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Conserved domains on  [gi|56181387|ref|NP_005852|]
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E3 ubiquitin-protein ligase CHIP isoform a [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RING-Ubox_CHIP cd16654
U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein ...
 227-297 7.26e-51

U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein (CHIP) and similar proteins; CHIP, also known as STIP1 homology and U box-containing protein 1 (STUB1), CLL-associated antigen KW-8, or Antigen NY-CO-7, is a multifunctional protein that functions both as a co-chaperone and an E3 ubiquitin-protein ligase. It couples protein folding and proteasome mediated degradation by interacting with heat shock proteins (e.g. HSC70) and ubiquitinating their misfolded client proteins, thereby targeting them for proteasomal degradation. It is also important for cellular differentiation and survival (or apoptosis), as well as susceptibility to stress. It targets a wide range of proteins, such as expanded ataxin-1, ataxin-3, huntingtin, and androgen receptor, which play roles in glucocorticoid response, tau degradation, and both p53 and cAMP signaling. CHIP contains an N-terminal tetratricopeptide repeat (TPR) domain responsible for protein-protein interaction, a highly charged middle coiled-coil (CC), and a C-terminal RING-like U-box domain acting as an ubiquitin ligase.


:

Pssm-ID: 438316 [Multi-domain]  Cd Length: 71  Bit Score: 161.97  E-value: 7.26e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56181387 227 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQEQLIPNLAMKEVIDAFISEN 297
Cdd:cd16654   1 VPDYLCCKISFELMRDPVITPSGITYERKDIEEHLQRVGHFDPITREPLTQDQLIPNLALKEAIEAFLEEN 71
CHIP_TPR_N pfam18391
CHIP N-terminal tetratricopeptide repeat domain; This is N-terminal tetratricopeptide repeat ...
 142-225 6.79e-29

CHIP N-terminal tetratricopeptide repeat domain; This is N-terminal tetratricopeptide repeat (TPR) domain found in C terminus of Hsp70 interacting proteins (CHIP). The TPR domain of CHIP binds directly to EEVD motifs located at the C termini of Hsc/Hsp70 and Hsp90.


:

Pssm-ID: 436460  Cd Length: 83  Bit Score: 105.75  E-value: 6.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387   142 AKKKRWNSIEERRIHQESELHSYLSRLIAAERERELEECQrNHEGDEDDSHVRAQQACIEAKHDKYMADMDELFSQVDEK 221
Cdd:pfam18391   1 ARKKRWNVQEEKRIKQEIELQSYLNRLIDEDKERQLAELE-LSEEGSDDEEKEEEIDEIEQECDEYLAELNNLFAQVDER 79


                  ....
gi 56181387   222 RKKR 225
Cdd:pfam18391  80 RRKR 83
Spy super family cl27809
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 25-124 4.87e-17

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


The actual alignment was detected with superfamily member COG3914:

Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 81.19  E-value: 4.87e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  25 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQ 104
Cdd:COG3914  77 LAALLELAALLLQALGRYEEALALYRRALALNPDNAEALFNLGNLLLALGRLEEALAALRRALALNPDFAEAYLNLGEAL 156

                        90       100
                ....*....|....*....|
gi 56181387 105 LEMESYDEAIANLQRAYSLA 124
Cdd:COG3914 157 RRLGRLEEAIAALRRALELD 176
 
Name Accession Description Interval E-value
RING-Ubox_CHIP cd16654
U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein ...
 227-297 7.26e-51

U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein (CHIP) and similar proteins; CHIP, also known as STIP1 homology and U box-containing protein 1 (STUB1), CLL-associated antigen KW-8, or Antigen NY-CO-7, is a multifunctional protein that functions both as a co-chaperone and an E3 ubiquitin-protein ligase. It couples protein folding and proteasome mediated degradation by interacting with heat shock proteins (e.g. HSC70) and ubiquitinating their misfolded client proteins, thereby targeting them for proteasomal degradation. It is also important for cellular differentiation and survival (or apoptosis), as well as susceptibility to stress. It targets a wide range of proteins, such as expanded ataxin-1, ataxin-3, huntingtin, and androgen receptor, which play roles in glucocorticoid response, tau degradation, and both p53 and cAMP signaling. CHIP contains an N-terminal tetratricopeptide repeat (TPR) domain responsible for protein-protein interaction, a highly charged middle coiled-coil (CC), and a C-terminal RING-like U-box domain acting as an ubiquitin ligase.


Pssm-ID: 438316 [Multi-domain]  Cd Length: 71  Bit Score: 161.97  E-value: 7.26e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56181387 227 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQEQLIPNLAMKEVIDAFISEN 297
Cdd:cd16654   1 VPDYLCCKISFELMRDPVITPSGITYERKDIEEHLQRVGHFDPITREPLTQDQLIPNLALKEAIEAFLEEN 71
U-box pfam04564
U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast ...
 227-299 6.40e-39

U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.


Pssm-ID: 398320 [Multi-domain]  Cd Length: 73  Bit Score: 131.66  E-value: 6.40e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56181387   227 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQEQLIPNLAMKEVIDAFISENGW 299
Cdd:pfam04564   1 IPDEFLDPITFELMTDPVILPSGITYDRSTIERHLLSVDPTDPFTREPLTHDQLIPNLELKAKIDAWLEEKRW 73
CHIP_TPR_N pfam18391
CHIP N-terminal tetratricopeptide repeat domain; This is N-terminal tetratricopeptide repeat ...
 142-225 6.79e-29

CHIP N-terminal tetratricopeptide repeat domain; This is N-terminal tetratricopeptide repeat (TPR) domain found in C terminus of Hsp70 interacting proteins (CHIP). The TPR domain of CHIP binds directly to EEVD motifs located at the C termini of Hsc/Hsp70 and Hsp90.


Pssm-ID: 436460  Cd Length: 83  Bit Score: 105.75  E-value: 6.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387   142 AKKKRWNSIEERRIHQESELHSYLSRLIAAERERELEECQrNHEGDEDDSHVRAQQACIEAKHDKYMADMDELFSQVDEK 221
Cdd:pfam18391   1 ARKKRWNVQEEKRIKQEIELQSYLNRLIDEDKERQLAELE-LSEEGSDDEEKEEEIDEIEQECDEYLAELNNLFAQVDER 79


                  ....
gi 56181387   222 RKKR 225
Cdd:pfam18391  80 RRKR 83
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
 230-293 2.39e-25

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 95.76  E-value: 2.39e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56181387    230 YLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGhFDPVTRSPLTQEQLIPNLAMKEVIDAF 293
Cdd:smart00504   1 EFLCPISLEVMKDPVILPSGQTYERSAIEKWLLSHG-TDPVTGQPLTHEDLIPNLALKSAIQEW 63
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 25-124 4.87e-17

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 81.19  E-value: 4.87e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  25 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQ 104
Cdd:COG3914  77 LAALLELAALLLQALGRYEEALALYRRALALNPDNAEALFNLGNLLLALGRLEEALAALRRALALNPDFAEAYLNLGEAL 156

                        90       100
                ....*....|....*....|
gi 56181387 105 LEMESYDEAIANLQRAYSLA 124
Cdd:COG3914 157 RRLGRLEEAIAALRRALELD 176
PLN03088 PLN03088
SGT1, suppressor of G2 allele of SKP1; Provisional
 26-126 2.41e-11

SGT1, suppressor of G2 allele of SKP1; Provisional


Pssm-ID: 215568 [Multi-domain]  Cd Length: 356  Bit Score: 63.65  E-value: 2.41e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387   26 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQL 105
Cdd:PLN03088   2 AKDLEDKAKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACM 81

                         90       100
                 ....*....|....*....|.
gi 56181387  106 EMESYDEAIANLQRAYSLAKE 126
Cdd:PLN03088  82 KLEEYQTAKAALEKGASLAPG 102
UFD2 COG5113
Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, ...
 219-298 3.21e-10

Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227444 [Multi-domain]  Cd Length: 929  Bit Score: 60.77  E-value: 3.21e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387 219 DEKRKKRDIPDYLCGKISFELMREPCITP-SGITYDRKDIEEHLQRvGHFDPVTRSPLTQEQLIPNLAMKEVIDAFISEN 297
Cdd:COG5113 843 VEEEDMGDVPDEFLDPLMFTIMKDPVKLPtSRITIDRSTIKAHLLS-DGTDPFNRMPLTLDDVTPNAELREKINRFYKCK 921


                .
gi 56181387 298 G 298
Cdd:COG5113 922 G 922
3a0801s09 TIGR00990
mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) ...
 21-96 6.90e-09

mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70); [Transport and binding proteins, Amino acids, peptides and amines]


Pssm-ID: 273380 [Multi-domain]  Cd Length: 615  Bit Score: 56.53  E-value: 6.90e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56181387    21 EKSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPlVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKA 96
Cdd:TIGR00990 122 ERKKYAAKLKEKGNKAYRNKDFNKAIKLYSKAIECKP-DPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKA 196
ANAPC3 pfam12895
Anaphase-promoting complex, cyclosome, subunit 3; Apc3, otherwise known as Cdc27, is one of ...
 40-120 2.17e-08

Anaphase-promoting complex, cyclosome, subunit 3; Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20.


Pssm-ID: 463743 [Multi-domain]  Cd Length: 82  Bit Score: 50.71  E-value: 2.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    40 RKYPEAAACYGRAITRNP--LVAVYYTnrALCYLKMQQHEQALADCRRAlELDGQSVKAHFFLGQCQLEMESYDEAIANL 117
Cdd:pfam12895   3 HQYKNAIFLAERLLAAEPesPEDAYLL--AQCLFLNGQYKRAYELLRKA-KLNGSSLGCRYLFAQCLLKLKKYDEALDAL 79


                  ...
gi 56181387   118 QRA 120
Cdd:pfam12895  80 GKA 82
ACL4-like cd24142
Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 ...
 65-127 2.28e-06

Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 (ACL4) acts as a chaperone for the L4 ribosomal subunit, encoded by RPL4A and RPL4B, and is required for hierarchical ribosome assembly. It is required for the soluble expression of newly synthesized RPL4 and for the protection of RPL4 from the Tom1-dependent cellular degradation machinery. ACL4 shields ribosomal protein L4 until timely release and insertion into the pre-ribosome is possible, once ribosomal protein L18 is present.


Pssm-ID: 467942 [Multi-domain]  Cd Length: 306  Bit Score: 48.39  E-value: 2.28e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56181387  65 NRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQ 127
Cdd:cd24142   5 EKAEELLDQGNFELALKFLQRALELEPNNVEALELLGEILLELGDVEEAREVLLRAIELDPDG 67
TPR smart00028
Tetratricopeptide repeats; Repeats present in 4 or more copies in proteins. Contain a minimum ...
 60-90 4.94e-06

Tetratricopeptide repeats; Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.


Pssm-ID: 197478 [Multi-domain]  Cd Length: 34  Bit Score: 42.43  E-value: 4.94e-06
                           10        20        30
                   ....*....|....*....|....*....|.
gi 56181387     60 AVYYTNRALCYLKMQQHEQALADCRRALELD 90
Cdd:smart00028   1 AEALYNLGNAYLKLGDYDEALEYYEKALELD 31
 
Name Accession Description Interval E-value
RING-Ubox_CHIP cd16654
U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein ...
 227-297 7.26e-51

U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein (CHIP) and similar proteins; CHIP, also known as STIP1 homology and U box-containing protein 1 (STUB1), CLL-associated antigen KW-8, or Antigen NY-CO-7, is a multifunctional protein that functions both as a co-chaperone and an E3 ubiquitin-protein ligase. It couples protein folding and proteasome mediated degradation by interacting with heat shock proteins (e.g. HSC70) and ubiquitinating their misfolded client proteins, thereby targeting them for proteasomal degradation. It is also important for cellular differentiation and survival (or apoptosis), as well as susceptibility to stress. It targets a wide range of proteins, such as expanded ataxin-1, ataxin-3, huntingtin, and androgen receptor, which play roles in glucocorticoid response, tau degradation, and both p53 and cAMP signaling. CHIP contains an N-terminal tetratricopeptide repeat (TPR) domain responsible for protein-protein interaction, a highly charged middle coiled-coil (CC), and a C-terminal RING-like U-box domain acting as an ubiquitin ligase.


Pssm-ID: 438316 [Multi-domain]  Cd Length: 71  Bit Score: 161.97  E-value: 7.26e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56181387 227 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQEQLIPNLAMKEVIDAFISEN 297
Cdd:cd16654   1 VPDYLCCKISFELMRDPVITPSGITYERKDIEEHLQRVGHFDPITREPLTQDQLIPNLALKEAIEAFLEEN 71
U-box pfam04564
U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast ...
 227-299 6.40e-39

U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.


Pssm-ID: 398320 [Multi-domain]  Cd Length: 73  Bit Score: 131.66  E-value: 6.40e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56181387   227 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQEQLIPNLAMKEVIDAFISENGW 299
Cdd:pfam04564   1 IPDEFLDPITFELMTDPVILPSGITYDRSTIERHLLSVDPTDPFTREPLTHDQLIPNLELKAKIDAWLEEKRW 73
CHIP_TPR_N pfam18391
CHIP N-terminal tetratricopeptide repeat domain; This is N-terminal tetratricopeptide repeat ...
 142-225 6.79e-29

CHIP N-terminal tetratricopeptide repeat domain; This is N-terminal tetratricopeptide repeat (TPR) domain found in C terminus of Hsp70 interacting proteins (CHIP). The TPR domain of CHIP binds directly to EEVD motifs located at the C termini of Hsc/Hsp70 and Hsp90.


Pssm-ID: 436460  Cd Length: 83  Bit Score: 105.75  E-value: 6.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387   142 AKKKRWNSIEERRIHQESELHSYLSRLIAAERERELEECQrNHEGDEDDSHVRAQQACIEAKHDKYMADMDELFSQVDEK 221
Cdd:pfam18391   1 ARKKRWNVQEEKRIKQEIELQSYLNRLIDEDKERQLAELE-LSEEGSDDEEKEEEIDEIEQECDEYLAELNNLFAQVDER 79


                  ....
gi 56181387   222 RKKR 225
Cdd:pfam18391  80 RRKR 83
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
 230-293 2.39e-25

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 95.76  E-value: 2.39e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56181387    230 YLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGhFDPVTRSPLTQEQLIPNLAMKEVIDAF 293
Cdd:smart00504   1 EFLCPISLEVMKDPVILPSGQTYERSAIEKWLLSHG-TDPVTGQPLTHEDLIPNLALKSAIQEW 63
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 25-124 4.87e-17

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 81.19  E-value: 4.87e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  25 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQ 104
Cdd:COG3914  77 LAALLELAALLLQALGRYEEALALYRRALALNPDNAEALFNLGNLLLALGRLEEALAALRRALALNPDFAEAYLNLGEAL 156

                        90       100
                ....*....|....*....|
gi 56181387 105 LEMESYDEAIANLQRAYSLA 124
Cdd:COG3914 157 RRLGRLEEAIAALRRALELD 176
NlpI COG4785
Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];
26-145 7.88e-17

Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 443815 [Multi-domain]  Cd Length: 223  Bit Score: 77.65  E-value: 7.88e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  26 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQL 105
Cdd:COG4785  73 AQLYYERGVAYDSLGDYDLAIADFDQALELDPDLAEAYNNRGLAYLLLGDYDAALEDFDRALELDPDYAYAYLNRGIALY 152

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 56181387 106 EMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAKKK 145
Cdd:COG4785 153 YLGRYELAIADLEKALELDPNDPERALWLYLAERKLDPEK 192
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 33-153 1.13e-16

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 80.04  E-value: 1.13e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  33 GNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDE 112
Cdd:COG3914 119 GNLLLALGRLEEALAALRRALALNPDFAEAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNALQDLGRLEE 198

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 56181387 113 AIANLQRAYSLAKEQRLNFGDDIPSALRIAKKKRWNSIEER 153
Cdd:COG3914 199 AIAAYRRALELDPDNADAHSNLLFALRQACDWEVYDRFEEL 239
RING-Ubox cd16453
U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that ...
 230-275 3.13e-16

U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that also includes the HECT family and the RING finger family. The E3 enzyme is ubiquitin-protein ligase that cooperates with a ubiquitin-activating enzyme (E1) and a ubiquitin-conjugating enzyme (E2), and plays a central role in determining the specificity of the ubiquitination system. It removes the ubiquitin molecule from the E2 enzyme and attaches it to the target substrate, forming a covalent bond between ubiquitin and the target. U-box proteins are characterized by the presence of a U-box domain of approximately 70 amino acids. The U-box is a modified form of the RING finger domain that lacks metal chelating cysteines and histidines. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms.


Pssm-ID: 438117 [Multi-domain]  Cd Length: 44  Bit Score: 71.05  E-value: 3.13e-16
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 56181387 230 YLCgKISFELMREPCITPSGITYDRKDIEEHLQRvGHFDPVTRSPL 275
Cdd:cd16453   1 FLC-PISGELMKDPVITPSGITYDRSAIERWLLS-DNTDPFTREPL 44
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
41-123 2.94e-15

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 73.89  E-value: 2.94e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG0457  57 RYEEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLALLELGRYDEAIEAYERA 136


                ...
gi 56181387 121 YSL 123
Cdd:COG0457 137 LEL 139
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 41-126 7.15e-15

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 70.03  E-value: 7.15e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG4235  32 RYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDPDNPEALYLLGLAAFQQGDYAEAIAAWQKL 111


                ....*.
gi 56181387 121 YSLAKE 126
Cdd:COG4235 112 LALLPA 117
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
41-120 1.23e-14

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 71.96  E-value: 1.23e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG0457  23 RYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKA 102
RING-Ubox_WDSUB1-like cd16655
U-box domain, a modified RING finger, found in WD repeat, SAM and U-box domain-containing ...
 228-283 1.27e-14

U-box domain, a modified RING finger, found in WD repeat, SAM and U-box domain-containing protein 1 (WDSUB1) and similar proteins; WDSUB1 is an uncharacterized protein containing seven WD40 repeats and a SAM domain in addition to the U-box. Its biological role remains unclear. This subfamily also includes many uncharacterized kinase domain-containing U-box (AtPUB) proteins and several MIF4G motif-containing AtPUB proteins from Arabidopsis.


Pssm-ID: 438317 [Multi-domain]  Cd Length: 55  Bit Score: 67.14  E-value: 1.27e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56181387 228 PDYLCgKISFELMREPCITPSGITYDRKDIEEHLQRvGHFDPVTRSPLTQEQLIPN 283
Cdd:cd16655   2 DEFLC-PITQELMRDPVVAADGHTYERSAIEEWLET-HNTSPMTRLPLSSTDLVPN 55
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
41-190 1.03e-13

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 69.27  E-value: 1.03e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG0457  91 RYEEALEDYDKALELDPDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELLEKL 170

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387 121 YSLAKEQRLNFGDDIPSALRIAKKKRWNSIEERRIHQESELHSYLSRLIAAERERELEECQRNHEGDEDD 190
Cdd:COG0457 171 EAAALAALLAAALGEAALALAAAEVLLALLLALEQALRKKLAILTLAALAELLLLALALLLALRLAALAL 240
RING-Ubox_UBE4A cd16657
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and ...
 229-297 1.10e-13

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and similar proteins; This subfamily includes yeast ubiquitin fusion degradation protein 2 (UFD2p) and its mammalian homolog, UBE4A. Yeast UFD2p, also known as ubiquitin conjugation factor E4 or UB fusion protein 2, is a polyubiquitin chain conjugation factor (E4) in the ubiquitin fusion degradation (UFD) pathway which catalyzes elongation of the ubiquitin chain through Lys48 linkage. It binds to substrates conjugated with one to three ubiquitin molecules and catalyzes the addition of further ubiquitin moieties in the presence of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3), yielding multiubiquitylated substrates that are targets for the 26S proteasome. UFD2p is implicated in cell survival under stress conditions and is essential for homoeostasis of unsaturated fatty acids. It interacts with UBL-UBA proteins Rad23 and Dsk2, which are involved in the endoplasmic reticulum-associated degradation, ubiquitin fusion degradation, and OLE-1 gene induction pathways. UBE4A is a U-box-type ubiquitin-protein ligase that is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. It may have a specific role in different biochemical processes other than ubiquitination, including growth or differentiation. Members of this family contain an N-terminal ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


Pssm-ID: 438319  Cd Length: 70  Bit Score: 64.99  E-value: 1.10e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387 229 DYLCGKISFELMREPCITP-SGITYDRKDIEEHLQRVGHfDPVTRSPLTQEQLIPNLAMKEVIDAFISEN 297
Cdd:cd16657   1 DEFLDPIMYTLMKDPVILPsSKVTVDRSTIKRHLLSDQT-DPFNRSPLTLDMVIPNEELKQKIEEFLAEK 69
RING-Ubox_PUB cd16664
U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and ...
 228-280 4.91e-12

U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and similar proteins; The plant PUB proteins, also known as U-box domain-containing proteins, are much more numerous in Arabidopsis which has 62 in comparison with the typical 6 in most animals. The majority of AtPUBs in this subfamily are known as ARM domain-containing PUB proteins, containing a C-terminally-located, tandem ARM (armadillo) repeat protein-interaction region in addition to the U-box domain. They have been implicated in the regulation of cell death and defense. They also play important roles in other plant-specific pathways, such as controlling both self-incompatibility and pseudo-self-incompatibility, as well as acting in abiotic stress. A subgroup of ARM domain-containing PUB proteins harbors a plant-specific U-box N-terminal domain.


Pssm-ID: 438326 [Multi-domain]  Cd Length: 53  Bit Score: 59.88  E-value: 4.91e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 56181387 228 PDYLCGkISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQEQL 280
Cdd:cd16664   2 EEFICP-ISLELMKDPVILATGQTYERAAIEKWLDSGNNTCPITGQPLTHTDL 53
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
41-128 6.85e-12

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 60.57  E-value: 6.85e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALAdCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG3063   7 DLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDPNNAEALLNLAELLLELGDYDEALAYLERA 85


                ....*...
gi 56181387 121 YSLAKEQR 128
Cdd:COG3063  86 LELDPSAL 93
RING-Ubox_LubX-like_rpt1 cd23149
first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX ...
 230-283 7.37e-12

first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins; LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the first one.


Pssm-ID: 438511 [Multi-domain]  Cd Length: 55  Bit Score: 59.42  E-value: 7.37e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 56181387 230 YLCgKISFELMREPCITPSGITYDRKDIEEHLqRVGHFDPVTRSPLTQEQLIPN 283
Cdd:cd23149   1 FTC-PITSGFMEDPVITPSGFSYERSAIERWL-ETKPEDPQTREPLTAKDLQPN 52
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 26-120 1.39e-11

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 60.98  E-value: 1.39e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  26 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQL 105
Cdd:COG4783   4 AEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALL 83

                        90
                ....*....|....*
gi 56181387 106 EMESYDEAIANLQRA 120
Cdd:COG4783  84 KAGDYDEALALLEKA 98
RING-Ubox_UBE4B cd16658
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and ...
 226-297 1.58e-11

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and similar proteins; UBE4B, also known as UFD2a, is a U-box-type ubiquitin-protein ligase that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor, which catalyzes formation of Lys27- and Lys33-linked polyubiquitin chains rather than the Lys48-linked chain. It is a mammalian homolog of yeast UFD2 ubiquitination factor and it participates in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. It is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. UBE4B has contradictory functions upon tumorigenesis as an oncogene or tumor suppressor in different types of cancers. It is essential for Hdm2 (also known as Mdm2)-mediated p53 degradation. It mediates p53 polyubiquitination and degradation, as well as inhibits p53-dependent transactivation and apoptosis, and thus plays an important role in regulating phosphorylated p53 following DNA damage. UBE4B is also associated with other pathways independent of the p53 family, such as polyglutamine aggregation and Wallerian degeneration, both of which are critical in neurodegenerative diseases. Moreover, UBE4B acts as a regulator of epidermal growth factor receptor (EGFR) degradation. It is recruited to endosomes in response to EGFR activation by binding to Hrs, a key component of endosomal sorting complex required for transport (ESCRT) 0, and then regulates endosomal sorting, affecting cellular levels of the EGFR and its downstream signaling. UBE4B contains a ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


Pssm-ID: 438320  Cd Length: 74  Bit Score: 59.21  E-value: 1.58e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56181387 226 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHfDPVTRSPLTQEQLIPNLAMKEVIDAFISEN 297
Cdd:cd16658   3 DAPDEFLDPLMDTLMTDPVILPSGTIMDRSIILRHLLNSQT-DPFNRQPLTEDMLEPVPELKERIQAWIREK 73
PLN03088 PLN03088
SGT1, suppressor of G2 allele of SKP1; Provisional
 26-126 2.41e-11

SGT1, suppressor of G2 allele of SKP1; Provisional


Pssm-ID: 215568 [Multi-domain]  Cd Length: 356  Bit Score: 63.65  E-value: 2.41e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387   26 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQL 105
Cdd:PLN03088   2 AKDLEDKAKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACM 81

                         90       100
                 ....*....|....*....|.
gi 56181387  106 EMESYDEAIANLQRAYSLAKE 126
Cdd:PLN03088  82 KLEEYQTAKAALEKGASLAPG 102
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 41-125 3.27e-11

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 60.74  E-value: 3.27e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG5010  69 DFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRA 148


                ....*
gi 56181387 121 YSLAK 125
Cdd:COG5010 149 LGTSP 153
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
53-123 5.01e-11

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 61.56  E-value: 5.01e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56181387  53 ITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL 123
Cdd:COG0457   1 LELDPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALEL 71
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 40-126 6.32e-11

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 61.67  E-value: 6.32e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  40 RKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQR 119
Cdd:COG2956 124 GDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEEAIAALER 203


                ....*..
gi 56181387 120 AYSLAKE 126
Cdd:COG2956 204 ALEQDPD 210
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 41-127 3.03e-10

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 57.51  E-value: 3.03e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG4783  53 DLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKA 132


                ....*..
gi 56181387 121 YSLAKEQ 127
Cdd:COG4783 133 LELDPDD 139
UFD2 COG5113
Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, ...
 219-298 3.21e-10

Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227444 [Multi-domain]  Cd Length: 929  Bit Score: 60.77  E-value: 3.21e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387 219 DEKRKKRDIPDYLCGKISFELMREPCITP-SGITYDRKDIEEHLQRvGHFDPVTRSPLTQEQLIPNLAMKEVIDAFISEN 297
Cdd:COG5113 843 VEEEDMGDVPDEFLDPLMFTIMKDPVKLPtSRITIDRSTIKAHLLS-DGTDPFNRMPLTLDDVTPNAELREKINRFYKCK 921


                .
gi 56181387 298 G 298
Cdd:COG5113 922 G 922
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 25-124 6.04e-10

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 58.97  E-value: 6.04e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  25 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQ 104
Cdd:COG2956 143 NAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELY 222

                        90       100
                ....*....|....*....|
gi 56181387 105 LEMESYDEAIANLQRAYSLA 124
Cdd:COG2956 223 EKLGDPEEALELLRKALELD 242
NlpI COG4785
Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];
54-123 2.24e-09

Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 443815 [Multi-domain]  Cd Length: 223  Bit Score: 56.46  E-value: 2.24e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  54 TRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL 123
Cdd:COG4785  67 LALPDLAQLYYERGVAYDSLGDYDLAIADFDQALELDPDLAEAYNNRGLAYLLLGDYDAALEDFDRALEL 136
3a0801s09 TIGR00990
mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) ...
 21-96 6.90e-09

mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70); [Transport and binding proteins, Amino acids, peptides and amines]


Pssm-ID: 273380 [Multi-domain]  Cd Length: 615  Bit Score: 56.53  E-value: 6.90e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56181387    21 EKSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPlVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKA 96
Cdd:TIGR00990 122 ERKKYAAKLKEKGNKAYRNKDFNKAIKLYSKAIECKP-DPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKA 196
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 44-123 2.14e-08

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 51.93  E-value: 2.14e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  44 EAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL 123
Cdd:COG4235   1 EAIARLRQALAANPNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALAL 80
ANAPC3 pfam12895
Anaphase-promoting complex, cyclosome, subunit 3; Apc3, otherwise known as Cdc27, is one of ...
 40-120 2.17e-08

Anaphase-promoting complex, cyclosome, subunit 3; Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20.


Pssm-ID: 463743 [Multi-domain]  Cd Length: 82  Bit Score: 50.71  E-value: 2.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    40 RKYPEAAACYGRAITRNP--LVAVYYTnrALCYLKMQQHEQALADCRRAlELDGQSVKAHFFLGQCQLEMESYDEAIANL 117
Cdd:pfam12895   3 HQYKNAIFLAERLLAAEPesPEDAYLL--AQCLFLNGQYKRAYELLRKA-KLNGSSLGCRYLFAQCLLKLKKYDEALDAL 79


                  ...
gi 56181387   118 QRA 120
Cdd:pfam12895  80 GKA 82
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 41-126 3.46e-08

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 53.58  E-value: 3.46e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:COG2956  91 LLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKA 170


                ....*.
gi 56181387 121 YSLAKE 126
Cdd:COG2956 171 LKLDPD 176
NlpI COG4785
Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];
25-132 4.84e-08

Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 443815 [Multi-domain]  Cd Length: 223  Bit Score: 52.61  E-value: 4.84e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  25 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQ 104
Cdd:COG4785 106 LAEAYNNRGLAYLLLGDYDAALEDFDRALELDPDYAYAYLNRGIALYYLGRYELAIADLEKALELDPNDPERALWLYLAE 185

                        90       100
                ....*....|....*....|....*...
gi 56181387 105 LEMEsYDEAIANLQRAYSLAKEQRLNFG 132
Cdd:COG4785 186 RKLD-PEKALALLLEDWATAYLLQGDTE 212
RING-Ubox_PRP19 cd16656
U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and ...
 231-282 1.62e-07

U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and similar proteins; Prp19, also known as nuclear matrix protein 200 (NMP200), senescence evasion factor (SNEV), or DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signaling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerization and is essential for its auto-ubiquitination activity in vitro or when overexpressed, a coiled-coil Prp19 homology region that mediates its tetramerization and interaction with CDC5L and SPF27, and a C-terminal seven-bladed WD40 beta-propeller type of leucine-rich architectural repeats that form an asymmetrical barrel-shaped structure important for substrate recognition and recruitment.


Pssm-ID: 438318  Cd Length: 54  Bit Score: 47.17  E-value: 1.62e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 56181387 231 LCGkISFELMREPCITP-SGITYDRKDIEEHLQRVGHfDPVTRSPLTQEQLIP 282
Cdd:cd16656   2 VCA-ISGEVPEEPVVSPkSGHVFEKRLIEKYIAENGT-DPVTGEPLTEEDLIE 52
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 36-119 2.50e-07

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 48.45  E-value: 2.50e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  36 LFVGRKYPEAAACYGRAITRNP---LVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVK---AHFFLGQCQLEMES 109
Cdd:COG1729   3 LLKAGDYDEAIAAFKAFLKRYPnspLAPDALYWLGEAYYALGDYDEAAEAFEKLLKRYPDSPKapdALLKLGLSYLELGD 82

                        90
                ....*....|
gi 56181387 110 YDEAIANLQR 119
Cdd:COG1729  83 YDKARATLEE 92
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 26-126 3.69e-07

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 49.19  E-value: 3.69e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  26 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQL 105
Cdd:COG5010  20 LRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYS 99

                        90       100
                ....*....|....*....|.
gi 56181387 106 EMESYDEAIANLQRAYSLAKE 126
Cdd:COG5010 100 RSGDKDEAKEYYEKALALSPD 120
TPR_12 pfam13424
Tetratricopeptide repeat;
58-126 4.52e-07

Tetratricopeptide repeat;


Pssm-ID: 315987 [Multi-domain]  Cd Length: 77  Bit Score: 46.61  E-value: 4.52e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56181387    58 LVAVYYTNRALCYLKMQQHEQALADCRRALEL--------DGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKE 126
Cdd:pfam13424   1 DVATALNNLAAVLRRLGRYDEALELLEKALEIarrllgpdHPLTATTLLNLGRLYLELGRYEEALELLERALALAEK 77
RING-Ubox_LubX-like_rpt2 cd23150
second U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein ...
 230-296 5.33e-07

second U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins; LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the second one.


Pssm-ID: 438512 [Multi-domain]  Cd Length: 69  Bit Score: 46.31  E-value: 5.33e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56181387 230 YLCgKISFELMREPCITPSGITYDRKDIEEHLQRVGHfDPVTRSPLTQEQLIPNLAMKEVIDAFISE 296
Cdd:cd23150   4 FLC-PISKTLIKTPVITAQGKVYDQEALSNFLIATGN-KDETGKKLSIDDVVVFDELYQQIKVYNFY 68
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 60-126 6.31e-07

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 47.88  E-value: 6.31e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56181387  60 AVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKE 126
Cdd:COG4783   4 AEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPD 70
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 35-127 1.13e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 48.96  E-value: 1.13e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  35 RLFVGRK-YPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEA 113
Cdd:COG2956  50 NLYRRRGeYDRAIRIHQKLLERDPDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKA 129

                        90
                ....*....|....
gi 56181387 114 IANLQRAYSLAKEQ 127
Cdd:COG2956 130 IEVLERLLKLGPEN 143
TPR_1 pfam00515
Tetratricopeptide repeat;
60-90 1.49e-06

Tetratricopeptide repeat;


Pssm-ID: 459840 [Multi-domain]  Cd Length: 34  Bit Score: 43.95  E-value: 1.49e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 56181387    60 AVYYTNRALCYLKMQQHEQALADCRRALELD 90
Cdd:pfam00515   1 AKALYNLGNAYFKLGKYDEALEYYEKALELN 31
ACL4-like cd24142
Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 ...
 65-127 2.28e-06

Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 (ACL4) acts as a chaperone for the L4 ribosomal subunit, encoded by RPL4A and RPL4B, and is required for hierarchical ribosome assembly. It is required for the soluble expression of newly synthesized RPL4 and for the protection of RPL4 from the Tom1-dependent cellular degradation machinery. ACL4 shields ribosomal protein L4 until timely release and insertion into the pre-ribosome is possible, once ribosomal protein L18 is present.


Pssm-ID: 467942 [Multi-domain]  Cd Length: 306  Bit Score: 48.39  E-value: 2.28e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56181387  65 NRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQ 127
Cdd:cd24142   5 EKAEELLDQGNFELALKFLQRALELEPNNVEALELLGEILLELGDVEEAREVLLRAIELDPDG 67
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 25-124 3.84e-06

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 48.07  E-value: 3.84e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  25 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQ 104
Cdd:COG3914  43 LALLLLAALAEAAAAALLALAAGEAAAAAAALLLLAALLELAALLLQALGRYEEALALYRRALALNPDNAEALFNLGNLL 122

                        90       100
                ....*....|....*....|
gi 56181387 105 LEMESYDEAIANLQRAYSLA 124
Cdd:COG3914 123 LALGRLEEALAALRRALALN 142
TPR smart00028
Tetratricopeptide repeats; Repeats present in 4 or more copies in proteins. Contain a minimum ...
 60-90 4.94e-06

Tetratricopeptide repeats; Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.


Pssm-ID: 197478 [Multi-domain]  Cd Length: 34  Bit Score: 42.43  E-value: 4.94e-06
                           10        20        30
                   ....*....|....*....|....*....|.
gi 56181387     60 AVYYTNRALCYLKMQQHEQALADCRRALELD 90
Cdd:smart00028   1 AEALYNLGNAYLKLGDYDEALEYYEKALELD 31
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
69-126 5.34e-06

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 44.01  E-value: 5.34e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56181387  69 CYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIAnLQRAYSLAKE 126
Cdd:COG3063   1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDPN 57
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 58-127 8.54e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 46.26  E-value: 8.54e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  58 LVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQ 127
Cdd:COG2956   6 AAALGWYFKGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDR 75
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 32-127 2.66e-05

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 45.46  E-value: 2.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    32 QGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYD 111
Cdd:TIGR02917 199 KGDLLLSLGNIELALAAYRKAIALRPNNIAVLLALATILIEAGEFEEAEKHADALLKKAPNSPLAHYLKALVDFQKKNYE 278

                          90
                  ....*....|....*.
gi 56181387   112 EAIANLQRAYSLAKEQ 127
Cdd:TIGR02917 279 DARETLQDALKSAPEY 294
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 31-124 4.64e-05

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 43.95  E-value: 4.64e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  31 EQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESY 110
Cdd:COG2956  13 FKGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALLELAQDYLKAGLL 92

                        90
                ....*....|....
gi 56181387 111 DEAIANLQRAYSLA 124
Cdd:COG2956  93 DRAEELLEKLLELD 106
ACL4-like cd24142
Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 ...
 26-128 9.43e-05

Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 (ACL4) acts as a chaperone for the L4 ribosomal subunit, encoded by RPL4A and RPL4B, and is required for hierarchical ribosome assembly. It is required for the soluble expression of newly synthesized RPL4 and for the protection of RPL4 from the Tom1-dependent cellular degradation machinery. ACL4 shields ribosomal protein L4 until timely release and insertion into the pre-ribosome is possible, once ribosomal protein L18 is present.


Pssm-ID: 467942 [Multi-domain]  Cd Length: 306  Bit Score: 43.39  E-value: 9.43e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387  26 AQELKEQGNrlfvgrkYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELD-GQSVKAHFFLGQcq 104
Cdd:cd24142   7 AEELLDQGN-------FELALKFLQRALELEPNNVEALELLGEILLELGDVEEAREVLLRAIELDpDGGYEKYLYLGQ-- 77

                        90       100
                ....*....|....*....|....
gi 56181387 105 leMESYDEAIANLQRAYSLAKEQR 128
Cdd:cd24142  78 --LSGGEEALQYYEKGIEILEEEL 99
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 78-126 1.50e-04

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 40.76  E-value: 1.50e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 56181387  78 QALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKE 126
Cdd:COG4235   1 EAIARLRQALAANPNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPD 49
LcrH_SycD TIGR02552
type III secretion low calcium response chaperone LcrH/SycD; Genes in this family are found in ...
 41-93 3.59e-04

type III secretion low calcium response chaperone LcrH/SycD; Genes in this family are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role. In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.


Pssm-ID: 274197 [Multi-domain]  Cd Length: 135  Bit Score: 39.97  E-value: 3.59e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 56181387    41 KYPEAAACYGRA--ITRNPLVAVYYTnrALCYLKMQQHEQALADCRRALELDGQS 93
Cdd:TIGR02552  66 EYEEAIDAYALAaaLDPDDPRPYFHA--AECLLALGEPESALKALDLAIEICGEN 118
LcrH_SycD TIGR02552
type III secretion low calcium response chaperone LcrH/SycD; Genes in this family are found in ...
 41-126 5.38e-04

type III secretion low calcium response chaperone LcrH/SycD; Genes in this family are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role. In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.


Pssm-ID: 274197 [Multi-domain]  Cd Length: 135  Bit Score: 39.20  E-value: 5.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    41 KYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:TIGR02552  32 RYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEPESALKALDLA 111


                  ....*.
gi 56181387   121 YSLAKE 126
Cdd:TIGR02552 112 IEICGE 117
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 40-127 8.54e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 40.84  E-value: 8.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    40 RKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQr 119
Cdd:TIGR02917 377 GDFEKAAEYLAKATELDPENAAARTQLGISKLSQGDPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAK- 455


                  ....*...
gi 56181387   120 aySLAKEQ 127
Cdd:TIGR02917 456 --KLEKKQ 461
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 21-162 8.69e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 40.84  E-value: 8.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    21 EKSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFF 99
Cdd:TIGR02917 561 ELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAaPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLL 640

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56181387   100 LGQCQLEMESYDEAIANLQRAYS---------LAKEQRLNFGDDIPSALRIAKKKRWNSIEERRIH-QESELH 162
Cdd:TIGR02917 641 LADAYAVMKNYAKAITSLKRALElkpdnteaqIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFeLEGDLY 713
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
35-90 9.86e-04

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 37.84  E-value: 9.86e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56181387  35 RLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELD 90
Cdd:COG3063  34 LLLLEQGRYDEAIALEKALKLDPNNAEALLNLAELLLELGDYDEALAYLERALELD 89
TPR_16 pfam13432
Tetratricopeptide repeat; This family is found predominantly at the C-terminus of ...
 31-93 1.44e-03

Tetratricopeptide repeat; This family is found predominantly at the C-terminus of transglutaminase enzyme core regions.


Pssm-ID: 433202 [Multi-domain]  Cd Length: 68  Bit Score: 36.55  E-value: 1.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56181387    31 EQGNRLFVGRKYPEAAACYGRAITRN---PLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQS 93
Cdd:pfam13432   2 ALARAALRAGDYDDAAAALEAALARFpesPDAAAALLLLGLAALRQGRLAEAAAAYRAALRAAPGD 67
type_IV_pilW TIGR02521
type IV pilus biogenesis/stability protein PilW; Members of this family are designated PilF ...
 41-144 1.51e-03

type IV pilus biogenesis/stability protein PilW; Members of this family are designated PilF and PilW. This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.


Pssm-ID: 131573 [Multi-domain]  Cd Length: 234  Bit Score: 39.24  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    41 KYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAhfFLGQCQLEMES--YDEAIAN 116
Cdd:TIGR02521 114 KYEQAMQQFEQAIEDPlyPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPES--LLELAELYYLRgqYKDARAY 191

                          90       100       110
                  ....*....|....*....|....*....|.
gi 56181387   117 LQRAYSLAkeqrlnfGDDIPS---ALRIAKK 144
Cdd:TIGR02521 192 LERYQQTY-------NQTAESlwlGIRIARA 215
TPR_16 pfam13432
Tetratricopeptide repeat; This family is found predominantly at the C-terminus of ...
 65-121 1.70e-03

Tetratricopeptide repeat; This family is found predominantly at the C-terminus of transglutaminase enzyme core regions.


Pssm-ID: 433202 [Multi-domain]  Cd Length: 68  Bit Score: 36.16  E-value: 1.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    65 NRALCYLKMQQHEQALADCRRALELDG---QSVKAHFFLGQCQLEMESYDEAIANLQRAY 121
Cdd:pfam13432   2 ALARAALRAGDYDDAAAALEAALARFPespDAAAALLLLGLAALRQGRLAEAAAAYRAAL 61
TPR_19 pfam14559
Tetratricopeptide repeat;
75-120 1.99e-03

Tetratricopeptide repeat;


Pssm-ID: 434038 [Multi-domain]  Cd Length: 65  Bit Score: 36.02  E-value: 1.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 56181387    75 QHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRA 120
Cdd:pfam14559   3 DYAEALELLEQALAEDPDNAEARLGLAEALLALGRLDEAEALLAAL 48
TPR_2 pfam07719
Tetratricopeptide repeat; This Pfam entry includes outlying Tetratricopeptide-like repeats ...
 60-90 3.75e-03

Tetratricopeptide repeat; This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.


Pssm-ID: 429619 [Multi-domain]  Cd Length: 33  Bit Score: 34.42  E-value: 3.75e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 56181387    60 AVYYTNRALCYLKMQQHEQALADCRRALELD 90
Cdd:pfam07719   1 AEALYNLGLAYYKLGDYEEALEAYEKALELD 31
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 68-122 4.32e-03

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 36.51  E-value: 4.32e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56181387  68 LCYLKMQQHEQALADCRRALELDGQSV---KAHFFLGQCQLEMESYDEAIANLQRAYS 122
Cdd:COG1729   1 KALLKAGDYDEAIAAFKAFLKRYPNSPlapDALYWLGEAYYALGDYDEAAEAFEKLLK 58
3a0801s09 TIGR00990
mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) ...
 38-126 6.20e-03

mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70); [Transport and binding proteins, Amino acids, peptides and amines]


Pssm-ID: 273380 [Multi-domain]  Cd Length: 615  Bit Score: 38.04  E-value: 6.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181387    38 VGRKYPEAAACYGRAITRNPL---VAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAI 114
Cdd:TIGR00990 306 ADESYEEAARAFEKALDLGKLgekEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAE 385

                          90
                  ....*....|..
gi 56181387   115 ANLQRAYSLAKE 126
Cdd:TIGR00990 386 EDFDKALKLNSE 397
 
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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