Psyllid ID: psy3604

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490------
Protein Sequence
MATSKDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRILSETGKLAPRVFQHFSEHSLRLSSDTMTEQCPRVRVPMVTEVNKHLNMSF
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHccccccccHHHHHHHHHHHcccccccHHHHccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccEEcccccccccccccccccHHHHHHHcccccccEEEEEEEEccccccccccccccEEEEEEccccccHHHHHHHHHHcccccccccccccccccccEEEEEEEEEEEEEEEcccHHHHHHHHHHcHHHHHHcccccccHHHHHHHHHcccccccccccccccccccccccccEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHccccccccccccHHHccccccccccHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccEEEEEEHHHHccHHHHHHHHHccccccEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccccHHHHHcccEEEEcccccccccccHHHHHcccccccccccccccccccccccEEccEEEEEEcccccccccccccccccHHHHHHHHHccccEEEEEEccccccccEEEEcccEEEEEEcccccccHHHHHHHHHHHccccccHcccccccccccEEEEEEEEEEEEEccccEEEEEEEEHHHHHHHHHHHcccccccHHHHHHHcccccccccccccccccccccccEEEEEcccccccccEEEccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHcccccccccccHEEcccccccHHHHHHHHHcccccccccHHHcccccEccEEEEEcccccccc
Coil and Loop (DISEMBL)
matskdtnrSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSShkerekedrigesegtcaevtsvedcyqrnwykRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELgipihgldtyakrpmrtvfppvapstqpkplsilqagvkqphpphippylplfpdphayirtpVVTLKIRskltspgeesddnelpyLKMLnnnlprdikvvawspvpekysaRFDCLFRNykywfpqagldIDAMHKAAQYLVgthdfrnlckmnvgngvvNFKRLVTHAGvtsawqnvqfndikevvdsepsfkkgqgnekpEIIQQLVDiekypriksaqfpwsstgattpneLFRRVFLLSFLAWVDQYRIRQTAHCNIftnlctfyvptylpslgEMIKDTVRESkctmgdldinhliegefdsrpgrilsetgklaprVFQHFSehslrlssdtmteqcprvrvpmvtEVNKHLNMSF
Flexible Loop (DISEMBL)
matskdtnrsllKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKvlsshkerekedrigesegtcaevtsvedcyqrnwYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLtspgeesddnelPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSepsfkkgqgnekpeIIQQLVDIEKYPRIKSaqfpwsstgattpnELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRILSETGKLAPRVFQHFSehslrlssdtmteqcprvrvpmvtevnkhlnmsf
Low Complexity Region (SEG)
MATSKDTNRsllkssvvallaEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQphpphippylplfpdphAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRILSETGKLAPRVFQHFSEHSLRLSSDTMTEQCPRVRVPMVTEVNKHLNMSF
Disordered region (IsUnstruct)
*************SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVL*****************TCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVF**************************IPPYLPLFPDPHAYIRTPVVTLKIR***************PYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV****************IIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDS***RIL*****LAPRVFQH************************************
Disordered Region (DISOPRED)
***********LKSSVVALLAEVGFDAADNAALETLVEICQACKYTC*****************************************YKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRP**********************************YLPLFPDPHAYIRTPVVTLKIRSKLT*****SDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESK********************************************************VRVPMVTEVNKHLN***
Disordered Region (DISEMBL)
**********LLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVL*****************TCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSK*********DNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRILSETGKLAPRVFQHFSEHSLRLSSDTMTEQCPRVRVPMVTEVNKHLNMSF
Disordered Region (DISPRO)
*******NRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQ**PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRILSETGKLAPRVFQHFSEHSLRLSSDTMTEQCPRVRVPMVTEVNKHL****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATSKDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRILSETGKLAPRVFQHFSEHSLRLSSDTMTEQCPRVRVPMVTEVNKHLNMSF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	496	2.2.26 [Sep-21-2011]
Q9JI38	481	tRNA pseudouridine(38/39)	yes	N/A	0.312	0.322	0.418	5e-31
Q3SX07	481	tRNA pseudouridine(38/39)	yes	N/A	0.272	0.280	0.461	5e-30
Q9BZE2	481	tRNA pseudouridine(38/39)	yes	N/A	0.312	0.322	0.418	5e-29
Q9VWY6	328	Transcription initiation	yes	N/A	0.221	0.335	0.454	3e-22
Q09524	402	Probable tRNA pseudouridi	yes	N/A	0.340	0.420	0.350	2e-21
P31115	442	tRNA pseudouridine(38/39)	yes	N/A	0.300	0.337	0.369	8e-21
Q7Z7C8	310	Transcription initiation	no	N/A	0.205	0.329	0.433	6e-19
Q9EQH4	308	Transcription initiation	no	N/A	0.205	0.331	0.433	9e-19
A7MAZ4	310	Transcription initiation	no	N/A	0.205	0.329	0.433	9e-19
Q5ZMS1	244	Transcription initiation	no	N/A	0.189	0.385	0.459	1e-17

>sp|Q9JI38|PUS3_MOUSE tRNA pseudouridine(38/39) synthase OS=Mus musculus GN=Pus3 PE=1 SV=2

 Score =  135 bits (341), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 77/184 (41%), Positives = 104/184 (56%), Gaps = 29/184 (15%)

Query: 196 VVTLKIRSKLTSPGEESDDN----------ELPYLKMLNNNLPRDIKVVAWSPVPEKYSA 245
           V++L +RS+  +  +  D N          E+ Y  +LN  LP DI+V+AW+PV   +SA
Sbjct: 128 VISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSFSA 187

Query: 246 RFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGV 305
           RF CL R Y+Y+FP+A LDI  M+ AAQ  VGTHDFRNLCKM+V NGV+NF+R +  A V
Sbjct: 188 RFSCLERTYRYFFPRADLDIATMNYAAQKYVGTHDFRNLCKMDVANGVINFQRTILCAQV 247

Query: 306 ------------TSAWQNVQFNDIKEVVDSEPS-------FKKGQGNEKPEIIQQLVDIE 346
                          +Q  QF  I +              F  GQG EKPEII +L++I+
Sbjct: 248 QLVAQSPGEERRQEPFQLCQFEVIGQAFLYHQVRCMMAILFLIGQGMEKPEIIDELLNIQ 307

Query: 347 KYPR 350
           K P+
Sbjct: 308 KNPQ 311

Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs. Also acts on position 38, but much less efficiently.
Mus musculus (taxid: 10090)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: 4EC: 5

>sp|Q3SX07|PUS3_BOVIN tRNA pseudouridine(38/39) synthase OS=Bos taurus GN=PUS3 PE=2 SV=1

 Score =  132 bits (333), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 71/154 (46%), Positives = 94/154 (61%), Gaps = 19/154 (12%)

Query: 216 ELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYL 275
           E+ Y  +LN  LP DI+V+AW+PV   +SARF CL R Y+Y+FP+A LDI  M+ AAQ  
Sbjct: 157 EIRYTHILNRVLPPDIRVLAWAPVETSFSARFSCLERTYRYFFPRANLDIVTMNYAAQKY 216

Query: 276 VGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKE---VVDSEPS------ 326
           VGTHDFRNLCKM+V NGV+NF+R +  A V    QN+     +E   +   E +      
Sbjct: 217 VGTHDFRNLCKMDVANGVINFQRTILSAQVQRVGQNLGEEGWQEPFQLCQFEVTGQAFLY 276

Query: 327 ----------FKKGQGNEKPEIIQQLVDIEKYPR 350
                     F  GQG EKPE+I +L++IEK P+
Sbjct: 277 HQVRCMMAVLFLIGQGMEKPEVIDELLNIEKNPQ 310

Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs.

Bos taurus (taxid: 9913)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 4

EC: 5

>sp|Q9BZE2|PUS3_HUMAN tRNA pseudouridine(38/39) synthase OS=Homo sapiens GN=PUS3 PE=1 SV=3

 Score =  129 bits (324), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 77/184 (41%), Positives = 101/184 (54%), Gaps = 29/184 (15%)

Query: 196 VVTLKIRSKLTSPGEESDDN----------ELPYLKMLNNNLPRDIKVVAWSPVPEKYSA 245
           V++L +RS+     +  D N          E+ Y  +LN  LP DI+++AW+PV   +SA
Sbjct: 127 VISLDLRSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSFSA 186

Query: 246 RFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGV 305
           RF CL R Y+Y+FP+A LDI  M  AAQ  VGTHDFRNLCKM+V NGV+NF+R +  A V
Sbjct: 187 RFSCLERTYRYFFPRADLDIVTMDYAAQKYVGTHDFRNLCKMDVANGVINFQRTILSAQV 246

Query: 306 T--------SAWQN----VQFNDIKEVVDSEPS-------FKKGQGNEKPEIIQQLVDIE 346
                      WQ      QF    +              F  GQG EKPEII +L++IE
Sbjct: 247 QLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFLIGQGMEKPEIIDELLNIE 306

Query: 347 KYPR 350
           K P+
Sbjct: 307 KNPQ 310

Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs.

Homo sapiens (taxid: 9606)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 4

EC: 5

>sp|Q9VWY6|TAF8_DROME Transcription initiation factor TFIID subunit 8 OS=Drosophila melanogaster GN=Taf8 PE=1 SV=1

 Score =  107 bits (266), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 50/110 (45%), Positives = 68/110 (61%)

Query: 87  NWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRP 146
           N     +T ++  +I E+G  +H++CEL+ R  P + DV LALI +GI I  LD Y ++ 
Sbjct: 37  NHSLETLTQMLQALIWEIGNSAHNYCELSGRTMPTVGDVSLALINMGISISNLDPYMRKE 96

Query: 147 MRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPV 196
                P     TQ +PLS+LQAG+K PHP ++P Y P  PDPHAYIRTP 
Sbjct: 97  THVPIPLPPQQTQQRPLSLLQAGIKAPHPHYVPSYFPPMPDPHAYIRTPT 146

TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.

Drosophila melanogaster (taxid: 7227)

>sp|Q09524|TG124_CAEEL Probable tRNA pseudouridine synthase tag-124 OS=Caenorhabditis elegans GN=tag-124 PE=3 SV=1

 Score =  103 bits (258), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 68/194 (35%), Positives = 103/194 (53%), Gaps = 25/194 (12%)

Query: 216 ELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYL 275
           ELPY+KMLN  LP+ I+V AW+PV + ++ARFDC  R YKY F +A L+++ M + A+ L
Sbjct: 129 ELPYVKMLNGVLPKTIRVFAWAPVAQTFNARFDCNRRTYKYSFAKADLNLEKMRQGAELL 188

Query: 276 VGTHDFRNLCK--MNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVD---SEPSF--- 327
           VG HDF N C+  MN    + ++ R V    V     + + ND+  +V+   S   F   
Sbjct: 189 VGEHDFSNFCQIDMNEKRLLQSYVRKVYEVKVEQVSTHPE-NDMYSMVELTVSGSGFLWH 247

Query: 328 ----------KKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLS 377
                     + G+ NE+P +I QL+D++KYP       P  +  + TP  LF   +   
Sbjct: 248 MIRYIVTILQEIGRENEQPSLISQLLDLKKYP-----SRPQYTLASDTPLCLFDCGYKSE 302

Query: 378 FLAW-VDQYRIRQT 390
            + W V  Y ++ T
Sbjct: 303 DVEWKVHDYTLKST 316

Formation of pseudouridine at position 38 and 39 in the anticodon stem and loop of transfer RNAs.

Caenorhabditis elegans (taxid: 6239)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|P31115|PUS3_YEAST tRNA pseudouridine(38/39) synthase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=DEG1 PE=1 SV=1

 Score =  102 bits (253), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 64/173 (36%), Positives = 92/173 (53%), Gaps = 24/173 (13%)

Query: 196 VVTLKIRSKLTSPGEE---SDDNELPYLKMLNNNLPRDIKV--VAWSPVPEKYSARFDCL 250
           V++L++RS LT   +    +D  E+PY+ +LN  LP DI++  V   P P  + ARF C+
Sbjct: 160 VISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLRP-PPNFDARFSCV 218

Query: 251 FRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAG------ 304
            R+YKY F    L+I+ M KAA Y VG  DFRN CK++    + NFKR +  +       
Sbjct: 219 HRHYKYIFNGKNLNIEKMSKAASYFVGERDFRNFCKLDGSKQITNFKRTIISSKILPLSE 278

Query: 305 -------VTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKYPR 350
                  V SA+   Q   +  ++     F  GQ  E PEI+ +L DIEK P+
Sbjct: 279 TFYCFDLVGSAFLWHQVRCMMAIL-----FLVGQSLEVPEIVLRLTDIEKTPQ 326

Formation of pseudouridines at positions 38 and 39 in the anticodon stem and loop of transfer RNAs.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 4

EC: 5

>sp|Q7Z7C8|TAF8_HUMAN Transcription initiation factor TFIID subunit 8 OS=Homo sapiens GN=TAF8 PE=1 SV=1

 Score = 95.9 bits (237), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/106 (43%), Positives = 63/106 (59%), Gaps = 4/106 (3%)

Query: 93  VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVF- 151
           +T ++   I E+G  +  +CE   R QP L+D+++ L+E+G  +  L  YAKR  R V  
Sbjct: 61  LTEMLQSYISEIGRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVDTLPAYAKRSQRMVIT 120

Query: 152 -PPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPV 196
            PPV  + QP     L AG  +PHPPHIP + P FPDPH YI+TP 
Sbjct: 121 APPV--TNQPVTPKALTAGQNRPHPPHIPSHFPEFPDPHTYIKTPT 164

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. Mediates both basal and activator-dependent transcription. Plays a role in the differentiation of preadipocyte fibroblasts to adipocytes, however, does not seem to play a role in differentiation of myoblasts. Required for the integration of TAF10 in the TAF complex. May be important for survival of cells of the inner cell mass which constitute the pluripotent cell population of the early embryo.

Homo sapiens (taxid: 9606)

>sp|Q9EQH4|TAF8_MOUSE Transcription initiation factor TFIID subunit 8 OS=Mus musculus GN=Taf8 PE=2 SV=1

 Score = 95.5 bits (236), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/106 (43%), Positives = 63/106 (59%), Gaps = 4/106 (3%)

Query: 93  VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVF- 151
           +T ++   I E+G  +  +CE   R QP L+D+++ L+E+G  +  L  YAKR  R V  
Sbjct: 59  LTEMLQSYISEIGRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVDTLPAYAKRSQRMVIT 118

Query: 152 -PPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPV 196
            PPV  + QP     L AG  +PHPPHIP + P FPDPH YI+TP 
Sbjct: 119 APPV--TNQPVTPKALTAGQNRPHPPHIPSHFPEFPDPHTYIKTPT 162

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. Mediates both basal and activator-dependent transcription. Plays a role in the differentiation of preadipocyte fibroblasts to adipocytes, however does not seem to play a role in differentiation of myoblasts. Required for the integration of TAF10 in the TAF complex (By similarity). May be important for survival of cells of the inner cell mass which constitute the pluripotent cell population of the early embryo.

Mus musculus (taxid: 10090)

>sp|A7MAZ4|TAF8_BOVIN Transcription initiation factor TFIID subunit 8 OS=Bos taurus GN=TAF8 PE=2 SV=1

 Score = 95.5 bits (236), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/106 (43%), Positives = 63/106 (59%), Gaps = 4/106 (3%)

Query: 93  VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVF- 151
           +T ++   I E+G  +  +CE   R QP L+D+++ L+E+G  +  L  YAKR  R V  
Sbjct: 61  LTEMLQSYISEIGRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVDTLPAYAKRSQRMVIT 120

Query: 152 -PPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPV 196
            PPV  + QP     L AG  +PHPPHIP + P FPDPH YI+TP 
Sbjct: 121 APPV--TNQPVTPKALTAGQNRPHPPHIPSHFPEFPDPHTYIKTPT 164

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. Mediates both basal and activator-dependent transcription. Plays a role in the differentiation of preadipocyte fibroblasts to adipocytes, however, does not seem to play a role in differentiation of myoblasts. Required for the integration of TAF10 in the TAF complex. May be important for survival of cells of the inner cell mass which constitute the pluripotent cell population of the early embryo.

Bos taurus (taxid: 9913)

>sp|Q5ZMS1|TAF8_CHICK Transcription initiation factor TFIID subunit 8 OS=Gallus gallus GN=TAF8 PE=2 SV=1

 Score = 92.0 bits (227), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/98 (45%), Positives = 58/98 (59%), Gaps = 4/98 (4%)

Query: 101 IKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVF--PPVAPST 158
           I E+G  +  +CE   R QP L+D+++ L+E+G  +  L  YAKR  R V   PPV  + 
Sbjct: 6   ISEIGRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVETLPAYAKRSQRMVITAPPV--TN 63

Query: 159 QPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPV 196
           QP     L AG  +PHP HIP Y P FPDPH YI+TP 
Sbjct: 64  QPVTPKALTAGQNKPHPSHIPGYFPEFPDPHTYIKTPT 101

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. Mediates both basal and activator-dependent transcription.

Gallus gallus (taxid: 9031)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	496
340724310	424	PREDICTED: tRNA pseudouridine synthase 3	0.316	0.370	0.439	1e-35
322786132	444	hypothetical protein SINV_14818 [Solenop	0.316	0.353	0.454	8e-35
383863340	420	PREDICTED: tRNA pseudouridine(38/39) syn	0.316	0.373	0.450	1e-34
350420811	424	PREDICTED: tRNA pseudouridine synthase 3	0.316	0.370	0.433	1e-34
332024452	443	tRNA pseudouridine synthase 3 [Acromyrme	0.316	0.354	0.454	5e-34
328777716	400	PREDICTED: tRNA pseudouridine synthase 3	0.316	0.392	0.421	9e-34
380027544	400	PREDICTED: tRNA pseudouridine(38/39) syn	0.316	0.392	0.427	1e-33
307177137	345	tRNA pseudouridine synthase 3 [Camponotu	0.316	0.455	0.439	1e-33
193666867	402	PREDICTED: tRNA pseudouridine synthase 3	0.419	0.517	0.387	8e-33
307212020	368	tRNA pseudouridine synthase 3 [Harpegnat	0.312	0.421	0.444	4e-32

>gi|340724310|ref|XP_003400525.1| PREDICTED: tRNA pseudouridine synthase 3-like [Bombus terrestris]

 Score =  157 bits (397), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/173 (43%), Positives = 111/173 (64%), Gaps = 16/173 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V+++ +RSKL    +   ++ELPY K+LN  LP +I+ +AW P    +SARF+C FR 
Sbjct: 133 SQVISIDLRSKLNPEDQCKLEDELPYCKILNRLLPSNIRCIAWCPASSNFSARFNCKFRT 192

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVT---SAWQ 310
           YKY+FP+  L+ID+M KA +Y +G HDFRN+CKM+V NGV N++R V  A V      ++
Sbjct: 193 YKYFFPRGNLNIDSMDKAVKYTIGEHDFRNICKMDVANGVTNYQRKVIDAKVCLYRRDFR 252

Query: 311 NVQFNDIKEVVDSEPS-------------FKKGQGNEKPEIIQQLVDIEKYPR 350
           N+   D+ +++ +  +             F  GQGNEKPEII +L+DIEKYPR
Sbjct: 253 NISGYDVCQLIITSQAFLWHQIRCLMGVLFLIGQGNEKPEIILELLDIEKYPR 305

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322786132|gb|EFZ12740.1| hypothetical protein SINV_14818 [Solenopsis invicta]

 Score =  154 bits (390), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 79/174 (45%), Positives = 109/174 (62%), Gaps = 17/174 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V++L IRSKL    + +  NELPY KMLN  LP +I+ VAW PV   +SARFDC +R 
Sbjct: 154 SQVISLDIRSKLAPEDQGNLSNELPYCKMLNRLLPTNIRCVAWCPVASNFSARFDCKYRR 213

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVT----SAW 309
           YKY+FP+  LDIDAM+KAA+Y+VG HDFRN+CKM+V NG++NFKR V  A V+     + 
Sbjct: 214 YKYFFPRGNLDIDAMNKAAKYVVGDHDFRNICKMDVANGIINFKRTVIDAKVSFVNEQSM 273

Query: 310 QNVQFNDIKEVVDSEPSF-------------KKGQGNEKPEIIQQLVDIEKYPR 350
           +     D+ E+  +  +F               GQ  E+PE+I +L+D E  P+
Sbjct: 274 EKSTGYDMCELEITSQAFLWHQIRCLMGILLLVGQRKEEPEVILKLLDTETCPQ 327

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383863340|ref|XP_003707139.1| PREDICTED: tRNA pseudouridine(38/39) synthase-like [Megachile rotundata]

 Score =  154 bits (389), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 78/173 (45%), Positives = 108/173 (62%), Gaps = 16/173 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V++L IRSKL    +   ++ELPY K+LN  LP +I+  AW PV +  SARFDC FR 
Sbjct: 134 SQVISLDIRSKLKPEDQNKLEDELPYCKILNRLLPSNIRCTAWCPVSDDVSARFDCKFRT 193

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQN-- 311
           YKY+FP+  L+IDAM KA +Y++G HDFRN+CKM+V NGVVN+ R +  A V+   QN  
Sbjct: 194 YKYFFPRGNLNIDAMDKAVKYIIGEHDFRNICKMDVANGVVNYMRTIMSAEVSLYRQNSK 253

Query: 312 -VQFNDIKEVVDSEPSF-------------KKGQGNEKPEIIQQLVDIEKYPR 350
            +   DI +++ +  +F               GQ  EKPE+I +L+DI K PR
Sbjct: 254 HISGYDICQLIITSQAFLWHQIRCLMGVLLLVGQEKEKPEVILELLDISKCPR 306

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350420811|ref|XP_003492633.1| PREDICTED: tRNA pseudouridine synthase 3-like [Bombus impatiens]

 Score =  154 bits (388), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 75/173 (43%), Positives = 110/173 (63%), Gaps = 16/173 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V+++ +RSKL    +   ++ELPY K+LN  LP +I+ +AW P    +SARF+C FR 
Sbjct: 133 SQVISIDLRSKLNPEDQCKLEDELPYCKILNRLLPSNIRCIAWCPASSNFSARFNCKFRT 192

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVT---SAWQ 310
           YKY+FP+  L+ID+M KA +Y +G HDFRN+CKM+V NGV N++R V  A V      ++
Sbjct: 193 YKYFFPRGNLNIDSMDKAVKYTIGEHDFRNICKMDVANGVTNYQRKVIDAKVCLYRRDFR 252

Query: 311 NVQFNDIKEVVDSEPS-------------FKKGQGNEKPEIIQQLVDIEKYPR 350
           N+   D+ +++ +  +             F  GQGNEKPEII +L+DIEK PR
Sbjct: 253 NISGYDVCQLIITSQAFLWHQIRCLMGVLFLIGQGNEKPEIILELLDIEKCPR 305

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332024452|gb|EGI64650.1| tRNA pseudouridine synthase 3 [Acromyrmex echinatior]

 Score =  152 bits (383), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 79/174 (45%), Positives = 114/174 (65%), Gaps = 17/174 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V++L +RS+L    +++  +ELPY K+LN  LP +I+ +AW PV   +SARFDC FR+
Sbjct: 136 SQVISLDVRSRLEPENQDNLSDELPYCKILNRLLPANIRCIAWCPVSSIFSARFDCKFRS 195

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAW-QNV 312
           Y+Y+FP+  LDI+AM KAA+Y++G HDFRN+CKM+V NGV+NFKR V  A V S   QNV
Sbjct: 196 YRYFFPRGNLDIEAMDKAAKYVIGDHDFRNICKMDVANGVINFKRTVMDARVNSLNDQNV 255

Query: 313 QFN---DIKEVVDSEPSF-------------KKGQGNEKPEIIQQLVDIEKYPR 350
           + +   D+ E+  +  +F               GQ  E+PEII +L+DIE  P+
Sbjct: 256 EKSTGYDMCELEITSQAFLWHQIRCLMGILLLIGQRKEEPEIILKLLDIETCPQ 309

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328777716|ref|XP_393954.4| PREDICTED: tRNA pseudouridine synthase 3-like [Apis mellifera]

 Score =  151 bits (381), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 73/173 (42%), Positives = 112/173 (64%), Gaps = 16/173 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V++L IRSKL    +   ++ELPY K+LN  LP +I+ +AW PVP  +SARF+C FR 
Sbjct: 117 SQVISLDIRSKLNPEDQYKLEDELPYCKILNRLLPSNIRCIAWCPVPNDFSARFNCKFRT 176

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGV---TSAWQ 310
           YKY+FP+  L+IDAM+KA +Y++G HDFRN+CKM+V NGV+N+ R V +A V      ++
Sbjct: 177 YKYFFPRGNLNIDAMNKAVKYIIGEHDFRNICKMDVANGVINYIRKVINAEVRMYRQDFR 236

Query: 311 NVQFNDIKEVVDSEPS-------------FKKGQGNEKPEIIQQLVDIEKYPR 350
           N+   D+ +++ +  +             F  G+G E+ EI+ +L+DIE  P+
Sbjct: 237 NISGYDMYQLIITSQAFLWHQIRCLMGVLFLIGEGKEEAEIMLELLDIENCPK 289

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380027544|ref|XP_003697482.1| PREDICTED: tRNA pseudouridine(38/39) synthase-like [Apis florea]

 Score =  150 bits (380), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 74/173 (42%), Positives = 110/173 (63%), Gaps = 16/173 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V++L IRSKL    +   ++ELPY KMLN  LP +I+ +AW PVP  +SARF+C FR 
Sbjct: 134 SQVISLDIRSKLNPEDQYKLEDELPYCKMLNRLLPSNIRCIAWCPVPNDFSARFNCKFRT 193

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVT---SAWQ 310
           YKY+FP+  L+IDAM KA +Y++G HDFRN+CKM+V NGV N+ R V +A V      ++
Sbjct: 194 YKYFFPRGNLNIDAMDKAVKYIIGEHDFRNICKMDVANGVTNYIRKVINAEVCMYRQDFR 253

Query: 311 NVQFNDIKEVVDSEPS-------------FKKGQGNEKPEIIQQLVDIEKYPR 350
           N+   D+ +++ +  +             F  G+G E+ EI+ +L+DIE  P+
Sbjct: 254 NISGYDMCQLIITSQAFLWHQIRCLMGVLFLIGEGKEEAEIMLKLLDIENCPK 306

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307177137|gb|EFN66370.1| tRNA pseudouridine synthase 3 [Camponotus floridanus]

 Score =  150 bits (379), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 76/173 (43%), Positives = 109/173 (63%), Gaps = 16/173 (9%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V++L IRS+L    + +   ELPY K+LN  LP +I+ +AW PV   +SARFDC +R 
Sbjct: 79  SQVISLDIRSRLEPENQHNLSEELPYCKILNRLLPTNIRCIAWCPVSPNFSARFDCKYRT 138

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQ 313
           YKY+FP++ LDIDAM K+ +Y +G HDFRN+CKM+V NGV+NFKR V  A V+ + QNV+
Sbjct: 139 YKYFFPKSNLDIDAMDKSVKYAIGDHDFRNICKMDVANGVINFKRTVIDAKVSMSNQNVE 198

Query: 314 ----FNDIKEVVDSEPSFKK------------GQGNEKPEIIQQLVDIEKYPR 350
               +N  +  + S+                 GQ  E+PEII +L++IE  P+
Sbjct: 199 KITGYNMCELEITSQAFLWHQIRCLMGILLLVGQRKEEPEIILKLLNIETCPQ 251

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193666867|ref|XP_001946781.1| PREDICTED: tRNA pseudouridine synthase 3-like isoform 1 [Acyrthosiphon pisum] gi|328702018|ref|XP_003241780.1| PREDICTED: tRNA pseudouridine synthase 3-like isoform 2 [Acyrthosiphon pisum]

 Score =  148 bits (373), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 132/245 (53%), Gaps = 37/245 (15%)

Query: 194 TPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 253
           + V++L +RS     G++S+  ELPY KMLN  LP+DI+VVAW PV + +SARFDC  R 
Sbjct: 119 SQVISLTVRSN----GDDSE--ELPYCKMLNRLLPKDIRVVAWGPVKDDFSARFDCGSRT 172

Query: 254 YKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQ 313
           YKYWFP+  LD+D M++A Q +VGTHDFRNLCKM+V NGVV F R +T A +    +N Q
Sbjct: 173 YKYWFPRGDLDVDLMNQAIQQVVGTHDFRNLCKMDVANGVVQFYRRITSADIKICSENNQ 232

Query: 314 FN-----DIKEVVDSEPSF-------------KKGQGNEKPEIIQQLVDIEKYPRIKSAQ 355
           F+     D+ E+     +F               G   E P I + L++IE  PR     
Sbjct: 233 FSKNRDYDMCELTIVGKAFLWHQIRCIVSVLILVGCRKENPNIFKDLLNIENCPRK---- 288

Query: 356 FPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPS--LGE 413
            P     +  P  LF   F    + WV    I   +   + T+L   +    + +  LGE
Sbjct: 289 -PQYCLASDLPLNLFDCQF--ENVNWV----IEDESISEVITSLQCSWATHMIKATMLGE 341

Query: 414 MIKDT 418
           M+K+T
Sbjct: 342 MLKNT 346

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307212020|gb|EFN87913.1| tRNA pseudouridine synthase 3 [Harpegnathos saltator]

 Score =  145 bits (367), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 76/171 (44%), Positives = 105/171 (61%), Gaps = 16/171 (9%)

Query: 196 VVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255
           V++L IRSKL    + +   ELPY K+LN  LP +I+ +AW P+   +SARFDC +R YK
Sbjct: 81  VISLDIRSKLEPEQQSNLSKELPYCKILNKLLPTNIRCIAWCPISSDFSARFDCKYRKYK 140

Query: 256 YWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFN 315
           Y+FP+  LDIDAM KA +Y++G  DFRN+CKM+V NGV NFKR V  A ++   Q V  +
Sbjct: 141 YFFPRGNLDIDAMDKAVKYVIGEFDFRNICKMDVANGVTNFKRKVIDAKISMNNQAVDKS 200

Query: 316 ---DIKEVVDSEPSF-------------KKGQGNEKPEIIQQLVDIEKYPR 350
              DI E+  +  +F               G+  E+PEII +L+DIE  P+
Sbjct: 201 TGYDICELEITSQAFLWHQIRCLMGILLLVGKKREEPEIISKLLDIETCPQ 251

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	496
UNIPROTKB|F1P3X5	379	PUS3 "tRNA pseudouridine synth	0.205	0.269	0.572	1.8e-31
ZFIN|ZDB-GENE-030131-9433	460	pus3 "pseudouridylate synthase	0.199	0.215	0.54	2.7e-27
UNIPROTKB|F1N5P3	481	PUS3 "tRNA pseudouridine synth	0.195	0.201	0.567	2.7e-27
UNIPROTKB|Q3SX07	481	PUS3 "tRNA pseudouridine(38/39	0.195	0.201	0.567	2.7e-27
UNIPROTKB|E2RGS6	480	PUS3 "tRNA pseudouridine synth	0.235	0.243	0.480	6.9e-27
MGI|MGI:1914299	481	Pus3 "pseudouridine synthase 3	0.191	0.197	0.577	8.2e-27
UNIPROTKB|Q9BZE2	481	PUS3 "tRNA pseudouridine(38/39	0.231	0.239	0.472	2.4e-26
RGD|1310757	479	Pus3 "pseudouridylate synthase	0.233	0.242	0.468	4.3e-26
UNIPROTKB|F1RVF1	479	LOC100739830 "tRNA pseudouridi	0.209	0.217	0.528	5.5e-26
UNIPROTKB|F1S759	479	LOC100739830 "tRNA pseudouridi	0.209	0.217	0.528	5.5e-26

UNIPROTKB|F1P3X5 PUS3 "tRNA pseudouridine synthase" [Gallus gallus (taxid:9031)]

 Score = 299 (110.3 bits), Expect = 1.8e-31, Sum P(2) = 1.8e-31
 Identities = 59/103 (57%), Positives = 73/103 (70%)

Query:   207 SPGEES-DDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDI 265
             S G+ S  + EL Y  +LN  LP DI+V+AW+PV   +SARF CL R Y+Y+FP A LD+
Sbjct:   145 SEGKSSKSEEELRYTHILNRVLPPDIRVLAWAPVEPDFSARFSCLKRTYRYFFPCADLDV 204

Query:   266 DAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA 308
               MH AAQ  VGTHDFRNLCKM+V NGV+NF+R +  A VT A
Sbjct:   205 ALMHTAAQRYVGTHDFRNLCKMDVANGVINFQRTILSAQVTWA 247

GO:0003723 "RNA binding" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0031119 "tRNA pseudouridine synthesis" evidence=IEA

ZFIN|ZDB-GENE-030131-9433 pus3 "pseudouridylate synthase 3" [Danio rerio (taxid:7955)]

 Score = 293 (108.2 bits), Expect = 2.7e-27, Sum P(2) = 2.7e-27
 Identities = 54/100 (54%), Positives = 73/100 (73%)

Query:   209 GEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAM 268
             G+ S D ELPY+K+LN  LP DI+++ W+PV   +SARFDC  R Y+Y+FP+  LD++ M
Sbjct:   148 GKTSAD-ELPYVKILNRVLPHDIRILQWAPVESGFSARFDCQSRTYRYYFPRGDLDLELM 206

Query:   269 HKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA 308
              +AA+   GTHDFRNLCKM+VGNGV+ F+R +  A V  A
Sbjct:   207 AEAAKRYEGTHDFRNLCKMDVGNGVLQFQRTILSASVQPA 246

GO:0003723 "RNA binding" evidence=IEA

GO:0009451 "RNA modification" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0016853 "isomerase activity" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

UNIPROTKB|F1N5P3 PUS3 "tRNA pseudouridine synthase" [Bos taurus (taxid:9913)]

 Score = 291 (107.5 bits), Expect = 2.7e-27, Sum P(2) = 2.7e-27
 Identities = 55/97 (56%), Positives = 70/97 (72%)

Query:   216 ELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYL 275
             E+ Y  +LN  LP DI+V+AW+PV   +SARF CL R Y+Y+FP+A LDI  M+ AAQ  
Sbjct:   157 EIRYTHILNRVLPPDIRVLAWAPVETSFSARFSCLERTYRYFFPRANLDIVTMNYAAQKY 216

Query:   276 VGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNV 312
             VGTHDFRNLCKM+V NGV+NF+R +  A V    QN+
Sbjct:   217 VGTHDFRNLCKMDVANGVINFQRTILSAQVQRVGQNL 253

GO:0031119 "tRNA pseudouridine synthesis" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q3SX07 PUS3 "tRNA pseudouridine(38/39) synthase" [Bos taurus (taxid:9913)]

 Score = 291 (107.5 bits), Expect = 2.7e-27, Sum P(2) = 2.7e-27
 Identities = 55/97 (56%), Positives = 70/97 (72%)

Query:   216 ELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYL 275
             E+ Y  +LN  LP DI+V+AW+PV   +SARF CL R Y+Y+FP+A LDI  M+ AAQ  
Sbjct:   157 EIRYTHILNRVLPPDIRVLAWAPVETSFSARFSCLERTYRYFFPRANLDIVTMNYAAQKY 216

Query:   276 VGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNV 312
             VGTHDFRNLCKM+V NGV+NF+R +  A V    QN+
Sbjct:   217 VGTHDFRNLCKMDVANGVINFQRTILSAQVQRVGQNL 253

GO:0005634 "nucleus" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

UNIPROTKB|E2RGS6 PUS3 "tRNA pseudouridine synthase" [Canis lupus familiaris (taxid:9615)]

 Score = 287 (106.1 bits), Expect = 6.9e-27, Sum P(2) = 6.9e-27
 Identities = 61/127 (48%), Positives = 79/127 (62%)

Query:   196 VVTLKIRSKLTSPGEESDDN----------ELPYLKMLNNNLPRDIKVVAWSPVPEKYSA 245
             V++L +RS         D N          E+ Y  +LN  LP DI+V+AW+PV   +SA
Sbjct:   126 VISLDLRSHFPEGSTSEDSNLKNEVNDVAKEIRYTHILNRVLPPDIRVLAWAPVEPSFSA 185

Query:   246 RFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGV 305
             RF CL R Y+Y+FP+A LDI  M+ AAQ  VGTHDFRNLCKM+V NGV+NF+R V  A V
Sbjct:   186 RFSCLERTYRYFFPRADLDIITMNYAAQKYVGTHDFRNLCKMDVANGVINFQRTVLFAQV 245

Query:   306 TSAWQNV 312
                 Q++
Sbjct:   246 ELVGQSL 252

GO:0031119 "tRNA pseudouridine synthesis" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1914299 Pus3 "pseudouridine synthase 3" [Mus musculus (taxid:10090)]

 Score = 289 (106.8 bits), Expect = 8.2e-27, Sum P(2) = 8.2e-27
 Identities = 56/97 (57%), Positives = 71/97 (73%)

Query:   211 ESDD--NELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAM 268
             E+DD   E+ Y  +LN  LP DI+V+AW+PV   +SARF CL R Y+Y+FP+A LDI  M
Sbjct:   151 EADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSFSARFSCLERTYRYFFPRADLDIATM 210

Query:   269 HKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGV 305
             + AAQ  VGTHDFRNLCKM+V NGV+NF+R +  A V
Sbjct:   211 NYAAQKYVGTHDFRNLCKMDVANGVINFQRTILCAQV 247

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0009451 "RNA modification" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IDA

GO:0016853 "isomerase activity" evidence=IEA

GO:0031119 "tRNA pseudouridine synthesis" evidence=IDA

UNIPROTKB|Q9BZE2 PUS3 "tRNA pseudouridine(38/39) synthase" [Homo sapiens (taxid:9606)]

 Score = 283 (104.7 bits), Expect = 2.4e-26, Sum P(2) = 2.4e-26
 Identities = 60/127 (47%), Positives = 81/127 (63%)

Query:   196 VVTLKIRSKLTSPGEESDD-----------NELPYLKMLNNNLPRDIKVVAWSPVPEKYS 244
             V++L +RS+    G +S+D            E+ Y  +LN  LP DI+++AW+PV   +S
Sbjct:   127 VISLDLRSQFPR-GRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSFS 185

Query:   245 ARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAG 304
             ARF CL R Y+Y+FP+A LDI  M  AAQ  VGTHDFRNLCKM+V NGV+NF+R +  A 
Sbjct:   186 ARFSCLERTYRYFFPRADLDIVTMDYAAQKYVGTHDFRNLCKMDVANGVINFQRTILSAQ 245

Query:   305 VTSAWQN 311
             V    Q+
Sbjct:   246 VQLVGQS 252

GO:0003723 "RNA binding" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0031119 "tRNA pseudouridine synthesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

RGD|1310757 Pus3 "pseudouridylate synthase 3" [Rattus norvegicus (taxid:10116)]

 Score = 281 (104.0 bits), Expect = 4.3e-26, Sum P(2) = 4.3e-26
 Identities = 59/126 (46%), Positives = 78/126 (61%)

Query:   196 VVTLKIRSKLTSPGEESDDN----------ELPYLKMLNNNLPRDIKVVAWSPVPEKYSA 245
             V++L +RS+     +  D N          E+ Y  +LN  LP DI+V+AW+P    +SA
Sbjct:   126 VISLDLRSQFPRSRDSEDSNLKDGADDIAKEIRYAHILNRVLPADIRVLAWAPAEPSFSA 185

Query:   246 RFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGV 305
             RF CL R Y+Y+FP A LDI  M+ AAQ  VGTHDFRNLCKM+V NGV NF+R +  A V
Sbjct:   186 RFSCLERTYRYFFPCADLDIATMNYAAQKYVGTHDFRNLCKMDVANGVTNFQRTILSAQV 245

Query:   306 TSAWQN 311
              +  Q+
Sbjct:   246 QTVAQS 251

GO:0003723 "RNA binding" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISO

GO:0031119 "tRNA pseudouridine synthesis" evidence=IEA;ISO

UNIPROTKB|F1RVF1 LOC100739830 "tRNA pseudouridine synthase" [Sus scrofa (taxid:9823)]

 Score = 281 (104.0 bits), Expect = 5.5e-26, Sum P(2) = 5.5e-26
 Identities = 56/106 (52%), Positives = 73/106 (68%)

Query:   210 EESDD--NELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDA 267
             +E +D   E+ Y  +LN  LP DI+V+AW+PV   +SARF CL R Y+Y+FP A LDI  
Sbjct:   148 DEVNDATKEIRYTHILNRVLPPDIRVLAWAPVEPSFSARFSCLERTYRYFFPHADLDIVT 207

Query:   268 MHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQ 313
             M+ AAQ  VGTHDFRNLCKM+V NGV NF+R +  A V    Q+++
Sbjct:   208 MNYAAQKYVGTHDFRNLCKMDVANGVTNFQRTILSAQVQLLSQSLE 253

GO:0008033 "tRNA processing" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

UNIPROTKB|F1S759 LOC100739830 "tRNA pseudouridine synthase" [Sus scrofa (taxid:9823)]

 Score = 281 (104.0 bits), Expect = 5.5e-26, Sum P(2) = 5.5e-26
 Identities = 56/106 (52%), Positives = 73/106 (68%)

Query:   210 EESDD--NELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDA 267
             +E +D   E+ Y  +LN  LP DI+V+AW+PV   +SARF CL R Y+Y+FP A LDI  
Sbjct:   148 DEVNDATKEIRYTHILNRVLPPDIRVLAWAPVEPSFSARFSCLERTYRYFFPHADLDIVT 207

Query:   268 MHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQ 313
             M+ AAQ  VGTHDFRNLCKM+V NGV NF+R +  A V    Q+++
Sbjct:   208 MNYAAQKYVGTHDFRNLCKMDVANGVTNFQRTILSAQVQLLSQSLE 253

GO:0008033 "tRNA processing" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	5.4.99.12	0.737
3rd Layer	5.4.99	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	496
cd02569	256	cd02569, PseudoU_synth_ScPus3, Pseudouridine synth	3e-56
COG0101	266	COG0101, TruA, Pseudouridylate synthase [Translati	1e-20
TIGR00071	227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	4e-20
PRK00021	244	PRK00021, truA, tRNA pseudouridine synthase A; Val	2e-18
cd00497	215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	8e-18
PRK14589	265	PRK14589, PRK14589, tRNA pseudouridine synthase AC	2e-16
cd02570	239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	2e-16
cd02866	219	cd02866, PseudoU_synth_TruA_Archea, Archeal pseudo	4e-14
PRK14586	245	PRK14586, PRK14586, tRNA pseudouridine synthase AC	1e-10
cd02568	245	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy	1e-09
PRK12434	245	PRK12434, PRK12434, tRNA pseudouridine synthase A;	3e-08
PRK14587	256	PRK14587, PRK14587, tRNA pseudouridine synthase AC	4e-08
cd08049	54	cd08049, TAF8, TATA Binding Protein (TBP) Associat	6e-07
pfam10406	51	pfam10406, TAF8_C, Transcription factor TFIID comp	2e-06
PRK14588	272	PRK14588, PRK14588, tRNA pseudouridine synthase AC	5e-06
smart00576	77	smart00576, BTP, Bromodomain transcription factors	2e-05
pfam07524	77	pfam07524, Bromo_TP, Bromodomain associated	2e-04
pfam07524	77	pfam07524, Bromo_TP, Bromodomain associated	7e-04

>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like

 Score =  187 bits (478), Expect = 3e-56
 Identities = 73/182 (40%), Positives = 97/182 (53%), Gaps = 32/182 (17%)

Query: 196 VVTLKIRSKLTSPGEES---------DDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSAR 246
           V++L +RS L                D+ ELPY K+LN  LP DI+++AW+PVP  +SAR
Sbjct: 61  VISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSAR 120

Query: 247 FDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVT 306
           F C+ R Y+Y+FP+  LDI+ M KAA+ L+G HDFRN CKM+V N V N+ R V  A V 
Sbjct: 121 FSCVSRTYRYFFPKGDLDIELMRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVE 180

Query: 307 ------SAWQNVQFN------------DIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKY 348
                        F              +  V+     F  GQG E P +I QL+D+EK 
Sbjct: 181 PVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVL-----FLIGQGLEPPSVISQLLDVEKN 235

Query: 349 PR 350
           PR
Sbjct: 236 PR 237

This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya. Length = 256

>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]

 Score = 91.2 bits (227), Expect = 1e-20
 Identities = 31/92 (33%), Positives = 45/92 (48%), Gaps = 16/92 (17%)

Query: 211 ESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAG-------- 262
            +D      ++ LN  LP DI+V+  + VP+ + ARF    R Y+Y    A         
Sbjct: 67  PADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAPLRPPFLAN 126

Query: 263 --------LDIDAMHKAAQYLVGTHDFRNLCK 286
                   LD+DAM +AA+ L+GTHDF +  K
Sbjct: 127 YVWHVPYPLDLDAMREAAKLLLGTHDFTSFRK 158

Length = 266

>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase

 Score = 88.9 bits (221), Expect = 4e-20
 Identities = 42/183 (22%), Positives = 70/183 (38%), Gaps = 47/183 (25%)

Query: 196 VVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255
           V++     ++        DN+L     LN  LP DI+V A +PV + + ARF    R+Y+
Sbjct: 60  VISFDTPKEIP-------DNKLNA--KLNALLPPDIRVKALAPVNDNFHARFSASKRHYR 110

Query: 256 YWFP-----QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQ 310
           Y         + LD++ M  AA+ L+G HDF N  K                +   S  +
Sbjct: 111 YILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSNFSKAK--------------SKSRSPIR 156

Query: 311 NVQFNDIKE-----VVDSEPS--------------FKKGQGNEKPEIIQQLVDIEKYPRI 351
            +    + E     + D   +                 G+G   PE + +L+D +K    
Sbjct: 157 TISDIKVSESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLA 216

Query: 352 KSA 354
            + 
Sbjct: 217 PTT 219

Members of this family are the tRNA modification enzyme TruA, tRNA pseudouridine(38-40) synthase. In a few species (e.g. Bacillus anthracis), TruA is represented by two paralogs [Protein synthesis, tRNA and rRNA base modification]. Length = 227

>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated

 Score = 84.4 bits (210), Expect = 2e-18
 Identities = 30/93 (32%), Positives = 43/93 (46%), Gaps = 18/93 (19%)

Query: 211 ESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-------------- 256
            +      + + LN  LP DI V+    VP+ + ARF    R Y+Y              
Sbjct: 67  PAPRPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRPARPPFLRG 126

Query: 257 ---WFPQAGLDIDAMHKAAQYLVGTHDFRNLCK 286
               +P   LD+DAM++AAQYL+G HDF +   
Sbjct: 127 YVWHYPYP-LDVDAMNEAAQYLLGEHDFTSFRA 158

Length = 244

>gnl|CDD|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA family

 Score = 81.7 bits (202), Expect = 8e-18
 Identities = 36/137 (26%), Positives = 52/137 (37%), Gaps = 15/137 (10%)

Query: 222 MLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDF 281
            LN  LP DI+V A   VP  + A   C  R Y+Y+ P   LD + +  AA   +GTHDF
Sbjct: 67  ALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIPSFPLDDERLKSAASRFLGTHDF 126

Query: 282 RNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQF---------NDIKEVVDSEPSFKKGQG 332
            N  K        N  R +           V           + ++ +V        G+G
Sbjct: 127 TNFSK----KDTRNTVRTIISIECKDLNPFVVVEFKAKSFLWHQVRRMVGF--LMLVGEG 180

Query: 333 NEKPEIIQQLVDIEKYP 349
              P  + +L+     P
Sbjct: 181 LHSPSSVSRLLAGPAPP 197

This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). Length = 215

>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional

 Score = 79.1 bits (195), Expect = 2e-16
 Identities = 27/65 (41%), Positives = 38/65 (58%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFR 282
           LN  LP DI    W+ VPE +  R+D + R Y+Y+F +   DI+AM  AA   +GTHDF 
Sbjct: 79  LNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYFSRPPSDINAMRDAAGEFIGTHDFS 138

Query: 283 NLCKM 287
              ++
Sbjct: 139 CFARV 143

Length = 265

>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial pseudouridine synthases similar to E

 Score = 78.3 bits (194), Expect = 2e-16
 Identities = 31/98 (31%), Positives = 46/98 (46%), Gaps = 20/98 (20%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDC-----------------LFRNYKYWFPQAGLDI 265
           LN+ LP DI+V++   VP+ + ARF                     R Y +  P+  LDI
Sbjct: 74  LNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRP-LDI 132

Query: 266 DAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHA 303
           +AM +AA+ L+GTHDF +      G    +  R +  A
Sbjct: 133 EAMQEAAKLLLGTHDFSSFRA--AGCQSKSTVRTIYRA 168

coli TruA. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators. Length = 239

>gnl|CDD|211343 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudouridine synthases

 Score = 71.3 bits (175), Expect = 4e-14
 Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 218 PYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVG 277
           P   M+N  LP+DI V+A + VPE +  R     + Y+Y       D++AM +AA+ L+G
Sbjct: 67  PIPPMINAKLPKDIWVLAGAKVPEDFDPRRWAHRKYYRYNLGS-DYDVEAMKEAAKKLIG 125

Query: 278 THDFRNLCKMN 288
           THDF N  K +
Sbjct: 126 THDFSNFSKRD 136

This group consists of archeal pseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs. Length = 219

>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional

 Score = 61.3 bits (149), Expect = 1e-10
 Identities = 31/77 (40%), Positives = 39/77 (50%), Gaps = 18/77 (23%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDC----------------LF-RNYKYWFPQAGLDI 265
           +N NLP DI V     VP+ +  RFD                 +F R Y +WFP   LD+
Sbjct: 80  MNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSKEKNVFLRKYVWWFPYE-LDL 138

Query: 266 DAMHKAAQYLVGTHDFR 282
           +AM KAA+YL G HDF 
Sbjct: 139 EAMRKAAKYLEGEHDFT 155

Length = 245

>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/ PUS2 like

 Score = 58.4 bits (142), Expect = 1e-09
 Identities = 31/96 (32%), Positives = 50/96 (52%), Gaps = 7/96 (7%)

Query: 189 HAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFD 248
           HA  R  VV+LK+   +    E     E   ++ LN++LP DI+V   + V + ++AR  
Sbjct: 61  HA-ARN-VVSLKV---IIDDPEGLGILED-LVEKLNSHLPSDIRVFGITRVTKSFNARKA 114

Query: 249 CLFRNYKYWFPQAGLD-IDAMHKAAQYLVGTHDFRN 283
           C  R Y+Y  P   L+ +   ++  +  VGTH+F N
Sbjct: 115 CDSRTYEYLLPTFALETLQRFNEILKEYVGTHNFHN 150

This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). Length = 245

>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed

 Score = 54.0 bits (130), Expect = 3e-08
 Identities = 27/79 (34%), Positives = 36/79 (45%), Gaps = 18/79 (22%)

Query: 220 LKMLNNNLPRDIKVVAWSPVPEKYSARF-----------------DCLFRNYKYWFPQAG 262
            K LN  LP DI V     V E++ AR+                 +   R Y     +  
Sbjct: 77  KKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEK- 135

Query: 263 LDIDAMHKAAQYLVGTHDF 281
           LD+ AM +AA+YLVG+HDF
Sbjct: 136 LDVKAMKEAAKYLVGSHDF 154

Length = 245

>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional

 Score = 54.1 bits (130), Expect = 4e-08
 Identities = 32/86 (37%), Positives = 45/86 (52%), Gaps = 8/86 (9%)

Query: 202 RSKLTSPGEESDDN------ELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255
           R   T PG  +  N      +LP L  +N+ LPR +   A + VPE ++ R     R Y 
Sbjct: 38  RGSRTDPGVSAVGNVVMTSQKLP-LGYVNSKLPRGVWAWAVAEVPEGFNPR-RAKRRRYL 95

Query: 256 YWFPQAGLDIDAMHKAAQYLVGTHDF 281
           Y  P  G D++AM +AA+ L GTHD+
Sbjct: 96  YVAPHWGEDVEAMREAAELLAGTHDY 121

Length = 256

>gnl|CDD|176263 cd08049, TAF8, TATA Binding Protein (TBP) Associated Factor 8

 Score = 45.7 bits (109), Expect = 6e-07
 Identities = 14/21 (66%), Positives = 15/21 (71%)

Query: 176 PHIPPYLPLFPDPHAYIRTPV 196
            HIP +LP FPDPH Y RTP 
Sbjct: 1   AHIPSWLPPFPDPHTYKRTPT 21

The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promoter recognition, or a role in the essential catalytic activity of the complex. The mouse ortholog of TAF8 is called taube nuss protein (TBN), and is required for early embryonic development. TBN mutant mice exhibit disturbances in the balance between cell death and cell survival in the early embryo. TAF8 plays a role in the differentiation of preadipocyte fibroblasts to adipocytes; it is also required for the integration of TAF10 into the TAF complex. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF8 is also a component of a small TAF complex (SMAT), which contains TAF8, TAF10 and SUPT7L. Several TAFs interact via histone-fold motifs. The histone fold (HFD) is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. TAF8 contains an H4 related histone fold motif, and interacts with several subunits of TFIID, including TBP and the histone-fold protein TAF10. Currently, five HF-containing TAF pairs have been described or suggested to exist in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10. Length = 54

>gnl|CDD|192573 pfam10406, TAF8_C, Transcription factor TFIID complex subunit 8 C-term

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 23/54 (42%), Positives = 27/54 (50%), Gaps = 9/54 (16%)

Query: 176 PHIPPYLPLFPDPHAYIRTPVVTL------KIRSKLTSPGEESDDNELPYLKML 223
            +IP +LP FP  H Y +TPV T       KIR KL    EES   E    K+L
Sbjct: 1   SYIPSWLPDFPPDHTYKKTPVYTEPVTDPRKIREKLV---EESRLAEKALRKLL 51

This is the C-terminal, Delta, part of the TAF8 protein. The N-terminal is generally the histone fold domain, Bromo_TP (pfam07524). TAF8 is one of the key subunits of the transcription factor for pol II, TFIID. TAF8 is one of the several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery. Length = 51

>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional

 Score = 48.0 bits (114), Expect = 5e-06
 Identities = 26/77 (33%), Positives = 34/77 (44%), Gaps = 16/77 (20%)

Query: 221 KMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAG----------------LD 264
           + LN +LP DI V      P  + ARF  + R Y+Y    A                 LD
Sbjct: 77  RGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGTLD 136

Query: 265 IDAMHKAAQYLVGTHDF 281
           + AM  A + L+GTHDF
Sbjct: 137 VAAMDAALKLLIGTHDF 153

Length = 272

>gnl|CDD|128846 smart00576, BTP, Bromodomain transcription factors and PHD domain containing proteins

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 18/34 (52%), Positives = 24/34 (70%)

Query: 101 IKEVGGLSHDFCELANRQQPMLADVLLALIELGI 134
           I+E+G  +H + ELA R +P L DV+LAL  LGI
Sbjct: 40  IQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73

subdomain of archael histone-like transcription factors. Length = 77

>gnl|CDD|219450 pfam07524, Bromo_TP, Bromodomain associated

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 16/34 (47%), Positives = 22/34 (64%)

Query: 101 IKEVGGLSHDFCELANRQQPMLADVLLALIELGI 134
           I+E+G  +  F E A R +P L DV+L L E+GI
Sbjct: 40  IQELGRQAKRFAEHAGRSEPTLFDVVLTLKEMGI 73

This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold. Length = 77

>gnl|CDD|219450 pfam07524, Bromo_TP, Bromodomain associated

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 9  RSLLKSSVVALLAEVGFDAADNAALETLVEICQACKY-TCLTVTAKVLSSHKER 61
            LLK  V  +L   GFD+A+ +ALETL +I Q   Y   L   AK  + H  R
Sbjct: 5  HDLLKVVVAQILETAGFDSAEESALETLTDIAQ--SYIQELGRQAKRFAEHAGR 56

This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold. Length = 77

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	496
PLN03078	513	Putative tRNA pseudouridine synthase; Provisional	100.0
PRK12434	245	tRNA pseudouridine synthase A; Reviewed	100.0
COG0101	266	TruA Pseudouridylate synthase [Translation, riboso	100.0
PRK14589	265	tRNA pseudouridine synthase ACD; Provisional	100.0
cd02569	256	PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Ps	100.0
PRK00021	244	truA tRNA pseudouridine synthase A; Validated	100.0
cd00497	224	PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudo	100.0
PRK14588	272	tRNA pseudouridine synthase ACD; Provisional	100.0
TIGR00071	227	hisT_truA pseudouridylate synthase I. universal so	100.0
PRK14586	245	tRNA pseudouridine synthase ACD; Provisional	100.0
cd02570	239	PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudou	100.0
cd02866	221	PseudoU_synth_TruA_Archea PseudoU_synth_archea: Ps	100.0
PRK14587	256	tRNA pseudouridine synthase ACD; Provisional	100.0
cd02568	245	PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: P	100.0
KOG2554|consensus	425		100.0
KOG2553|consensus	416		100.0
KOG4393|consensus	295		99.95
KOG4336|consensus	323		99.88
KOG2389|consensus	353		99.78
smart00576	77	BTP Bromodomain transcription factors and PHD doma	99.65
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	99.64
PF01416	105	PseudoU_synth_1: tRNA pseudouridine synthase; Inte	99.6
PF10406	51	TAF8_C: Transcription factor TFIID complex subunit	97.54
cd08049	54	TAF8 TATA Binding Protein (TBP) Associated Factor	97.49
PF10105	187	DUF2344: Uncharacterized protein conserved in bact	96.75
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	96.7
cd00076	85	H4 Histone H4, one of the four histones, along wit	96.4
PTZ00015	102	histone H4; Provisional	96.17
PLN00035	103	histone H4; Provisional	96.08
smart00803	65	TAF TATA box binding protein associated factor. TA	95.61
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	95.12
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	94.99
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	92.53
PF02969	66	TAF: TATA box binding protein associated factor (T	92.24
smart00417	74	H4 Histone H4.	89.7
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	87.34
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	87.33
KOG3334|consensus	148		82.69

>PLN03078 Putative tRNA pseudouridine synthase; Provisional

Probab=100.00  E-value=6.3e-52  Score=439.32  Aligned_cols=325  Identities=17%  Similarity=0.167  Sum_probs=247.2

Q ss_pred             chhhhhhhhhhhhhcceeeeeeeeeccccHHHhhhcC--CCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCC
Q psy3604          80 VEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELAN--RQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPS  157 (496)
Q Consensus        80 ~~~~~~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~ag--RTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~  157 (496)
                      ..+-+-..+.....++++++.|+|+|+.|+|||.+.+  ...++.+.++.||..+|...+.-.                 
T Consensus        56 ~~~~~~~~~w~~~~krrvaL~IaYdGt~Y~G~Q~Q~n~~~~~TVEg~LE~AL~k~~~I~e~n~-----------------  118 (513)
T PLN03078         56 NSDQGGGMKWESARKKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNY-----------------  118 (513)
T ss_pred             ccCCCCCCCcccccceEEEEEEEEcCCCcceeeECCCCCCCCCHHHHHHHHHHHHhCcccccc-----------------
Confidence            3333445555566778889999999999999998876  245789999999998764211100                 


Q ss_pred             CCCCCchhccccccCCCCCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEE
Q psy3604         158 TQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWS  237 (496)
Q Consensus       158 ~~p~~~~fL~aG~~~~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~  237 (496)
                                 |    .+..|--..++|||+||||++||++|+++.+  ...|..+.+...|...||++||+||||+++.
T Consensus       119 -----------~----~~~ki~~~rAgRTDkGVHA~gQVvsf~l~~p--~~~~~~d~~~~~L~~~LN~~LP~DIRVl~v~  181 (513)
T PLN03078        119 -----------G----NLHKIGWARSSRTDKGVHSLATMISLKMEIP--ENAWKDDPDGIALAKFINSHLPDNIRVFSIL  181 (513)
T ss_pred             -----------c----cccceeEEeeccCCcCccccccEEEEeccCc--chhccccchHHHHHHHHHhcCCCCeEEEEEE
Confidence                       0    0001111346789999999999999998542  1111112334578899999999999999999


Q ss_pred             ecCCCCCccccCCceeEEEecCCC-------------CccHHHHHHHHHHccccccccccccccccCC------------
Q psy3604         238 PVPEKYSARFDCLFRNYKYWFPQA-------------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNG------------  292 (496)
Q Consensus       238 ~V~~~FhARfsa~~R~Y~Y~~~~~-------------~LDie~M~eAak~fvGtHDF~nF~~~~~~~~------------  292 (496)
                      +|+++|||||+|++|+|+|+||..             ..|+++|++|+++|+|+|||+|||.......            
T Consensus       182 ~V~~~FhAR~sc~sRtY~Y~iP~~~~~~k~~f~~~~~~~dI~kMneAl~~fiGtHDFhNFT~r~~y~~~~~~~~~~~~~~  261 (513)
T PLN03078        182 PAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEFNSILNGFEGEHPFHNYTARSKYRKKLPGKHKQRNGA  261 (513)
T ss_pred             ECCCCcCCCCCCCceEEEEEEccccccCCCccchhhhHHHHHHHHHHHHhcccccCcccccCCCccCccccccccccccc
Confidence            999999999999999999999751             0279999999999999999999986531100            


Q ss_pred             -----------------------------------------------------------------------CCCceEEEE
Q psy3604         293 -----------------------------------------------------------------------VVNFKRLVT  301 (496)
Q Consensus       293 -----------------------------------------------------------------------~~stvRtI~  301 (496)
                                                                                             ..+..|.|+
T Consensus       262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wl~e~d~~d~i~~s~~R~I~  341 (513)
T PLN03078        262 VSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSGSSDENEDILKFQSSQVQIRARWLHEPDETDRISASHFRKIF  341 (513)
T ss_pred             cccccccccccccccccccccccccchhhhhccccccccccccccccccccccchhhhhhhccCCccccccchhheEEEE
Confidence                                                                                   003379999


Q ss_pred             EEEEEec-----ceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCee
Q psy3604         302 HAGVTSA-----WQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNEL  369 (496)
Q Consensus       302 ~i~i~~~-----~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L  369 (496)
                      +|.+...     .+++.|+|.|+||     |  ||++++|++|..+++.|..+|....+  +   .+|+||   ++||+|
T Consensus       342 ~~~~~~~~~~~g~~fv~i~I~GqSFmlhQIRKMIG~~~aV~rg~~~~~~i~~~L~~~~r--~---~~P~AP---~~GL~L  413 (513)
T PLN03078        342 RCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIRLSLTKFSR--I---VLPLAP---SEVLIL  413 (513)
T ss_pred             EeecCCccccCCceEEEEEEEehhHHHHHHHHHHHHHHHHHhccCCHHHHHHHhccccc--c---ccccCC---CcceEE
Confidence            9988542     2799999999999     8  99999999999999999999986433  2   345776   999999


Q ss_pred             eeeccCCCCcccccchHHHH--HHHHHHHhhhhcccccccccchhhhhhhccccchhhcccCcccccccccccCCCCcch
Q psy3604         370 FRRVFLLSFLAWVDQYRIRQ--TAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRIL  447 (496)
Q Consensus       370 ~~V~Y~~~~l~f~~~~~~~~--~~~~~i~~~~~~~y~~~~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  447 (496)
                      ++|.|+..+..=......+.  -..+.+.+.+.+||..+++|+|+++++.+.++|++|++|||       +|++||+.||
T Consensus       414 ~~~~F~~yn~~~~~~~p~~~~~~e~e~~~~~i~eF~~~~i~p~i~~~~~~~~~~w~~w~~nl~-------~~~~~~~~~~  486 (513)
T PLN03078        414 RGNSFSVRKKPGNIKRPGMETMNESEEILKGVEEFYRAVMLPQVSKFLDPSKPPWKEWVENLD-------RFTSIPDAQL  486 (513)
T ss_pred             EeeeccccccccccCCCCccccccHHHHHHHHHHHHHHhhhHHHHHHhccccchHHHHHHHHH-------hhcCCCHHHH
Confidence            99999732111000111121  13334467778888899999999999999999999999999       9999999999


Q ss_pred             hhhccc
Q psy3604         448 SETGKL  453 (496)
Q Consensus       448 ~e~~~~  453 (496)
                      +|||+-
T Consensus       487 ~~v~~~  492 (513)
T PLN03078        487 DEVRKA  492 (513)
T ss_pred             HHHHHH
Confidence            999974

>PRK12434 tRNA pseudouridine synthase A; Reviewed

Probab=100.00  E-value=5.4e-48  Score=382.18  Aligned_cols=221  Identities=24%  Similarity=0.256  Sum_probs=188.7

Q ss_pred             ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604          95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH  174 (496)
Q Consensus        95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~  174 (496)
                      .+|++.|+|+|+.++|||.+.+...++.+.++.||..++..          +                ..+.        
T Consensus         2 ~~~~l~i~YdGt~y~G~Q~Q~~~~~TVq~~le~aL~~~~~~----------~----------------~~~~--------   47 (245)
T PRK12434          2 RNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTGE----------E----------------IEII--------   47 (245)
T ss_pred             ceEEEEEEECCCccceEeeCCCCCCCHHHHHHHHHHHHhCC----------C----------------eEEE--------
Confidence            46789999999999999998754456788888888875421          0                0112        


Q ss_pred             CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604         175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY  254 (496)
Q Consensus       175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y  254 (496)
                             .++|||+||||++||++|+++..+         ++..+..+||+.||+||+|+++.+||++|||||+|++|+|
T Consensus        48 -------~agRTD~GVHA~~qv~~f~~~~~~---------~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y  111 (245)
T PRK12434         48 -------GCGRTDAGVHALNQVANFQTDEKL---------SEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTY  111 (245)
T ss_pred             -------EeccCCCCcCccCcEEEEEcCCCC---------CHHHHHHHHHccCCCCeEEEEEEECCCCcccccCCCcEEE
Confidence                   246799999999999999987643         5778999999999999999999999999999999999999


Q ss_pred             EEecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEee
Q psy3604         255 KYWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIK  318 (496)
Q Consensus       255 ~Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G  318 (496)
                      +|+|+.                .++|+++|++|++.|+|+|||+|||+.+  +..++++|+|+++++.+.++++.|+|+|
T Consensus       112 ~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~--~~~~~~~R~I~~~~v~~~~~~~~i~i~g  189 (245)
T PRK12434        112 LYKIWNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTSFTNAK--SKKKSTVREIYSIDIMEEDGFVQIRVSG  189 (245)
T ss_pred             EEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcCHHhhcCCC--CCCCCCEEEEEEEEEEEeCCEEEEEEEe
Confidence            999852                4689999999999999999999999764  2357999999999999888899999999


Q ss_pred             Cce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         319 EVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       319 ~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                      +||     |  ||+|++||+|++++++|+++|+.+++  ..     ..|+|||+||+|++|.|
T Consensus       190 ~~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r--~~-----~~~~APa~GL~L~~V~Y  245 (245)
T PRK12434        190 NGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDR--NQ-----ANCTAPASGLYLENVEY  245 (245)
T ss_pred             cHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCc--cc-----CCCccCCCCCEEeEeEC
Confidence            999     7  99999999999999999999997543  21     12356699999999998

>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.3e-48  Score=384.06  Aligned_cols=227  Identities=23%  Similarity=0.266  Sum_probs=194.9

Q ss_pred             eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604          96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP  175 (496)
Q Consensus        96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p  175 (496)
                      +|++.|+|+|+.++|||.|++- .++.++++.||..++....                          .+..+       
T Consensus         3 ri~l~iaYdGt~f~G~Q~Qp~~-~TVQ~~le~aL~~i~~~~~--------------------------~i~~A-------   48 (266)
T COG0101           3 RIALKIAYDGTRFHGWQRQPNV-RTVQGELEKALSKIGGESV--------------------------RVIGA-------   48 (266)
T ss_pred             eEEEEEEEcCCceeeeccCCCC-CCHHHHHHHHHHHhcCCcc--------------------------eeEEe-------
Confidence            7899999999999999999774 5688889999998775311                          12333       


Q ss_pred             CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604         176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK  255 (496)
Q Consensus       176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~  255 (496)
                              .|||+||||.+||+||+++...         .+..|..+||+.||+||+|+++++||++|||||+|.+|+|+
T Consensus        49 --------GRTD~GVHA~gqv~hfd~~~~~---------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaRfsa~~R~Y~  111 (266)
T COG0101          49 --------GRTDAGVHALGQVVHFDTPADR---------PLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYR  111 (266)
T ss_pred             --------cCCCcCccccccEEEEEcCCcc---------cHHHHHHHHHhcCCCCcEEEEEEECCCCCCCcccccceEEE
Confidence                    4699999999999999987643         37899999999999999999999999999999999999999


Q ss_pred             EecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeC
Q psy3604         256 YWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKE  319 (496)
Q Consensus       256 Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~  319 (496)
                      |+|+.                .+||+++|++|++.|+|+|||+|||+.+.  +..|++|+|++++|.+.++.+.|+|+|+
T Consensus       112 Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~aa~~l~G~HDF~sF~~~~~--~~~s~vRti~~~~v~~~~~~i~i~i~g~  189 (266)
T COG0101         112 YIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFRKAGC--QSKSPVRTIYRIDVSRDGDLIVIDISGN  189 (266)
T ss_pred             EEEcCccCCChhhhcccccccCcCCHHHHHHHHHHccccccchhhccCCC--ccCCCeEEEEEEEEEecCCEEEEEEEeC
Confidence            99863                35799999999999999999999999753  3458999999999999999999999999


Q ss_pred             ce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCccccc
Q psy3604         320 VV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVD  383 (496)
Q Consensus       320 sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~  383 (496)
                      ||     |  ||+|++||+|++++++|.++|+.+++.  .  ..+   +|||+||+|++|.|+ +..++..
T Consensus       190 sFL~~mVR~iVg~l~~vg~g~~~~~~i~~ll~~~~r~--~--~~~---~Apa~GL~L~~v~Y~-~~~~~~~  252 (266)
T COG0101         190 SFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRK--L--AGP---TAPAEGLYLVRVDYP-EDFELPE  252 (266)
T ss_pred             hhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhccCcc--c--CCC---CCCCCccEEEeeccC-Ccccccc
Confidence            99     7  999999999999999999999964432  2  233   556999999999997 3344443

>PRK14589 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=1.1e-47  Score=383.49  Aligned_cols=249  Identities=21%  Similarity=0.260  Sum_probs=203.6

Q ss_pred             eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604          96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP  175 (496)
Q Consensus        96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p  175 (496)
                      +|++.|+|+|+.++|||.+.+ ..++.+.++.||..++... +..     +                ..+          
T Consensus         2 ~~~l~i~YdGt~y~G~Q~Q~~-~~TVq~~Le~aL~~~~~~~-~~~-----~----------------~~i----------   48 (265)
T PRK14589          2 RLAFRISYIGTRFFGSQYQPD-QRTVEGEFIAACRRLGLFS-DWR-----E----------------AGF----------   48 (265)
T ss_pred             cEEEEEEEcCCCeeeeeeCCC-CCCHHHHHHHHHHHhhCcc-CCc-----e----------------eeE----------
Confidence            578899999999999999887 3467888889998877421 000     0                011          


Q ss_pred             CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604         176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK  255 (496)
Q Consensus       176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~  255 (496)
                           ..++|||+||||++||++|+++.            +..+...||+.||+||+|+++.+|+++|||||+|++|+|+
T Consensus        49 -----~~agRTDaGVHA~gqv~~f~~~~------------~~~~~~~lN~~LP~dI~V~~~~~v~~~FhAR~~a~~R~Y~  111 (265)
T PRK14589         49 -----ALAGRTDRGVHARGQVLAFSTHK------------PERAVEALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYR  111 (265)
T ss_pred             -----EEeccCCcCccccccEEEEEeCC------------hHHHHHHHHhhCCCCeEEEEEEEcCCCCCcccCCceeEEE
Confidence                 23567999999999999999752            4578899999999999999999999999999999999999


Q ss_pred             EecCCCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHH
Q psy3604         256 YWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFK  328 (496)
Q Consensus       256 Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~  328 (496)
                      |+|+..++|+++|++|++.|+|+|||+|||+.+    .++++|+|+++++.+.++.+.|+|+|+||     |  ||+|++
T Consensus       112 Y~i~~~~lD~~~m~~a~~~f~G~HDF~~F~~~~----~~~~vRtI~~i~v~~~~~~~~~~i~G~~FL~~mVR~mVG~ll~  187 (265)
T PRK14589        112 YYFSRPPSDINAMRDAAGEFIGTHDFSCFARVE----GKSPVRTILRIRVFSDGGFPVFEVTAQSFLWHMVRCMAGALLQ  187 (265)
T ss_pred             EEEecCccHHHHHHHHHHHccCCccHHHHhccC----CCCCeEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHHH
Confidence            999989999999999999999999999999863    46899999999999988899999999999     7  999999


Q ss_pred             HhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccccchHHHHH----HHHHHHhhhhcccc
Q psy3604         329 KGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQT----AHCNIFTNLCTFYV  404 (496)
Q Consensus       329 VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~~~~~~~~----~~~~i~~~~~~~y~  404 (496)
                      ||+|++++++|+++|+.+++.     ..+   +|||+||+|++|.|+.   +|....++...    ++.+.+...+.++.
T Consensus       188 vg~G~~~~~~i~~~L~~~~r~-----~~~---~APa~GL~L~~V~Y~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  256 (265)
T PRK14589        188 IGEGEMEPDDIERLLSGPCKR-----KVK---PAPAEGLVLWDVDCGL---TFTPIPADPRSVRRIARQRREAHLMETVY  256 (265)
T ss_pred             HhCCCCCHHHHHHHHhCcCCC-----CCC---ccCCCCcEEeeeecCC---ccccccchHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999975432     122   4569999999999962   77766555421    33334444555555


Q ss_pred             ccccc
Q psy3604         405 PTYLP  409 (496)
Q Consensus       405 ~~~lp  409 (496)
                      ..+||
T Consensus       257 ~~~~~  261 (265)
T PRK14589        257 ALLLP  261 (265)
T ss_pred             HHhcc
Confidence            56665

>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like

Probab=100.00  E-value=3.3e-47  Score=378.68  Aligned_cols=233  Identities=35%  Similarity=0.542  Sum_probs=188.4

Q ss_pred             eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604         100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP  179 (496)
Q Consensus       100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP  179 (496)
                      .|+|+|+.|+|||.+.+...++.+.++.||..++.--+. .     +                ..+.             
T Consensus         2 ~i~YdGt~y~G~Q~Q~~~~~TVq~~Le~aL~~~~~i~~~-~-----~----------------~~~~-------------   46 (256)
T cd02569           2 RFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDR-Q-----T----------------SNYS-------------   46 (256)
T ss_pred             EEEEeCCcceeeeECCCCCCCHHHHHHHHHHHhcCCCCC-C-----c----------------eeEE-------------
Confidence            689999999999998763356888889999987631000 0     0                1111             


Q ss_pred             CCCCCCCCcccccccceEEEeecccCCCCC---C------CCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCC
Q psy3604         180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPG---E------ESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL  250 (496)
Q Consensus       180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~---~------~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~  250 (496)
                        .++|||+||||++||++|++...++...   +      ........+..+||++||+||+|+++.+|+++|||||+|+
T Consensus        47 --~agRTD~GVHA~~qv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~  124 (256)
T cd02569          47 --RCGRTDKGVSAFGQVISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSARFSCV  124 (256)
T ss_pred             --eecccCccccccCcEEEEEecCCCCccccccccccccccccchHHHHHHHHHhhCCCCcEEEEEEECCCCcCCCccCC
Confidence              3467999999999999999976542210   0      0011224688999999999999999999999999999999


Q ss_pred             ceeEEEecCCCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecc------eEEEEEEeeCce---
Q psy3604         251 FRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAW------QNVQFNDIKEVV---  321 (496)
Q Consensus       251 ~R~Y~Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~------~~i~i~I~G~sF---  321 (496)
                      +|+|+|+|+...+|+++|++|+++|+|+|||+|||+.+.+++.++++|+|++++|.+.+      +++.|+|+|+||   
T Consensus       125 ~R~Y~Y~i~~~~ldi~~m~~a~~~f~G~HDF~~F~~~~~~~~~~~~~RtI~~~~v~~~~~~~~~~~~~~~~i~g~~FL~~  204 (256)
T cd02569         125 SRTYRYFFPKGDLDIELMRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWH  204 (256)
T ss_pred             ceEEEEEecCCCCCHHHHHHHHHHhhCCcchHHHhccCcccCCCCCceEEEEEEEEEccCCCCCCcEEEEEEEEcHHHHH
Confidence            99999999999999999999999999999999999864333457999999999998864      789999999999   


Q ss_pred             --e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         322 --D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       322 --R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                        |  ||+|++||+|++++++|+++|+.+.+...+  .++   +|||+||+|++|.|
T Consensus       205 mVR~mvg~ll~vg~G~~~~~~i~~~L~~~~r~~~~--~~~---~Ap~~GL~L~~v~~  256 (256)
T cd02569         205 QVRCMMAVLFLIGQGLEPPSVISQLLDVEKNPRKP--QYT---MASEVPLVLYDCGF  256 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHhCccccCCC--CcC---cCCCCCcEEEEeeC
Confidence              7  999999999999999999999986543322  112   45699999999987

This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.

>PRK00021 truA tRNA pseudouridine synthase A; Validated

Probab=100.00  E-value=6.5e-47  Score=374.08  Aligned_cols=220  Identities=25%  Similarity=0.293  Sum_probs=189.3

Q ss_pred             ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604          95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH  174 (496)
Q Consensus        95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~  174 (496)
                      .++++.|+|+|+.++|||.+.+ ..++.+.++.||..++..  .                        ..+..       
T Consensus         2 ~~~~l~i~YdGt~y~G~q~q~~-~~TVq~~le~aL~~~~~~--~------------------------~~~~~-------   47 (244)
T PRK00021          2 MRIALTIEYDGTNFHGWQRQPN-GRTVQGELEKALSKLAGE--P------------------------VRVIG-------   47 (244)
T ss_pred             eEEEEEEEECCCccceeeeCCC-CCCHHHHHHHHHHHHhCC--C------------------------eEEEE-------
Confidence            4678999999999999999877 347888889999987751  0                        11222       


Q ss_pred             CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604         175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY  254 (496)
Q Consensus       175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y  254 (496)
                              ++|||+||||++||++|+++..+         ++..+...||+.||+||+|+++.+||++|||||+|++|+|
T Consensus        48 --------agRTD~GVHA~~qvv~~~~~~~~---------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~F~aR~~a~~R~Y  110 (244)
T PRK00021         48 --------AGRTDAGVHALGQVAHFDTPAPR---------PPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRY  110 (244)
T ss_pred             --------EccCCCcccccCcEEEEEeCCCC---------CHHHHHHHHHhcCCCCEEEEEeEecCCCcCcCcCCCceEE
Confidence                    45799999999999999997643         6778999999999999999999999999999999999999


Q ss_pred             EEecCCC----------------CccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEee
Q psy3604         255 KYWFPQA----------------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIK  318 (496)
Q Consensus       255 ~Y~~~~~----------------~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G  318 (496)
                      +|+++..                .+|+++|++|++.|+|+|||+|||+.+  .+.++++|+|.+++|.++++++.|+|+|
T Consensus       111 ~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~HdF~~F~~~~--~~~~~~~R~I~~~~v~~~~~~~~i~i~g  188 (244)
T PRK00021        111 RYRIYNRPARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSFRASG--CQSKSPVRTIYEADVTREGDFIVFDISA  188 (244)
T ss_pred             EEEEecCCCCChhhCCcEEEeCCCCcHHHHHHHHHHhcCceeeeeeeCCC--CCCCCCeEEEEEEEEEEcCCEEEEEEEE
Confidence            9998743                489999999999999999999998653  3467999999999999888899999999


Q ss_pred             Cce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         319 EVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       319 ~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                      +||     |  ||+|++||+|++++++|+++|+.+.+.  .  ..+   +|||+||+|++|.|
T Consensus       189 ~sFL~~qVR~mvg~l~~vg~g~~~~~~i~~~L~~~~~~--~--~~~---~APa~GL~L~~v~Y  244 (244)
T PRK00021        189 NGFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRT--L--AGP---TAPAEGLYLVEVDY  244 (244)
T ss_pred             chhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcc--c--CCC---ccCCCCCEEeeeEC
Confidence            999     7  999999999999999999999975432  2  223   45699999999988

>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family

Probab=100.00  E-value=5.2e-47  Score=370.64  Aligned_cols=217  Identities=35%  Similarity=0.542  Sum_probs=184.7

Q ss_pred             eeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCCC
Q psy3604         101 IKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPP  180 (496)
Q Consensus       101 L~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP~  180 (496)
                      |+|+|+.++|||.+.+- .++.+.++.||..++.. +++.     +                ..+               
T Consensus         1 i~YdGt~f~G~Q~Q~~~-~TVq~~le~aL~~~~~~-~~~~-----~----------------~~i---------------   42 (224)
T cd00497           1 IAYDGWKYHGFQRQPDV-PTVEGELFKALLKTGLI-ESPK-----P----------------SNY---------------   42 (224)
T ss_pred             CEEcCCceeeEeeCcCC-CCHHHHHHHHHHHhhCc-CCCc-----c----------------eeE---------------
Confidence            58999999999999773 46888899999887642 1100     0                112               


Q ss_pred             CCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecCC
Q psy3604         181 YLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQ  260 (496)
Q Consensus       181 ~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~~  260 (496)
                      ..++|||+||||++||++|+++..+         +  .+...||+.||+||+|+++.+|+++|||||+|++|+|+|+++.
T Consensus        43 ~~agRTD~GVHA~~qv~~~~~~~~~---------~--~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~  111 (224)
T cd00497          43 SRAGRTDKGVSALGQVVSLETRSKL---------K--PYPDILNGLLPKDIRVLAWAPVPEDFHARFSCVSRTYRYYFPG  111 (224)
T ss_pred             EEeccccccccccccEEEEEECCCc---------H--HHHHHHHhhCCCCcEEEEEEEeCCCCCCCcccCeEEEEEEECC
Confidence            2356799999999999999997543         1  7999999999999999999999999999999999999999998


Q ss_pred             CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHHHhCCC
Q psy3604         261 AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFKKGQGN  333 (496)
Q Consensus       261 ~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~VG~G~  333 (496)
                      ..+|+++|++|++.|+|+|||+|||+.+.  ..++++|+|.++++.+.++++.|+|+|+||     |  ||+|++||+|+
T Consensus       112 ~~~d~~~m~~a~~~f~G~HDF~~F~~~~~--~~~~~~RtI~~~~v~~~~~~~~i~i~g~sFL~~mVR~mvg~ll~vg~g~  189 (224)
T cd00497         112 GDLDIEAMREAAKLLLGTHDFRNFCKKDG--RKKNPVRTIISAEVEEVDDFYVFEVKGKSFLWHQVRRIVAALFLVGQGL  189 (224)
T ss_pred             CCcCHHHHHHHHHHccCcccHHHhcCCCC--CCCCCeEEEEEEEEEecCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCCC
Confidence            89999999999999999999999998642  347999999999999888899999999999     6  99999999999


Q ss_pred             CCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         334 EKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       334 ~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                      +++++|+++|+.+.+...+      .++|||+||+|++|.|
T Consensus       190 ~~~~~i~~~l~~~~~~~~~------~~~APa~GL~L~~V~Y  224 (224)
T cd00497         190 EPPSIISRLLDEEKRPSKP------QYPAPPEPLVLWDCKY  224 (224)
T ss_pred             CCHHHHHHHHhcCCcccCC------CCcCCCCCcEEeeeeC
Confidence            9999999999875432211      1246699999999988

This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly ph

>PRK14588 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=1.1e-46  Score=377.98  Aligned_cols=227  Identities=19%  Similarity=0.198  Sum_probs=191.0

Q ss_pred             ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604          95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH  174 (496)
Q Consensus        95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~  174 (496)
                      ++|++.|+|+|+.++|||.+.+- .++.+.++.||..+.-.          +                ..+.        
T Consensus         2 ~~~~l~iaYdGt~f~G~Q~Q~~~-~TVq~~Le~aL~~l~~~----------~----------------i~i~--------   46 (272)
T PRK14588          2 RTIALLLEYDGTDFAGSQWQTDG-RTVQGALEAAWQALTQE----------R----------------RRIV--------   46 (272)
T ss_pred             ceEEEEEEEcCCceeeeEECCCC-CCHHHHHHHHHHHhhCC----------C----------------ceEE--------
Confidence            46899999999999999998772 35677777888765310          0                0112        


Q ss_pred             CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604         175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY  254 (496)
Q Consensus       175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y  254 (496)
                             .++|||+||||++||++|+++..+         ++..+...||+.||+||+|+++.+|+++|||||+|++|+|
T Consensus        47 -------~AgRTDaGVHA~gQv~~f~~~~~~---------~~~~l~~~LN~~LP~dI~V~~v~~v~~~FhaR~~a~~R~Y  110 (272)
T PRK14588         47 -------LAGRTDAGVHARGQVAHVQTDTRH---------SLATIWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREY  110 (272)
T ss_pred             -------EecCCCcCcCccccEEEEEcCCCC---------CHHHHHHHHHhcCCCCeEEEEEEECCCCcCcccCCCcEEE
Confidence                   346799999999999999986543         5778999999999999999999999999999999999999


Q ss_pred             EEecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEec----ceEEEE
Q psy3604         255 KYWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA----WQNVQF  314 (496)
Q Consensus       255 ~Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~----~~~i~i  314 (496)
                      +|+|+.                ..+|+++|++|++.|+|+|||+|||+..   ..++++|+|+++++.+.    ++.+.|
T Consensus       111 ~Y~i~~~~~~~p~~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~~~~---~~~~~vRtI~~~~~~~~~~~~~~~i~~  187 (272)
T PRK14588        111 RYVIDCAPAPSPQLRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAFTTAP---QEGSTVRTCYWARCTDTEWFGRPLLAI  187 (272)
T ss_pred             EEEEcCCCCCChhhcCceEecCCCCCHHHHHHHHHHccCCcchHhhcCCC---CCCCCeEEEEEEEEEEcccCCCCEEEE
Confidence            999852                4689999999999999999999999862   35789999999999875    368999


Q ss_pred             EEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccc
Q psy3604         315 NDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWV  382 (496)
Q Consensus       315 ~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~  382 (496)
                      +|+|+||     |  ||+|++||+|++++++|+++|+.+++  ..     ..|+|||+||+|++|.|++..+.|.
T Consensus       188 ~i~g~~FL~~mVR~mVg~ll~vg~g~~~~~~i~~~L~~~~r--~~-----~~~~APa~GL~L~~V~Y~~~~~~~~  255 (272)
T PRK14588        188 EVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDR--RL-----AGPTAPAHGLYLTAVRYPPGLIRWV  255 (272)
T ss_pred             EEEEchhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCc--cc-----CCCCCCCCCcEEeeEecCchhcccc
Confidence            9999999     7  99999999999999999999987543  22     2235569999999999987777776

>TIGR00071 hisT_truA pseudouridylate synthase I

Probab=100.00  E-value=2.8e-46  Score=366.11  Aligned_cols=214  Identities=25%  Similarity=0.335  Sum_probs=184.7

Q ss_pred             eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604          96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP  175 (496)
Q Consensus        96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p  175 (496)
                      ++++.|+|+|+.++|||.+.+ ..++.+.++.||..++..          +                ..+.         
T Consensus         2 ~~~l~i~YdGt~f~G~Q~Q~~-~~TVq~~le~aL~~~~~~----------~----------------i~~~---------   45 (227)
T TIGR00071         2 KIALKIAYDGSNYHGWQRQPN-KRTVQGELEKALEAIGKK----------K----------------ITIM---------   45 (227)
T ss_pred             eEEEEEEEcCCCeeEEeECcC-CCCHHHHHHHHHHHHhCC----------C----------------eeEE---------
Confidence            568899999999999999987 346788888999886641          0                0112         


Q ss_pred             CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604         176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK  255 (496)
Q Consensus       176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~  255 (496)
                            .++|||+||||++||++|+++..+         ++..+..+||++||+||+|+++.+|+++|||||+|++|+|+
T Consensus        46 ------~agRTD~GVHA~~qv~~f~~~~~~---------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaR~~a~~R~Y~  110 (227)
T TIGR00071        46 ------SAGRTDKGVHAMGQVISFDTPKEI---------PDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYR  110 (227)
T ss_pred             ------eeccCcCCccccccEEEEEecCCC---------CHHHHHHHHHccCCCCEEEEEEEeCCCCcCCCCCCCcEEEE
Confidence                  345799999999999999997643         56789999999999999999999999999999999999999


Q ss_pred             EecCCC-----CccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--h
Q psy3604         256 YWFPQA-----GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--S  323 (496)
Q Consensus       256 Y~~~~~-----~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--V  323 (496)
                      |+|+..     .+|+++|++|++.|+|+|||+|||+..  .+.++++|+|++++|.+.++++.|+|+|+||     |  |
T Consensus       111 Y~i~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~--~~~~~~~R~i~~~~v~~~~~~~~i~i~g~~FL~~mVR~mv  188 (227)
T TIGR00071       111 YILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSNFSKAK--SKSRSPIRTISDIKVSESGEYIIFDIIGNSFLWHMVRKIV  188 (227)
T ss_pred             EEEccCcccCCCCCHHHHHHHHHHccCcccHHHhcCCC--CCCCCCeEEEEEEEEEEcCCEEEEEEEecHHHHHHHHHHH
Confidence            999865     699999999999999999999999764  3467999999999999988999999999999     7  9


Q ss_pred             hHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCee
Q psy3604         324 EPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNEL  369 (496)
Q Consensus       324 GtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L  369 (496)
                      |+|++||+|++++++|+++|+.+++...       .|+|||+||+|
T Consensus       189 g~l~~vg~g~~~~~~i~~~L~~~~r~~~-------~~~APa~GL~L  227 (227)
T TIGR00071       189 GALVLVGRGKLPPEWVAKLLDAKKRNLA-------PTTAPANGLYL  227 (227)
T ss_pred             HHHHHHHCCCCCHHHHHHHHhcCCcccC-------CCCCCCCCCcC
Confidence            9999999999999999999987553221       23456999998

universal so far, single copy in all prokaryotes, 3 in yeast. Trusted cutoff for orthology is about 100 based on 1 match only in complete prokaryote with length 200.

>PRK14586 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=4e-46  Score=368.83  Aligned_cols=220  Identities=22%  Similarity=0.250  Sum_probs=185.1

Q ss_pred             ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604          95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH  174 (496)
Q Consensus        95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~  174 (496)
                      .+|++.|+|+|+.++|||.+.+ ..++.+.++.||..+.-.          +                -.+.        
T Consensus         2 ~~~~l~i~YdGt~f~G~Q~Q~~-~~TVq~~le~aL~~~~~~----------~----------------i~~~--------   46 (245)
T PRK14586          2 KRVAAVVSYDGSNFFGYQGQPD-VRTVQGVFEDALERIFKQ----------R----------------IYTQ--------   46 (245)
T ss_pred             eEEEEEEEEcCCceeeEEECCC-CCCHHHHHHHHHHHHhCC----------C----------------eeEE--------
Confidence            4689999999999999999987 236777788888775310          0                0122        


Q ss_pred             CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604         175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY  254 (496)
Q Consensus       175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y  254 (496)
                             .++|||+||||++||++|+++..        ..++..+..+||++||+||+|+++.+||++|||||+|++|+|
T Consensus        47 -------~agRTD~GVHA~~qv~~f~~~~~--------~~~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y  111 (245)
T PRK14586         47 -------AAGRTDTGVHANGQVIAFNCPND--------RMTEEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIY  111 (245)
T ss_pred             -------EecCCccCCCccCcEEEEEecCC--------cCCHHHHHHHHHccCCCCeEEEEEEECCCCcCcccCCCcEEE
Confidence                   24579999999999999998754        136789999999999999999999999999999999999999


Q ss_pred             EEecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEe-cceEEEEEEe
Q psy3604         255 KYWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTS-AWQNVQFNDI  317 (496)
Q Consensus       255 ~Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~-~~~~i~i~I~  317 (496)
                      +|+|+.                .++|+++|++|++.|+|+|||+|| +..  .+.++++|+|+++++.+ .++.+.|+|+
T Consensus       112 ~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~l~G~HDF~~F-~~~--~~~~~~vR~I~~~~~~~~~~~~i~~~i~  188 (245)
T PRK14586        112 HYFILTSKEKNVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSF-KTG--SDERNPVRTIYRIRILRLKKDLILIRVE  188 (245)
T ss_pred             EEEEecCCCCChhhCCceEEeCCCCCHHHHHHHHHHccCcchHHhh-cCC--CCCCCCcEEEEEEEEEEccCCEEEEEEE
Confidence            999852                368999999999999999999999 432  34679999999999988 4788999999


Q ss_pred             eCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         318 KEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       318 G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                      |+||     |  ||+|++||+|++++++|.++|+.+++.  .     ..++|||+||+|++|.|
T Consensus       189 g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~--~-----~~~~APa~GL~L~~v~f  245 (245)
T PRK14586        189 GRSFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRS--K-----AAGTAPAHGLYLYKVLF  245 (245)
T ss_pred             echhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcc--c-----CCCccCCCCCEEeEeEC
Confidence            9999     7  999999999999999999999976532  1     12356699999999987

>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like

Probab=100.00  E-value=7.4e-46  Score=365.34  Aligned_cols=215  Identities=23%  Similarity=0.304  Sum_probs=185.2

Q ss_pred             eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604         100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP  179 (496)
Q Consensus       100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP  179 (496)
                      .|+|+|+.++|||.+.+ ..++.+.++.||..++..          +                ..+..            
T Consensus         2 ~i~Y~Gt~f~G~q~q~~-~~TVq~~le~aL~~~~~~----------~----------------~~i~~------------   42 (239)
T cd02570           2 TIEYDGTNFSGWQRQPN-GRTVQGELEKALSKIAGE----------P----------------VRVIG------------   42 (239)
T ss_pred             EEEEeCCccceeeeCCC-CCCHHHHHHHHHHHHhCC----------C----------------eEEEE------------
Confidence            58999999999999987 357888888999887631          0                12222            


Q ss_pred             CCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604         180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFP  259 (496)
Q Consensus       180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~  259 (496)
                         ++|||+||||++||++|+++..+         ++..+...||+.||+||+|+++.+|+++|||||+|++|+|+|+|+
T Consensus        43 ---agRTD~GVHA~~qvv~~~~~~~~---------~~~~~~~~lN~~Lp~dI~v~~i~~v~~~F~aR~~a~~R~Y~Y~i~  110 (239)
T cd02570          43 ---AGRTDAGVHALGQVAHFDTPSEI---------PLEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRIL  110 (239)
T ss_pred             ---ECcCCCCcCccccEEEEEECCCC---------CHHHHHHHHHccCCCCEEEEEEEECCCCcCcccCCCceEEEEEEc
Confidence               45799999999999999997643         577899999999999999999999999999999999999999997


Q ss_pred             CC----------------CccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce--
Q psy3604         260 QA----------------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV--  321 (496)
Q Consensus       260 ~~----------------~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF--  321 (496)
                      ..                .+|+++|++|++.|+|+|||+|||+.+.  ..++++|+|+++++.+.++++.|+|+|+||  
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~d~~~m~~a~~~f~G~HdF~~F~~~~~--~~~~~~R~I~~~~v~~~~~~~~i~i~g~sFL~  188 (239)
T cd02570         111 NRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGC--QSKSTVRTIYRADVYREGDLIVFEIRANGFLY  188 (239)
T ss_pred             cCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcchhhhCCCCC--CCCCCeEEEEEEEEEEeCCEEEEEEEEcHHHH
Confidence            43                6899999999999999999999998642  357999999999999888899999999999  


Q ss_pred             ---e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         322 ---D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       322 ---R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                         |  ||+|++||+|++++++|+++|+.+.+.  .  .   .|+|||+||+|++|.|
T Consensus       189 ~qVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~--~--~---~~~APa~GL~L~~v~Y  239 (239)
T cd02570         189 HMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRT--A--A---GPTAPAHGLYLVKVEY  239 (239)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcc--c--C---CCCcCCCCCEEeeeEC
Confidence               7  999999999999999999999865432  1  1   2345699999999988

This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.

>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,

Probab=100.00  E-value=6.4e-46  Score=362.26  Aligned_cols=213  Identities=24%  Similarity=0.334  Sum_probs=181.2

Q ss_pred             eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604         100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP  179 (496)
Q Consensus       100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP  179 (496)
                      .|+|+|+.++|||.+.+ ..++.+.++.||..++... +-     .+                ..+              
T Consensus         2 ~i~Y~Gt~y~G~q~q~~-~~TVq~~le~aL~~~~~~~-~~-----~~----------------i~~--------------   44 (221)
T cd02866           2 KVAYDGTPYHGFQRQPD-VRTVEGELIKALRRLGIIE-SP-----KR----------------PRL--------------   44 (221)
T ss_pred             EEEEeCCceeeeeeCCC-CCCHHHHHHHHHHHhhccc-cC-----Cc----------------eEE--------------
Confidence            58999999999999987 3467777888888775321 00     00                112              


Q ss_pred             CCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604         180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFP  259 (496)
Q Consensus       180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~  259 (496)
                       ..++|||+||||++||++|+++..            . +..+||+.||+||+|+++.+||++|||||+|++|+|+|+++
T Consensus        45 -~~agRTD~GVHA~~qv~~f~~~~~------------~-~~~~lN~~LP~dI~v~~~~~v~~~F~ar~~a~~r~Y~Y~i~  110 (221)
T cd02866          45 -YSAGRTDAGVSALGNVVAFETEKE------------L-TPPAINNALPKDIRVWAWAKVPEDFHPRRDARRRYYRYYLG  110 (221)
T ss_pred             -EEEcCCccccCccccEEEEEeCcH------------H-HHHHHHhhCCCCEEEEEEEEeCCCCCCCccCCeEEEEEEEC
Confidence             235679999999999999998631            1 78999999999999999999999999999999999999999


Q ss_pred             CCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHHHhCC
Q psy3604         260 QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFKKGQG  332 (496)
Q Consensus       260 ~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~VG~G  332 (496)
                      ...+|+++|++|++.|+|+|||+|||+.+    ..+++|+|+++++.+.++++.|+|+|+||     |  ||+|++||+|
T Consensus       111 ~~~ld~~~m~~a~~~~~G~HDF~~F~~~~----~~~~~R~I~~~~~~~~~~~~~~~i~g~~FL~~mVR~mvg~ll~vg~g  186 (221)
T cd02866         111 AEDYDVEAMAEAAKKLIGTHDFSNFSKRD----GRDPVRTIERIEIRENGEFLVIDVVGESFLWNMVRRIVGALSLVGKG  186 (221)
T ss_pred             CCcCCHHHHHHHHHHhcCCcCHHHhhCCC----CCCCcEEEEEEEEEEcCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCC
Confidence            88999999999999999999999999853    13899999999999888999999999999     7  9999999999


Q ss_pred             CCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         333 NEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       333 ~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                      ++++++|+++|+.+.+...       .++|||+||+|++|.|
T Consensus       187 ~~~~~~i~~~l~~~~~~~~-------~~~APa~GL~L~~v~Y  221 (221)
T cd02866         187 KRENEWVDKLLDGEFRKKD-------GVPAPPEGLILVDVKY  221 (221)
T ss_pred             CCCHHHHHHHHhCCCcccC-------CCCCCCCCcEEEEeeC
Confidence            9999999999997553221       2246699999999988

This group consists of archealpseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs.

>PRK14587 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=6.7e-45  Score=361.54  Aligned_cols=224  Identities=22%  Similarity=0.212  Sum_probs=186.0

Q ss_pred             eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604          96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP  175 (496)
Q Consensus        96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p  175 (496)
                      +|++.|+|+|+.++|||.+.+   ++.+.+..||..+                                 +.        
T Consensus         2 ~~~l~i~YdGt~f~G~Q~Q~~---TVq~~Le~aL~~i---------------------------------~~--------   37 (256)
T PRK14587          2 PYLYRIAYDGTLFYGFTGHPN---SLEPALRRVFGEI---------------------------------LG--------   37 (256)
T ss_pred             cEEEEEEECCCcccceecCcc---hHHHHHHHHHHHh---------------------------------cc--------
Confidence            578899999999999999877   3455555555431                                 00        


Q ss_pred             CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604         176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK  255 (496)
Q Consensus       176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~  255 (496)
                            .++|||+||||++||++|.  ..+         +    ..+||+.||+||+|+++.+|+++||||+ |++|+|+
T Consensus        38 ------~agRTDaGVHA~~qv~~~~--~~~---------~----~~~LN~~LP~dI~V~~~~~V~~~FhaR~-a~~R~Y~   95 (256)
T PRK14587         38 ------RGSRTDPGVSAVGNVVMTS--QKL---------P----LGYVNSKLPRGVWAWAVAEVPEGFNPRR-AKRRRYL   95 (256)
T ss_pred             ------CccCCccCCCcccCEEEEC--CcC---------C----HHHHHhcCCCCeEEEEEEECCCCcCcCc-ccceEEE
Confidence                  0567999999999999973  222         2    4789999999999999999999999997 9999999


Q ss_pred             EecCCCCccHHHHHHHHHHccccccccccccccccCCCCC-ceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHH
Q psy3604         256 YWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVN-FKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSF  327 (496)
Q Consensus       256 Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~s-tvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv  327 (496)
                      |+++...+|+++|++|++.|+|+|||+|||+.+.  ..++ ++|+|++++|.+.++.+.|+|+|+||     |  ||+|+
T Consensus        96 Y~i~~~~lDi~~m~~aa~~l~G~HDF~~F~~~~~--~~~~~~vRtI~~i~v~~~~~~i~i~i~g~sFL~~mVR~mVG~Ll  173 (256)
T PRK14587         96 YVAPHWGEDVEAMREAAELLAGTHDYSSFIQRRG--EKATPTVTTVYEIGVELRGDLIYLYFVGRGFRNKMIRKMAWAIL  173 (256)
T ss_pred             EEEccCcchHHHHHHHHHHhcCCcChHHhccCCC--CCCCCCEEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHH
Confidence            9998788999999999999999999999997642  2345 99999999999888899999999999     7  99999


Q ss_pred             HHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccccchHHHHHHHHHHHhh
Q psy3604         328 KKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTN  398 (496)
Q Consensus       328 ~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~~~~~~~~~~~~i~~~  398 (496)
                      +||+|++++++|+++|+.. +  ..  ..++   |||+||+|++|.|+   .+|..+++++.++...+++.
T Consensus       174 ~Vg~G~~~~~~i~~~L~~~-r--~~--~~~~---APa~GL~L~~V~Y~---~~~~~~~~~~~~~~~~~~~~  233 (256)
T PRK14587        174 AAGRGVLSRRDIAELLERP-R--PG--AVPS---APAEGLVLLDIEYD---VKFQVDYTALRKAYVYFLSK  233 (256)
T ss_pred             HHhCCCCCHHHHHHHHhcC-c--cc--CCCC---CCCCCCEEeeeccC---ccccCChHHHHHHHHHHHHH
Confidence            9999999999999999843 2  22  2334   55999999999996   28888888887766665544

>cd02568 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like

Probab=100.00  E-value=1.5e-44  Score=357.43  Aligned_cols=230  Identities=19%  Similarity=0.172  Sum_probs=186.8

Q ss_pred             eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604         100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP  179 (496)
Q Consensus       100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP  179 (496)
                      .|+|+|+.++|||.+.+--.++.+.++.||..++...+.   ..+                             .+..|.
T Consensus         2 ~i~Y~Gt~f~G~Q~Q~~~~~TVq~~le~aL~~~~~~~~~---~~~-----------------------------~~~~~~   49 (245)
T cd02568           2 LFGYCGTGYHGMQYNPGNYKTIEGELERALVKAGAISES---NAG-----------------------------DPKKIG   49 (245)
T ss_pred             EEEEeCCCccccccCCCCCCChHHHHHHHHHHcCCcCcc---ccC-----------------------------Chhhcc
Confidence            689999999999999873246788888999987742110   000                             001122


Q ss_pred             CCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604         180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFP  259 (496)
Q Consensus       180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~  259 (496)
                      -..++|||+||||++||++|+++..+++.    ..++..+..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+
T Consensus        50 ~~~agRTD~GVHA~~qv~~~~~~~~~~~~----~~~~~~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~  125 (245)
T cd02568          50 FSRAARTDKGVHAARNVVSLKVIIDDPEG----LGIGEDLVEKLNSHLPEDIRVFGITRVTKSFNARKACDSRTYEYLLP  125 (245)
T ss_pred             eeeecccccchhheeeEEEEEEecccccc----ccchHHHHHHHHccCCCceEEEEEEcCCCCCCcchhhhcceeEEECC
Confidence            23467899999999999999997654110    12267899999999999999999999999999999999999999999


Q ss_pred             CCC-ccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEec------ceEEEEEEeeCce-----e--hhH
Q psy3604         260 QAG-LDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA------WQNVQFNDIKEVV-----D--SEP  325 (496)
Q Consensus       260 ~~~-LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~------~~~i~i~I~G~sF-----R--VGt  325 (496)
                      ... +|+++|++|++.|+|+|||+|||+... ...++++|+|.++++.+.      ++++.|+|+|+||     |  ||+
T Consensus       126 ~~~~~d~~~m~~a~~~~~G~HdF~~F~~~~~-~~~~~~~R~i~~~~~~~~~~~~~~~~~i~i~i~g~~FL~~mVR~mvg~  204 (245)
T cd02568         126 TFALETLDRFNEILKLYVGTHNFHNFTVRKK-FEDPSANRFIISFYVSEPFVIEEGLEWVSIEIHGQSFMLHQIRKMIGL  204 (245)
T ss_pred             cccHhHHHHHHHHHHHhhCccccccCccccc-ccCCCceeEEEEEEEecceeecCCccEEEEEEEechHHHHHHHHHHHH
Confidence            877 699999999999999999999998642 235789999999999874      3789999999999     7  999


Q ss_pred             HHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604         326 SFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF  374 (496)
Q Consensus       326 Lv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y  374 (496)
                      |++||+|+++++.|+++|+....   .  ..   |+|||+||+|++|.|
T Consensus       205 l~~vg~g~~~~~~i~~~L~~~~~---~--~~---~~APa~GL~L~~v~y  245 (245)
T cd02568         205 AIAIVRGGAPESLIDLSFNKAKR---I--II---PLAPGLGLLLEYPHF  245 (245)
T ss_pred             HHHHHcCCCCHHHHHHHhccccc---c--cc---cCCCCcceeEecccC
Confidence            99999999999999999985322   1  12   345699999999988

This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U

>KOG2554|consensus

Probab=100.00  E-value=1.6e-44  Score=363.49  Aligned_cols=251  Identities=34%  Similarity=0.554  Sum_probs=219.5

Q ss_pred             hcceeeeeeeeeccccHHHhhhcCCCC-CCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhcccccc
Q psy3604          93 VTSVIGLVIKEVGGLSHDFCELANRQQ-PMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVK  171 (496)
Q Consensus        93 ~~~~i~~yL~~lG~sa~~~ae~agRTq-p~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~  171 (496)
                      -++.|++-|.|+|+.|.|++-+...-. ++.+-+..||....+. .+..                     +-+|      
T Consensus        64 ~kR~IAlkiaY~GW~Y~Gla~Qe~T~~~TIEg~l~eAL~kt~Li-es~~---------------------~~~y------  115 (425)
T KOG2554|consen   64 SKRHIALKIAYLGWNYQGLAPQEHTNNPTIEGKLFEALKKTRLI-ESRQ---------------------TCNY------  115 (425)
T ss_pred             cceEEEEEEEEeccccCceecCCCCCCcchHHHHHHHHHhhhcc-cCcc---------------------cccc------
Confidence            479999999999999999998844333 6788899999875542 1111                     0122      


Q ss_pred             CCCCCCCCCCCCCCCCcccccccceEEEeecccCCCCC------CCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCc
Q psy3604         172 QPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPG------EESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSA  245 (496)
Q Consensus       172 ~~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~------~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhA  245 (496)
                               +.+.|||+||+|.+||+++.+++.++..+      .+.+..+..|...||++||+||||.+|++||+.|+|
T Consensus       116 ---------sRCGRTDKGVSAfgQviSl~lRS~~p~~~s~~~~~~~a~~~Ei~Y~~mLN~vLP~dIRi~awapvp~~FsA  186 (425)
T KOG2554|consen  116 ---------SRCGRTDKGVSAFGQVISLVLRSRIPMPDSQRDAVATADSEEIPYVHMLNRVLPPDIRIVAWAPVPPTFSA  186 (425)
T ss_pred             ---------cccCCcccchhhhhheeeeeeeccCCCchhhhccccccccccccHHHHHhccCCCcceEEEEecCCCCccc
Confidence                     35678999999999999999998876642      223456889999999999999999999999999999


Q ss_pred             cccCCceeEEEecCCCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecce---EEEEEEeeCce-
Q psy3604         246 RFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQ---NVQFNDIKEVV-  321 (496)
Q Consensus       246 Rfsa~~R~Y~Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~---~i~i~I~G~sF-  321 (496)
                      ||+|..|+|+|+|+..+|||++|++||.+|+|+|||+|||+.+..++..|..|+|.+++|...++   .+.|+|.|++| 
T Consensus       187 RFsC~~RtYrY~F~k~dLdI~~M~kAA~l~vGe~DFrNFCK~D~~n~vtny~Rti~s~kV~~~~~~~~my~ldi~g~AFL  266 (425)
T KOG2554|consen  187 RFSCVQRTYRYYFPKKDLDIDRMSKAASLLVGEHDFRNFCKIDVSNGVTNYERTILSAKVEDVGQTPGMYYLDIQGSAFL  266 (425)
T ss_pred             eeehhhceeeEeccCCCcCHHHHHHHHHHHhcchhhhhhhhhcchhhhHHHHhhhheeeEEEcCCCCceEEEEeechhhH
Confidence            99999999999999999999999999999999999999999987666788999999999987664   59999999999 


Q ss_pred             ----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccccch
Q psy3604         322 ----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQY  385 (496)
Q Consensus       322 ----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~~~  385 (496)
                          |  |++|+.||+|...|+.|.++|+.++.|.+|  +|.+|.   ..+|+|.+|.|-.++++|....
T Consensus       267 wHqVRcimaiL~liGq~~E~p~lI~dLldIek~P~kP--qY~mA~---~~PL~LydC~f~~e~~ew~~~~  331 (425)
T KOG2554|consen  267 WHQVRCIMAILFLIGQGLEQPSLISDLLDIEKNPQKP--QYTMAS---DYPLELYDCDFHRENVEWRHDT  331 (425)
T ss_pred             HHHHHHHHHHHHHhccccCCchHHHHHHhcccCCCCc--eeeecc---CCceEEEecCCCCccccccccc
Confidence                8  999999999999999999999999999999  999998   9999999999977899997754

>KOG2553|consensus

Probab=100.00  E-value=1.1e-38  Score=328.14  Aligned_cols=273  Identities=15%  Similarity=0.151  Sum_probs=222.6

Q ss_pred             hcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccC
Q psy3604          93 VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQ  172 (496)
Q Consensus        93 ~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~  172 (496)
                      .++++++.+.|+|.+|||+|-+.+ .++|.+|++.||..+|...+.=.                 .+|            
T Consensus        35 ~KrKVail~gY~G~gY~GmQ~N~~-~kTIEgeL~~al~~aGaI~e~n~-----------------~dp------------   84 (416)
T KOG2553|consen   35 RKRKVAILLGYCGTGYHGMQYNPP-LKTIEGELFEALFKAGAISESNA-----------------GDP------------   84 (416)
T ss_pred             cceEEEEEEEeccCCccceecCCC-CCchHHHHHHHHHHcCCcccccc-----------------cCh------------
Confidence            557789999999999999999999 48999999999999997533211                 111            


Q ss_pred             CCCCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCce
Q psy3604         173 PHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFR  252 (496)
Q Consensus       173 ~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R  252 (496)
                         .+|---.++|||+||||.+|||++++..+           ...++..||..||++||||++.+|++.||+|..|.+|
T Consensus        85 ---kk~~~~raARTDKGVhA~~nviSlK~~~~-----------~~~lv~~lN~~Lp~~IRv~~v~r~~k~F~pr~~CdsR  150 (416)
T KOG2553|consen   85 ---KKIGFARAARTDKGVHAAGNVISLKLELD-----------DPELVEKLNEILPEQIRVWGVKRVTKSFNPRKQCDSR  150 (416)
T ss_pred             ---HHhhhHHhhccccchhhhhheeEEEEeeC-----------cHHHHHHHhhhCCcceEEEEEEecCCCCCccccccce
Confidence               11222357889999999999999998742           3678999999999999999999999999999999999


Q ss_pred             eEEEecCC------CC---------------------------------------------ccHHHHHHHHHHccccccc
Q psy3604         253 NYKYWFPQ------AG---------------------------------------------LDIDAMHKAAQYLVGTHDF  281 (496)
Q Consensus       253 ~Y~Y~~~~------~~---------------------------------------------LDie~M~eAak~fvGtHDF  281 (496)
                      +|.|++|.      .+                                             -.++.++++++.++|+|||
T Consensus       151 ~YeYllPtfal~~p~~~~~~~~~~~~~~e~~~~f~~~~~~~~~~~~s~~~~~~~~~yr~s~~~l~~~~~~ls~Y~GthnF  230 (416)
T KOG2553|consen  151 TYEYLLPTFALAPPKPSSLLEVDIQYDKEFEKEFWNTYPLSAKERLSGQDRKTESGYRLSEEKLEVFNTILSKYVGTHNF  230 (416)
T ss_pred             eEEEecceeeecCCCCccHHHhhhhhhhhhhhhhccccchhhhhhhcccccccccceeeCHHHHHHHHHHHHHhhccccc
Confidence            99999872      11                                             1367889999999999999


Q ss_pred             cccccccccCCCCCceEEEEEEEEEe-------cceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccC
Q psy3604         282 RNLCKMNVGNGVVNFKRLVTHAGVTS-------AWQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEK  347 (496)
Q Consensus       282 ~nF~~~~~~~~~~stvRtI~~i~i~~-------~~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~  347 (496)
                      ||||..+. ..+++..|.|.++.+.+       .-+||.+.|+|+||     |  ||++++|.|+..+.+.|+..|+...
T Consensus       231 HNfT~~~~-~~dpss~R~I~s~~~~~pfv~~~~~~e~V~i~i~GQSFMLHQIRKMVglav~i~R~~~p~~~i~~af~~~~  309 (416)
T KOG2553|consen  231 HNFTTGKD-FTDPSSNRFIKSFTVSEPFVINDEGVEFVKIKIHGQSFMLHQIRKMVGLAVLIVRSGAPASTIQRAFNKEH  309 (416)
T ss_pred             ceecccCC-CCCccccceeeEEEecCcceeccCCceEEEEEEEcchhHHHHHHHHHHHHHHHHhcCCCHHHHHHhhCCCc
Confidence            99998763 35789999999998872       23799999999999     7  9999999999999999999998433


Q ss_pred             CCCCCCCCCCCCCCCCCCCCeeeeeccC----------CCCcccccchHHHHHHHHHHHhhhhcccccccccchhhhhhh
Q psy3604         348 YPRIKSAQFPWSSTGATTPNELFRRVFL----------LSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKD  417 (496)
Q Consensus       348 ~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~----------~~~l~f~~~~~~~~~~~~~i~~~~~~~y~~~~lp~i~~~~~~  417 (496)
                      +.     .+|+||   ++||+|.++.|.          ++.++|.+.+..++.++..           ++.++|-+. ..
T Consensus       310 ri-----~IP~AP---~~gLlL~~~~F~~yn~~~~~~~~e~i~~~~~e~ei~~fk~~-----------~Iy~~I~~~-E~  369 (416)
T KOG2553|consen  310 KI-----NIPKAP---GEGLLLEEPHFESYNRKFRPSGHEEIDWDDYEEEIDQFKEK-----------HIYSHIIKT-EE  369 (416)
T ss_pred             cc-----cccCCC---cceEEeecccccccccccCCCCcCCcCHHHHHHHHHHHHHH-----------HhchHHhhh-Hh
Confidence            33     455887   999999999996          5778888877777666665           345544433 24


Q ss_pred             ccccchhhcccCc
Q psy3604         418 TVRESKCTMGDLD  430 (496)
Q Consensus       418 ~~~~~~~~~~~~~  430 (496)
                      .-..|.+|+..||
T Consensus       370 ~~~~f~~wl~~l~  382 (416)
T KOG2553|consen  370 KEGVFAIWLSSLN  382 (416)
T ss_pred             hhhhHHHHHHHHh
Confidence            4567999999999

>KOG4393|consensus

Probab=99.95  E-value=4e-27  Score=229.91  Aligned_cols=181  Identities=14%  Similarity=0.115  Sum_probs=149.8

Q ss_pred             CCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcC-CC--CcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604         183 PLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNL-PR--DIKVVAWSPVPEKYSARFDCLFRNYKYWFP  259 (496)
Q Consensus       183 p~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~L-P~--DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~  259 (496)
                      .+|||+||||..+++++.++...       .........++|..| ++  ||+|+++..||.+|||||+|.+|+|.|++.
T Consensus        54 ssrtDa~Vha~~naa~~~vpr~s-------g~~~~~~~~a~nt~l~~k~gdirV~dv~~Vps~FhaR~sassRtY~YRla  126 (295)
T KOG4393|consen   54 SSRTDAGVHAYLNAAHYIVPRFS-------GSQQQAKDRAVNTVLQRKDGDIRVIDVRCVPSNFHARYSASSRTYFYRLA  126 (295)
T ss_pred             cCCCchhhheeeeeEEEEeeccc-------CCcHHHHHHHHhccccCCCCceEEEEeeecCcchhheecccceeEEEEee
Confidence            35799999999999999997653       124455667777766 44  999999999999999999999999999974


Q ss_pred             -----------------CCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEec--------------
Q psy3604         260 -----------------QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA--------------  308 (496)
Q Consensus       260 -----------------~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~--------------  308 (496)
                                       +..||..+|++|+++|+|+|||.+|++..  +....+++|+..+.+...              
T Consensus       127 ~g~d~l~~fERd~cW~lp~~lna~kmqeaa~lf~G~hdfsaf~~at--s~~y~P~~t~rr~sv~~~g~~~a~~~~~~~e~  204 (295)
T KOG4393|consen  127 SGSDPLSIFERDRCWHLPEELNARKMQEAAPLFEGSHDFSAFTEAT--STVYFPSITERRLSVLNNGDPLACSNQPETEG  204 (295)
T ss_pred             cCCCccChhhhcccccCCcccCHHHHHhhhhhhccchhhhhhhcCC--CCCCCCcccceeeeecccCCccccccCCcccc
Confidence                             25789999999999999999999999875  457788888888888532              


Q ss_pred             --ceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccC
Q psy3604         309 --WQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFL  375 (496)
Q Consensus       309 --~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~  375 (496)
                        .+++.+++.++||     |  ++.||.+|.+.++...++.+|+.+.....-.-+.+.|   ||+||+|..|.|.
T Consensus       205 ~~~~~~nve~e~~gflyrQvRrm~a~LV~~g~~al~~~qv~~iLe~~~~~~l~k~~~~va---pphglfL~sv~Y~  277 (295)
T KOG4393|consen  205 VTTNVGNVEGETEGFLYRQVRRMRAYLVTAGSRALLYHQVLYILEVRDIVGLLKCVGTVA---PPHGLFLSSVEYV  277 (295)
T ss_pred             ceeeeEEEEEEecchHHHHHHhhheeeeeecccccchhhhhhhhhccchhhhhhccCCCC---CCccceeeeEEec
Confidence              2679999999999     3  8999999999999999999999876432222244445   5999999999996

>KOG4336|consensus

Probab=99.88  E-value=6e-23  Score=204.01  Aligned_cols=136  Identities=42%  Similarity=0.707  Sum_probs=118.1

Q ss_pred             HHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhh
Q psy3604          10 SLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWY   89 (496)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y   89 (496)
                      ++|..+|.+||+++|||.++++|+|+|++++++                                               
T Consensus         5 ~vl~~VV~~Ll~~~gfd~is~~aletlvell~~-----------------------------------------------   37 (323)
T KOG4336|consen    5 RVLAPVVSNLLKTKGFDSISNAALETLVELLQS-----------------------------------------------   37 (323)
T ss_pred             hHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHH-----------------------------------------------
Confidence            489999999999999999999999999999997                                               


Q ss_pred             hhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccC-CCc---ccCCCCCCCCC-----C
Q psy3604          90 KRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKR-PMR---TVFPPVAPSTQ-----P  160 (496)
Q Consensus        90 ~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~-p~r---~~lP~~p~~~~-----p  160 (496)
                                ||.++|+++|.||+++|||+|+.+||..+|++|||.++.|..|.+. ++.   ..++.+++..+     +
T Consensus        38 ----------yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~v~sL~~~~q~~~~sl~~~~~~aP~~~~q~~ds~~  107 (323)
T KOG4336|consen   38 ----------YIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIKVSSLYAYFQKQEFSLWSVLIAAPENQEQEEDSEQ  107 (323)
T ss_pred             ----------HHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCChhhhHHHHHhccchhhhccccCCCcCCccccccc
Confidence                      7899999999999999999999999999999999999999998753 332   33444444443     3


Q ss_pred             CCchhccccccCCCCCCCCCCCCCCCCcccccccceEEEeec
Q psy3604         161 KPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIR  202 (496)
Q Consensus       161 ~~~~fL~aG~~~~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~  202 (496)
                      .+...+..|.+.++|.|||+|||+|||+|||..+++...-..
T Consensus       108 ~~~~~l~~gv~~php~yIpshLPpfPdpHTYi~Tpi~~~p~t  149 (323)
T KOG4336|consen  108 QPELLLTLGVSRPHPKYIPSHLPPFPDPHTYIKTPIYKVPDT  149 (323)
T ss_pred             cchHhhhcCCCCCCCccccccCCCCCCCcccccCCccCCCCC
Confidence            445667899999999999999999999999999999877543

>KOG2389|consensus

Probab=99.78  E-value=5.3e-19  Score=179.00  Aligned_cols=141  Identities=29%  Similarity=0.512  Sum_probs=120.7

Q ss_pred             CchHHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchh
Q psy3604           3 TSKDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVED   82 (496)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (496)
                      ...+|++++++.+|+|+|+.+||++.+++||++|+++++.                                        
T Consensus        22 ~~~~ya~sla~~avaQIcqslg~~~~~~sale~Ltd~~~q----------------------------------------   61 (353)
T KOG2389|consen   22 EEAEYAFSLARVAVAQICQSLGYSSTQNSALETLTDVLQQ----------------------------------------   61 (353)
T ss_pred             hHHHHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHH----------------------------------------
Confidence            4679999999999999999999999999999999999996                                        


Q ss_pred             hhhhhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCC---------CCccc-------c----
Q psy3604          83 CYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPI---------HGLDT-------Y----  142 (496)
Q Consensus        83 ~~~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v---------~gL~~-------y----  142 (496)
                                       ||+.+|+.+|.|++++||++||++|+++||.++|+++         +.|.+       |    
T Consensus        62 -----------------yvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s~~~~~~~~~s~~L~ds~v~rdii~~~g  124 (353)
T KOG2389|consen   62 -----------------YVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSASLGASGSSGESHCLLDSKVLRDIIIFNG  124 (353)
T ss_pred             -----------------HHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhhcccccccchhHHHhhhhhHHHHHhhcc
Confidence                             8999999999999999999999999999999999988         55555       1    


Q ss_pred             -c-cCCCcccCCCCCCCCCCCCchhccccc--cCCCCCCCCCCCC-CCCCcccccccceEEEee
Q psy3604         143 -A-KRPMRTVFPPVAPSTQPKPLSILQAGV--KQPHPPHIPPYLP-LFPDPHAYIRTPVVTLKI  201 (496)
Q Consensus       143 -~-k~p~r~~lP~~p~~~~p~~~~fL~aG~--~~~~p~hIP~~Lp-~~~D~~v~a~~qVvsf~l  201 (496)
                       + +.||..++|.||++.... .++++.|.  ..+++.|||.||| +|||.+.+...+-.+...
T Consensus       125 ~~eevpF~~~lP~Fp~s~s~~-k~~l~~~~~g~~pp~~~Ip~wLP~~fp~~~~~~~s~e~~~~~  187 (353)
T KOG2389|consen  125 KAEEVPFKDDLPRFPVSKSVN-KPFLKFGSVGAEPPGESIPIWLPPAFPDLEGCSKSPEGNVTV  187 (353)
T ss_pred             ccccCCCCCCCCccccccccc-cCCCCccccCCCCCCccccccCCCCCCCcccCCCCccccccc
Confidence             1 358999999999876532 34444443  2489999999999 999999999988555554

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=99.65  E-value=1.8e-16  Score=130.85  Aligned_cols=76  Identities=42%  Similarity=0.680  Sum_probs=73.1

Q ss_pred             hHHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhh
Q psy3604           5 KDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCY   84 (496)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (496)
                      ++|.|++|+.+|+++|++.||+.++++|+|+|+++++.                                          
T Consensus         1 ~~~~~~ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~------------------------------------------   38 (77)
T smart00576        1 NELAFALLRIAVAQILESAGFDSFQESALETLTDILQS------------------------------------------   38 (77)
T ss_pred             CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHH------------------------------------------
Confidence            57999999999999999999999999999999999997                                          


Q ss_pred             hhhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCC
Q psy3604          85 QRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIH  137 (496)
Q Consensus        85 ~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~  137 (496)
                                     |+..+|+.++.||+++||++|++.||.+||+++|++++
T Consensus        39 ---------------yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~~~   76 (77)
T smart00576       39 ---------------YIQELGRTAHSYAELAGRTEPNLGDVVLALENLGISVG   76 (77)
T ss_pred             ---------------HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcccC
Confidence                           78999999999999999999999999999999999865

subdomain of archael histone-like transcription factors

>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO)

Probab=99.64  E-value=2.7e-16  Score=129.55  Aligned_cols=77  Identities=40%  Similarity=0.625  Sum_probs=73.7

Q ss_pred             hHHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhh
Q psy3604           5 KDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCY   84 (496)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (496)
                      +++.+++|+.+|+++|..+||++++++|||+|++++..                                          
T Consensus         1 ~e~~~~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~------------------------------------------   38 (77)
T PF07524_consen    1 DEFARSLLRRSVAQILKHAGFDSASPSALDTLTDILQR------------------------------------------   38 (77)
T ss_pred             CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHH------------------------------------------
Confidence            57999999999999999999999999999999999996                                          


Q ss_pred             hhhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCC
Q psy3604          85 QRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHG  138 (496)
Q Consensus        85 ~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~g  138 (496)
                                     ||+.+|+.++.|++++||++|++.||.++|.+||+++++
T Consensus        39 ---------------yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~v~e   77 (77)
T PF07524_consen   39 ---------------YLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGISVNE   77 (77)
T ss_pred             ---------------HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Confidence                           789999999999999999999999999999999998763

The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].

>PF01416 PseudoU_synth_1: tRNA pseudouridine synthase; InterPro: IPR020097 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones

Probab=99.60  E-value=1.1e-17  Score=144.35  Aligned_cols=98  Identities=20%  Similarity=0.206  Sum_probs=80.0

Q ss_pred             HHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHH
Q psy3604         271 AAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLV  343 (496)
Q Consensus       271 Aak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL  343 (496)
                      |++.|+|+|||++|++.+.  ...+++|+|.++.+...++++. +|+|+||     |  ||+++.+|+|..+++.|.++|
T Consensus         1 A~~~~~G~HdF~~f~~~~~--~~~~~~r~i~~~~~~~~~~~~~-~i~g~~Fl~~~vR~~vg~~~~~~~G~~~~~~i~~~L   77 (105)
T PF01416_consen    1 AAKLYVGTHDFSGFQKQKT--VEKNTIRTIFSIDIIEEGDVVV-EIHGNSFLRHQVRIMVGTLLRTGRGVHSLEQIAELL   77 (105)
T ss_dssp             -CCEETCEEECCGCSSCS---HHHHHCCCEEEEECCCCCCEEE-EEEESS--TTHHHHHHCCCCHHHTTSCEEECCCCCH
T ss_pred             CcceeEecCCCcCCEECCc--ccccHHHHHHHHhhhcCCCEEE-EEEecccccccchhhhHHHHHHhcCCCCHHHHHHHH
Confidence            6788999999999998743  2368999999999999889999 9999999     6  999999999999999999999


Q ss_pred             hccCCCCCCCCCCCCCCCCCCCCCeeeeeccC
Q psy3604         344 DIEKYPRIKSAQFPWSSTGATTPNELFRRVFL  375 (496)
Q Consensus       344 ~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~  375 (496)
                      +...++..+. .+..|   |+.||+|++|.||
T Consensus        78 ~~~~~~~~~~-ri~~a---p~~gL~L~~v~y~  105 (105)
T PF01416_consen   78 NSKLRPKAPP-RILTA---PAVGLYLFHVRYD  105 (105)
T ss_dssp             HHHSCTTS-T-EEEEE---EECCECCEECCTT
T ss_pred             hccCccccCC-Cccee---eCCCCCceEeeCc
Confidence            9876442220 12234   5999999999995

Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents pseudouridine synthase I (TruA). TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1VS3_B 2NR0_B 2NQP_D 1DJ0_A 2NRE_A.

>PF10406 TAF8_C: Transcription factor TFIID complex subunit 8 C-term ; InterPro: IPR019473 This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID []

Probab=97.54  E-value=3.4e-05  Score=59.16  Aligned_cols=25  Identities=52%  Similarity=1.088  Sum_probs=22.8

Q ss_pred             CCCCCCCCCCCCcccccccceEEEe
Q psy3604         176 PHIPPYLPLFPDPHAYIRTPVVTLK  200 (496)
Q Consensus       176 ~hIP~~Lp~~~D~~v~a~~qVvsf~  200 (496)
                      +|||+|||+|||+|||..|++..-.
T Consensus         1 ~~IP~~lP~fP~~HTY~~Tp~~~~~   25 (51)
T PF10406_consen    1 SHIPDWLPPFPPPHTYKRTPIYNER   25 (51)
T ss_pred             CCCcccCCCCCCCcccccCCCCCCC
Confidence            5999999999999999999998654

The adjacent N-terminal region generally contains a histone fold domain (IPR006565 from INTERPRO). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery [].

>cd08049 TAF8 TATA Binding Protein (TBP) Associated Factor 8

Probab=97.49  E-value=4.6e-05  Score=59.06  Aligned_cols=25  Identities=56%  Similarity=1.145  Sum_probs=22.5

Q ss_pred             CCCCCCCCCCCCcccccccceEEEe
Q psy3604         176 PHIPPYLPLFPDPHAYIRTPVVTLK  200 (496)
Q Consensus       176 ~hIP~~Lp~~~D~~v~a~~qVvsf~  200 (496)
                      .|||+|||+|||+|||..+++..-.
T Consensus         1 ~hIP~~LP~FP~~HTY~~Tp~~~~~   25 (54)
T cd08049           1 AHIPSWLPPFPDPHTYKRTPTYSER   25 (54)
T ss_pred             CCCCcCCCCCCCchhhccCCCCCCC
Confidence            5999999999999999999997553

The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promo

>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function

Probab=96.75  E-value=0.02  Score=55.25  Aligned_cols=116  Identities=12%  Similarity=0.234  Sum_probs=76.3

Q ss_pred             cccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecCCCCccHHH
Q psy3604         188 PHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDA  267 (496)
Q Consensus       188 ~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~~~~LDie~  267 (496)
                      -|+.+.+-++.+.+..+         .++..+...||+.||++|+|.++..+|....+ ..+.-..+.|.+.....+.+.
T Consensus        55 vGv~S~~E~~di~l~~~---------~~~~~~~~rLn~~lP~Gl~i~~~~~i~~~~~s-l~~~i~~~~Y~i~~~~~~~~~  124 (187)
T PF10105_consen   55 VGVESLAEYMDIELEED---------IDPEEVLERLNAVLPEGLRILEAEEIPPKAPS-LMALINAAEYRITLPEIDEEE  124 (187)
T ss_pred             CceeeccEEEEEEEecC---------CCHHHHHHHHHHhCCCCCEEEEEEEccCCCcc-hhhhcceEEEEEEecCCCHHH
Confidence            47888999999998754         37889999999999999999999999855443 234446677776555777888


Q ss_pred             HHHHHHHccccccccccccc-cccCC-CCCceEEEEEEEEEecceEEEE
Q psy3604         268 MHKAAQYLVGTHDFRNLCKM-NVGNG-VVNFKRLVTHAGVTSAWQNVQF  314 (496)
Q Consensus       268 M~eAak~fvGtHDF~nF~~~-~~~~~-~~stvRtI~~i~i~~~~~~i~i  314 (496)
                      +++++..|.-..++ ...+. +.+.. ..+-.-.|.++++...++.+.|
T Consensus       125 ~~~~~~~~~~~~~~-~v~k~~Kkg~~~~~dir~~i~~l~~~~~~~~~~l  172 (187)
T PF10105_consen  125 LEEAIEAFLAAEEI-IVEKRTKKGKKKEIDIRPYIKDLELEGSEDNIVL  172 (187)
T ss_pred             HHHHHHHHHCCCCE-EEEEeCCCCceEEEEhHHhhheEEEEeCCCeEEE
Confidence            88888777655432 12222 11111 1122234556667665544444

>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=96.70  E-value=0.0019  Score=57.77  Aligned_cols=64  Identities=19%  Similarity=0.193  Sum_probs=58.1

Q ss_pred             HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604          14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV   93 (496)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~   93 (496)
                      .+|.++|++.|=...++.+...|.|.+.+                                                   
T Consensus         5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~r---------------------------------------------------   33 (117)
T cd07979           5 RVIAAILKSMGITEYEPRVINQLLEFAYR---------------------------------------------------   33 (117)
T ss_pred             HHHHHHHHHCCCCccCHHHHHHHHHHHHH---------------------------------------------------
Confidence            46889999999999999999999999996                                                   


Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCC
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGI  134 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi  134 (496)
                            |..+++..+..|++|+||..-..+||.+|+...+-
T Consensus        34 ------y~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~   68 (117)
T cd07979          34 ------YTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD   68 (117)
T ss_pred             ------HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence                  67788999999999999999999999999987553

The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi

>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution

Probab=96.40  E-value=0.0054  Score=52.01  Aligned_cols=75  Identities=17%  Similarity=0.251  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhh
Q psy3604           7 TNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQR   86 (496)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (496)
                      ....+-+.+|..|....|=.-+...|.+.+.++++.                                            
T Consensus        10 ~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~--------------------------------------------   45 (85)
T cd00076          10 NIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKS--------------------------------------------   45 (85)
T ss_pred             hhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHH--------------------------------------------
Confidence            334455778889999999999999999999999996                                            


Q ss_pred             hhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCC
Q psy3604          87 NWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHG  138 (496)
Q Consensus        87 ~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~g  138 (496)
                                   |+.++.+.+-.|++|+||..-+..||..||+.+|-.+-|
T Consensus        46 -------------~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~yg   84 (85)
T cd00076          46 -------------YLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG   84 (85)
T ss_pred             -------------HHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCccC
Confidence                         678889999999999999999999999999999966544

>PTZ00015 histone H4; Provisional

Probab=96.17  E-value=0.0069  Score=53.01  Aligned_cols=74  Identities=23%  Similarity=0.276  Sum_probs=65.6

Q ss_pred             HHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhh
Q psy3604           8 NRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRN   87 (496)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (496)
                      .+.+.+.+|..|+...|=.-+...|.+.+.++++.                                             
T Consensus        28 i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~---------------------------------------------   62 (102)
T PTZ00015         28 IRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKA---------------------------------------------   62 (102)
T ss_pred             ccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHH---------------------------------------------
Confidence            34566889999999999999999999999999986                                             


Q ss_pred             hhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCC
Q psy3604          88 WYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHG  138 (496)
Q Consensus        88 ~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~g  138 (496)
                                  |+.++.+.+-.|++|++|..-+..||.+||...|-.+-|
T Consensus        63 ------------~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~yg  101 (102)
T PTZ00015         63 ------------FLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLYG  101 (102)
T ss_pred             ------------HHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCCC
Confidence                        678889999999999999999999999999999875543

>PLN00035 histone H4; Provisional

Probab=96.08  E-value=0.011  Score=51.89  Aligned_cols=72  Identities=19%  Similarity=0.223  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhh
Q psy3604          11 LLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYK   90 (496)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~   90 (496)
                      +=+.+|..|+...|=.-+...|.+.|.++++.                                                
T Consensus        30 ipk~~IrRLARr~GvkRIS~~ay~elr~vle~------------------------------------------------   61 (103)
T PLN00035         30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKI------------------------------------------------   61 (103)
T ss_pred             CCHHHHHHHHHHcCcccchHHHHHHHHHHHHH------------------------------------------------
Confidence            44567888999999999999999999999996                                                


Q ss_pred             hhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCc
Q psy3604          91 RAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGL  139 (496)
Q Consensus        91 r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL  139 (496)
                               |+.++.+.+-.|++|++|..-+..||.+||...|-.+-||
T Consensus        62 ---------~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~lyGf  101 (103)
T PLN00035         62 ---------FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF  101 (103)
T ss_pred             ---------HHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCCCC
Confidence                     6778889999999999999999999999999999876665

>smart00803 TAF TATA box binding protein associated factor

Probab=95.61  E-value=0.016  Score=46.62  Aligned_cols=61  Identities=21%  Similarity=0.222  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhh
Q psy3604          13 KSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRA   92 (496)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~   92 (496)
                      +.+|..+.+..|.+.....|.+.|.+.++.                                                  
T Consensus         5 ~~~i~ria~~~Gi~ris~~a~~~l~~~~e~--------------------------------------------------   34 (65)
T smart00803        5 KETIKDVAESLGIGNLSDEAAKLLAEDVEY--------------------------------------------------   34 (65)
T ss_pred             HHHHHHHHHHCCCccccHHHHHHHHHHHHH--------------------------------------------------
Confidence            356778888999999999999999999984                                                  


Q ss_pred             hcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604          93 VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI  130 (496)
Q Consensus        93 ~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~  130 (496)
                             ++.++.+.+-.|++|++|+.-+..||..||.
T Consensus        35 -------rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803       35 -------RIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             -------HHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence                   6788999999999999999999999999873

TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.

>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]

Probab=95.12  E-value=0.024  Score=48.69  Aligned_cols=69  Identities=28%  Similarity=0.357  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhh
Q psy3604          12 LKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKR   91 (496)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r   91 (496)
                      =+.-|..++.+.|=+-++..|.+.|.+.++.                                                 
T Consensus        21 p~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~-------------------------------------------------   51 (91)
T COG2036          21 PKAPVRRILRKAGAERVSSSAIEELQEALEE-------------------------------------------------   51 (91)
T ss_pred             CchHHHHHHHHHhHHHhhHHHHHHHHHHHHH-------------------------------------------------
Confidence            3455777888888889999999999999997                                                 


Q ss_pred             hhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCC
Q psy3604          92 AVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIH  137 (496)
Q Consensus        92 ~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~  137 (496)
                              |+.+++..+.-+|.|+||..-...||.+++..+|..+.
T Consensus        52 --------~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~   89 (91)
T COG2036          52 --------YLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIY   89 (91)
T ss_pred             --------HHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence                    78899999999999999999999999999999987643

>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=94.99  E-value=0.035  Score=50.65  Aligned_cols=61  Identities=18%  Similarity=0.215  Sum_probs=48.5

Q ss_pred             HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604          14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV   93 (496)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~   93 (496)
                      .+|.+||++.|-+..++.....|.|.+.+                                                   
T Consensus        16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayR---------------------------------------------------   44 (129)
T PF02291_consen   16 RVIHLILKSMGVTEYEPRVVNQLLEFAYR---------------------------------------------------   44 (129)
T ss_dssp             HHHHHHHHHTT---B-THHHHHHHHHHHH---------------------------------------------------
T ss_pred             HHHHHHHHHcCCcccCHHHHHHHHHHHHH---------------------------------------------------
Confidence            57889999999999999999999999985                                                   


Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE  131 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~  131 (496)
                            |..++=..++.|++|+||+.....||-+|..-
T Consensus        45 ------Yt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~   76 (129)
T PF02291_consen   45 ------YTSDVLEDAQVYADHAGRSTIDADDVRLAIQS   76 (129)
T ss_dssp             ------HHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHHhcccccCChHHHHHHHHH
Confidence                  45556668899999999999999999999983

TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.

>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C

Probab=92.53  E-value=0.18  Score=41.88  Aligned_cols=65  Identities=17%  Similarity=0.172  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHHHhCccc---cChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhh
Q psy3604           9 RSLLKSSVVALLAEVGFDA---ADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQ   85 (496)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (496)
                      ++-|.-+|+.+|++.+=+.   +.+.++..|+|++-.                                           
T Consensus         4 Kaal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~-------------------------------------------   40 (76)
T PF15630_consen    4 KAALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYK-------------------------------------------   40 (76)
T ss_dssp             HHHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHH-------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHH-------------------------------------------
Confidence            5667889999999996433   788999999999875                                           


Q ss_pred             hhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604          86 RNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI  130 (496)
Q Consensus        86 ~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~  130 (496)
                                    ++..+|+.-..|+.|+||+.-+.+||.+...
T Consensus        41 --------------q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R   71 (76)
T PF15630_consen   41 --------------QLENLAKDLEAFAKHAGRSTINMDDVKLLAR   71 (76)
T ss_dssp             --------------HHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred             --------------HHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence                          5678899999999999999999999988654

>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex

Probab=92.24  E-value=0.26  Score=39.98  Aligned_cols=61  Identities=20%  Similarity=0.226  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhh
Q psy3604          13 KSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRA   92 (496)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~   92 (496)
                      +.+|-.+-+.+|....+..+...|.+-++-                                                  
T Consensus         6 ~esvk~iAes~Gi~~l~de~a~~La~dvey--------------------------------------------------   35 (66)
T PF02969_consen    6 QESVKDIAESLGISNLSDEAAKALAEDVEY--------------------------------------------------   35 (66)
T ss_dssp             HHHHHHHHHHTT---B-HHHHHHHHHHHHH--------------------------------------------------
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHH--------------------------------------------------
Confidence            456777888999999999999999888872                                                  


Q ss_pred             hcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604          93 VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI  130 (496)
Q Consensus        93 ~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~  130 (496)
                             -|.++-..+..|+.|+.|+.-+..||..||+
T Consensus        36 -------rlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen   36 -------RLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             -------HHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             -------HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence                   4677888899999999999999999999984

TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.

>smart00417 H4 Histone H4

Probab=89.70  E-value=0.2  Score=41.45  Aligned_cols=65  Identities=15%  Similarity=0.204  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhh
Q psy3604           6 DTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQ   85 (496)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (496)
                      |....+-+-+|..|+...|=.-....|.+.|.++++.                                           
T Consensus         9 d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~-------------------------------------------   45 (74)
T smart00417        9 DNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKS-------------------------------------------   45 (74)
T ss_pred             hhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHH-------------------------------------------
Confidence            4445566788999999999999999999999999986                                           


Q ss_pred             hhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHH
Q psy3604          86 RNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLL  127 (496)
Q Consensus        86 ~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~  127 (496)
                                    |+.++.+.+-.|++++||..-+..||..
T Consensus        46 --------------~l~~I~rdav~~a~ha~RKTV~~~DV~~   73 (74)
T smart00417       46 --------------FLENVVRDAVTYTEHARRKTVTAMDVVY   73 (74)
T ss_pred             --------------HHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence                          6778899999999999999888999865

>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=87.34  E-value=0.94  Score=47.62  Aligned_cols=70  Identities=19%  Similarity=0.223  Sum_probs=60.9

Q ss_pred             HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604          14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV   93 (496)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~   93 (496)
                      .+|..+.+.+|-+..+..|...|.+.++.                                                   
T Consensus         3 ~~i~~ia~~~Gi~~~~~~a~~~La~~~e~---------------------------------------------------   31 (343)
T cd08050           3 ESIKLIAESLGIDSLSDEVAQLLAEDVEY---------------------------------------------------   31 (343)
T ss_pred             hHHHHHHHHcCCCcCCHHHHHHHHHHHHH---------------------------------------------------
Confidence            46778889999999999999999999884                                                   


Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCcccc
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTY  142 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y  142 (496)
                            ++.++.+.|..||++++|+.-+.+||-.||+..++.  -|-+|
T Consensus        32 ------~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e--plyG~   72 (343)
T cd08050          32 ------RLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE--PLYGF   72 (343)
T ss_pred             ------HHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC--cccCC
Confidence                  678899999999999999999999999999997764  44444

The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as

>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=87.33  E-value=1.4  Score=36.01  Aligned_cols=59  Identities=22%  Similarity=0.234  Sum_probs=49.7

Q ss_pred             HHHHHHHh-CccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhhc
Q psy3604          16 VVALLAEV-GFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVT   94 (496)
Q Consensus        16 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~~   94 (496)
                      +-.++.++ +-...++.|.+.|.++++.                                                    
T Consensus         7 l~~lv~~id~~~~~~~da~~~l~~~~e~----------------------------------------------------   34 (72)
T cd07981           7 LQELLKEIDPREQLDPDVEELLLEIADD----------------------------------------------------   34 (72)
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHHHHHH----------------------------------------------------
Confidence            33444444 4467999999999999996                                                    


Q ss_pred             ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604          95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE  131 (496)
Q Consensus        95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~  131 (496)
                           |+..++..+..+|.|+||......||.++|+.
T Consensus        35 -----fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r   66 (72)
T cd07981          35 -----FVDDVVEDACRLAKHRKSDTLEVKDVQLHLER   66 (72)
T ss_pred             -----HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence                 77888899999999999999999999999986

The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind

>KOG3334|consensus

Probab=82.69  E-value=2.2  Score=39.55  Aligned_cols=61  Identities=16%  Similarity=0.205  Sum_probs=53.3

Q ss_pred             HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604          14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV   93 (496)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~   93 (496)
                      .+|+++|.++|-..-++-...-|.|...+                                                   
T Consensus        17 ~~i~~iL~s~GI~eyEprVi~qlLefa~r---------------------------------------------------   45 (148)
T KOG3334|consen   17 RVIASILKSLGIQEYEPRVINQLLEFAYR---------------------------------------------------   45 (148)
T ss_pred             HHHHHHHHHcCccccChHHHHHHHHHHHH---------------------------------------------------
Confidence            46899999999999999999999998885                                                   


Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE  131 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~  131 (496)
                            |.+.+=..+..|++|++++.-..+||-+|..-
T Consensus        46 ------Ytt~vL~DA~vys~HA~ka~i~~eDVrlA~~~   77 (148)
T KOG3334|consen   46 ------YTTTVLDDAKVYSSHAKKATIDAEDVRLAIQM   77 (148)
T ss_pred             ------HHHHHHHHHHHHHHhccCCCCcHHHHHHHHHH
Confidence                  44555568899999999999999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	496
1vs3_A	249	Crystal Structure Of The Trna Pseudouridine Synthas		1e-04

>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua From Thermus Thermophilus Hb8 Length = 249

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 37/81 (45%), Gaps = 18/81 (22%)
Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-----------------WFPQAGLDI 265
           LN  LP D+KVV    V   + AR D L+R Y+Y                 W  +  LD+
Sbjct: 79  LNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRP-LDL 137
Query: 266 DAMHKAAQYLVGTHDFRNLCK 286
           +AM +A   L+G H+F    K
Sbjct: 138 EAMEEALSLLLGRHNFLGFAK 158

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	496
1vs3_A	249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	9e-18
1dj0_A	264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	2e-17
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08

>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural NPPSFA, national project on protein structural and function analyses; 2.25A {Thermus thermophilus} Length = 249

 Score = 81.7 bits (203), Expect = 9e-18
 Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 18/76 (23%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-----------------WFPQAGLDI 265
           LN  LP D+KVV    V   + AR D L+R Y+Y                 W  +  LD+
Sbjct: 79  LNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRP-LDL 137

Query: 266 DAMHKAAQYLVGTHDF 281
           +AM +A   L+G H+F
Sbjct: 138 EAMEEALSLLLGRHNF 153

>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif, RNA-modifying enzyme, lyase; 1.50A {Escherichia coli} SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A Length = 264

 Score = 81.0 bits (201), Expect = 2e-17
 Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 18/76 (23%)

Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-----------------WFPQAGLDI 265
           +N NLP DI V     VP+ + ARF    R Y+Y                  F +  LD 
Sbjct: 81  VNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEP-LDA 139

Query: 266 DAMHKAAQYLVGTHDF 281
           + MH+AAQ L+G +DF
Sbjct: 140 ERMHRAAQCLLGENDF 155

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.8 bits (136), Expect = 1e-08
 Identities = 65/497 (13%), Positives = 145/497 (29%), Gaps = 123/497 (24%)

Query: 13  KSSVVALLAE----------------VGFDAADNAALETLVEICQACKYTCLTVTAKVLS 56
           K+ V   +                  +    +    LE L ++        +       S
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL-----YQIDPNWTSRS 217

Query: 57  SHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVTSVIGLVIKEVGGLSH----DF- 111
            H    K  RI   +        +    +   Y+  +     LV+  V         +  
Sbjct: 218 DHSSNIK-LRIHSIQ------AELRRLLKSKPYENCL-----LVLLNVQNAKAWNAFNLS 265

Query: 112 CE-LANRQQPMLADVLLALIELGIPI-HGLDTYAKRPMRTVF-----------PPVAPST 158
           C+ L   +   + D L A     I + H   T     ++++            P    +T
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325

Query: 159 QPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNEL- 217
            P+ LSI+   ++         +         ++    +T  I S L       +  E  
Sbjct: 326 NPRRLSIIAESIRD-GLATWDNWK--------HVNCDKLTTIIESSL----NVLEPAEYR 372

Query: 218 PYLKML-----NNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAA 272
                L     + ++P  +  + W  V +            Y        ++        
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL------VEKQ----PK 422

Query: 273 QYLVGTHD--FRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSF--- 327
           +  +           K+   N     + +V H  +   + +   +D+      +  +   
Sbjct: 423 ESTISIPSIYLELKVKLE--NEYALHRSIVDHYNIPKTFDS---DDLIPPYLDQYFYSHI 477

Query: 328 ----KKGQGNEKPEIIQQL-VD---IEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFL 379
               K  +  E+  + + + +D   +E+  +I+     W+++G+           +L+ L
Sbjct: 478 GHHLKNIEHPERMTLFRMVFLDFRFLEQ--KIRHDSTAWNASGS-----------ILNTL 524

Query: 380 AWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEF 439
             +  Y+     +   +  L    +  +LP + E +   +  SK T    D+  +     
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAIL-DFLPKIEENL---IC-SKYT----DLLRIA---L 572

Query: 440 DSRPGRILSETGKLAPR 456
            +    I  E  K   R
Sbjct: 573 MAEDEAIFEEAHKQVQR 589

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	496
d1dj0a_	264	Pseudouridine synthase I TruA {Escherichia coli [T	100.0
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	95.91
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	94.69
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	94.08
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	89.53
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	86.41
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	84.32
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	80.82

>d1dj0a_ d.265.1.1 (A:) Pseudouridine synthase I TruA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase I TruA
domain: Pseudouridine synthase I TruA
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=4.6e-45  Score=360.22  Aligned_cols=222  Identities=22%  Similarity=0.227  Sum_probs=190.4

Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCC
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQP  173 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~  173 (496)
                      +++|++.|+|+|+.++|||.+.+. .++.+.++.||...+..          +                ..+.       
T Consensus         3 ~~r~al~i~Y~Gt~f~G~Q~Q~~~-~TVq~~Le~aL~~~~~~----------~----------------~~~~-------   48 (264)
T d1dj0a_           3 VYKIALGIEYDGSKYYGWQRQNEV-RSVQEKLEKALSQVANE----------P----------------ITVF-------   48 (264)
T ss_dssp             CEEEEEEEEECCTTSSCSCCTTCS-SCHHHHHHHHHHHHHTS----------C----------------CCEE-------
T ss_pred             cEEEEEEEEEECCCeeeEeECcCC-CCHHHHHHHHHHHhhCC----------C----------------eEEE-------
Confidence            356899999999999999999873 56788888898875321          1                0122       


Q ss_pred             CCCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCcee
Q psy3604         174 HPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN  253 (496)
Q Consensus       174 ~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~  253 (496)
                              .++|||+||||++||++|+++..         .+...+...||+.||+||+|+++.+|+++|||||+|++|+
T Consensus        49 --------~agRTD~GVhA~~qv~~~~~~~~---------~~~~~~~~~lN~~Lp~dI~i~~~~~v~~~F~aR~~a~~r~  111 (264)
T d1dj0a_          49 --------CAGRTDAGVHGTGQVVHFETTAL---------RKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARR  111 (264)
T ss_dssp             --------ESSCCCTTCEEEEEEEEEEESCC---------CCHHHHHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEE
T ss_pred             --------EeecccCCcceeeEEEEEeeccc---------hhhhhhhcccccccccccccccceeccccccchhhhhhcc
Confidence                    24679999999999999999764         3678999999999999999999999999999999999999


Q ss_pred             EEEecC----------------CCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEe
Q psy3604         254 YKYWFP----------------QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDI  317 (496)
Q Consensus       254 Y~Y~~~----------------~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~  317 (496)
                      |+|++.                ...+|+++|++|++.|+|+|||+|||+.+.  ...+++|+|..+.+.+.++++.|+|+
T Consensus       112 Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~hdF~~F~~~~~--~~~~~~r~i~~~~~~~~~~~i~i~i~  189 (264)
T d1dj0a_         112 YRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQC--QSRTPWRNVMHINVTRHGPYVVVDIK  189 (264)
T ss_dssp             EEEEEECSSSCCCTTTTSSEECCSCCCHHHHHHHHGGGCEEEECGGGCCTTC--CCSCCEEEEEEEEEEEETTEEEEEEE
T ss_pred             cceeeccccccccccccccccccCCcchHHHHHHHhhccCcccccccccccc--cCCCcccccccccceecCcEEEEEec
Confidence            999874                247899999999999999999999998753  35689999999999999999999999


Q ss_pred             eCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccC
Q psy3604         318 KEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFL  375 (496)
Q Consensus       318 G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~  375 (496)
                      |+||     |  ||+|++||+|++++++|+++|+.+.+  ..  ..   ++|||+||+|++|.|+
T Consensus       190 g~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r--~~--~~---~~APa~GL~L~~V~Y~  247 (264)
T d1dj0a_         190 ANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDR--TL--AA---ATAKAEGLYLVAVDYP  247 (264)
T ss_dssp             ESCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCG--GG--SC---CCCCSTTEEEEEEECC
T ss_pred             hhHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhcCCc--cc--Cc---cccCCCCCEEcccccC
Confidence            9999     7  99999999999999999999987542  22  22   3456999999999996

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=95.91  E-value=0.0014  Score=51.91  Aligned_cols=70  Identities=19%  Similarity=0.208  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhh
Q psy3604          10 SLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWY   89 (496)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y   89 (496)
                      .+-+.+|-.+....|-...+..|.++|.+++..                                               
T Consensus         9 gI~k~~i~Riar~~Gv~ris~d~~~~l~~~l~~-----------------------------------------------   41 (82)
T d2huec1           9 GITKPAIRRLARRGGVKRISGLIYEETRGVLKV-----------------------------------------------   41 (82)
T ss_dssp             SSCHHHHHHHHHHTTCCEECTTHHHHHHHHHHH-----------------------------------------------
T ss_pred             CcCHHHHHHHHHHcCcccchHHHHHHHHHHHHH-----------------------------------------------
Confidence            344678888999999999999999999999985                                               


Q ss_pred             hhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCC
Q psy3604          90 KRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPI  136 (496)
Q Consensus        90 ~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v  136 (496)
                                ++.++.+.+-.||+|++|..-+..||..||..+|-.+
T Consensus        42 ----------~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g~pl   78 (82)
T d2huec1          42 ----------FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL   78 (82)
T ss_dssp             ----------HHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCEEE
T ss_pred             ----------HHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcCCCC
Confidence                      6888999999999999999999999999999877443

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

Probab=94.69  E-value=0.024  Score=42.53  Aligned_cols=61  Identities=15%  Similarity=0.198  Sum_probs=53.5

Q ss_pred             HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604          14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV   93 (496)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~   93 (496)
                      ..|-.+.++.|-......|.+.|.+.++.                                                   
T Consensus         7 a~I~ri~k~~~~~ris~ea~~~l~~~~e~---------------------------------------------------   35 (68)
T d1htaa_           7 APIGRIIKNAGAERVSDDARIALAKVLEE---------------------------------------------------   35 (68)
T ss_dssp             HHHHHHHHHTTCSCCCHHHHHHHHHHHHH---------------------------------------------------
T ss_pred             HHHHHHHHHCCcchhhHHHHHHHHHHHHH---------------------------------------------------
Confidence            45666777788888999999999888884                                                   


Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE  131 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~  131 (496)
                            ||.++...+..+|++++|..-+..||..||+.
T Consensus        36 ------fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~   67 (68)
T d1htaa_          36 ------MGEEIASEAVKLAKHAGRKTIKAEDIELARKM   67 (68)
T ss_dssp             ------HHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHT
T ss_pred             ------HHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence                  78999999999999999999999999999974

>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.08  E-value=0.034  Score=42.26  Aligned_cols=60  Identities=17%  Similarity=0.227  Sum_probs=52.4

Q ss_pred             HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604          14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV   93 (496)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~   93 (496)
                      ..|.+||++.|-...++.....|.|..-+                                                   
T Consensus         5 ~~i~~iL~~~GV~~yeprV~~qlLef~yR---------------------------------------------------   33 (68)
T d1tafa_           5 QVIMSILKELNVQEYEPRVVNQLLEFTFR---------------------------------------------------   33 (68)
T ss_dssp             HHHHHHHHHTTCCCBCTHHHHHHHHHHHH---------------------------------------------------
T ss_pred             HHHHHHHHHcCCccccHHHHHHHHHHHHH---------------------------------------------------
Confidence            46889999999999999999999999875                                                   


Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI  130 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~  130 (496)
                            |.+.+=..+..|++|+||++.+.+||-+|..
T Consensus        34 ------Ytt~VL~DA~vys~HA~k~~id~dDVkLAi~   64 (68)
T d1tafa_          34 ------YVTSILDDAKVYANHARKKTIDLDDVRLATE   64 (68)
T ss_dssp             ------HHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Confidence                  3455556788899999999999999999875

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon (Pyrococcus horikoshii) [TaxId: 53953]

Probab=89.53  E-value=0.15  Score=37.77  Aligned_cols=59  Identities=22%  Similarity=0.303  Sum_probs=49.0

Q ss_pred             HHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhhc
Q psy3604          15 SVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVT   94 (496)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~~   94 (496)
                      .|-.+..+.|=..+...|.+.|...++-                                                    
T Consensus         7 ~I~rI~k~~~~~ris~ea~~~l~~a~e~----------------------------------------------------   34 (66)
T d1ku5a_           7 PVDRLIRKAGAERVSEQAAKVLAEYLEE----------------------------------------------------   34 (66)
T ss_dssp             HHHHHHHHTTCSEECHHHHHHHHHHHHH----------------------------------------------------
T ss_pred             HHHHHHHhCcccccHHHHHHHHHHHHHH----------------------------------------------------
Confidence            4445555666667888888888888874                                                    


Q ss_pred             ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604          95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI  130 (496)
Q Consensus        95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~  130 (496)
                           ||.++...++.++++.||..-...||..||+
T Consensus        35 -----Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_          35 -----YAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             -----HHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             -----HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence                 7899999999999999999899999999985

>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)62
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=86.41  E-value=0.53  Score=35.58  Aligned_cols=61  Identities=20%  Similarity=0.255  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhh
Q psy3604          13 KSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRA   92 (496)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~   92 (496)
                      ..+|-.+.+.+|+......+...|.+=++                                               |   
T Consensus         9 ~esik~iAeS~Gi~~l~de~a~~LA~Dve-----------------------------------------------Y---   38 (70)
T d1tafb_           9 AESMKVIAESIGVGSLSDDAAKELAEDVS-----------------------------------------------I---   38 (70)
T ss_dssp             HHHHHHHHHHTTCCCBCHHHHHHHHHHHH-----------------------------------------------H---
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHH-----------------------------------------------H---
Confidence            45677888999999999999999988776                                               2   


Q ss_pred             hcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604          93 VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI  130 (496)
Q Consensus        93 ~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~  130 (496)
                             -|.++-..+..||+|+.|+.-+..||-.||+
T Consensus        39 -------Rl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_          39 -------KLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             -------HHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             -------HHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence                   4667778899999999999999999999984

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

Probab=84.32  E-value=0.44  Score=40.90  Aligned_cols=61  Identities=18%  Similarity=0.271  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604          14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV   93 (496)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~   93 (496)
                      ..|-.++++.|-......|++.|.+.++.                                                   
T Consensus        83 a~IkRi~k~~g~~ris~dA~~~l~~~~E~---------------------------------------------------  111 (151)
T d1f1ea_          83 ATVRRILKRAGIERASSDAVDLYNKLICR---------------------------------------------------  111 (151)
T ss_dssp             HHHHHHHHHTTCCEECHHHHHHHHHHHHH---------------------------------------------------
T ss_pred             HHHHHHHHcCCcchhhHHHHHHHHHHHHH---------------------------------------------------
Confidence            45666777889999999999999999984                                                   


Q ss_pred             cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604          94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE  131 (496)
Q Consensus        94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~  131 (496)
                            |+.++...+..+|.+++|..-+..||..|+..
T Consensus       112 ------fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~  143 (151)
T d1f1ea_         112 ------ATEELGEKAAEYADEDGRKTVQGEDVEKAITY  143 (151)
T ss_dssp             ------HHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence                  78899999999999999999999999999985

>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit beta (Nf-Yb3)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.82  E-value=1.2  Score=34.44  Aligned_cols=35  Identities=23%  Similarity=0.355  Sum_probs=32.5

Q ss_pred             eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCC
Q psy3604         100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGI  134 (496)
Q Consensus       100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi  134 (496)
                      ||++++..+...+...+|..-+..||..|+..+|.
T Consensus        37 Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~   71 (87)
T d1n1ja_          37 FISFITSEASERCHQEKRKTINGEDILFAMSTLGF   71 (87)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCc
Confidence            78899999999999999999999999999999875