRWDGTLPKNVPAGSTPETSGGIGLGAWVSVGD 211
Cdd:pfam18668  15 TFSEGATLNSPREEILYDDEKQMYRWTGAFPKVVPAASTPDSTGGVGDGAWIYVGD 70
Pectate_lyase_3 super family cl40625
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure ...
 240-356 8.13e-03

Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28.


The actual alignment was detected with superfamily member pfam12708:

Pssm-ID: 403800 [Multi-domain]  Cd Length: 213  Bit Score: 38.45  E-value: 8.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653 240 DVRGWGAKGDGVTDSTENIAASLSSQKA------VVASEGVFS-SSGINSNY-CNL--DGRGSGVLSHRSS-TGNYLVFN 308
Cdd:pfam12708   3 NVKDYGAKGDGVTDDTAAIQKAIDDGGAtttpavVYFPPGTYLvSSPIILYSgTVLvgDGNNPPVLKAAPNfVGAGLIDG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2085572653 309 NPRTG-------------RLSNITVESNKATDTTQGQQVslAGGSDVTVSDVNFSNVKGTG 356
Cdd:pfam12708  83 DPYTGggpgiintnnfyrQIRNLVIDITGVAPGATGIHW--QVAQATSLQNVVFEMSFGSG 141
 
Name Accession Description Interval E-value
Peptidase_S74_CIMCD cd10144
Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F ...
 716-829 3.39e-49

Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F endosialidase and related proteins; This peptidase S74 family includes C-terminal intramolecular chaperone domain (CIMCD) of Escherichia coli phage K1F endosialidase, Bacillus phage GA-1 neck appendage protein, and Bacteriophage T5 L-shaped tail fibre. This domain acts as a molecular chaperone; during virus particle assembly, the CIMCD of phage tailspike proteins induces the homo-trimerization of phage tailspike proteins by chaperoning the formation of a triple beta-helix. Homo-trimeric phage tailspike proteins are then auto-cleaved by the CIMCD domain. This family also includes the peptidase S74 Intramolecular Chaperone Auto-processing (ICA) domain of mammalian Myrf. The ICA domain drives the homo-oligomerization of Myrf in the endoplasmic reticulum (ER) membrane. The homo-oligomeric Myrf is proteolyzed by the ICA domain, releasing its N-terminal fragments from the ER membrane.


Pssm-ID: 381748 [Multi-domain]  Cd Length: 113  Bit Score: 169.04  E-value: 3.39e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653 716 SDARDKTEPLNISDALLDAWSEVDFVQFQYLDRIEEKGaDSARWHFGIIAQRAKEAFERHGIDAHRYGFLCFDSWDDVYE 795
Cdd:cd10144     1 SDARLKTEIREIDDAELDAWKKVRFVQYKWKEAVAEKG-DDARLHFGVIAQEVIAAFEDAGLDAGKYGILCYDEWDAVTD 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2085572653 796 EDANgYRKLITPAGSRYGIRYEEVLILEAALMRR 829
Cdd:cd10144    80 EVIT-MENVGIEAGERYGTRYDELLIFEAAAQRR 112
PHA00430 PHA00430
tail fiber protein
 11-113 3.05e-16

tail fiber protein


Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 83.02  E-value: 3.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653  11 NTQYRIEFDYLARTFVVVTLVNSSNptlnRVLEVGRDYRFLNPTMIEM---LVDQSGFDIVRIHRQT-GTDLVVDFRNGS 86
Cdd:PHA00430   17 NVDFNIPFEYLARKFVVVTLIGVDR----KELILNQDYRFATKTTISTtkaWGPADGYTLIEIRRFTsATDRLVDFTDGS 92

                          90       100
                  ....*....|....*....|....*..
gi 2085572653  87 VLTASDLTNSELQAIHIAEEGRDQTVD 113
Cdd:PHA00430   93 ILRAYDLNISQIQTLHVAEEARDLTAD 119
Tail_spike_N pfam18668
Tail spike TSP1/Gp66 receptor binding N-terminal domain; Bacteriophages recognize and bind to ...
 156-211 9.59e-16

Tail spike TSP1/Gp66 receptor binding N-terminal domain; Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs of podovirus G7C tailspikes gp63.1 and gp66 are essential for infection of its natural host bacterium E. coli 4s. Gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The two N-terminal domains show 70% sequence identity to the N-terminal region of the CBA120 phage tailspike 1 (orf210, TSP1). The N-terminal domain of TSP1 is the virion head binding domain that interfaces with the phage baseplate. The N-terminal domain can be further divided into two subdomains, each beginning with a alpha-helix followed by an anti-parallel beta-sandwich. Subdomain two folds similarly to the chitin binding domain of Chitinase from Bacillus circulans.


Pssm-ID: 408449  Cd Length: 70  Bit Score: 72.60  E-value: 9.59e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2085572653 156 SFEKGYNVTTWSEVLLWEEDGDYYRWDGTLPKNVPAGSTPETSGGIGLGAWVSVGD 211
Cdd:pfam18668  15 TFSEGATLNSPREEILYDDEKQMYRWTGAFPKVVPAASTPDSTGGVGDGAWIYVGD 70
Peptidase_S74 pfam13884
Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the ...
 716-773 1.05e-12

Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, pfam12219. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope.


Pssm-ID: 404724  Cd Length: 56  Bit Score: 63.42  E-value: 1.05e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2085572653 716 SDARDKTEPLNISDALLDAWSEVDFVQFQYLDrieEKGADSARWHFGIIAQRAKEAFE 773
Cdd:pfam13884   1 SDRRLKTNIKPIDENALDKIEQLEPVSYDYKD---EKGEDGARRHIGVIAQEVEEVFP 55
Phage_T7_tail pfam03906
Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube ...
 11-113 1.99e-12

Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube surrounded by six kinked tail-fibres, which are oligomers of the viral protein gp17.


Pssm-ID: 427579 [Multi-domain]  Cd Length: 157  Bit Score: 65.76  E-value: 1.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653  11 NTQYRIEFDYLARTFVVVTLVNssnptlnRVLEVGRDYRFLNPTMIEMLVDQSGFDIVRIHRQTG-TDLVVDFRNGSVLT 89
Cdd:pfam03906  17 NRDFNIPFEYLARAHVVVTVDR-------KVLTINTDYRWADRYTISLTKAPADGTVVELRRVTPtTDRLVDFTDGSTLR 89

                          90       100
                  ....*....|....*....|....
gi 2085572653  90 ASDLTNSELQAIHIAEEGRDQTVD 113
Cdd:pfam03906  90 AYDLNVAQIQTMHVAQEARDLTTA 113
Pectate_lyase_3 pfam12708
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure ...
 240-356 8.13e-03

Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28.


Pssm-ID: 403800 [Multi-domain]  Cd Length: 213  Bit Score: 38.45  E-value: 8.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653 240 DVRGWGAKGDGVTDSTENIAASLSSQKA------VVASEGVFS-SSGINSNY-CNL--DGRGSGVLSHRSS-TGNYLVFN 308
Cdd:pfam12708   3 NVKDYGAKGDGVTDDTAAIQKAIDDGGAtttpavVYFPPGTYLvSSPIILYSgTVLvgDGNNPPVLKAAPNfVGAGLIDG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2085572653 309 NPRTG-------------RLSNITVESNKATDTTQGQQVslAGGSDVTVSDVNFSNVKGTG 356
Cdd:pfam12708  83 DPYTGggpgiintnnfyrQIRNLVIDITGVAPGATGIHW--QVAQATSLQNVVFEMSFGSG 141
 
Name Accession Description Interval E-value
Peptidase_S74_CIMCD cd10144
Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F ...
 716-829 3.39e-49

Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F endosialidase and related proteins; This peptidase S74 family includes C-terminal intramolecular chaperone domain (CIMCD) of Escherichia coli phage K1F endosialidase, Bacillus phage GA-1 neck appendage protein, and Bacteriophage T5 L-shaped tail fibre. This domain acts as a molecular chaperone; during virus particle assembly, the CIMCD of phage tailspike proteins induces the homo-trimerization of phage tailspike proteins by chaperoning the formation of a triple beta-helix. Homo-trimeric phage tailspike proteins are then auto-cleaved by the CIMCD domain. This family also includes the peptidase S74 Intramolecular Chaperone Auto-processing (ICA) domain of mammalian Myrf. The ICA domain drives the homo-oligomerization of Myrf in the endoplasmic reticulum (ER) membrane. The homo-oligomeric Myrf is proteolyzed by the ICA domain, releasing its N-terminal fragments from the ER membrane.


Pssm-ID: 381748 [Multi-domain]  Cd Length: 113  Bit Score: 169.04  E-value: 3.39e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653 716 SDARDKTEPLNISDALLDAWSEVDFVQFQYLDRIEEKGaDSARWHFGIIAQRAKEAFERHGIDAHRYGFLCFDSWDDVYE 795
Cdd:cd10144     1 SDARLKTEIREIDDAELDAWKKVRFVQYKWKEAVAEKG-DDARLHFGVIAQEVIAAFEDAGLDAGKYGILCYDEWDAVTD 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2085572653 796 EDANgYRKLITPAGSRYGIRYEEVLILEAALMRR 829
Cdd:cd10144    80 EVIT-MENVGIEAGERYGTRYDELLIFEAAAQRR 112
PHA00430 PHA00430
tail fiber protein
 11-113 3.05e-16

tail fiber protein


Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 83.02  E-value: 3.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653  11 NTQYRIEFDYLARTFVVVTLVNSSNptlnRVLEVGRDYRFLNPTMIEM---LVDQSGFDIVRIHRQT-GTDLVVDFRNGS 86
Cdd:PHA00430   17 NVDFNIPFEYLARKFVVVTLIGVDR----KELILNQDYRFATKTTISTtkaWGPADGYTLIEIRRFTsATDRLVDFTDGS 92

                          90       100
                  ....*....|....*....|....*..
gi 2085572653  87 VLTASDLTNSELQAIHIAEEGRDQTVD 113
Cdd:PHA00430   93 ILRAYDLNISQIQTLHVAEEARDLTAD 119
Tail_spike_N pfam18668
Tail spike TSP1/Gp66 receptor binding N-terminal domain; Bacteriophages recognize and bind to ...
 156-211 9.59e-16

Tail spike TSP1/Gp66 receptor binding N-terminal domain; Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs of podovirus G7C tailspikes gp63.1 and gp66 are essential for infection of its natural host bacterium E. coli 4s. Gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The two N-terminal domains show 70% sequence identity to the N-terminal region of the CBA120 phage tailspike 1 (orf210, TSP1). The N-terminal domain of TSP1 is the virion head binding domain that interfaces with the phage baseplate. The N-terminal domain can be further divided into two subdomains, each beginning with a alpha-helix followed by an anti-parallel beta-sandwich. Subdomain two folds similarly to the chitin binding domain of Chitinase from Bacillus circulans.


Pssm-ID: 408449  Cd Length: 70  Bit Score: 72.60  E-value: 9.59e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2085572653 156 SFEKGYNVTTWSEVLLWEEDGDYYRWDGTLPKNVPAGSTPETSGGIGLGAWVSVGD 211
Cdd:pfam18668  15 TFSEGATLNSPREEILYDDEKQMYRWTGAFPKVVPAASTPDSTGGVGDGAWIYVGD 70
Peptidase_S74 pfam13884
Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the ...
 716-773 1.05e-12

Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, pfam12219. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope.


Pssm-ID: 404724  Cd Length: 56  Bit Score: 63.42  E-value: 1.05e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2085572653 716 SDARDKTEPLNISDALLDAWSEVDFVQFQYLDrieEKGADSARWHFGIIAQRAKEAFE 773
Cdd:pfam13884   1 SDRRLKTNIKPIDENALDKIEQLEPVSYDYKD---EKGEDGARRHIGVIAQEVEEVFP 55
Phage_T7_tail pfam03906
Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube ...
 11-113 1.99e-12

Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube surrounded by six kinked tail-fibres, which are oligomers of the viral protein gp17.


Pssm-ID: 427579 [Multi-domain]  Cd Length: 157  Bit Score: 65.76  E-value: 1.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653  11 NTQYRIEFDYLARTFVVVTLVNssnptlnRVLEVGRDYRFLNPTMIEMLVDQSGFDIVRIHRQTG-TDLVVDFRNGSVLT 89
Cdd:pfam03906  17 NRDFNIPFEYLARAHVVVTVDR-------KVLTINTDYRWADRYTISLTKAPADGTVVELRRVTPtTDRLVDFTDGSTLR 89

                          90       100
                  ....*....|....*....|....
gi 2085572653  90 ASDLTNSELQAIHIAEEGRDQTVD 113
Cdd:pfam03906  90 AYDLNVAQIQTMHVAQEARDLTTA 113
Pectate_lyase_3 pfam12708
Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure ...
 240-356 8.13e-03

Pectate lyase superfamily protein; This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28.


Pssm-ID: 403800 [Multi-domain]  Cd Length: 213  Bit Score: 38.45  E-value: 8.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085572653 240 DVRGWGAKGDGVTDSTENIAASLSSQKA------VVASEGVFS-SSGINSNY-CNL--DGRGSGVLSHRSS-TGNYLVFN 308
Cdd:pfam12708   3 NVKDYGAKGDGVTDDTAAIQKAIDDGGAtttpavVYFPPGTYLvSSPIILYSgTVLvgDGNNPPVLKAAPNfVGAGLIDG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2085572653 309 NPRTG-------------RLSNITVESNKATDTTQGQQVslAGGSDVTVSDVNFSNVKGTG 356
Cdd:pfam12708  83 DPYTGggpgiintnnfyrQIRNLVIDITGVAPGATGIHW--QVAQATSLQNVVFEMSFGSG 141
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH