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Conserved domains on  [gi|359385725|ref|NP_001240721|]
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zinc finger protein 444 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 21-98 4.85e-40

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


:

Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 135.69  E-value: 4.85e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 359385725   21 HRFRRFHLGDAPGPREALGLLRALCRDWLRPEVHTKEQMLELLVLEQFLSALPADTQAWVCSRQPQSGEEAVALLEEL 98
Cdd:pfam02023   6 QRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAEDL 83
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
178-279 2.51e-06

FOG: Zn-finger [General function prediction only];


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 48.92  E-value: 2.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725 178 TSCPECGKTSLKPAHLLRHRQSHSGE-------KPHACPECGKAFRRKEHLRRHRDT--HPGSPgspgpalrplparEKP 248
Cdd:COG5048  255 SSASESPRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGES-------------LKP 321

                         90       100       110
                 ....*....|....*....|....*....|...
gi 359385725 249 HACCE--CGKTFYWREHLVRHRKTHSGARPFAC 279
Cdd:COG5048  322 FSCPYslCGKLFSRNDALKRHILLHTSISPAKE 354
KREPA super family cl49620
Kinetoplastid RNA Editing Protein A (KREPA); The KREPA 1-6 (TbMP81, 63, 42, 24, 19, and 18, ...
 122-225 2.19e-05

Kinetoplastid RNA Editing Protein A (KREPA); The KREPA 1-6 (TbMP81, 63, 42, 24, 19, and 18, respectively) proteins are components of the RNA editing complex of parasitic protozoans such as Trypanosoma and Leishmania species. These parasites have a uniquely organized mitochondrial genome, the kinetoplast. Most kinetoplast-transcribed mRNAs are cryptic and encode multiple subunits for the electron transport chain following maturation through a uridine insertion/deletion process called RNA editing. KREPAs participate in the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. The editosome, a high molecular mass enzyme complex, carries out the reaction with the help of critical enzymes and structural proteins. Five related editosome proteins KREPA1 (TbMP81), KREPA2 (TbMP63), KREPA3 (TbMP42), KREPA4 (TbMP24), KREPA5 (TbMP19), and KREPA6 (TbMP18) play critical roles in the structure and auxiliary functions of the editing process without any predicted catalytic function. The KREPA1, KREPA2, and KREPA3 proteins contain C2H2 zinc finger motifs and KREPA4 and KREPA6, contain RNA-binding domains but all have a conserved C-terminal sequences that resemble an oligonucleotide-binding (OB)-fold domain. Thus, this group of five proteins is likely to be involved in protein-protein and/or protein-RNA interactions. RNA editing is crucial for the parasite's survival in both its bloodstream and procyclic form life cycle stages which allows the parasite to adapt to its environment and maintain its viability.


The actual alignment was detected with superfamily member cd23959:

Pssm-ID: 483960 [Multi-domain]  Cd Length: 424  Bit Score: 45.63  E-value: 2.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725 122 GATGGKEDSGMIPLGTAPGAEGPAPGDSQAVrpykqEPSSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHllrhRQSHS 201
Cdd:cd23959  171 AAQQSSASPGEVASPFASGTVSASPFATATD-----TAPSSGAPDGFPAEASAPSPFAAPASAASFPAAPV----ANGEA 241

                         90       100
                 ....*....|....*....|....
gi 359385725 202 GEKPHACPECGKAFRRKEHLRRHR 225
Cdd:cd23959  242 ATPTHACTICGKAFSTHEGLRMHS 265
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 277-299 5.80e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


:

Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 33.81  E-value: 5.80e-03
                          10        20
                  ....*....|....*....|...
gi 359385725  277 FACWECGKGFGRREHVLRHQRIH 299
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 21-98 4.85e-40

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 135.69  E-value: 4.85e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 359385725   21 HRFRRFHLGDAPGPREALGLLRALCRDWLRPEVHTKEQMLELLVLEQFLSALPADTQAWVCSRQPQSGEEAVALLEEL 98
Cdd:pfam02023   6 QRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAEDL 83
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 16-99 4.58e-38

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.


Pssm-ID: 153421  Cd Length: 85  Bit Score: 130.46  E-value: 4.58e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725  16 LDSPWHRFRRFHLGDAPGPREALGLLRALCRDWLRPEVHTKEQMLELLVLEQFLSALPADTQAWVCSRQPQSGEEAVALL 95
Cdd:cd07936    1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80


                 ....
gi 359385725  96 EELW 99
Cdd:cd07936   81 EDLL 84
SCAN smart00431
leucine rich region;
22-117 1.58e-36

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 127.42  E-value: 1.58e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725    22 RFRRFHLGDAPGPREALGLLRALCRDWLRPEVHTKEQMLELLVLEQFLSALPADTQAWVCSRQPQSGEEAVALLEEL-WG 100
Cdd:smart00431   7 RFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLLEDLeRE 86

                           90
                   ....*....|....*..
gi 359385725   101 PAASPDGSSATRVPQDV 117
Cdd:smart00431  87 LDEPGQQVSAHVHGQEV 103
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
178-279 2.51e-06

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 48.92  E-value: 2.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725 178 TSCPECGKTSLKPAHLLRHRQSHSGE-------KPHACPECGKAFRRKEHLRRHRDT--HPGSPgspgpalrplparEKP 248
Cdd:COG5048  255 SSASESPRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGES-------------LKP 321

                         90       100       110
                 ....*....|....*....|....*....|...
gi 359385725 249 HACCE--CGKTFYWREHLVRHRKTHSGARPFAC 279
Cdd:COG5048  322 FSCPYslCGKLFSRNDALKRHILLHTSISPAKE 354
zf-H2C2_2 pfam13465
Zinc-finger double domain;
192-217 6.31e-06

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 42.36  E-value: 6.31e-06
                          10        20
                  ....*....|....*....|....*.
gi 359385725  192 HLLRHRQSHSGEKPHACPECGKAFRR 217
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 122-225 2.19e-05

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 45.63  E-value: 2.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725 122 GATGGKEDSGMIPLGTAPGAEGPAPGDSQAVrpykqEPSSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHllrhRQSHS 201
Cdd:cd23959  171 AAQQSSASPGEVASPFASGTVSASPFATATD-----TAPSSGAPDGFPAEASAPSPFAAPASAASFPAAPV----ANGEA 241

                         90       100
                 ....*....|....*....|....
gi 359385725 202 GEKPHACPECGKAFRRKEHLRRHR 225
Cdd:cd23959  242 ATPTHACTICGKAFSTHEGLRMHS 265
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 60-181 1.69e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 40.05  E-value: 1.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725  60 LELLVLEqfLSALPADTQawVCSRQPQSGEEAVALLEELWGPAASPDGSsatrVPQDVTQGPGATGGKedSGMIPLGTAP 139
Cdd:PRK14959 352 LELLLLN--LAMLPRLMP--VESLRPSGGGASAPSGSAAEGPASGGAAT----IPTPGTQGPQGTAPA--AGMTPSSAAP 421

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 359385725 140 GAEGPAPGDSQAVrPYKQEPSSPPLApGLPAFLAA--PGTTSCP 181
Cdd:PRK14959 422 ATPAPSAAPSPRV-PWDDAPPAPPRS-GIPPRPAPrmPEASPVP 463
ZnF_C2H2 smart00355
zinc finger;
206-228 4.88e-03

zinc finger;


Pssm-ID: 197676  Cd Length: 23  Bit Score: 33.98  E-value: 4.88e-03
                           10        20
                   ....*....|....*....|...
gi 359385725   206 HACPECGKAFRRKEHLRRHRDTH 228
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 277-299 5.80e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 33.81  E-value: 5.80e-03
                          10        20
                  ....*....|....*....|...
gi 359385725  277 FACWECGKGFGRREHVLRHQRIH 299
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
 110-248 5.98e-03

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 38.06  E-value: 5.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725  110 ATRVPQDVTQGPGATGGKEDSGMIPLGTAPGAEGPAPGDSQAVRPYKQEPSSpplapglpafLAAPGTTSCPECGKTSlk 189
Cdd:TIGR00599  98 FLRIPKTTPVENPDLAGPENSSKIELIEESESDGVDAEDEDLQRSATSSRAL----------AARSTADILQLSSDPS-- 165

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 359385725  190 PAHLLRHRQSHSGEKPHACPECGKAFRRKEHLRRHRDTHPGSPGSPGPALRPLPAREKP 248
Cdd:TIGR00599 166 KRNDADYRSEPPNEGLVQCPICQQRMPEKAVERHLDSECLGSPSLGASTTFPTESNPHN 224
 
Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 21-98 4.85e-40

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 135.69  E-value: 4.85e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 359385725   21 HRFRRFHLGDAPGPREALGLLRALCRDWLRPEVHTKEQMLELLVLEQFLSALPADTQAWVCSRQPQSGEEAVALLEEL 98
Cdd:pfam02023   6 QRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAEDL 83
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 16-99 4.58e-38

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.


Pssm-ID: 153421  Cd Length: 85  Bit Score: 130.46  E-value: 4.58e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725  16 LDSPWHRFRRFHLGDAPGPREALGLLRALCRDWLRPEVHTKEQMLELLVLEQFLSALPADTQAWVCSRQPQSGEEAVALL 95
Cdd:cd07936    1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80


                 ....
gi 359385725  96 EELW 99
Cdd:cd07936   81 EDLL 84
SCAN smart00431
leucine rich region;
22-117 1.58e-36

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 127.42  E-value: 1.58e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725    22 RFRRFHLGDAPGPREALGLLRALCRDWLRPEVHTKEQMLELLVLEQFLSALPADTQAWVCSRQPQSGEEAVALLEEL-WG 100
Cdd:smart00431   7 RFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLLEDLeRE 86

                           90
                   ....*....|....*..
gi 359385725   101 PAASPDGSSATRVPQDV 117
Cdd:smart00431  87 LDEPGQQVSAHVHGQEV 103
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
178-279 2.51e-06

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 48.92  E-value: 2.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725 178 TSCPECGKTSLKPAHLLRHRQSHSGE-------KPHACPECGKAFRRKEHLRRHRDT--HPGSPgspgpalrplparEKP 248
Cdd:COG5048  255 SSASESPRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGES-------------LKP 321

                         90       100       110
                 ....*....|....*....|....*....|...
gi 359385725 249 HACCE--CGKTFYWREHLVRHRKTHSGARPFAC 279
Cdd:COG5048  322 FSCPYslCGKLFSRNDALKRHILLHTSISPAKE 354
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
160-232 4.44e-06

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 48.15  E-value: 4.44e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 359385725 160 SSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHLLRHRQSHSGEKPHAC--PECGKAFRRKEHLRRHRDTHPGSP 232
Cdd:COG5048   16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNP 90
zf-H2C2_2 pfam13465
Zinc-finger double domain;
192-217 6.31e-06

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 42.36  E-value: 6.31e-06
                          10        20
                  ....*....|....*....|....*.
gi 359385725  192 HLLRHRQSHSGEKPHACPECGKAFRR 217
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 122-225 2.19e-05

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 45.63  E-value: 2.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725 122 GATGGKEDSGMIPLGTAPGAEGPAPGDSQAVrpykqEPSSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHllrhRQSHS 201
Cdd:cd23959  171 AAQQSSASPGEVASPFASGTVSASPFATATD-----TAPSSGAPDGFPAEASAPSPFAAPASAASFPAAPV----ANGEA 241

                         90       100
                 ....*....|....*....|....
gi 359385725 202 GEKPHACPECGKAFRRKEHLRRHR 225
Cdd:cd23959  242 ATPTHACTICGKAFSTHEGLRMHS 265
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 206-228 3.58e-05

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 39.98  E-value: 3.58e-05
                          10        20
                  ....*....|....*....|...
gi 359385725  206 HACPECGKAFRRKEHLRRHRDTH 228
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 147-272 2.44e-04

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 42.40  E-value: 2.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725 147 GDSQAVR--PYKQEPSSPPLAPGLPAFLAAPGTtscpecgktslkpahllrhRQSHSGEKPHACP--ECGKAFRRKEHLR 222
Cdd:COG5189  308 GEMIDVRklPCTNSSSNGKLAHGGERNIDTPSR-------------------MLKVKDGKPYKCPveGCNKKYKNQNGLK 368

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 359385725 223 RHR-DTHPGSPGSPGPALRP---LPAREKPHACCECGKTFYWREHLVRHRKtHS 272
Cdd:COG5189  369 YHMlHGHQNQKLHENPSPEKmniFSAKDKPYRCEVCDKRYKNLNGLKYHRK-HS 421
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 60-181 1.69e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 40.05  E-value: 1.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725  60 LELLVLEqfLSALPADTQawVCSRQPQSGEEAVALLEELWGPAASPDGSsatrVPQDVTQGPGATGGKedSGMIPLGTAP 139
Cdd:PRK14959 352 LELLLLN--LAMLPRLMP--VESLRPSGGGASAPSGSAAEGPASGGAAT----IPTPGTQGPQGTAPA--AGMTPSSAAP 421

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 359385725 140 GAEGPAPGDSQAVrPYKQEPSSPPLApGLPAFLAA--PGTTSCP 181
Cdd:PRK14959 422 ATPAPSAAPSPRV-PWDDAPPAPPRS-GIPPRPAPrmPEASPVP 463
ZnF_C2H2 smart00355
zinc finger;
206-228 4.88e-03

zinc finger;


Pssm-ID: 197676  Cd Length: 23  Bit Score: 33.98  E-value: 4.88e-03
                           10        20
                   ....*....|....*....|...
gi 359385725   206 HACPECGKAFRRKEHLRRHRDTH 228
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 277-299 5.80e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 33.81  E-value: 5.80e-03
                          10        20
                  ....*....|....*....|...
gi 359385725  277 FACWECGKGFGRREHVLRHQRIH 299
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
 110-248 5.98e-03

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 38.06  E-value: 5.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359385725  110 ATRVPQDVTQGPGATGGKEDSGMIPLGTAPGAEGPAPGDSQAVRPYKQEPSSpplapglpafLAAPGTTSCPECGKTSlk 189
Cdd:TIGR00599  98 FLRIPKTTPVENPDLAGPENSSKIELIEESESDGVDAEDEDLQRSATSSRAL----------AARSTADILQLSSDPS-- 165

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 359385725  190 PAHLLRHRQSHSGEKPHACPECGKAFRRKEHLRRHRDTHPGSPGSPGPALRPLPAREKP 248
Cdd:TIGR00599 166 KRNDADYRSEPPNEGLVQCPICQQRMPEKAVERHLDSECLGSPSLGASTTFPTESNPHN 224
 
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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