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Conserved domains on  [gi|1134612243|ref|NP_001335163|]
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F-box DNA helicase 1 isoform 2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
F-box_FBXO18 cd22095
F-box domain found in F-box only protein 18 (FBXO18) and similar proteins; FBXO18, also called ...
 135-182 1.89e-25

F-box domain found in F-box only protein 18 (FBXO18) and similar proteins; FBXO18, also called FBX18, or F-box DNA helicase 1 (FBH1), is a 3'-5' DNA helicase and the substrate-recognition component of the SCF(FBH1) E3 ubiquitin ligase complex that plays a key role in response to stalled/damaged replication forks. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


:

Pssm-ID: 438867  Cd Length: 48  Bit Score: 99.66  E-value: 1.89e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1134612243 135 HICRLPSEVLRHIFAFLPVEDLYWNLSLVCHLWREIINDPLFIPWKKL 182
Cdd:cd22095     1 HIQQLPEELLRNIFAFLPAEDLYQNISLVCRHWRDIVSDPLFIPWKKL 48
UvrD super family cl33806
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
365-857 1.84e-23

Superfamily I DNA or RNA helicase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0210:

Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 106.56  E-value: 1.84e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 365 QLTHEQQLILNHKMEPLQVVkimAFAGTGKTSTLVKYA------EKWSQSRFLYVTF-NKS-------IAKQAELVFPSN 430
Cdd:COG0210     6 GLNPEQRAAVEHPEGPLLVL---AGAGSGKTRVLTHRIayliaeGGVDPEQILAVTFtNKAaremrerIEALLGRLARGL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 431 VICkTFHSMAYSHVGRKYQLKKKLNlfkltPF----------MVNSVLAE----GKGGFIRaklvckTLENFFASA-DEE 495
Cdd:COG0210    83 WVG-TFHSLALRILRRHAELLGLPP-----NFtildgddqlrLIKELLKElgldEKRFPPR------ELLSLISRAkNEG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 496 LTIDHVPIWCKNSHGQRVMV------EQSEKLNG-------VLEASRLWDNmrklgeckeeayqmtHDGYLKLWQlskpl 562
Cdd:COG0210   151 LTPEELAELLAADPEWRAAAelyeayQERLRANNaldfddlLLLAVRLLEE---------------NPEVLEKYQ----- 210

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 563 lASFDAIFVDEAQDCTPAIMNIV--LSQPCGKIF-VGDPHQQIYTFRGA--VN-ALFTV--PHTHVFYLTQSFRFGVEI- 633
Cdd:COG0210   211 -NRFRYILVDEYQDTNPAQYELLrlLAGDGRNLCvVGDDDQSIYGFRGAdpENiLRFEKdfPDAKVIKLEQNYRSTQNIl 289

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 634 -----------------------------AYVGATILD----VCKRVRKktlvggNHQSGIR-GDIkgqvALLSRTNA-- 677
Cdd:COG0210   290 daanaviannpgrlgknlwtdngegekvrLYVAPDEEEearfVADEIRE------LHEEGVPlSDI----AVLYRTNAqs 359

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 678 NVFDEA-------VRVTEGESP-------------------------ARIH--LIGGIKSFGLDRI--------IDIWTL 715
Cdd:COG0210   360 RALEEAlrragipYRVVGGLRFyeraeikdllaylrllanpdddvalLRILnvPRRGIGAATLERLreaareegISLLEA 439

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 716 LQ--------PEEERRK----RDLIIK----------DRFIRRWVHKegfSGFKRYVTAAEDKELEAKIA-------VVE 766
Cdd:COG0210   440 LRdlgelaglSGRAAKAlrrfAELLEAlraaaerlplEELLEALLDE---SGYEEELREEAGEEAERRLEnleelvdAAA 516

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 767 KYNIR-----IPELVERIErcHIDDLDFAEY-----ILGTVHKAKGLEFDTVHVLddfvkvpcarhNLAQ--LPHFRveS 834
Cdd:COG0210   517 RFEERnpgasLEAFLEELA--LLSDLDAADEdedavTLMTLHAAKGLEFPVVFLV-----------GLEEglFPHQR--S 581

                         650       660
                  ....*....|....*....|....*...
gi 1134612243 835 FS-----EDEWNLLYVAVTRAKKRLIMT 857
Cdd:COG0210   582 LDdeeelEEERRLFYVAITRARERLYLT 609
 
Name Accession Description Interval E-value
F-box_FBXO18 cd22095
F-box domain found in F-box only protein 18 (FBXO18) and similar proteins; FBXO18, also called ...
 135-182 1.89e-25

F-box domain found in F-box only protein 18 (FBXO18) and similar proteins; FBXO18, also called FBX18, or F-box DNA helicase 1 (FBH1), is a 3'-5' DNA helicase and the substrate-recognition component of the SCF(FBH1) E3 ubiquitin ligase complex that plays a key role in response to stalled/damaged replication forks. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438867  Cd Length: 48  Bit Score: 99.66  E-value: 1.89e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1134612243 135 HICRLPSEVLRHIFAFLPVEDLYWNLSLVCHLWREIINDPLFIPWKKL 182
Cdd:cd22095     1 HIQQLPEELLRNIFAFLPAEDLYQNISLVCRHWRDIVSDPLFIPWKKL 48
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
365-857 1.84e-23

Superfamily I DNA or RNA helicase [Replication, recombination and repair];


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 106.56  E-value: 1.84e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 365 QLTHEQQLILNHKMEPLQVVkimAFAGTGKTSTLVKYA------EKWSQSRFLYVTF-NKS-------IAKQAELVFPSN 430
Cdd:COG0210     6 GLNPEQRAAVEHPEGPLLVL---AGAGSGKTRVLTHRIayliaeGGVDPEQILAVTFtNKAaremrerIEALLGRLARGL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 431 VICkTFHSMAYSHVGRKYQLKKKLNlfkltPF----------MVNSVLAE----GKGGFIRaklvckTLENFFASA-DEE 495
Cdd:COG0210    83 WVG-TFHSLALRILRRHAELLGLPP-----NFtildgddqlrLIKELLKElgldEKRFPPR------ELLSLISRAkNEG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 496 LTIDHVPIWCKNSHGQRVMV------EQSEKLNG-------VLEASRLWDNmrklgeckeeayqmtHDGYLKLWQlskpl 562
Cdd:COG0210   151 LTPEELAELLAADPEWRAAAelyeayQERLRANNaldfddlLLLAVRLLEE---------------NPEVLEKYQ----- 210

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 563 lASFDAIFVDEAQDCTPAIMNIV--LSQPCGKIF-VGDPHQQIYTFRGA--VN-ALFTV--PHTHVFYLTQSFRFGVEI- 633
Cdd:COG0210   211 -NRFRYILVDEYQDTNPAQYELLrlLAGDGRNLCvVGDDDQSIYGFRGAdpENiLRFEKdfPDAKVIKLEQNYRSTQNIl 289

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 634 -----------------------------AYVGATILD----VCKRVRKktlvggNHQSGIR-GDIkgqvALLSRTNA-- 677
Cdd:COG0210   290 daanaviannpgrlgknlwtdngegekvrLYVAPDEEEearfVADEIRE------LHEEGVPlSDI----AVLYRTNAqs 359

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 678 NVFDEA-------VRVTEGESP-------------------------ARIH--LIGGIKSFGLDRI--------IDIWTL 715
Cdd:COG0210   360 RALEEAlrragipYRVVGGLRFyeraeikdllaylrllanpdddvalLRILnvPRRGIGAATLERLreaareegISLLEA 439

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 716 LQ--------PEEERRK----RDLIIK----------DRFIRRWVHKegfSGFKRYVTAAEDKELEAKIA-------VVE 766
Cdd:COG0210   440 LRdlgelaglSGRAAKAlrrfAELLEAlraaaerlplEELLEALLDE---SGYEEELREEAGEEAERRLEnleelvdAAA 516

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 767 KYNIR-----IPELVERIErcHIDDLDFAEY-----ILGTVHKAKGLEFDTVHVLddfvkvpcarhNLAQ--LPHFRveS 834
Cdd:COG0210   517 RFEERnpgasLEAFLEELA--LLSDLDAADEdedavTLMTLHAAKGLEFPVVFLV-----------GLEEglFPHQR--S 581

                         650       660
                  ....*....|....*....|....*...
gi 1134612243 835 FS-----EDEWNLLYVAVTRAKKRLIMT 857
Cdd:COG0210   582 LDdeeelEEERRLFYVAITRARERLYLT 609
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 761-858 3.11e-23

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 94.43  E-value: 3.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 761 KIAVVEKYNIRIPELVERIERCHIDDLDFAEYILGTVHKAKGLEFDTVHVLDDFVKvpcarhnlaqlphfrvesfsEDEW 840
Cdd:cd18786    12 KGVVLTPYHRDRAYLNQYLQGLSLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTAN--------------------SLTP 71

                          90
                  ....*....|....*...
gi 1134612243 841 NLLYVAVTRAKKRLIMTK 858
Cdd:cd18786    72 RRLYVALTRARKRLVIYD 89
F-box-like pfam12937
F-box-like; This is an F-box-like family.
 136-183 2.98e-12

F-box-like; This is an F-box-like family.


Pssm-ID: 463757 [Multi-domain]  Cd Length: 45  Bit Score: 61.73  E-value: 2.98e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLY 183
Cdd:pfam12937   1 LSSLPDEILLQIFSYLDPKDLL-RLALVCRRWRELASDDSL--WRRLC 45
UvrD_C pfam13361
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 732-861 1.95e-11

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 433145 [Multi-domain]  Cd Length: 377  Bit Score: 67.05  E-value: 1.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 732 RFIRRWVHKEGfsGFKRYVTAAEDKEleaKIAVVEKYNIRIPELVERI-----ERCHIDDLDFAEYIlgTVHKAKGLEFD 806
Cdd:pfam13361 256 EALRDFLEKLE--NLRELYSILREYD---DIEETPEPEDALRNFLEIAtlsnsELEGSDIKERIPIM--TIHQAKGLEFD 328

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1134612243 807 TVHVLDDFVKVpcarhnlaqLPHFR---VESFSEDEWNLLYVAVTRAKKRLIMTKSLE 861
Cdd:pfam13361 329 TVFLAGLEEGI---------FPSYRsikDEGNLEEERRLFYVAITRAKKRLYISYSKS 377
PRK13909 PRK13909
RecB-like helicase;
771-862 3.78e-08

RecB-like helicase;


Pssm-ID: 237554 [Multi-domain]  Cd Length: 910  Bit Score: 57.67  E-value: 3.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 771 RIPELVERIERChiDDLDFAEYILG----TVHKAKGLEFDTVHVLDDFVKvPCARH----------NLAQLpHFRV---E 833
Cdd:PRK13909  585 DIEEFLFKLEPC--DKEIASEESKGvqimTVHKSKGLEFEHVIVCDRLGK-PNSDSsnllfeydgiELWQI-YYRIkgrE 660

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1134612243 834 SF---------------SEDEWNLLYVAVTRAKKRLIMTKSLEN 862
Cdd:PRK13909  661 NFdkdyaralekekalkYEEEINVLYVAFTRAKNSLIVVKKDES 704
FBOX smart00256
A Receptor for Ubiquitination Targets;
139-182 1.23e-05

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 42.81  E-value: 1.23e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1134612243  139 LPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKL 182
Cdd:smart00256   1 LPDEILEEILSKLDPKDLL-RLRKVSRKWRSLIDSHDF--WFKL 41
recB TIGR00609
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ...
 774-859 3.60e-05

exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273172 [Multi-domain]  Cd Length: 1087  Bit Score: 47.81  E-value: 3.60e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243  774 ELVERIERCHiDDLDFAEYIlgTVHKAKGLEFDTV--------HVLDDFVKVPCARH-----NLAQLPHF----RVESFS 836
Cdd:TIGR00609  638 EEEEEIIRLE-SDAELVKIV--TIHKSKGLEYPIVflpfitdaKKSNFASLHDQHSHeyqlyDFNQSEENqklaRVERLA 714

                           90       100
                   ....*....|....*....|...
gi 1134612243  837 EDeWNLLYVAVTRAKKRLIMTKS 859
Cdd:TIGR00609  715 ED-LRLLYVALTRAKKQLFIGIA 736
 
Name Accession Description Interval E-value
F-box_FBXO18 cd22095
F-box domain found in F-box only protein 18 (FBXO18) and similar proteins; FBXO18, also called ...
 135-182 1.89e-25

F-box domain found in F-box only protein 18 (FBXO18) and similar proteins; FBXO18, also called FBX18, or F-box DNA helicase 1 (FBH1), is a 3'-5' DNA helicase and the substrate-recognition component of the SCF(FBH1) E3 ubiquitin ligase complex that plays a key role in response to stalled/damaged replication forks. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438867  Cd Length: 48  Bit Score: 99.66  E-value: 1.89e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1134612243 135 HICRLPSEVLRHIFAFLPVEDLYWNLSLVCHLWREIINDPLFIPWKKL 182
Cdd:cd22095     1 HIQQLPEELLRNIFAFLPAEDLYQNISLVCRHWRDIVSDPLFIPWKKL 48
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
365-857 1.84e-23

Superfamily I DNA or RNA helicase [Replication, recombination and repair];


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 106.56  E-value: 1.84e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 365 QLTHEQQLILNHKMEPLQVVkimAFAGTGKTSTLVKYA------EKWSQSRFLYVTF-NKS-------IAKQAELVFPSN 430
Cdd:COG0210     6 GLNPEQRAAVEHPEGPLLVL---AGAGSGKTRVLTHRIayliaeGGVDPEQILAVTFtNKAaremrerIEALLGRLARGL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 431 VICkTFHSMAYSHVGRKYQLKKKLNlfkltPF----------MVNSVLAE----GKGGFIRaklvckTLENFFASA-DEE 495
Cdd:COG0210    83 WVG-TFHSLALRILRRHAELLGLPP-----NFtildgddqlrLIKELLKElgldEKRFPPR------ELLSLISRAkNEG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 496 LTIDHVPIWCKNSHGQRVMV------EQSEKLNG-------VLEASRLWDNmrklgeckeeayqmtHDGYLKLWQlskpl 562
Cdd:COG0210   151 LTPEELAELLAADPEWRAAAelyeayQERLRANNaldfddlLLLAVRLLEE---------------NPEVLEKYQ----- 210

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 563 lASFDAIFVDEAQDCTPAIMNIV--LSQPCGKIF-VGDPHQQIYTFRGA--VN-ALFTV--PHTHVFYLTQSFRFGVEI- 633
Cdd:COG0210   211 -NRFRYILVDEYQDTNPAQYELLrlLAGDGRNLCvVGDDDQSIYGFRGAdpENiLRFEKdfPDAKVIKLEQNYRSTQNIl 289

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 634 -----------------------------AYVGATILD----VCKRVRKktlvggNHQSGIR-GDIkgqvALLSRTNA-- 677
Cdd:COG0210   290 daanaviannpgrlgknlwtdngegekvrLYVAPDEEEearfVADEIRE------LHEEGVPlSDI----AVLYRTNAqs 359

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 678 NVFDEA-------VRVTEGESP-------------------------ARIH--LIGGIKSFGLDRI--------IDIWTL 715
Cdd:COG0210   360 RALEEAlrragipYRVVGGLRFyeraeikdllaylrllanpdddvalLRILnvPRRGIGAATLERLreaareegISLLEA 439

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 716 LQ--------PEEERRK----RDLIIK----------DRFIRRWVHKegfSGFKRYVTAAEDKELEAKIA-------VVE 766
Cdd:COG0210   440 LRdlgelaglSGRAAKAlrrfAELLEAlraaaerlplEELLEALLDE---SGYEEELREEAGEEAERRLEnleelvdAAA 516

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 767 KYNIR-----IPELVERIErcHIDDLDFAEY-----ILGTVHKAKGLEFDTVHVLddfvkvpcarhNLAQ--LPHFRveS 834
Cdd:COG0210   517 RFEERnpgasLEAFLEELA--LLSDLDAADEdedavTLMTLHAAKGLEFPVVFLV-----------GLEEglFPHQR--S 581

                         650       660
                  ....*....|....*....|....*...
gi 1134612243 835 FS-----EDEWNLLYVAVTRAKKRLIMT 857
Cdd:COG0210   582 LDdeeelEEERRLFYVAITRARERLYLT 609
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 761-858 3.11e-23

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 94.43  E-value: 3.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 761 KIAVVEKYNIRIPELVERIERCHIDDLDFAEYILGTVHKAKGLEFDTVHVLDDFVKvpcarhnlaqlphfrvesfsEDEW 840
Cdd:cd18786    12 KGVVLTPYHRDRAYLNQYLQGLSLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTAN--------------------SLTP 71

                          90
                  ....*....|....*...
gi 1134612243 841 NLLYVAVTRAKKRLIMTK 858
Cdd:cd18786    72 RRLYVALTRARKRLVIYD 89
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 566-857 4.55e-16

3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440692 [Multi-domain]  Cd Length: 866  Bit Score: 83.09  E-value: 4.55e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 566 FDAIFVDEAQDCTPAIMNIV-------LSQPCGKIFVGDPHQQIYTFRGA------------------------------ 608
Cdd:COG1074   285 YRHILVDEFQDTSPLQWEILrrlageaLADGRTLFLVGDPKQSIYRFRGAdpelflearralegrvdgerltlttnfrst 364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 609 ------VNALFT---------VPHTHVFYLTQSFRFGVEIAYVGATILD---------------VCKRVRKKTLVGGNHQ 658
Cdd:COG1074   365 pevvdaVNALFAqlmgagfgeIPYEPVEALRPGAYPAVELWPLEPDDVSeedarerearavaarIRRLLAEGTTVEGGGR 444

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 659 SGIRGDIkgqvALLSRTN------ANVFDEA---VRVTEG----ESPA----------------RIHLIGGIKS--FGLD 707
Cdd:COG1074   445 PVRPGDI----AVLVRTRseaaaiARALKAAgipVAASDRlslfESPEvrdllallrallnpedDLALAAVLRSplFGLS 520

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 708 -----------RIIDIWT-LLQPEEERRKRDLIikdRFIRRWVHKEGFS----------GFKRYVTAAEDKE-------- 757
Cdd:COG1074   521 dedlaalaadrKGESLWEaLRAYERLARALERL---RALRELARRLGLAellerlleetGLLERLLALPGGErrlanllh 597

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 758 LEAKIAVVEKYNIR----IPELVERIERCHIDDLDFAEYILG---------TVHKAKGLEFDTVHVLDDFvkvpcARHNL 824
Cdd:COG1074   598 LDELLQLALEYEQTggpgLAGFLRWLERLIEDGGDEEKRRLEsdadavrimTIHKSKGLEFPVVFLPALR-----ERARA 672

                         410       420       430
                  ....*....|....*....|....*....|...
gi 1134612243 825 AQLphfrvesfsEDEWNLLYVAVTRAKKRLIMT 857
Cdd:COG1074   673 EEL---------AEELRLLYVALTRARDRLVLS 696
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 369-627 3.89e-14

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 71.78  E-value: 3.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 369 EQQLILNHKMEPLQVVkimAFAGTGKTSTLV-KYA-----EKWSQSRFLYVTFNKSIAKQ-----AELV---FPSNVICK 434
Cdd:cd17932     3 EQREAVTHPDGPLLVL---AGAGSGKTRVLThRIAylileGGVPPERILAVTFTNKAAKEmrerlRKLLgeqLASGVWIG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 435 TFHSMAYshvgrkyqlkkklnlfkltpfmvnsvlaegkggfiraklvcKTLENFFASADeeltidhvpiwcknshgqrvm 514
Cdd:cd17932    80 TFHSFAL-----------------------------------------RILRRYGDFDD--------------------- 97

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 515 veqseklnGVLEASRLWDNMRKLGEckeeAYQmthdgylklwqlskpllASFDAIFVDEAQDCTPAIMNIV--LSQPCGK 592
Cdd:cd17932    98 --------LLLYALELLEENPDVRE----KLQ-----------------SRFRYILVDEYQDTNPLQYELLklLAGDGKN 148

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1134612243 593 IF-VGDPHQQIYTFRGAVNALFT-----VPHTHVFYLTQSF 627
Cdd:cd17932   149 LFvVGDDDQSIYGFRGADPENILdfekdFPDAKVIKLEENY 189
COG3972 COG3972
Superfamily I DNA and RNA helicases [Replication, recombination and repair];
364-869 6.72e-13

Superfamily I DNA and RNA helicases [Replication, recombination and repair];


Pssm-ID: 443172 [Multi-domain]  Cd Length: 565  Bit Score: 72.56  E-value: 6.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 364 IQLTHEQQLILnhKMEPLQVVKIMAFAGTGKTSTL----VKYAEKWSQSRFLYVTFNKSIAKQaelvfpsnvicktfhsm 439
Cdd:COG3972   158 AVLDLQQERIA--RSIPDGPQRIRGVAGSGKTVLLaakaAYLALKHPGWRILVTCFNRSLADH----------------- 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 440 ayshvgrkyqlkkklnlfkltpfmvnsvlaegkggfIRAKLvcktlENFFASADEELTIDHVPIWCKNSHGQRVMVEQSE 519
Cdd:COG3972   219 ------------------------------------LRDLI-----PRFLRRFSNGEPEDNVKLIVFHAWGGKLLKQYGI 257

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 520 KLNGVLEASRLWDNmrklgECKEeayqmthdgYLKLWQLSKPLlASFDAIFVDEAQDCTPAIMNIV---LSQPCGKIFV- 595
Cdd:COG3972   258 PPLTFSQPNEAFDE-----ACKA---------LLEAIQGEIIP-PIYDAILIDEAQDFEPEFLRLLyqlLKPPKKRLIWa 322

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 596 GDPHQQIY--TFRGAVNALFTVPHTHVfyLTQSFRFGVEIAYVGATILDVCKRVRKktLVGGNHQSGIRgDIKGQVALLS 673
Cdd:COG3972   323 YDEAQNIYgrKIPSAGGIPAGIGRDTI--LKKNYRNTRPILTFAHAFGMGLLRPPG--LLQGDAEDYEV-ERPGDKVTLI 397

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 674 RTNANVFDEavrvteGESPArihliggIKSFGldriidiwtllQPEEERRKrdliIKDRfIRRWVHKEGFsgfkryvtAA 753
Cdd:COG3972   398 RPPEPAGRK------GPLPE-------FKKYD-----------DRAEELEA----IAEE-IKKNLRDEGL--------RP 440

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 754 EDkeleakIAVV----EKYNIRIPELVERIERCHID------DLDFAEYI------LGTVHKAKGLEFDTVHVLddfvkv 817
Cdd:COG3972   441 SD------IAVIylgnNEAKELGDRLAAALERQGIDsyiagaRSDPNFFWkdggvtISTIHRAKGLEAPVVIIV------ 508

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1134612243 818 pcarhNLAQLPHFrvESFsEDEWNLLYVAVTRAKKRLIMTKSLENILTLAGE 869
Cdd:COG3972   509 -----GLDQLAKG--ESL-ERLRNLLYVAMTRARGWLVVSGSGESMAELYDE 552
F-box-like pfam12937
F-box-like; This is an F-box-like family.
 136-183 2.98e-12

F-box-like; This is an F-box-like family.


Pssm-ID: 463757 [Multi-domain]  Cd Length: 45  Bit Score: 61.73  E-value: 2.98e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLY 183
Cdd:pfam12937   1 LSSLPDEILLQIFSYLDPKDLL-RLALVCRRWRELASDDSL--WRRLC 45
SF1_C_UvrD cd18807
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ...
 794-857 1.01e-11

C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350194 [Multi-domain]  Cd Length: 150  Bit Score: 63.79  E-value: 1.01e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1134612243 794 LGTVHKAKGLEFDTVHVLD---DFVKVPCARHNLAQLPhfrvESFSEdEWNLLYVAVTRAKKRLIMT 857
Cdd:cd18807    88 LMTIHASKGLEFPVVFIVGlgeGFIPSDASYHAAKEDE----ERLEE-ERRLLYVALTRAKKELYLV 149
UvrD_C pfam13361
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 732-861 1.95e-11

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 433145 [Multi-domain]  Cd Length: 377  Bit Score: 67.05  E-value: 1.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 732 RFIRRWVHKEGfsGFKRYVTAAEDKEleaKIAVVEKYNIRIPELVERI-----ERCHIDDLDFAEYIlgTVHKAKGLEFD 806
Cdd:pfam13361 256 EALRDFLEKLE--NLRELYSILREYD---DIEETPEPEDALRNFLEIAtlsnsELEGSDIKERIPIM--TIHQAKGLEFD 328

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1134612243 807 TVHVLDDFVKVpcarhnlaqLPHFR---VESFSEDEWNLLYVAVTRAKKRLIMTKSLE 861
Cdd:pfam13361 329 TVFLAGLEEGI---------FPSYRsikDEGNLEEERRLFYVAITRAKKRLYISYSKS 377
UvrD_C_2 pfam13538
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 796-857 5.24e-10

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 463913 [Multi-domain]  Cd Length: 52  Bit Score: 55.66  E-value: 5.24e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1134612243 796 TVHKAKGLEFDTVHVLDDfvkvpcarhNLAQLPHFrvesfsEDEWNLLYVAVTRAKKRLIMT 857
Cdd:pfam13538   6 TVHKAQGSEFPAVFLVDP---------DLTAHYHS------MLRRRLLYTAVTRARKKLVLV 52
HelD COG3973
DNA helicase IV [Replication, recombination and repair];
569-857 5.67e-10

DNA helicase IV [Replication, recombination and repair];


Pssm-ID: 443173 [Multi-domain]  Cd Length: 699  Bit Score: 63.35  E-value: 5.67e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 569 IFVDEAQDCTP----AIMNIVlsqPCGKI-FVGDPHQQIYTFRGA------VNALFTvPHTHVFYLTQSFRFGVEIAyvg 637
Cdd:COG3973   473 VVVDEAQDLSPmqwrVLKRRF---PSASFtIVGDLAQAIHPYRGAesweevLEPLGG-DRARLVELTKSYRSTAEIM--- 545

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 638 atilDVCKRVRKKTLVGGNHQSGIRgdikgqvallsRTnanvfDEAVRVTEGESPARIHliggiksfglDRIIDIWTLLQ 717
Cdd:COG3973   546 ----EFANRVLRAAGPDLPPPESVR-----------RH-----GEPPRVVRVPSEAELA----------AAVVEAVRELL 595

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 718 PEEERR-----KRDLIIKDrfIRRWVHKegfsGFKRYVTAAEDKELEAKIAVVekyniripelverierchiddldfaey 792
Cdd:COG3973   596 AEGEGTiavicKTAREAEA--LYAALKA----GLPVTLIDDESEELEAGVVVL--------------------------- 642

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1134612243 793 ilgTVHKAKGLEFDTVHVLDdfvkvpcarhnlaqlPHFRVESfSEDEWNLLYVAVTRAKKRLIMT 857
Cdd:COG3973   643 ---PAYLAKGLEFDAVVVVD---------------PDEIVYE-SPRGRRLLYVALTRATHRLTVL 688
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 593-856 4.94e-09

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 59.99  E-value: 4.94e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 593 IFVGDPHQ----QiytfRGAV-NALFTVPHTHVFYLTQSFRFGVEiayvgATILDVCKRVRKktlvgGNHQSGIRGDikg 667
Cdd:COG0507   250 ILVGDPDQlpsvG----AGAVlRDLIESGTVPVVELTEVYRQADD-----SRIIELAHAIRE-----GDAPEALNAR--- 312

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 668 qvallsrtnanvfDEAVRVTEGESPARIhliggiksfgLDRIIDIWTllqpEEERRKRDLII-----KD-----RFIRRW 737
Cdd:COG0507   313 -------------YADVVFVEAEDAEEA----------AEAIVELYA----DRPAGGEDIQVlaptnAGvdalnQAIREA 365

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 738 VHKEGfsGFKRYVTAAEDKELEA------------------KIAVVEKYNIRIPELV---ERIERCHIDDLDFAEYILG- 795
Cdd:COG0507   366 LNPAG--ELERELAEDGELELYVgdrvmftrndydlgvfngDIGTVLSIDEDEGRLTvrfDGREIVTYDPSELDQLELAy 443

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1134612243 796 --TVHKAKGLEFDTVHVLddfvkvpcarhnlaqLPHFRVESFSedeWNLLYVAVTRAKKRLIM 856
Cdd:COG0507   444 aiTVHKSQGSTFDRVILV---------------LPSEHSPLLS---RELLYTALTRARELLTL 488
F-box_FBXO6-like cd22168
F-box domain found in F-box only proteins FBXO6, FBXO44 and similar proteins; This subfamily ...
 135-185 1.62e-08

F-box domain found in F-box only proteins FBXO6, FBXO44 and similar proteins; This subfamily includes FBXO6 and FBXO44. FBXO6, also called FBX6, F-box protein that recognizes sugar chains 2 (FBS2), or F-box/G-domain protein 2 (FBG2), is a substrate-recognition component of SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complexes. It is involved in the endoplasmic reticulum-associated degradation pathway (ERAD) for misfolded lumenal proteins, by recognizing and binding sugar chains on unfolded glycoproteins that are retro-translocated into the cytosol and promoting their ubiquitination and subsequent degradation. FBXO6 can recognize and bind denatured glycoproteins, which are modified with not only high-mannose but also complex-type oligosaccharides. It also recognizes sulfated glycans. FBXO6 is involved in DNA damage response by specifically recognizing activated CHEK1 (phosphorylated on 'Ser-345'), promoting its ubiquitination and degradation. FBXO44, also called FBXO6A, FBX44, or F-box/G-domain protein 3 (FBG3), is a substrate-recognition component of an SCF-type E3 ubiquitin ligase complex. It interacts with SKP1 and CUL1. FBXO44 mediates BRCA1 ubiquitination and degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438939 [Multi-domain]  Cd Length: 82  Bit Score: 52.29  E-value: 1.62e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1134612243 135 HICRLPSEVLRHIFAFLPVEDLYWNLSLVCHLWREIINDPLFipWKKLYHR 185
Cdd:cd22168     3 TISDLPEDVLLEILSLVPARDLILSCRLVCSRWRDLVDLPTL--WKRKCQR 51
F-box_SF cd09917
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 138-172 1.79e-08

F-box domain superfamily; This short domain is commonly found at the N-terminus of various proteins, and typically co-occurs with one or more other conserved domains or motifs, such as leucine rich repeats, WD40 repeats, kelch, tub, spry, and others. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. One of the best researched roles of F-box proteins is their participation in SCF (Skp1-Cul1-F-box protein), a multi-protein complex that functions as a ubiquitin E3 ligase, where the role of the F-box protein is to recruit target substrates. Gene families containing the F-box are found greatly expanded in narrow taxonomic lineages, such as flowering plants and nematodes. In this hierarchical classification, many of the subfamilies are named according to their domain architectures.


Pssm-ID: 438852  Cd Length: 35  Bit Score: 50.91  E-value: 1.79e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134612243 138 RLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIIN 172
Cdd:cd09917     2 DLPDEILLKILSYLDPRDLL-RLSLVCKRWRELAS 35
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 136-176 3.21e-08

F-box domain; This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 425796  Cd Length: 43  Bit Score: 50.23  E-value: 3.21e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLyWNLSLVCHLWREIINDPLF 176
Cdd:pfam00646   1 LLDLPDDLLLEILSRLDPKDL-LRLSLVSKRWRSLVDSLKL 40
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 366-610 3.37e-08

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 55.71  E-value: 3.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 366 LTHEQQLILNHkmePLQVVKIMAFAGTGKTSTLV-KYA-----EKWSQSRFLYVTF-NKS-------IAKQAELVFPSNV 431
Cdd:pfam00580   1 LNPEQRKAVTH---LGGPLLVLAGAGSGKTRVLTeRIAylileGGIDPEEILAVTFtNKAaremkerILKLLGKAELSEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 432 ICKTFHSMAYS-------HVGRKyQLKKKLNLFKLTPFMVNSVLAEGKG---GFIRAKLVCKTLENFfasADEELTIDHV 501
Cdd:pfam00580  78 NISTFHSFCLRilrkyanRIGLL-PNFSILDELDQLALLKELLEKDRLNldpKLLRKLELKELISKA---KNRLLSPEEL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 502 PIWCKNSHGQRVMV-----EQSEKLNGVLEASRLwdnmrkLGECKEeayqmthdgylkLWQLSKPLLAS----FDAIFVD 572
Cdd:pfam00580 154 QQGAADPRDKLAAEfyqeyQERLKENNALDFDDL------LLLTLE------------LLRSDPELLEAyrerFKYILVD 215

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1134612243 573 EAQDCTPA---IMNIVLSQPCGKIFVGDPHQQIYTFRGAVN 610
Cdd:pfam00580 216 EFQDTNPIqyrLLKLLAGGHENLFLVGDPDQSIYGFRGADI 256
PRK13909 PRK13909
RecB-like helicase;
771-862 3.78e-08

RecB-like helicase;


Pssm-ID: 237554 [Multi-domain]  Cd Length: 910  Bit Score: 57.67  E-value: 3.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243 771 RIPELVERIERChiDDLDFAEYILG----TVHKAKGLEFDTVHVLDDFVKvPCARH----------NLAQLpHFRV---E 833
Cdd:PRK13909  585 DIEEFLFKLEPC--DKEIASEESKGvqimTVHKSKGLEFEHVIVCDRLGK-PNSDSsnllfeydgiELWQI-YYRIkgrE 660

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1134612243 834 SF---------------SEDEWNLLYVAVTRAKKRLIMTKSLEN 862
Cdd:PRK13909  661 NFdkdyaralekekalkYEEEINVLYVAFTRAKNSLIVVKKDES 704
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 791-856 5.91e-08

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 50.64  E-value: 5.91e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1134612243 791 EYILG---TVHKAKGLEFDTVHVLddfvkvpcarhnlaqLPhfrvESFSEDEWNLLYVAVTRAKKRLIM 856
Cdd:cd18809    29 ERLQAyamTIHKSQGSEFDRVIVV---------------LP----TSHPMLSRGLLYTALTRARKLLTL 78
F-box_FBXO33 cd22104
F-box domain found in F-box only protein 33 (FBXO33) and similar proteins; FBXO33, also called ...
 138-182 9.90e-07

F-box domain found in F-box only protein 33 (FBXO33) and similar proteins; FBXO33, also called FBX33, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It exerts similar functions as F-box involved in polyQ pathogenesis (FipoQ) in modulating the ubiquitination and solubility of expanded SCA3-polyQ proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438876  Cd Length: 48  Bit Score: 46.48  E-value: 9.90e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1134612243 138 RLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKL 182
Cdd:cd22104     3 NLPSVVLVHIFSYLPPRDRL-RASSTCRRWREALFHPSL--WRSL 44
F-box_FBXL4 cd22117
F-box domain found in F-box/LRR-repeat protein 4 (FBXL4) and similar proteins; FBXL4, also ...
 139-185 1.52e-06

F-box domain found in F-box/LRR-repeat protein 4 (FBXL4) and similar proteins; FBXL4, also called F-box and leucine-rich repeat protein 4, or F-box protein FBL4/FBL5, is part of an SCF (SKP1-cullin-F-box) protein ligase complex. It serves as a clock output molecule that regulates sleep through promotion of rhythmic degradation of the GABA(A) receptor. Biallelic pathogenic variants in FBXL4 are associated with an encephalopathic mtDNA maintenance defect syndrome that is a multi-system disease characterized by lactic acidemia, developmental delay, and hypotonia. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438889  Cd Length: 47  Bit Score: 45.69  E-value: 1.52e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1134612243 139 LPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLYHR 185
Cdd:cd22117     4 LPYELIQLILSYLDLPSLC-RLSQTCKLFRKHCYDPLL--WKELNLQ 47
F-box_FBXO45 cd22111
F-box domain found in F-box only protein 45 (FBXO45) and similar proteins; FBXO45, also called ...
 138-172 9.49e-06

F-box domain found in F-box only protein 45 (FBXO45) and similar proteins; FBXO45, also called FBX45, or F-box/SPRY domain-containing protein 1, functions as the substrate-recognition component of E3 ubiquitin ligase complexes. It is critical for synaptogenesis, neuronal migration, and synaptic transmission. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438883  Cd Length: 36  Bit Score: 43.04  E-value: 9.49e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134612243 138 RLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIIN 172
Cdd:cd22111     3 RLPSRVLEVIFSYLDLPDLR-NCSLVCKSWYRLLN 36
FBOX smart00256
A Receptor for Ubiquitination Targets;
139-182 1.23e-05

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 42.81  E-value: 1.23e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1134612243  139 LPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKL 182
Cdd:smart00256   1 LPDEILEEILSKLDPKDLL-RLRKVSRKWRSLIDSHDF--WFKL 41
F-box_FBXO10 cd22090
F-box domain found in F-box only protein 10 (FBXO10) and similar proteins; FBXO10, also called ...
 135-183 1.60e-05

F-box domain found in F-box only protein 10 (FBXO10) and similar proteins; FBXO10, also called FBX10, or PRMT11, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The SCF(FBXO10) complex mediates ubiquitination and degradation of BCL2, an anti-apoptotic protein, thereby playing a role in apoptosis by controlling the stability of BCL2. It also associates with the receptor for advanced glycation end products (RAGE) to mediate its ubiquitination and degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438862  Cd Length: 50  Bit Score: 43.11  E-value: 1.60e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1134612243 135 HICRLPSEVLRHIFAFLPVEDLyWNLSLVCHLWREIINDPLFIPWKKLY 183
Cdd:cd22090     1 EVTGLPLELWRLILAYLPVRDL-CRCCQVCRAWYELILSLDSTRWKQLY 48
recB TIGR00609
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ...
 774-859 3.60e-05

exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273172 [Multi-domain]  Cd Length: 1087  Bit Score: 47.81  E-value: 3.60e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134612243  774 ELVERIERCHiDDLDFAEYIlgTVHKAKGLEFDTV--------HVLDDFVKVPCARH-----NLAQLPHF----RVESFS 836
Cdd:TIGR00609  638 EEEEEIIRLE-SDAELVKIV--TIHKSKGLEYPIVflpfitdaKKSNFASLHDQHSHeyqlyDFNQSEENqklaRVERLA 714

                           90       100
                   ....*....|....*....|...
gi 1134612243  837 EDeWNLLYVAVTRAKKRLIMTKS 859
Cdd:TIGR00609  715 ED-LRLLYVALTRAKKQLFIGIA 736
F-box_4 pfam15966
F-box;
135-170 1.28e-04

F-box;


Pssm-ID: 464958  Cd Length: 116  Bit Score: 42.28  E-value: 1.28e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1134612243 135 HICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREI 170
Cdd:pfam15966   4 SLSSLPFEVLQHIASFLDSFSLS-QLSLVSRLMREV 38
F-box_FBXL12 cd22123
F-box domain found in F-box/LRR-repeat protein 12 (FBXL12) and similar proteins; FBXL12, also ...
 139-173 1.32e-04

F-box domain found in F-box/LRR-repeat protein 12 (FBXL12) and similar proteins; FBXL12, also called F-box and leucine-rich repeat protein 12, or F-box protein FBL12, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It mediates the polyubiquitination and proteasomal degradation of calcium/calmodulin dependent protein kinase I (CAMK1) leading to disruption of cyclin D1/CDK4 complex assembly, which results in G1 cell cycle arrest in lung epithelia. It regulates T-cell differentiation in a cell-autonomous manner. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438895  Cd Length: 42  Bit Score: 40.03  E-value: 1.32e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134612243 139 LPSEVLRHIFAFLPVEDLYWNlSLVCHLWREIIND 173
Cdd:cd22123     4 LPENVLLEILSYLPVRDLLRI-SRVCKRWRRLVYD 37
F-box_FBXO4 cd22085
F-box domain found in F-box only protein 4 (FBXO4) and similar proteins; FBXO4, also called ...
 136-185 1.61e-04

F-box domain found in F-box only protein 4 (FBXO4) and similar proteins; FBXO4, also called FBX4, is a specific substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex that catalyzes the ubiquitination and subsequent degradation of cyclin D1 and Trx1. It recognizes TERF1 and promotes its ubiquitination together with UBE2D1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438857  Cd Length: 50  Bit Score: 40.09  E-value: 1.61e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLYHR 185
Cdd:cd22085     3 LNHLPIDLQLYILSFLSPHDLC-QLGLTSHYWHTLVRDPLL--WRYFLLR 49
F-box_FBXO15 cd22093
F-box domain found in F-box only protein 15 (FBXO15) and similar proteins; FBXO15, also called ...
 136-183 1.63e-04

F-box domain found in F-box only protein 15 (FBXO15) and similar proteins; FBXO15, also called FBX15, has a novel dual molecular function by controlling transcriptional repression and being part of SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligases, which is essential for stress response, gliotoxin production and virulence in the opportunistic human pathogen Aspergillus fumigatus. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438865  Cd Length: 46  Bit Score: 39.93  E-value: 1.63e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLY 183
Cdd:cd22093     1 IERLPSEILLKILSYLDASSLL-CISCVNKLFYQLANDNAL--WRKLY 45
F-box_FBXW5 cd22132
F-box domain found in F-box/WD repeat-containing protein 5 (FBXW5) and similar proteins; FBXW5, ...
 139-184 1.77e-04

F-box domain found in F-box/WD repeat-containing protein 5 (FBXW5) and similar proteins; FBXW5, also called F-box and WD-40 domain-containing protein 5, is the substrate-recognition component of both SCF (SKP1-CUL1-F-box protein) and DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438904 [Multi-domain]  Cd Length: 46  Bit Score: 39.90  E-value: 1.77e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1134612243 139 LPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLYH 184
Cdd:cd22132     4 LPDSLLLHIFSYLSPKDLL-AAGQVCKQWYRVSRDEFL--WKELFY 46
F-box_FBXO42 cd22110
F-box domain found in F-box only protein 42 (FBXO42) and similar proteins; FBXO42, also called ...
 139-173 2.09e-04

F-box domain found in F-box only protein 42 (FBXO42) and similar proteins; FBXO42, also called FBX42, or just one F-box and Kelch domain-containing protein (JFK), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It specifically recognizes p53/TP53, promoting its ubiquitination and degradation. FBXO42 is also involved in the ubiquitin-proteasome system that may play a role in the pathogenesis of Parkinson's disease (PD). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438882  Cd Length: 38  Bit Score: 39.63  E-value: 2.09e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134612243 139 LPSEVLRHIFAFLPVEDLYWNLSLVCHLWREIIND 173
Cdd:cd22110     4 LPEEILEYILSYLSPYGDLKSAALVCKRWHRIIKG 38
F-box_FBXL8 cd22121
F-box domain found in F-box/LRR-repeat protein 8 (FBXL8) and similar proteins; FBXL8, also ...
 138-171 2.51e-04

F-box domain found in F-box/LRR-repeat protein 8 (FBXL8) and similar proteins; FBXL8, also called F-box and leucine-rich repeat protein 8, or F-box protein FBL8, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438893  Cd Length: 35  Bit Score: 39.27  E-value: 2.51e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1134612243 138 RLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREII 171
Cdd:cd22121     2 ALPEEILVHIFRHLSLRDRY-AAAQVCKHWREAA 34
recB TIGR00609
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ...
 566-608 3.16e-04

exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273172 [Multi-domain]  Cd Length: 1087  Bit Score: 44.73  E-value: 3.16e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1134612243  566 FDAIFVDEAQDCTP---AIMN-IVLSQPCGK-IFVGDPHQQIYTFRGA 608
Cdd:TIGR00609  297 YPIALIDEFQDTDPqqyRIFSkLFIAQKETSlFLIGDPKQAIYSFRGA 344
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 563-609 7.14e-04

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 40.55  E-value: 7.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1134612243 563 LASFDAIFVDEAQDCTPAIMNIV--LSQPCGK-IFVGDPHQQIYTFRGAV 609
Cdd:cd17914    44 AAQLDNILVDEAAQILEPETSRLidLALDQGRvILVGDHDQLGPVWRGAV 93
F-box_FBXO13 cd22092
F-box domain found in F-box only protein 13 (FBXO13) and similar proteins; FBXO13, also called ...
 135-182 7.37e-04

F-box domain found in F-box only protein 13 (FBXO13) and similar proteins; FBXO13, also called FBX13, F-box/LRR-repeat protein 17 (FBL17), or F-box and leucine-rich repeat protein 17 (FBXL17), is the substrate-recognition component of SCF(FBXL17) E3 ubiquitin ligase complex, a key component of a quality control pathway required to ensure functional dimerization of BTB domain-containing proteins (dimerization quality control, DQC). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438864  Cd Length: 49  Bit Score: 38.17  E-value: 7.37e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1134612243 135 HICRLPSEVLRHIFAFLPVEDLYWNLSLVCHLWREIINDPLFipWKKL 182
Cdd:cd22092     1 NINQLPDSILLKIFSYLSLQERCLSASLVCKYWRDLCLDSQF--WKQI 46
F-box_AtSKIP19-like cd22164
F-box domain found in Arabidopsis thaliana SKP1-interacting partner 19 (AtSKIP19) and similar ...
 139-183 7.48e-04

F-box domain found in Arabidopsis thaliana SKP1-interacting partner 19 (AtSKIP19) and similar proteins; AtSKIP19, also called F-box protein SKIP19, or F-box/LRR-repeat protein 20 (FBL20), is a component of SCF (SPK1/ASK-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with CUL1 and SPK1B/ASK2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438935 [Multi-domain]  Cd Length: 47  Bit Score: 38.35  E-value: 7.48e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1134612243 139 LPSEVLRHIFAFLPVEDLYWNLSLVCHLWREIINDPLFipWKKLY 183
Cdd:cd22164     5 LPDDLTASILSRLGAIDILTNAQKVCKLWRRICKDPSM--WRVID 47
F-box_FBXO3 cd22084
F-box domain found in F-box only protein 3 (FBXO3) and similar proteins; FBXO3, also called ...
 136-186 7.77e-04

F-box domain found in F-box only protein 3 (FBXO3) and similar proteins; FBXO3, also called FBX3, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. It also promotes ubiquitylation and transcriptional activity of AIRE (autoimmune regulator). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438856  Cd Length: 49  Bit Score: 38.01  E-value: 7.77e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLYHRY 186
Cdd:cd22084     1 LDDLPSDPLLNILSFLDYRDLI-SCSQVCRRLNQLCSHDPL--WKRLCKKY 48
F-box_FBXW2 cd22131
F-box domain found in F-box/WD repeat-containing protein 2 (FBXW2) and similar proteins; FBXW2, ...
 136-172 8.61e-04

F-box domain found in F-box/WD repeat-containing protein 2 (FBXW2) and similar proteins; FBXW2, also called F-box and WD-40 domain-containing protein 2, or protein MD6, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It acts as a tumor suppressor by promoting SKP2 degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438903  Cd Length: 40  Bit Score: 37.69  E-value: 8.61e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIIN 172
Cdd:cd22131     3 LKLLPLELSFYLLSFLDPESLL-TCCLVSKQWNKVIS 38
F-box_FBXO11 cd22091
F-box domain found in F-box only protein 11 (FBXO11) and similar proteins; FBXO11, also called ...
 139-183 1.33e-03

F-box domain found in F-box only protein 11 (FBXO11) and similar proteins; FBXO11, also called FBX11, protein arginine N-methyltransferase 9 (PRMT9), or vitiligo-associated protein 1 (VIT-1), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as DTL/CDT2, BCL6 and PRDM1/BLIMP1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438863  Cd Length: 45  Bit Score: 37.40  E-value: 1.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1134612243 139 LPSEVLRHIFAFLPVEDLyWNLSLVCHLWREIINDPLFipWKKLY 183
Cdd:cd22091     4 LPDEVLLKIFSYLLEQDL-CRAAQVCKRFNTLANDPEL--WKRLY 45
F-box_FBXO36 cd22106
F-box domain found in F-box only protein 36 (FBXO36) and similar proteins; FBXO36, also called ...
 136-184 1.63e-03

F-box domain found in F-box only protein 36 (FBXO36) and similar proteins; FBXO36, also called FBX36, likely functions as the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438878  Cd Length: 46  Bit Score: 37.17  E-value: 1.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLYH 184
Cdd:cd22106     1 LVRLPDKLLLYIISYLDLEDIA-RLSQTSKRFKKLCNSDEL--WEKIYM 46
F-box_FBXO30-like cd22101
F-box domain found in F-box only protein 30 (FBXO30), F-box only protein 40 (FBXO40) and ...
 136-170 2.16e-03

F-box domain found in F-box only protein 30 (FBXO30), F-box only protein 40 (FBXO40) and similar proteins; FBXO30, also called FBX30, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It is required for muscle atrophy following denervation. FBXO30 regulates mammopoiesis by targeting the bipolar mitotic kinesin Eg5. FBXO40, also called FBX40, or muscle disease-related protein, is a probable substrate-recognition component of an SCF-type E3 ubiquitin ligase complex that may function in myogenesis. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438873  Cd Length: 45  Bit Score: 36.97  E-value: 2.16e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREI 170
Cdd:cd22101     1 LSSLPFEILQHIARFLDSFSLC-NLSLVSRLMREV 34
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 796-854 2.81e-03

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 41.28  E-value: 2.81e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1134612243 796 TVHKAKGLEFDTVHVlddfvkvpcarhnlaQLPHFRVESFSEDewnLLYVAVTRAKKRL 854
Cdd:TIGR01447 521 TVHKSQGSEFDHVIL---------------ILPNGNSPVLTRE---LLYTGITRAKDQL 561
F-box_FBXL6 cd22119
F-box domain found in F-box/LRR-repeat protein 6 (FBXL6) and similar proteins; FBXL6, also ...
 138-176 3.10e-03

F-box domain found in F-box/LRR-repeat protein 6 (FBXL6) and similar proteins; FBXL6, also called F-box and leucine-rich repeat protein 6, or F-box protein FBL6 (FBL6A), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438891  Cd Length: 47  Bit Score: 36.46  E-value: 3.10e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1134612243 138 RLPSEVLRHIFAFL-----PVEDLYwNLSLVCHLWREIINDPLF 176
Cdd:cd22119     3 RLPPEILVKIFQFAvategAVPLLC-RLSRVCRLWREVALDPSL 45
F-box_FBXO31 cd22102
F-box domain found in F-box only protein 31 (FBXO31) and similar proteins; FBXO31, also called ...
 136-172 4.26e-03

F-box domain found in F-box only protein 31 (FBXO31) and similar proteins; FBXO31, also called FBX31, or FBXO14, is a component of an SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in G1 arrest following DNA damage. It specifically recognizes phosphorylated cyclin-D1 (CCND1), promoting its ubiquitination and degradation by the proteasome, resulting in G1 arrest. FBXO31 may act as a tumor suppressor. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438874  Cd Length: 48  Bit Score: 36.25  E-value: 4.26e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1134612243 136 ICRLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIIN 172
Cdd:cd22102     1 ILDLPPELLVEIFSSLPGTDLP-SLAQVCKKFREILN 36
recB PRK10876
exonuclease V subunit beta; Provisional
 571-608 5.27e-03

exonuclease V subunit beta; Provisional


Pssm-ID: 236784 [Multi-domain]  Cd Length: 1181  Bit Score: 40.72  E-value: 5.27e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1134612243  571 VDEAQDCTPA----IMNIVLSQP-CGKIFVGDPHQQIYTFRGA 608
Cdd:PRK10876   383 IDEFQDTDPQqyriFRRIYRHQPeTALLLIGDPKQAIYAFRGA 425
F-box_AtSKIP31-like cd22166
F-box domain found in Arabidopsis thaliana SKP1-interacting partner 31 (AtSKIP31) and similar ...
 138-183 8.00e-03

F-box domain found in Arabidopsis thaliana SKP1-interacting partner 31 (AtSKIP31) and similar proteins; AtSKIP31, also called F-box protein SKIP31, is a component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with SKP1A/ASK1 and SPK1B/ASK2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438937  Cd Length: 46  Bit Score: 35.13  E-value: 8.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1134612243 138 RLPSEVLRHIFAFLPVEDLYwNLSLVCHLWREIINDPLFipWKKLY 183
Cdd:cd22166     3 KLPPELFRHILKFLSPEDLT-SCATVCRFLRGAASDESL--WRRLY 45
F-box_FBA cd22083
F-box domain found in the F-box associated (FBA) family of F-box proteins; The F-box ...
 139-171 8.37e-03

F-box domain found in the F-box associated (FBA) family of F-box proteins; The F-box associated (FBA) family is composed of FBXO2, FBXO6, FBXO17, FBXO27, and FBXO44, which contain a conserved G domain that mediates substrate binding. Members of this family play diverse roles in glycoprotein quality control. They bind high mannose and sulfated glycoproteins, with one FBA protein, FBXO44, failing to bind any glycans on the tested arrays. FBA proteins are components of canonical SCF (Skp1, Cullin1, and Rbx1) complexes, yet FBXO2 bound very little Cullin1, suggesting that FBXO2 may exist primarily as a heterodimer with Skp1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438855  Cd Length: 37  Bit Score: 35.06  E-value: 8.37e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1134612243 139 LPSEVLRHIFAFLPVEDLYWNLSLVCHLWREII 171
Cdd:cd22083     4 IPEELLLEILTHVPATSLITNCRLVCTLWRDII 36
 
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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