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Conserved domains on  [gi|42562972|ref|NP_176723|]
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global transcription factor group B1 [Arabidopsis thaliana]

Protein Classification

DLD and SH2_Cterm_SPT6_like domain-containing protein( domain architecture ID 13863247)

protein containing domains YqgFc, DLD, SH2_Nterm_SPT6_like, and SH2_Cterm_SPT6_like

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1204-1408 1.28e-94

SH2 domain;


:

Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 304.07  E-value: 1.28e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972   1204 KEKARKEKELVRKHFKSRMIVHPRFQNITADQATEYLSDKDFGESIVRPSSRGLNFLTLTLKIYDGVYAHKEIAEGGKEN 1283
Cdd:pfam14633    5 EELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELDKEN 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972   1284 KditslQCIGKTLTIGEDTFEDLDEVMDRYVDPLVSHLKTMLNYRKFRKGTKSEVDDLLRIEKGENPSRIVYCFGISHEH 1363
Cdd:pfam14633   85 E-----FSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKDGTKEEVEEWLREEKKANPKRSPYAFCLSHKH 159

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 42562972   1364 PGTFILSYIRSTNP--HHEYIGLYPKGFKFRKRMFEDIDRLVAYFQR 1408
Cdd:pfam14633  160 PGYFLLSFKANKNSrvHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
Tex super family cl34417
Transcriptional accessory protein Tex/SPT6 [Transcription];
340-1020 3.80e-28

Transcriptional accessory protein Tex/SPT6 [Transcription];


The actual alignment was detected with superfamily member COG2183:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 122.83  E-value: 3.80e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  340 IPFIAMYRKEQcrslldTGDFDganqgkkpETKwhkvfwmIHDLDKKWLLLRkrkmalhgyytkryEEESRRvydetrln 419
Cdd:COG2183   33 VPFIARYRKEA------TGGLD--------EVQ-------LRTIEERLTYLR--------------ELEKRR-------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  420 lnqylfESVIKSLK--------------VAETEREVDDvdskfnLHFPpgeigvdegqYKrPKRKSQYSICSKAGLweva 485
Cdd:COG2183   70 ------ETILKSIEeqgkltpelkakieAADTKQELED------LYLP----------YK-PKRRTKATIAREKGL---- 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  486 nkfgysaEQLGLALsleklvdeLEDAKETPEEMAKNFVCAM--FENSLAVLKGARHMAAVEISCEPSVKKYVRGIYMENA 563
Cdd:COG2183  123 -------EPLADLL--------LAQPTGDPEAEAAKYINEEkgVADVEAALDGARDILAERISEDAELRGKLRELLWKEG 187

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  564 VVSTSPTA---DGNTVIDSFHQFSgikwlreKPLSKFEGAQWLLIQKGEEEKLLQVTFKLPENYMNRLIsdcNEHYlsvg 640
Cdd:COG2183  188 VLVSKVKKgkeEEGAKFRDYFDYS-------EPLKKIPSHRILALNRGEKEGVLKVKLEPDEEEAEAYI---ARRF---- 253

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  641 VSKYAQLWNEQRKLILEDALHAFLLPSMEKEARSLLTSRAksrllseygqalwnkvsagpyqkkemdinlDEEA------ 714
Cdd:COG2183  254 IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKA------------------------------EEEAikvfae 303

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  715 --------AP----RVMAccWGPGkppntF------VMLDSSGEVLD--VLY--AGsltsrsQNvndqQRKKSdQDRVLK 772
Cdd:COG2183  304 nlrdlllaAPaggkVVLG--LDPG-----FrtgckvAVVDETGKLLDtaTIYphPP------QN----KWEEA-AKTLAA 365

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  773 FMMDHQPHVVALGavNLSCTRLKDdiyEVIFQMVEEKPRDVghgmddlSIVYVDESLPRLYENSRISGEQLPQQSGNVRR 852
Cdd:COG2183  366 LIKKYKVELIAIG--NGTASRETE---QFVAELIKELDLKV-------QYVIVSEAGASVYSASELAREEFPDLDVTVRG 433

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  853 AVALGRYLQNPLA-MVatlcgpgreilswKLHP----------------LENflQLDEkygmveqVMVDITNQVGIDINL 915
Cdd:COG2183  434 AVSIARRLQDPLAeLV-------------KIDPksigvgqyqhdvnqkkLKR--SLDA-------VVEDCVNAVGVDLNT 491

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  916 AashdwffSP--LQFISGLGPrkaaSLQRSLV--RA--GSIFVRKDLI-MHGLGKKVFVNAAGFLRIRRSGlaasssqfi 988
Cdd:COG2183  492 A-------SAplLSYVSGLNP----TLAKNIVayRDenGAFKSRKELLkVPRLGPKAFEQAAGFLRIRDGD--------- 551

                        730       740       750
                 ....*....|....*....|....*....|....
gi 42562972  989 DLLDDTRIHPESYSLAQELAKDI-YD-EDVRGDS 1020
Cdd:COG2183  552 NPLDNSAVHPESYPVVEKILKDLgVSvKDLIGNK 585
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1102-1174 7.61e-08

Ribosomal protein S1-like RNA-binding domain;


:

Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.07  E-value: 7.61e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42562972    1102 EGRIVQASVRRLQNGRAICVLDSGLTGMLMKEDFSDDgrDIVDLADQLKEGDILTCKIKSIQKQRYQVFLICK 1174
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
HHH_9 super family cl40179
HHH domain;
991-1070 9.56e-05

HHH domain;


The actual alignment was detected with superfamily member pfam17674:

Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 42.14  E-value: 9.56e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    991 LDDTRIHPESYSLAQELAKDiydedvrgdsnddedaIEMAIEHVRDRPASLRKVVLDEYLaskKRENKKETYSNIIRELS 1070
Cdd:pfam17674    3 LDNTAIHPESYPLAEKILKD----------------LGLDLKDLIGNSALLKKLDPKKLA---EEEVGLPTLKDILEELA 63
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
 86-118 1.07e-03

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


:

Pssm-ID: 464226  Cd Length: 89  Bit Score: 39.77  E-value: 1.07e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 42562972     86 DEGLDEDDYLLLQDNNVKFKKRQ---YKRLKKAQRE 118
Cdd:pfam14632   54 DDRLDEDDLDLIEENTGVKRRRSsskFKRLKRGHDD 89
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1204-1408 1.28e-94

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 304.07  E-value: 1.28e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972   1204 KEKARKEKELVRKHFKSRMIVHPRFQNITADQATEYLSDKDFGESIVRPSSRGLNFLTLTLKIYDGVYAHKEIAEGGKEN 1283
Cdd:pfam14633    5 EELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELDKEN 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972   1284 KditslQCIGKTLTIGEDTFEDLDEVMDRYVDPLVSHLKTMLNYRKFRKGTKSEVDDLLRIEKGENPSRIVYCFGISHEH 1363
Cdd:pfam14633   85 E-----FSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKDGTKEEVEEWLREEKKANPKRSPYAFCLSHKH 159

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 42562972   1364 PGTFILSYIRSTNP--HHEYIGLYPKGFKFRKRMFEDIDRLVAYFQR 1408
Cdd:pfam14633  160 PGYFLLSFKANKNSrvHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
SH2_Cterm_SPT6_like cd09928
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ...
 1324-1410 1.44e-34

C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198182  Cd Length: 89  Bit Score: 127.73  E-value: 1.44e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972 1324 MLNYRKFRKGTKSEVDDLLRIEKGENPSRIVYCFGISHEHPGTFILSYI-RSTNPHHEYIGLYPKGFKFRKRMFEDIDRL 1402
Cdd:cd09928    2 MLNHHKYFRGTKEEVEKLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLpANTRVRHEYVKVTPDGFRFRGQVFPSVDSL 81


                 ....*...
gi 42562972 1403 VAYFQRHI 1410
Cdd:cd09928   82 LNWFKEHF 89
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
340-1020 3.80e-28

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 122.83  E-value: 3.80e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  340 IPFIAMYRKEQcrslldTGDFDganqgkkpETKwhkvfwmIHDLDKKWLLLRkrkmalhgyytkryEEESRRvydetrln 419
Cdd:COG2183   33 VPFIARYRKEA------TGGLD--------EVQ-------LRTIEERLTYLR--------------ELEKRR-------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  420 lnqylfESVIKSLK--------------VAETEREVDDvdskfnLHFPpgeigvdegqYKrPKRKSQYSICSKAGLweva 485
Cdd:COG2183   70 ------ETILKSIEeqgkltpelkakieAADTKQELED------LYLP----------YK-PKRRTKATIAREKGL---- 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  486 nkfgysaEQLGLALsleklvdeLEDAKETPEEMAKNFVCAM--FENSLAVLKGARHMAAVEISCEPSVKKYVRGIYMENA 563
Cdd:COG2183  123 -------EPLADLL--------LAQPTGDPEAEAAKYINEEkgVADVEAALDGARDILAERISEDAELRGKLRELLWKEG 187

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  564 VVSTSPTA---DGNTVIDSFHQFSgikwlreKPLSKFEGAQWLLIQKGEEEKLLQVTFKLPENYMNRLIsdcNEHYlsvg 640
Cdd:COG2183  188 VLVSKVKKgkeEEGAKFRDYFDYS-------EPLKKIPSHRILALNRGEKEGVLKVKLEPDEEEAEAYI---ARRF---- 253

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  641 VSKYAQLWNEQRKLILEDALHAFLLPSMEKEARSLLTSRAksrllseygqalwnkvsagpyqkkemdinlDEEA------ 714
Cdd:COG2183  254 IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKA------------------------------EEEAikvfae 303

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  715 --------AP----RVMAccWGPGkppntF------VMLDSSGEVLD--VLY--AGsltsrsQNvndqQRKKSdQDRVLK 772
Cdd:COG2183  304 nlrdlllaAPaggkVVLG--LDPG-----FrtgckvAVVDETGKLLDtaTIYphPP------QN----KWEEA-AKTLAA 365

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  773 FMMDHQPHVVALGavNLSCTRLKDdiyEVIFQMVEEKPRDVghgmddlSIVYVDESLPRLYENSRISGEQLPQQSGNVRR 852
Cdd:COG2183  366 LIKKYKVELIAIG--NGTASRETE---QFVAELIKELDLKV-------QYVIVSEAGASVYSASELAREEFPDLDVTVRG 433

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  853 AVALGRYLQNPLA-MVatlcgpgreilswKLHP----------------LENflQLDEkygmveqVMVDITNQVGIDINL 915
Cdd:COG2183  434 AVSIARRLQDPLAeLV-------------KIDPksigvgqyqhdvnqkkLKR--SLDA-------VVEDCVNAVGVDLNT 491

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  916 AashdwffSP--LQFISGLGPrkaaSLQRSLV--RA--GSIFVRKDLI-MHGLGKKVFVNAAGFLRIRRSGlaasssqfi 988
Cdd:COG2183  492 A-------SAplLSYVSGLNP----TLAKNIVayRDenGAFKSRKELLkVPRLGPKAFEQAAGFLRIRDGD--------- 551

                        730       740       750
                 ....*....|....*....|....*....|....
gi 42562972  989 DLLDDTRIHPESYSLAQELAKDI-YD-EDVRGDS 1020
Cdd:COG2183  552 NPLDNSAVHPESYPVVEKILKDLgVSvKDLIGNK 585
HHH_7 pfam14635
Helix-hairpin-helix motif;
875-975 1.58e-22

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 93.76  E-value: 1.58e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    875 REILSWKLHPLENFLQLDEKYGMVEQVMVDITNQVGIDINLAASHDWFFSPLQFISGLGPRKAASLQRSLVRAGS-IFVR 953
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGrLDNR 80

                           90       100
                   ....*....|....*....|...
gi 42562972    954 KDLIMHG-LGKKVFVNAAGFLRI 975
Cdd:pfam14635   81 SQLITKCiMGPKVFMNCAGFLII 103
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 716-833 5.90e-19

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 83.39  E-value: 5.90e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972     716 PRVMACCwgPGKPPNTFVMLDSSGEVLDVLYAGSLTsrsqnvndqqRKKSDQDRVLKFMMDHQPHVVALGAVNLSCTRLK 795
Cdd:smart00732    1 KRVLGLD--PGRKGIGVAVVDETGKLADPLEVIPRT----------NKEADAARLKKLIKKYQPDLIVIGLPLNMNGTAS 68

                            90       100       110
                    ....*....|....*....|....*....|....*...
gi 42562972     796 DDIYEVIFQMVEEKPrdvghgmdDLSIVYVDESLPRLY 833
Cdd:smart00732   69 RETEEAFAELLKERF--------NLPVVLVDERLATVY 98
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1102-1174 7.61e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.07  E-value: 7.61e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42562972    1102 EGRIVQASVRRLQNGRAICVLDSGLTGMLMKEDFSDDgrDIVDLADQLKEGDILTCKIKSIQKQRYQVFLICK 1174
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
HHH_9 pfam17674
HHH domain;
991-1070 9.56e-05

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 42.14  E-value: 9.56e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    991 LDDTRIHPESYSLAQELAKDiydedvrgdsnddedaIEMAIEHVRDRPASLRKVVLDEYLaskKRENKKETYSNIIRELS 1070
Cdd:pfam17674    3 LDNTAIHPESYPLAEKILKD----------------LGLDLKDLIGNSALLKKLDPKKLA---EEEVGLPTLKDILEELA 63
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
 86-118 1.07e-03

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


Pssm-ID: 464226  Cd Length: 89  Bit Score: 39.77  E-value: 1.07e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 42562972     86 DEGLDEDDYLLLQDNNVKFKKRQ---YKRLKKAQRE 118
Cdd:pfam14632   54 DDRLDEDDLDLIEENTGVKRRRSsskFKRLKRGHDD 89
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1204-1408 1.28e-94

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 304.07  E-value: 1.28e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972   1204 KEKARKEKELVRKHFKSRMIVHPRFQNITADQATEYLSDKDFGESIVRPSSRGLNFLTLTLKIYDGVYAHKEIAEGGKEN 1283
Cdd:pfam14633    5 EELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELDKEN 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972   1284 KditslQCIGKTLTIGEDTFEDLDEVMDRYVDPLVSHLKTMLNYRKFRKGTKSEVDDLLRIEKGENPSRIVYCFGISHEH 1363
Cdd:pfam14633   85 E-----FSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKDGTKEEVEEWLREEKKANPKRSPYAFCLSHKH 159

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 42562972   1364 PGTFILSYIRSTNP--HHEYIGLYPKGFKFRKRMFEDIDRLVAYFQR 1408
Cdd:pfam14633  160 PGYFLLSFKANKNSrvHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
SH2_Cterm_SPT6_like cd09928
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ...
 1324-1410 1.44e-34

C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198182  Cd Length: 89  Bit Score: 127.73  E-value: 1.44e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972 1324 MLNYRKFRKGTKSEVDDLLRIEKGENPSRIVYCFGISHEHPGTFILSYI-RSTNPHHEYIGLYPKGFKFRKRMFEDIDRL 1402
Cdd:cd09928    2 MLNHHKYFRGTKEEVEKLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLpANTRVRHEYVKVTPDGFRFRGQVFPSVDSL 81


                 ....*...
gi 42562972 1403 VAYFQRHI 1410
Cdd:cd09928   82 LNWFKEHF 89
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
 1225-1313 6.28e-33

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198174  Cd Length: 85  Bit Score: 122.73  E-value: 6.28e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972 1225 HPRFQNITADQATEYLSDKDFGESIVRPSSRGLNFLTLTLKIYDGVYAHKEIAEGGKENKditslQCIGKTLTIGEDTFE 1304
Cdd:cd09918    2 HPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENP-----FSLGKELIIGGEEYE 76


                 ....*....
gi 42562972 1305 DLDEVMDRY 1313
Cdd:cd09918   77 DLDEIIARF 85
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
340-1020 3.80e-28

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 122.83  E-value: 3.80e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  340 IPFIAMYRKEQcrslldTGDFDganqgkkpETKwhkvfwmIHDLDKKWLLLRkrkmalhgyytkryEEESRRvydetrln 419
Cdd:COG2183   33 VPFIARYRKEA------TGGLD--------EVQ-------LRTIEERLTYLR--------------ELEKRR-------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  420 lnqylfESVIKSLK--------------VAETEREVDDvdskfnLHFPpgeigvdegqYKrPKRKSQYSICSKAGLweva 485
Cdd:COG2183   70 ------ETILKSIEeqgkltpelkakieAADTKQELED------LYLP----------YK-PKRRTKATIAREKGL---- 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  486 nkfgysaEQLGLALsleklvdeLEDAKETPEEMAKNFVCAM--FENSLAVLKGARHMAAVEISCEPSVKKYVRGIYMENA 563
Cdd:COG2183  123 -------EPLADLL--------LAQPTGDPEAEAAKYINEEkgVADVEAALDGARDILAERISEDAELRGKLRELLWKEG 187

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  564 VVSTSPTA---DGNTVIDSFHQFSgikwlreKPLSKFEGAQWLLIQKGEEEKLLQVTFKLPENYMNRLIsdcNEHYlsvg 640
Cdd:COG2183  188 VLVSKVKKgkeEEGAKFRDYFDYS-------EPLKKIPSHRILALNRGEKEGVLKVKLEPDEEEAEAYI---ARRF---- 253

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  641 VSKYAQLWNEQRKLILEDALHAFLLPSMEKEARSLLTSRAksrllseygqalwnkvsagpyqkkemdinlDEEA------ 714
Cdd:COG2183  254 IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKA------------------------------EEEAikvfae 303

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  715 --------AP----RVMAccWGPGkppntF------VMLDSSGEVLD--VLY--AGsltsrsQNvndqQRKKSdQDRVLK 772
Cdd:COG2183  304 nlrdlllaAPaggkVVLG--LDPG-----FrtgckvAVVDETGKLLDtaTIYphPP------QN----KWEEA-AKTLAA 365

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  773 FMMDHQPHVVALGavNLSCTRLKDdiyEVIFQMVEEKPRDVghgmddlSIVYVDESLPRLYENSRISGEQLPQQSGNVRR 852
Cdd:COG2183  366 LIKKYKVELIAIG--NGTASRETE---QFVAELIKELDLKV-------QYVIVSEAGASVYSASELAREEFPDLDVTVRG 433

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  853 AVALGRYLQNPLA-MVatlcgpgreilswKLHP----------------LENflQLDEkygmveqVMVDITNQVGIDINL 915
Cdd:COG2183  434 AVSIARRLQDPLAeLV-------------KIDPksigvgqyqhdvnqkkLKR--SLDA-------VVEDCVNAVGVDLNT 491

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972  916 AashdwffSP--LQFISGLGPrkaaSLQRSLV--RA--GSIFVRKDLI-MHGLGKKVFVNAAGFLRIRRSGlaasssqfi 988
Cdd:COG2183  492 A-------SAplLSYVSGLNP----TLAKNIVayRDenGAFKSRKELLkVPRLGPKAFEQAAGFLRIRDGD--------- 551

                        730       740       750
                 ....*....|....*....|....*....|....
gi 42562972  989 DLLDDTRIHPESYSLAQELAKDI-YD-EDVRGDS 1020
Cdd:COG2183  552 NPLDNSAVHPESYPVVEKILKDLgVSvKDLIGNK 585
HHH_7 pfam14635
Helix-hairpin-helix motif;
875-975 1.58e-22

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 93.76  E-value: 1.58e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    875 REILSWKLHPLENFLQLDEKYGMVEQVMVDITNQVGIDINLAASHDWFFSPLQFISGLGPRKAASLQRSLVRAGS-IFVR 953
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGrLDNR 80

                           90       100
                   ....*....|....*....|...
gi 42562972    954 KDLIMHG-LGKKVFVNAAGFLRI 975
Cdd:pfam14635   81 SQLITKCiMGPKVFMNCAGFLII 103
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 716-833 5.90e-19

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 83.39  E-value: 5.90e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972     716 PRVMACCwgPGKPPNTFVMLDSSGEVLDVLYAGSLTsrsqnvndqqRKKSDQDRVLKFMMDHQPHVVALGAVNLSCTRLK 795
Cdd:smart00732    1 KRVLGLD--PGRKGIGVAVVDETGKLADPLEVIPRT----------NKEADAARLKKLIKKYQPDLIVIGLPLNMNGTAS 68

                            90       100       110
                    ....*....|....*....|....*....|....*...
gi 42562972     796 DDIYEVIFQMVEEKPrdvghgmdDLSIVYVDESLPRLY 833
Cdd:smart00732   69 RETEEAFAELLKERF--------NLPVVLVDERLATVY 98
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 716-871 3.21e-15

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 74.52  E-value: 3.21e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    716 PRVMACCWGPGKP--PNTFVMLDSSGEVLDVLyagsltSRSQNVNDQQRKKSDQDRVLKFMMDHQPHVVALGAVNLSCTR 793
Cdd:pfam14639    5 PRVLGVAFGSGRFddAIICVLVNGEGEVTDFL------KLAWREFDRENKAQFEETLKKFLLSKKPHVIGVSGENRDAQK 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42562972    794 LKDDIYEVIFQMveekprDVGHGMDDLSIVYVDESLPRLYENSRISGEQLPQQSGNVRRAVALGRYLQNPLAMVATLC 871
Cdd:pfam14639   79 FYEDVQRVLHEL------EQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1102-1174 7.61e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.07  E-value: 7.61e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42562972    1102 EGRIVQASVRRLQNGRAICVLDSGLTGMLMKEDFSDDgrDIVDLADQLKEGDILTCKIKSIQKQRYQVFLICK 1174
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 908-973 2.56e-05

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 43.24  E-value: 2.56e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42562972    908 QVGIDINLAASHDwffspLQFISGLGPRKAaslqRSLVR---AGSIFV-RKDLI-MHGLGKKVFVNAAGFL 973
Cdd:pfam12836    1 AVGVDINTASAEL-----LSRVPGLGPKLA----KNIVEyreENGPFRsREDLLkVKGLGPKTFEQLAGFL 62
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 340-568 4.22e-05

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 45.86  E-value: 4.22e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    340 IPFIAMYRKEQcrslldTGDFDganqgkkpETKwhkvfwmIHDLDKKWLLLRkrkmalhgyytkryEEESRRvydetrln 419
Cdd:pfam09371   25 VPFIARYRKEA------TGGLD--------EVQ-------LREIEERLEYLR--------------ELEKRK-------- 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    420 lnqylfESVIKSLK--------------VAETEREVDDvdskfnLHFPpgeigvdegqYKrPKRKSQYSIcskaglweva 485
Cdd:pfam09371   62 ------ETILKSIEeqgkltdelkaaieAADTLTELED------LYLP----------YK-PKRRTKATI---------- 108

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    486 nkfgysAEQLGlalsLEKLVDELEdAKETPEEMAKNFVCAM--FENSLAVLKGARHMAAVEISCEPSVKKYVRGIYMENA 563
Cdd:pfam09371  109 ------AREKG----LEPLADAIL-AQPDPEEEAAKYINPEkgVADVEEALAGARDIIAERISEDAELRKKLRELLWREG 177


                   ....*
gi 42562972    564 VVSTS 568
Cdd:pfam09371  178 VIVSK 182
HHH_9 pfam17674
HHH domain;
991-1070 9.56e-05

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 42.14  E-value: 9.56e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562972    991 LDDTRIHPESYSLAQELAKDiydedvrgdsnddedaIEMAIEHVRDRPASLRKVVLDEYLaskKRENKKETYSNIIRELS 1070
Cdd:pfam17674    3 LDNTAIHPESYPLAEKILKD----------------LGLDLKDLIGNSALLKKLDPKKLA---EEEVGLPTLKDILEELA 63
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
 86-118 1.07e-03

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


Pssm-ID: 464226  Cd Length: 89  Bit Score: 39.77  E-value: 1.07e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 42562972     86 DEGLDEDDYLLLQDNNVKFKKRQ---YKRLKKAQRE 118
Cdd:pfam14632   54 DDRLDEDDLDLIEENTGVKRRRSsskFKRLKRGHDD 89
 
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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