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Conserved domains on  [gi|258597147|ref|XP_001347604|]
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RNA polymerase II-associated protein 1, putative [Plasmodium falciparum 3D7]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPAP1_C pfam08620
RPAP1-like, C-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in ...
 241-318 4.08e-14

RPAP1-like, C-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.


:

Pssm-ID: 462538  Cd Length: 69  Bit Score: 68.72  E-value: 4.08e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 258597147   241 EIRFDFQGKLriqinekLYNEKENKIIFNhfNGLYHHNEEPLNSGYTLPEILYLCQSSYNNQVCISLKILKHVFINMH 318
Cdd:pfam08620    1 ELRFDFKGNL-------IPPSESSDIPTH--LGLHHHGDDPEAAGYTLPELAHLSRSTVPAQRCIALQTLGRILYKLG 69
LbR-like super family cl17507
Left-handed beta-roll, including virulence factors and various other proteins; This family ...
 519-585 8.81e-07

Left-handed beta-roll, including virulence factors and various other proteins; This family contains a variety of protein domains with a left-handed beta-roll structure including cell surface adhesion proteins, bacterial virulence factors, and ice-binding proteins, and other activities. UspA1 Head And Neck Domain and YadA of Yersinia are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric beta-rolls of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region. The collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix. These domains form a left handed beta roll made up of a series of short repeated elements.


The actual alignment was detected with superfamily member cd12796:

Pssm-ID: 248061 [Multi-domain]  Cd Length: 114  Bit Score: 49.32  E-value: 8.81e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 258597147  519 NDVLNGNNDISNG-NNDISNGNNDISNGNNDISNGNNDISNGNNDISnGNNDISNGNNDISNDNNETV 585
Cdd:cd12796    47 NNTVSGNNHVVTGsNNVVTGNGNTVSGSNNVVSGSNNTVSGGNNTVS-GSNNTVSGSNHIVSGNNKVV 113
 
Name Accession Description Interval E-value
RPAP1_C pfam08620
RPAP1-like, C-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in ...
 241-318 4.08e-14

RPAP1-like, C-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.


Pssm-ID: 462538  Cd Length: 69  Bit Score: 68.72  E-value: 4.08e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 258597147   241 EIRFDFQGKLriqinekLYNEKENKIIFNhfNGLYHHNEEPLNSGYTLPEILYLCQSSYNNQVCISLKILKHVFINMH 318
Cdd:pfam08620    1 ELRFDFKGNL-------IPPSESSDIPTH--LGLHHHGDDPEAAGYTLPELAHLSRSTVPAQRCIALQTLGRILYKLG 69
LbR_Ice_bind cd12796
Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium ...
 519-585 8.81e-07

Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix.


Pssm-ID: 240609 [Multi-domain]  Cd Length: 114  Bit Score: 49.32  E-value: 8.81e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 258597147  519 NDVLNGNNDISNG-NNDISNGNNDISNGNNDISNGNNDISNGNNDISnGNNDISNGNNDISNDNNETV 585
Cdd:cd12796    47 NNTVSGNNHVVTGsNNVVTGNGNTVSGSNNVVSGSNNTVSGGNNTVS-GSNNTVSGSNHIVSGNNKVV 113
Hia COG5295
Autotransporter adhesin [Intracellular trafficking, secretion, and vesicular transport, ...
 519-587 3.71e-04

Autotransporter adhesin [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444098 [Multi-domain]  Cd Length: 785  Bit Score: 45.53  E-value: 3.71e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 258597147  519 NDVLNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDIS--NDNNE-TVHN 587
Cdd:COG5295   600 TDAVNGGGAVATGDNSVAVGNNAQASGANSVALGAGATATANNSVALGAGSVADRANTVSvgSAGAErQITN 671
PTZ00441 PTZ00441
sporozoite surface protein 2 (SSP2); Provisional
 480-573 5.24e-03

sporozoite surface protein 2 (SSP2); Provisional


Pssm-ID: 240420 [Multi-domain]  Cd Length: 576  Bit Score: 41.49  E-value: 5.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 258597147  480 EDQNIEEDIPDDLEDQMGDIYFLDENNDIYETKINEVDKNDVLNGNNDISNGNNDISNGNNDISNGNNDISNGNNdisNG 559
Cdd:PTZ00441  401 SNKEVPEDVPMEPEDDRDNNFNEPKKPENKGDGQNEPVIPKPLDNERDQSNKNKQVNPGNRHNSEDRYTRPHGRN---NE 477

                          90
                  ....*....|....
gi 258597147  560 NNDISNGNNDISNG 573
Cdd:PTZ00441  478 NRNYNNKNSDIPKH 491
 
Name Accession Description Interval E-value
RPAP1_C pfam08620
RPAP1-like, C-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in ...
 241-318 4.08e-14

RPAP1-like, C-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.


Pssm-ID: 462538  Cd Length: 69  Bit Score: 68.72  E-value: 4.08e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 258597147   241 EIRFDFQGKLriqinekLYNEKENKIIFNhfNGLYHHNEEPLNSGYTLPEILYLCQSSYNNQVCISLKILKHVFINMH 318
Cdd:pfam08620    1 ELRFDFKGNL-------IPPSESSDIPTH--LGLHHHGDDPEAAGYTLPELAHLSRSTVPAQRCIALQTLGRILYKLG 69
LbR_Ice_bind cd12796
Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium ...
 519-585 8.81e-07

Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix.


Pssm-ID: 240609 [Multi-domain]  Cd Length: 114  Bit Score: 49.32  E-value: 8.81e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 258597147  519 NDVLNGNNDISNG-NNDISNGNNDISNGNNDISNGNNDISNGNNDISnGNNDISNGNNDISNDNNETV 585
Cdd:cd12796    47 NNTVSGNNHVVTGsNNVVTGNGNTVSGSNNVVSGSNNTVSGGNNTVS-GSNNTVSGSNHIVSGNNKVV 113
LbR_Ice_bind cd12796
Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium ...
 525-582 4.24e-06

Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix.


Pssm-ID: 240609 [Multi-domain]  Cd Length: 114  Bit Score: 47.39  E-value: 4.24e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 258597147  525 NNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNDNN 582
Cdd:cd12796    40 HNVLSGNNNTVSGNNHVVTGSNNVVTGNGNTVSGSNNVVSGSNNTVSGGNNTVSGSNN 97
LbR_Ice_bind cd12796
Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium ...
 504-582 1.29e-05

Ice-binding protein, left-handed beta-roll; The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix.


Pssm-ID: 240609 [Multi-domain]  Cd Length: 114  Bit Score: 45.85  E-value: 1.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 258597147  504 ENNDIYETKINEVDKND----VLNGNNDISNGNND-ISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDIS 578
Cdd:cd12796     7 FKNRVLSGSENNVIAGGqnlvVSGSNNLVSGGNHNvLSGNNNTVSGNNHVVTGSNNVVTGNGNTVSGSNNVVSGSNNTVS 86


                  ....
gi 258597147  579 NDNN 582
Cdd:cd12796    87 GGNN 90
LbR_YadA-like cd12820
YadA-like, left-handed beta-roll; This group contains the collagen-binding domain virulence ...
 523-581 3.16e-05

YadA-like, left-handed beta-roll; This group contains the collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins, including Moraxella catarrhalis UspA-like proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. These domains form a left handed beta roll made up of a series of short repeated elements. UspA1 and UspA2 are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric left-handed parallel beta-helices of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region.


Pssm-ID: 240612 [Multi-domain]  Cd Length: 126  Bit Score: 45.18  E-value: 3.16e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 258597147  523 NGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNDN 581
Cdd:cd12820    68 SGENSSAFGSNNTASGNNSSAFGYNNTASGENSTAFGNNSKASGENSTALGNGNKASGN 126
LbR_YadA-like cd12820
YadA-like, left-handed beta-roll; This group contains the collagen-binding domain virulence ...
 524-584 1.92e-04

YadA-like, left-handed beta-roll; This group contains the collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins, including Moraxella catarrhalis UspA-like proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. These domains form a left handed beta roll made up of a series of short repeated elements. UspA1 and UspA2 are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric left-handed parallel beta-helices of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region.


Pssm-ID: 240612 [Multi-domain]  Cd Length: 126  Bit Score: 42.87  E-value: 1.92e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 258597147  524 GNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDIS--NDNNET 584
Cdd:cd12820    62 GYGNKASGENSSAFGSNNTASGNNSSAFGYNNTASGENSTAFGNNSKASGENSTAlgNGNKAS 124
Hia COG5295
Autotransporter adhesin [Intracellular trafficking, secretion, and vesicular transport, ...
 519-587 3.71e-04

Autotransporter adhesin [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444098 [Multi-domain]  Cd Length: 785  Bit Score: 45.53  E-value: 3.71e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 258597147  519 NDVLNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDIS--NDNNE-TVHN 587
Cdd:COG5295   600 TDAVNGGGAVATGDNSVAVGNNAQASGANSVALGAGATATANNSVALGAGSVADRANTVSvgSAGAErQITN 671
LbR-like cd12813
Left-handed beta-roll, including virulence factors and various other proteins; This family ...
 517-582 5.18e-04

Left-handed beta-roll, including virulence factors and various other proteins; This family contains a variety of protein domains with a left-handed beta-roll structure including cell surface adhesion proteins, bacterial virulence factors, and ice-binding proteins, and other activities. UspA1 Head And Neck Domain and YadA of Yersinia are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric beta-rolls of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region. The collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix. These domains form a left handed beta roll made up of a series of short repeated elements.


Pssm-ID: 240610 [Multi-domain]  Cd Length: 99  Bit Score: 40.99  E-value: 5.18e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 258597147  517 DKNDVLnGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNG-NNDISNGNNDISNGNNDISNDNN 582
Cdd:cd12813    30 DNNSAS-GSNSTAVGGANTATGSNAVASGTNAIVTDDNAVASGnNNLASGSNSTALGGHSTVTGSNS 95
Hia COG5295
Autotransporter adhesin [Intracellular trafficking, secretion, and vesicular transport, ...
 524-583 4.52e-03

Autotransporter adhesin [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444098 [Multi-domain]  Cd Length: 785  Bit Score: 41.68  E-value: 4.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 258597147  524 GNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNDNNE 583
Cdd:COG5295   598 TDTDAVNGGGAVATGDNSVAVGNNAQASGANSVALGAGATATANNSVALGAGSVADRANT 657
LbR_YadA-like cd12820
YadA-like, left-handed beta-roll; This group contains the collagen-binding domain virulence ...
 523-584 5.10e-03

YadA-like, left-handed beta-roll; This group contains the collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins, including Moraxella catarrhalis UspA-like proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. These domains form a left handed beta roll made up of a series of short repeated elements. UspA1 and UspA2 are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric left-handed parallel beta-helices of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region.


Pssm-ID: 240612 [Multi-domain]  Cd Length: 126  Bit Score: 38.63  E-value: 5.10e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 258597147  523 NGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNGNNDISNDNNET 584
Cdd:cd12820    54 SGENSTAFGYGNKASGENSSAFGSNNTASGNNSSAFGYNNTASGENSTAFGNNSKASGENST 115
PTZ00441 PTZ00441
sporozoite surface protein 2 (SSP2); Provisional
 480-573 5.24e-03

sporozoite surface protein 2 (SSP2); Provisional


Pssm-ID: 240420 [Multi-domain]  Cd Length: 576  Bit Score: 41.49  E-value: 5.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 258597147  480 EDQNIEEDIPDDLEDQMGDIYFLDENNDIYETKINEVDKNDVLNGNNDISNGNNDISNGNNDISNGNNDISNGNNdisNG 559
Cdd:PTZ00441  401 SNKEVPEDVPMEPEDDRDNNFNEPKKPENKGDGQNEPVIPKPLDNERDQSNKNKQVNPGNRHNSEDRYTRPHGRN---NE 477

                          90
                  ....*....|....
gi 258597147  560 NNDISNGNNDISNG 573
Cdd:PTZ00441  478 NRNYNNKNSDIPKH 491
COG2931 COG2931
Ca2+-binding protein, RTX toxin-related [Secondary metabolites biosynthesis, transport and ...
 487-577 6.82e-03

Ca2+-binding protein, RTX toxin-related [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442175 [Multi-domain]  Cd Length: 252  Bit Score: 40.27  E-value: 6.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 258597147  487 DIPDDLEDQMGDIYFLDENNDIYETKINEVDKNDVLNGNNDISNGNNDISNGNNDISNGNNDISNGNND---ISNGNNDI 563
Cdd:COG2931    53 GGGGGGGGGGGGGGLDGGGGGGGGDGGGGGGGDDTDGGGDGGDGGGGGTGDDTGDGGGGNDTLTGGDGNdtlTGGAGDDT 132

                          90
                  ....*....|....*...
gi 258597147  564 SNGN--NDISNGN--NDI 577
Cdd:COG2931   133 LYGGagNDTLTGGagNDT 150
 
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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