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Conserved domains on  [gi|15223228|ref|NP_174531|]
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RING/U-box superfamily protein [Arabidopsis thaliana]

Protein Classification

RING-HC finger protein( domain architecture ID 17786959)

RING-HC finger protein may function as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination

CATH:  3.30.40.10
Gene Ontology:  GO:0008270
PubMed:  19489725|11007473
SCOP:  3000160

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RING-HC_MIP1-like cd23128
RING finger, HC subclass, found in Arabidopsis thaliana MND1-interacting protein 1 (MIP1) and ...
648-706 4.44e-23

RING finger, HC subclass, found in Arabidopsis thaliana MND1-interacting protein 1 (MIP1) and similar proteins; This subfamily includes Arabidopsis thaliana MIP1, RING finger protein 4 (RF4) and RING finger protein 298 (RF298). MIP1 interacts with MND1, HOP2 and XRI1. RF4 and RF298 are putative E3 ubiquitin-protein ligase that may mediate E2-dependent protein ubiquitination. Members of this subfamily contain a typical C3HC4-type RING-HC finger.


:

Pssm-ID: 438490 [Multi-domain]  Cd Length: 55  Bit Score: 92.57  E-value: 4.44e-23
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15223228 648 NYDRECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASnnggSKVTCPCCRGLVQQRIRI 706
Cdd:cd23128   1 KRERECVMCMEEERSVVFLPCAHQVVCSGCNDLHEKK----GMRECPSCRGEIQERIRV 55
DUF6592 pfam20235
Family of unknown function (DUF6592); This putative domain is found in plant E3-ligase ...
84-204 4.08e-22

Family of unknown function (DUF6592); This putative domain is found in plant E3-ligase proteins. The function of this domain is unknown. The domain is about 120 amino acids in length.


:

Pssm-ID: 466386  Cd Length: 116  Bit Score: 91.98  E-value: 4.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    84 HLEFLYNQAVSKL-LElgyEERVALKAVLSNGHCYGELDVLTNIVNNSLSYLNSGGGGGGSNGNGEDRTEtgftDLRDLE 162
Cdd:pfam20235   2 KIHGFYLEALSRLpTE---ELPALHRALLDAGHCYGPLDPVSNIILNTIWYPATRESPGEDLKGDMISTD----DLRRLE 74
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 15223228   163 EYSLAGMIYLLQQVKPNLSKGDAMWCLLMSELHVGRASTLDV 204
Cdd:pfam20235  75 SRSLDGLVAFLRSYFPYLTTGDALWYLLLADADLLVAVRLIE 116
Smc super family cl34174
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
374-605 2.01e-07

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


The actual alignment was detected with superfamily member COG1196:

Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 54.56  E-value: 2.01e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 374 LLHQVKDFEKKVKERKEWAQKNAMQAAQKVSEEL---AELKTLSSEREGIQLLKKGKQAVEESTAKRFTDKEIELRKACS 450
Cdd:COG1196 230 LLLKLRELEAELEELEAELEELEAELEELEAELAeleAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEE 309
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 451 QNDRANVIVRKLENQNAEIRAEREGSKLSASESLKACMEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLA 530
Cdd:COG1196 310 RRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELL 389
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15223228 531 ----QITEYEKEIEAKwRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKA 605
Cdd:COG1196 390 ealrAAAELAAQLEEL-EEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAE 467
 
Name Accession Description Interval E-value
RING-HC_MIP1-like cd23128
RING finger, HC subclass, found in Arabidopsis thaliana MND1-interacting protein 1 (MIP1) and ...
648-706 4.44e-23

RING finger, HC subclass, found in Arabidopsis thaliana MND1-interacting protein 1 (MIP1) and similar proteins; This subfamily includes Arabidopsis thaliana MIP1, RING finger protein 4 (RF4) and RING finger protein 298 (RF298). MIP1 interacts with MND1, HOP2 and XRI1. RF4 and RF298 are putative E3 ubiquitin-protein ligase that may mediate E2-dependent protein ubiquitination. Members of this subfamily contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438490 [Multi-domain]  Cd Length: 55  Bit Score: 92.57  E-value: 4.44e-23
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15223228 648 NYDRECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASnnggSKVTCPCCRGLVQQRIRI 706
Cdd:cd23128   1 KRERECVMCMEEERSVVFLPCAHQVVCSGCNDLHEKK----GMRECPSCRGEIQERIRV 55
DUF6592 pfam20235
Family of unknown function (DUF6592); This putative domain is found in plant E3-ligase ...
84-204 4.08e-22

Family of unknown function (DUF6592); This putative domain is found in plant E3-ligase proteins. The function of this domain is unknown. The domain is about 120 amino acids in length.


Pssm-ID: 466386  Cd Length: 116  Bit Score: 91.98  E-value: 4.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    84 HLEFLYNQAVSKL-LElgyEERVALKAVLSNGHCYGELDVLTNIVNNSLSYLNSGGGGGGSNGNGEDRTEtgftDLRDLE 162
Cdd:pfam20235   2 KIHGFYLEALSRLpTE---ELPALHRALLDAGHCYGPLDPVSNIILNTIWYPATRESPGEDLKGDMISTD----DLRRLE 74
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 15223228   163 EYSLAGMIYLLQQVKPNLSKGDAMWCLLMSELHVGRASTLDV 204
Cdd:pfam20235  75 SRSLDGLVAFLRSYFPYLTTGDALWYLLLADADLLVAVRLIE 116
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
650-703 6.76e-12

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 464042 [Multi-domain]  Cd Length: 50  Bit Score: 60.47  E-value: 6.76e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15223228   650 DRECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNggskvTCPCCRGLVQQR 703
Cdd:pfam13920   2 DLLCVICLDRPRNVVLLPCGHLCLCEECAERLLRKKK-----KCPICRQPIESV 50
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
374-605 2.01e-07

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 54.56  E-value: 2.01e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 374 LLHQVKDFEKKVKERKEWAQKNAMQAAQKVSEEL---AELKTLSSEREGIQLLKKGKQAVEESTAKRFTDKEIELRKACS 450
Cdd:COG1196 230 LLLKLRELEAELEELEAELEELEAELEELEAELAeleAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEE 309
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 451 QNDRANVIVRKLENQNAEIRAEREGSKLSASESLKACMEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLA 530
Cdd:COG1196 310 RRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELL 389
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15223228 531 ----QITEYEKEIEAKwRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKA 605
Cdd:COG1196 390 ealrAAAELAAQLEEL-EEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAE 467
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
398-645 2.69e-06

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 50.83  E-value: 2.69e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    398 QAAQKVSEELAELKTLSSEREGIQLLKKGKQAveestakRFTDKEIELRKAcsqNDRANVIVRKLENQNAEIrAEREGSK 477
Cdd:TIGR02168  236 ELREELEELQEELKEAEEELEELTAELQELEE-------KLEELRLEVSEL---EEEIEELQKELYALANEI-SRLEQQK 304
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    478 LSASESLKacmEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLAQITEYEKEIEAKWrQEQKAKEEALAQM 557
Cdd:TIGR02168  305 QILRERLA---NLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAEL-EELESRLEELEEQ 380
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    558 EEEQRSKEAAEghnKRKLETLRLKIeldfQRHKDDHQRLEQELGRLKASSDSDSSHISNNAwkpKKSQGENIAKLLEEID 637
Cdd:TIGR02168  381 LETLRSKVAQL---ELQIASLNNEI----ERLEARLERLEDRRERLQQEIEELLKKLEEAE---LKELQAELEELEEELE 450

                   ....*...
gi 15223228    638 KLEGSYDN 645
Cdd:TIGR02168  451 ELQEELER 458
CCDC158 pfam15921
Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. ...
331-622 1.37e-05

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.


Pssm-ID: 464943 [Multi-domain]  Cd Length: 1112  Bit Score: 48.58  E-value: 1.37e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    331 GQQPRKSGSEESVSTVLEK-FRDLNLDDNLESVGVDDKDCVIVDLLHQVKDFE-KKVKerkewaqknamqAAQKVSEELA 408
Cdd:pfam15921  579 GQHGRTAGAMQVEKAQLEKeINDRRLELQEFKILKDKKDAKIRELEARVSDLElEKVK------------LVNAGSERLR 646
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    409 ELKTLSSEREgiQLLKKGKQAVEESTAKRfTDKEIELRKACSQNDRANVIVRKLENQNAEIRAEREGSKlsasESLKAcM 488
Cdd:pfam15921  647 AVKDIKQERD--QLLNEVKTSRNELNSLS-EDYEVLKRNFRNKSEEMETTTNKLKMQLKSAQSELEQTR----NTLKS-M 718
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    489 EASKKEKKCLKklVAWEKQILKLQDEITAEKEKIKALYKTLAQITE---YEKEIEAKWRQEQKA---KEEALAQMEEEQR 562
Cdd:pfam15921  719 EGSDGHAMKVA--MGMQKQITAKRGQIDALQSKIQFLEEAMTNANKekhFLKEEKNKLSQELSTvatEKNKMAGELEVLR 796
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15223228    563 SKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKASSDSDSSHI------SNNAWKPK 622
Cdd:pfam15921  797 SQERRLKEKVANMEVALDKASLQFAECQDIIQRQEQESVRLKLQHTLDVKELqgpgytSNSSMKPR 862
PTZ00121 PTZ00121
MAEBL; Provisional
383-655 2.84e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.83  E-value: 2.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   383 KKVKERKEWAQKNAMQAAQKVSE-ELAELKTLSSEREGIQLLKKGKQAVEESTAKRFT-DKEIELRKAcsqndranVIVR 460
Cdd:PTZ00121 1516 KKAEEAKKADEAKKAEEAKKADEaKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEeDKNMALRKA--------EEAK 1587
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   461 KLENQNAE--IRAEREGSKLSASESLKACMEASKKEKKCLKKLVawEKQILKLQDEITAEKEKIKALYKTLAQITEYEKE 538
Cdd:PTZ00121 1588 KAEEARIEevMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEE--KKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAE 1665
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   539 IEAKWRQEQKAKEEALAQMEEEQRSKEAA--EGHNKRKLETLRLKIELdfQRHKDDHQRLEQELGRLKASS-DSDSSHIS 615
Cdd:PTZ00121 1666 EAKKAEEDKKKAEEAKKAEEDEKKAAEALkkEAEEAKKAEELKKKEAE--EKKKAEELKKAEEENKIKAEEaKKEAEEDK 1743
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 15223228   616 NNAWKPKKSQGENiaKLLEEIDKLEGSYDNEANYDRECII 655
Cdd:PTZ00121 1744 KKAEEAKKDEEEK--KKIAHLKKEEEKKAEEIRKEKEAVI 1781
 
Name Accession Description Interval E-value
RING-HC_MIP1-like cd23128
RING finger, HC subclass, found in Arabidopsis thaliana MND1-interacting protein 1 (MIP1) and ...
648-706 4.44e-23

RING finger, HC subclass, found in Arabidopsis thaliana MND1-interacting protein 1 (MIP1) and similar proteins; This subfamily includes Arabidopsis thaliana MIP1, RING finger protein 4 (RF4) and RING finger protein 298 (RF298). MIP1 interacts with MND1, HOP2 and XRI1. RF4 and RF298 are putative E3 ubiquitin-protein ligase that may mediate E2-dependent protein ubiquitination. Members of this subfamily contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438490 [Multi-domain]  Cd Length: 55  Bit Score: 92.57  E-value: 4.44e-23
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15223228 648 NYDRECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASnnggSKVTCPCCRGLVQQRIRI 706
Cdd:cd23128   1 KRERECVMCMEEERSVVFLPCAHQVVCSGCNDLHEKK----GMRECPSCRGEIQERIRV 55
DUF6592 pfam20235
Family of unknown function (DUF6592); This putative domain is found in plant E3-ligase ...
84-204 4.08e-22

Family of unknown function (DUF6592); This putative domain is found in plant E3-ligase proteins. The function of this domain is unknown. The domain is about 120 amino acids in length.


Pssm-ID: 466386  Cd Length: 116  Bit Score: 91.98  E-value: 4.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    84 HLEFLYNQAVSKL-LElgyEERVALKAVLSNGHCYGELDVLTNIVNNSLSYLNSGGGGGGSNGNGEDRTEtgftDLRDLE 162
Cdd:pfam20235   2 KIHGFYLEALSRLpTE---ELPALHRALLDAGHCYGPLDPVSNIILNTIWYPATRESPGEDLKGDMISTD----DLRRLE 74
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 15223228   163 EYSLAGMIYLLQQVKPNLSKGDAMWCLLMSELHVGRASTLDV 204
Cdd:pfam20235  75 SRSLDGLVAFLRSYFPYLTTGDALWYLLLADADLLVAVRLIE 116
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
650-703 6.76e-12

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 464042 [Multi-domain]  Cd Length: 50  Bit Score: 60.47  E-value: 6.76e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15223228   650 DRECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNggskvTCPCCRGLVQQR 703
Cdd:pfam13920   2 DLLCVICLDRPRNVVLLPCGHLCLCEECAERLLRKKK-----KCPICRQPIESV 50
RING-HC_BIRC2_3_7 cd16713
RING finger, HC subclass, found in apoptosis protein c-IAP1, c-IAP2, livin, and similar ...
650-707 5.47e-11

RING finger, HC subclass, found in apoptosis protein c-IAP1, c-IAP2, livin, and similar proteins; The cellular inhibitor of apoptosis protein c-IAPs function as ubiquitin E3 ligases that mediate the ubiquitination of substrates involved in apoptosis, nuclear factor-kappaB (NF-kappaB) signaling, and oncogenesis. Unlike other IAPs, such as XIAP, c-IAPs exhibit minimal binding to caspases and may not play an important role in the inhibition of these proteases. c-IAP1, also known as baculoviral IAP repeat-containing protein BIRC2, IAP-2, RING finger protein 48, or TNFR2-TRAF-signaling complex protein 2, is a potent regulator of the tumor necrosis factor (TNF) receptor family and NF-kappaB signaling pathways in the cytoplasm. It can also regulate E2F1 transcription factor-mediated control of cyclin transcription in the nucleus. c-IAP2, also known as BIRC3, IAP-1, apoptosis inhibitor 2 (API2), or IAP homolog C, also influences ubiquitin-dependent pathways that modulate innate immune signalling by activation of NF-kappaB. c-IAPs contain three N-terminal baculoviral IAP repeat (BIR) domains that enable interactions with proteins, a ubiquitin-association (UBA) domain that is responsible for the binding of polyubiquitin (polyUb), a caspase activation and recruitment domain (CARD) that serves as a protein interaction surface, and a C3HC4-type RING-HC finger at the carboxyl terminus that is required for ubiquitin ligase activity. Livin, also known as baculoviral IAP repeat-containing protein 7 (BIRC7), kidney inhibitor of apoptosis protein (KIAP), melanoma inhibitor of apoptosis protein (ML-IAP), or RING finger protein 50, was identified as the melanoma IAP. It plays crucial roles in apoptosis, cell proliferation, and cell cycle control. Its anti-apoptotic activity is regulated by the inhibition of caspase-3, -7, and -9. Its E3 ubiquitin-ligase-like activity promotes degradation of Smac/DIABLO, a critical endogenous regulator of all IAPs. Unlike other family members, mammalian livin contains a single BIR domain and a C3HC4-type RING-HC finger. The UBA domain can be detected in non-mammalian homologs of livin.


Pssm-ID: 438373 [Multi-domain]  Cd Length: 57  Bit Score: 58.25  E-value: 5.47e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15223228 650 DRECIICMKDEVSVVFLPCAHQVVCGSCSDSFfasnnggskVTCPCCRGLVQQRIRIF 707
Cdd:cd16713   7 ERTCKVCMDKEVSIVFIPCGHLVVCTECAPSL---------RKCPICRATIKGTVRTF 55
RING-HC_LRSAM1 cd16515
RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing ...
652-706 1.78e-10

RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins; LRSAM1, also known as Tsg101-associated ligase (TAL), or RIFLE, is an E3 ubiquitin-protein ligase that physically associates with, and selectively ubiquitylates, Tsg101, an E2-like molecule that regulates vesicular trafficking processes in yeast and mammals. It regulates a Tsg101-associated complex responsible for the sorting of cargo into cytoplasm-containing vesicles that bud at the multivesicular body and at the plasma membrane. LRSAM1 is a multidomain protein containing an N-terminal leucine-rich repeat (LRR), followed by several recognizable motifs, including an ezrin-radixin-moezin (ERM) domain, a coiled-coil (CC) region, a SAM domain, and a C-terminal C3HC4-type RING-HC finger domain.


Pssm-ID: 438178 [Multi-domain]  Cd Length: 48  Bit Score: 56.53  E-value: 1.78e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15223228 652 ECIICMKDEVSVVFLPCAHQVVCGSCSDSFFasnnggskvTCPCCRGLVQQRIRI 706
Cdd:cd16515   3 ECVVCMDAESQVIFLPCGHVCCCQTCSSSLS---------TCPLCRADITQRVRI 48
RING-HC_IAPs cd16510
RING finger, HC subclass, found in inhibitor of apoptosis proteins (IAPs); IAPs are frequently ...
651-698 1.19e-08

RING finger, HC subclass, found in inhibitor of apoptosis proteins (IAPs); IAPs are frequently overexpressed in cancer and associated with tumor cell survival, chemoresistance, disease progression, and poor prognosis. They function primarily as negative regulators of cell death. They regulate caspases and apoptosis through the inhibition of specific members of the caspase family of cysteine proteases. In addition, IAPs has been implicated in a multitude of other cellular processes, including inflammatory signalling and immunity, mitogenic kinase signalling, proliferation and mitosis, as well as cell invasion and metastasis. IAPs in this family includes cellular inhibitor of apoptosis protein c-IAP1 (BIRC2) and c-IAP2 (BIRC3), XIAP (BIRC4), BIRC7, and BIRC8, all of which contain three N-terminal baculoviral IAP repeat (BIR) domains that enable interactions with proteins, a ubiquitin-association (UBA) domain that is responsible for the binding of polyubiquitin (polyUb), and a C3HC4-type RING-HC finger at the carboxyl terminus that is required for ubiquitin ligase activity. The UBA domain is only absent in mammalian homologs of BIRC7. Moreover, c-IAPs contains an additional caspase activation and recruitment domain (CARD) between the UBA and C3HC4-type RING-HC domains. The CARD domain may serve as a protein interaction surface.


Pssm-ID: 438173 [Multi-domain]  Cd Length: 40  Bit Score: 51.10  E-value: 1.19e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFfasnnggskVTCPCCRG 698
Cdd:cd16510   2 KLCKICMDREVNIVFLPCGHLVTCAQCAASL---------RKCPICRT 40
RING-HC_XBAT35-like cd23129
RING finger, HC subclass, found in Arabidopsis thaliana protein XB3 homolog 5 (XBAT35) and ...
652-707 1.98e-08

RING finger, HC subclass, found in Arabidopsis thaliana protein XB3 homolog 5 (XBAT35) and similar proteins; XBAT35, also known as ankyrin repeat domain and RING finger-containing protein XBAT35, or RING-type E3 ubiquitin transferase XBAT35, has no E3 ubiquitin-protein ligase activity observed when associated with the E2 enzyme UBC8 in vitro. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438491 [Multi-domain]  Cd Length: 54  Bit Score: 51.11  E-value: 1.98e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15223228 652 ECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNGgskvtCPCCRGLVQQRIRIF 707
Cdd:cd23129   4 ECVVCMDAPRDAVCVPCGHVAGCMSCLKALMQSSPL-----CPICRAPVRQVIKVY 54
mRING-HC-C3HC5_NEU1 cd16647
Modified RING finger, HC subclass (C3HC5-type), found in neuralized-like protein NEURL1A, ...
652-707 7.08e-08

Modified RING finger, HC subclass (C3HC5-type), found in neuralized-like protein NEURL1A, NEURL1B, and similar proteins; This subfamily includes Drosophila neuralized (D-neu) protein, and its two mammalian homologs, NEURL1A and NEURL1B. D-neu is a regulator of the developmentally important Notch signaling pathway. NEURL1A, also known as NEURL1, NEU, neuralized 1, or RING finger protein 67 (RNF67), is a mammalian homolog of D-neu. It functions as an E3 ubiquitin-protein ligase that directly interacts with and monoubiquitinates cytoplasmic polyadenylation element-binding protein 3 (CPEB3), an RNA binding protein and a translational regulator of local protein synthesis, which facilitates hippocampal plasticity and hippocampal-dependent memory storage. It also acts as a potential tumor suppressor that causes apoptosis and downregulates Notch target genes in medulloblastoma. NEURL1B, also known as neuralized-2 (NEUR2) or neuralized-like protein 3, is another mammalian homolog of D-neu protein. It functions as an E3 ubiquitin-protein ligase that interacts with and ubiquitinates Delta. Thus, it plays a role in the endocytic pathways for Notch signaling by working cooperatively with another E3 ligase, Mind bomb-1 (Mib1), in Delta endocytosis to hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs)-positive vesicles. Members of this subfamily contain two neuralized homology regions (NHRs) responsible for Neural-ligand interactions and a modified C3HC5-type RING-HC finger required for ubiquitin ligase activity. The C3HC5-type RING-HC finger is distinguished from typical C3HC4-type RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438309 [Multi-domain]  Cd Length: 53  Bit Score: 49.22  E-value: 7.08e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15223228 652 ECIICMKDEVSVVFLPCAHQVVCGSCSDSffASNNGGSkvtCPCCRGLVQQRIRIF 707
Cdd:cd16647   3 ECVICYERPVDTVLYRCGHMCMCYDCALQ--LKRRGGS---CPICRAPIKDVIKIY 53
RING-HC_MEX3B cd16721
RING finger, HC subclass, found in RNA-binding protein MEX3B; MEX3B, also known as RING finger ...
651-707 1.22e-07

RING finger, HC subclass, found in RNA-binding protein MEX3B; MEX3B, also known as RING finger and KH domain-containing protein 3 (RKHD3), or RING finger protein 195 (RNF195), is an RNA-binding phosphoprotein that localizes in P-bodies and stress granules, which are two structures involved in the storage and turnover of mRNAs. It regulates the spatial organization of the Rap1 pathway that orchestrates Sertoli cell functions. It has a 3' long conserved untranslated region (3'LCU)-mediated fine-tuning system for mRNA regulation in early vertebrate development such as anteroposterior (AP) patterning and signal transduction. MEX3B contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3B shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway.


Pssm-ID: 438381 [Multi-domain]  Cd Length: 58  Bit Score: 48.91  E-value: 1.22e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNnggsKVTCPCCRGLVQQRIRIF 707
Cdd:cd16721   5 RDCSICFESEVIAALVPCGHNLFCMECANRICEKN----EPQCPVCHAAVTQAIRIF 57
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
374-605 2.01e-07

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 54.56  E-value: 2.01e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 374 LLHQVKDFEKKVKERKEWAQKNAMQAAQKVSEEL---AELKTLSSEREGIQLLKKGKQAVEESTAKRFTDKEIELRKACS 450
Cdd:COG1196 230 LLLKLRELEAELEELEAELEELEAELEELEAELAeleAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEE 309
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 451 QNDRANVIVRKLENQNAEIRAEREGSKLSASESLKACMEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLA 530
Cdd:COG1196 310 RRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELL 389
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15223228 531 ----QITEYEKEIEAKwRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKA 605
Cdd:COG1196 390 ealrAAAELAAQLEEL-EEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAE 467
RING-HC_BIRC4_8 cd16714
RING finger, HC subclass, found in E3 ubiquitin-protein ligase XIAP, baculoviral IAP ...
653-707 2.99e-07

RING finger, HC subclass, found in E3 ubiquitin-protein ligase XIAP, baculoviral IAP repeat-containing protein 8 (BIRC8) and similar proteins; XIAP, also known as baculoviral IAP repeat-containing protein 4 (BIRC4), IAP-like protein (ILP), inhibitor of apoptosis protein 3 (IAP-3), or X-linked inhibitor of apoptosis protein (X-linked IAP), is a potent suppressor of apoptosis that directly inhibits specific members of the caspase family of cysteine proteases, including caspase-3, -7, and -9. It promotes proteasomal degradation of caspase-3 and enhances its anti-apoptotic effect in Fas-induced cell death. The ubiquitin-protein ligase (E3) activity of XIAP also exhibits in the ubiquitination of second mitochondria-derived activator of caspases (Smac). The mitochondrial proteins, Smac/DIABLO and Omi/HtrA2, can inhibit the antiapoptotic activity of XIAP. XIAP has also been implicated in several intracellular signaling cascades involved in the cellular response to stress, such as the c-Jun N-terminal kinase (JNK), the nuclear factor-kappaB (NF-kappaB), and the transforming growth factor-beta (TGF-beta) pathways. Moreover, XIAP can regulate copper homeostasis by interacting with MURR1. BIRC8, also known as inhibitor of apoptosis-like protein 2, IAP-like protein 2, ILP-2, or testis-specific inhibitor of apoptosis, is a tissue-specific homolog of E3 ubiquitin-protein ligase XIAP. It has been implicated in the control of apoptosis in the testis by direct inhibition of caspase 9. Both XIAP and BIRC8 contain three N-terminal baculoviral IAP repeat (BIR) domains, a ubiquitin-association (UBA) domain and a C3HC4-type RING-HC finger at the carboxyl terminus.


Pssm-ID: 438374 [Multi-domain]  Cd Length: 64  Bit Score: 47.83  E-value: 2.99e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15223228 653 CIICMKDEVSVVFLPCAHQVVCGSCSDSFfasnnggskVTCPCCRGLVQQRIRIF 707
Cdd:cd16714  17 CKICMDRNISIVFIPCGHLVTCKQCAEAL---------DKCPICCTVITFKQKIF 62
RING-HC_MEX3 cd16518
RING finger, HC subclass, found in RNA-binding proteins of the evolutionarily-conserved MEX-3 ...
651-707 3.02e-07

RING finger, HC subclass, found in RNA-binding proteins of the evolutionarily-conserved MEX-3 family; MEX-3 phosphoproteins are found in vertebrates. They are mediators of post-transcriptional regulation in different organisms, and have been implicated in many core biological processes, including embryonic development, epithelial homeostasis, immune responses, metabolism, and cancer. They contain two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. They shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The RNA-binding protein MEX-3 from nematode Caenorhabditis elegans is the founding member of the MEX-3 family. Due to the lack of a RING-HC finger, it is not included here.


Pssm-ID: 438181 [Multi-domain]  Cd Length: 53  Bit Score: 47.75  E-value: 3.02e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNGgskvTCPCCRGLVQQRIRIF 707
Cdd:cd16518   1 RDCVVCFESEVVAALVPCGHNLFCMECANRICEKSDP----ECPVCHTPVTQAIRIF 53
mRING-HC-C3HC5_CGRF1-like cd16649
Modified RING finger, HC subclass (C3HC5-type), found in RING finger proteins, RNF26, RNF197 ...
651-697 4.61e-07

Modified RING finger, HC subclass (C3HC5-type), found in RING finger proteins, RNF26, RNF197 (CGRRF1), RNF156 (MGRN1), RNF157 and similar proteins; This subfamily corresponds to a group of RING finger proteins containing a modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. Cell growth regulator with RING finger domain protein 1 (CGRRF1), also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. RNF26 is an E3 ubiquitin ligase that temporally regulates virus-triggered type I interferon induction by increasing the stability of Mediator of IRF3 activation, MITA, also known as STING, through K11-linked polyubiquitination after viral infection and promoting degradation of IRF3, another important component required for virus-triggered interferon induction. Mahogunin ring finger-1 (MGRN1), also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in the brain. It is a homolog of the E3 ligase MGRN1. In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis.


Pssm-ID: 438311 [Multi-domain]  Cd Length: 40  Bit Score: 46.55  E-value: 4.61e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFfasnnggSKVTCPCCR 697
Cdd:cd16649   1 GLCVVCLENPASVLLLPCRHLCLCEVCAKGL-------RGKTCPICR 40
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
386-605 1.03e-06

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 52.25  E-value: 1.03e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 386 KERKEWAQKNaMQAAQkvsEELAELKTLSSEREGiQLLKKGKQAveeSTAKRFTDKEIELRKAcsqndRANVIVRKLENQ 465
Cdd:COG1196 171 KERKEEAERK-LEATE---ENLERLEDILGELER-QLEPLERQA---EKAERYRELKEELKEL-----EAELLLLKLREL 237
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 466 NAEIRAEREGSKLSASESLKAcmeaskkekkcLKKLVAWEKQILKLQDEITAEKEKIKA----LYKTLAQITEYEKEIEA 541
Cdd:COG1196 238 EAELEELEAELEELEAELEEL-----------EAELAELEAELEELRLELEELELELEEaqaeEYELLAELARLEQDIAR 306
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15223228 542 KwRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKA 605
Cdd:COG1196 307 L-EERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLE 369
RING-HC_MEX3A cd16720
RING finger, HC subclass, found in RNA-binding protein MEX3A; MEX3A, also known as RING finger ...
651-707 1.04e-06

RING finger, HC subclass, found in RNA-binding protein MEX3A; MEX3A, also known as RING finger and KH domain-containing protein 4 (RKHD4), is an RNA-binding phosphoprotein that localizes in P-bodies and stress granules, which are two structures involved in the storage and turnover of mRNAs. It has been implicated in the regulation of tumorigenesis. It controls the polarity and stemness of intestinal epithelial cells through the post-transcriptional regulation of the homeobox transcription factor CDX2, which plays a crucial role in intestinal cell fate specification, both during normal development and in tumorigenic processes involving intestinal reprogramming. Moreover, it exhibits a transforming activity when overexpressed in gastric epithelial cells. MEX3A contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3A shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway.


Pssm-ID: 438380 [Multi-domain]  Cd Length: 56  Bit Score: 46.10  E-value: 1.04e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNGgskvTCPCCRGLVQQRIRIF 707
Cdd:cd16720   3 RDCMVCFESEVTAALVPCGHNLFCMECAVRICERNEP----ECPVCHALATQAIRIF 55
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
387-599 1.38e-06

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 51.86  E-value: 1.38e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 387 ERKEWAQKNAMQAAQKVSEELAEL-KTLSSEREGIQLLKKGKQAVEEstakRFTDKEIELRKACSQNDRANVIVRKLENQ 465
Cdd:COG1196 270 EELRLELEELELELEEAQAEEYELlAELARLEQDIARLEERRRELEE----RLEELEEELAELEEELEELEEELEELEEE 345
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 466 NAEIRAEREGSKLSASESLKACMEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALyktLAQITEYEKEIEAKwRQ 545
Cdd:COG1196 346 LEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEEL---EEAEEALLERLERL-EE 421
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 15223228 546 EQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQE 599
Cdd:COG1196 422 ELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAELLEEAALL 475
mRING-HC-C3HC5_MGRN1-like cd16789
Modified RING finger, HC subclass (C3HC5-type), found in mahogunin RING finger protein 1 ...
651-697 1.51e-06

Modified RING finger, HC subclass (C3HC5-type), found in mahogunin RING finger protein 1 (MGRN1), RING finger protein 157 (RNF157) and similar proteins; MGRN1, also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. MGRN1 interacts with cytosolic prion proteins (PrPs) that are linked with neurodegeneration. It also interacts with expanded polyglutamine proteins, and suppresses misfolded polyglutamine aggregation and cytotoxicity. Moreover, MGRN1 inhibits melanocortin receptor signaling by competition with Galphas, suggesting a novel pathway for melanocortin signaling from the cell surface to the nucleus. MGRN1 also interacts with and ubiquitylates TSG101, a key component of the endosomal sorting complex required for transport (ESCRT)-I, and regulates endosomal trafficking. A null mutation in the gene encoding MGRN1 causes spongiform neurodegeneration, suggesting a link between dysregulation of endosomal trafficking and spongiform neurodegeneration. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in the brain. It is a homolog of the E3 ligase mahogunin ring finger-1 (MGRN1). In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis. Both MGRN1 and RNF157 contain a modified C3HC5-type RING-HC finger, and a functionally uncharacterized region, known as domain associated with RING2 (DAR2), N-terminal to the RING finger. The C3HC5-type RING-HC finger is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438443 [Multi-domain]  Cd Length: 42  Bit Score: 45.37  E-value: 1.51e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSF-FASNNggskvtCPCCR 697
Cdd:cd16789   1 SECVICLSDPRDTAVLPCRHLCLCSDCAEVLrYQSNK------CPICR 42
RING-HC_CARP cd16500
RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein CARP-1, ...
653-707 1.60e-06

RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein CARP-1, CARP-2 and similar proteins; The CARP subfamily includes CARP-1 and CARP-2 proteins, both of which are E3 ubiquitin ligases that ubiquitinate apical caspases and target them for proteasome-mediated degradation. As a novel group of caspase regulators with a FYVE-type zinc finger domain, they do not localize to membranes in the cell and are involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8, and caspase 10. Moreover, they stabilize MDM2 by inhibiting MDM2 self-ubiquitination, as well as by targeting 14-3-3sigma for degradation. They work together with MDM2 to enhance p53 degradation, thereby inhibiting p53-mediated cell death. CARPs contain an N-terminal FYVE-like domain that can serve as a membrane-targeting or endosome localizing signal and a C-terminal C3HC4-type RING-HC finger domain.


Pssm-ID: 438163 [Multi-domain]  Cd Length: 48  Bit Score: 45.46  E-value: 1.60e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15223228 653 CIICMKDEVSVVFLPCAHQVVCGSCsdsffasnngGSKVT-CPCCRGLVQQRIRIF 707
Cdd:cd16500   3 CKICMDAAIDCVLLECGHMVTCTDC----------GKKLSeCPICRQYVVRVVHFF 48
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
398-645 2.69e-06

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 50.83  E-value: 2.69e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    398 QAAQKVSEELAELKTLSSEREGIQLLKKGKQAveestakRFTDKEIELRKAcsqNDRANVIVRKLENQNAEIrAEREGSK 477
Cdd:TIGR02168  236 ELREELEELQEELKEAEEELEELTAELQELEE-------KLEELRLEVSEL---EEEIEELQKELYALANEI-SRLEQQK 304
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    478 LSASESLKacmEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLAQITEYEKEIEAKWrQEQKAKEEALAQM 557
Cdd:TIGR02168  305 QILRERLA---NLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAEL-EELESRLEELEEQ 380
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    558 EEEQRSKEAAEghnKRKLETLRLKIeldfQRHKDDHQRLEQELGRLKASSDSDSSHISNNAwkpKKSQGENIAKLLEEID 637
Cdd:TIGR02168  381 LETLRSKVAQL---ELQIASLNNEI----ERLEARLERLEDRRERLQQEIEELLKKLEEAE---LKELQAELEELEEELE 450

                   ....*...
gi 15223228    638 KLEGSYDN 645
Cdd:TIGR02168  451 ELQEELER 458
RING-HC_MEX3D cd16723
RING finger, HC subclass, found in RNA-binding protein MEX3D; MEX3D, also known as RING finger ...
651-707 3.29e-06

RING finger, HC subclass, found in RNA-binding protein MEX3D; MEX3D, also known as RING finger and KH domain-containing protein 1 (RKHD1), RING finger protein 193 (RNF193), or TINO, is an RNA-binding phosphoprotein that controls the stability of the transcripts coding for the anti-apoptotic protein BCL-2, and negatively regulates BCL-2 in HeLa cells. MEX3D contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3D shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway.


Pssm-ID: 438383 [Multi-domain]  Cd Length: 64  Bit Score: 44.91  E-value: 3.29e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFFasnnGGSKVTCPCCRGLVQQRIRIF 707
Cdd:cd16723  11 RECVVCFESEVIAALVPCGHNLFCMECAIRIC----GKSEPECPACHTPATQAIHIF 63
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
652-696 4.56e-06

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 44.01  E-value: 4.56e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 15223228 652 ECIICMKDEVSVVFLPCAHqVVCGSCSDSFFASNNggskVTCPCC 696
Cdd:cd16449   2 ECPICLERLKDPVLLPCGH-VFCRECIRRLLESGS----IKCPIC 41
mRING-HC-C3HC5_MAPL cd16648
Modified RING finger, HC subclass (C3HC5-type), found in mitochondrial-anchored protein ligase ...
650-707 6.48e-06

Modified RING finger, HC subclass (C3HC5-type), found in mitochondrial-anchored protein ligase (MAPL) and similar proteins; MAPL, also known as MULAN, mitochondrial ubiquitin ligase activator of NFKB 1, E3 SUMO-protein ligase MUL1, E3 ubiquitin-protein ligase MUL1, growth inhibition and death E3 ligase (GIDE), putative NF-kappa-B-activating protein 266, or RING finger protein 218 (RNF218), is a multifunctional mitochondrial outer membrane protein involved in several processes specific to metazoan (multicellular animal) cells, such as NF-kappaB activation, innate immunity and antiviral signaling, suppression of PINK1/parkin defects, mitophagy in skeletal muscle, and caspase-dependent apoptosis. MAPL contains a unique BAM (beside a membrane)/GIDE (growth inhibition death E3 ligase) domain and a C-terminal modified cytosolic C3HC5-type RING-HC finger which is distinguished from typical C3HC4-type RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438310 [Multi-domain]  Cd Length: 52  Bit Score: 43.61  E-value: 6.48e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15223228 650 DRECIICMKDEVSVVFLPCAHqvVCgSCSDSFFASNnggSKVTCPCCRGLVQQRIRIF 707
Cdd:cd16648   1 DNACVICLSNPRSCVFLECGH--VC-SCIECYEALP---SPKKCPICRSFIKRVVPLY 52
CCDC158 pfam15921
Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. ...
331-622 1.37e-05

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.


Pssm-ID: 464943 [Multi-domain]  Cd Length: 1112  Bit Score: 48.58  E-value: 1.37e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    331 GQQPRKSGSEESVSTVLEK-FRDLNLDDNLESVGVDDKDCVIVDLLHQVKDFE-KKVKerkewaqknamqAAQKVSEELA 408
Cdd:pfam15921  579 GQHGRTAGAMQVEKAQLEKeINDRRLELQEFKILKDKKDAKIRELEARVSDLElEKVK------------LVNAGSERLR 646
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    409 ELKTLSSEREgiQLLKKGKQAVEESTAKRfTDKEIELRKACSQNDRANVIVRKLENQNAEIRAEREGSKlsasESLKAcM 488
Cdd:pfam15921  647 AVKDIKQERD--QLLNEVKTSRNELNSLS-EDYEVLKRNFRNKSEEMETTTNKLKMQLKSAQSELEQTR----NTLKS-M 718
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    489 EASKKEKKCLKklVAWEKQILKLQDEITAEKEKIKALYKTLAQITE---YEKEIEAKWRQEQKA---KEEALAQMEEEQR 562
Cdd:pfam15921  719 EGSDGHAMKVA--MGMQKQITAKRGQIDALQSKIQFLEEAMTNANKekhFLKEEKNKLSQELSTvatEKNKMAGELEVLR 796
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15223228    563 SKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKASSDSDSSHI------SNNAWKPK 622
Cdd:pfam15921  797 SQERRLKEKVANMEVALDKASLQFAECQDIIQRQEQESVRLKLQHTLDVKELqgpgytSNSSMKPR 862
RING-HC_RNF141 cd16545
RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; ...
652-697 1.61e-05

RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; RNF141, also known as zinc finger protein 230 (ZNF230), is a RING finger protein present primarily in the nuclei of spermatogonia, the acrosome, and the tail of spermatozoa. It may have a broad function during early development of vertebrates. It plays an important role in spermatogenesis, including spermatogenic cell proliferation and sperm maturation, as well as motility and fertilization. It also exhibits DNA binding activity. RNF141/ZNF230 gene mutations may be associated with azoospermia. RNF141 contains a C3HC4-type RING finger domain that may function as an activator module in transcription.


Pssm-ID: 438207 [Multi-domain]  Cd Length: 40  Bit Score: 42.46  E-value: 1.61e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15223228 652 ECIICMkDEVSVVFLPCAHqVVCGSCSDSFFASNNggskvTCPCCR 697
Cdd:cd16545   2 ECCICM-DRKADLILPCAH-SYCQKCIDKWSDRHR-----TCPICR 40
RING-HC_MEX3C cd16722
RING finger, HC subclass, found in RNA-binding protein MEX3C; MEX3C, also known as RING finger ...
651-707 1.75e-05

RING finger, HC subclass, found in RNA-binding protein MEX3C; MEX3C, also known as RING finger and KH domain-containing protein 2 (RKHD2), or RING finger protein 194 (RNF194), is an RNA-binding phosphoprotein that acts as a suppressor of chromosomal instability. It functions as an ubiquitin E3 ligase responsible for the post-transcriptional, HLA-A allotype-specific regulation of MHC class I molecules (MHC-I). It also modifies retinoic acid inducible gene-1 (RIG-I) in stress granules and plays a critical role in eliciting antiviral immune responses. Moreover, MEX3C plays an essential role in normal postnatal growth via enhancing the local expression of insulin-like growth factor 1 (IGF1) in bone. It may also be involved in metabolic regulation of energy balance. MEX3C contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3C shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway.


Pssm-ID: 438382 [Multi-domain]  Cd Length: 55  Bit Score: 42.66  E-value: 1.75e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNGgskvTCPCCRGLVQQRIRIF 707
Cdd:cd16722   2 HDCVICFENEVIAALVPCGHNLFCMECANKICEKETP----SCPVCQTAVTQAIQIH 54
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
386-597 2.17e-05

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 48.01  E-value: 2.17e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 386 KERKEWAQKNAmQAAQKVSEELAELKTLSSEREGIQLLKKGKQAVEESTAKRFTDKEIELRKAcsQNDRANVIVRKLENQ 465
Cdd:COG1196 323 EELAELEEELE-ELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEEL--AEELLEALRAAAELA 399
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 466 NAEIRAEREgskLSASESLKAcmeaskkekkclkklvAWEKQILKLQDEITAEKEKIKALYKTLAQITEYEKEIEAkwrq 545
Cdd:COG1196 400 AQLEELEEA---EEALLERLE----------------RLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEE---- 456
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 15223228 546 EQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLE 597
Cdd:COG1196 457 EEEALLELLAELLEEAALLEAALAELLEELAEAAARLLLLLEAEADYEGFLE 508
PTZ00121 PTZ00121
MAEBL; Provisional
383-655 2.84e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.83  E-value: 2.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   383 KKVKERKEWAQKNAMQAAQKVSE-ELAELKTLSSEREGIQLLKKGKQAVEESTAKRFT-DKEIELRKAcsqndranVIVR 460
Cdd:PTZ00121 1516 KKAEEAKKADEAKKAEEAKKADEaKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEeDKNMALRKA--------EEAK 1587
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   461 KLENQNAE--IRAEREGSKLSASESLKACMEASKKEKKCLKKLVawEKQILKLQDEITAEKEKIKALYKTLAQITEYEKE 538
Cdd:PTZ00121 1588 KAEEARIEevMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEE--KKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAE 1665
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   539 IEAKWRQEQKAKEEALAQMEEEQRSKEAA--EGHNKRKLETLRLKIELdfQRHKDDHQRLEQELGRLKASS-DSDSSHIS 615
Cdd:PTZ00121 1666 EAKKAEEDKKKAEEAKKAEEDEKKAAEALkkEAEEAKKAEELKKKEAE--EKKKAEELKKAEEENKIKAEEaKKEAEEDK 1743
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 15223228   616 NNAWKPKKSQGENiaKLLEEIDKLEGSYDNEANYDRECII 655
Cdd:PTZ00121 1744 KKAEEAKKDEEEK--KKIAHLKKEEEKKAEEIRKEKEAVI 1781
zf-RING_2 pfam13639
Ring finger domain;
652-697 5.45e-05

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 40.85  E-value: 5.45e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15223228   652 ECIIC---MKDEVSVVFLPCAHqVVCGSCSDSFFASNNggskvTCPCCR 697
Cdd:pfam13639   2 ECPICleeFEEGDKVVVLPCGH-HFHRECLDKWLRSSN-----TCPLCR 44
mRING-HC-C3HC5_MGRN1 cd16816
Modified RING finger, HC subclass (C3HC5-type), found in mahogunin RING finger protein 1 ...
644-697 9.47e-05

Modified RING finger, HC subclass (C3HC5-type), found in mahogunin RING finger protein 1 (MGRN1) and similar proteins; MGRN1, also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. MGRN1 interacts with cytosolic prion proteins (PrPs) that are linked with neurodegeneration. It also interacts with expanded polyglutamine proteins, and suppresses misfolded polyglutamine aggregation and cytotoxicity. Moreover, MGRN1 inhibits melanocortin receptor signaling by competition with Galphas, suggesting a novel pathway for melanocortin signaling from the cell surface to the nucleus. Furthermore, MGRN1 interacts with and ubiquitylates TSG101, a key component of the endosomal sorting complex required for transport (ESCRT)-I, and regulates endosomal trafficking. A null mutation in the gene encoding MGRN1 causes spongiform neurodegeneration, suggesting a link between dysregulation of endosomal trafficking and spongiform neurodegeneration. MGRN1 contains a modified C3HC5-type RING-HC finger, a conserved PSAP motif necessary for interaction between MGRN1 and TSG101. In addition, MGRN1 harbors a functionally uncharacterized region, as known as the domain associated with RING2 (DAR2), N-terminal to the RING finger. The C3HC5-type RING-HC finger is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438465  Cd Length: 58  Bit Score: 40.82  E-value: 9.47e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15223228 644 DNEANYDRECIICMKDEVSVVFLPCAHQVVCGSCSDSF-FASNNggskvtCPCCR 697
Cdd:cd16816   2 DENSDNSNECVVCLSDLRDTLILPCRHLCLCNSCADTLrYQANN------CPICR 50
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
461-605 9.61e-05

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 45.22  E-value: 9.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   461 KLENQNAEIRAEREGSKLSASESLKacmEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLAQITEYEKEIE 540
Cdd:TIGR02794  47 AVAQQANRIQQQKKPAAKKEQERQK---KLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEE 123
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228   541 AKWRQ------------EQKAKEEALAQMEEEQRSKEAAEghNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKA 605
Cdd:TIGR02794 124 AKAKQaaeakakaeaeaERKAKEEAAKQAEEEAKAKAAAE--AKKKAEEAKKKAEAEAKAKAEAEAKAKAEEAKAKA 198
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
363-568 1.62e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 44.41  E-value: 1.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  363 GVDDKDCVIVD----------LLHQVKDFEKKVKERKEWAQKNAMQAAQKVSEELAELKTLSSEREGIQllKKGKQAVEE 432
Cdd:PRK09510  46 GGSVIDAVMVDpgavveqynrQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQ--EQKKQAEEA 123
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  433 STAKRFTDKEIELRKAcsqndranvivrkLENQNAEIRAEREgSKLSASESLKACMEASKKEKKClkklvAWEKQILKLQ 512
Cdd:PRK09510 124 AKQAALKQKQAEEAAA-------------KAAAAAKAKAEAE-AKRAAAAAKKAAAEAKKKAEAE-----AAKKAAAEAK 184
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228  513 DEITAE-KEKIKALYKTLAqiteyEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAE 568
Cdd:PRK09510 185 KKAEAEaAAKAAAEAKKKA-----EAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKA 236
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
371-644 1.73e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 45.06  E-value: 1.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    371 IVDLLHQVKDFEKK---VKERKEWAQKNAMQAAQKVSEELAELKTLSSER---EGIQLLKKGKQAVEestakrFTDKEIE 444
Cdd:TIGR02169  158 IIDEIAGVAEFDRKkekALEELEEVEENIERLDLIIDEKRQQLERLRRERekaERYQALLKEKREYE------GYELLKE 231
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    445 LRKACSQndranviVRKLENQNAEIRAEREGSKLSASESLKACMEASKKEKKClkklvawEKQILKL-QDEITAEKEKIK 523
Cdd:TIGR02169  232 KEALERQ-------KEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEEL-------NKKIKDLgEEEQLRVKEKIG 297
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    524 alyKTLAQITEYEKEIEAKWRQEQKAKEEaLAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRL 603
Cdd:TIGR02169  298 ---ELEAEIASLERSIAEKERELEDAEER-LAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAEL 373
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 15223228    604 KASSDsdsshiSNNAWKPK-KSQGENIAKLLEEIDKLEGSYD 644
Cdd:TIGR02169  374 EEVDK------EFAETRDElKDYREKLEKLKREINELKRELD 409
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
398-600 1.91e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 45.03  E-value: 1.91e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  398 QAAQKVSEELAELKTLSSEREgiQLLKKGKQAVEesTAKRFTDKEiELRKACSQ--NDRANVIVRKLEnQNAEIRAEREG 475
Cdd:PRK02224 475 ERVEELEAELEDLEEEVEEVE--ERLERAEDLVE--AEDRIERLE-ERREDLEEliAERRETIEEKRE-RAEELRERAAE 548
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  476 SKLSASESLKACMEASKKEKKCLKKLVAWEKQilklQDEITAEKEKIKALYKTLAQITEYEKEIEAkwRQEqkaKEEALA 555
Cdd:PRK02224 549 LEAEAEEKREAAAEAEEEAEEAREEVAELNSK----LAELKERIESLERIRTLLAAIADAEDEIER--LRE---KREALA 619
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 15223228  556 QMEEEQRSKEAAEGHNKRKLETlrlkiELD---FQRHKDDHQRLEQEL 600
Cdd:PRK02224 620 ELNDERRERLAEKRERKRELEA-----EFDearIEEAREDKERAEEYL 662
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
373-605 1.95e-04

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 44.96  E-value: 1.95e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    373 DLLHQVKDFEKKVKERKEWAQKNAMQAAQKVSEELAELKT--LSSEREGIQLLKKGKQAVEESTAK--RFTDKEIELRKA 448
Cdd:pfam02463  190 IDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEYLLYLdyLKLNEERIDLLQELLRDEQEEIESskQEIEKEEEKLAQ 269
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    449 CSQNDRANVIVRKLENQNAEIRAEREGSKLSASESLKacmeasKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKAL--- 525
Cdd:pfam02463  270 VLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLE------RRKVDDEEKLKESEKEKKKAEKELKKEKEEIEELeke 343
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    526 YKTLAQITEYEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKA 605
Cdd:pfam02463  344 LKELEIKREAEEEEEEELEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKSEEEKEAQLLLELARQLEDLLKE 423
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
416-605 2.01e-04

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 44.76  E-value: 2.01e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 416 EREGIQLLKKGKQAvEESTAKRFTDKEIELRKACSQNDRANVIVRKLENQNAEI-RAEREGSKLSAS----ESLKACMEA 490
Cdd:COG4717  52 EKEADELFKPQGRK-PELNLKELKELEEELKEAEEKEEEYAELQEELEELEEELeELEAELEELREEleklEKLLQLLPL 130
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 491 SKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLAQITEYEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAEGH 570
Cdd:COG4717 131 YQELEALEAELAELPERLEELEERLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRLAE 210
                       170       180       190
                ....*....|....*....|....*....|....*
gi 15223228 571 NKRKLETLRLKIEldfqRHKDDHQRLEQELGRLKA 605
Cdd:COG4717 211 LEEELEEAQEELE----ELEEELEQLENELEAAAL 241
mRING-HC-C3HC5_RNF157 cd16817
Modified RING finger, HC subclass (C3HC5-type), found in RING finger protein 157 (RNF157) and ...
652-697 2.06e-04

Modified RING finger, HC subclass (C3HC5-type), found in RING finger protein 157 (RNF157) and similar proteins; RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in brain. It is a homolog of the E3 ligase mahogunin ring finger-1 (MGRN1). In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis. RNF157 contains a modified C3HC5-type RING-HC finger, and a functionally uncharacterized region, known as domain associated with RING2 (DAR2), N-terminal to the RING finger. The C3HC5-type RING-HC finger is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438466 [Multi-domain]  Cd Length: 60  Bit Score: 39.69  E-value: 2.06e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15223228 652 ECIICMKDEVSVVFLPCAHQVVCGSCSDSF-FASNNggskvtCPCCR 697
Cdd:cd16817   6 ECVVCLSDVRDTLILPCRHLCLCNACADTLrYQANN------CPICR 46
mRING-HC-C3HC5_NEU1B cd16786
Modified RING finger, HC subclass (C3HC5-type), found in neuralized-like protein 1B (NEURL1B); ...
650-707 2.48e-04

Modified RING finger, HC subclass (C3HC5-type), found in neuralized-like protein 1B (NEURL1B); NEURL1B, also known as neuralized-2 (NEUR2) or neuralized-like protein 3, is a mammalian homolog of the Drosophila neuralized (D-neu) protein. It functions as an E3 ubiquitin-protein ligase that interacts with and ubiquitinates Delta. Thus, it plays a role in the endocytic pathways for Notch signaling through working cooperatively with another E3 ligase, Mind bomb-1 (Mib1), in Delta endocytosis to hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs)-positive vesicles. NEURL1B contains two neuralized homology regions (NHRs) responsible for Neural-ligand interactions and a modified C3HC5-type RING-HC finger required for ubiquitin ligase activity. The C3HC5-type RING-HC finger is distinguished from typical C3HC4-type RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438440 [Multi-domain]  Cd Length: 57  Bit Score: 39.54  E-value: 2.48e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15223228 650 DRECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNGgskvTCPCCRGLVQQRIRIF 707
Cdd:cd16786   2 NGECTVCFDSEVDTVIYTCGHMCLCNSCGLKLKRQINA----CCPICRRVIKDVIKIY 55
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
375-640 3.00e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 44.29  E-value: 3.00e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    375 LHQVKDFEKKVKERKEWAQKNAMQAAQKVSEELAELKTLSSEREGIQL-LKKGKQAVEestakrftdkEIELRKACSQND 453
Cdd:TIGR02169  725 IEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEdLHKLEEALN----------DLEARLSHSRIP 794
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    454 RANVIVRKLENQNAEIRAEREG--SKLSASESLKACMEASKKEKkclkklvawEKQILKLQDEITAEKEKIKALYKTLAQ 531
Cdd:TIGR02169  795 EIQAELSKLEEEVSRIEARLREieQKLNRLTLEKEYLEKEIQEL---------QEQRIDLKEQIKSIEKEIENLNGKKEE 865
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    532 ITEYEKEIEAKWRQeqkaKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKASSDSDS 611
Cdd:TIGR02169  866 LEEELEELEAALRD----LESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKG 941
                          250       260       270
                   ....*....|....*....|....*....|
gi 15223228    612 SHISNNAWKPKKSQ-GENIAKLLEEIDKLE 640
Cdd:TIGR02169  942 EDEEIPEEELSLEDvQAELQRVEEEIRALE 971
mRING-HC-C3HC5_CGRF1 cd16787
Modified RING finger, HC subclass (C3HC5-type), found in cell growth regulator with RING ...
651-697 4.13e-04

Modified RING finger, HC subclass (C3HC5-type), found in cell growth regulator with RING finger domain protein 1 (CGRRF1) and similar proteins; CGRRF1, also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. CGRRF1 contains a C-terminal modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438441 [Multi-domain]  Cd Length: 38  Bit Score: 38.12  E-value: 4.13e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFFAsnnggskvtCPCCR 697
Cdd:cd16787   1 KDCVVCQNAPVNRVLLPCRHACVCDECFKRLQR---------CPMCR 38
RING-HC_MIB2_rpt1 cd16726
first RING finger, HC subclass, found in mind bomb 2 (MIB2) and similar proteins; MIB2, also ...
652-678 6.20e-04

first RING finger, HC subclass, found in mind bomb 2 (MIB2) and similar proteins; MIB2, also known as novel zinc finger protein (Novelzin), putative NF-kappa-B-activating protein 002N, skeletrophin, or zinc finger ZZ type with ankyrin repeat domain protein 1, is a large, multi-domain E3 ubiquitin-protein ligase that promotes ubiquitination of the cytoplasmic tails of Notch ligands. It promotes Delta ubiquitylation and endocytosis in Notch activation. Overexpression of MIB2 activates NF-kappaB and interferon-stimulated response element (ISRE) reporter activity. Moreover, MIB2 acts as a novel component of the activated B-cell CLL/lymphoma 10 (BCL10) complex and controls BCL10-dependent NF-kappaB activation. It also functions as a founder myoblast-specific protein that regulates myoblast fusion and muscle stability. MIB2 contains an MZM region with two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region consisting of two C3HC4-type RING-HC fingers. This model corresponds to the first RING-HC finger.


Pssm-ID: 438386  Cd Length: 38  Bit Score: 37.81  E-value: 6.20e-04
                        10        20
                ....*....|....*....|....*..
gi 15223228 652 ECIICMKDEVSVVFLPCAHQVVCGSCS 678
Cdd:cd16726   2 ECLVCSELAALVRFEPCQHSIVCEECA 28
RING-HC_NEURL3 cd16552
RING finger, HC subclass, found in neuralized-like protein 3 (NEURL3) and similar proteins; ...
652-697 6.73e-04

RING finger, HC subclass, found in neuralized-like protein 3 (NEURL3) and similar proteins; NEURL3, also known as lung-inducible neuralized-related C3HC4 RING domain protein (LINCR), is a novel inflammation-induced E3 ubiquitin-protein ligase encoded by LINCR, a glucocorticoid-attenuated response gene induced in the lung during endotoxemia. It is expressed in alveolar epithelial type II cells, preferentially interacts with the ubiquitin-conjugating enzyme UbcH6, and generates polyubiquitin chains linked via non-canonical lysine residues. Overexpression of NEURL3 in the developing lung epithelium inhibits distal differentiation and induces cystic changes in the Notch signaling pathway. NEURL3 contains an N-terminal neuralized homology repeat (NHR) domain similar to the SPRY (SPla and the RYanodine receptor) domain and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438214 [Multi-domain]  Cd Length: 50  Bit Score: 37.99  E-value: 6.73e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15223228 652 ECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNnggskVTCPCCR 697
Cdd:cd16552   3 ECAICFHHTANTRLVPCGHSHFCGSCAWHIFRDT-----ARCPVCR 43
RING-HC_MYLIP cd16523
RING finger, HC subclass, found in myosin regulatory light chain interacting protein (MYLIP) ...
653-707 6.83e-04

RING finger, HC subclass, found in myosin regulatory light chain interacting protein (MYLIP) and similar proteins; MYLIP, also known as inducible degrader of the low-density lipoprotein (LDL)-receptor (IDOL), or MIR, is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of myosin regulatory light chain (MRLC), LDLR, VLDLR, and LRP8. Its activity depends on E2 ubiquitin-conjugating enzymes of the UBE2D family. MYLIP stimulates clathrin-independent endocytosis and acts as a sterol-dependent inhibitor of cellular cholesterol uptake by binding directly to the cytoplasmic tail of the LDLR and promoting its ubiquitination via the UBE2D1/E1 complex. The ubiquitinated LDLR then enters the multivesicular body (MVB) protein-sorting pathway and is shuttled to the lysosome for degradation. Moreover, MYLIP has been identified as a novel ERM-like protein that affects cytoskeleton interactions regulating cell motility, such as neurite outgrowth. The ERM proteins includes ezrin, radixin, and moesin, which are cytoskeletal effector proteins linking actin to membrane-bound proteins at the cell surface. MYLIP contains an ERM-homology domain and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438186 [Multi-domain]  Cd Length: 52  Bit Score: 37.94  E-value: 6.83e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15223228 653 CIICMKDEVSVVFLPCAHQVVCGSCSDSFFAsnnggskvtCPCCRGLVQQRIRIF 707
Cdd:cd16523   5 CMVCCEEEINSAFCPCGHMVCCESCAAQLQS---------CPVCRSRVEHVQHVY 50
RING-HC_CblA-like cd16501
RING finger, HC subclass, found in Dictyostelium discoideum Cbl-like protein A (CblA) and ...
653-707 7.49e-04

RING finger, HC subclass, found in Dictyostelium discoideum Cbl-like protein A (CblA) and similar proteins; CblA is a Dictyostelium homolog of the Cbl proteins which are multi-domain proteins acting as key negative regulators of various receptor and non-receptor tyrosine kinase signaling. CblA upregulates STATc tyrosine phosphorylation by downregulating PTP3, the protein tyrosine phosphatase responsible for dephosphorylating STATc. STATc is a signal transducer and activator of transcription protein. Like other Cbl proteins, CblA contains a tyrosine-kinase-binding domain (TKB), a proline-rich domain, a C3HC4-type RING-HC finger, and an ubiquitin-associated (UBA) domain. TKB, also known as a phosphotyrosine binding PTB domain, is composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain. This family also includes Drosophila melanogaster defense repressor 1 (Dnr1) that was identified as an inhibitor of Dredd activity in the absence of a microbial insult in Drosophila S2 cells. It inhibits the Drosophila initiator caspases Dredd and Dronc. Moreover, Dnr1 acts as a negative regulator of the Imd (immune deficiency) innate immune-response pathway. Its mutations cause neurodegeneration in Drosophila by activating the innate immune response in the brain. Dnr1 contains a FERM N-terminal domain followed by a region rich in glutamine and serine residues, a central FERM domain, and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438164 [Multi-domain]  Cd Length: 53  Bit Score: 37.85  E-value: 7.49e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15223228 653 CIICMKDEVSVVFLPCAHQVVCGSCSDSFfasnnggskVTCPCCRGLVQQRIRIF 707
Cdd:cd16501   8 CVVCMDAPIDTVFLECGHLACCRLCSKRL---------RVCPICRQPISRVVRIF 53
RING-HC_RNF170 cd16553
RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; ...
650-697 7.65e-04

RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; RNF170, also known as putative LAG1-interacting protein, is an endoplasmic reticulum (ER) membrane-bound E3 ubiquitin-protein ligase that mediates ubiquitination-dependent degradation of type-I inositol 1,4,5-trisphosphate (IP3) receptors (ITPR1) via the endoplasmic-reticulum-associated protein degradation (ERAD) pathway. A point mutation (arginine to cysteine at position 199) in the RNF170 gene is linked with autosomal-dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. RNF170 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438215 [Multi-domain]  Cd Length: 57  Bit Score: 38.04  E-value: 7.65e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15223228 650 DRECIICMKDEVSVVFLPCAHqVVCGSCSDSFFASNNGGSKVTCPCCR 697
Cdd:cd16553   1 DMECPICLQDARFPVETNCGH-LFCGPCIITYWRHGSWLGAVSCPVCR 47
PTZ00121 PTZ00121
MAEBL; Provisional
382-640 8.88e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.82  E-value: 8.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   382 EKKVKE--RKEWAQKNAMQAaqKVSEELAELKTLSSEREGIQLLKKGKQAVEESTAKRFTDkeiELRKAcSQNDRANVIV 459
Cdd:PTZ00121 1223 AKKAEAvkKAEEAKKDAEEA--KKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKAD---ELKKA-EEKKKADEAK 1296
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   460 RKLENQNAEIRAEREGSKLSASESLKACMEASKKEKKCLKKlvAWEKqilKLQDEITAEKEKIKalyKTLAQITEYEKEI 539
Cdd:PTZ00121 1297 KAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKK--AEEA---KKAAEAAKAEAEAA---ADEAEAAEEKAEA 1368
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   540 EAKWRQEQKAKEEALAQMEEEQRSKEAAEG---HNKRKLETLRLKIE----LDFQRHKDDHQRLEQELGRlKASSDSDSS 612
Cdd:PTZ00121 1369 AEKKKEEAKKKADAAKKKAEEKKKADEAKKkaeEDKKKADELKKAAAakkkADEAKKKAEEKKKADEAKK-KAEEAKKAD 1447
                         250       260
                  ....*....|....*....|....*...
gi 15223228   613 HISNNAWKPKKSqgENIAKLLEEIDKLE 640
Cdd:PTZ00121 1448 EAKKKAEEAKKA--EEAKKKAEEAKKAD 1473
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
373-605 1.04e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 42.74  E-value: 1.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    373 DLLHQVKDFEKKVKERKEWAQKN--AMQAAQKVSEEL-AELKTLSSEREGIQLLKKGKQAVEESTAKRFTDKEIELRKAC 449
Cdd:TIGR02168  751 QLSKELTELEAEIEELEERLEEAeeELAEAEAEIEELeAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLE 830
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    450 SQNDRANVIVRKLENQNAEIRAEREGSKLSASESLKACMEAskkekkclkklvawEKQILKLQDEITAEKEKIKALYKTL 529
Cdd:TIGR02168  831 RRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEEL--------------ESELEALLNERASLEEALALLRSEL 896
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    530 AQITEYEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHK-------DDHQRLEQELGR 602
Cdd:TIGR02168  897 EELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRIDNLQERLSEEYSLTLEEAEalenkieDDEEEARRRLKR 976

                   ...
gi 15223228    603 LKA 605
Cdd:TIGR02168  977 LEN 979
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
377-640 1.13e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 42.36  E-value: 1.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  377 QVKDFEKKVKERKEwAQKNAMQAAQKVSEELAELKTLSSEREGIQLLKKGKQAVEESTAKRFTDKEIELRKacsqndran 456
Cdd:PRK03918 460 ELKRIEKELKEIEE-KERKLRKELRELEKVLKKESELIKLKELAEQLKELEEKLKKYNLEELEKKAEEYEK--------- 529
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  457 vIVRKLENQNAEIRA-EREGSKLSASESLKACMEASKKEKKCLKKLVawEKQILKL----QDEITAEKEKIKALYKTLAQ 531
Cdd:PRK03918 530 -LKEKLIKLKGEIKSlKKELEKLEELKKKLAELEKKLDELEEELAEL--LKELEELgfesVEELEERLKELEPFYNEYLE 606
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  532 ITEYEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRLKASSDSDS 611
Cdd:PRK03918 607 LKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAELEELE 686
                        250       260       270
                 ....*....|....*....|....*....|.
gi 15223228  612 SHISNNA--WKPKKSQGENIAKLLEEIDKLE 640
Cdd:PRK03918 687 KRREEIKktLEKLKEELEEREKAKKELEKLE 717
RING-HC_UNKL cd16772
RING finger, HC subclass, found in RING finger protein unkempt-like (UNKL) and similar ...
651-698 1.24e-03

RING finger, HC subclass, found in RING finger protein unkempt-like (UNKL) and similar proteins; UNKL, also known as zinc finger CCCH domain-containing protein 5-like, is a putative E3 ubiquitin-protein ligase that may participate in a protein complex showing an E3 ligase activity regulated by RAC1. It shows high sequence similarity with RING finger protein unkempt (UNK), which is a metazoan-specific zinc finger protein enriched in embryonic brains, and may play a broad regulatory role during the formation of the central nervous system (CNS). UNKL contains several CCCH-type zinc fingers at the N-terminus, and a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438428  Cd Length: 44  Bit Score: 37.07  E-value: 1.24e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSdsffasnngGSKVTCPCCRG 698
Cdd:cd16772   1 KKCIVCQERDRSIVLQPCQHYVLCEHCA---------ASKPECPYCKT 39
PTZ00121 PTZ00121
MAEBL; Provisional
377-640 1.47e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.05  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   377 QVKDFEKKVKERKEWAQKNAMQAAQKVSEELAELKTLSSEREGIQLLKKGKQAVEESTAKRFTD--KEIELRKA------ 448
Cdd:PTZ00121 1123 KAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEvrKAEELRKAedarka 1202
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   449 ----CSQNDRANVIVRKLEN-QNAEIRAEREGSKLSASESLKAcmEASKKEKKCLKKLVAWEKQILKLQDEITAEkEKIK 523
Cdd:PTZ00121 1203 eaarKAEEERKAEEARKAEDaKKAEAVKKAEEAKKDAEEAKKA--EEERNNEEIRKFEEARMAHFARRQAAIKAE-EARK 1279
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   524 AlyKTLAQITEYEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQELGRL 603
Cdd:PTZ00121 1280 A--DELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAAD 1357
                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 15223228   604 KASSDSDSSHISNNAWKPKKSQGENIAKLLEEIDKLE 640
Cdd:PTZ00121 1358 EAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394
RING-HC_RGLG_plant cd16729
RING finger, HC subclass, found in RING domain ligase RGLG1, RGLG2 and similar proteins from ...
650-707 1.62e-03

RING finger, HC subclass, found in RING domain ligase RGLG1, RGLG2 and similar proteins from plant; RGLG1 is a ubiquitously expressed E3 ubiquitin-protein ligase that interacts with UBC13 and, together with UBC13, catalyzes the formation of K63-linked polyubiquitin chains, which is involved in DNA damage repair. RGLG1 mediates the formation of canonical, K48-linked polyubiquitin chains that target proteins for degradation. It also regulates apical dominance by acting on the auxin transport proteins abundance. RGLG1 has overlapping functions with its closest sequelog, RGLG2. They both function as RING E3 ligases that interact with ethylene response factor 53 (ERF53) in the nucleus and negatively regulate the plant drought stress response. Members of this subfamily contain a Von Willebrand factor type A (vWA) domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438389  Cd Length: 48  Bit Score: 37.07  E-value: 1.62e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15223228 650 DRECIICMKDEVSVVFlPCAHQVvCGSCsdsffasnnGGSKVTCPCCRGLVQQRIRIF 707
Cdd:cd16729   2 DQLCPICLSNPKDMAF-GCGHQT-CCEC---------GQSLTHCPICRQPITTRIKLY 48
mRING-HC-C3HC5_RNF26 cd16788
Modified RING finger, HC subclass (C3HC5-type), found in RING finger protein 26 (RNF26) and ...
651-707 1.98e-03

Modified RING finger, HC subclass (C3HC5-type), found in RING finger protein 26 (RNF26) and similar proteins; RNF26 is an E3 ubiquitin ligase that temporally regulates virus-triggered type I interferon induction by increasing the stability of Mediator of IRF3 activation, MITA, also known as STING, through K11-linked polyubiquitination of MITA after viral infection, and promoting the degradation of IRF3, another important component required for virus-triggered interferon induction. Although RNF26 substrates of ubiquitination remain unclear at present, RNF26 upregulation in gastric cancer might be implicated in carcinogenesis through dysregulation of growth regulators. RNF26 contains an N-terminal leucine zipper domain and a C-terminal modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438442 [Multi-domain]  Cd Length: 60  Bit Score: 37.01  E-value: 1.98e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228 651 RECIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNggSKVTCPCCRGLVQQRIRIF 707
Cdd:cd16788   6 KKCVICQDQSKTVLILPCRHMCLCRQCANILLQQPV--YRRNCPLCRTMILQTLDVY 60
mRING-HC-C4C4_Asi1p-like cd16616
Modified RING finger, HC subclass (C4C4-type), found in Saccharomyces cerevisiae amino acid ...
650-697 1.99e-03

Modified RING finger, HC subclass (C4C4-type), found in Saccharomyces cerevisiae amino acid sensor-independent protein Asi1p, Asi3p and similar proteins; Asi1p and Asi3p are inner nuclear membrane proteins that act as negative regulators of SPS (Ssy1-Ptr3-Ssy5)-sensor signaling in yeast. Together with Asi2p, they assemble into an Asi complex that functions in the SPS amino acid sensing pathway involved in degradation of Stp1 and Stp2 transcription factors. Both Asi1p and Asi3p contain five membrane-spanning domains, as well as highly conserved RING fingers at their extreme C termini, which are C4C4-type RING finger motifs whose overall folding is similar to that of the C3HC4-type RING-HC finger.


Pssm-ID: 438278  Cd Length: 53  Bit Score: 36.94  E-value: 1.99e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15223228 650 DRECIICMKDEVSVVFLPCAHQVVCGSCSDSfFASNNggsKVTCPCCR 697
Cdd:cd16616   1 DLSCVICKSNPRNIVLWPCRCLALCDDCRLS-LAMRG---FHTCVCCR 44
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
652-697 2.04e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 36.96  E-value: 2.04e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15223228 652 ECIICMKDEVSVVFLPCAHQvVCGSCSDSFFASNNGgskVTCPCCR 697
Cdd:cd16568   6 ECIICHEYLYEPMVTTCGHT-YCYTCLNTWFKSNRS---LSCPDCR 47
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
399-567 2.21e-03

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 41.09  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   399 AAQKVSEELAELKTLSSER-------------EGIQLLKKGKQAVEESTAKRFtdKEIELRKACSQNDRAnvivRKLE-- 463
Cdd:pfam15709 334 SRDRLRAERAEMRRLEVERkrreqeeqrrlqqEQLERAEKMREELELEQQRRF--EEIRLRKQRLEEERQ----RQEEee 407
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   464 -NQNAEIRAEREGSKLSASESLKACMEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIkalyktLAQITEyEKEIEAK 542
Cdd:pfam15709 408 rKQRLQLQAAQERARQQQEEFRRKLQELQRKKQQEEAERAEAEKQRQKELEMQLAEEQKR------LMEMAE-EERLEYQ 480
                         170       180
                  ....*....|....*....|....*
gi 15223228   543 wRQEQKAKEEALAQMEEEQRSKEAA 567
Cdd:pfam15709 481 -RQKQEAEEKARLEAEERRQKEEEA 504
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
392-600 2.29e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 40.90  E-value: 2.29e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 392 AQKNAMQAAQKVSEELAELKTLSSEREGIQLLKKGKQAVEESTAKRFTDKEIELRKACSQNDRANVIVRKLENQNAEIRA 471
Cdd:COG4942  18 QADAAAEAEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRA 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 472 EREGSKLSASESLKACMEASKKEK----------KCLKKLVAWEKQILK-LQDEITAEKEKIKALYKTLAQITEYEKEIE 540
Cdd:COG4942  98 ELEAQKEELAELLRALYRLGRQPPlalllspedfLDAVRRLQYLKYLAPaRREQAEELRADLAELAALRAELEAERAELE 177
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228 541 AKwRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRLKIELDFQRHKDDHQRLEQEL 600
Cdd:COG4942 178 AL-LAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEELEALIARLEAEA 236
RING-HC_CARP2 cd16707
RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein 2 (CARP-2) ...
653-707 2.48e-03

RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein 2 (CARP-2) and similar proteins; CARP-2, also known as rififylin, caspase regulator CARP2, FYVE-RING finger protein Sakura (Fring), RING finger and FYVE-like domain-containing protein 1, RING finger protein 189 (RNF189), or RING finger protein 34-like, is an endosome-associated E3 ubiquitin-protein ligase that targets internalized receptor interacting kinase (RIP) for proteasome-mediated degradation. It acts as a negative regulator of tumor necrosis factor (TNF)-induced nuclear factor (NF)-kappaB activation. It also regulates the p53 signaling pathway by degrading 14-3-3sigma and stabilizing MDM2. As a caspase regulator, CARP2 does not localize to membranes in the cell and is involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10. CARP2 contains an N-terminal FYVE-like domain and a C-terminal C3HC4-type RING-HC finger domain.


Pssm-ID: 438367 [Multi-domain]  Cd Length: 50  Bit Score: 36.49  E-value: 2.48e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15223228 653 CIICMKDEVSVVFLPCAHQVVCGSCsdsffasnnGGSKVTCPCCRGLVQQRIRIF 707
Cdd:cd16707   5 CKICMDSPIDCVLLECGHMVTCTKC---------GKRMSECPICRQYVIRAVHVF 50
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
650-703 2.59e-03

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA.


Pssm-ID: 438172 [Multi-domain]  Cd Length: 53  Bit Score: 36.51  E-value: 2.59e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15223228 650 DRECIICMKDEVSVVFLPCAHqVVCGSCSDSFFASNNGgskvTCPCCRGLVQQR 703
Cdd:cd16509   3 DEECAICLDSLTNPVITPCAH-VFCRRCICEVIQREKA----KCPMCRAPLSAS 51
RING-HC_RNF213 cd16561
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...
650-702 3.20e-03

RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; RNF213, also known as ALK lymphoma oligomerization partner on chromosome 17 or Moyamoya steno-occlusive disease-associated AAA+ and RING finger protein (mysterin), is an intracellular soluble protein that functions as an E3 ubiquitin-protein ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. It plays a unique role in endothelial cells for proper gene expression in response to inflammatory signals from the environment. Mutations in RNF213 may be associated with Moyamoya disease (MMD), an idiopathic cerebrovascular occlusive disorder prevalent in East Asia. It also acts as a nuclear marker for acanthomorph phylogeny. RNF213 contains two tandem enzymatically active AAA+ ATPase modules and a C3HC4-type RING-HC finger. It can form a huge ring-shaped oligomeric complex.


Pssm-ID: 438223 [Multi-domain]  Cd Length: 50  Bit Score: 36.10  E-value: 3.20e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15223228 650 DRECIICMKDEVSVVFLPCAHqVVCGSCSDSFFASNNggskvTCPCCRGLVQQ 702
Cdd:cd16561   2 EQECSICLEDLNDPVKLPCDH-VFCEECIRQWLPGQM-----SCPLCRTELPD 48
PTZ00121 PTZ00121
MAEBL; Provisional
384-640 3.34e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 40.89  E-value: 3.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   384 KVKERKEWAQKNAMQAAQKvSEELAELKTLSSEREGIQLLKKG--KQAVEESTAKRFTDKEI--ELRKACSQNDRANVIV 459
Cdd:PTZ00121 1346 EAAKAEAEAAADEAEAAEE-KAEAAEKKKEEAKKKADAAKKKAeeKKKADEAKKKAEEDKKKadELKKAAAAKKKADEAK 1424
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   460 RKLE--------NQNAEIRAEREGSKLSASESLKACMEASKKEKKCLKKLVAWEKQILKLQDEITAEKEKIKALYKTLAQ 531
Cdd:PTZ00121 1425 KKAEekkkadeaKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKK 1504
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   532 ITEYEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAEGHNKRK------------------LETLRlkieldfqRHKDDH 593
Cdd:PTZ00121 1505 AAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKadelkkaeelkkaeekkkAEEAK--------KAEEDK 1576
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 15223228   594 QRLEQELGRLKASSDSDSSHISNNAWKPKKSQGENIAKLLEEIDKLE 640
Cdd:PTZ00121 1577 NMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAE 1623
DUF3584 pfam12128
Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. ...
392-641 3.44e-03

Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication.


Pssm-ID: 432349 [Multi-domain]  Cd Length: 1191  Bit Score: 40.98  E-value: 3.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    392 AQKNAMQAAQKVSEELAELKTLSSEREGIQLLKKGKQAVEEstakrFTDKEIELRKACSQNDRanVIVRKLENQNAEIRA 471
Cdd:pfam12128  664 SEKDKKNKALAERKDSANERLNSLEAQLKQLDKKHQAWLEE-----QKEQKREARTEKQAYWQ--VVEGALDAQLALLKA 736
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    472 EREGSKLSASESLKACMEASKKEKKCLKKLvawEKQILKLQDEITAEKEKIKALYKTLAQITEYEKEIEAKWRQEQKAKE 551
Cdd:pfam12128  737 AIAARRSGAKAELKALETWYKRDLASLGVD---PDVIAKLKREIRTLERKIERIAVRRQEVLRYFDWYQETWLQRRPRLA 813
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228    552 EALAQMEEEQRSkeaAEGHNKRKLETLRLKI-ELDFQRHKDDHQ--RLEQELGRLKASSDS-DSSHISNNAWKPKKSQGE 627
Cdd:pfam12128  814 TQLSNIERAISE---LQQQLARLIADTKLRRaKLEMERKASEKQqvRLSENLRGLRCEMSKlATLKEDANSEQAQGSIGE 890
                          250
                   ....*....|....
gi 15223228    628 NIAKLLEEIDKLEG 641
Cdd:pfam12128  891 RLAQLEDLKLKRDY 904
CALCOCO1 pfam07888
Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are ...
428-604 4.04e-03

Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.


Pssm-ID: 462303 [Multi-domain]  Cd Length: 488  Bit Score: 40.26  E-value: 4.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   428 QAVEESTAKRFTDKEIELRKACSQNDRanviVRKLENQNAEIRAEREGSKLSASEslkacMEASKKEKKCLKKLVAWEKQ 507
Cdd:pfam07888  48 QAQEAANRQREKEKERYKRDREQWERQ----RRELESRVAELKEELRQSREKHEE-----LEEKYKELSASSEELSEEKD 118
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228   508 ILKLQDEitAEKEKIKALYKTLAQITEYEKEIEAKWRQEQKAKEEALAQMEEEQRSKEAAEGHNKRKLETLRlKIELDFQ 587
Cdd:pfam07888 119 ALLAQRA--AHEARIRELEEDIKTLTQRVLERETELERMKERAKKAGAQRKEEEAERKQLQAKLQQTEEELR-SLSKEFQ 195
                         170
                  ....*....|....*..
gi 15223228   588 RHKDDHQRLEQELGRLK 604
Cdd:pfam07888 196 ELRNSLAQRDTQVLQLQ 212
RING-HC_SPL2-like cd23145
RING finger, HC subclass, found in Arabidopsis thaliana SP1-like protein 2 (SPL2) and similar ...
653-697 4.25e-03

RING finger, HC subclass, found in Arabidopsis thaliana SP1-like protein 2 (SPL2) and similar proteins; SPL2, also known as RING-type E3 ubiquitin transferase SPL2, acts as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. SPL2 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438507 [Multi-domain]  Cd Length: 47  Bit Score: 35.64  E-value: 4.25e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 15223228 653 CIICMKDEVSVVFLPCAHQVVCGSCSDSFFASNNGgskvTCPCCR 697
Cdd:cd23145   6 CVVCLLRRRRVAFIECGHRVCCELCARRVTREANP----RCPVCR 46
RING-HC_ULS1-like cd23136
RING finger, HC subclass, found in Saccharomyces cerevisiae ubiquitin ligase for SUMO ...
653-700 5.07e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae ubiquitin ligase for SUMO conjugates protein 1 (ULS1) and similar proteins; ULS1, also called role in silencing protein 1, is an ATP-dependent helicase involved in mating type switching and in silencing interference through its interaction with the silencing regulator SIR4. It cooperates with UBC4 and UBC5 to mediate ubiquitination of SUMO conjugates. ULS1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438498 [Multi-domain]  Cd Length: 76  Bit Score: 36.52  E-value: 5.07e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15223228 653 CIICMK---DEVSVVFLPCAHqVVCGSCSDSFFASN------NGGSKVTCPCCRGLV 700
Cdd:cd23136   7 CPVCFDvvgEESIVILAGCGH-MICDGCVENFFEEQreekegTGNRSAPCLTCKKLV 62
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
505-605 5.40e-03

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 39.79  E-value: 5.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223228  505 EKQILKLQDEITAEKEKIKALYKtlaqitEYEKEIEAKWRQEQKAKEEALAQME-EEQRSKEAAEGHNKRKLETLRLkiE 583
Cdd:PRK09510  86 QQQAEELQQKQAAEQERLKQLEK------ERLAAQEQKKQAEEAAKQAALKQKQaEEAAAKAAAAAKAKAEAEAKRA--A 157
                         90       100
                 ....*....|....*....|..
gi 15223228  584 LDFQRHKDDHQRLEQELGRLKA 605
Cdd:PRK09510 158 AAAKKAAAEAKKKAEAEAAKKA 179
RING-HC_CARP1 cd16706
RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein 1 (CARP1) ...
650-707 5.56e-03

RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein 1 (CARP1) and similar proteins; CARP1, also known as caspase regulator CARP1, FYVE-RING finger protein Momo, RING finger homologous to inhibitor of apoptosis protein (RFI), RING finger protein 34 (RNF34), or RING finger protein RIFF, is a nuclear protein that functions as a specific E3 ubiquitin ligase for the transcriptional coactivator PGC-1alpha, a master regulator of energy metabolism and adaptive thermogenesis in the brown fat cell which negatively regulates brown fat cell metabolism. It is preferentially expressed in esophageal, gastric, and colorectal cancers, suggesting a possible association with the development of digestive tract cancers. It regulates the p53 signaling pathway by degrading 14-3-3 sigma and stabilizing MDM2. CARP1 does not localize to membranes in the cell and is involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10. CARP1 contains an N-terminal FYVE-like domain and a C-terminal C3HC4-type RING-HC finger domain.


Pssm-ID: 438366 [Multi-domain]  Cd Length: 54  Bit Score: 35.77  E-value: 5.56e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15223228 650 DRECIICMKDEVSVVFLPCAHQVVCGSCsdsffasnnGGSKVTCPCCRGLVQQRIRIF 707
Cdd:cd16706   4 DNLCRICMDAVIDCVLLECGHMVTCTKC---------GKRMSECPICRQYVVRAVHVF 52
RING-HC_MIB2_rpt2 cd16728
second RING finger, HC subclass, found in mind bomb 2 (MIB2) and similar proteins; MIB2, also ...
653-707 6.57e-03

second RING finger, HC subclass, found in mind bomb 2 (MIB2) and similar proteins; MIB2, also known as novel zinc finger protein (Novelzin), putative NF-kappa-B-activating protein 002N, skeletrophin, or zinc finger ZZ type with ankyrin repeat domain protein 1, is a large, multi-domain E3 ubiquitin-protein ligase that promotes ubiquitination of the cytoplasmic tails of Notch ligands. Especially, it promotes Delta ubiquitylation and endocytosis in Notch activation. Overexpression of MIB2, activates NF-kappaB and interferon-stimulated response element (ISRE) reporter activity. Moreover, MIB2 acts as a novel component of the activated B-cell CLL/lymphoma 10 (BCL10) complex and controls BCL10-dependent NF-kappaB activation. It also functions as a founder myoblast-specific protein that regulates myoblast fusion and muscle stability. MIB2 contains an MZM region with two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region consisting of two C3HC4-type RING-HC fingers. This model corresponds to the second RING-HC finger.


Pssm-ID: 438388  Cd Length: 51  Bit Score: 35.22  E-value: 6.57e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15223228 653 CIICMKDEVSVVFlPCAHqvvcGSCSDSffasnnGGSKVTCPCCRGLVQQRIRIF 707
Cdd:cd16728   7 CPICIDNHIKLVF-QCGH----GSCIEC------SSALKACPICRQAIRERIQIF 50
RING-HC_RNF168 cd16550
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...
653-697 8.02e-03

RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates, such as H2A and H2AX with H2AK13/15 ubiquitylation, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. Moreover, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for the interaction with K63 linked poly-ubiquitin.


Pssm-ID: 438212 [Multi-domain]  Cd Length: 48  Bit Score: 35.04  E-value: 8.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 15223228 653 CIICMKDEVSVVFLPCAHQvVCGSCsdsfFASNNGGSKVTCPCCR 697
Cdd:cd16550   3 CPICLEILVEPVTLPCNHT-LCMPC----FQSTVEKASLCCPLCR 42
 
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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