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Conserved domains on  [gi|2462578331|ref|XP_054200430|]
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cyclin-T2 isoform X4 [Homo sapiens]

Protein Classification

cyclin family protein( domain architecture ID 1750054)

cyclin family protein may associate with and activate its cognate cyclin-dependent kinase (CDK)

CATH:  1.10.472.10
Gene Ontology:  GO:0000079|GO:0019901|GO:0007049
PubMed:  14744433|30185601|15269391|15840440
SCOP:  4001102

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 1-88 3.85e-57

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


The actual alignment was detected with superfamily member cd20598:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 114  Bit Score: 186.82  E-value: 3.85e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578331   1 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIR 80
Cdd:cd20598    27 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPSRLKRIR 106


                  ....*...
gi 2462578331  81 NWRANQAA 88
Cdd:cd20598   107 NWRANQAA 114
ROM1 super family cl34999
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
 121-252 1.58e-03

RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG5422:

Pssm-ID: 227709 [Multi-domain]  Cd Length: 1175  Bit Score: 41.42  E-value: 1.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578331  121 PTNPSFQK-PST------SAFPAPVPLNS-GNISVQDSHTSDNLSMLATGMPSTSYGLSSHQEWPQH--QDSARTEQLYS 190
Cdd:COG5422    115 PASDSLSFnPSStqsrkdSGPGDGSPVQKrKNPLLPSSSTHGTHPPIVFTDNNGSHAGAPNARSRKEipSLGSQSMQLPS 194

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462578331  191 QKQETSLSGSQYNiNFQQGPSISLHSGLHHRPDKISDHSSVKQEYTHKAGSS-KHHGPISTTP 252
Cdd:COG5422    195 PHFRQKFSSSDTS-NGFSYPSIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSgASLISSNITP 256
 
Name Accession Description Interval E-value
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 1-88 3.85e-57

second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II). CCNT2 contains two cyclin boxs. The model responds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410301 [Multi-domain]  Cd Length: 114  Bit Score: 186.82  E-value: 3.85e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578331   1 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIR 80
Cdd:cd20598    27 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPSRLKRIR 106


                  ....*...
gi 2462578331  81 NWRANQAA 88
Cdd:cd20598   107 NWRANQAA 114
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
 121-252 1.58e-03

RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms];


Pssm-ID: 227709 [Multi-domain]  Cd Length: 1175  Bit Score: 41.42  E-value: 1.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578331  121 PTNPSFQK-PST------SAFPAPVPLNS-GNISVQDSHTSDNLSMLATGMPSTSYGLSSHQEWPQH--QDSARTEQLYS 190
Cdd:COG5422    115 PASDSLSFnPSStqsrkdSGPGDGSPVQKrKNPLLPSSSTHGTHPPIVFTDNNGSHAGAPNARSRKEipSLGSQSMQLPS 194

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462578331  191 QKQETSLSGSQYNiNFQQGPSISLHSGLHHRPDKISDHSSVKQEYTHKAGSS-KHHGPISTTP 252
Cdd:COG5422    195 PHFRQKFSSSDTS-NGFSYPSIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSgASLISSNITP 256
 
Name Accession Description Interval E-value
CYCLIN_CCNT2_rpt2 cd20598
second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory ...
 1-88 3.85e-57

second cyclin box found in cyclin-T2 (CCNT2); CCNT2, also termed CycT2, is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II). CCNT2 contains two cyclin boxs. The model responds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410301 [Multi-domain]  Cd Length: 114  Bit Score: 186.82  E-value: 3.85e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578331   1 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIR 80
Cdd:cd20598    27 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPSRLKRIR 106


                  ....*...
gi 2462578331  81 NWRANQAA 88
Cdd:cd20598   107 NWRANQAA 114
CYCLIN_CCNT1_rpt2 cd20597
second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor ...
 1-83 1.46e-50

second cyclin box found in cyclin-T1 (CCNT1); CCNT1, also termed CycT1, is a host factor essential for HIV-1 replication in CD4 T cells and macrophages. It is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin-T1) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). CCNT1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410300 [Multi-domain]  Cd Length: 109  Bit Score: 169.10  E-value: 1.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578331   1 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIR 80
Cdd:cd20597    27 MATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIW 106


                  ...
gi 2462578331  81 NWR 83
Cdd:cd20597   107 NWR 109
CYCLIN_CCNT_rpt2 cd20539
second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, ...
 1-66 2.00e-39

second cyclin box found in cyclin-T (CCNT) family; The CCNT family includes two C-type cyclins, cyclin-T1 (CCNT1) and cyclin-T2 (CCNT2), both of which are regulatory subunits of the cyclin-dependent kinase pair (CDK9/cyclin-T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410242 [Multi-domain]  Cd Length: 92  Bit Score: 138.56  E-value: 2.00e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462578331   1 MATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFL 66
Cdd:cd20539    27 LATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPRSSEGKDWYEYVDPSLTLEELDELTSEFL 92
CYCLIN_CCNK_rpt2 cd20531
second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA ...
 9-70 1.80e-13

second cyclin box found in cyclin-K (CCNK) and similar proteins; CCNK is a novel RNA polymerase II-associated C-type cyclin possessing both carboxy-terminal domain kinase and Cdk-activating kinase activity. It is a regulatory subunit of cyclin-dependent kinases that mediates the activation of these target kinases. It plays a role in transcriptional regulation by controlling the phosphorylation of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A). CCNK contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410234 [Multi-domain]  Cd Length: 101  Bit Score: 66.59  E-value: 1.80e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462578331   9 TTFCLQYKPTVIACVCIHLACKWSNWEIP---VSTDGKHWWEYVDPTVTLELLDELTHeflQILE 70
Cdd:cd20531    38 TTLCLQWEPEIIAVALMYLAAKLSKFDLQdwtSKPPGKRWWEQFVEDVSLEVLEDICH---QVLD 99
CYCLIN_AcCycT_rpt2 cd20588
second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; ...
 9-70 2.96e-08

second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins; CycTs associate with their partner cyclin-dependent kinases (CDKs) to trigger their kinase activity. CycTs show high sequence similarity with metazoan cyclin-K (CCNK). CycTs contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410291 [Multi-domain]  Cd Length: 93  Bit Score: 51.38  E-value: 2.96e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462578331   9 TTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDgKHWWEYVDptVTLELLDELTHEFLQILE 70
Cdd:cd20588    35 TSLCLQFKPHHIAAGAIFLAAKFLKVKLPCDGR-KVWWQEFD--VTPRQLEEVSNQMLELYE 93
CYCLIN_CCNM_CCNQ_rpt2 cd20535
second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ...
 7-68 1.47e-07

second cyclin box found in cyclin-M (CCNM) family; The CCNM family proteins, also called ancient conserved domain proteins (ACDPs), are evolutionarily conserved Mg2+ transporters. CCNM, also called cyclin-Q (CCNQ), or CDK10-activating cyclin, or cyclin-related protein FAM58A, associates with CDK10 to promote its kinase activity. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410238 [Multi-domain]  Cd Length: 104  Bit Score: 49.56  E-value: 1.47e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462578331   7 HLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDG-KHWWEYVDPTVTLELLDELTHEFLQI 68
Cdd:cd20535    39 YHSPLCLQFKPQHIALAVIYLALQVYGVKVPPEEEAeKPWWQAFCEDLTKETIDEIIEDIINV 101
CYCLIN_SpCG1C_ScCTK2-like_rpt2 cd20546
second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces ...
 7-67 2.98e-07

second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2), and similar proteins; Cyclin pch1 is essential for progression through the whole cell cycle. It is a homolog of cyclin T; it forms a heterodimer with its partner kinase, cyclin-dependent kinase 9 (CDK9), that can phosphorylate both the pol II C-terminal domain (CTD) and the CTD of transcription elongation factor Spt5. Yeast Cdk9/Pch1, with mRNA capping enzyme Pct1, may also form an elongation checkpoint for mRNA quality control. CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. This group also includes yeast RNA polymerase II holoenzyme cyclin-like subunit, a component of the SRB8-11 complex, a regulatory module of the Mediator complex which is involved in regulation of basal and activated RNA polymerase II-dependent transcription. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410249 [Multi-domain]  Cd Length: 97  Bit Score: 48.52  E-value: 2.98e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462578331   7 HLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKH--WWEYVDptVTLELLDELTHEFLQ 67
Cdd:cd20546    33 YRTPLCLLYPPHVIAAAAIYLAAKLLGIDLELSPNEKLneWWELFG--VDEEEIADAINEILD 93
CYCLIN_CCNL_rpt2 cd20533
second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 ...
 4-70 4.63e-07

second cyclin box found in cyclin-L (CCNL) family; The CCNL family includes two cyclins, CCNL1 and CCNL2. CCNL1 is involved in regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL2 is a novel RNA polymerase II-associated cyclin involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.


Pssm-ID: 410236 [Multi-domain]  Cd Length: 92  Bit Score: 47.98  E-value: 4.63e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462578331   4 NSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPvstDGKHWWEYVDptVTLELLDELThefLQILE 70
Cdd:cd20533    30 NDSLRTDLCVRYPPEVIACACIYLAARELGIPLP---LPPPWWELFD--VSKEDIEEIC---LTILE 88
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
 121-252 1.58e-03

RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms];


Pssm-ID: 227709 [Multi-domain]  Cd Length: 1175  Bit Score: 41.42  E-value: 1.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578331  121 PTNPSFQK-PST------SAFPAPVPLNS-GNISVQDSHTSDNLSMLATGMPSTSYGLSSHQEWPQH--QDSARTEQLYS 190
Cdd:COG5422    115 PASDSLSFnPSStqsrkdSGPGDGSPVQKrKNPLLPSSSTHGTHPPIVFTDNNGSHAGAPNARSRKEipSLGSQSMQLPS 194

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462578331  191 QKQETSLSGSQYNiNFQQGPSISLHSGLHHRPDKISDHSSVKQEYTHKAGSS-KHHGPISTTP 252
Cdd:COG5422    195 PHFRQKFSSSDTS-NGFSYPSIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSgASLISSNITP 256
 
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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