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Conserved domains on  [gi|920604359|ref|WP_053015872|]
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BppU family phage baseplate upper protein [Staphylococcus haemolyticus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 314-380 1.42e-08

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


:

Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 51.57  E-value: 1.42e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 920604359 314 DFDNptqITKSGFYYLYKPV------NGPVTLNGMLIVIYANANYMKFIYTPYTSNEVHIRTK-SGDWLPWQSI 380
Cdd:cd19958    9 DLNT---LTTPGFYYQSANAnattalNYPVAGAGYLEVYRYGGGGVTQIYTPYNSGRIYVRTRyNGTWSAWKEI 79
BppU_N super family cl11256
BppU N-terminal domain; This is the N-terminal domain of baseplate upper proteins (BppU, also ...
 9-165 3.13e-08

BppU N-terminal domain; This is the N-terminal domain of baseplate upper proteins (BppU, also known as ORF48) which is found in phage from a number of different bacteria. The N-terminal domain exhibits a beta-sandwich immunoglobulin fold.


The actual alignment was detected with superfamily member pfam10651:

Pssm-ID: 431419  Cd Length: 141  Bit Score: 52.33  E-value: 3.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359    9 IDLEEEAYLKPISDRGIGFYNLDKNTAQFQFRVTKDNLPLLISTNNVKgyaffkqITVKNGDRPSTSgVLDVEFIDPMTG 88
Cdd:pfam10651   3 ITLDTTAQNNKIKQTGIRFRTGDSNTAVLNFKITKNGQPLDLTGLTAK-------FELVKPDDGSIV-SDELEILDAKKG 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 920604359   89 LIGVTVPPWFLKSVtnstvlGEVYLSLNDYKNEDKddTVVLGTFQFEVKDSLVNQIssDVKVSYIRMFDDLRDELEK 165
Cdd:pfam10651  75 KFKYVLPEEVLKHV------GKVKAYFSVFKEDDQ--VISTRNFSFNVEKSLVEDG--IVSSDYIEDFEDLIEEVTE 141
CC_brat-like super family cl29238
coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family ...
 161-238 1.23e-05

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family contains the coiled-coil (CC) region of Drosophila brain tumor (Brat), a translational repressor that belongs to the tripartite motif (TRIM) protein superfamily. TRIM proteins play important roles in various cellular processes and are involved in many diseases which consists of two B-box domains and a coiled-coil (CC) domain at the N-terminal region, and an NHL domain at the C-terminus. Brat localizes at the basal cortex during asymmetric division of Drosophila neuroblasts by directly interacting with the scaffolding protein Miranda (Mira), which it does through the CC-NHL domain tandem, indicating that the function of the Brat CC domain is to assemble Brat-NHL in dimeric form which is necessary for Mira binding. Brat CC forms an elongated antiparallel dimer similar to its other TRIM protein counterparts, but the overall length of Brat CC dimer is shorter than the TRIMs.


The actual alignment was detected with superfamily member smart00502:

Pssm-ID: 475168  Cd Length: 127  Bit Score: 44.56  E-value: 1.23e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 920604359   161 DELEKKVEQLKKDIGSTQSLIDTIKQLSTSATQAIQKAKDDSINSINTNKTDALNNIEEQTTLSLAQIDSKKNDVQSG 238
Cdd:smart00502  10 TKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQLESLTQK 87
 
Name Accession Description Interval E-value
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 314-380 1.42e-08

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 51.57  E-value: 1.42e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 920604359 314 DFDNptqITKSGFYYLYKPV------NGPVTLNGMLIVIYANANYMKFIYTPYTSNEVHIRTK-SGDWLPWQSI 380
Cdd:cd19958    9 DLNT---LTTPGFYYQSANAnattalNYPVAGAGYLEVYRYGGGGVTQIYTPYNSGRIYVRTRyNGTWSAWKEI 79
BppU_N pfam10651
BppU N-terminal domain; This is the N-terminal domain of baseplate upper proteins (BppU, also ...
 9-165 3.13e-08

BppU N-terminal domain; This is the N-terminal domain of baseplate upper proteins (BppU, also known as ORF48) which is found in phage from a number of different bacteria. The N-terminal domain exhibits a beta-sandwich immunoglobulin fold.


Pssm-ID: 431419  Cd Length: 141  Bit Score: 52.33  E-value: 3.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359    9 IDLEEEAYLKPISDRGIGFYNLDKNTAQFQFRVTKDNLPLLISTNNVKgyaffkqITVKNGDRPSTSgVLDVEFIDPMTG 88
Cdd:pfam10651   3 ITLDTTAQNNKIKQTGIRFRTGDSNTAVLNFKITKNGQPLDLTGLTAK-------FELVKPDDGSIV-SDELEILDAKKG 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 920604359   89 LIGVTVPPWFLKSVtnstvlGEVYLSLNDYKNEDKddTVVLGTFQFEVKDSLVNQIssDVKVSYIRMFDDLRDELEK 165
Cdd:pfam10651  75 KFKYVLPEEVLKHV------GKVKAYFSVFKEDDQ--VISTRNFSFNVEKSLVEDG--IVSSDYIEDFEDLIEEVTE 141
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
 161-238 1.23e-05

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 44.56  E-value: 1.23e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 920604359   161 DELEKKVEQLKKDIGSTQSLIDTIKQLSTSATQAIQKAKDDSINSINTNKTDALNNIEEQTTLSLAQIDSKKNDVQSG 238
Cdd:smart00502  10 TKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQLESLTQK 87
DUF1542 pfam07564
Domain of Unknown Function (DUF1542); This domain is found in several cell surface proteins, ...
 160-218 2.27e-03

Domain of Unknown Function (DUF1542); This domain is found in several cell surface proteins, such as extracellular matrix-binding protein ebh. Some members are involved in antibiotic resistance (e.g Swiss:Q9RL69 and Swiss:Q9LCJ9) and/or cellular adhesion. In some proteins it is repeated more than fifteen times, being the most repeated domain in streptococci. This is a predominantly alpha-helical domain that form a long, thin, fibre-like structure and it has been proposed to function as a stalk that helps the adhesive non-repeat region (NRR) of proteins protrude beyond the cell surface.


Pssm-ID: 429541 [Multi-domain]  Cd Length: 77  Bit Score: 36.80  E-value: 2.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 920604359  160 RDELEKKVEQLKKDIGST--------QSLIDTIKQLSTSATQAIQKAKDDsiNSINTNKTDALNNIE 218
Cdd:pfam07564   6 KAAIDQAANEKKNEINNNpdatdeekQEAINQVNQAKNQAINNINNATTN--QDVDQAKNNGINAIN 70
235kDa-fam TIGR01612
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ...
 116-273 8.34e-03

reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.


Pssm-ID: 130673 [Multi-domain]  Cd Length: 2757  Bit Score: 38.88  E-value: 8.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359   116 NDYKNEDKDDTVVLGTFQFEVKDSLVNQISSDV-----------KVS-YIRMFDDLRDELEK---KVEQLKKDIGSTqsl 180
Cdd:TIGR01612  874 NKIKAEISDDKLNDYEKKFNDSKSLINEINKSIeeeyqnintlkKVDeYIKICENTKESIEKfhnKQNILKEILNKN--- 950

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359   181 IDTIKQlstsaTQAIQKAKDDSINSINTNKTDALNNIeeQTTLSLAQIDSKKNDVQSGFEIAKTAF-QNSVDQNTQTFDA 259
Cdd:TIGR01612  951 IDTIKE-----SNLIEKSYKDKFDNTLIDKINELDKA--FKDASLNDYEAKNNELIKYFNDLKANLgKNKENMLYHQFDE 1023

                          170
                   ....*....|....
gi 920604359   260 KVTDANNLIDKKVN 273
Cdd:TIGR01612 1024 KEKATNDIEQKIED 1037
 
Name Accession Description Interval E-value
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 314-380 1.42e-08

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 51.57  E-value: 1.42e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 920604359 314 DFDNptqITKSGFYYLYKPV------NGPVTLNGMLIVIYANANYMKFIYTPYTSNEVHIRTK-SGDWLPWQSI 380
Cdd:cd19958    9 DLNT---LTTPGFYYQSANAnattalNYPVAGAGYLEVYRYGGGGVTQIYTPYNSGRIYVRTRyNGTWSAWKEI 79
BppU_N pfam10651
BppU N-terminal domain; This is the N-terminal domain of baseplate upper proteins (BppU, also ...
 9-165 3.13e-08

BppU N-terminal domain; This is the N-terminal domain of baseplate upper proteins (BppU, also known as ORF48) which is found in phage from a number of different bacteria. The N-terminal domain exhibits a beta-sandwich immunoglobulin fold.


Pssm-ID: 431419  Cd Length: 141  Bit Score: 52.33  E-value: 3.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359    9 IDLEEEAYLKPISDRGIGFYNLDKNTAQFQFRVTKDNLPLLISTNNVKgyaffkqITVKNGDRPSTSgVLDVEFIDPMTG 88
Cdd:pfam10651   3 ITLDTTAQNNKIKQTGIRFRTGDSNTAVLNFKITKNGQPLDLTGLTAK-------FELVKPDDGSIV-SDELEILDAKKG 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 920604359   89 LIGVTVPPWFLKSVtnstvlGEVYLSLNDYKNEDKddTVVLGTFQFEVKDSLVNQIssDVKVSYIRMFDDLRDELEK 165
Cdd:pfam10651  75 KFKYVLPEEVLKHV------GKVKAYFSVFKEDDQ--VISTRNFSFNVEKSLVEDG--IVSSDYIEDFEDLIEEVTE 141
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
 161-238 1.23e-05

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 44.56  E-value: 1.23e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 920604359   161 DELEKKVEQLKKDIGSTQSLIDTIKQLSTSATQAIQKAKDDSINSINTNKTDALNNIEEQTTLSLAQIDSKKNDVQSG 238
Cdd:smart00502  10 TKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQLESLTQK 87
DUF1542 pfam07564
Domain of Unknown Function (DUF1542); This domain is found in several cell surface proteins, ...
 160-218 2.27e-03

Domain of Unknown Function (DUF1542); This domain is found in several cell surface proteins, such as extracellular matrix-binding protein ebh. Some members are involved in antibiotic resistance (e.g Swiss:Q9RL69 and Swiss:Q9LCJ9) and/or cellular adhesion. In some proteins it is repeated more than fifteen times, being the most repeated domain in streptococci. This is a predominantly alpha-helical domain that form a long, thin, fibre-like structure and it has been proposed to function as a stalk that helps the adhesive non-repeat region (NRR) of proteins protrude beyond the cell surface.


Pssm-ID: 429541 [Multi-domain]  Cd Length: 77  Bit Score: 36.80  E-value: 2.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 920604359  160 RDELEKKVEQLKKDIGST--------QSLIDTIKQLSTSATQAIQKAKDDsiNSINTNKTDALNNIE 218
Cdd:pfam07564   6 KAAIDQAANEKKNEINNNpdatdeekQEAINQVNQAKNQAINNINNATTN--QDVDQAKNNGINAIN 70
ClyA_Cry6Aa-like cd22656
Bacillus thuringiensis crystal 6Aa (Cry6Aa) toxin, and similar proteins; This model includes ...
 110-279 8.05e-03

Bacillus thuringiensis crystal 6Aa (Cry6Aa) toxin, and similar proteins; This model includes pesticidal Cry6Aa toxin from Bacillus thuringiensis, one of the many parasporal crystal (Cry) toxins produced during the sporulation phase of growth. Many of these proteins are toxic to numerous insect species and have been effectively used as proteinaceous insecticides to directly kill insect pests; some have been used to control insect growth on transgenic agricultural plants. Cry6Aa exists as a protoxin, which is activated by cleavage using trypsin. Structure studies for Cry6Aa support a mechanism of action by pore formation, similar to cytolysin A (ClyA)-type alpha pore-forming toxins (alpha-PFTs) such as HblB, and bioassay and mutation studies show that Cry6Aa is an active pore-forming toxin. Cry6Aa shows atypical features compared to other members of alpha-PFTs, including internal repeat sequences and small loop regions within major alpha helices.


Pssm-ID: 439154 [Multi-domain]  Cd Length: 309  Bit Score: 38.50  E-value: 8.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359 110 EVYLSLNDYKNEDKDDTVVLGTFQFEVKDsLVNQISSDVKVSYIrmfDDLRDELEK-----------KVEQLKKDIGSTQ 178
Cdd:cd22656  139 KVVDKLTDFENQTEKDQTALETLEKALKD-LLTDEGGAIARKEI---KDLQKELEKlneeyaaklkaKIDELKALIADDE 214

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359 179 SLIDTIKQLSTSATQAiqkakDDSINSINTNKTDALNNIEEqttlslaqidskkndVQSGFEIAKTAFQN---SVDQNTQ 255
Cdd:cd22656  215 AKLAAALRLIADLTAA-----DTDLDNLLALIGPAIPALEK---------------LQGAWQAIATDLDSlkdLLEDDIS 274

                        170       180       190
                 ....*....|....*....|....*....|...
gi 920604359 256 TFDAKV---TDANNLIDK------KVNDFQTNG 279
Cdd:cd22656  275 KIPAAIlakLELEKAIEKwnelaeKADKFRQNA 307
235kDa-fam TIGR01612
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ...
 116-273 8.34e-03

reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.


Pssm-ID: 130673 [Multi-domain]  Cd Length: 2757  Bit Score: 38.88  E-value: 8.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359   116 NDYKNEDKDDTVVLGTFQFEVKDSLVNQISSDV-----------KVS-YIRMFDDLRDELEK---KVEQLKKDIGSTqsl 180
Cdd:TIGR01612  874 NKIKAEISDDKLNDYEKKFNDSKSLINEINKSIeeeyqnintlkKVDeYIKICENTKESIEKfhnKQNILKEILNKN--- 950

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 920604359   181 IDTIKQlstsaTQAIQKAKDDSINSINTNKTDALNNIeeQTTLSLAQIDSKKNDVQSGFEIAKTAF-QNSVDQNTQTFDA 259
Cdd:TIGR01612  951 IDTIKE-----SNLIEKSYKDKFDNTLIDKINELDKA--FKDASLNDYEAKNNELIKYFNDLKANLgKNKENMLYHQFDE 1023

                          170
                   ....*....|....
gi 920604359   260 KVTDANNLIDKKVN 273
Cdd:TIGR01612 1024 KEKATNDIEQKIED 1037
 
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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