Psyllid ID: psy3263

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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-------33
Protein Sequence
MFIFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVAMNQNTNQDMN
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHcccEEEccccccccEEEEcccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccEEEEEEcccccEEEEcccccEEEEEEcccccEEEcccccccccEEEccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHcccccccccccHHHHcEEEEEEccccccEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEccccccccEEEEEEEccccEEEccccccccEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEEEcEEEEEEEEcccccHHHHHHHcccEEEEccccccccEEEEcccccccHHHHHHHHHHHHHHHHccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccEEEEEEccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccccEEcEEEEccccccccc
Coil and Loop (DISEMBL)
mfifvvpsinpfgckIKALRAKTntyiktpvrgeepvfvvTGRKEDVARAKREILSAADHFSALRAsrksgalsplspptgvpghvtieVRVPYKVVGLvvgpkgatiKRIQHQtntyivtpsrdkepvfevtgnfpegpgfeshhgQKIVFILTSnlysffdcrifqrmnhhvfsgssgcssasssssssacaphsstqldlgsiwsgmssldkdeglgdspsfdaspvnpssiwsyppvsstspsgsisgsrqcylcndrevthalipcghnffcsecaertcdfdrtcpmcrvpvNQAMRIIFNQFlfgklwepvamnqntnqdmn
Flexible Loop (DISEMBL)
mfifvvpsinpfgckikALRAKTntyiktpvrgeepvfvvtgrkedVARAKREILSAADHFSALRASRksgalsplspptgvpghvTIEVRVPYKVVGLVVgpkgatikriqhqtntyivtpsrdkepVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVAMNQNTNQDMN
Low Complexity Region (SEG)
MFIFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFsgssgcssasssssssacaphssTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWsyppvsstspsgsisgsRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVAMNQNTNQDMN
Disordered region (IsUnstruct)
*FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA*********************************VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVF*******************************************************************************QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVA**********
Disordered Region (DISOPRED)
**IFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDV****************************************IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPE*P*****HGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDS***************************ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVAM*********
Disordered Region (DISEMBL)
MFIFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHV*************************QLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSY***************RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVAMNQNTNQDMN
Disordered Region (DISPRO)
MFIFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK********PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMN****************************************S****************************************SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVAMNQN******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFIFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPVAMNQNTNQDMN
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	329	2.2.26 [Sep-21-2011]
Q05A36	652	RNA-binding E3 ubiquitin-	yes	N/A	0.735	0.371	0.477	2e-51
Q5U5Q3	659	RNA-binding E3 ubiquitin-	yes	N/A	0.735	0.367	0.477	2e-51
Q69Z36	601	RNA-binding protein MEX3B	no	N/A	0.410	0.224	0.764	2e-50
A1L3F4	507	RNA-binding protein MEX3B	N/A	N/A	0.544	0.353	0.598	7e-50
Q6ZN04	569	RNA-binding protein MEX3B	no	N/A	0.379	0.219	0.804	1e-49
A1L020	520	RNA-binding protein MEX3A	no	N/A	0.364	0.230	0.788	8e-49
Q86XN8	651	RNA-binding protein MEX3D	no	N/A	0.379	0.192	0.765	2e-47
Q3UE17	643	RNA-binding protein MEX3D	no	N/A	0.376	0.192	0.773	5e-47
Q8JHV9	401	Baculoviral IAP repeat-co	N/A	N/A	0.203	0.167	0.323	6e-06
A9ULZ2	345	Baculoviral IAP repeat-co	N/A	N/A	0.203	0.194	0.323	1e-05

>sp|Q05A36|MEX3C_MOUSE RNA-binding E3 ubiquitin-protein ligase MEX3C OS=Mus musculus GN=Mex3c PE=2 SV=2

 Score =  203 bits (516), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 136/285 (47%), Positives = 168/285 (58%), Gaps = 43/285 (15%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
           GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct: 245 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 304

Query: 72  -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
            AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct: 305 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 364

Query: 131 EVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHV-FSGSSGCSSASSSS- 188
           EVTG  PE         +  + + T N     +   F      V F G +  S+  SS+ 
Sbjct: 365 EVTG-MPENVDRAREEIEMHIAMRTGNYIELNEENDFHYNGTDVSFEGGTLGSAWLSSNP 423

Query: 189 -----------------------------SSSACAPHSSTQ-LDLGSIWSG--MSSLDKD 216
                                         S+  A  S T     G+ W G  + S+  +
Sbjct: 424 VPPSRARMMSNYRNDSSSSLGSGSTDSYFGSNRLADFSPTSPFSTGNFWFGDTLPSVGSE 483

Query: 217 EGLGDSPSFDASPVNPSSIWS-YPPVSSTS-----PSGSISGSRQ 255
           +   DSP+FD+ P +  +IW+ + PV+  S     PSG++   R+
Sbjct: 484 DLTVDSPAFDSLPTSAQTIWTPFEPVNPLSGFGSDPSGNMKTQRR 528

RNA-binding protein. May be involved in post-transcriptional regulatory mechanisms.
Mus musculus (taxid: 10090)

>sp|Q5U5Q3|MEX3C_HUMAN RNA-binding E3 ubiquitin-protein ligase MEX3C OS=Homo sapiens GN=MEX3C PE=1 SV=3

 Score =  203 bits (516), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 136/285 (47%), Positives = 168/285 (58%), Gaps = 43/285 (15%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
           GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct: 252 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 311

Query: 72  -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
            AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct: 312 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 371

Query: 131 EVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHV-FSGSSGCSSASSSS- 188
           EVTG  PE         +  + + T N     +   F      V F G +  S+  SS+ 
Sbjct: 372 EVTG-MPENVDRAREEIEMHIAMRTGNYIELNEENDFHYNGTDVSFEGGTLGSAWLSSNP 430

Query: 189 -----------------------------SSSACAPHSSTQ-LDLGSIWSG--MSSLDKD 216
                                         S+  A  S T     G+ W G  + S+  +
Sbjct: 431 VPPSRARMISNYRNDSSSSLGSGSTDSYFGSNRLADFSPTSPFSTGNFWFGDTLPSVGSE 490

Query: 217 EGLGDSPSFDASPVNPSSIWS-YPPVSSTS-----PSGSISGSRQ 255
           +   DSP+FD+ P +  +IW+ + PV+  S     PSG++   R+
Sbjct: 491 DLAVDSPAFDSLPTSAQTIWTPFEPVNPLSGFGSDPSGNMKTQRR 535

RNA-binding protein. May be involved in post-transcriptional regulatory mechanisms.

Homo sapiens (taxid: 9606)

>sp|Q69Z36|MEX3B_MOUSE RNA-binding protein MEX3B OS=Mus musculus GN=Mex3b PE=2 SV=2

 Score =  199 bits (507), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 107/140 (76%), Positives = 119/140 (85%), Gaps = 5/140 (3%)

Query: 3   IFVVPSINPF--GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH 60
           I   PS+ P+  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+H
Sbjct: 106 ISPTPSLEPWLPGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEH 165

Query: 61  FSALRASR-KSGALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY 118
           FS +RASR K+ AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TY
Sbjct: 166 FSMIRASRNKNTALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTY 225

Query: 119 IVTPSRDKEPVFEVTGNFPE 138
           IVTPSRDKEPVFEVTG  PE
Sbjct: 226 IVTPSRDKEPVFEVTG-MPE 244

RNA-binding protein. May be involved in post-transcriptional regulatory mechanisms.

Mus musculus (taxid: 10090)

>sp|A1L3F4|MEX3B_XENLA RNA-binding protein MEX3B OS=Xenopus laevis GN=mex3b PE=2 SV=1

 Score =  197 bits (502), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 112/187 (59%), Positives = 125/187 (66%), Gaps = 8/187 (4%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGA 72
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR   A
Sbjct: 79  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVALARREIISAAEHFSMIRASRNKNA 138

Query: 73  LS----PLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
            +     +  P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEP
Sbjct: 139 AALNGGSVPAPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEP 198

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHV---FSGSSGCSSAS 185
           VFEVTG  PE         +  + + T  L    D   F      V     GS    S  
Sbjct: 199 VFEVTG-MPENVDRAREEIEAHIAVRTGGLIEVADENDFHANGTDVGFDLHGSLWSKSNQ 257

Query: 186 SSSSSSA 192
           SS S  A
Sbjct: 258 SSGSRKA 264

RNA-binding protein. May be involved in post-transcriptional regulatory mechanisms.

Xenopus laevis (taxid: 8355)

>sp|Q6ZN04|MEX3B_HUMAN RNA-binding protein MEX3B OS=Homo sapiens GN=MEX3B PE=1 SV=1

 Score =  197 bits (500), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 103/128 (80%), Positives = 113/128 (88%), Gaps = 3/128 (2%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR K+ 
Sbjct: 86  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASRNKNT 145

Query: 72  ALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
           AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct: 146 ALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 205

Query: 131 EVTGNFPE 138
           EVTG  PE
Sbjct: 206 EVTG-MPE 212

RNA-binding protein. May be involved in post-transcriptional regulatory mechanisms.

Homo sapiens (taxid: 9606)

>sp|A1L020|MEX3A_HUMAN RNA-binding protein MEX3A OS=Homo sapiens GN=MEX3A PE=1 SV=1

 Score =  194 bits (493), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 97/123 (78%), Positives = 111/123 (90%), Gaps = 3/123 (2%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
           GCKIKALRAKTNTYIKTPVRGEEPVF+VTGR+EDVA A+REI+SAA+HFS +RASR KSG
Sbjct: 152 GCKIKALRAKTNTYIKTPVRGEEPVFMVTGRREDVATARREIISAAEHFSMIRASRNKSG 211

Query: 72  ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE 131
           A   ++P   +PG VTI VRVPY+VVGLVVGPKGATIKRIQ QTNTYI+TPSRD++PVFE
Sbjct: 212 AAFGVAP--ALPGQVTIRVRVPYRVVGLVVGPKGATIKRIQQQTNTYIITPSRDRDPVFE 269

Query: 132 VTG 134
           +TG
Sbjct: 270 ITG 272

RNA binding protein, may be involved in post-transcriptional regulatory mechanisms.

Homo sapiens (taxid: 9606)

>sp|Q86XN8|MEX3D_HUMAN RNA-binding protein MEX3D OS=Homo sapiens GN=MEX3D PE=1 SV=3

 Score =  189 bits (481), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 98/128 (76%), Positives = 108/128 (84%), Gaps = 3/128 (2%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
           GCKIKALRAKTNTYIKTPVRGEEPVF+VTGRKEDV  AKREILSAA+HFS +RA+R K+G
Sbjct: 199 GCKIKALRAKTNTYIKTPVRGEEPVFIVTGRKEDVEMAKREILSAAEHFSIIRATRSKAG 258

Query: 72  AL-SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
            L      P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF
Sbjct: 259 GLPGAAQGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVF 318

Query: 131 EVTGNFPE 138
            VTG  PE
Sbjct: 319 AVTG-MPE 325

RNA binding protein, may be involved in post-transcriptional regulatory mechanisms.

Homo sapiens (taxid: 9606)

>sp|Q3UE17|MEX3D_MOUSE RNA-binding protein MEX3D OS=Mus musculus GN=Mex3d PE=2 SV=2

 Score =  188 bits (478), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 99/128 (77%), Positives = 110/128 (85%), Gaps = 4/128 (3%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
           GCKIKALRAKTNTYIKTPVRGEEPVF+VTGRKEDV  AKREILSA +HFS +RA+R K+G
Sbjct: 180 GCKIKALRAKTNTYIKTPVRGEEPVFIVTGRKEDVEMAKREILSA-EHFSLIRATRSKAG 238

Query: 72  ALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
            LS  +P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF
Sbjct: 239 GLSGATPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVF 298

Query: 131 EVTGNFPE 138
            VTG  PE
Sbjct: 299 AVTG-MPE 305

RNA binding protein, may be involved in post-transcriptional regulatory mechanisms.

Mus musculus (taxid: 10090)

>sp|Q8JHV9|BIR7A_XENLA Baculoviral IAP repeat-containing protein 7-A OS=Xenopus laevis GN=birc7-a PE=1 SV=1

 Score = 52.0 bits (123), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 237 SYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 296
           S PP+S+      +   R C +C D++V+   +PCGH   C+ECA       R CP+CR 
Sbjct: 335 SAPPLSTEEQLRRLKEERMCKVCMDKDVSMLFVPCGHLVVCTECAPNL----RHCPICRA 390

Query: 297 PVNQAMRIIFN 307
            +  ++R   +
Sbjct: 391 AIRGSVRAFMS 401

Weak apoptotic suppressor. Has E3 ubiquitin-protein ligase activity. Weak inhibitor of caspase activity.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|A9ULZ2|BIR7B_XENLA Baculoviral IAP repeat-containing protein 7-B OS=Xenopus laevis GN=birc7-b PE=2 SV=2

 Score = 51.2 bits (121), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 237 SYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 296
           S PP+S+      +   R C +C D++V+   +PCGH   C+ECA       R CP+CR 
Sbjct: 279 SGPPLSTEEQLQRLKEERMCKVCMDKDVSMLFVPCGHLVVCTECAPNL----RHCPICRA 334

Query: 297 PVNQAMRIIFN 307
            +  ++R   +
Sbjct: 335 AIRGSVRAFMS 345

Weak apoptotic suppressor. Has E3 ubiquitin-protein ligase activity. Weak inhibitor of caspase activity.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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	329
219522040	428	mex-3 protein [Tribolium castaneum] gi|2	0.866	0.665	0.578	2e-85
270002843	410	hypothetical protein TcasGA2_TC001207 [T	0.866	0.695	0.578	3e-85
66510891	425	PREDICTED: RNA-binding protein MEX3B-lik	0.869	0.672	0.550	1e-80
350414446	425	PREDICTED: RNA-binding protein MEX3B-lik	0.869	0.672	0.550	1e-80
340715365	425	PREDICTED: RNA-binding protein MEX3B-lik	0.869	0.672	0.550	1e-80
380020079	425	PREDICTED: RNA-binding protein MEX3B-lik	0.869	0.672	0.544	2e-79
383860805	418	PREDICTED: RNA-binding protein MEX3B-lik	0.857	0.674	0.549	4e-79
332022800	422	RNA-binding protein MEX3A [Acromyrmex ec	0.838	0.654	0.548	1e-75
345483953	444	PREDICTED: RNA-binding protein MEX3B-lik	0.875	0.648	0.495	1e-74
322797035	326	hypothetical protein SINV_16493 [Solenop	0.875	0.883	0.556	1e-74

>gi|219522040|ref|NP_001137201.1| mex-3 protein [Tribolium castaneum] gi|218464687|emb|CAM28380.2| KH domain protein [Tribolium castaneum]

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 187/323 (57%), Positives = 220/323 (68%), Gaps = 38/323 (11%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK--- 69
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA+AKREILSAA+HFS +RASRK   
Sbjct: 108 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAKAKREILSAAEHFSQIRASRKNNL 167

Query: 70  ----SGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 125
               SGA +P  PP  +PGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRD
Sbjct: 168 AGLGSGASTPPGPPANIPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRD 227

Query: 126 KEPVFEVTGNFPEGPGFESHHGQKIVFILTSN-----------------LYSFFDCRIFQ 168
           KEPVFEVTG  PE         +  + + T N                 LY      I  
Sbjct: 228 KEPVFEVTG-LPESVESARREIEAHIAMRTGNGASMGLGGLDDGDLFSSLYKSGLSSILN 286

Query: 169 RMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDAS 228
            +    F  +   + +SS S SS+ +  SS   DLG+IW   SS ++DEGLGDSPSFD+S
Sbjct: 287 YIEPEQFPMTGSSTFSSSGSCSSSSS--SSGGRDLGAIW---SSSERDEGLGDSPSFDSS 341

Query: 229 PVNPSSIWSYPPVS------STSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAE 282
               SSIWSYPPV+      STSP+ S+ GS +C +C + +VTHAL+PCGHNFFC ECA 
Sbjct: 342 -TALSSIWSYPPVAPSRPSNSTSPADSLLGSAKCLVCGEAKVTHALVPCGHNFFCMECAN 400

Query: 283 RTCD-FDRTCPMCRVPVNQAMRI 304
           R CD  +  CP+C +P  QA+RI
Sbjct: 401 RVCDGTEAQCPVCSLPAIQAIRI 423

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270002843|gb|EEZ99290.1| hypothetical protein TcasGA2_TC001207 [Tribolium castaneum]

 Score =  321 bits (823), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 187/323 (57%), Positives = 220/323 (68%), Gaps = 38/323 (11%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK--- 69
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA+AKREILSAA+HFS +RASRK   
Sbjct: 90  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAKAKREILSAAEHFSQIRASRKNNL 149

Query: 70  ----SGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 125
               SGA +P  PP  +PGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRD
Sbjct: 150 AGLGSGASTPPGPPANIPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRD 209

Query: 126 KEPVFEVTGNFPEGPGFESHHGQKIVFILTSN-----------------LYSFFDCRIFQ 168
           KEPVFEVTG  PE         +  + + T N                 LY      I  
Sbjct: 210 KEPVFEVTG-LPESVESARREIEAHIAMRTGNGASMGLGGLDDGDLFSSLYKSGLSSILN 268

Query: 169 RMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDAS 228
            +    F  +   + +SS S SS+ +  SS   DLG+IW   SS ++DEGLGDSPSFD+S
Sbjct: 269 YIEPEQFPMTGSSTFSSSGSCSSSSS--SSGGRDLGAIW---SSSERDEGLGDSPSFDSS 323

Query: 229 PVNPSSIWSYPPVS------STSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAE 282
               SSIWSYPPV+      STSP+ S+ GS +C +C + +VTHAL+PCGHNFFC ECA 
Sbjct: 324 -TALSSIWSYPPVAPSRPSNSTSPADSLLGSAKCLVCGEAKVTHALVPCGHNFFCMECAN 382

Query: 283 RTCD-FDRTCPMCRVPVNQAMRI 304
           R CD  +  CP+C +P  QA+RI
Sbjct: 383 RVCDGTEAQCPVCSLPAIQAIRI 405

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66510891|ref|XP_623265.1| PREDICTED: RNA-binding protein MEX3B-like isoform 2 [Apis mellifera]

 Score =  306 bits (783), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 181/329 (55%), Positives = 217/329 (65%), Gaps = 43/329 (13%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 101 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 160

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 161 GALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 220

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGC------- 181
           VFEVTG  PE         +  + + T    +  D  +   +         GC       
Sbjct: 221 VFEVTG-LPESVEAARREIEAHIALRTGTGTTLDDSELLSVLCRGGLGSILGCLDPPGSN 279

Query: 182 -----------SSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPV 230
                      S + SSSSSS+ AP  +   DL +IW   + +++DEGLG+SPSF++   
Sbjct: 280 GSNGSSGAFSSSGSCSSSSSSSGAPGLN---DLVAIWG--AGMERDEGLGESPSFESQTA 334

Query: 231 NPSSIWSYPPV------------SSTSPSGSI--SGSRQCYLCNDREVTHALIPCGHNFF 276
           + SSIWS+P V            S TSP+ S+   G R+C +C D+EVT AL+PCGHN F
Sbjct: 335 SASSIWSFPGVALPSRPSPPASASPTSPTDSLLGGGRRECVVCGDKEVTAALVPCGHNHF 394

Query: 277 CSECAERTCD-FDRTCPMCRVPVNQAMRI 304
           C +C  R C+  D +CP+C  PV QA+RI
Sbjct: 395 CLDCGNRVCESSDPSCPVCSRPVLQALRI 423

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350414446|ref|XP_003490320.1| PREDICTED: RNA-binding protein MEX3B-like [Bombus impatiens]

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 181/329 (55%), Positives = 217/329 (65%), Gaps = 43/329 (13%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 101 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 160

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 161 GALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 220

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGC------- 181
           VFEVTG  PE         +  + + T    +  D  +   +         GC       
Sbjct: 221 VFEVTG-LPESVEAARREIEAHIALRTGTGTTLDDSELLSVLCRGGLGSILGCLDPPGSN 279

Query: 182 -----------SSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPV 230
                      S + SSSSSS+ AP  +   DL +IW   + +++DEGLG+SPSF++   
Sbjct: 280 GSNGSSGAFSSSGSCSSSSSSSGAPGLN---DLVAIWG--AGMERDEGLGESPSFESQTA 334

Query: 231 NPSSIWSYPPV------------SSTSPSGSI--SGSRQCYLCNDREVTHALIPCGHNFF 276
           + SSIWS+P V            S TSP+ S+   G R+C +C D+EVT AL+PCGHN F
Sbjct: 335 SASSIWSFPGVPLPSRPSPPASASPTSPTDSLLGGGRRECVVCGDKEVTAALVPCGHNHF 394

Query: 277 CSECAERTCD-FDRTCPMCRVPVNQAMRI 304
           C +C  R C+  D +CP+C  PV QA+RI
Sbjct: 395 CLDCGNRVCESSDPSCPICSRPVLQALRI 423

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340715365|ref|XP_003396185.1| PREDICTED: RNA-binding protein MEX3B-like [Bombus terrestris]

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 181/329 (55%), Positives = 217/329 (65%), Gaps = 43/329 (13%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 101 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 160

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 161 GALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 220

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGC------- 181
           VFEVTG  PE         +  + + T    +  D  +   +         GC       
Sbjct: 221 VFEVTG-LPESVEAARREIEAHIALRTGTGATLDDSELLSVLCRGGLGSILGCLDPPGSN 279

Query: 182 -----------SSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPV 230
                      S + SSSSSS+ AP  +   DL +IW   + +++DEGLG+SPSF++   
Sbjct: 280 GSNGSSGAFSSSGSCSSSSSSSGAPGIN---DLVAIWG--AGMERDEGLGESPSFESQTA 334

Query: 231 NPSSIWSYPPV------------SSTSPSGSI--SGSRQCYLCNDREVTHALIPCGHNFF 276
           + SSIWS+P V            S TSP+ S+   G R+C +C D+EVT AL+PCGHN F
Sbjct: 335 SASSIWSFPGVALPSRPSPPASASPTSPTDSLLGGGRRECVVCGDKEVTAALVPCGHNHF 394

Query: 277 CSECAERTCD-FDRTCPMCRVPVNQAMRI 304
           C +C  R C+  D +CP+C  PV QA+RI
Sbjct: 395 CLDCGNRVCESSDPSCPICSRPVLQALRI 423

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380020079|ref|XP_003693924.1| PREDICTED: RNA-binding protein MEX3B-like [Apis florea]

 Score =  301 bits (772), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 179/329 (54%), Positives = 217/329 (65%), Gaps = 43/329 (13%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 101 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 160

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 161 GALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 220

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGC------- 181
           VFEVTG  PE         +  + + T    +  D  +   +         GC       
Sbjct: 221 VFEVTG-LPESVEAARREIEAHIALRTGTGTTLDDSELLSVLCRGGLGSILGCLDPPGSN 279

Query: 182 -----------SSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPV 230
                      S + SSSSSS+ AP  +   DL +IW   + +++DEGLG+SPSF++   
Sbjct: 280 GSNGSSGAFSSSGSCSSSSSSSGAPGLN---DLVAIWG--AGMERDEGLGESPSFESQTA 334

Query: 231 NPSSIWSYPPV------------SSTSPSGSI--SGSRQCYLCNDREVTHALIPCGHNFF 276
           + SSIWS+P V            S TSP+ S+   G R+C +C D+EVT AL+PCGHN F
Sbjct: 335 SASSIWSFPGVALPSRPSPPASASPTSPTDSLLGGGRRECVVCGDKEVTAALVPCGHNHF 394

Query: 277 CSECAERTCDF-DRTCPMCRVPVNQAMRI 304
           C +C  + C+  + +CP+C  PV QA+RI
Sbjct: 395 CLDCGNQVCERPNPSCPVCSRPVLQALRI 423

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383860805|ref|XP_003705879.1| PREDICTED: RNA-binding protein MEX3B-like [Megachile rotundata]

 Score =  301 bits (770), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 179/326 (54%), Positives = 217/326 (66%), Gaps = 44/326 (13%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 101 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 160

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 161 GALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 220

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGC------- 181
           VFEVTG  PE         +  + + T    S  D  +   +         GC       
Sbjct: 221 VFEVTG-LPESVEAARREIEAHIALRTGTGPSLDDSELLSVLCRGGLGSILGCLDPPGSN 279

Query: 182 -----------SSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPV 230
                      S + SSSSSS+ AP  +   D+ +IW   + +++DE LG+SPSF+++  
Sbjct: 280 GSNGSNGAFSSSGSCSSSSSSSGAPGLN---DIVAIWG--AGVERDESLGESPSFESA-- 332

Query: 231 NPSSIWSYPPVS-----------STSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSE 279
             SSIWS+P V+            TSP+ S+ G R+C +C D+EVT AL+PCGHN FC +
Sbjct: 333 --SSIWSFPGVALPSRPSPPGSIPTSPTDSLLGRRECVVCGDKEVTSALVPCGHNHFCLD 390

Query: 280 CAERTCD-FDRTCPMCRVPVNQAMRI 304
           C+ R C+  D +CP+C  PV QA+RI
Sbjct: 391 CSNRVCESSDPSCPVCSRPVLQALRI 416

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022800|gb|EGI63073.1| RNA-binding protein MEX3A [Acromyrmex echinatior]

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 174/317 (54%), Positives = 211/317 (66%), Gaps = 41/317 (12%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 45  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 104

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PP  VPGH+TI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 105 GALLGAPPGPPATVPGHITIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 164

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFD--------CR-------IFQRMNHH 173
           VFEVTG  PE         Q  + + T       D        CR         Q M+  
Sbjct: 165 VFEVTG-LPESVEAARREIQAHITLRTGTAPGVVDDTDLLGVLCRGGLGSVLGIQSMDQP 223

Query: 174 VFSGSSGCSSASSSSSSSACAPHSSTQL---DLGSIWSGMSSLDKDEGLGDSPSFDASPV 230
             + SS  + A SSS+S + +  S+  +   DL +IW+G   +++DEG+G+SPSF++ P 
Sbjct: 224 GSNSSSSSNGAFSSSASCSSSSSSTGGIGMNDLVAIWNG---IERDEGIGESPSFESQPT 280

Query: 231 NPSSIWSYPPV------------SSTSPSGSISGS--RQCYLCNDREVTHALIPCGHNFF 276
           + SSIWS+P V            S  SP+ S+ G   R C +C ++EVT AL+PCGHN F
Sbjct: 281 STSSIWSFPSVALPSRPSPPATASPASPTDSLLGGARRDCVVCGEKEVTAALVPCGHNLF 340

Query: 277 CSECAERTCD-FDRTCP 292
           C +C  R C+  D +CP
Sbjct: 341 CMDCGNRVCENQDPSCP 357

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345483953|ref|XP_001604798.2| PREDICTED: RNA-binding protein MEX3B-like [Nasonia vitripennis]

 Score =  286 bits (731), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 169/341 (49%), Positives = 210/341 (61%), Gaps = 53/341 (15%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 110 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 169

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PP  VPGH+TI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 170 GALLGAPPGPPASVPGHITIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 229

Query: 129 VFEVTGNFPEGPG-----FESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGCSS 183
           VFEVTG  PE         ++H  Q+   +L   ++   D  + + +         GC  
Sbjct: 230 VFEVTG-LPESVAAARTEIQAHITQR-TGVLPLCMHEEKD--LLEVLCRGGLGSILGCLD 285

Query: 184 ASSSSSSSACAPHSSTQL----------------DLGSIWSGMSSLDKDEGLGDSPSFDA 227
               +  S  +  + +                  DL +IW   + +++DEG+G+SPSF++
Sbjct: 286 PPGGAKGSNGSSGAFSSSGSCSSSSSSTGAPGLNDLVAIWG--AGMERDEGIGESPSFES 343

Query: 228 SPVNPSSIWSYPPVS---------------------STSPSGSISGSRQCYLCNDREVTH 266
              + SSIWS+P V+                      T      +G R+C +C D++VT 
Sbjct: 344 QTASASSIWSFPGVALPSRPSPPASASPASPTDSLLGTGSGNGSTGVRECVVCGDKDVTT 403

Query: 267 ALIPCGHNFFCSECAERTC-DFDRTCPMCRVPVNQAMRIIF 306
           AL+PCGH  FC EC  R C   + TCP+C  PV QA+RII 
Sbjct: 404 ALVPCGHKHFCLECGHRICMSSEPTCPVCSKPVLQALRIII 444

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322797035|gb|EFZ19349.1| hypothetical protein SINV_16493 [Solenopsis invicta]

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 183/329 (55%), Positives = 219/329 (66%), Gaps = 41/329 (12%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 70
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 1   GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 60

Query: 71  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           GAL  +P  PPT +PGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 61  GALLGAPPGPPTTMPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 120

Query: 129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFD--------CR-------IFQRMNHH 173
           VFEVTG  PE         Q  + + T       D        CR         Q ++  
Sbjct: 121 VFEVTG-LPESVEAARREIQAHITLRTGTAPGVVDESDLLGALCRGGLSSVIAIQSIDQP 179

Query: 174 VFSGSSGCSSASSSSSSSACAPHSSTQL---DLGSIWSGMSSLDKDEGLGDSPSFDASPV 230
             + SS  + A SSS+S + +  S+  +   DL +IW GM   ++DEGLG+SPSF++ P 
Sbjct: 180 GSNSSSSSNGAFSSSASCSSSSSSTGGMGMNDLVAIWGGM---ERDEGLGESPSFESQPT 236

Query: 231 NPSSIWSYPPV------------SSTSPSGSISGS--RQCYLCNDREVTHALIPCGHNFF 276
           + SSIWS+P V            S  SP+ S+ G+  R C +C D+EVT AL+PCGHN F
Sbjct: 237 STSSIWSFPSVTLPSRPSPPATASPASPTDSLLGNARRDCVVCGDKEVTAALVPCGHNLF 296

Query: 277 CSECAERTCDF-DRTCPMCRVPVNQAMRI 304
           C +C  R CD  D +CP+C   V Q +RI
Sbjct: 297 CMDCGNRVCDSQDPSCPVCSRRVLQVLRI 325

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

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	329
UNIPROTKB|F1N0W7	516	MEX3C "Uncharacterized protein	0.379	0.242	0.812	6.5e-68
UNIPROTKB|Q5U5Q3	659	MEX3C "RNA-binding E3 ubiquiti	0.379	0.189	0.812	6.5e-68
MGI|MGI:2652843	652	Mex3c "mex3 homolog C (C. eleg	0.379	0.191	0.812	6.5e-68
RGD|1309023	511	Mex3c "mex-3 homolog C (C. ele	0.379	0.244	0.812	6.5e-68
UNIPROTKB|D4A2R5	464	Mex3c "Protein Mex3c" [Rattus	0.379	0.269	0.812	6.5e-68
UNIPROTKB|F1PAZ0	621	MEX3C "Uncharacterized protein	0.379	0.201	0.812	8.3e-68
UNIPROTKB|J9P0S0	414	MEX3C "Uncharacterized protein	0.379	0.301	0.812	8.3e-68
UNIPROTKB|I3LE70	387	MEX3C "Uncharacterized protein	0.379	0.322	0.812	1.3e-67
ZFIN|ZDB-GENE-030131-2628	537	mex3b "mex-3 homolog B (C. ele	0.455	0.279	0.670	6.4e-66
MGI|MGI:1918252	601	Mex3b "mex3 homolog B (C. eleg	0.398	0.217	0.779	1.4e-64

UNIPROTKB|F1N0W7 MEX3C "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 507 (183.5 bits), Expect = 6.5e-68, Sum P(3) = 6.5e-68
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:   109 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 168

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   169 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 228

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   229 EVTG-MPE 235

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q5U5Q3 MEX3C "RNA-binding E3 ubiquitin-protein ligase MEX3C" [Homo sapiens (taxid:9606)]

 Score = 507 (183.5 bits), Expect = 6.5e-68, Sum P(3) = 6.5e-68
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:   252 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 311

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   312 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 371

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   372 EVTG-MPE 378

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

MGI|MGI:2652843 Mex3c "mex3 homolog C (C. elegans)" [Mus musculus (taxid:10090)]

 Score = 507 (183.5 bits), Expect = 6.5e-68, Sum P(3) = 6.5e-68
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:   245 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 304

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   305 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 364

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   365 EVTG-MPE 371

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|1309023 Mex3c "mex-3 homolog C (C. elegans)" [Rattus norvegicus (taxid:10116)]

 Score = 507 (183.5 bits), Expect = 6.5e-68, Sum P(3) = 6.5e-68
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:   104 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 163

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   164 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 223

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   224 EVTG-MPE 230

GO:0003723 "RNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA;ISO

UNIPROTKB|D4A2R5 Mex3c "Protein Mex3c" [Rattus norvegicus (taxid:10116)]

 Score = 507 (183.5 bits), Expect = 6.5e-68, Sum P(3) = 6.5e-68
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:    57 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 116

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   117 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 176

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   177 EVTG-MPE 183

GO:0003723 "RNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

UNIPROTKB|F1PAZ0 MEX3C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 506 (183.2 bits), Expect = 8.3e-68, Sum P(3) = 8.3e-68
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:   214 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 273

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   274 PALGGLSCGPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 333

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   334 EVTG-MPE 340

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|J9P0S0 MEX3C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 506 (183.2 bits), Expect = 8.3e-68, Sum P(3) = 8.3e-68
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:     7 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 66

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:    67 PALGGLSCGPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 126

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   127 EVTG-MPE 133

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|I3LE70 MEX3C "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 507 (183.5 bits), Expect = 1.3e-67, Sum P(3) = 1.3e-67
 Identities = 104/128 (81%), Positives = 113/128 (88%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:     1 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 60

Query:    72 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:    61 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 120

Query:   131 EVTGNFPE 138
             EVTG  PE
Sbjct:   121 EVTG-MPE 127

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-030131-2628 mex3b "mex-3 homolog B (C. elegans)" [Danio rerio (taxid:7955)]

 Score = 495 (179.3 bits), Expect = 6.4e-66, Sum P(3) = 6.4e-66
 Identities = 104/155 (67%), Positives = 120/155 (77%)

Query:    13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 71
             GCKIKALRAKTNTYIKTPVRGEEPVFVVTGR+EDVA A+REI+SAA+HFS +RASR K+ 
Sbjct:    78 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRREDVAMARREIISAAEHFSMIRASRNKNS 137

Query:    72 ALS---PLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
             +L+    +  P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEP
Sbjct:   138 SLNGNATVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEP 197

Query:   129 VFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFD 163
             VFEVTG  PE         +  + + T  L  F D
Sbjct:   198 VFEVTG-MPENVDRAREEIEAHIAMRTGGLIEFTD 231

GO:0003723 "RNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

MGI|MGI:1918252 Mex3b "mex3 homolog B (C. elegans)" [Mus musculus (taxid:10090)]

 Score = 514 (186.0 bits), Expect = 1.4e-64, Sum P(2) = 1.4e-64
 Identities = 106/136 (77%), Positives = 118/136 (86%)

Query:     7 PSINPF--GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSAL 64
             PS+ P+  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +
Sbjct:   110 PSLEPWLPGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMI 169

Query:    65 RASR-KSGALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP 122
             RASR K+ AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTP
Sbjct:   170 RASRNKNTALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTP 229

Query:   123 SRDKEPVFEVTGNFPE 138
             SRDKEPVFEVTG  PE
Sbjct:   230 SRDKEPVFEVTG-MPE 244

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" 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

No EC number assignment, probably not an enzyme!

---

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	329
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	2e-11
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-10
pfam00013	59	pfam00013, KH_1, KH domain	3e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-10
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	6e-07
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-06
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	8e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-05
pfam13014	42	pfam13014, KH_3, KH domain	3e-05
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-05
pfam00013	59	pfam00013, KH_1, KH domain	6e-05
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	7e-05
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	9e-05
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	0.001
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	0.003
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	0.003
smart00184	40	smart00184, RING, Ring finger	0.004

>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger)

 Score = 57.8 bits (140), Expect = 2e-11
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
              C +C +R      +PCGH   C ECA+R     + CP+CR P+  
Sbjct: 2   DDLCVICLERPRNVVFLPCGHLCLCEECAKR-LRSKKKCPICRQPIES 48

Length = 49

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGNF 136
           VTIEV +P   VGL++G  G+TIK+I+ +T   I +     +E V E+TG  
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPP 54

Length = 68

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 54.9 bits (133), Expect = 3e-10
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 87  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNF 136
           T  + +P   VG ++G  G+ IK I+ +T   I  P  D++    ++G  
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP-DDRDDTVTISGTP 49

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 54.5 bits (132), Expect = 4e-10
 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)

Query: 87  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGN 135
           T  V VP  +VG ++G  G+TIK I+ +T   I  P      +E +  +TG 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT 52

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 253 SRQCYLCNDREV-THALIPCGHNFFCSECAERTCDFDRTCPMCR 295
             +C +C D       L PCGH  FC EC  R       CP+CR
Sbjct: 2   ELECPICLDLLRDPVVLTPCGH-VFCRECILRYLKKKSKCPICR 44

Length = 45

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

Query: 13 GCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREIL 55
          G  IK +R +T   IK P  G   EE +  +TG  E V +AK  IL
Sbjct: 19 GSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 42.5 bits (101), Expect = 8e-06
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 87  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
           T EV +P K+   ++G KG+ I++I  +T   I  P    + 
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKS 42

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 13 GCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 56
          G  IK +  +T   I  P  G  E V  +TG  E+V +A   IL 
Sbjct: 22 GSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILE 66

Length = 68

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)

Query: 97  VGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTG 134
           VG ++G  G TIK I+ +T   I  P       E +  +TG
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 254 RQCYLCNDREVTHALI---PCGHNFFCSECAERTCDFDRTCPMCRVP 297
            +C +C D       +   PCGH  F  EC ++      TCP+CR P
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGH-VFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 39.9 bits (94), Expect = 6e-05
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI 54
          G  IK +R +T   I+ P    +    ++G  E V +AK  I
Sbjct: 19 GSNIKEIREETGVKIRIP-DDRDDTVTISGTPEQVEKAKELI 59

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

 Score = 39.4 bits (92), Expect = 7e-05
 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

Query: 255 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPV 298
           +C +C +       L+PCGH F C  C ++       TCP+CR P+
Sbjct: 1   ECPICLEEFREPVVLLPCGHVF-CRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 39.4 bits (93), Expect = 9e-05
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREIL 55
          I   G  I+ +  +T   I+ P  G +     +TG KE+V +AK EIL
Sbjct: 15 IGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL 62

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II)

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
           + I + V     GLV+G KG  I+ +Q      +
Sbjct: 25  IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension. Length = 68

>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18

 Score = 38.8 bits (90), Expect = 0.003
 Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 226 DASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTC 285
           D   +  SS W   P+ S  P   +  S +C++C D      L  C H F CS C  R  
Sbjct: 2   DELDITDSSDWLTTPIPSLYP---LDTSLRCHICKDFFDVPVLTSCSHTF-CSLCIRRCL 57

Query: 286 DFDRTCPMCRVP 297
                CP+CR  
Sbjct: 58  SNQPKCPLCRAE 69

All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 397

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 35.5 bits (83), Expect = 0.003
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 92  VPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK----EPVFEVTGNF 136
           VP    G ++G  G+TIK I+ +T   I           E V  ++G  
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKP 54

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|214546 smart00184, RING, Ring finger

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 256 CYLCNDREVTHA-LIPCGHNFFCSECAERTCDFD-RTCPMC 294
           C +C +  +    ++PCGH F C  C  +  +    TCP+C
Sbjct: 1   CPICLEEYLKDPVILPCGHTF-CRSCIRKWLESGNNTCPIC 40

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s). Length = 40

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	329
KOG2113|consensus	394		99.97
KOG1676|consensus	600		99.9
KOG1676|consensus	600		99.88
KOG2191|consensus	402		99.86
KOG2193|consensus	584		99.76
KOG2193|consensus	584		99.74
KOG2190|consensus	485		99.72
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.67
PRK13763	180	putative RNA-processing protein; Provisional	99.6
KOG2192|consensus	390		99.57
KOG2192|consensus	390		99.57
KOG2113|consensus	394		99.33
KOG2190|consensus	485		99.25
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.22
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.21
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.17
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.16
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.15
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.12
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.11
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.08
PF13014	43	KH_3: KH domain	99.07
KOG2191|consensus	402		99.07
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.06
KOG4172|consensus	62		99.04
PF13014	43	KH_3: KH domain	99.02
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.01
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.0
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.93
KOG4265|consensus	349		98.88
KOG0317|consensus	293		98.78
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.77
KOG0823|consensus	230		98.77
smart00322	69	KH K homology RNA-binding domain.	98.76
smart00322	69	KH K homology RNA-binding domain.	98.75
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.75
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.74
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.65
PHA02929	238	N1R/p28-like protein; Provisional	98.65
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.6
KOG0287|consensus	442		98.59
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.53
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.52
KOG0320|consensus	187		98.51
PRK13763	180	putative RNA-processing protein; Provisional	98.49
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.47
KOG2279|consensus	608		98.43
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.43
PHA02926	242	zinc finger-like protein; Provisional	98.35
PF14634	44	zf-RING_5: zinc-RING finger domain	98.33
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.29
KOG2208|consensus	753		98.24
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.22
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.22
KOG1571|consensus	355		98.21
KOG2177|consensus	386		98.21
KOG4275|consensus	350		98.19
PRK08406	140	transcription elongation factor NusA-like protein;	98.19
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.13
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.13
KOG2164|consensus	513		98.1
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.07
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.06
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.0
KOG0978|consensus	698		97.97
KOG0119|consensus	554		97.94
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.89
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	97.86
KOG0824|consensus	324		97.83
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.81
KOG0311|consensus	381		97.73
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.72
KOG0336|consensus	629		97.71
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.7
KOG1588|consensus	259		97.7
KOG4159|consensus	398		97.69
KOG1785|consensus	563		97.68
KOG0802|consensus	543		97.66
KOG1100|consensus	207		97.56
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	97.54
KOG4628|consensus	348		97.51
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.36
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.36
KOG2208|consensus	753		97.36
KOG2879|consensus	298		97.35
KOG2814|consensus	345		97.32
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.21
KOG1588|consensus	259		97.17
KOG4692|consensus	489		97.13
KOG2279|consensus	608		97.12
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	97.11
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.03
COG5152	259	Uncharacterized conserved protein, contains RING a	96.98
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.95
KOG0336|consensus	629		96.88
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.88
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.86
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.86
TIGR01953	341	NusA transcription termination factor NusA. This m	96.83
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.82
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.76
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.76
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.73
KOG0297|consensus	391		96.72
KOG1813|consensus	313		96.67
KOG1039|consensus	344		96.58
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.58
KOG2660|consensus	331		96.54
KOG0119|consensus	554		96.5
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.47
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.45
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.32
KOG0828|consensus	636		96.24
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.19
KOG0804|consensus	493		96.18
PRK12704	520	phosphodiesterase; Provisional	95.99
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.9
PRK00468	75	hypothetical protein; Provisional	95.69
PRK02821	77	hypothetical protein; Provisional	95.65
PRK12704	520	phosphodiesterase; Provisional	95.61
KOG4367|consensus	699		95.59
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.59
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	95.42
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	95.39
KOG2814|consensus	345		95.38
KOG1734|consensus	328		95.32
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.27
KOG3002|consensus	299		95.26
KOG0825|consensus	1134		95.17
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	95.16
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	95.14
KOG1002|consensus	791		95.1
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.07
PRK00106	535	hypothetical protein; Provisional	95.05
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.92
PRK01064	78	hypothetical protein; Provisional	94.85
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.78
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	94.75
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	94.73
PRK00106	535	hypothetical protein; Provisional	94.6
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.56
KOG1001|consensus	674		94.53
KOG0827|consensus	465		94.35
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.16
KOG3039|consensus	303		94.15
KOG3800|consensus	300		94.01
PRK00468	75	hypothetical protein; Provisional	93.8
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	93.78
COG5219	1525	Uncharacterized conserved protein, contains RING Z	93.69
PRK02821	77	hypothetical protein; Provisional	93.57
PF04641	260	Rtf2: Rtf2 RING-finger	93.48
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	93.46
KOG1645|consensus	463		93.45
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	93.41
PRK08406	140	transcription elongation factor NusA-like protein;	93.34
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.31
COG5175	480	MOT2 Transcriptional repressor [Transcription]	93.16
KOG4739|consensus	233		92.96
COG1837	76	Predicted RNA-binding protein (contains KH domain)	92.89
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	92.79
PRK12705	508	hypothetical protein; Provisional	92.11
KOG4185|consensus	296		91.88
KOG0826|consensus	357		91.88
KOG3273|consensus	252		91.69
PRK01064	78	hypothetical protein; Provisional	91.68
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	91.55
KOG1814|consensus	445		91.23
PRK12705	508	hypothetical protein; Provisional	91.09
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	91.01
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	91.0
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	90.9
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	90.84
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	90.78
KOG2932|consensus	389		90.75
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	90.74
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.3
COG1855	604	ATPase (PilT family) [General function prediction	89.9
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	89.7
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	89.31
KOG4362|consensus	684		89.28
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	88.62
PHA02825	162	LAP/PHD finger-like protein; Provisional	88.23
COG1782	637	Predicted metal-dependent RNase, consists of a met	88.13
KOG3579|consensus	352		87.95
PRK13764	602	ATPase; Provisional	87.85
KOG4369|consensus	2131		87.7
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	86.91
KOG4369|consensus	2131		86.79
KOG1493|consensus	84		86.45
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	86.33
KOG1428|consensus	3738		86.17
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	85.04
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	84.9
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	84.72
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	84.68
PHA03096	284	p28-like protein; Provisional	84.6
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	84.29
PRK06418	166	transcription elongation factor NusA-like protein;	84.0
PRK06418	166	transcription elongation factor NusA-like protein;	83.73
KOG2930|consensus	114		83.72
KOG2874|consensus	356		83.64
KOG3161|consensus	861		82.83
PHA02862	156	5L protein; Provisional	82.67
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	81.63
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	81.14
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	80.45
KOG1067|consensus	760		80.22

>KOG2113|consensus

Probab=99.97  E-value=3.1e-32  Score=252.61  Aligned_cols=289  Identities=35%  Similarity=0.374  Sum_probs=200.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      +|+.|+|+||++||.||+||++||+.|.++++++|.|+|.+|+|++|+++|.+.+|||...++.+...++....   ..+
T Consensus        36 ~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~s~Sgg~~~~---s~s  112 (394)
T KOG2113|consen   36 HVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASRSFSGGTNGA---SAS  112 (394)
T ss_pred             cceeecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCccccceeeeeeecccccCCCccc---ccc
Confidence            69999999999999999999999999999999999999999999999999999999999999999888776542   357


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-------chhhhhh----hhhh-
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-------GFESHHG----QKIV-  151 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-------eie~~i~----d~~~-  151 (329)
                      ++.+.++.+|.++||+++|.+|++||+||+.++.+|..|.++.++++.++| .|++|       |||+++.    |+|. 
T Consensus       113 ~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg-~~~nC~kra~s~eie~ta~~ra~~i~d~  191 (394)
T KOG2113|consen  113 GQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTG-APKNCVKRARSCEIEQTAVTRAGQIHDT  191 (394)
T ss_pred             CCCceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEec-CCcchhhhccccchhhhhhhhhhccccC
Confidence            889999999999999999999999999999999999999999999999999 99996       8888776    3333 


Q ss_pred             ------hhhcCCCCCCcccc-------cccccccC-----ccCCCC-CCCCCCCCCCC---CCCCCCCCCCCCCcceecC
Q psy3263         152 ------FILTSNLYSFFDCR-------IFQRMNHH-----VFSGSS-GCSSASSSSSS---SACAPHSSTQLDLGSIWSG  209 (329)
Q Consensus       152 ------~~~~~~~~~~~~~~-------~~~~~~~~-----~~~~~~-~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~  209 (329)
                            ..-+-.+.=++...       .||+.||-     +..... +..+.+.||..   .+..+     -....+|..
T Consensus       192 dndf~~~la~v~l~v~~~~~a~~~~~~~~~~s~f~~~~~~n~~~~~~~~~sss~~~~~s~~~~~~~-----~~~~~~~~s  266 (394)
T KOG2113|consen  192 DNDFAGQLAGVSLMVQKQQQAQQQMQEAQQQSMFYRRAFGNSNPFNQKEMSSSPFGMESSLGLDAL-----LRSFPSMRS  266 (394)
T ss_pred             CccccccccccchhhhhHHHHHHHHhhcCccchHHHhcccCCCccchhhccCCCcccccccccccc-----hhhhhhhhc
Confidence                  22221111122111       22222331     000000 00011111110   00001     123445554


Q ss_pred             CCCCCCCCCCCCCCCcCCC------CCCCCccccCCCC---------------------------CCCCCCCCCCCCccc
Q psy3263         210 MSSLDKDEGLGDSPSFDAS------PVNPSSIWSYPPV---------------------------SSTSPSGSISGSRQC  256 (329)
Q Consensus       210 ~~~~~~~~~~~~w~~~~~~------~~~~~~~~~~~~~---------------------------sp~~~~~~l~~~~~C  256 (329)
                      ....+.++|.+++.+....      +.++...|..-+.                           .--.+++-|-..+.|
T Consensus       267 s~t~~~~~g~g~s~~~~~~~~~~~~~~~~~~~~~~~~s~~~i~~~e~~s~~~~~~~a~~~~~l~~~~~~~~~~~~s~~~~  346 (394)
T KOG2113|consen  267 SLTPESLSGTGLSRPSLGGGQSAKQDLPTYDYWGTNNSLNDIMENEILSRKYDALSAWSSMGLEKREESPTNGLMSSLKG  346 (394)
T ss_pred             cCCcccccccCCCccccCCccccccCCCcCCccccCcchhhhhhhhhhhhhcchhhccccccchhccccccccchhhccc
Confidence            3333445555444333222      1223333332110                           001123445567899


Q ss_pred             ccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchh
Q psy3263         257 YLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR  303 (329)
Q Consensus       257 ~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~  303 (329)
                      .+|-+.....++.+|+|++||.+|+..  .....||+|.......++
T Consensus       347 ~~~~~~~~st~~~~~~~n~~~~~~a~~--s~~~~~~~c~~~~~~~~~  391 (394)
T KOG2113|consen  347 TSAGFGLLSTIWSGGNMNLSPGSLASA--SASPTSSTCDHNDHTLVP  391 (394)
T ss_pred             ccccCceeeeEeecCCcccChhhhhhc--ccCCccccccccceeeee
Confidence            999999999999999999999999982  236899999876654443

>KOG1676|consensus

Probab=99.90  E-value=1.9e-23  Score=208.46  Aligned_cols=139  Identities=23%  Similarity=0.211  Sum_probs=115.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPP   79 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p   79 (329)
                      -||.||||+||+||+|+.+|||||+|-++++    ||.+.|.|+++.|++|.++|.++++     .+.....++...++|
T Consensus       240 ~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~-----~~~~~~~~~~~~G~P  314 (600)
T KOG1676|consen  240 KVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIA-----EAEAGAGGGMGGGAP  314 (600)
T ss_pred             ceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHH-----HHhccCCCCcCCCCc
Confidence            5999999999999999999999999976555    9999999999999999999999963     222233333333444


Q ss_pred             CCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC-C----CCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263          80 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-D----KEPVFEVTGNFPEGPGFES-HHGQKIV  151 (329)
Q Consensus        80 ~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~-~----~e~~i~ItG~~pe~veie~-~i~d~~~  151 (329)
                      ..   ...+++.||..++|+||||||+|||.|.+++||++.++.. +    +|++|+|+| .+.+|+++. +|++.+.
T Consensus       315 ~~---~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG-~~~QIdhAk~LIr~kvg  388 (600)
T KOG1676|consen  315 GL---VAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRG-DKRQIDHAKQLIRDKVG  388 (600)
T ss_pred             cc---eeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEec-CcccchHHHHHHHHHhc
Confidence            22   1378999999999999999999999999999999999865 2    799999999 999998888 5556555

>KOG1676|consensus

Probab=99.88  E-value=3.3e-22  Score=199.64  Aligned_cols=147  Identities=22%  Similarity=0.210  Sum_probs=119.3

Q ss_pred             eeeeeeecCCChHHHHHHHHhCCeEEecCCCC-----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCC
Q psy3263           3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRGE-----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS   77 (329)
Q Consensus         3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~   77 (329)
                      +-+|+||||+|||||+||+++|+++.+-.++.     .+.+.|+|.++.|+.|+.++++++      ++......+..+.
T Consensus       148 ~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil------~e~~~~~~g~~~~  221 (600)
T KOG1676|consen  148 NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADIL------REEDDEVPGSGGH  221 (600)
T ss_pred             cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHH------HhcccCCCccccc
Confidence            35899999999999999999999999876554     456799999999999999999994      4333332222233


Q ss_pred             CCCCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----CCCeEEEECCCCCCcchhh-hhhhhhhh
Q psy3263          78 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNFPEGPGFES-HHGQKIVF  152 (329)
Q Consensus        78 ~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~e~~i~ItG~~pe~veie~-~i~d~~~~  152 (329)
                      .....-++.+++|.||...||+||||+|++||+|+.+||++|+|-+++    .||.+.|.| +++.|+.++ +|.+++..
T Consensus       222 ~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG-~~d~ie~Aa~lI~eii~~  300 (600)
T KOG1676|consen  222 AGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIG-TVDQIEHAAELINEIIAE  300 (600)
T ss_pred             cCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeec-CHHHHHHHHHHHHHHHHH
Confidence            322334557999999999999999999999999999999999996655    599999999 999997777 77788875


Q ss_pred             hhcC
Q psy3263         153 ILTS  156 (329)
Q Consensus       153 ~~~~  156 (329)
                      .-++
T Consensus       301 ~~~~  304 (600)
T KOG1676|consen  301 AEAG  304 (600)
T ss_pred             Hhcc
Confidence            5444

>KOG2191|consensus

Probab=99.86  E-value=8.3e-22  Score=184.62  Aligned_cols=130  Identities=27%  Similarity=0.325  Sum_probs=107.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS   77 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~   77 (329)
                      -+|.||||||++|.+||.+||++||+++..|      ||++.|+|+.|++......|++.+      |+......+....
T Consensus        49 AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKi------re~p~~~~k~v~~  122 (402)
T KOG2191|consen   49 AAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKI------REKPQAVAKPVDI  122 (402)
T ss_pred             cccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHH------HHhHHhhcCCccc
Confidence            3799999999999999999999999997766      999999999999999999999984      4433333332211


Q ss_pred             -CCCCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC-CC-----CCCeEEEECCCCCCc
Q psy3263          78 -PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS-RD-----KEPVFEVTGNFPEGP  140 (329)
Q Consensus        78 -~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~-~~-----~e~~i~ItG~~pe~v  140 (329)
                       -|-..+....+.+.||+...|.||||||+|||.|+|++|++|+|.+ .+     .||+|++.| .+|+.
T Consensus       123 ~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sg-e~e~~  191 (402)
T KOG2191|consen  123 LQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSG-EPEQN  191 (402)
T ss_pred             cCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecC-CHHHH
Confidence             1212233356899999999999999999999999999999999974 33     699999999 99998

>KOG2193|consensus

Probab=99.76  E-value=5.2e-19  Score=170.28  Aligned_cols=142  Identities=22%  Similarity=0.297  Sum_probs=120.9

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPP   79 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p   79 (329)
                      |||.||||.|.|||.|-..|.++|++-..+.    |+.++|-|++|...+|.++|++++.    -.+...          
T Consensus       209 yvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimq----kEA~~~----------  274 (584)
T KOG2193|consen  209 YVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQ----KEAVDD----------  274 (584)
T ss_pred             eeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHH----Hhhhcc----------
Confidence            8999999999999999999999999974333    8999999999999999999999853    111111          


Q ss_pred             CCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC------CCCeEEEECCCCCCc-chhhhhhhhhhh
Q psy3263          80 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNFPEGP-GFESHHGQKIVF  152 (329)
Q Consensus        80 ~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------~e~~i~ItG~~pe~v-eie~~i~d~~~~  152 (329)
                       .....+.++++-.+.+||.+|||-|..||+|+++||++|.|.+-.      .||+|+|.| .-|.| ..|+.|...+..
T Consensus       275 -k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre  352 (584)
T KOG2193|consen  275 -KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLRE  352 (584)
T ss_pred             -chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHH
Confidence             112346678888999999999999999999999999999998633      599999999 88888 888899999999


Q ss_pred             hhcCCCCCC
Q psy3263         153 ILTSNLYSF  161 (329)
Q Consensus       153 ~~~~~~~~~  161 (329)
                      .||+++.++
T Consensus       353 ~yEnDl~a~  361 (584)
T KOG2193|consen  353 CYENDLAAM  361 (584)
T ss_pred             HHhhhHHHh
Confidence            999976654

>KOG2193|consensus

Probab=99.74  E-value=1.1e-18  Score=168.04  Aligned_cols=137  Identities=26%  Similarity=0.356  Sum_probs=106.4

Q ss_pred             eeeeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHHhh-hhh-HhhhcccCC---
Q psy3263           3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSAAD-HFS-ALRASRKSG---   71 (329)
Q Consensus         3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i~e-~~~-~~~~~~~~~---   71 (329)
                      .|||+||||.|.+||+|+++|||+|.+.+--|      ||.|+|.|..|+|.+|..+|...+. .|. .+++-.-.+   
T Consensus       289 ~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~  368 (584)
T KOG2193|consen  289 NLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLP  368 (584)
T ss_pred             chhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCC
Confidence            58999999999999999999999999975443      9999999999999999999988753 111 122211111   


Q ss_pred             CC--------------C-CCC-CCC------------CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          72 AL--------------S-PLS-PPT------------GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        72 ~~--------------~-~~~-~p~------------~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      .+              . .++ +|.            ..+.+.++++.||...||.|||++|..||+|...+||.|+|.+
T Consensus       369 P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIap  448 (584)
T KOG2193|consen  369 PGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAP  448 (584)
T ss_pred             cccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecC
Confidence            00              0 000 110            1235678899999999999999999999999999999999976


Q ss_pred             CC----CCCeEEEECCCCCCc
Q psy3263         124 RD----KEPVFEVTGNFPEGP  140 (329)
Q Consensus       124 ~~----~e~~i~ItG~~pe~v  140 (329)
                      .+    .+|.|+|+| .|+..
T Consensus       449 pE~pdvseRMViItG-ppeaq  468 (584)
T KOG2193|consen  449 PEIPDVSERMVIITG-PPEAQ  468 (584)
T ss_pred             CCCCCcceeEEEecC-ChHHH
Confidence            44    789999999 88766

>KOG2190|consensus

Probab=99.72  E-value=2.5e-17  Score=165.71  Aligned_cols=125  Identities=24%  Similarity=0.321  Sum_probs=101.6

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEec---CCCCcceEEEec---------CHHHHHHHHHHHHHHhhhhhHhhhcccCCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTP---VRGEEPVFVVTG---------RKEDVARAKREILSAADHFSALRASRKSGA   72 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip---~~~~ervi~ItG---------~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~   72 (329)
                      ||.||||+|..||+||.+|.++|++-   +...||+|+|+|         ..+++.+|.++|...++   .........+
T Consensus        54 vG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~---~d~~~~~d~~  130 (485)
T KOG2190|consen   54 VGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE---EDDEAAEDNG  130 (485)
T ss_pred             ceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc---ccccccccCC
Confidence            79999999999999998888888875   334499999999         99999999999987643   0001111111


Q ss_pred             CCCCCCCCCCCC-ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----CCCeEEEECCCCCCc
Q psy3263          73 LSPLSPPTGVPG-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNFPEGP  140 (329)
Q Consensus        73 ~~~~~~p~~~~g-~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~e~~i~ItG~~pe~v  140 (329)
                      +.       .+. ..+.++.||..++|.||||+|+.||+|++.|||+|++.++.    .+|.|+|+| .++.|
T Consensus       131 ~~-------~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG-~~~av  195 (485)
T KOG2190|consen  131 ED-------ASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG-EPDAV  195 (485)
T ss_pred             cc-------ccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcC-chHHH
Confidence            11       111 38999999999999999999999999999999999998763    789999999 99988

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.67  E-value=1.4e-16  Score=140.64  Aligned_cols=128  Identities=16%  Similarity=0.156  Sum_probs=95.9

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEE---ecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVV---TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPT   80 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~I---tG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~   80 (329)
                      .+|.|||+||++||+|+++||++|++..  ++..|.|   ++.++++.+|++.|.++..-|..-.|-..           
T Consensus         8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~--~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l-----------   74 (172)
T TIGR03665         8 RIGVLIGKGGETKKEIEERTGVKLDIDS--ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKL-----------   74 (172)
T ss_pred             HhhhHhCCchhHHHHHHHHhCcEEEEEc--CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHh-----------
Confidence            4789999999999999999999999984  3345677   89999999999999987542211100000           


Q ss_pred             CCCCc-eEEEEEecC---------cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhh
Q psy3263          81 GVPGH-VTIEVRVPY---------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQK  149 (329)
Q Consensus        81 ~~~g~-~t~~i~VP~---------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~  149 (329)
                       .... ....+.|+.         +..|.|||++|+|++.||+.|||+|.++.    ..|.|.| .+++++++. +|.++
T Consensus        75 -~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~i~~l  148 (172)
T TIGR03665        75 -LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIG-DPEQVQIAREAIEML  148 (172)
T ss_pred             -cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEEC-CHHHHHHHHHHHHHH
Confidence             0111 112233443         47999999999999999999999999985    6799999 999996655 66554


Q ss_pred             h
Q psy3263         150 I  150 (329)
Q Consensus       150 ~  150 (329)
                      +
T Consensus       149 i  149 (172)
T TIGR03665       149 I  149 (172)
T ss_pred             H
Confidence            4

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.60  E-value=2.3e-15  Score=133.88  Aligned_cols=124  Identities=17%  Similarity=0.192  Sum_probs=90.4

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEE----ecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVV----TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPT   80 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~I----tG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~   80 (329)
                      +|.|||++|++||.|+++||++|++..  ++..|.|    +++++++++|+++|.+++.-|..-.+-...          
T Consensus        14 ig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~----------   81 (180)
T PRK13763         14 IGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLL----------   81 (180)
T ss_pred             hhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHh----------
Confidence            689999999999999999999999984  3355677    589999999999999986422211110000          


Q ss_pred             CCCCceEE-EEEe---------cCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhh
Q psy3263          81 GVPGHVTI-EVRV---------PYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHG  147 (329)
Q Consensus        81 ~~~g~~t~-~i~V---------P~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~  147 (329)
                        ...... .+.+         ..+.+|+|||++|+|+|.||+.|||+|.++.+    .|.|.| .+++++++. +|.
T Consensus        82 --gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~----~v~i~G-~~~~~~~A~~~I~  152 (180)
T PRK13763         82 --DDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK----TVAIIG-DPEQVEIAREAIE  152 (180)
T ss_pred             --CCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC----EEEEEe-CHHHHHHHHHHHH
Confidence              000111 1111         12579999999999999999999999999743    488999 999995544 443

>KOG2192|consensus

Probab=99.57  E-value=8.5e-15  Score=134.47  Aligned_cols=142  Identities=23%  Similarity=0.334  Sum_probs=104.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEec----CCCCcceEEEecCHHHHHHHHHHHHHHhhh-------------------
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTP----VRGEEPVFVVTGRKEDVARAKREILSAADH-------------------   60 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip----~~~~ervi~ItG~~e~v~~A~~~I~~i~e~-------------------   60 (329)
                      +.|.||||+|++||+||++..++.++-    +...+||+.+.|.+.+|..+.+.|++.+..                   
T Consensus       133 ~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~  212 (390)
T KOG2192|consen  133 LAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETY  212 (390)
T ss_pred             hccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCccc
Confidence            458899999999999999999999985    233389999999999999999999887631                   


Q ss_pred             ----hhHhhhccc-CCCCCC----CCCCCC--------------------------------------------------
Q psy3263          61 ----FSALRASRK-SGALSP----LSPPTG--------------------------------------------------   81 (329)
Q Consensus        61 ----~~~~~~~~~-~~~~~~----~~~p~~--------------------------------------------------   81 (329)
                          |.|+-..+. ..+.++    .+||+.                                                  
T Consensus       213 dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQg  292 (390)
T KOG2192|consen  213 DYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQG  292 (390)
T ss_pred             ccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCC
Confidence                122111111 000000    000000                                                  


Q ss_pred             -----------------CC-CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCc
Q psy3263          82 -----------------VP-GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGP  140 (329)
Q Consensus        82 -----------------~~-g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~v  140 (329)
                                       +. ..+|.+|.||.+.-|.||||||++||+|++++||.|++...-   .+++|+|+| +.+++
T Consensus       293 Gs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItG-TqdQI  371 (390)
T KOG2192|consen  293 GSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQI  371 (390)
T ss_pred             CCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEec-cHHHH
Confidence                             00 136889999999999999999999999999999999996522   689999999 88888


Q ss_pred             chhhhh
Q psy3263         141 GFESHH  146 (329)
Q Consensus       141 eie~~i  146 (329)
                      .-+.++
T Consensus       372 qnAQYL  377 (390)
T KOG2192|consen  372 QNAQYL  377 (390)
T ss_pred             hhHHHH
Confidence            555433

>KOG2192|consensus

Probab=99.57  E-value=1.5e-14  Score=132.79  Aligned_cols=128  Identities=18%  Similarity=0.273  Sum_probs=103.8

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecC-CCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPV-RGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~-~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      .|.||||||++||+||.++|+.|++|. .+.+|+++|+...+-|-.-.+.|+--+|+..                  ..+
T Consensus        59 agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f------------------~~~  120 (390)
T KOG2192|consen   59 AGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGF------------------QLP  120 (390)
T ss_pred             ccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCC------------------CCC
Confidence            478999999999999999999999994 4559999999999888877777765544111                  223


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC----CCCCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTGNFPEGP-GFESHHGQKIV  151 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~----~~~e~~i~ItG~~pe~v-eie~~i~d~~~  151 (329)
                      ....+++.|+..+.|.|||+.|+.||+++++..++++|-.    ...+|++.|.| .|.+| ++-..|.|.+.
T Consensus       121 ~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g-~~k~v~~~i~~il~~i~  192 (390)
T KOG2192|consen  121 SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGG-KPKRVVECIKIILDLIS  192 (390)
T ss_pred             CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecC-CcchHHHHHHHHHHHhh
Confidence            3377899999999999999999999999999999998753    44899999999 99999 44445555444

>KOG2113|consensus

Probab=99.33  E-value=9e-13  Score=123.39  Aligned_cols=160  Identities=28%  Similarity=0.365  Sum_probs=108.8

Q ss_pred             CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-----chhh---hhhhhhhh
Q psy3263          81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-----GFES---HHGQKIVF  152 (329)
Q Consensus        81 ~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-----eie~---~i~d~~~~  152 (329)
                      ..+++.|+.+.||+++|+.|+|++|.+||.||++|.+||..|.+.++|+|.+|| .+++|     +|++   |+.-... 
T Consensus        21 ~~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg-~~edv~~aRrei~saaeH~~l~~~-   98 (394)
T KOG2113|consen   21 SIGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTG-RHEDVRRARREIPSAAEHFGLIRA-   98 (394)
T ss_pred             CCCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceecc-CchhHHHHhhcCccccceeeeeee-
Confidence            566889999999999999999999999999999999999999999999999999 99998     3333   3221100 


Q ss_pred             hhcCCCCCCcccccccccccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceecCCCCCCCCCCCCCCCCcCCCCCCC
Q psy3263         153 ILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNP  232 (329)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~  232 (329)
                                         +.+    ++....++.           ..+....+...              |+-+. +  
T Consensus        99 -------------------s~s----~Sgg~~~~s-----------~s~qt~sy~sv--------------P~rvv-g--  127 (394)
T KOG2113|consen   99 -------------------SRS----FSGGTNGAS-----------ASGQTTSYVSV--------------PLRVV-G--  127 (394)
T ss_pred             -------------------ccc----ccCCCcccc-----------ccCCCceeeec--------------cceee-e--
Confidence                               000    000000000           00000000000              00000 0  


Q ss_pred             CccccCCCCCCCCCCCCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccchhhh
Q psy3263         233 SSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRII  305 (329)
Q Consensus       233 ~~~~~~~~~sp~~~~~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~~i~  305 (329)
                                  +-..+-.....|.+|++.....+.++|+|..||.+|+...+.+ ...|++|...+.+...+.
T Consensus       128 ------------lvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta~~ra~~i~  189 (394)
T KOG2113|consen  128 ------------LVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTAVTRAGQIH  189 (394)
T ss_pred             ------------eccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhhhhhhhccc
Confidence                        0011224567899999999999999999999999999888666 777999988776665553

>KOG2190|consensus

Probab=99.25  E-value=4.3e-11  Score=120.86  Aligned_cols=131  Identities=20%  Similarity=0.254  Sum_probs=95.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCC----CCcceEEEecCHHHHHHHHHHHHHHhhhhhHh-----hhc---cc--
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVR----GEEPVFVVTGRKEDVARAKREILSAADHFSAL-----RAS---RK--   69 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~----~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~-----~~~---~~--   69 (329)
                      -+|.||||+|++||+||++|||+|++..+    ..+|.|+|.|.+++|.+|...|...+..+...     ...   +.  
T Consensus       148 q~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~  227 (485)
T KOG2190|consen  148 QVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSA  227 (485)
T ss_pred             heeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcc
Confidence            48999999999999999999999999754    33899999999999999999998875321100     000   00  


Q ss_pred             CCCCCCC----CCC--CC------CCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263          70 SGALSPL----SPP--TG------VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG  134 (329)
Q Consensus        70 ~~~~~~~----~~p--~~------~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG  134 (329)
                      ..++...    ...  .+      .+.+....+.+|...++.|||++|..|+.|++.+|+.|.+-....+++|+++.
T Consensus       228 ~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~  304 (485)
T KOG2190|consen  228 SQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISA  304 (485)
T ss_pred             cccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeecc
Confidence            0000000    000  00      01223356789999999999999999999999999999997766558888776

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.22  E-value=2.1e-11  Score=90.62  Aligned_cols=51  Identities=25%  Similarity=0.276  Sum_probs=46.9

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC----CcceEEEecCHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREI   54 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~----~ervi~ItG~~e~v~~A~~~I   54 (329)
                      +||.||||+|++||+|+++|||+|+++...    .+|+|+|+|++++|.+|+.+|
T Consensus        10 ~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396          10 QAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             HcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            589999999999999999999999998543    379999999999999999987

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.21  E-value=1.6e-11  Score=90.17  Aligned_cols=52  Identities=33%  Similarity=0.446  Sum_probs=47.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREIL   55 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~   55 (329)
                      ++|.||||+|++|++|+++|||+|++|...+ ++.|+|+|++++|.+|+.+|+
T Consensus        10 ~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394          10 LHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             HhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHhC
Confidence            6899999999999999999999999996543 788999999999999999873

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.17  E-value=1.9e-11  Score=90.95  Aligned_cols=54  Identities=30%  Similarity=0.482  Sum_probs=49.2

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC----CCCCeEEEECCCCCCcc
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGNFPEGPG  141 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~----~~e~~i~ItG~~pe~ve  141 (329)
                      ++++.||.+.+|.|||++|++||+|+++|||+|.+++.    +++|+|+|+| .++++.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G-~~~~v~   58 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG-KPSAVQ   58 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEe-CHHHHH
Confidence            46899999999999999999999999999999999864    3689999999 999883

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=99.16  E-value=7e-11  Score=86.98  Aligned_cols=48  Identities=25%  Similarity=0.281  Sum_probs=44.6

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREI   54 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I   54 (329)
                      +||.||||+|++||+|+++|||+|+++.   ++.|.|+|+ ++++++|+.+|
T Consensus        12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393          12 KIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             heeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHh
Confidence            6899999999999999999999999985   357899998 99999999987

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.15  E-value=2.6e-11  Score=88.97  Aligned_cols=54  Identities=31%  Similarity=0.486  Sum_probs=49.0

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCcc
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGPG  141 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~ve  141 (329)
                      +.++.||.+++|.|||++|++|++|+++|||+|.+|... .++.|+|+| .+++|+
T Consensus         1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G-~~~~v~   55 (62)
T cd02394           1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITG-PKENVE   55 (62)
T ss_pred             CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEc-CHHHHH
Confidence            357899999999999999999999999999999999855 678899999 888883

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.12  E-value=3.5e-11  Score=87.68  Aligned_cols=51  Identities=29%  Similarity=0.439  Sum_probs=46.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI   54 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I   54 (329)
                      ++|.||||+|++||+|+++|||+|+++.++++..|+|+|++++|++|+++|
T Consensus        10 ~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen   10 LVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             HHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred             HcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence            578999999999999999999999999665344899999999999999987

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=99.11  E-value=3.1e-11  Score=85.14  Aligned_cols=48  Identities=40%  Similarity=1.012  Sum_probs=43.2

Q ss_pred             CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +..|.||++...+++++||||.+||..|+.++.+....||+||+++.+
T Consensus         2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen    2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES   49 (50)
T ss_dssp             HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred             cCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence            578999999999999999999999999999999999999999998864

...

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.08  E-value=1.6e-11  Score=89.45  Aligned_cols=54  Identities=33%  Similarity=0.597  Sum_probs=48.9

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcc
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPG  141 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~ve  141 (329)
                      |.++.||.+++|+|||++|++||+|+++|||+|.++.++++..|+|+| .+++|+
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~   54 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVE   54 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHH
Confidence            689999999999999999999999999999999998775334899999 999883

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>PF13014 KH_3: KH domain

Probab=99.07  E-value=1.7e-10  Score=78.80  Aligned_cols=39  Identities=36%  Similarity=0.485  Sum_probs=35.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecC---C-CCcceEEEec
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPV---R-GEEPVFVVTG   42 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~---~-~~ervi~ItG   42 (329)
                      |||.||||+|++||+|+++|||+|++|+   . ..+++|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            6899999999999999999999999997   2 2389999998

>KOG2191|consensus

Probab=99.07  E-value=1.7e-10  Score=109.01  Aligned_cols=121  Identities=21%  Similarity=0.225  Sum_probs=91.8

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHHhhhhhH----hhhcccCCCC-
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSAADHFSA----LRASRKSGAL-   73 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i~e~~~~----~~~~~~~~~~-   73 (329)
                      -|.||||+|.+||.++|++++.|++++..+      ||+++|.|.+|+..+|..+|++.+...++    +..+.....| 
T Consensus       143 ag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGp  222 (402)
T KOG2191|consen  143 AGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGP  222 (402)
T ss_pred             ccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCc
Confidence            378999999999999999999999984332      89999999999999999999998642221    2222111111 


Q ss_pred             ----CCCCCCC-----CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC
Q psy3263          74 ----SPLSPPT-----GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD  125 (329)
Q Consensus        74 ----~~~~~p~-----~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~  125 (329)
                          .+.+.|+     -.+...+..+-|+....|..-|.||.++-.|-..+|+.|.+++.-
T Consensus       223 vaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l  283 (402)
T KOG2191|consen  223 VANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQAL  283 (402)
T ss_pred             ccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeecccc
Confidence                1111111     133456678889999999999999999999999999999998754

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=99.06  E-value=1.6e-10  Score=85.06  Aligned_cols=54  Identities=22%  Similarity=0.285  Sum_probs=47.5

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcch
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGF  142 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~vei  142 (329)
                      .+..+.||.+++|.|||+||++||+|+++|||+|.++.   ++.|.|+|+.+++++.
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~   55 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEK   55 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHH
Confidence            46789999999999999999999999999999999987   4679999933788743

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG4172|consensus

Probab=99.04  E-value=2.1e-11  Score=86.29  Aligned_cols=53  Identities=28%  Similarity=0.778  Sum_probs=48.7

Q ss_pred             cccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccchhhhh
Q psy3263         254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~~i~~  306 (329)
                      .+|.||+|...+.++.-|||.|+|.+|..++++. ...||+||+++...++.+.
T Consensus         8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~   61 (62)
T KOG4172|consen    8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYR   61 (62)
T ss_pred             cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhc
Confidence            6999999999999999999999999999999886 8899999999988877653

>PF13014 KH_3: KH domain

Probab=99.02  E-value=3.9e-10  Score=77.06  Aligned_cols=39  Identities=38%  Similarity=0.635  Sum_probs=35.6

Q ss_pred             ccceeecCCCchHHHHHHhcCceEEcCC----CCCCCeEEEEC
Q psy3263          96 VVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTG  134 (329)
Q Consensus        96 ~vG~IIGkgG~tIk~Iq~~tga~I~ip~----~~~e~~i~ItG  134 (329)
                      +||+|||++|++||+|+++|||+|+||+    .+++++|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999999998    22788899998

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=99.01  E-value=3.3e-10  Score=82.92  Aligned_cols=52  Identities=37%  Similarity=0.592  Sum_probs=47.7

Q ss_pred             EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCc
Q psy3263          88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGP  140 (329)
Q Consensus        88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~v  140 (329)
                      .++.||.+++|+|||++|++|++|+++|||+|.++...   .++.|+|+| .++++
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G-~~~~v   56 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITG-TPEAV   56 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEc-CHHHH
Confidence            57999999999999999999999999999999998763   688899999 87777

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=99.00  E-value=9.5e-10  Score=80.49  Aligned_cols=52  Identities=38%  Similarity=0.485  Sum_probs=47.4

Q ss_pred             eeeeeeecCCChHHHHHHHHhCCeEEecCCC---CcceEEEecCHHHHHHHHHHH
Q psy3263           3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREI   54 (329)
Q Consensus         3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~---~ervi~ItG~~e~v~~A~~~I   54 (329)
                      -+||.|||++|++|++|+++||++|.++...   .++.|.|.|+.+++++|+.+|
T Consensus         9 ~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           9 SLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             hhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence            3789999999999999999999999999653   378899999999999999887

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A

Probab=98.93  E-value=5.8e-10  Score=76.06  Aligned_cols=38  Identities=39%  Similarity=0.940  Sum_probs=31.0

Q ss_pred             cccccccCcccEEeCCCChhccHhhHHhhcCC--C--CCCccc
Q psy3263         256 CYLCNDREVTHALIPCGHNFFCSECAERTCDF--D--RTCPMC  294 (329)
Q Consensus       256 C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~--~~CP~C  294 (329)
                      |+||++.+.+|+.++|||+ ||..|+.++++.  .  ..||.|
T Consensus         1 CpiC~~~~~~Pv~l~CGH~-FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSLPCGHS-FCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-SSSSE-EEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCccccCCcCH-HHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999999999999999 999999999988  2  479987

>KOG4265|consensus

Probab=98.88  E-value=6.4e-10  Score=106.56  Aligned_cols=58  Identities=28%  Similarity=0.764  Sum_probs=52.0

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQ  308 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~~  308 (329)
                      +...+|+||+...++.+++||.|.|+|..|++.+.-+...||+||+++...+.+...+
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~~~~  345 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIYVNK  345 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhhheecccc
Confidence            4468999999999999999999999999999999877889999999998887776554

>KOG0317|consensus

Probab=98.78  E-value=2.8e-09  Score=99.50  Aligned_cols=51  Identities=31%  Similarity=0.806  Sum_probs=46.4

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  301 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~  301 (329)
                      .+....|.+|++...+|...||||. ||+.|+..|+.....||+||..+...
T Consensus       236 ~~a~~kC~LCLe~~~~pSaTpCGHi-FCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNPSATPCGHI-FCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCCCCceEEEecCCCCCCcCcCcch-HHHHHHHHHHccccCCCcccccCCCc
Confidence            3566899999999999999999999 99999999999999999999988543

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=98.77  E-value=1.8e-08  Score=84.00  Aligned_cols=58  Identities=24%  Similarity=0.315  Sum_probs=50.0

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC--------------------cceEEEecC---HHHHHHHHHHHHHHh
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE--------------------EPVFVVTGR---KEDVARAKREILSAA   58 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--------------------ervi~ItG~---~e~v~~A~~~I~~i~   58 (329)
                      |+|+|.|||.+|.+||+|+++|||+|.|-.++.                    .-.|.|++.   .+++++|+.+|..++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            899999999999999999999999999986531                    245788885   499999999999885


Q ss_pred             h
Q psy3263          59 D   59 (329)
Q Consensus        59 e   59 (329)
                      .
T Consensus        94 ~   94 (120)
T cd02395          94 K   94 (120)
T ss_pred             c
Confidence            3

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG0823|consensus

Probab=98.77  E-value=2.8e-09  Score=96.82  Aligned_cols=49  Identities=29%  Similarity=0.684  Sum_probs=44.5

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC---CCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~~  300 (329)
                      ...++|-||+|..++|++..|||. ||+.|+.+|++.   ...||+|+..+..
T Consensus        45 ~~~FdCNICLd~akdPVvTlCGHL-FCWpClyqWl~~~~~~~~cPVCK~~Vs~   96 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDPVVTLCGHL-FCWPCLYQWLQTRPNSKECPVCKAEVSI   96 (230)
T ss_pred             CCceeeeeeccccCCCEEeecccc-eehHHHHHHHhhcCCCeeCCcccccccc
Confidence            456899999999999999999999 999999999987   7789999998843

>smart00322 KH K homology RNA-binding domain

Probab=98.76  E-value=2.8e-08  Score=72.28  Aligned_cols=55  Identities=35%  Similarity=0.379  Sum_probs=49.5

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC-CcceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-~ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      ++|.+||++|.+|++|+++||++|.++... ...++.|.|..+++..|+.+|.+.+
T Consensus        13 ~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322       13 KVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             hcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            579999999999999999999999998554 3688999999999999999998764

>smart00322 KH K homology RNA-binding domain

Probab=98.75  E-value=1.4e-08  Score=73.87  Aligned_cols=63  Identities=40%  Similarity=0.536  Sum_probs=53.9

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCcchhh-hhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGPGFES-HHGQK  149 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~veie~-~i~d~  149 (329)
                      .+.++.||...+|.+||++|++|++|++.+|++|.++... ....++|.| .+++++.+. +|.+.
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g-~~~~v~~a~~~i~~~   67 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITG-PPENVEKAAELILEI   67 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEc-CHHHHHHHHHHHHHH
Confidence            5788999999999999999999999999999999998755 677899999 888884443 65543

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=98.75  E-value=4.2e-09  Score=70.41  Aligned_cols=38  Identities=39%  Similarity=1.065  Sum_probs=33.7

Q ss_pred             cccccccCccc-EEeCCCChhccHhhHHhhcCCCCCCccc
Q psy3263         256 CYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMC  294 (329)
Q Consensus       256 C~IC~e~~~~~-~~lpCgH~~fC~~Cl~~~~~~~~~CP~C  294 (329)
                      |+||++.+.++ +.++|||. ||.+|+.++.+....||+|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~-fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHS-FCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEE-EEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCcCEECCCCCc-hhHHHHHHHHHCcCCCcCC
Confidence            89999999999 58999999 9999999999888899998

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.74  E-value=6.4e-09  Score=92.75  Aligned_cols=49  Identities=29%  Similarity=0.714  Sum_probs=42.9

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC----------------CCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF----------------DRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~----------------~~~CP~Cr~~i~~  300 (329)
                      .++.+|+||++...++++++|||. ||..|+..|+..                ...||+||..+..
T Consensus        16 ~~~~~CpICld~~~dPVvT~CGH~-FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         16 GGDFDCNICLDQVRDPVVTLCGHL-FCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCccCCccCCCcCCCcEEcCCCch-hHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            457899999999999999999999 999999998631                4689999999854

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.65  E-value=1.2e-08  Score=100.60  Aligned_cols=52  Identities=31%  Similarity=0.685  Sum_probs=47.2

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +.++..+.|.||.+.+.++++++|||. ||..|+..++.....||+|+..+..
T Consensus        21 ~~Le~~l~C~IC~d~~~~PvitpCgH~-FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        21 YPLDTSLRCHICKDFFDVPVLTSCSHT-FCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             cccccccCCCcCchhhhCccCCCCCCc-hhHHHHHHHHhCCCCCCCCCCcccc
Confidence            457888999999999999999999999 9999999998887789999998743

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.65  E-value=1.5e-08  Score=93.76  Aligned_cols=50  Identities=30%  Similarity=0.746  Sum_probs=42.1

Q ss_pred             CCcccccccccCcc--------cEEeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263         252 GSRQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  302 (329)
Q Consensus       252 ~~~~C~IC~e~~~~--------~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~  302 (329)
                      .+.+|+||++.+.+        +++.+|+|. ||..|+.+|++....||+||..+....
T Consensus       173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~-FC~~CI~~Wl~~~~tCPlCR~~~~~v~  230 (238)
T PHA02929        173 KDKECAICMEKVYDKEIKNMYFGILSNCNHV-FCIECIDIWKKEKNTCPVCRTPFISVI  230 (238)
T ss_pred             CCCCCccCCcccccCccccccceecCCCCCc-ccHHHHHHHHhcCCCCCCCCCEeeEEe
Confidence            45799999997654        256689999 999999999988899999999887544

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A

Probab=98.60  E-value=1.1e-08  Score=70.02  Aligned_cols=40  Identities=30%  Similarity=0.819  Sum_probs=34.8

Q ss_pred             ccccccccCc---ccEEeCCCChhccHhhHHhhcCCCCCCcccc
Q psy3263         255 QCYLCNDREV---THALIPCGHNFFCSECAERTCDFDRTCPMCR  295 (329)
Q Consensus       255 ~C~IC~e~~~---~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr  295 (329)
                      .|+||++.+.   ..+.++|+|. ||.+|+..|++....||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHV-FHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEE-EEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCe-eCHHHHHHHHHhCCcCCccC
Confidence            6999999873   4567899999 99999999999888999997

...

>KOG0287|consensus

Probab=98.59  E-value=1.1e-08  Score=97.12  Aligned_cols=66  Identities=23%  Similarity=0.596  Sum_probs=53.9

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhhhhhhhhcchhhh
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPV  318 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~~~~~~~v~~~~  318 (329)
                      +..-+.|-||+|.+..|++.||+|+ ||.-|++..+...+.||.|+..++..  .++++++++++++..
T Consensus        20 lD~lLRC~IC~eyf~ip~itpCsHt-fCSlCIR~~L~~~p~CP~C~~~~~Es--~Lr~n~il~Eiv~S~   85 (442)
T KOG0287|consen   20 LDDLLRCGICFEYFNIPMITPCSHT-FCSLCIRKFLSYKPQCPTCCVTVTES--DLRNNRILDEIVKSL   85 (442)
T ss_pred             hHHHHHHhHHHHHhcCceeccccch-HHHHHHHHHhccCCCCCceecccchh--hhhhhhHHHHHHHHH
Confidence            4566899999999999999999999 99999999999999999999988553  344555555554433

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.53  E-value=1.4e-07  Score=83.47  Aligned_cols=52  Identities=17%  Similarity=0.088  Sum_probs=48.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      .+|+||||+|++++.||+.|||+|.++    +..|.|.|.+++++.|+++|.++++
T Consensus        99 ~~griIG~~G~t~~~ie~~t~~~i~i~----~~~v~i~G~~~~~~~A~~~i~~li~  150 (172)
T TIGR03665        99 IKGRIIGEGGKTRRIIEELTGVSISVY----GKTVGIIGDPEQVQIAREAIEMLIE  150 (172)
T ss_pred             HHhhhcCCCcHHHHHHHHHHCCeEEEc----CCEEEEECCHHHHHHHHHHHHHHHc
Confidence            368999999999999999999999998    3778999999999999999999864

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>smart00504 Ubox Modified RING finger domain

Probab=98.52  E-value=6.5e-08  Score=70.74  Aligned_cols=46  Identities=15%  Similarity=0.238  Sum_probs=42.4

Q ss_pred             CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      ++.|+||.+.+.+|+.++|||. ||..|+..+++....||+|+.++.
T Consensus         1 ~~~Cpi~~~~~~~Pv~~~~G~v-~~~~~i~~~~~~~~~cP~~~~~~~   46 (63)
T smart00504        1 EFLCPISLEVMKDPVILPSGQT-YERRAIEKWLLSHGTDPVTGQPLT   46 (63)
T ss_pred             CcCCcCCCCcCCCCEECCCCCE-EeHHHHHHHHHHCCCCCCCcCCCC
Confidence            3689999999999999999999 999999999988889999999874

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>KOG0320|consensus

Probab=98.51  E-value=3.5e-08  Score=86.32  Aligned_cols=49  Identities=31%  Similarity=0.793  Sum_probs=41.4

Q ss_pred             CCCcccccccccCccc--EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTH--ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~--~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +....|+||++....-  +...|||. ||..|++..++....||+||+.++.
T Consensus       129 ~~~~~CPiCl~~~sek~~vsTkCGHv-FC~~Cik~alk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVPVSTKCGHV-FCSQCIKDALKNTNKCPTCRKKITH  179 (187)
T ss_pred             ccccCCCceecchhhccccccccchh-HHHHHHHHHHHhCCCCCCcccccch
Confidence            3447999999977654  45799999 9999999999999999999987743

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.49  E-value=2e-07  Score=83.06  Aligned_cols=52  Identities=17%  Similarity=0.105  Sum_probs=47.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      .+|+||||+|+++|.||+.|||+|.++    +..+.|.|.+++++.|++.|.++++
T Consensus       105 ~~griIG~~G~~~k~ie~~t~~~i~i~----~~~v~i~G~~~~~~~A~~~I~~li~  156 (180)
T PRK13763        105 IKGRIIGEGGKTRRIIEELTGVDISVY----GKTVAIIGDPEQVEIAREAIEMLIE  156 (180)
T ss_pred             HhhheeCCCcHHHHHHHHHHCcEEEEc----CCEEEEEeCHHHHHHHHHHHHHHHc
Confidence            479999999999999999999999998    3448899999999999999998864

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.47  E-value=7.4e-08  Score=64.74  Aligned_cols=38  Identities=34%  Similarity=1.011  Sum_probs=35.3

Q ss_pred             cccccccCcccE-EeCCCChhccHhhHHhhcC-C-CCCCccc
Q psy3263         256 CYLCNDREVTHA-LIPCGHNFFCSECAERTCD-F-DRTCPMC  294 (329)
Q Consensus       256 C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~-~-~~~CP~C  294 (329)
                      |.||++.+.++. +++|||. ||..|+.++++ . ...||+|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~-fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHS-FCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEE-EEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCCEEecCCCc-chHHHHHHHHHhcCCccCCcC
Confidence            899999999999 8999999 99999999998 3 7889998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>KOG2279|consensus

Probab=98.43  E-value=8.6e-08  Score=96.11  Aligned_cols=118  Identities=25%  Similarity=0.349  Sum_probs=95.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCC--CCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVR--GEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTG   81 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~--~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~   81 (329)
                      +|.+|+||+|++||.|+.+|+++|.+-.+  +++++-++.|-+..|.+|+.++..+..     +                
T Consensus        78 ~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~-----~----------------  136 (608)
T KOG2279|consen   78 AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILT-----E----------------  136 (608)
T ss_pred             ceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHh-----c----------------
Confidence            68899999999999999999999999643  347888888899999999999988753     1                


Q ss_pred             CCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcchhh
Q psy3263          82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGFES  144 (329)
Q Consensus        82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~veie~  144 (329)
                       ...+..+.-+|.+.++.|+|++|++|..|..-++++|.+-.+-   ..+.+.|.| ....++++.
T Consensus       137 -~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~-qqk~~~~a~  200 (608)
T KOG2279|consen  137 -NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISG-QQKEVAAAK  200 (608)
T ss_pred             -CCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceeccc-ccchHHHHH
Confidence             1114556778999999999999999999999999999987544   455677777 555554444

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Probab=98.43  E-value=1.5e-07  Score=63.03  Aligned_cols=43  Identities=35%  Similarity=1.015  Sum_probs=36.6

Q ss_pred             ccccccccCcccEEe-CCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263         255 QCYLCNDREVTHALI-PCGHNFFCSECAERTCDF-DRTCPMCRVPV  298 (329)
Q Consensus       255 ~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i  298 (329)
                      .|.||++.+.+++.+ +|||. ||..|+..+... ...||+|+..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~-~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHV-FCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCCh-hcHHHHHHHHHhCcCCCCCCCCcC
Confidence            599999998666655 59999 999999999887 78899998753

>PHA02926 zinc finger-like protein; Provisional

Probab=98.35  E-value=1.9e-07  Score=84.62  Aligned_cols=51  Identities=25%  Similarity=0.616  Sum_probs=40.3

Q ss_pred             CCCcccccccccCcc---------cEEeCCCChhccHhhHHhhcCC------CCCCcccccccccch
Q psy3263         251 SGSRQCYLCNDREVT---------HALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQAM  302 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~---------~~~lpCgH~~fC~~Cl~~~~~~------~~~CP~Cr~~i~~~~  302 (329)
                      ..+.+|.||+|...+         .++.+|+|. ||..|+..|...      ...||+||..+....
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHs-FCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~  233 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHI-FCITCINIWHRTRRETGASDNCPICRTRFRNIT  233 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCch-HHHHHHHHHHHhccccCcCCcCCCCcceeeeec
Confidence            456899999997532         356799999 999999999874      356999999886543

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.33  E-value=3.8e-07  Score=62.58  Aligned_cols=41  Identities=32%  Similarity=0.877  Sum_probs=35.0

Q ss_pred             ccccccccC---cccEEeCCCChhccHhhHHhhcCCCCCCccccc
Q psy3263         255 QCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDRTCPMCRV  296 (329)
Q Consensus       255 ~C~IC~e~~---~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~  296 (329)
                      .|.+|++.+   ..+.+++|||. ||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~-~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHI-FCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCH-HHHHHHHhhcCCCCCCcCCCC
Confidence            488999888   35668999999 999999999855789999985

>smart00184 RING Ring finger

Probab=98.29  E-value=5e-07  Score=58.37  Aligned_cols=38  Identities=34%  Similarity=1.027  Sum_probs=34.4

Q ss_pred             cccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccc
Q psy3263         256 CYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMC  294 (329)
Q Consensus       256 C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~C  294 (329)
                      |.||++....++.++|+|. ||..|+..+.+. ...||+|
T Consensus         1 C~iC~~~~~~~~~~~C~H~-~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHT-FCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCCh-HHHHHHHHHHHhCcCCCCCC
Confidence            7899999989999999999 999999999874 6789987

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

>KOG2208|consensus

Probab=98.24  E-value=1.8e-06  Score=91.98  Aligned_cols=115  Identities=21%  Similarity=0.293  Sum_probs=93.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   82 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~   82 (329)
                      ++.-++||+|.+|.+|++++.+.|.++..++ +..++++|...++++|.+.+..+..                     ..
T Consensus       357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~---------------------ei  415 (753)
T KOG2208|consen  357 ELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIA---------------------EI  415 (753)
T ss_pred             hhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHH---------------------hh
Confidence            4567899999999999999999999997544 6788999999999999999988743                     11


Q ss_pred             CC-ceEEEEEecCcccceeecCCCchHHHHHHhcC-ceEEcCCCCCCCe-EEEECCCCCCc
Q psy3263          83 PG-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTN-TYIVTPSRDKEPV-FEVTGNFPEGP  140 (329)
Q Consensus        83 ~g-~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tg-a~I~ip~~~~e~~-i~ItG~~pe~v  140 (329)
                      ++ .....+.+|...+..|||.+|+.|..|...++ .+|+++.....+. .++.| .-..+
T Consensus       416 ~n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~~~~~-~~~dv  475 (753)
T KOG2208|consen  416 LNSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMVTIRG-ISKDV  475 (753)
T ss_pred             hcccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccceEec-ccccc
Confidence            11 24456889999999999999999999999999 8999887664333 66666 55555

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Probab=98.22  E-value=4.8e-07  Score=84.66  Aligned_cols=50  Identities=30%  Similarity=0.705  Sum_probs=45.5

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      |...+.|-||-+.+..++..+|||. ||.-|+++.+...+.||+||.+...
T Consensus        22 LDs~lrC~IC~~~i~ip~~TtCgHt-FCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          22 LDSMLRCRICDCRISIPCETTCGHT-FCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             chhHHHhhhhhheeecceecccccc-hhHHHHHHHhcCCCCCccccccHHh
Confidence            4556899999999999999999999 9999999999999999999998643

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A

Probab=98.22  E-value=3.6e-07  Score=62.61  Aligned_cols=30  Identities=33%  Similarity=0.978  Sum_probs=21.0

Q ss_pred             cccccccCcc----cEEeCCCChhccHhhHHhhcCC
Q psy3263         256 CYLCNDREVT----HALIPCGHNFFCSECAERTCDF  287 (329)
Q Consensus       256 C~IC~e~~~~----~~~lpCgH~~fC~~Cl~~~~~~  287 (329)
                      |+||.+ +.+    |+.|+|||. ||.+|++++...
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~-~c~~cl~~l~~~   34 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHV-FCKDCLQKLSKK   34 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-E-EEHHHHHHHHHH
T ss_pred             CCcccc-ccCCCCCCEEEeCccH-HHHHHHHHHHhc
Confidence            899999 877    899999999 999999999774

>KOG1571|consensus

Probab=98.21  E-value=5.8e-07  Score=86.51  Aligned_cols=53  Identities=25%  Similarity=0.702  Sum_probs=45.8

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      +.....|.||.+.+.+++++||||.|.|..|...+    ..||+||+.+....+.|.
T Consensus       302 ~~~p~lcVVcl~e~~~~~fvpcGh~ccct~cs~~l----~~CPvCR~rI~~~~k~y~  354 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKSAVFVPCGHVCCCTLCSKHL----PQCPVCRQRIRLVRKRYR  354 (355)
T ss_pred             cCCCCceEEecCCccceeeecCCcEEEchHHHhhC----CCCchhHHHHHHHHHHhc
Confidence            34456999999999999999999999999998886    679999999988777664

>KOG2177|consensus

Probab=98.21  E-value=4.7e-07  Score=83.18  Aligned_cols=47  Identities=34%  Similarity=0.851  Sum_probs=42.6

Q ss_pred             CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV  296 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~  296 (329)
                      .+.+...|+||++.+.+++++||+|+ ||..|+..++.....||.||.
T Consensus         9 ~~~~~~~C~iC~~~~~~p~~l~C~H~-~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFREPVLLPCGHN-FCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hccccccChhhHHHhhcCccccccch-HhHHHHHHhcCCCcCCcccCC
Confidence            45678999999999999999999999 999999999876679999995

>KOG4275|consensus

Probab=98.19  E-value=2e-07  Score=87.13  Aligned_cols=52  Identities=31%  Similarity=0.797  Sum_probs=47.1

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      .....|.||++...+.++|+|||..-|.+|-+++    ..||+||+.+....++|.
T Consensus       298 ~~~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~rvvrif~  349 (350)
T KOG4275|consen  298 ATRRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYIVRVVRIFR  349 (350)
T ss_pred             hHHHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHHHHHHhhhc
Confidence            3478999999999999999999999999999887    699999999988888875

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.19  E-value=2e-06  Score=73.70  Aligned_cols=93  Identities=16%  Similarity=0.105  Sum_probs=64.9

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      .||..||++|++|++|++..|-+|++-...+              .++..|..++.......-.          .. ...
T Consensus        42 ~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------d~~~fI~n~l~Pa~V~~v~----------I~-~~~   96 (140)
T PRK08406         42 DMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------DPEEFIKNIFAPAAVRSVT----------IK-KKN   96 (140)
T ss_pred             CccccCCcCchHHHHHHHHhCCceEEEEcCC--------------CHHHHHHHHcCCCEEEEEE----------EE-ecC
Confidence            3699999999999999999998888753333              1344444442100000000          00 112


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      +.....+.|+.+..|..|||+|.+|+.+++-++-++.+
T Consensus        97 ~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         97 GDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             CcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            23667888999999999999999999999999998876

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis

Probab=98.13  E-value=1.8e-06  Score=65.73  Aligned_cols=48  Identities=21%  Similarity=0.390  Sum_probs=40.3

Q ss_pred             CCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         252 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +.+.|+||.+.+.+|+++||||. |+..|+.+|+.. ...||+|+.++..
T Consensus         3 ~~f~CpIt~~lM~dPVi~~~G~t-yer~~I~~~l~~~~~~~P~t~~~l~~   51 (73)
T PF04564_consen    3 DEFLCPITGELMRDPVILPSGHT-YERSAIERWLEQNGGTDPFTRQPLSE   51 (73)
T ss_dssp             GGGB-TTTSSB-SSEEEETTSEE-EEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred             cccCCcCcCcHhhCceeCCcCCE-EcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence            56899999999999999999999 999999999999 9999999998864

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=98.13  E-value=2.1e-05  Score=70.24  Aligned_cols=121  Identities=17%  Similarity=0.236  Sum_probs=85.5

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-----CHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-----RKEDVARAKREILSAADHFSALRASRKSGALSPLSPP   79 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-----~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p   79 (329)
                      +|.+||+.|+.-|.|.+.+++++.+.  .++..|.|..     +|-.+.+|++.|.++..-|+--.|-.-..        
T Consensus        19 ~~~lig~~g~v~k~ie~~~~~~~~iD--~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~--------   88 (194)
T COG1094          19 IGVLIGKWGEVKKAIEEKTGVKLRID--SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLE--------   88 (194)
T ss_pred             heeeecccccchHHHHhhcCeEEEEE--CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhc--------
Confidence            57899999999999999999999997  4445555543     57899999999988743222211111100        


Q ss_pred             CCCCCceEEE-EEe------c----CcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh
Q psy3263          80 TGVPGHVTIE-VRV------P----YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES  144 (329)
Q Consensus        80 ~~~~g~~t~~-i~V------P----~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~  144 (329)
                          ....+. |.+      +    .+..|.|||++|.|-+.|++.|+|+|.+-..    .|.|-| .+++|+++.
T Consensus        89 ----d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~----tVaiiG-~~~~v~iAr  155 (194)
T COG1094          89 ----DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK----TVAIIG-GFEQVEIAR  155 (194)
T ss_pred             ----CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc----EEEEec-ChhhhHHHH
Confidence                011111 111      1    2456999999999999999999999999543    689999 999995444

>KOG2164|consensus

Probab=98.10  E-value=1e-06  Score=88.21  Aligned_cols=54  Identities=24%  Similarity=0.707  Sum_probs=45.3

Q ss_pred             CcccccccccCcccEEeCCCChhccHhhHHhhcCC-----CCCCccccccccc--chhhhhh
Q psy3263         253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVNQ--AMRIIFN  307 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-----~~~CP~Cr~~i~~--~~~i~~~  307 (329)
                      +..|+||++.+.-|+...|||. ||..|+-+.|..     ...||+|+..|..  ...++..
T Consensus       186 ~~~CPICL~~~~~p~~t~CGHi-FC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e  246 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRTNCGHI-FCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIE  246 (513)
T ss_pred             CCcCCcccCCCCcccccccCce-eeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeec
Confidence            6799999999999998899999 999999988766     5799999998855  4444443

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=98.07  E-value=3.1e-06  Score=70.65  Aligned_cols=58  Identities=24%  Similarity=0.398  Sum_probs=42.8

Q ss_pred             CcccceeecCCCchHHHHHHhcCceEEcCCCC-------------------CC-CeEEEECCC--CCCc-chhhhhhhhh
Q psy3263          94 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-------------------KE-PVFEVTGNF--PEGP-GFESHHGQKI  150 (329)
Q Consensus        94 ~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-------------------~e-~~i~ItG~~--pe~v-eie~~i~d~~  150 (329)
                      ++++|.|||+||+|||+|+++|||+|.|-.+.                   ++ -.|.|+++.  .+.+ ++..+|..++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999998651                   22 348999955  3566 2333555444


Q ss_pred             h
Q psy3263         151 V  151 (329)
Q Consensus       151 ~  151 (329)
                      .
T Consensus        94 ~   94 (120)
T cd02395          94 K   94 (120)
T ss_pred             c
Confidence            4

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.06  E-value=1.7e-06  Score=80.24  Aligned_cols=48  Identities=31%  Similarity=0.728  Sum_probs=41.9

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHh-hcCC-CCCCcccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAER-TCDF-DRTCPMCRVPVN  299 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~-~~~~-~~~CP~Cr~~i~  299 (329)
                      ..+..|.+|++....++-.+|||. ||..|+.. |..+ ...||+||+...
T Consensus       213 ~~d~kC~lC~e~~~~ps~t~CgHl-FC~~Cl~~~~t~~k~~~CplCRak~~  262 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCTPCGHL-FCLSCLLISWTKKKYEFCPLCRAKVY  262 (271)
T ss_pred             ccccceeeeecccCCcccccccch-hhHHHHHHHHHhhccccCchhhhhcc
Confidence            567899999999999999999999 99999998 6666 455999999763

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.00  E-value=4.7e-06  Score=63.47  Aligned_cols=41  Identities=32%  Similarity=0.771  Sum_probs=33.2

Q ss_pred             cccccccccCc-------------ccEEeCCCChhccHhhHHhhcCCCCCCcccc
Q psy3263         254 RQCYLCNDREV-------------THALIPCGHNFFCSECAERTCDFDRTCPMCR  295 (329)
Q Consensus       254 ~~C~IC~e~~~-------------~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr  295 (329)
                      ..|.||++.+.             ..++.+|||. |...|+.+|++....||+||
T Consensus        20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~-FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHI-FHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEE-EEHHHHHHHHTTSSB-TTSS
T ss_pred             CcccccChhhhChhhhhcCCccccceEecccCCC-EEHHHHHHHHhcCCcCCCCC
Confidence            35999998772             1245699999 99999999999988999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

>KOG0978|consensus

Probab=97.97  E-value=1.4e-06  Score=90.82  Aligned_cols=49  Identities=31%  Similarity=0.784  Sum_probs=44.4

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN  299 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~  299 (329)
                      +.+-+.|++|.++.++.++..|||. ||..|++..... ...||.|...|-
T Consensus       640 yK~~LkCs~Cn~R~Kd~vI~kC~H~-FC~~Cvq~r~etRqRKCP~Cn~aFg  689 (698)
T KOG0978|consen  640 YKELLKCSVCNTRWKDAVITKCGHV-FCEECVQTRYETRQRKCPKCNAAFG  689 (698)
T ss_pred             HHhceeCCCccCchhhHHHHhcchH-HHHHHHHHHHHHhcCCCCCCCCCCC
Confidence            3566899999999999999999998 999999998777 899999999983

>KOG0119|consensus

Probab=97.94  E-value=2.1e-05  Score=78.44  Aligned_cols=58  Identities=26%  Similarity=0.318  Sum_probs=47.1

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC------------------cc-eEEEecC-HHHHHHHHHHHHHHhh
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE------------------EP-VFVVTGR-KEDVARAKREILSAAD   59 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------------------er-vi~ItG~-~e~v~~A~~~I~~i~e   59 (329)
                      |+|||+|||..|.|.|+|++||||+|.|=.++.                  |+ -+.|++. .|.|++|...|..+++
T Consensus       152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~  229 (554)
T KOG0119|consen  152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQ  229 (554)
T ss_pred             cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999999853111                  32 4678875 6788899999888764

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=97.89  E-value=3.3e-06  Score=62.31  Aligned_cols=45  Identities=31%  Similarity=0.713  Sum_probs=26.1

Q ss_pred             CCCcccccccccCcccE-EeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         251 SGSRQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      ++.+.|.+|.+.+..|+ +-.|.|. ||..|+.....  ..||+|+.+.
T Consensus         5 e~lLrCs~C~~~l~~pv~l~~CeH~-fCs~Ci~~~~~--~~CPvC~~Pa   50 (65)
T PF14835_consen    5 EELLRCSICFDILKEPVCLGGCEHI-FCSSCIRDCIG--SECPVCHTPA   50 (65)
T ss_dssp             HHTTS-SSS-S--SS-B---SSS---B-TTTGGGGTT--TB-SSS--B-
T ss_pred             HHhcCCcHHHHHhcCCceeccCccH-HHHHHhHHhcC--CCCCCcCChH
Confidence            45678999999999997 5799999 99999987544  4699999987

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

Probab=97.86  E-value=6.5e-06  Score=79.48  Aligned_cols=47  Identities=36%  Similarity=0.843  Sum_probs=41.0

Q ss_pred             CCCcccccccccCc-------------ccEEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         251 SGSRQCYLCNDREV-------------THALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       251 ~~~~~C~IC~e~~~-------------~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      .++..|.||+|.+.             .|.-+||||- |-.+|++.|++....||+||.++
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHi-lHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHI-LHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccce-eeHHHHHHHHHhccCCCcccCcc
Confidence            56789999999742             2467899998 99999999999999999999995

>KOG0824|consensus

Probab=97.83  E-value=7.6e-06  Score=77.14  Aligned_cols=50  Identities=24%  Similarity=0.733  Sum_probs=44.8

Q ss_pred             CCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccch
Q psy3263         252 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAM  302 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~  302 (329)
                      -..+|.||+.....|+.++|+|. ||..|++...+. +..|++||.+|+..+
T Consensus         6 ~~~eC~IC~nt~n~Pv~l~C~Hk-FCyiCiKGsy~ndk~~CavCR~pids~i   56 (324)
T KOG0824|consen    6 KKKECLICYNTGNCPVNLYCFHK-FCYICIKGSYKNDKKTCAVCRFPIDSTI   56 (324)
T ss_pred             cCCcceeeeccCCcCccccccch-hhhhhhcchhhcCCCCCceecCCCCcch
Confidence            45699999999999999999999 999999998777 677999999997754

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.81  E-value=1.3e-05  Score=76.49  Aligned_cols=47  Identities=23%  Similarity=0.752  Sum_probs=36.2

Q ss_pred             CcccccccccC-cccE---Ee-CCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         253 SRQCYLCNDRE-VTHA---LI-PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       253 ~~~C~IC~e~~-~~~~---~l-pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +..|++|.... .++-   ++ +|||+ ||..|+.+++.. ...||.|+..+..
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~-~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHT-LCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCc-ccHHHHHHHhcCCCCCCCCCCCccch
Confidence            45899999842 2221   22 79999 999999998866 6789999998754

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0311|consensus

Probab=97.73  E-value=2.6e-06  Score=81.78  Aligned_cols=52  Identities=21%  Similarity=0.461  Sum_probs=44.7

Q ss_pred             CCCCCcccccccccCcccEE-eCCCChhccHhhHHhhcCC-CCCCcccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQA  301 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~  301 (329)
                      .+..+..|+||++..+.++. ..|+|. ||.+|+..-+.. ...||.||+.+...
T Consensus        39 ~~~~~v~c~icl~llk~tmttkeClhr-fc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   39 MFDIQVICPICLSLLKKTMTTKECLHR-FCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             HhhhhhccHHHHHHHHhhcccHHHHHH-HHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            45678999999999988774 479999 999999998887 89999999987544

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.72  E-value=3.1e-05  Score=66.36  Aligned_cols=93  Identities=15%  Similarity=0.079  Sum_probs=63.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      -||..||++|++|++|++..|-+|++-...+        .+      ...|..++.        +.......  .. ..+
T Consensus        43 ~vG~~IG~~G~rIk~i~el~gekIdVVeys~--------D~------~~fI~N~l~--------PA~V~~V~--i~-~~~   97 (141)
T TIGR01952        43 EMGAAIGKGGENVKRLEELIGKSIELIEYSE--------NL------EEFVANKLA--------PAEVKNVT--VS-EFN   97 (141)
T ss_pred             CccccCCCCchHHHHHHHhcCCeeEEEEcCC--------CH------HHHHHHcCC--------CceEEEEE--EE-cCC
Confidence            3789999999999999999998888753322        21      122222210        00000000  00 113


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      +.....+.||.+..++.|||+|.+|+...+-++-++.+
T Consensus        98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952        98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI  135 (141)
T ss_pred             CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence            45677899999999999999999999999999988865

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>KOG0336|consensus

Probab=97.71  E-value=8.2e-05  Score=73.36  Aligned_cols=57  Identities=28%  Similarity=0.196  Sum_probs=51.2

Q ss_pred             eeeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      .|||.+|||||++||+||..||++|++-..+.+-.|+|-|..+--.+|+..|...++
T Consensus        56 ~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~  112 (629)
T KOG0336|consen   56 EMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQD  112 (629)
T ss_pred             hhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhh
Confidence            489999999999999999999999999877778889999999988889888877654

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.70  E-value=7.3e-05  Score=78.89  Aligned_cols=62  Identities=23%  Similarity=0.302  Sum_probs=50.2

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQKI  150 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~~  150 (329)
                      ...++.||.+++|.|||+||.+||+|+++||++|.+..   +..|.|.+...+.++.+. +|.++.
T Consensus       578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~  640 (719)
T TIGR02696       578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIA  640 (719)
T ss_pred             eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhh
Confidence            67789999999999999999999999999999999864   567999996666663222 444433

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>KOG1588|consensus

Probab=97.70  E-value=7.8e-05  Score=69.36  Aligned_cols=32  Identities=34%  Similarity=0.433  Sum_probs=29.8

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCC
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRG   33 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~   33 (329)
                      |+|||+|+|..|.++|+|+++|+|+|-|-.++
T Consensus       106 fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg  137 (259)
T KOG1588|consen  106 FNFVGRILGPRGNSLKRLEEETGCKIMIRGRG  137 (259)
T ss_pred             CccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence            89999999999999999999999999996544

>KOG4159|consensus

Probab=97.69  E-value=1.7e-05  Score=78.57  Aligned_cols=50  Identities=34%  Similarity=0.895  Sum_probs=45.9

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +..+++|.||+..+..++.+||||. ||..|+.+.+.+...||.||..+..
T Consensus        81 ~~sef~c~vc~~~l~~pv~tpcghs-~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   81 IRSEFECCVCSRALYPPVVTPCGHS-FCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             ccchhhhhhhHhhcCCCcccccccc-ccHHHHHHHhccCCCCccccccccc
Confidence            3678999999999999999999999 9999999988889999999998854

>KOG1785|consensus

Probab=97.68  E-value=1.4e-05  Score=77.79  Aligned_cols=55  Identities=29%  Similarity=0.798  Sum_probs=47.4

Q ss_pred             cccccccccCcccEEeCCCChhccHhhHHhhcCC--CCCCcccccccccchhhhhhhh
Q psy3263         254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQAMRIIFNQF  309 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~~~~i~~~~~  309 (329)
                      ..|.||-|..++..+-||||. +|..|+..|...  ...||.||..|...-++....|
T Consensus       370 eLCKICaendKdvkIEPCGHL-lCt~CLa~WQ~sd~gq~CPFCRcEIKGte~viid~F  426 (563)
T KOG1785|consen  370 ELCKICAENDKDVKIEPCGHL-LCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVIIDPF  426 (563)
T ss_pred             HHHHHhhccCCCcccccccch-HHHHHHHhhcccCCCCCCCceeeEeccccceeeecc
Confidence            589999999999999999999 999999999866  6899999999977666554433

>KOG0802|consensus

Probab=97.66  E-value=1.3e-05  Score=82.85  Aligned_cols=47  Identities=28%  Similarity=0.704  Sum_probs=42.9

Q ss_pred             CCCcccccccccCcc-----cEEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         251 SGSRQCYLCNDREVT-----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~-----~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      ..+..|.||.|.+..     +..++|+|. ||..|++.|+++...||.||..+
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hi-fh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLPCGHI-FHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             hcCCeeeeechhhccccccccceeecccc-hHHHHHHHHHHHhCcCCcchhhh
Confidence            346899999999988     789999999 99999999999999999999954

>KOG1100|consensus

Probab=97.56  E-value=2.4e-05  Score=71.20  Aligned_cols=48  Identities=40%  Similarity=0.953  Sum_probs=40.4

Q ss_pred             cccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhh
Q psy3263         254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  305 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~  305 (329)
                      ..|..|.+.....+++||.|.++|..|....    ..||+|+.+......++
T Consensus       159 ~~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~----~~CPiC~~~~~s~~~v~  206 (207)
T KOG1100|consen  159 RSCRKCGEREATVLLLPCRHLCLCGICDESL----RICPICRSPKTSSVEVN  206 (207)
T ss_pred             ccceecCcCCceEEeecccceEecccccccC----ccCCCCcChhhceeecc
Confidence            3499999999999999999999999998753    57999999877665543

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.54  E-value=3.8e-05  Score=72.51  Aligned_cols=47  Identities=23%  Similarity=0.675  Sum_probs=40.1

Q ss_pred             CCcccccccccCcc---cEEeCCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263         252 GSRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN  299 (329)
Q Consensus       252 ~~~~C~IC~e~~~~---~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~  299 (329)
                      ...+|.||++.+..   .+.+||.|. |-..|+.+|+.. ...||+||.++.
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~-FH~~Cv~kW~~~y~~~CPvCrt~iP  372 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHR-FHVGCVDKWLLGYSNKCPVCRTAIP  372 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCce-echhHHHHHHhhhcccCCccCCCCC
Confidence            34799999998742   347899999 999999999985 889999999874

>KOG4628|consensus

Probab=97.51  E-value=4e-05  Score=74.36  Aligned_cols=47  Identities=21%  Similarity=0.647  Sum_probs=39.6

Q ss_pred             cccccccccCccc---EEeCCCChhccHhhHHhhcCC-CCCCcccccccccc
Q psy3263         254 RQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQA  301 (329)
Q Consensus       254 ~~C~IC~e~~~~~---~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~  301 (329)
                      ..|.||+|.+..-   ..|||.|. |-..|+..|+.+ ...||+|++.+...
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~-FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHK-FHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCc-hhhccchhhHhhcCccCCCCCCcCCCC
Confidence            4999999988643   36899999 999999999999 46699999987443

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.36  E-value=0.00028  Score=74.86  Aligned_cols=61  Identities=15%  Similarity=0.173  Sum_probs=47.9

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-chhhhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQK  149 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d~  149 (329)
                      ...++.||.+.+|.|||+||++||+|+++||++|.|-.   +..|.|.+...+.+ +...+|..+
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---dG~V~i~~~~~~~~~~a~~~I~~~  612 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---DGTVKIAASDGEAAEAAIKMIEGI  612 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---CeEEEEEECcHHHHHHHHHHHHhh
Confidence            67789999999999999999999999999999999954   46678887344444 333355443

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=97.36  E-value=0.00044  Score=61.92  Aligned_cols=51  Identities=20%  Similarity=0.165  Sum_probs=47.2

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      .|+|||++|-|-+.|++-||++|.+-    ...|-|-|..++|+.|+++|..+++
T Consensus       113 kgRIIG~~GkTr~~IE~lt~~~I~V~----g~tVaiiG~~~~v~iAr~AVemli~  163 (194)
T COG1094         113 KGRIIGREGKTRRAIEELTGVYISVY----GKTVAIIGGFEQVEIAREAVEMLIN  163 (194)
T ss_pred             hceeeCCCchHHHHHHHHhCCeEEEe----CcEEEEecChhhhHHHHHHHHHHHc
Confidence            48999999999999999999999998    6678999999999999999988864

>KOG2208|consensus

Probab=97.36  E-value=0.00013  Score=77.97  Aligned_cols=136  Identities=18%  Similarity=0.219  Sum_probs=91.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhhhhh--------------Hhhhcc
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFS--------------ALRASR   68 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e~~~--------------~~~~~~   68 (329)
                      ++++||||||.+|+.++.++.+.|.+|...+ .+...+.|..+.+..+.-.|.+.+.+..              ......
T Consensus       211 ~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~~~~~~~~  290 (753)
T KOG2208|consen  211 LHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRLPRFIRGI  290 (753)
T ss_pred             chhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhhcccccccccc
Confidence            5789999999999999999999999995444 4555666666655555555444321000              000000


Q ss_pred             c------------CCCCCCCCCCCC---------------------------CCCceEEEEEecCcccceeecCCCchHH
Q psy3263          69 K------------SGALSPLSPPTG---------------------------VPGHVTIEVRVPYKVVGLVVGPKGATIK  109 (329)
Q Consensus        69 ~------------~~~~~~~~~p~~---------------------------~~g~~t~~i~VP~~~vG~IIGkgG~tIk  109 (329)
                      .            .......-++..                           ......+.+.+-.+.+..|+||+|+.|.
T Consensus       291 ~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~v~GK~~~ni~  370 (753)
T KOG2208|consen  291 PGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKFVIGKKGANIE  370 (753)
T ss_pred             ccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhhhcCCCCccHH
Confidence            0            000000000000                           0123557788888999999999999999


Q ss_pred             HHHHhcCceEEcCC-CCCCCeEEEECCCCCCc
Q psy3263         110 RIQHQTNTYIVTPS-RDKEPVFEVTGNFPEGP  140 (329)
Q Consensus       110 ~Iq~~tga~I~ip~-~~~e~~i~ItG~~pe~v  140 (329)
                      +|++++.+.|.++. .+++..+.++| .-.++
T Consensus       371 ki~e~~~~~i~~~~~~~~~~~v~~~~-~~~~~  401 (753)
T KOG2208|consen  371 KIREESQVKIDLPKQGSNNKKVVITG-VSAND  401 (753)
T ss_pred             HHHHhhhhceecccccCCCCCeEEec-cccch
Confidence            99999999999998 44778899999 88887

>KOG2879|consensus

Probab=97.35  E-value=0.00017  Score=67.31  Aligned_cols=49  Identities=27%  Similarity=0.693  Sum_probs=42.0

Q ss_pred             CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF--DRTCPMCRVPVN  299 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~  299 (329)
                      .+.+.+|++|.+....|... +|||. ||..|+..-+..  ...||.|.....
T Consensus       236 ~t~~~~C~~Cg~~PtiP~~~~~C~Hi-yCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIPHVIGKCGHI-YCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccCCceeeccCCCCCCCeeeccccce-eehhhhhhhhcchhhcccCccCCCCc
Confidence            35678999999999999865 59999 999999887665  689999988764

>KOG2814|consensus

Probab=97.32  E-value=0.00034  Score=67.03  Aligned_cols=56  Identities=25%  Similarity=0.204  Sum_probs=47.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC--cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      |.|.|||++|.|-|+|++||+++|.+|.+.+  +.++.+.+..+.|.+|.++|..+++
T Consensus        67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~id  124 (345)
T KOG2814|consen   67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLID  124 (345)
T ss_pred             HhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHH
Confidence            5689999999999999999999999997664  4444445578999999999988765

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.21  E-value=0.00037  Score=62.65  Aligned_cols=94  Identities=19%  Similarity=0.145  Sum_probs=63.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      -||..||++|.+|+.|+++.|-+|++-...++          -    ...|..++.        +........-   ..+
T Consensus        86 ~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d----------~----~~fI~nal~--------Pa~v~~V~~~---~~d  140 (190)
T COG0195          86 PVGACIGKRGSRVKAVSEELGEKIDVVEWSED----------P----AEFIKNALA--------PAEVLSVNIK---EDD  140 (190)
T ss_pred             chhhhccCCChHHHHHHHHhCCceEEEEeCCC----------H----HHHHHHhcC--------cceEeEEEEE---eCC
Confidence            37899999999999999999977776422221          1    122222210        0000000000   001


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      + ....+.||.+..++.|||+|.+++.+.+-||-+|.+-.
T Consensus       141 ~-~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         141 G-HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             C-cEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            2 26788899999999999999999999999999999854

>KOG1588|consensus

Probab=97.17  E-value=0.0012  Score=61.49  Aligned_cols=40  Identities=33%  Similarity=0.597  Sum_probs=35.0

Q ss_pred             CceEEEEEecC------cccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          84 GHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        84 g~~t~~i~VP~------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      -..+..|.||.      ++||.|+|++|.|+|+|+++|||+|-|=.
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG  135 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG  135 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence            34677888876      58999999999999999999999999953

>KOG4692|consensus

Probab=97.13  E-value=0.0002  Score=68.94  Aligned_cols=50  Identities=22%  Similarity=0.539  Sum_probs=45.4

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ..++..|+||+..+.++++.||+|. -|..|+.+.+.+.+.|-.|+..+..
T Consensus       419 ~sEd~lCpICyA~pi~Avf~PC~H~-SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPINAVFAPCSHR-SCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CcccccCcceecccchhhccCCCCc-hHHHHHHHHHhcCCeeeEecceeee
Confidence            3577899999999999999999999 9999999999999999999887643

>KOG2279|consensus

Probab=97.12  E-value=0.00049  Score=69.68  Aligned_cols=136  Identities=18%  Similarity=0.161  Sum_probs=92.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHHhhhhh----------HhhhcccC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAADHFS----------ALRASRKS   70 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i~e~~~----------~~~~~~~~   70 (329)
                      .|+.|+||+|++|+.++.-++++|.+-..+-   .+...|.|....++.|+.++.+.++...          +.|.-+..
T Consensus       150 ~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~  229 (608)
T KOG2279|consen  150 SVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQ  229 (608)
T ss_pred             hcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCC
Confidence            3789999999999999999999999986554   7888899999999999999877553211          11111100


Q ss_pred             C-----CCC------C-------------CCCC--------------------CCCCC-------ceEEEEEecCcccce
Q psy3263          71 G-----ALS------P-------------LSPP--------------------TGVPG-------HVTIEVRVPYKVVGL   99 (329)
Q Consensus        71 ~-----~~~------~-------------~~~p--------------------~~~~g-------~~t~~i~VP~~~vG~   99 (329)
                      .     .++      .             .+.+                    .+.+|       ...-.+.+|...+|.
T Consensus       230 p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~  309 (608)
T KOG2279|consen  230 PINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGD  309 (608)
T ss_pred             CccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccc
Confidence            0     000      0             0000                    00001       122478899999999


Q ss_pred             eecCCCchHHHHHHhcCceEEcCCCC-CCC-----eEEEECCCCCCc
Q psy3263         100 VVGPKGATIKRIQHQTNTYIVTPSRD-KEP-----VFEVTGNFPEGP  140 (329)
Q Consensus       100 IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~-----~i~ItG~~pe~v  140 (329)
                      +||..|++++.+...+++++.|-... ..+     ++.+.| ...-+
T Consensus       310 lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~eg-kqh~~  355 (608)
T KOG2279|consen  310 LIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEG-KQHYE  355 (608)
T ss_pred             hhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecc-hhHHH
Confidence            99999999999999999999886544 333     355666 44433

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger

Probab=97.11  E-value=0.0004  Score=54.28  Aligned_cols=31  Identities=35%  Similarity=0.730  Sum_probs=27.1

Q ss_pred             EeCCCChhccHhhHHhhcCC---CCCCcccccccc
Q psy3263         268 LIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN  299 (329)
Q Consensus       268 ~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~  299 (329)
                      .-.|+|. |-..|+.+|+..   ...||+||++..
T Consensus        49 ~g~C~H~-FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   49 WGKCSHN-FHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             eccCccH-HHHHHHHHHHccccCCCCCCCcCCeee
Confidence            4479999 999999999986   689999999764

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.03  E-value=0.0011  Score=70.13  Aligned_cols=51  Identities=18%  Similarity=0.178  Sum_probs=44.3

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAA   58 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~   58 (329)
                      +|.|||.||.+||+|+++||++|++..   +-.|.|.+ ..+.+++|+.+|..++
T Consensus       589 i~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~  640 (719)
T TIGR02696       589 IGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIA  640 (719)
T ss_pred             hhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhh
Confidence            688999999999999999999999973   34566766 6899999999999885

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=96.98  E-value=0.00025  Score=63.43  Aligned_cols=47  Identities=28%  Similarity=0.631  Sum_probs=42.5

Q ss_pred             CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .+.|.||...+..|+...|||. ||..|+.+-.+....|-+|.+....
T Consensus       196 PF~C~iCKkdy~spvvt~CGH~-FC~~Cai~~y~kg~~C~~Cgk~t~G  242 (259)
T COG5152         196 PFLCGICKKDYESPVVTECGHS-FCSLCAIRKYQKGDECGVCGKATYG  242 (259)
T ss_pred             ceeehhchhhccchhhhhcchh-HHHHHHHHHhccCCcceecchhhcc
Confidence            3799999999999999999999 9999999988888999999886544

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=96.95  E-value=0.001  Score=70.62  Aligned_cols=52  Identities=19%  Similarity=0.199  Sum_probs=43.5

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHh
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +|.|||+||.+||+|+++||++|++-.  +..+.......+.+++|++.|..+.
T Consensus       562 I~~vIG~gGk~Ik~I~~~tg~~I~i~d--dG~V~i~~~~~~~~~~a~~~I~~~~  613 (684)
T TIGR03591       562 IRDVIGPGGKVIREITEETGAKIDIED--DGTVKIAASDGEAAEAAIKMIEGIT  613 (684)
T ss_pred             HHhhcCCCcHHHHHHHHHHCCEEEEec--CeEEEEEECcHHHHHHHHHHHHhhh
Confidence            688999999999999999999999963  3444444557899999999998774

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>KOG0336|consensus

Probab=96.88  E-value=0.00049  Score=67.99  Aligned_cols=51  Identities=35%  Similarity=0.473  Sum_probs=46.9

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG  134 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG  134 (329)
                      +....-+.+-.++||.|||+||+.||+||..|.++|++-+.+.+-.|+|-|
T Consensus        45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg   95 (629)
T KOG0336|consen   45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFG   95 (629)
T ss_pred             CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEec
Confidence            455667888999999999999999999999999999999999888899999

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=96.88  E-value=0.0014  Score=59.08  Aligned_cols=33  Identities=27%  Similarity=0.263  Sum_probs=29.6

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE   34 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~   34 (329)
                      .+|||+|||..|.|.|+|++.|+|+|-|-..+.
T Consensus       162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs  194 (269)
T COG5176         162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS  194 (269)
T ss_pred             cceeEEEecCCcchHHHHHHHhCCeEEEecccc
Confidence            379999999999999999999999999975554

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.86  E-value=0.001  Score=65.42  Aligned_cols=92  Identities=14%  Similarity=0.038  Sum_probs=65.1

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||++|.+|++|.++. |=+|++-...+++.              ..|..++.        +......  ..  . +
T Consensus       253 vGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~--------------~fI~Nal~--------Pa~V~~V--~i--~-~  305 (374)
T PRK12328        253 IGATVGVKGVRINAVSKELNGENIDCIEYSNVPE--------------IFIARALA--------PAIISSV--KI--E-E  305 (374)
T ss_pred             HHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhCC--------CceeeEE--EE--c-C
Confidence            7899999999999999998 87888764444322              22322210        0000000  00  1 2


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      ......+.||.+..++.|||+|.+++-..+-||.+|.|-+
T Consensus       306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            3367889999999999999999999999999999999853

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.86  E-value=0.0012  Score=71.41  Aligned_cols=52  Identities=19%  Similarity=0.258  Sum_probs=44.4

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCce-EEcCCCCCCCeEEEECCCCCCc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY-IVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~-I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ....+.||.+++|.|||+||.|||+|+++||+. |.+-.   +-.|.|.+...+.+
T Consensus       685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---dg~V~I~a~d~~~i  737 (891)
T PLN00207        685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---DGTVKITAKDLSSL  737 (891)
T ss_pred             eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---CeeEEEEeCCHHHH
Confidence            677899999999999999999999999999999 77744   45688888566666

>TIGR01953 NusA transcription termination factor NusA

Probab=96.83  E-value=0.0026  Score=62.18  Aligned_cols=93  Identities=19%  Similarity=0.220  Sum_probs=65.0

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||++|.+|+.|.++. |-+|++-...+++.              ..|..++.        +......  .-. . +
T Consensus       245 vga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~--------------~fi~nal~--------Pa~v~~v--~i~-~-~  298 (341)
T TIGR01953       245 VGACVGPKGSRIQAISKELNGEKIDIIEYSDDPA--------------EFIANALS--------PAKVISV--EVL-D-E  298 (341)
T ss_pred             ceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhcC--------CceEEEE--EEE-c-C
Confidence            7999999999999999998 88888764444332              12222210        0000000  000 1 1


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      ......+.||.+..++.|||+|.+++-...-||.+|.|-+
T Consensus       299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            2357889999999999999999999999999999999854

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=96.82  E-value=0.0016  Score=47.69  Aligned_cols=37  Identities=22%  Similarity=0.303  Sum_probs=34.2

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      .....+.||.+.+|..|||+|.+|+.+++.+|-+|.+
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3788999999999999999999999999999988875

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=96.76  E-value=0.00095  Score=64.28  Aligned_cols=52  Identities=29%  Similarity=0.760  Sum_probs=43.7

Q ss_pred             CCCCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC--CCCCccccccc
Q psy3263         246 PSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPV  298 (329)
Q Consensus       246 ~~~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i  298 (329)
                      ..+..+++..|.||-+...-..++||+|. .|.-|+-++..-  .+.||+||..-
T Consensus        54 addtDEen~~C~ICA~~~TYs~~~PC~H~-~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          54 ADDTDEENMNCQICAGSTTYSARYPCGHQ-ICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccccccccceeEEecCCceEEEeccCCch-HHHHHHHHHHHHHhccCCCcccccc
Confidence            34456788999999999888889999999 999999876444  78999999864

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=96.76  E-value=0.00071  Score=63.97  Aligned_cols=43  Identities=35%  Similarity=0.717  Sum_probs=37.5

Q ss_pred             cccccccccCcccEEeC-CCChhccHhhHHhhcCC-CCCCcccccc
Q psy3263         254 RQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF-DRTCPMCRVP  297 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~lp-CgH~~fC~~Cl~~~~~~-~~~CP~Cr~~  297 (329)
                      +.|+.|..++.+++..| |+|. ||.+|+...+.. ...||.|...
T Consensus       275 LkCplc~~Llrnp~kT~cC~~~-fc~eci~~al~dsDf~CpnC~rk  319 (427)
T COG5222         275 LKCPLCHCLLRNPMKTPCCGHT-FCDECIGTALLDSDFKCPNCSRK  319 (427)
T ss_pred             ccCcchhhhhhCcccCccccch-HHHHHHhhhhhhccccCCCcccc
Confidence            79999999999999775 6888 999999876665 8999999873

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.73  E-value=0.0037  Score=61.59  Aligned_cols=95  Identities=16%  Similarity=0.149  Sum_probs=66.5

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||++|.+|++|.++. |-+|++-...+++.              ..|..++.        +......  ... . +
T Consensus       247 vGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~--------------~fi~nal~--------Pa~v~~v--~i~-~-~  300 (362)
T PRK12327        247 KGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA--------------EFVANALS--------PAKVVSV--EVD-D-E  300 (362)
T ss_pred             hheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhCC--------CceEEEE--EEE-c-C
Confidence            7999999999999999998 88888764444321              22322210        0000000  000 1 2


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD  125 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~  125 (329)
                      ......+.||.+..++.|||+|.+++-...-||.+|.|-+.+
T Consensus       301 ~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~  342 (362)
T PRK12327        301 EEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES  342 (362)
T ss_pred             CCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence            336788999999999999999999999999999999986544

>KOG0297|consensus

Probab=96.72  E-value=0.00085  Score=66.76  Aligned_cols=56  Identities=25%  Similarity=0.611  Sum_probs=49.1

Q ss_pred             CCCCCcccccccccCcccEE-eCCCChhccHhhHHhhcCCCCCCcccccccccchhhh
Q psy3263         249 SISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  305 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~  305 (329)
                      ++++++.|++|.....+|+. ..|||. ||..|+..+......||.|+..+.....+.
T Consensus        17 ~~~~~l~C~~C~~vl~~p~~~~~cgh~-fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~   73 (391)
T KOG0297|consen   17 PLDENLLCPICMSVLRDPVQTTTCGHR-FCAGCLLESLSNHQKCPVCRQELTQAEELP   73 (391)
T ss_pred             CCcccccCccccccccCCCCCCCCCCc-ccccccchhhccCcCCcccccccchhhccC
Confidence            37888999999999999998 599999 999999999888899999999886654443

>KOG1813|consensus

Probab=96.67  E-value=0.00083  Score=63.47  Aligned_cols=46  Identities=24%  Similarity=0.678  Sum_probs=42.3

Q ss_pred             cccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +.|.||...+.+++...|+|. ||..|+..-.+....|++|.+.+..
T Consensus       242 f~c~icr~~f~~pVvt~c~h~-fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYFYRPVVTKCGHY-FCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             ccccccccccccchhhcCCce-eehhhhccccccCCcceeccccccc
Confidence            679999999999999999999 9999999988888999999987754

>KOG1039|consensus

Probab=96.58  E-value=0.0011  Score=64.76  Aligned_cols=51  Identities=29%  Similarity=0.759  Sum_probs=41.9

Q ss_pred             CCCcccccccccCcccE-----E---eCCCChhccHhhHHhhcC--C-----CCCCcccccccccch
Q psy3263         251 SGSRQCYLCNDREVTHA-----L---IPCGHNFFCSECAERTCD--F-----DRTCPMCRVPVNQAM  302 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~-----~---lpCgH~~fC~~Cl~~~~~--~-----~~~CP~Cr~~i~~~~  302 (329)
                      ..+..|-||++...+..     +   .+|.|. ||..|+..|..  +     .+.||.||.......
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~-~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~  224 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHS-FCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVN  224 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchh-hhhcHhHhhhhhhccccccccCCCcccCcccccc
Confidence            45789999999887766     4   679999 99999999983  3     589999999875544

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.58  E-value=0.0034  Score=63.89  Aligned_cols=93  Identities=18%  Similarity=0.229  Sum_probs=65.2

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||++|.+|+.|..+. |=+|++-...+++.              ..|...+.     .+   .....   .. . .
T Consensus       247 vga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~--------------~fi~nal~-----pa---~v~~v---~~-~-~  299 (470)
T PRK09202        247 VGACVGMRGSRIQAISNELGGEKIDIILWSDDPA--------------QFIINALS-----PA---EVSSV---VV-D-E  299 (470)
T ss_pred             hHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhCC-----CC---EEEEE---EE-e-C
Confidence            7999999999999999998 88888764444332              22222210     00   00000   00 0 1


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  124 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~  124 (329)
                      ......+.||....++-|||+|.+|+...+.||.+|.|-..
T Consensus       300 ~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        300 DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            12578899999999999999999999999999999998653

>KOG2660|consensus

Probab=96.54  E-value=0.00051  Score=65.76  Aligned_cols=51  Identities=24%  Similarity=0.678  Sum_probs=44.6

Q ss_pred             CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  301 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~  301 (329)
                      +.....|.+|...+.++.++ -|-|. ||..|+.+.+.....||.|...+.+.
T Consensus        12 ~n~~itC~LC~GYliDATTI~eCLHT-FCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDATTITECLHT-FCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             cccceehhhccceeecchhHHHHHHH-HHHHHHHHHHHHhccCCccceeccCc
Confidence            34567999999999999855 79999 99999999999899999999888554

>KOG0119|consensus

Probab=96.50  E-value=0.005  Score=61.87  Aligned_cols=57  Identities=30%  Similarity=0.554  Sum_probs=43.5

Q ss_pred             CceEEEEEecC------cccceeecCCCchHHHHHHhcCceEEcCC-----------CC-------CCCe-EEEECCCCC
Q psy3263          84 GHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPS-----------RD-------KEPV-FEVTGNFPE  138 (329)
Q Consensus        84 g~~t~~i~VP~------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~-----------~~-------~e~~-i~ItG~~pe  138 (329)
                      +..+.+|.||.      ++||+|||..|.|.|+|+.+|||+|.|=.           ++       +|++ +.|++.+-|
T Consensus       136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e  215 (554)
T KOG0119|consen  136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE  215 (554)
T ss_pred             cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence            34556677764      78999999999999999999999999943           11       3444 788885556


Q ss_pred             Cc
Q psy3263         139 GP  140 (329)
Q Consensus       139 ~v  140 (329)
                      +|
T Consensus       216 ki  217 (554)
T KOG0119|consen  216 KI  217 (554)
T ss_pred             HH
Confidence            66

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=96.47  E-value=0.0054  Score=55.44  Aligned_cols=31  Identities=29%  Similarity=0.654  Sum_probs=28.6

Q ss_pred             cccceeecCCCchHHHHHHhcCceEEcCCCC
Q psy3263          95 KVVGLVVGPKGATIKRIQHQTNTYIVTPSRD  125 (329)
Q Consensus        95 ~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~  125 (329)
                      ++||+|||+.|.|.|++++.|+|+|-|-..-
T Consensus       163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             ceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            7999999999999999999999999996544

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.45  E-value=0.0056  Score=61.38  Aligned_cols=94  Identities=19%  Similarity=0.173  Sum_probs=65.2

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||++|.+|+.|..+. |=+|++-...+++.              ..|..++.        +......  ... . +
T Consensus       279 vGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~--------------~fI~NaLs--------PA~V~~V--~i~-~-~  332 (449)
T PRK12329        279 VGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA--------------TYIANALS--------PARVDEV--RLV-D-P  332 (449)
T ss_pred             hhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhcC--------CceeeEE--EEE-c-C
Confidence            7999999999999999998 87888754444322              22222210        0000000  000 1 2


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  124 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~  124 (329)
                      ......+.||.+..++-|||+|.+++-...-||-+|.|-..
T Consensus       333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~  373 (449)
T PRK12329        333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS  373 (449)
T ss_pred             CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence            23567899999999999999999999999999999998653

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=96.32  E-value=0.006  Score=63.74  Aligned_cols=52  Identities=21%  Similarity=0.287  Sum_probs=44.0

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ...++.|+.+.++-+||+||.+||+|.++||++|.+-   ++..|.|.+...+.+
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~  603 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESA  603 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHH
Confidence            6678899999999999999999999999999999996   455688888333444

>KOG0828|consensus

Probab=96.24  E-value=0.0017  Score=65.21  Aligned_cols=49  Identities=29%  Similarity=0.686  Sum_probs=39.5

Q ss_pred             CCCCcccccccccC-----------------cccEEeCCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263         250 ISGSRQCYLCNDRE-----------------VTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN  299 (329)
Q Consensus       250 l~~~~~C~IC~e~~-----------------~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~  299 (329)
                      .+....|+||+...                 .+.++.||.|. |-..|+.+|.+. +-.||+||.++.
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~Hi-fH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHI-FHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHH-HHHHHHHHHHhhhcccCCccCCCCC
Confidence            45678999999632                 22456799998 999999999996 669999999875

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.19  E-value=0.0052  Score=65.47  Aligned_cols=62  Identities=18%  Similarity=0.273  Sum_probs=45.8

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      ....+.||.+.++.+||+||.|||+|+++||+.|.+   +++-.|.|.+...+.+ +...+|..+.
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi---~d~G~v~i~~~~~~~~~~a~~~I~~~~  616 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI---EDDGTVKIAATDGEAAEAAKERIEGIT  616 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCcccc---CCCceEEEEcccHHHHHHHHHHHHHhc
Confidence            556777899999999999999999999999998877   3345677888445555 2223444433

>KOG0804|consensus

Probab=96.18  E-value=0.0029  Score=62.87  Aligned_cols=47  Identities=28%  Similarity=0.663  Sum_probs=37.7

Q ss_pred             CCCCcccccccccCcccE----EeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHA----LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~----~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      +.+-..|+||+|++-.-+    ...|.|. |-..|+..|+.  .+||+||.-..
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hs-fh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHS-FHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccc-cchHHHhhccc--CcChhhhhhcC
Confidence            455679999999886443    5799999 99999999976  58999987443

>PRK12704 phosphodiesterase; Provisional

Probab=95.99  E-value=0.018  Score=59.46  Aligned_cols=53  Identities=19%  Similarity=0.339  Sum_probs=44.5

Q ss_pred             ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCC
Q psy3263          85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEG  139 (329)
Q Consensus        85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~  139 (329)
                      .++-.|.+|+ ++-|.|||+-|.+||.+..-||+-|.|.  |+..+|.|||..|-.
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~~~~~r  262 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPIR  262 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc--CCCCeEEEecCChhh
Confidence            3556788998 7779999999999999999999999994  455678899966666

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.90  E-value=0.0043  Score=44.50  Aligned_cols=47  Identities=26%  Similarity=0.721  Sum_probs=37.5

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .....|..|...-...+++||||. .|..|..-.  ....||.|.+++..
T Consensus         5 ~~~~~~~~~~~~~~~~~~~pCgH~-I~~~~f~~~--rYngCPfC~~~~~~   51 (55)
T PF14447_consen    5 QPEQPCVFCGFVGTKGTVLPCGHL-ICDNCFPGE--RYNGCPFCGTPFEF   51 (55)
T ss_pred             ccceeEEEccccccccccccccce-eeccccChh--hccCCCCCCCcccC
Confidence            345678899988888889999999 999997543  24789999998853

>PRK00468 hypothetical protein; Provisional

Probab=95.69  E-value=0.012  Score=45.03  Aligned_cols=31  Identities=29%  Similarity=0.468  Sum_probs=27.6

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhc
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQT  115 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~t  115 (329)
                      ...+++.|..+-+|.||||+|.+|+.|+.--
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3678899999999999999999999998753

>PRK02821 hypothetical protein; Provisional

Probab=95.65  E-value=0.012  Score=45.25  Aligned_cols=33  Identities=30%  Similarity=0.383  Sum_probs=29.0

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCc
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT  117 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga  117 (329)
                      ...+.+.|..+-+|.||||+|.+|+.|+.--.+
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            377899999999999999999999999987543

>PRK12704 phosphodiesterase; Provisional

Probab=95.61  E-value=0.022  Score=58.79  Aligned_cols=54  Identities=15%  Similarity=0.107  Sum_probs=44.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~e   59 (329)
                      |-|+||||.|-|||.|+.-||+-|-|.  +...+|+|+| .+-.-+.|+..+..++.
T Consensus       221 mkgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~~~~~rre~a~~~l~~l~~  275 (520)
T PRK12704        221 MKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPIRREIARLALEKLVQ  275 (520)
T ss_pred             hhcceeCCCcchHHHHHHHhCCeEEEc--CCCCeEEEecCChhhHHHHHHHHHHHHh
Confidence            569999999999999999999998886  4456778999 56666678887777653

>KOG4367|consensus

Probab=95.59  E-value=0.0073  Score=59.90  Aligned_cols=37  Identities=24%  Similarity=0.628  Sum_probs=34.1

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF  287 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~  287 (329)
                      +++++.|+||..-+.+|.++||+|+ +|..|+..+..+
T Consensus         1 meeelkc~vc~~f~~epiil~c~h~-lc~~ca~~~~~~   37 (699)
T KOG4367|consen    1 MEEELKCPVCGSFYREPIILPCSHN-LCQACARNILVQ   37 (699)
T ss_pred             CcccccCceehhhccCceEeecccH-HHHHHHHhhccc
Confidence            3678999999999999999999999 999999988766

>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B

Probab=95.59  E-value=0.0061  Score=42.63  Aligned_cols=42  Identities=29%  Similarity=0.745  Sum_probs=21.6

Q ss_pred             cccccccCc--ccEEe--CCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263         256 CYLCNDREV--THALI--PCGHNFFCSECAERTCDF-DRTCPMCRVPV  298 (329)
Q Consensus       256 C~IC~e~~~--~~~~l--pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i  298 (329)
                      |++|.+.+.  +..+.  +||+. .|..|..++.+. ...||-||+++
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~-IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQ-ICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS-----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCc-HHHHHHHHHHhccCCCCCCCCCCC
Confidence            677887662  22345  57998 999999999975 89999999875

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=95.42  E-value=0.014  Score=63.44  Aligned_cols=51  Identities=24%  Similarity=0.201  Sum_probs=42.5

Q ss_pred             eeeeecCCChHHHHHHHHhCCe-EEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263           5 VVPSINPFGCKIKALRAKTNTY-IKTPVRGEEPVFVVTG-RKEDVARAKREILSAA   58 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~-I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~   58 (329)
                      +|.|||.||.+||+|+++||+. |++-.  +.. |.|.+ ..+.+++|+..|..+.
T Consensus       696 i~~vIG~GGktIk~I~eetg~~~Idi~d--dg~-V~I~a~d~~~i~~A~~~I~~l~  748 (891)
T PLN00207        696 VNMIIGSGGKKVKSIIEETGVEAIDTQD--DGT-VKITAKDLSSLEKSKAIISSLT  748 (891)
T ss_pred             HHHHhcCCchhHHHHHHHHCCCccCcCC--Cee-EEEEeCCHHHHHHHHHHHHHHh
Confidence            5789999999999999999999 88863  333 45555 7899999999998884

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=95.39  E-value=0.016  Score=42.48  Aligned_cols=25  Identities=12%  Similarity=0.034  Sum_probs=23.2

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEe
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKT   29 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~i   29 (329)
                      +|..|||+|.+|+.++..+|-+|++
T Consensus        36 ~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          36 LGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             ceeeECCCCHHHHHHHHHHCCCeEE
Confidence            5899999999999999999988875

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>KOG2814|consensus

Probab=95.38  E-value=0.0078  Score=57.87  Aligned_cols=53  Identities=21%  Similarity=0.426  Sum_probs=45.9

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP  140 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v  140 (329)
                      ...+.|+..+.|.|||+.|.|-|+|+++|+++|.+|.+. +...|+|+| .-.++
T Consensus        58 ~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~-~~~~~  111 (345)
T KOG2814|consen   58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIG-ISRNC  111 (345)
T ss_pred             hhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEee-hhHHH
Confidence            346789999999999999999999999999999999766 777788888 55555

>KOG1734|consensus

Probab=95.32  E-value=0.0092  Score=55.89  Aligned_cols=49  Identities=24%  Similarity=0.594  Sum_probs=39.9

Q ss_pred             CCCcccccccccCc----------ccEEeCCCChhccHhhHHhhcCC--CCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREV----------THALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~----------~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~  300 (329)
                      .++..|.||-....          +...+.|+|. |-..|++-|+-.  ...||.|+..++.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHv-FHEfCIrGWcivGKkqtCPYCKekVdl  282 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHV-FHEFCIRGWCIVGKKQTCPYCKEKVDL  282 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccc-hHHHhhhhheeecCCCCCchHHHHhhH
Confidence            34679999987553          3346899999 999999999877  7899999988743

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.27  E-value=0.041  Score=56.75  Aligned_cols=58  Identities=17%  Similarity=0.310  Sum_probs=45.7

Q ss_pred             ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh
Q psy3263          85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES  144 (329)
Q Consensus        85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~  144 (329)
                      .++..|.+|+ ++-|.|||+-|.+||.+...||+-|.|.  |+...|.|+|-.|-.-||+.
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~fdp~rreia~  261 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPVRREIAR  261 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc--CCCCeEEecCCchHHHHHHH
Confidence            3556788999 6779999999999999999999999994  44557889995555444443

>KOG3002|consensus

Probab=95.26  E-value=0.013  Score=56.38  Aligned_cols=63  Identities=22%  Similarity=0.494  Sum_probs=47.3

Q ss_pred             CCCCCCCcccccccccCcccEEeCC--CChhccHhhHHhhcCCCCCCcccccccccchhhhhhhhhhhcch
Q psy3263         247 SGSISGSRQCYLCNDREVTHALIPC--GHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLW  315 (329)
Q Consensus       247 ~~~l~~~~~C~IC~e~~~~~~~lpC--gH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~~~~~~~v~  315 (329)
                      .....+-++|+||++....|.. .|  ||. .|..|-.++   ...||.||.++. .+|.+..+.....+.
T Consensus        42 ~~~~~~lleCPvC~~~l~~Pi~-QC~nGHl-aCssC~~~~---~~~CP~Cr~~~g-~~R~~amEkV~e~~~  106 (299)
T KOG3002|consen   42 TLLDLDLLDCPVCFNPLSPPIF-QCDNGHL-ACSSCRTKV---SNKCPTCRLPIG-NIRCRAMEKVAEAVL  106 (299)
T ss_pred             cccchhhccCchhhccCcccce-ecCCCcE-ehhhhhhhh---cccCCccccccc-cHHHHHHHHHHHhce
Confidence            3344566899999999988864 66  898 999998655   578999999998 556666555555443

>KOG0825|consensus

Probab=95.17  E-value=0.0039  Score=65.58  Aligned_cols=51  Identities=24%  Similarity=0.385  Sum_probs=42.0

Q ss_pred             CCCcccccccccCcccE---EeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263         251 SGSRQCYLCNDREVTHA---LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  302 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~---~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~  302 (329)
                      .....|++|+....+-.   -.+|+|- ||..|+..|......||+||..|.+.+
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~-FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEKHTAHY-FCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhccccccccc-cHHHHhhhhhhhcccCchhhhhhheee
Confidence            34578999997665543   3599999 999999999999999999999886654

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C

Probab=95.16  E-value=0.015  Score=42.20  Aligned_cols=41  Identities=22%  Similarity=0.344  Sum_probs=29.6

Q ss_pred             CCcccccccccCcccEE-eCCCChhccHhhHHhhcCC--CCCCcc
Q psy3263         252 GSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF--DRTCPM  293 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~--~~~CP~  293 (329)
                      -.+.|+|.+..+.+|+. ..|+|. |..+.+..++..  ...||+
T Consensus        10 ~~~~CPiT~~~~~~PV~s~~C~H~-fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDPVKSKKCGHT-FEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSEEEESSS--E-EEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCCcCcCCCCCe-ecHHHHHHHHHhcCCCCCCC
Confidence            35799999999999986 599999 999999999944  789998

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=95.14  E-value=0.034  Score=58.27  Aligned_cols=52  Identities=23%  Similarity=0.306  Sum_probs=43.2

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHHHHHhh
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREILSAAD   59 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I~~i~e   59 (329)
                      .+.+||+||.+||+|.++||++|++-   ++..+.|.+. .+.+.+|+..|..+++
T Consensus       563 I~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~~~ak~~I~~i~~  615 (692)
T COG1185         563 IRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESAKKAKERIEAITR  615 (692)
T ss_pred             HhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHHHHHHHHHHHHHh
Confidence            35689999999999999999999997   3445567665 5899999999998853

>KOG1002|consensus

Probab=95.10  E-value=0.0063  Score=61.68  Aligned_cols=47  Identities=30%  Similarity=0.759  Sum_probs=40.7

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-----CCCCccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPV  298 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-----~~~CP~Cr~~i  298 (329)
                      .++.+|.+|.+...++....|.|. ||.-|+......     ...||+|...+
T Consensus       534 k~~~~C~lc~d~aed~i~s~ChH~-FCrlCi~eyv~~f~~~~nvtCP~C~i~L  585 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDYIESSCHHK-FCRLCIKEYVESFMENNNVTCPVCHIGL  585 (791)
T ss_pred             cCceeecccCChhhhhHhhhhhHH-HHHHHHHHHHHhhhcccCCCCccccccc
Confidence            456899999999999999999999 999999776544     68999998876

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]

Probab=95.07  E-value=0.027  Score=43.26  Aligned_cols=31  Identities=42%  Similarity=0.588  Sum_probs=27.7

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHh
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQ  114 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~  114 (329)
                      ...++++.|...-+|.||||+|.||+.|+.-
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            3467899999999999999999999999865

>PRK00106 hypothetical protein; Provisional

Probab=95.05  E-value=0.055  Score=55.93  Aligned_cols=58  Identities=19%  Similarity=0.343  Sum_probs=45.6

Q ss_pred             ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh
Q psy3263          85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES  144 (329)
Q Consensus        85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~  144 (329)
                      .++..|.+|+ ++-|.|||+-|.+|+.+..-||+-|.|.  |+...|.|+|-.|-.-||+.
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp~~v~lS~fdpvRReiAr  282 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID--DTPEVVVLSGFDPIRREIAR  282 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc--CCCCeEEEeCCChHHHHHHH
Confidence            3556788999 6779999999999999999999999994  45557889995554444433

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.92  E-value=0.25  Score=44.62  Aligned_cols=101  Identities=17%  Similarity=0.151  Sum_probs=72.4

Q ss_pred             eeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCCCc
Q psy3263           6 VPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGH   85 (329)
Q Consensus         6 G~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~g~   85 (329)
                      -+|...+|..++.|-+..|++|.+.  -++..+.|+|++..++.+...|.+++.                        ..
T Consensus        38 ~LLl~~~~~~L~~l~~~~~~~I~~~--~~~~~i~I~g~k~~~~~i~~~i~~~l~------------------------~i   91 (210)
T PF14611_consen   38 FLLLTGNGRILENLAARNGAKIEVS--RSENRIRITGTKSTAEYIEASINEILS------------------------NI   91 (210)
T ss_pred             eeeecCCchHHHHHHHhcCceEEEe--cCCcEEEEEccHHHHHHHHHHHHHHHh------------------------hc
Confidence            4677889999999988889999997  445678999999999999999988853                        11


Q ss_pred             eEEEEEecCcccceee-c---CCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263          86 VTIEVRVPYKVVGLVV-G---PKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG  134 (329)
Q Consensus        86 ~t~~i~VP~~~vG~II-G---kgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG  134 (329)
                      .+..+.++.-.--+.. +   .....++.|++.|+++|....+++.  +.|++
T Consensus        92 ~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~~~--~~i~~  142 (210)
T PF14611_consen   92 RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDGNK--LKISW  142 (210)
T ss_pred             EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCCCe--EEEEE
Confidence            4444555432111111 1   1356789999999999998776643  44444

>PRK01064 hypothetical protein; Provisional

Probab=94.85  E-value=0.038  Score=42.69  Aligned_cols=32  Identities=28%  Similarity=0.436  Sum_probs=28.1

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhc
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT  115 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~t  115 (329)
                      ....+++.|..+-.|.+|||+|.+|+.||.-.
T Consensus        28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            34678899999999999999999999998853

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.78  E-value=0.052  Score=55.98  Aligned_cols=54  Identities=15%  Similarity=0.109  Sum_probs=43.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~e   59 (329)
                      |=|+||||.|-|||.|+.-||+-|-|.  +...+|+|+| .|-.-+-|+..|..++.
T Consensus       215 ~kgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~fdp~rreia~~~l~~li~  269 (514)
T TIGR03319       215 MKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPVRREIARMALEKLIQ  269 (514)
T ss_pred             hhccccCCCcchHHHHHHHhCceEEEc--CCCCeEEecCCchHHHHHHHHHHHHHHH
Confidence            459999999999999999999998886  3345677888 67777778777766653

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=94.75  E-value=0.028  Score=59.94  Aligned_cols=51  Identities=20%  Similarity=0.253  Sum_probs=42.1

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAA   58 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~   58 (329)
                      ++.+||.||.+||+|+++||++|++-  ++ -.|.|.+ ..+.+++|++.|..+.
T Consensus       565 I~~vIG~gg~~ik~I~~~~~~~idi~--d~-G~v~i~~~~~~~~~~a~~~I~~~~  616 (693)
T PRK11824        565 IRDVIGPGGKTIREITEETGAKIDIE--DD-GTVKIAATDGEAAEAAKERIEGIT  616 (693)
T ss_pred             HHHHhcCCchhHHHHHHHHCCccccC--CC-ceEEEEcccHHHHHHHHHHHHHhc
Confidence            57899999999999999999988873  33 3356666 7899999999998874

>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins

Probab=94.73  E-value=0.022  Score=39.96  Aligned_cols=40  Identities=33%  Similarity=0.775  Sum_probs=31.5

Q ss_pred             ccccccc--cCcccEEeCCC-----ChhccHhhHHhhcCC--CCCCcccc
Q psy3263         255 QCYLCND--REVTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCR  295 (329)
Q Consensus       255 ~C~IC~e--~~~~~~~lpCg-----H~~fC~~Cl~~~~~~--~~~CP~Cr  295 (329)
                      .|.||++  ...++...||.     |. +-.+|+.+|...  ...||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~-vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKY-VHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhH-HHHHHHHHHHHHcCCCcCCCCC
Confidence            4889997  44566778995     55 788999999966  56999995

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

>PRK00106 hypothetical protein; Provisional

Probab=94.60  E-value=0.067  Score=55.35  Aligned_cols=54  Identities=19%  Similarity=0.126  Sum_probs=43.7

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~e   59 (329)
                      |=|+||||.|-|||.|+.-||+-|-|.  +....|+|+| .|-.-+-|+..+..++.
T Consensus       236 mkGriIGreGrNir~~E~~tGvdliid--dtp~~v~lS~fdpvRReiAr~~le~Li~  290 (535)
T PRK00106        236 MKGRIIGREGRNIRTLESLTGIDVIID--DTPEVVVLSGFDPIRREIARMTLESLIK  290 (535)
T ss_pred             hhcceeCCCcchHHHHHHHhCceEEEc--CCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence            459999999999999999999988886  4445677888 67777778877766653

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.56  E-value=0.024  Score=52.61  Aligned_cols=50  Identities=22%  Similarity=0.234  Sum_probs=42.9

Q ss_pred             EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ..+.||..+++.+||++|.+|+.|.+.+++.|.+-.   +-.|.|+|+.++++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---NG~VwI~~~~~~~~  196 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---NGRIWIKGPDEEDE  196 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---CcEEEEeeCCHHHH
Confidence            568899999999999999999999999999999843   35688999555566

>KOG1001|consensus

Probab=94.53  E-value=0.015  Score=61.59  Aligned_cols=45  Identities=31%  Similarity=0.885  Sum_probs=39.6

Q ss_pred             cccccccccCcccEEeCCCChhccHhhHHhhcCC--CCCCccccccccc
Q psy3263         254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQ  300 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~  300 (329)
                      ..|.+|.+ ...++..+|+|. ||.+|+....+.  ...||.||..+..
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~-~c~~c~~~~i~~~~~~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHD-FCVECLKKSIQQSENAPCPLCRNVLKE  501 (674)
T ss_pred             cccccccc-cccceeecccch-HHHHHHHhccccccCCCCcHHHHHHHH
Confidence            79999999 777888999999 999999998887  5679999987743

>KOG0827|consensus

Probab=94.35  E-value=0.02  Score=56.16  Aligned_cols=44  Identities=27%  Similarity=0.773  Sum_probs=33.4

Q ss_pred             cccccccccCccc---E-EeCCCChhccHhhHHhhcCC---CCCCccccccc
Q psy3263         254 RQCYLCNDREVTH---A-LIPCGHNFFCSECAERTCDF---DRTCPMCRVPV  298 (329)
Q Consensus       254 ~~C~IC~e~~~~~---~-~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i  298 (329)
                      -.|.||.+.+-..   . +-.|||. |-..|+..|.+.   .+.||.|+-.+
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhi-fh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHI-FHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             ceeeEeccCCccccccccccchhhH-HHHHHHHHHHccCCccCCCCceeecc
Confidence            4899996654322   1 3359999 999999999998   46899999433

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.16  E-value=0.073  Score=49.40  Aligned_cols=53  Identities=23%  Similarity=0.153  Sum_probs=42.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I~~i~e   59 (329)
                      +++.+||++|.+|+.|.++|++.|.+-.   +-.|-|.|. .+++++|++.|..+.+
T Consensus       155 ~i~~lig~~g~~i~~l~~~~~~~I~ig~---NG~VwI~~~~~~~~~~a~~~I~~~e~  208 (235)
T PRK04163        155 KVPRVIGKKGSMINMLKEETGCDIIVGQ---NGRIWIKGPDEEDEEIAIEAIKKIER  208 (235)
T ss_pred             HHHhhcCCCChhHhhhhhhhCcEEEEcC---CcEEEEeeCCHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999953   234567775 6699999999987643

>KOG3039|consensus

Probab=94.15  E-value=0.034  Score=51.53  Aligned_cols=48  Identities=25%  Similarity=0.414  Sum_probs=41.8

Q ss_pred             CCcccccccccCccc----EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         252 GSRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~----~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ....|++|.+.+.++    ++-||||. ||.+|..++......||+|-.++..
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~V-v~~ecvEklir~D~v~pv~d~plkd  271 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHV-VTKECVEKLIRKDMVDPVTDKPLKD  271 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcE-eeHHHHHHhccccccccCCCCcCcc
Confidence            457899999988765    36799999 9999999999999999999998744

>KOG3800|consensus

Probab=94.01  E-value=0.029  Score=53.07  Aligned_cols=43  Identities=28%  Similarity=0.818  Sum_probs=33.5

Q ss_pred             ccccccccC-cccE----EeCCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263         255 QCYLCNDRE-VTHA----LIPCGHNFFCSECAERTCDF-DRTCPMCRVPV  298 (329)
Q Consensus       255 ~C~IC~e~~-~~~~----~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i  298 (329)
                      .|++|.... .+|.    .-+|+|+ .|.+|..++... ...||.|...+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~-lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHR-LCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeeccccch-HHHHHHHHHHhcCCCCCCcccchh
Confidence            588887533 2332    2399999 999999999888 88999998765

>PRK00468 hypothetical protein; Provisional

Probab=93.80  E-value=0.034  Score=42.63  Aligned_cols=19  Identities=26%  Similarity=0.202  Sum_probs=16.8

Q ss_pred             eeeeecCCChHHHHHHHHh
Q psy3263           5 VVPSINPFGCKIKALRAKT   23 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T   23 (329)
                      +|+||||+|.+|++||.--
T Consensus        41 ~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         41 MGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CcceecCCChhHHHHHHHH
Confidence            5999999999999999653

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=93.78  E-value=0.1  Score=44.88  Aligned_cols=85  Identities=21%  Similarity=0.110  Sum_probs=56.2

Q ss_pred             CCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHH---HHHHHHHHHHhhhhhHhhhcccCCCCCCC-CCCCCCCCce
Q psy3263          11 PFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDV---ARAKREILSAADHFSALRASRKSGALSPL-SPPTGVPGHV   86 (329)
Q Consensus        11 kgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v---~~A~~~I~~i~e~~~~~~~~~~~~~~~~~-~~p~~~~g~~   86 (329)
                      ..|.-||+|-.+-.-+|.+=           ..+...   +.|++.|.+++-      +..    +... .+     ...
T Consensus        23 ~~~dli~~lAk~lrKRIvvR-----------~dps~l~~~e~A~~~I~~ivP------~ea----~i~di~F-----d~~   76 (145)
T cd02410          23 EDGDLVKDLAKDLRKRIVIR-----------PDPSVLKPPEEAIKIILEIVP------EEA----GITDIYF-----DDD   76 (145)
T ss_pred             cccHHHHHHHHHHhceEEEc-----------CChhhcCCHHHHHHHHHHhCC------Ccc----CceeeEe-----cCC
Confidence            45677777777777666653           333322   458888888741      110    0100 00     124


Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      |-+|.|-.+.-|++||++|.++++|..+||=.-.+
T Consensus        77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v  111 (145)
T cd02410          77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKV  111 (145)
T ss_pred             CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence            56788888999999999999999999999987666

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=93.69  E-value=0.021  Score=61.51  Aligned_cols=49  Identities=22%  Similarity=0.607  Sum_probs=39.0

Q ss_pred             CCCCcccccccccCc-------ccEEeCCCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263         250 ISGSRQCYLCNDREV-------THALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN  299 (329)
Q Consensus       250 l~~~~~C~IC~e~~~-------~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~  299 (329)
                      +.+..+|.||+....       ....-.|.|. |-..|+.+|...  ...||+||..++
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknK-FH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNK-FHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhh-hhHHHHHHHHHhcCCCCCCccccccc
Confidence            567789999997542       1123469999 999999999988  789999998765

>PRK02821 hypothetical protein; Provisional

Probab=93.57  E-value=0.038  Score=42.59  Aligned_cols=21  Identities=24%  Similarity=0.150  Sum_probs=18.2

Q ss_pred             eeeeecCCChHHHHHHHHhCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNT   25 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga   25 (329)
                      +|+||||+|.+|++||.--.+
T Consensus        42 ~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         42 LGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CcceeCCCCchHHHHHHHHHH
Confidence            699999999999999976544

>PF04641 Rtf2: Rtf2 RING-finger

Probab=93.48  E-value=0.049  Score=51.25  Aligned_cols=50  Identities=22%  Similarity=0.453  Sum_probs=39.8

Q ss_pred             CCCCcccccccccCcc----cEEeCCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263         250 ISGSRQCYLCNDREVT----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  301 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~----~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~  301 (329)
                      ....+.|+|....+..    .++.||||. |+..++..+. ....||+|-.++...
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V-~s~~alke~k-~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCV-FSEKALKELK-KSKKCPVCGKPFTEE  163 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCE-eeHHHHHhhc-ccccccccCCccccC
Confidence            3567899999987742    346699999 9999999995 356799999998644

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=93.46  E-value=0.043  Score=38.16  Aligned_cols=46  Identities=24%  Similarity=0.691  Sum_probs=27.6

Q ss_pred             ccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263         255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  302 (329)
Q Consensus       255 ~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~  302 (329)
                      -|.-|+-..  .-++.|.....|..|+..++.....||+|..++...+
T Consensus         4 nCKsCWf~~--k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtki   49 (50)
T PF03854_consen    4 NCKSCWFAN--KGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTKI   49 (50)
T ss_dssp             ---SS-S----SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----S
T ss_pred             cChhhhhcC--CCeeeecchhHHHHHHHHHhccccCCCcccCcCcccc
Confidence            467777443  3478896555999999999999999999999886544

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

>KOG1645|consensus

Probab=93.45  E-value=0.044  Score=54.15  Aligned_cols=47  Identities=30%  Similarity=0.635  Sum_probs=38.6

Q ss_pred             CCcccccccccCccc-----EEeCCCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263         252 GSRQCYLCNDREVTH-----ALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN  299 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~-----~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~  299 (329)
                      ....|+||++...-+     +.+.|||. |-.+|+++|+.+  ...||.|.....
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghl-Fgs~cie~wl~k~~~~~cp~c~~kat   56 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHL-FGSQCIEKWLGKKTKMQCPLCSGKAT   56 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeeccccc-ccHHHHHHHHhhhhhhhCcccCChhH
Confidence            357899999976543     36799999 999999999976  789999987653

>cd02409 KH-II KH-II (K homology RNA-binding domain, type II)

Probab=93.41  E-value=0.13  Score=37.10  Aligned_cols=34  Identities=29%  Similarity=0.481  Sum_probs=28.1

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceE
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI  119 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I  119 (329)
                      ..+.+.+.....|.+||++|.+|+.+++.++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            5556666666789999999999999999998665

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=93.34  E-value=0.088  Score=45.10  Aligned_cols=38  Identities=24%  Similarity=0.289  Sum_probs=34.1

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      ..+-+.|+...+|..||++|++||.|++..|-+|.+-.
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve   69 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE   69 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence            56778889999999999999999999999999998743

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.31  E-value=0.04  Score=41.52  Aligned_cols=35  Identities=26%  Similarity=0.302  Sum_probs=30.2

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceE
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI  119 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I  119 (329)
                      ...+.+.+..+..|.+|||+|.|++.||.-.+..+
T Consensus        28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            46788999999999999999999999998765544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=93.16  E-value=0.042  Score=53.11  Aligned_cols=48  Identities=25%  Similarity=0.636  Sum_probs=37.3

Q ss_pred             CCcccccccccCcc--cEEe--CCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         252 GSRQCYLCNDREVT--HALI--PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       252 ~~~~C~IC~e~~~~--~~~l--pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      ++..|+.|+|.+-.  .-+.  |||.. .|..|...+.+. ...||.||+.++.
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~-ic~fc~~~irq~lngrcpacrr~y~d   65 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQ-ICQFCYNNIRQNLNGRCPACRRKYDD   65 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccH-HHHHHHHHHHhhccCCChHhhhhccc
Confidence            34459999987642  2233  67888 999999999888 8999999998744

>KOG4739|consensus

Probab=92.96  E-value=0.045  Score=50.59  Aligned_cols=41  Identities=27%  Similarity=0.771  Sum_probs=30.0

Q ss_pred             ccccccccCc-ccE-EeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         255 QCYLCNDREV-THA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       255 ~C~IC~e~~~-~~~-~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      -|-.|+-... ++. ++.|+|. ||..|......  ..||+|++.+
T Consensus         5 hCn~C~~~~~~~~f~LTaC~Hv-fC~~C~k~~~~--~~C~lCkk~i   47 (233)
T KOG4739|consen    5 HCNKCFRFPSQDPFFLTACRHV-FCEPCLKASSP--DVCPLCKKSI   47 (233)
T ss_pred             EeccccccCCCCceeeeechhh-hhhhhcccCCc--ccccccccee
Confidence            4667765443 333 6799999 99999876532  3899999985

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]

Probab=92.89  E-value=0.056  Score=41.53  Aligned_cols=18  Identities=28%  Similarity=0.303  Sum_probs=16.4

Q ss_pred             eeeeecCCChHHHHHHHH
Q psy3263           5 VVPSINPFGCKIKALRAK   22 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~   22 (329)
                      +|.+|||+|-+|++||.-
T Consensus        41 ~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          41 MGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             ccceecCCChhHHHHHHH
Confidence            589999999999999964

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A

Probab=92.79  E-value=0.04  Score=41.54  Aligned_cols=46  Identities=22%  Similarity=0.541  Sum_probs=22.7

Q ss_pred             CcccccccccCc-c---cEE----eCCCChhccHhhHHhhcCC-----------CCCCcccccccc
Q psy3263         253 SRQCYLCNDREV-T---HAL----IPCGHNFFCSECAERTCDF-----------DRTCPMCRVPVN  299 (329)
Q Consensus       253 ~~~C~IC~e~~~-~---~~~----lpCgH~~fC~~Cl~~~~~~-----------~~~CP~Cr~~i~  299 (329)
                      +.+|.||+.... +   +.+    -.|++. |-..|+..|+..           ...||.|++++.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~-fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKK-FHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCH-HHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            468999998754 2   211    267777 888999999764           236999999874

>PRK12705 hypothetical protein; Provisional

Probab=92.11  E-value=0.15  Score=52.57  Aligned_cols=52  Identities=13%  Similarity=0.065  Sum_probs=37.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSA   57 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i   57 (329)
                      |=|+||||.|.|||.++..||+-|-|.  +...+|+|++ .+..-+.|+..+..+
T Consensus       209 mkGriIGreGrNir~~E~~tGvdliid--dtp~~V~ls~fdp~rreia~~~l~~L  261 (508)
T PRK12705        209 MKGRIIGREGRNIRAFEGLTGVDLIID--DTPEAVVISSFNPIRREIARLTLEKL  261 (508)
T ss_pred             hhccccCccchhHHHHHHhhCCceEec--CCccchhhcccCccchHHHHHHHHHH
Confidence            459999999999999999999998886  3333445555 355555555555544

>KOG4185|consensus

Probab=91.88  E-value=0.11  Score=49.36  Aligned_cols=44  Identities=30%  Similarity=0.821  Sum_probs=37.0

Q ss_pred             cccccccccCc------ccEEeCCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263         254 RQCYLCNDREV------THALIPCGHNFFCSECAERTCDF-DRTCPMCRVPV  298 (329)
Q Consensus       254 ~~C~IC~e~~~------~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i  298 (329)
                      ..|-||-+.+.      .|..+.|||. +|..|+..+... ...||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~-~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHT-ICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCce-ehHhHHHHHhcCceeeccCCCCcc
Confidence            47888987664      3567789999 999999999888 77899999984

>KOG0826|consensus

Probab=91.88  E-value=0.089  Score=50.68  Aligned_cols=47  Identities=19%  Similarity=0.438  Sum_probs=39.0

Q ss_pred             CCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      .+...|++|....+++..+ -.|-. ||..|+.........||+-..+.
T Consensus       298 ~~~~~CpvClk~r~Nptvl~vSGyV-fCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEVSGYV-FCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             CccccChhHHhccCCCceEEecceE-EeHHHHHHHHHhcCCCCccCCcc
Confidence            4557999999988877654 56888 99999999988889999976665

>KOG3273|consensus

Probab=91.69  E-value=0.078  Score=47.86  Aligned_cols=50  Identities=16%  Similarity=0.091  Sum_probs=46.1

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHh
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +|+|+||+|.|=-.|+.-|.++|-+.    +..|.|-|..+++..|++.|-+++
T Consensus       180 IGRiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~~~niriAR~avcsLI  229 (252)
T KOG3273|consen  180 IGRIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGAFQNIRIARDAVCSLI  229 (252)
T ss_pred             HHHhhcCCCcceeeeeccceeEEEec----CceEEEeecchhhHHHHHhhHhhh
Confidence            69999999999999999999999997    567899999999999999998874

>PRK01064 hypothetical protein; Provisional

Probab=91.68  E-value=0.11  Score=40.20  Aligned_cols=19  Identities=32%  Similarity=0.284  Sum_probs=16.9

Q ss_pred             eeeeecCCChHHHHHHHHh
Q psy3263           5 VVPSINPFGCKIKALRAKT   23 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T   23 (329)
                      +|.+|||+|.+|++||.-.
T Consensus        41 ~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         41 IGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             ceEEECCCCccHHHHHHHH
Confidence            4999999999999999754

>cd02409 KH-II KH-II (K homology RNA-binding domain, type II)

Probab=91.55  E-value=0.13  Score=37.12  Aligned_cols=23  Identities=22%  Similarity=0.169  Sum_probs=20.7

Q ss_pred             eeeeecCCChHHHHHHHHhCCeE
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYI   27 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I   27 (329)
                      .|.+|||+|.+|++|+..++-.+
T Consensus        36 ~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          36 PGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             CceEECCCCccHHHHHHHHHHHc
Confidence            57899999999999999998665

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>KOG1814|consensus

Probab=91.23  E-value=0.078  Score=52.51  Aligned_cols=34  Identities=24%  Similarity=0.777  Sum_probs=27.8

Q ss_pred             CCCcccccccccCcc---cEEeCCCChhccHhhHHhhc
Q psy3263         251 SGSRQCYLCNDREVT---HALIPCGHNFFCSECAERTC  285 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~---~~~lpCgH~~fC~~Cl~~~~  285 (329)
                      .....|.||++...-   -.++||+|. ||..|+....
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv-~Ck~C~kdY~  218 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLPCSHV-FCKSCLKDYF  218 (445)
T ss_pred             hhcccceeeehhhcCcceeeecccchH-HHHHHHHHHH
Confidence            456899999998764   347899999 9999998764

>PRK12705 hypothetical protein; Provisional

Probab=91.09  E-value=0.41  Score=49.31  Aligned_cols=54  Identities=15%  Similarity=0.236  Sum_probs=41.0

Q ss_pred             ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      .++-.|.+|+ ++-|.|||+-|.+|+.+...||+-|.|...+  +.|.|++-.|..-
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp--~~V~ls~fdp~rr  251 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP--EAVVISSFNPIRR  251 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc--cchhhcccCccch
Confidence            3555778898 6669999999999999999999999995433  3466666344443

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function

Probab=91.01  E-value=0.18  Score=43.94  Aligned_cols=20  Identities=20%  Similarity=0.580  Sum_probs=17.6

Q ss_pred             CCcccccccccCcccEEeCC
Q psy3263         252 GSRQCYLCNDREVTHALIPC  271 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~~~lpC  271 (329)
                      ++..|+||+|.+-++|+|-|
T Consensus         1 ed~~CpICme~PHNAVLLlC   20 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLC   20 (162)
T ss_pred             CCccCceeccCCCceEEEEe
Confidence            35689999999999999877

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=91.00  E-value=0.077  Score=39.97  Aligned_cols=28  Identities=25%  Similarity=0.236  Sum_probs=22.5

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVR   32 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~   32 (329)
                      ||..||++|.+||.|.++. |-+|++=..
T Consensus        19 vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen   19 VGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             HHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             ceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            6889999999999999999 888887533

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

Probab=90.90  E-value=0.19  Score=38.80  Aligned_cols=31  Identities=29%  Similarity=0.475  Sum_probs=27.6

Q ss_pred             EeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         268 LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       268 ~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      .--|.|. |-..|+.+|+.....||++|+...
T Consensus        51 wG~CnHa-FH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          51 WGVCNHA-FHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             EEecchH-HHHHHHHHHHhhCCCCCCCCceeE
Confidence            3479999 999999999999999999998763

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=90.84  E-value=0.19  Score=38.37  Aligned_cols=38  Identities=26%  Similarity=0.444  Sum_probs=30.7

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      ..+.+.+..+..|.+|||+|+|++.||.-+...++-..
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~~   61 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRNT   61 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhcc
Confidence            34667777788999999999999999998776665443

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=90.78  E-value=0.087  Score=40.02  Aligned_cols=35  Identities=26%  Similarity=0.427  Sum_probs=29.6

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEE
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV  120 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~  120 (329)
                      ..+.+.+....-|.|||++|++|++|.+..+-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            44677788899999999999999999988776664

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>KOG2932|consensus

Probab=90.75  E-value=0.094  Score=50.18  Aligned_cols=43  Identities=37%  Similarity=0.835  Sum_probs=29.9

Q ss_pred             ccccccccCccc-EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         255 QCYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       255 ~C~IC~e~~~~~-~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      -|.-|---.... ..+||.|. ||.+|+..-  ..+.||.|--++..
T Consensus        92 fCd~Cd~PI~IYGRmIPCkHv-FCl~CAr~~--~dK~Cp~C~d~Vqr  135 (389)
T KOG2932|consen   92 FCDRCDFPIAIYGRMIPCKHV-FCLECARSD--SDKICPLCDDRVQR  135 (389)
T ss_pred             eecccCCcceeeecccccchh-hhhhhhhcC--ccccCcCcccHHHH
Confidence            466665333322 26799999 999998654  36799999877643

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0

Probab=90.74  E-value=0.13  Score=43.59  Aligned_cols=48  Identities=21%  Similarity=0.736  Sum_probs=40.3

Q ss_pred             CcccccccccCcccEEe----CCCChhccHhhHHhhcCC---CCCCcccccccccc
Q psy3263         253 SRQCYLCNDREVTHALI----PCGHNFFCSECAERTCDF---DRTCPMCRVPVNQA  301 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~l----pCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~~~  301 (329)
                      --+|-||.|...+..++    =||-+ .|..|.-.+|+.   .+.||+|+..+...
T Consensus        80 lYeCnIC~etS~ee~FLKPneCCgY~-iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   80 LYECNICKETSAEERFLKPNECCGYS-ICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             ceeccCcccccchhhcCCcccccchH-HHHHHHHHHHHHcccCCCCCccccccccc
Confidence            35899999988887765    38998 999999988887   78999999988543

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=90.30  E-value=0.19  Score=37.80  Aligned_cols=34  Identities=32%  Similarity=0.380  Sum_probs=26.3

Q ss_pred             EEEecCcc-----cceeecCCCchHHHHHHhc-CceEEcC
Q psy3263          89 EVRVPYKV-----VGLVVGPKGATIKRIQHQT-NTYIVTP  122 (329)
Q Consensus        89 ~i~VP~~~-----vG~IIGkgG~tIk~Iq~~t-ga~I~ip  122 (329)
                      .+.|-...     +|..||++|++||.|.++. |-+|.+-
T Consensus         6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            34455555     8999999999999999999 8888874

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=89.90  E-value=0.21  Score=50.54  Aligned_cols=43  Identities=28%  Similarity=0.377  Sum_probs=38.2

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK  126 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~  126 (329)
                      +.....+.||.+.++.+|||+|.+|++|.+..|.+|.+-..+.
T Consensus       484 gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         484 GDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             cCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            4466789999999999999999999999999999999966553

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=89.70  E-value=0.1  Score=48.32  Aligned_cols=46  Identities=26%  Similarity=0.756  Sum_probs=34.5

Q ss_pred             CCccccccccc-Cccc--EEe--C-CCChhccHhhHHhhcCC-CCCCc--cccccc
Q psy3263         252 GSRQCYLCNDR-EVTH--ALI--P-CGHNFFCSECAERTCDF-DRTCP--MCRVPV  298 (329)
Q Consensus       252 ~~~~C~IC~e~-~~~~--~~l--p-CgH~~fC~~Cl~~~~~~-~~~CP--~Cr~~i  298 (329)
                      .+..|++|... .-+|  .++  | |-|. +|.+|..++... ...||  -|.+-+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHr-mCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHR-MCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHH-HHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            35689999853 3333  222  5 9999 999999999888 78899  786644

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=89.31  E-value=0.42  Score=41.07  Aligned_cols=36  Identities=19%  Similarity=0.269  Sum_probs=32.5

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcC
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP  122 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip  122 (329)
                      .+-+.|....+|..||++|++||.|++..|-+|.+-
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV   69 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI   69 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence            667788889999999999999999999999998874

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>KOG4362|consensus

Probab=89.28  E-value=0.098  Score=55.11  Aligned_cols=48  Identities=19%  Similarity=0.581  Sum_probs=41.8

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC---CCCCcccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN  299 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~  299 (329)
                      ....+|+||......++++.|.|. ||..|+...+..   ...||+|+..+.
T Consensus        19 ~k~lEc~ic~~~~~~p~~~kc~~~-~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   19 QKILECPICLEHVKEPSLLKCDHI-FLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             hhhccCCceeEEeeccchhhhhHH-HHhhhhhceeeccCccccchhhhhhhh
Confidence            456899999999999999999999 999999887766   578999997653

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=88.62  E-value=0.51  Score=36.62  Aligned_cols=36  Identities=17%  Similarity=0.202  Sum_probs=29.8

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      ..++|.|-...-|+|||++|++|++|++.-.....+
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            346778888888999999999999999987666655

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=88.23  E-value=0.43  Score=41.60  Aligned_cols=48  Identities=21%  Similarity=0.486  Sum_probs=36.1

Q ss_pred             CCCCcccccccccCcccEEeCCCChh----ccHhhHHhhcCC--CCCCccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNF----FCSECAERTCDF--DRTCPMCRVPV  298 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~----fC~~Cl~~~~~~--~~~CP~Cr~~i  298 (329)
                      ...+..|-||++... ....||....    .-.+|+++|...  ...|++|+.++
T Consensus         5 s~~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y   58 (162)
T PHA02825          5 SLMDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY   58 (162)
T ss_pred             CCCCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence            456789999998764 3345775321    246899999887  78999999987

>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]

Probab=88.13  E-value=0.85  Score=46.74  Aligned_cols=92  Identities=22%  Similarity=0.122  Sum_probs=60.3

Q ss_pred             eecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCCCceE
Q psy3263           8 SINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT   87 (329)
Q Consensus         8 IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~g~~t   87 (329)
                      ++-+.|.-||+|-.+...||.+-++-   .+  .-.   -+.|++.|.+++-      +.....   .-.+     ...+
T Consensus        43 ~~~~~~dlik~lAk~lrKRI~iR~dP---sv--l~~---~e~A~~~I~eivP------~ea~i~---~i~F-----d~~t  100 (637)
T COG1782          43 LFAKDGDLIKDLAKDLRKRIIIRPDP---SV--LKP---PEEARKIILEIVP------EEAGIT---DIYF-----DDDT  100 (637)
T ss_pred             HhccchhHHHHHHHHHhhceEeccCc---hh--cCC---HHHHHHHHHHhCc------cccCce---eEEe-----cCCC
Confidence            45567888899988888888874222   11  112   2457777877741      111100   0000     1245


Q ss_pred             EEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      -+|.|-.+.=|++|||+|++.++|.++||-.-++
T Consensus       101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~i  134 (637)
T COG1782         101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKI  134 (637)
T ss_pred             ceEEEEecCCceEEecCchHHHHHHHHhCCccee
Confidence            6788889999999999999999999999875544

>KOG3579|consensus

Probab=87.95  E-value=0.38  Score=45.59  Aligned_cols=45  Identities=27%  Similarity=0.715  Sum_probs=35.4

Q ss_pred             CcccccccccCcccEEeCC----CChhccHhhHHhhcCC-----------CCCCccccccc
Q psy3263         253 SRQCYLCNDREVTHALIPC----GHNFFCSECAERTCDF-----------DRTCPMCRVPV  298 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~lpC----gH~~fC~~Cl~~~~~~-----------~~~CP~Cr~~i  298 (329)
                      .+.|.+|.|++.|+-++.|    .|. ||+.|-+...++           ..+||+-...+
T Consensus       268 pLcCTLC~ERLEDTHFVQCPSVp~HK-FCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~v  327 (352)
T KOG3579|consen  268 PLCCTLCHERLEDTHFVQCPSVPSHK-FCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNV  327 (352)
T ss_pred             ceeehhhhhhhccCceeecCCCcccc-eecccCHHHHHhhcCCCceeCCCCCcCcccCCcc
Confidence            4899999999999999998    688 999998776554           24677665544

>PRK13764 ATPase; Provisional

Probab=87.85  E-value=0.35  Score=50.88  Aligned_cols=43  Identities=28%  Similarity=0.317  Sum_probs=38.4

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK  126 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~  126 (329)
                      ......|.||.+.++.+|||||.+|++|.++.|.+|.+-..+.
T Consensus       479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~  521 (602)
T PRK13764        479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE  521 (602)
T ss_pred             cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence            4467889999999999999999999999999999999965553

>KOG4369|consensus

Probab=87.70  E-value=0.24  Score=54.81  Aligned_cols=53  Identities=21%  Similarity=0.110  Sum_probs=46.0

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecC----CCCcceEEEecCHHHHHHHHHHHHHH
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPV----RGEEPVFVVTGRKEDVARAKREILSA   57 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~----~~~ervi~ItG~~e~v~~A~~~I~~i   57 (329)
                      ..++|||||.+|+.+|+-||+.|.+-+    +..||.+.+.|+++.+.-|...|.-.
T Consensus      1351 ~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~ 1407 (2131)
T KOG4369|consen 1351 SSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLP 1407 (2131)
T ss_pred             hhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccce
Confidence            468999999999999999999998853    22389999999999999999888654

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=86.91  E-value=0.14  Score=38.42  Aligned_cols=23  Identities=22%  Similarity=0.147  Sum_probs=19.3

Q ss_pred             eeeeecCCChHHHHHHHHhCCeE
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYI   27 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I   27 (329)
                      .|.||||.|.++++||.-.+..+
T Consensus        40 ~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   40 AGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             CHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             cceEECCCCeeHHHHHHHHHHHH
Confidence            47899999999999998766544

>KOG4369|consensus

Probab=86.79  E-value=0.3  Score=54.13  Aligned_cols=61  Identities=15%  Similarity=0.100  Sum_probs=50.7

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC----CCCCCeEEEECCCCCCcchhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTGNFPEGPGFESHHG  147 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~----~~~e~~i~ItG~~pe~veie~~i~  147 (329)
                      ..-.+.+|....-.|||+||.+|..++.-||+.|.+-+    +..||.+.+.| .|+.+..+.++.
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg-~p~~~r~a~~~I 1404 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKG-RPPSQRVATSPI 1404 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCC-CChhhhhhhccc
Confidence            34566788888899999999999999999999999965    22589999999 999996665443

>KOG1493|consensus

Probab=86.45  E-value=0.24  Score=37.96  Aligned_cols=29  Identities=31%  Similarity=0.675  Sum_probs=25.3

Q ss_pred             CCCChhccHhhHHhhcCC---CCCCcccccccc
Q psy3263         270 PCGHNFFCSECAERTCDF---DRTCPMCRVPVN  299 (329)
Q Consensus       270 pCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~  299 (329)
                      -|.|. |-..|+.+|...   ...||+||+...
T Consensus        50 ~C~h~-fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   50 YCLHA-FHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             HHHHH-HHHHHHHHHhcCccccccCCcchheeE
Confidence            69998 999999999876   679999998653

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=86.33  E-value=0.34  Score=36.92  Aligned_cols=26  Identities=19%  Similarity=0.147  Sum_probs=22.3

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEec
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTP   30 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip   30 (329)
                      .|.+|||.|+++++||--++..++-.
T Consensus        35 ~g~LIGk~G~tL~AlQ~L~~~~~~~~   60 (77)
T cd02414          35 IGLLIGKRGKTLDALQYLANLVLNRN   60 (77)
T ss_pred             CCeEECCCCccHHHHHHHHHHHHhhc
Confidence            48899999999999999988776654

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG1428|consensus

Probab=86.17  E-value=0.37  Score=54.49  Aligned_cols=50  Identities=22%  Similarity=0.637  Sum_probs=38.6

Q ss_pred             CCCcccccccccCcc--c-EEeCCCChhccHhhHHhhcCC----------CCCCcccccccccc
Q psy3263         251 SGSRQCYLCNDREVT--H-ALIPCGHNFFCSECAERTCDF----------DRTCPMCRVPVNQA  301 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~--~-~~lpCgH~~fC~~Cl~~~~~~----------~~~CP~Cr~~i~~~  301 (329)
                      ..+..|.||+...-.  | ..+.|+|. |-..|.+++++.          .-.||+|..++...
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~C~Hi-FHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~ 3546 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHI-FHLQCCRRVLENRWLGPRITFGFISCPICKNKINHI 3546 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecCCccc-hhHHHHHHHHHhcccCCeeEEeeeecccccchhhhH
Confidence            456789999975532  2 36899999 999999888765          34899999887543

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=85.04  E-value=0.29  Score=37.12  Aligned_cols=23  Identities=22%  Similarity=0.248  Sum_probs=19.7

Q ss_pred             eeeecCCChHHHHHHHHhCCeEE
Q psy3263           6 VPSINPFGCKIKALRAKTNTYIK   28 (329)
Q Consensus         6 G~IIGkgG~~Ik~Lr~~Tga~I~   28 (329)
                      |.+|||+|++|++|+++.+-.+.
T Consensus        37 ~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   37 GIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             HHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             cHhHHhhhHHHHHHHHHHHHHHh
Confidence            67999999999999998876654

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans

Probab=84.90  E-value=0.92  Score=44.73  Aligned_cols=24  Identities=29%  Similarity=0.733  Sum_probs=18.8

Q ss_pred             ccHhhHHhhcCC-------------CCCCcccccccc
Q psy3263         276 FCSECAERTCDF-------------DRTCPMCRVPVN  299 (329)
Q Consensus       276 fC~~Cl~~~~~~-------------~~~CP~Cr~~i~  299 (329)
                      -|.+|+.+|...             ...||.||+.+.
T Consensus       315 WC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  315 WCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             HHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            488999887532             468999999875

They are purported to be transmembrane protein-precursors but their function is unknown.

>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3

Probab=84.72  E-value=0.8  Score=37.37  Aligned_cols=32  Identities=25%  Similarity=0.546  Sum_probs=26.4

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCce
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY  118 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~  118 (329)
                      .++|.|-...-|+|||++|++|++|++.....
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~   93 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQKL   93 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence            36677777778999999999999998876554

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=84.68  E-value=0.46  Score=37.72  Aligned_cols=33  Identities=30%  Similarity=0.721  Sum_probs=26.8

Q ss_pred             CCCCcccccccccCcccE--EeCCCChhccHhhHHh
Q psy3263         250 ISGSRQCYLCNDREVTHA--LIPCGHNFFCSECAER  283 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~--~lpCgH~~fC~~Cl~~  283 (329)
                      +.++..|.+|...+...+  ..||||. |...|+.|
T Consensus        75 i~~~~~C~vC~k~l~~~~f~~~p~~~v-~H~~C~~r  109 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGNSVFVVFPCGHV-VHYSCIKR  109 (109)
T ss_pred             ECCCCCccCcCCcCCCceEEEeCCCeE-EecccccC
Confidence            456778999999887655  5699998 99999764

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>PHA03096 p28-like protein; Provisional

Probab=84.60  E-value=0.47  Score=45.38  Aligned_cols=42  Identities=21%  Similarity=0.245  Sum_probs=30.4

Q ss_pred             cccccccccCcc--------cEEeCCCChhccHhhHHhhcCC---CCCCccccc
Q psy3263         254 RQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDF---DRTCPMCRV  296 (329)
Q Consensus       254 ~~C~IC~e~~~~--------~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~  296 (329)
                      ..|.||++....        ..+-.|-|. ||..|+..|...   ...||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~-fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHE-FNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcH-HHHHHHHHHHHhhhhcccCccccc
Confidence            789999986542        234589999 999999988665   444555544

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=84.29  E-value=0.61  Score=36.17  Aligned_cols=26  Identities=15%  Similarity=0.243  Sum_probs=22.0

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEec
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTP   30 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip   30 (329)
                      -|.+|||+|++|++|+++-.....++
T Consensus        41 Pg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          41 TQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             CceEECCCchhHHHHHHHHHHHhCCC
Confidence            37899999999999999987766664

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=84.00  E-value=1.1  Score=39.46  Aligned_cols=36  Identities=11%  Similarity=0.108  Sum_probs=30.0

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcC
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP  122 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip  122 (329)
                      ..+-+.|-... |+-|||+|.+||++++..|-+|.+-
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV   96 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV   96 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence            34555665555 9999999999999999999999974

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=83.73  E-value=0.84  Score=40.25  Aligned_cols=26  Identities=23%  Similarity=0.086  Sum_probs=23.7

Q ss_pred             eeeecCCChHHHHHHHHhCCeEEecC
Q psy3263           6 VPSINPFGCKIKALRAKTNTYIKTPV   31 (329)
Q Consensus         6 G~IIGkgG~~Ik~Lr~~Tga~I~ip~   31 (329)
                      |.-|||+|.+||+|+++.|-+|.+-.
T Consensus        72 g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         72 RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             cccccccchHHHHHHHHhCCcEEEEE
Confidence            67899999999999999999998863

>KOG2930|consensus

Probab=83.72  E-value=0.54  Score=38.08  Aligned_cols=29  Identities=24%  Similarity=0.456  Sum_probs=26.1

Q ss_pred             EeCCCChhccHhhHHhhcCCCCCCcccccc
Q psy3263         268 LIPCGHNFFCSECAERTCDFDRTCPMCRVP  297 (329)
Q Consensus       268 ~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~  297 (329)
                      ---|.|. |-.-|+.+|++....||+|.+.
T Consensus        78 WG~CNHa-FH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   78 WGVCNHA-FHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             eeecchH-HHHHHHHHHHhhcCcCCCcCcc
Confidence            3479999 9999999999999999999775

>KOG2874|consensus

Probab=83.64  E-value=1.8  Score=41.18  Aligned_cols=47  Identities=23%  Similarity=0.314  Sum_probs=41.2

Q ss_pred             eeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHH
Q psy3263           7 PSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSA   57 (329)
Q Consensus         7 ~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i   57 (329)
                      ++||..|.|+|+|+=-|+|+|-+.    ...|.+.|+...+..+++-+.+-
T Consensus       162 RLiGpng~TLKAlelLT~CYilVq----G~TVsaiGpfkGlkevr~IV~Dc  208 (356)
T KOG2874|consen  162 RLIGPNGSTLKALELLTNCYILVQ----GNTVSAIGPFKGLKEVRKIVEDC  208 (356)
T ss_pred             HhcCCCchhHHHHHHHhhcEEEee----CcEEEeecCcchHHHHHHHHHHH
Confidence            589999999999999999999997    45678889999999988887663

>KOG3161|consensus

Probab=82.83  E-value=0.51  Score=49.34  Aligned_cols=43  Identities=21%  Similarity=0.581  Sum_probs=32.9

Q ss_pred             CCCcccccccccC----cccEEeCCCChhccHhhHHhhcCCCCCCcccccc
Q psy3263         251 SGSRQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP  297 (329)
Q Consensus       251 ~~~~~C~IC~e~~----~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~  297 (329)
                      .+-+.|.||+..+    ..|+.+-|||. .|..|++.+..  ..|| |...
T Consensus         9 ~~~l~c~ic~n~f~~~~~~Pvsl~cght-ic~~c~~~lyn--~scp-~~~D   55 (861)
T KOG3161|consen    9 VLLLLCDICLNLFVVQRLEPVSLQCGHT-ICGHCVQLLYN--ASCP-TKRD   55 (861)
T ss_pred             HHHhhchHHHHHHHHHhcCcccccccch-HHHHHHHhHhh--ccCC-CCcc
Confidence            3457899997665    35778899999 99999988755  5777 5543

>PHA02862 5L protein; Provisional

Probab=82.67  E-value=0.92  Score=39.03  Aligned_cols=44  Identities=23%  Similarity=0.577  Sum_probs=33.9

Q ss_pred             cccccccccCcccEEeCCCChh----ccHhhHHhhcCC--CCCCccccccc
Q psy3263         254 RQCYLCNDREVTHALIPCGHNF----FCSECAERTCDF--DRTCPMCRVPV  298 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~lpCgH~~----fC~~Cl~~~~~~--~~~CP~Cr~~i  298 (329)
                      ..|-||++...+. ..||..+.    .-.+|+.+|...  ...|++|+.++
T Consensus         3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY   52 (156)
T PHA02862          3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY   52 (156)
T ss_pred             CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence            5799999987554 46875321    346999999987  78999999987

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=81.63  E-value=0.6  Score=32.82  Aligned_cols=43  Identities=26%  Similarity=0.455  Sum_probs=21.1

Q ss_pred             cccccccccCcccE-EeCCCChhccHhhH---HhhcCC-CCCCcccccc
Q psy3263         254 RQCYLCNDREVTHA-LIPCGHNFFCSECA---ERTCDF-DRTCPMCRVP  297 (329)
Q Consensus       254 ~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl---~~~~~~-~~~CP~Cr~~  297 (329)
                      +.|++.+.....|+ ...|.|. -|++=.   ....+. ...||+|.++
T Consensus         3 L~CPls~~~i~~P~Rg~~C~H~-~CFDl~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRGKNCKHL-QCFDLESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSEEEETT--SS---EEHHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeCccCCcCccc-ceECHHHHHHHhhccCCeECcCCcCc
Confidence            67999999999998 5699998 554331   111112 6789999864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=81.14  E-value=2.5  Score=44.88  Aligned_cols=36  Identities=33%  Similarity=0.374  Sum_probs=31.9

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      .|-+|.|-.+.-|+||||+|+|+++|.++||=.-++
T Consensus        93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~  128 (630)
T TIGR03675        93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKV  128 (630)
T ss_pred             CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeE
Confidence            456788889999999999999999999999987666

This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.

>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein

Probab=80.45  E-value=1.8  Score=33.59  Aligned_cols=29  Identities=17%  Similarity=0.397  Sum_probs=22.9

Q ss_pred             EEEEecCcccceeecCCCchHHHHHHhcC
Q psy3263          88 IEVRVPYKVVGLVVGPKGATIKRIQHQTN  116 (329)
Q Consensus        88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tg  116 (329)
                      +++.|-...-|.+||++|++|+++++.-.
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~   68 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEILE   68 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence            45555557789999999999999987753

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG1067|consensus

Probab=80.22  E-value=1.8  Score=44.93  Aligned_cols=51  Identities=20%  Similarity=0.232  Sum_probs=40.6

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ...++.|+......+||++|-..|+|+.+||+.-.    -++..|+|-.+++..+
T Consensus       597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~----vDe~t~~i~A~~~~am  647 (760)
T KOG1067|consen  597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQ----VDEGTFSIFAPTQAAM  647 (760)
T ss_pred             eeeEEeecchhhheeecCccceeeeEeeeccceee----ecCceEEEEecCHHHH
Confidence            67789999999999999999999999999994322    2566788888444444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	329
2dgr_A	83	Solution Structure Of The Second Kh Domain In Ring		2e-17
3t6p_A	345	Iap Antagonist-Induced Conformational Change In Cia		2e-05
4auq_B	62	Structure Of Birc7-Ubch5b-Ub Complex. Length = 62		4e-05
3eb5_A	74	Structure Of The Ciap2 Ring Domain Length = 74		1e-04
4ic3_A	74	Crystal Structure Of The F495l Mutant Xiap Ring Dom		4e-04
2ecg_A	75	Solution Structure Of The Ring Domain Of The Baculo		6e-04
4ic2_A	74	Crystal Structure Of The Xiap Ring Domain Length =		7e-04

>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger And Kh Domain Containing Protein 1 Length = 83

Iteration: 1
 Score = 86.7 bits (213), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 43/54 (79%), Positives = 47/54 (87%), Gaps = 1/54 (1%)
Query: 85  HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPE 138
             TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF VTG  PE
Sbjct: 9   QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTG-MPE 61

>pdb|3T6P|A Chain A, Iap Antagonist-Induced Conformational Change In Ciap1 Promotes E3 Ligase Activation Via Dimerization Length = 345

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN 307
           R C +C D+EV+   IPCGH   C ECA       R CP+CR  +   +R   +
Sbjct: 296 RTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGTVRTFLS 345

>pdb|4AUQ|B Chain B, Structure Of Birc7-Ubch5b-Ub Complex. Length = 62

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN 307
           R C +C DR V+   +PCGH   C+ECA       + CP+CR PV   +R   +
Sbjct: 14  RTCKVCLDRAVSIVFVPCGH-LVCAECAPGL----QLCPICRAPVRSRVRTFLS 62

>pdb|3EB5|A Chain A, Structure Of The Ciap2 Ring Domain Length = 74

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN 307
           R C +C D+EV+   IPCGH   C +CA       R CP+CR  +   +R   +
Sbjct: 25  RTCKVCMDKEVSIVFIPCGHLVVCKDCAPSL----RKCPICRSTIKGTVRTFLS 74

>pdb|4IC3|A Chain A, Crystal Structure Of The F495l Mutant Xiap Ring Domain Length = 74

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN 307
           C +C DR +    +PCGH   C +CAE        CPMC   +    +I+ +
Sbjct: 27  CKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKILMS 74

>pdb|2ECG|A Chain A, Solution Structure Of The Ring Domain Of The Baculoviral Iap Repeat-Containing Protein 4 From Homo Sapiens Length = 75

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN 307
           C +C DR +    +PCGH   C +CAE        CPMC   +    +I  +
Sbjct: 28  CKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKIFMS 75

>pdb|4IC2|A Chain A, Crystal Structure Of The Xiap Ring Domain Length = 74

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN 307
           C +C DR +    +PCGH   C +CAE        CPMC   +    +I  +
Sbjct: 27  CKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKIFMS 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	329
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	6e-25
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-12
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-23
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-21
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-07
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-04
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-19
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	8e-09
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-19
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-13
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	5e-07
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	5e-13
2ea5_A	68	Cell growth regulator with ring finger domain prot	3e-12
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-12
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-08
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	5e-12
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	6e-12
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	8e-04
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-12
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-11
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	5e-07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	5e-11
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-08
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	8e-11
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	1e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	8e-04
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	3e-10
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-09
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-05
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	6e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	6e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-08
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-08
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-07
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	1e-07
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-07
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	4e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	4e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	5e-05
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	7e-07
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	7e-07
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	8e-07
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-06
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-06
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	2e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-06
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	2e-05
1we8_A	104	Tudor and KH domain containing protein; structural	2e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	2e-05
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	4e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	5e-05
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	6e-05
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	7e-05
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	8e-05
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	1e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	1e-04
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	2e-04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	3e-04
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	4e-04
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	5e-04
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	5e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	6e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	8e-04

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 95.4 bits (237), Expect = 6e-25
 Identities = 42/57 (73%), Positives = 46/57 (80%)

Query: 78  PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG 134
                 G  TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF VTG
Sbjct: 2   SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTG 58

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 61.5 bits (149), Expect = 1e-12
 Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 4/63 (6%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 68
          + P G  IK ++ +T+TYI TP R +EPVF VTG  E+V RA+ EI    +    LR+  
Sbjct: 25 VGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEI----EAHITLRSGP 80

Query: 69 KSG 71
           SG
Sbjct: 81 SSG 83

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 93.0 bits (231), Expect = 5e-23
 Identities = 26/134 (19%), Positives = 45/134 (33%), Gaps = 11/134 (8%)

Query: 13  GCKIKALRAKTNTYIK------TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRA 66
           G  I  L+ +T   IK            E V ++ G  E +      I           A
Sbjct: 25  GQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNVA 84

Query: 67  SRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 126
             +  ++              +++ VP    GL++G  GAT+K I  Q+  ++    +  
Sbjct: 85  KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD 144

Query: 127 EP-----VFEVTGN 135
                  V  V+G 
Sbjct: 145 GINLQNRVVTVSGE 158

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 53.7 bits (129), Expect = 6e-09
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 6/60 (10%)

Query: 82  VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGN 135
           +     ++V +P    G ++G  G TI ++Q +T   I ++ S+D  P     V  + G 
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 88.7 bits (220), Expect = 1e-21
 Identities = 26/131 (19%), Positives = 41/131 (31%), Gaps = 16/131 (12%)

Query: 13  GCKIKALRAKTNTYIKTPVRGEEP-----VFVVTGRKEDVARAKREILSAADHFSALRAS 67
           G  IK L+ +    +     G +         + G    V +A   ++            
Sbjct: 21  GETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ---- 76

Query: 68  RKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-- 125
                        G      I+V VP   VG+V+G  G  IK+IQ+     I     D  
Sbjct: 77  ----GGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT 132

Query: 126 -KEPVFEVTGN 135
             E +  + G 
Sbjct: 133 GPEKIAHIMGP 143

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 49.4 bits (118), Expect = 2e-07
 Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 5/54 (9%)

Query: 87  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-----VFEVTGN 135
             E+ +P    GLV+G  G TIK++Q +    ++      +         + G+
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD 56

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 3/46 (6%)

Query: 13  GCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREIL 55
           G  IK ++      I+       G E +  + G  +    A R I 
Sbjct: 110 GEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIIN 155

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 82.9 bits (205), Expect = 2e-19
 Identities = 22/128 (17%), Positives = 42/128 (32%), Gaps = 14/128 (10%)

Query: 13  GCKIKALRAKTNTYIK-TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSG 71
           G  +K +R ++   I  +     E +  + G    + +A   I+             +  
Sbjct: 24  GESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKL---------EEDI 74

Query: 72  ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK----E 127
           + S  +        VT+ + VP    G ++G  G  IK I+  T   +           E
Sbjct: 75  SSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTE 134

Query: 128 PVFEVTGN 135
               + G 
Sbjct: 135 RAITIAGI 142

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 52.9 bits (127), Expect = 8e-09
 Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGN 135
           +TI + +  K VG ++G KG ++K+++ ++   I ++     E +  + G 
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGP 55

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 83.0 bits (205), Expect = 2e-19
 Identities = 29/138 (21%), Positives = 41/138 (29%), Gaps = 15/138 (10%)

Query: 13  GCKIKALRAKTNTYIK-TPVRGEEP--VFVVTGRKEDVARAKREILS------AADHFSA 63
           G  IK ++      I+  P  G  P  +  +TG  +    A   I        A +    
Sbjct: 22  GEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPGGP 81

Query: 64  LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123
               R  G            G       VP    GL++G  G TIK I  Q+   I    
Sbjct: 82  GPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQR 141

Query: 124 R------DKEPVFEVTGN 135
                      +F + G 
Sbjct: 142 NPPPNADPNMKLFTIRGT 159

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 52.6 bits (126), Expect = 2e-08
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 84  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGN 135
           G   I+V +P   VG+V+G  G  IK+IQ+     I   P     P  + ++TG 
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP 55

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 66.3 bits (162), Expect = 2e-13
 Identities = 31/134 (23%), Positives = 50/134 (37%), Gaps = 25/134 (18%)

Query: 13  GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRAS 67
           G  IK L    +  IK     TP      V ++TG  E   +A+  I         L+  
Sbjct: 22  GQHIKQLSRFASASIKIAPPETPDSKVRMV-IITGPPEAQFKAQGRIYGK------LKEE 74

Query: 68  RKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TP 122
              G              +   +RVP    G V+G  G T+  +Q+ T   +V     TP
Sbjct: 75  NFFGP--------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTP 126

Query: 123 SRDKEPVFEVTGNF 136
             + + + ++ G+F
Sbjct: 127 DENDQVIVKIIGHF 140

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 47.8 bits (114), Expect = 5e-07
 Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 85  HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD---KEPVFEVTGN 135
              ++V +P + VG ++G KG  IK++    +  I + P      K  +  +TG 
Sbjct: 2   QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP 56

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A Length = 79

 Score = 62.9 bits (153), Expect = 5e-13
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 304
           +  C +C + E+     PCGH   C  CA +     ++CP+CR  V     +
Sbjct: 18  AMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHVQHV 65

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 68

 Score = 60.2 bits (146), Expect = 3e-12
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 242 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 301
            S+    S   S+ C +C +  V   L+PC H   C  C +      + CPMCR  V ++
Sbjct: 4   GSSGVEPSEENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYF----QQCPMCRQFVQES 59

Query: 302 MRI 304
             +
Sbjct: 60  FAL 62

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 60.5 bits (147), Expect = 4e-12
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGNFPEG 139
            +  V +P +    V+G  G  ++ ++ +T T I  P   D     ++TG   EG
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT-KEG 70

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGEEPVFV-VTGRKEDVARAKREILSAADHFSALRAS 67
          I   G K++ L  KT T I+ P   +    + +TG KE + +A+ E+L  +      R+ 
Sbjct: 32 IGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQDK-RSG 90

Query: 68 RKSG 71
            SG
Sbjct: 91 PSSG 94

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 59.8 bits (145), Expect = 5e-12
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 304
            + C +C DR +    +PCGH   C +CAE        CPMC   +    +I
Sbjct: 25  EKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKI 72

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 60.1 bits (146), Expect = 6e-12
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 77  SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 131
               G       E+ +P    GLV+G  G TIK++Q +    ++     + + + +    
Sbjct: 5   DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR 64

Query: 132 VTGNF 136
           + G+ 
Sbjct: 65  IIGDP 69

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 7/49 (14%), Positives = 16/49 (32%), Gaps = 5/49 (10%)

Query: 13 GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILS 56
          G  IK L+ +    +      +     +    + G    V +A   ++ 
Sbjct: 33 GETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMD 81

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 59.7 bits (145), Expect = 7e-12
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 5/64 (7%)

Query: 77  SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 131
           S     PG+   E+ +P    GLV+G  G TIK++Q +    +V       +   +    
Sbjct: 6   SGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR 65

Query: 132 VTGN 135
           +TG+
Sbjct: 66  ITGD 69

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 5/48 (10%)

Query: 13 GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREIL 55
          G  IK L+ +    +          G +    +TG    V +AK  +L
Sbjct: 34 GETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVL 81

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 58.7 bits (142), Expect = 2e-11
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-VFEVTG 134
           VTIEV VP+ +   V+G KG+ I+++  +    I  P+ + +  +  +TG
Sbjct: 17  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITG 66

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREILSAADHFSALRAS 67
          I   G  I+ +  +    I  P    +  +  +TG   ++ RAK  +L       A +  
Sbjct: 32 IGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQAEQED 91

Query: 68 RK 69
          R 
Sbjct: 92 RA 93

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 57.5 bits (139), Expect = 5e-11
 Identities = 11/48 (22%), Positives = 22/48 (45%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT 133
           V+ +V + ++V   ++G +G  I++I  +    I  P         VT
Sbjct: 17  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVT 64

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGEEP--VFVVTGRKEDVARAKREILSAADHF 61
          I   G  I+ +  +    I+ P  G        VTG  E+V  A   IL+  + +
Sbjct: 32 IGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY 86

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B* Length = 63

 Score = 56.0 bits (135), Expect = 8e-11
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 254 RQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF 306
           + C LC  R     +I    GH   C  CA R      +CP+C+  +   +++  
Sbjct: 8   KPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVFI 62

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A Length = 345

 Score = 61.1 bits (146), Expect = 1e-10
 Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 4/52 (7%)

Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF 306
            C +C D+EV+   IPCGH   C ECA       R CP+CR  +   +R   
Sbjct: 297 TCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGTVRTFL 344

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 77  SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVT 133
           +  TG      I+V VP   VG+V+G  G  IK+IQ+     I         P  +  + 
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61

Query: 134 GNF 136
           G  
Sbjct: 62  GPP 64

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 37.5 bits (87), Expect = 8e-04
 Identities = 13/75 (17%), Positives = 20/75 (26%), Gaps = 3/75 (4%)

Query: 13  GCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK 69
           G  IK ++      I+       G E +  + G  +    A R I        +      
Sbjct: 30  GEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGPPGPP 89

Query: 70  SGALSPLSPPTGVPG 84
            G   P        G
Sbjct: 90  GGPGMPPGGRGRGRG 104

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A Length = 64

 Score = 54.4 bits (131), Expect = 3e-10
 Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 247 SGSISGSRQCYLCNDREVTHALIP--CGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 304
           S  ++    C +C  R     ++    GH   C  CA++    ++ CP+CR P+   +  
Sbjct: 2   SLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLT 61

Query: 305 IF 306
            F
Sbjct: 62  YF 63

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 53.1 bits (128), Expect = 1e-09
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGNFPEG 139
             +E+ + +K    ++G  GA I RI+ Q    +  P   +K  +  + G+ P+G
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGD-PQG 58

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 56
          I   G  I  ++ +    ++ P   E   +  + G  + V +AKRE+L 
Sbjct: 20 IGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLE 68

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 51.7 bits (124), Expect = 6e-09
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 74  SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VF 130
           S  S        +T E +VP  +VG ++G  G  I RIQ ++   I + P     P    
Sbjct: 3   SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62

Query: 131 EVTGN 135
            +TG 
Sbjct: 63  MLTGT 67

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 51.7 bits (124), Expect = 6e-09
 Identities = 12/46 (26%), Positives = 21/46 (45%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE 131
             + V V  K    ++G KGA I +I+ + +  I  P +D     +
Sbjct: 17  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQ 62

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 4/48 (8%)

Query: 13 GCKIKALRAKTNTYIKTPVRGEEP----VFVVTGRKEDVARAKREILS 56
          G  I  +R + +  I+ P + +         +TG +++   A+  IL 
Sbjct: 36 GAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILR 83

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389

 Score = 54.4 bits (130), Expect = 2e-08
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRIIFNQF 309
           S  + C +C + +    + PCGH   C+ C     + + + CP CR  +     I+ + F
Sbjct: 330 STFQLCKICAENDKDVKIEPCGHLM-CTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPF 388

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 242 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 299
            S+  +       +C +C    V    +PC H F C  C +      + C +CR  + 
Sbjct: 4   GSSGNTAPSLTVPECAICLQTCVHPVSLPCKHVF-CYLCVKGASWLGKRCALCRQEIP 60

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 51.6 bits (123), Expect = 3e-08
 Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKL 314
           QC +C++  +    + C H+F CS C          CP+CR  +      +       K+
Sbjct: 66  QCIICSEYFIEAVTLNCAHSF-CSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKM 124

Query: 315 WE 316
             
Sbjct: 125 VN 126

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 12/52 (23%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 84  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTG 134
             +TI + +  K VG ++G KG ++K+++ ++   I ++     E +  + G
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAG 54

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 47.5 bits (113), Expect = 1e-07
 Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 1/45 (2%)

Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 299
           +C++C        +  C H F C  CA         C +C  P  
Sbjct: 17  RCFICRQAFQNPVVTKCRHYF-CESCALEHFRATPRCYICDQPTG 60

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 2/47 (4%)

Query: 255 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
            C +C         +  C H F C  C  R   +   CP C + V+Q
Sbjct: 17  LCSICKGYLIDATTITECLHTF-CKSCIVRHFYYSNRCPKCNIVVHQ 62

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 6/56 (10%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGN 135
             +E+ VP  +VG ++G  G T+   Q  T   I ++   +  P        +TG+
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 46.8 bits (111), Expect = 2e-07
 Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 8/66 (12%)

Query: 242 SSTSPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMC 294
            S+      SG+  C +C D                CGH F CS+C   +     TCP C
Sbjct: 4   GSSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTC 62

Query: 295 RVPVNQ 300
           R  +N 
Sbjct: 63  RKKINH 68

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 46.6 bits (111), Expect = 3e-07
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 6/56 (10%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGN 135
             +E+ VP  +VG ++G  G T+   Q  T   I ++   +  P        +TG+
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 6/49 (12%)

Query: 255 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
            C LC        T  +I C H+F C  C  R  +  + CP+C V V++
Sbjct: 17  MCVLCGGYFIDATT--IIECLHSF-CKTCIVRYLETSKYCPICDVQVHK 62

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 8/43 (18%), Positives = 16/43 (37%)

Query: 87  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPV 129
             +  V   ++GL +G  GA I++ +       +    D    
Sbjct: 5   HEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTF 47

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 41.9 bits (98), Expect = 5e-05
 Identities = 23/131 (17%), Positives = 39/131 (29%), Gaps = 35/131 (26%)

Query: 4   FVVPS------INPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSA 57
           F+V        I   G  I+  R          +  +   F + G  +D  +  R  L  
Sbjct: 8   FIVREDLMGLAIGTHGANIQQARKVPGV-TAIDLDEDTCTFHIYGEDQDAVKKARSFLEF 66

Query: 58  ADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT 117
           A+                              ++VP  +VG V+G  G  I+ I  ++  
Sbjct: 67  AEDV----------------------------IQVPRNLVGKVIGKNGKLIQEIVDKSGV 98

Query: 118 YIVTPSRDKEP 128
             V    + E 
Sbjct: 99  VRVRIEAENEK 109

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 45.1 bits (107), Expect = 7e-07
 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 251 SGSRQCYLC-NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQF 309
           + + +C +C  D       +PC H F C  C  R    + TCP+C+VPV   +  I +  
Sbjct: 3   TVAERCPICLEDPSNYSMALPCLHAF-CYVCITRWIRQNPTCPLCKVPVESVVHTIESDS 61

Query: 310 LFGK 313
            FG 
Sbjct: 62  EFGD 65

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 45.4 bits (108), Expect = 7e-07
 Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 81  GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGNF 136
            +   +T +V +P  + G ++G  G  IK+I+H++   I +    +  ++ +  +TG  
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71

 Score = 45.2 bits (107), Expect = 8e-07
 Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 245 SPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297
           +     SG+  C +C D                CGH F CS+C   +     TCP CR  
Sbjct: 2   TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTCRKK 60

Query: 298 VNQ 300
           +N 
Sbjct: 61  INH 63

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 82  VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGN 135
           +    T E+ +P  ++G ++G +GA I  I+  +   I +    +        +TG+
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS 58

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGNF 136
           +T +V +P  + G ++G  G  IK+I+H++   I +    +  ++ +  +TG  
Sbjct: 14  ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGN 135
            + E+ +P  ++G ++G +GA I  I+  +   I +    +        +TG+
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS 57

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 255 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFL 310
           +C +C +   +   +  C HN+ CS C  +   +   CP C V V +   +  N+ L
Sbjct: 24  RCGICFEYFNIAMIIPQCSHNY-CSLCIRKFLSYKTQCPTCCVTVTEP-DLKNNRIL 78

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 8/60 (13%)

Query: 84  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-------VFEVTGNF 136
               +   +P    GLV+G  G  +K I  QT  ++   SR   P       +F + G+ 
Sbjct: 5   PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFV-EISRQLPPNGDPNFKLFIIRGSP 63

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 2/37 (5%)

Query: 269 IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRI 304
           +PC H   C  C + T +     CP CR  V+   R 
Sbjct: 31  LPCNHTL-CKPCFQSTVEKASLCCPFCRRRVSSWTRY 66

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 4/44 (9%)

Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
           +C  C        L+PC H   CS C E +      CP+C+ P 
Sbjct: 8   RCQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPW 47

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 12/75 (16%)

Query: 66  ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-----V 120
           +S  SG L+  +P       V  ++ VP + VG ++G  G TI+ I   +   I      
Sbjct: 2   SSGSSGILTENTP-------VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES 54

Query: 121 TPSRDKEPVFEVTGN 135
             +     + +++G 
Sbjct: 55  EGTLLLSRLIKISGT 69

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 28/138 (20%), Positives = 43/138 (31%), Gaps = 8/138 (5%)

Query: 177 GSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIW 236
           GSS      SS      +P +S           + +             D          
Sbjct: 2   GSSHHHHHHSSGLVPRGSPSASKVYKASDSAEAIEAFQLTPQQQHLIREDCQNQKLWDEV 61

Query: 237 SYPPVSSTSPSGSISGSRQCYLCND---REVTHALIPCGHNFFCSECAERTCDFD-RTCP 292
               V   +    +  S  C  C +   + VT     C HN  C +C +R+      +CP
Sbjct: 62  LSHLVEGPNFLKKLEQSFMCVCCQELVYQPVT---TECFHN-VCKDCLQRSFKAQVFSCP 117

Query: 293 MCRVPVNQAMRIIFNQFL 310
            CR  + Q   +I N+ L
Sbjct: 118 ACRHDLGQNYIMIPNEIL 135

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 10/48 (20%), Positives = 19/48 (39%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT 133
             +EV +P K+   ++G KG  I+ I  +     +    +      V 
Sbjct: 17  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVV 64

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 9/77 (11%)

Query: 240 PVSSTSPSGSISGSR---QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDR---TCPM 293
           P S +     +S      QC  C +         C HN  C +C +R+  F     +CP 
Sbjct: 36  PASGSPFQLFLSKVEETFQCICCQELVFRPITTVCQHNV-CKDCLDRS--FRAQVFSCPA 92

Query: 294 CRVPVNQAMRIIFNQFL 310
           CR  + ++  +  NQ L
Sbjct: 93  CRYDLGRSYAMQVNQPL 109

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64

 Score = 39.4 bits (92), Expect = 6e-05
 Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)

Query: 270 PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
            CGH F CS+C   +     TCP CR  +N 
Sbjct: 27  ECGHVF-CSQCLRDSLKNANTCPTCRKKINH 56

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 131

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 81  GVPGHVTIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG 134
            +   V+ +V +P         VGL++GP+G T+K I+ + N  I+   R K  V E   
Sbjct: 2   AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMI--RGKGSVKEGKV 59

Query: 135 NFPEGPGFESHHGQKIVFI 153
              +G             +
Sbjct: 60  GRKDGQMLPGEDEPLHALV 78

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 40.3 bits (94), Expect = 8e-05
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 255 QCYLCNDREVTHALIP-CGHNFFCSECAER-TCDFDRTCPMCRVPVNQAMRIIFNQFL 310
           +C++C ++     L P C     C  C  R   +    CP CR P+     ++  ++ 
Sbjct: 24  RCFICMEKLRDARLCPHCSKLC-CFSCIRRWLTEQRAQCPHCRAPLQLRE-LVNCRWA 79

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
           +C +C D      L PC H  FC +C ++  D  R CP+CR+ +
Sbjct: 17  ECCICMDGRADLIL-PCAH-SFCQKCIDKWSDRHRNCPICRLQM 58

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 41.6 bits (97), Expect = 1e-04
 Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 3/119 (2%)

Query: 9   INPFGCKIKALRAKTNTYIK-TPVRGEEPVFVV--TGRKEDVARAKREILSAADHFSALR 65
           I   G   K +  +T T I      GE  +     T     V +A+  +L+    FS  R
Sbjct: 49  IGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPER 108

Query: 66  ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 124
           A R       L         +  E     +V G ++G KG T + I+  +   +    +
Sbjct: 109 AFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGK 167

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)

Query: 269 IPCGHNFFCSECAERTCDFDRT---CPMCRVPVNQ 300
           I CGHN FC +C  +  +       CP+C+  V +
Sbjct: 36  IDCGHN-FCLKCITQIGETSCGFFKCPLCKTSVRK 69

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 112

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 4/35 (11%)

Query: 269 IPCGHNFFCSECAERTCDFDR---TCPMCRVPVNQ 300
             C H  FC  C  +  +  +    CP+C+  + +
Sbjct: 37  TKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDITK 70

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 8/39 (20%)

Query: 269 IPCGHNFFCSECAERTCDFDRT-------CPMCRVPVNQ 300
           + CGH+  C  C   +     T       CP+C +  + 
Sbjct: 28  LDCGHS-LCRACITVSNKEAVTSMGGKSSCPVCGISYSF 65

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 7/38 (18%)

Query: 269 IPCGHNFFCSECAERTCDFDRT------CPMCRVPVNQ 300
             C H+ FC  C     + +R       CP+CRVP   
Sbjct: 35  ADCNHS-FCRACITLNYESNRNTDGKGNCPVCRVPYPF 71

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 117

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 8/47 (17%)

Query: 255 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
           +C  C +     V   L  C H F CS C          CP+C  P 
Sbjct: 24  RCSRCTNILREPVC--LGGCEHIF-CSNCVSDC--IGTGCPVCYTPA 65

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 7/38 (18%)

Query: 269 IPCGHNFFCSECAERTCD------FDRTCPMCRVPVNQ 300
           + CGH+ FC  C             + +CP+CR+    
Sbjct: 35  LDCGHS-FCQACLTANHKKSMLDKGESSCPVCRISYQP 71

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B Length = 165

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 5/59 (8%)

Query: 255 QCYLCND--REVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRIIFNQFL 310
            C +C D  +  T     C H F C++C         + CP CR  +     +  +   
Sbjct: 56  MCPICLDMLKN-TMTTKECLHRF-CADCIITALRSGNKECPTCRKKLVSKRSLRPDPNF 112

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 37.0 bits (86), Expect = 8e-04
 Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 4/35 (11%)

Query: 268 LIPCGHNFFCSECAERTCDFDR---TCPMCRVPVN 299
           L+ CGH   C +C E+          CP C     
Sbjct: 34  LLHCGHT-ICRQCLEKLLASSINGVRCPFCSKITR 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	329
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.9
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.9
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.9
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.89
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.89
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.74
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.71
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.62
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.6
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.48
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.46
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.36
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.33
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.32
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.31
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.31
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.31
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.3
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.3
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.29
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.29
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.29
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.29
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.28
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.28
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.28
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.28
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.27
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.27
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.27
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.27
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.26
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.26
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.25
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.25
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.25
1we8_A	104	Tudor and KH domain containing protein; structural	99.25
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.25
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.24
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.24
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.23
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.23
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.23
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.22
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.22
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.22
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.21
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.21
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.2
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.19
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.18
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.18
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.18
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.17
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.17
1we8_A	104	Tudor and KH domain containing protein; structural	99.16
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.15
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.15
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.13
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.13
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.13
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.12
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.11
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.11
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.09
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.09
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.08
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.08
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.08
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.07
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.07
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.04
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.04
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.03
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.02
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.02
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.02
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.01
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.01
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.01
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.0
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.0
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.99
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	98.98
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.98
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	98.97
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.96
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.96
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.95
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.95
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.95
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.94
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.94
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	98.92
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.92
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.91
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.9
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.87
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.85
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.84
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.84
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.83
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.83
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.82
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.79
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.78
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.78
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.77
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.76
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.75
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.74
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.73
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.7
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.69
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.68
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.65
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.59
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.58
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.58
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.56
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.52
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.51
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.5
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.45
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.39
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.23
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.23
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.18
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.16
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.14
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.04
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	97.97
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.87
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.82
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.67
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.66
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	97.39
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.21
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.83
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.73
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	96.62
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.55
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.45
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	95.64
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.63
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.94
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.52
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.07
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	92.47
3nw0_A	238	Non-structural maintenance of chromosomes element	91.46
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	90.57
2cxc_A	144	NUSA; transcription termination, RNA binding prote	89.51
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	83.46

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.90  E-value=5e-25  Score=193.26  Aligned_cols=144  Identities=24%  Similarity=0.275  Sum_probs=108.5

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC------CcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS   77 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~------~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~   77 (329)
                      +||.||||+|++||+||++|||+|+++..+      .+|+|+|+|.+++|++|+.+|.+++..+....+... . .....
T Consensus        16 ~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~~-~-~~~~~   93 (178)
T 2anr_A           16 AAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNVAKTE-P-VSILQ   93 (178)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCCC-------------
T ss_pred             HeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCCccccCC-c-ccccC
Confidence            579999999999999999999999998643      378999999999999999999998642211000000 0 00000


Q ss_pred             C--CCCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-----CCCeEEEECCCCCCcch-hhhhhhh
Q psy3263          78 P--PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGNFPEGPGF-ESHHGQK  149 (329)
Q Consensus        78 ~--p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-----~e~~i~ItG~~pe~vei-e~~i~d~  149 (329)
                      +  ..+.....+.++.||.+++|.||||+|++||+|+++|||+|++++.+     .++.|+|+| .+++|+. ..+|.+.
T Consensus        94 ~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~  172 (178)
T 2anr_A           94 PQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSG-EPEQNRKAVELIIQK  172 (178)
T ss_dssp             ------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEES-SHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHH
Confidence            0  00123457899999999999999999999999999999999998764     468999999 9998833 3366554


Q ss_pred             h
Q psy3263         150 I  150 (329)
Q Consensus       150 ~  150 (329)
                      +
T Consensus       173 i  173 (178)
T 2anr_A          173 I  173 (178)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=99.90  E-value=2.5e-24  Score=186.15  Aligned_cols=133  Identities=20%  Similarity=0.262  Sum_probs=108.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC----CcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPP   79 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~----~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p   79 (329)
                      +||.||||+|++||+||++|||+|+++..+    .+|+|+|+|+++++.+|+.+|++++.      +....       .|
T Consensus        13 ~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~------e~~~~-------~~   79 (163)
T 3krm_A           13 AVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLK------EENFF-------GP   79 (163)
T ss_dssp             GHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHH------HTTSS-------CS
T ss_pred             hcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh------ccccc-------cc
Confidence            579999999999999999999999998643    48999999999999999999998753      11000       01


Q ss_pred             CCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----C-CCeEEEECCCCCCcchh-hhhhhhhh
Q psy3263          80 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----K-EPVFEVTGNFPEGPGFE-SHHGQKIV  151 (329)
Q Consensus        80 ~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~-e~~i~ItG~~pe~veie-~~i~d~~~  151 (329)
                       ......+.++.||.+++|.||||+|++||+|+++|||+|.++.+.    + ++.|+|+| .+++|+.+ .+|.+++.
T Consensus        80 -~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~  155 (163)
T 3krm_A           80 -KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIG-HFYASQMAQRKIRDILA  155 (163)
T ss_dssp             -SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             -ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHHH
Confidence             223457889999999999999999999999999999999998653    2 33799999 99999333 36666554

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=99.90  E-value=3.2e-24  Score=185.12  Aligned_cols=139  Identities=20%  Similarity=0.195  Sum_probs=108.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC-----CcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSP   78 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-----~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~   78 (329)
                      +||.||||+|++||+||++|||+|+++.++     .+++|+|+|.+++|.+|+.+|.++++.      ....  +.....
T Consensus        12 ~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e------~~~~--~~~~~~   83 (164)
T 2jvz_A           12 KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE------RDQG--GFGDRN   83 (164)
T ss_dssp             CHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTC------SSSC--CCSSCS
T ss_pred             heeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh------ccCC--CCCCcc
Confidence            589999999999999999999999997543     378999999999999999999998541      1100  000000


Q ss_pred             CCCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263          79 PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGFES-HHGQKIV  151 (329)
Q Consensus        79 p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~veie~-~i~d~~~  151 (329)
                      ........+.++.||.+++|.||||+|++||+|+++|||+|.+++.+   .++.|+|+| .+++|+.+. +|.+++.
T Consensus        84 ~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~  159 (164)
T 2jvz_A           84 EYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG-PPDRCEHAARIINDLLQ  159 (164)
T ss_dssp             SCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEES-CHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEc-CHHHHHHHHHHHHHHHh
Confidence            00112235688999999999999999999999999999999998755   368899999 899994333 6665543

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=99.89  E-value=2.6e-24  Score=185.47  Aligned_cols=137  Identities=18%  Similarity=0.228  Sum_probs=108.5

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC-CcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   82 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~   82 (329)
                      ++|.||||+|++||+||++|||+|+++..+ .+|+|+|+|++++|.+|+.+|.++++..  ....  ..+.    . ...
T Consensus        15 ~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~--~~~~--~~~~----~-~~~   85 (160)
T 2jzx_A           15 EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEED--ISSS--MTNS----T-AAS   85 (160)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCSEEEEECCTTTEEEEEEEEEHHHHHHHHHHHHHHHHHH--HTSC--CCSS----S-CCC
T ss_pred             heeeeECCCcHHHHHHHHHHCCEEEEcCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhh--cccc--CCCC----c-cCC
Confidence            479999999999999999999999999654 4789999999999999999999875421  1100  0000    0 011


Q ss_pred             CCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----CCCeEEEECCCCCCcchh-hhhhhhh
Q psy3263          83 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNFPEGPGFE-SHHGQKI  150 (329)
Q Consensus        83 ~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~e~~i~ItG~~pe~veie-~~i~d~~  150 (329)
                      ....+.++.||.+++|.||||||++||+|+++|||+|+++++.    +++.|+|+| .+++|+.+ .+|.+++
T Consensus        86 ~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i  157 (160)
T 2jzx_A           86 RPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAG-IPQSIIECVKQICVVM  157 (160)
T ss_dssp             CCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Confidence            2247899999999999999999999999999999999998632    678999999 99999333 3555544

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=99.89  E-value=5.4e-24  Score=186.14  Aligned_cols=145  Identities=20%  Similarity=0.189  Sum_probs=105.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC---CcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCC--C-CCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGAL--S-PLS   77 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~---~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~--~-~~~   77 (329)
                      +||.||||+|++||+||++|||+|+++...   .+|+|+|+|++++|++|+.+|.++++.+..-........+  . ...
T Consensus        13 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~~~p~~~~~~~~~   92 (174)
T 1j4w_A           13 AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQ   92 (174)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC------------------
T ss_pred             heeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCCCC
Confidence            579999999999999999999999997432   3789999999999999999999986533210000000000  0 000


Q ss_pred             ---CCCCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC------CCCCeEEEECCCCCCcchhh-hhh
Q psy3263          78 ---PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGNFPEGPGFES-HHG  147 (329)
Q Consensus        78 ---~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~------~~e~~i~ItG~~pe~veie~-~i~  147 (329)
                         ......+..+.++.||.+++|.||||+|++||+|+++|||+|+++++      ..++.|+|+| ++++|+.+. +|.
T Consensus        93 ~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~  171 (174)
T 1j4w_A           93 GNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQIDYARQLIE  171 (174)
T ss_dssp             -----------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEEC-CHHHHHHHHHHHH
T ss_pred             CccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEEC-CHHHHHHHHHHHH
Confidence               00011234688999999999999999999999999999999999865      2568899999 999994433 655


Q ss_pred             hh
Q psy3263         148 QK  149 (329)
Q Consensus       148 d~  149 (329)
                      ++
T Consensus       172 ~~  173 (174)
T 1j4w_A          172 EK  173 (174)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.74  E-value=5.2e-19  Score=171.22  Aligned_cols=149  Identities=17%  Similarity=0.170  Sum_probs=109.3

Q ss_pred             eeeeeecCCC--hHHHHHHHHhCCeEEecCCC--------CcceEEEecCHHHHHHHHHHHHHHh---------------
Q psy3263           4 FVVPSINPFG--CKIKALRAKTNTYIKTPVRG--------EEPVFVVTGRKEDVARAKREILSAA---------------   58 (329)
Q Consensus         4 ~VG~IIGkgG--~~Ik~Lr~~Tga~I~ip~~~--------~ervi~ItG~~e~v~~A~~~I~~i~---------------   58 (329)
                      ||+.||||||  ++|++|+++|||+|++|.++        ....|+|+|.+++|++|+.+|.+++               
T Consensus        40 ~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~Pl~i~~elp~~~i~~  119 (376)
T 3n89_A           40 YYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCHFTVFMALSKMKMPL  119 (376)
T ss_dssp             GHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCEEEEEEECTTCSSCH
T ss_pred             hhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCCceEEEEccccccCc
Confidence            6789999999  99999999999999999655        1467999999999999999998741               


Q ss_pred             -hhhhHhhhcccCCCCCCC-------------------CCCC---------------------CCCCceEEEEEecCccc
Q psy3263          59 -DHFSALRASRKSGALSPL-------------------SPPT---------------------GVPGHVTIEVRVPYKVV   97 (329)
Q Consensus        59 -e~~~~~~~~~~~~~~~~~-------------------~~p~---------------------~~~g~~t~~i~VP~~~v   97 (329)
                       +....+..  ....++..                   |+..                     ......+.++.|+..+|
T Consensus       120 ~~l~~~I~q--q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e~~~~~~~s~~v~V~~~~H  197 (376)
T 3n89_A          120 HELQAHVRQ--NPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLSTYYV  197 (376)
T ss_dssp             HHHHHHHHH--CCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--CCCSSCEEEEEEEEGGGH
T ss_pred             chhhhhhcc--ceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhhcccccceEEEEEeCHHHH
Confidence             11112221  11111110                   1100                     01124688999999999


Q ss_pred             ceeecCCC--chHHHHHHhcCceEEcCCCCC-------CCeEEEECCCCCCc-chhhhhhhhhh--hhhc
Q psy3263          98 GLVVGPKG--ATIKRIQHQTNTYIVTPSRDK-------EPVFEVTGNFPEGP-GFESHHGQKIV--FILT  155 (329)
Q Consensus        98 G~IIGkgG--~tIk~Iq~~tga~I~ip~~~~-------e~~i~ItG~~pe~v-eie~~i~d~~~--~~~~  155 (329)
                      ..|||++|  ..|++|+++|||+|.+|..++       ...|+|+| .+++| ++..+|.+++.  ..||
T Consensus       198 ~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItG-s~e~V~~Ark~I~~lLPv~l~Fd  266 (376)
T 3n89_A          198 DQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVG-NIDNVLKARRYIMDLLPISMCFN  266 (376)
T ss_dssp             HHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEES-CHHHHHHHHHHHHHTSEEEEEEE
T ss_pred             HHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEe-CHHHHHHHHHHHHhhCCEEEEEe
Confidence            99999999  677999999999999997532       24699999 99999 55558888887  5566

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.71  E-value=1.2e-18  Score=148.47  Aligned_cols=113  Identities=16%  Similarity=0.240  Sum_probs=87.7

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEec--CCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTP--VRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTG   81 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip--~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~   81 (329)
                      +||.+|||+|++|++|++++|  |++.  .++.+..+...+.+++|.+|+.++ .+                        
T Consensus        14 ~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~~~~~~i~~~~~p~~v~~~~~~l-~~------------------------   66 (144)
T 2qnd_A           14 LMGLAIGTHGANIQQARKVPG--VTAIDLDEDTCTFHIYGEDQDAVKKARSFL-EF------------------------   66 (144)
T ss_dssp             GHHHHHCGGGHHHHHHHTSTT--EEEEEEETTTTEEEEEESSHHHHHHHHHHH-CE------------------------
T ss_pred             ceeeEECCChhHHHHHHHHHC--CeEeccCCCchheeeccCCHHHHHHHHHhh-hc------------------------
Confidence            589999999999999999999  5543  333345554556799999997743 22                        


Q ss_pred             CCCceEEEEEecCcccceeecCCCchHHHHHHhcCc-eEEcCCCC------CCC--eEEEECCCCCCcchhh-hhhh
Q psy3263          82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT-YIVTPSRD------KEP--VFEVTGNFPEGPGFES-HHGQ  148 (329)
Q Consensus        82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga-~I~ip~~~------~e~--~i~ItG~~pe~veie~-~i~d  148 (329)
                          ...++.||.+.+|++|||+|++||.|++.||+ +|+|++.+      +++  .|+|+| ++++|+.+. +|.+
T Consensus        67 ----~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G-~~~~v~~Ak~li~~  138 (144)
T 2qnd_A           67 ----AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVG-TKDSIANATVLLDY  138 (144)
T ss_dssp             ----EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEE-EHHHHHHHHHHHHH
T ss_pred             ----ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEe-CHHHHHHHHHHHHH
Confidence                13789999999999999999999999999997 99998643      133  389999 999994443 4443

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=2.9e-16  Score=121.55  Aligned_cols=69  Identities=64%  Similarity=0.971  Sum_probs=62.5

Q ss_pred             CCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhh
Q psy3263          80 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQK  149 (329)
Q Consensus        80 ~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~  149 (329)
                      ++.+++.++++.||+++||+||||||++||+||++|||+|++|+++++++|+|+| .+++++.+. +|.+.
T Consensus         4 ~~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~~~~~v~ItG-~~e~v~~A~~~I~~~   73 (83)
T 2dgr_A            4 GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTG-MPENVDRAREEIEAH   73 (83)
T ss_dssp             CCSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSSSCCEEEEEE-CTTTHHHHHHHHHHH
T ss_pred             CCCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCCCCCeEEEEc-CHHHHHHHHHHHHHH
Confidence            3778899999999999999999999999999999999999999888899999999 999995544 66664

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.60  E-value=5.4e-16  Score=140.54  Aligned_cols=128  Identities=20%  Similarity=0.191  Sum_probs=92.6

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-----HHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-----KEDVARAKREILSAADHFSALRASRKSGALSPLSPP   79 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-----~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p   79 (329)
                      +|.|||++|++||.|+++||++|++..  ++..|+|.|.     ++++++|+++|.+++.-|..-.+....         
T Consensus        45 ig~lIG~gGk~Ik~I~e~tgvkI~I~~--~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~g~~ll---------  113 (219)
T 2e3u_A           45 IAVLIGKKGQTKKEIEKRTKTKITIDS--ETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLL---------  113 (219)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTEEEEECT--TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHHHGGGG---------
T ss_pred             hhhhhcccHHHHHHHHHHHCcEEEEEc--CCCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCccccceec---------
Confidence            688999999999999999999999973  3456788775     699999999999986311111110000         


Q ss_pred             CCCCCceEEEEEec-----------CcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhh
Q psy3263          80 TGVPGHVTIEVRVP-----------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHG  147 (329)
Q Consensus        80 ~~~~g~~t~~i~VP-----------~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~  147 (329)
                        .++.....+.++           .+.+|+||||+|+|||.|++.|||+|.++.    +.|.|.| .+++++++. +|.
T Consensus       114 --~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~----~~v~i~G-~~~~i~~A~~~i~  186 (219)
T 2e3u_A          114 --NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG----KTVAIIG-NPIQIEIAKTAIE  186 (219)
T ss_dssp             --STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET----TEEEEEE-CHHHHHHHHHHHH
T ss_pred             --cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC----eEEEEEe-CHHHHHHHHHHHH
Confidence              011111123322           247899999999999999999999999963    5799999 999995544 454


Q ss_pred             hhh
Q psy3263         148 QKI  150 (329)
Q Consensus       148 d~~  150 (329)
                      +++
T Consensus       187 ~li  189 (219)
T 2e3u_A          187 KLA  189 (219)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=9.3e-15  Score=113.09  Aligned_cols=55  Identities=45%  Similarity=0.665  Sum_probs=52.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +||.||||+|++||+||++|||+|++|.++++++|+|+|.+++|++|+++|.+++
T Consensus        20 ~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~~~~~v~ItG~~e~v~~A~~~I~~~i   74 (83)
T 2dgr_A           20 VVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEIEAHI   74 (83)
T ss_dssp             HHHHHHTTTTSSHHHHHHHTTCEEECCCSSSCCEEEEEECTTTHHHHHHHHHHHH
T ss_pred             HeeeeECCCchHHHHHHHHhCCeEEecCCCCCCeEEEEcCHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999998888899999999999999999999874

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.46  E-value=3.3e-14  Score=126.10  Aligned_cols=122  Identities=19%  Similarity=0.218  Sum_probs=94.4

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEe-----cCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVT-----GRKEDVARAKREILSAADHFSALRASRKSGALSPLSPP   79 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~It-----G~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p   79 (329)
                      ||.|||++|+++|.|++++|++|++.  ..++.++|.     |.+.++.+|++.|.+++.-|+.-.+..-..        
T Consensus        15 vg~liGk~g~~~k~i~e~~g~~i~id--~~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~e~A~~Ll~--------   84 (191)
T 1tua_A           15 LGAVIGPRGEVKAEIMRRTGTVITVD--TENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAFRLLE--------   84 (191)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTEEEEEE--TTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHHHGGGGS--------
T ss_pred             hhHHHhcCHhHHHHHHHHHCcEEEEE--cCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHHHhhhccc--------
Confidence            68899999999999999999999996  346677888     999999999999998876554433321111        


Q ss_pred             CCCCCceEEEEEec----------CcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh
Q psy3263          80 TGVPGHVTIEVRVP----------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES  144 (329)
Q Consensus        80 ~~~~g~~t~~i~VP----------~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~  144 (329)
                         +......+.++          .+..|.||||+|.|||.|++.|||+|.+...    .|.|.| .+++++++.
T Consensus        85 ---Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~~----~v~i~G-~~~~i~~Ar  151 (191)
T 1tua_A           85 ---EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGEY----EVAIIG-DYERAMAAK  151 (191)
T ss_dssp             ---TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECSS----EEEEEE-EHHHHHHHH
T ss_pred             ---CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcCC----EEEEEe-ChHHHHHHH
Confidence               11111223333          3568999999999999999999999999643    799999 999995544

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.36  E-value=4e-13  Score=101.25  Aligned_cols=56  Identities=18%  Similarity=0.224  Sum_probs=51.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      ++|.||||||++||+||++|||+|+++..+. +|+|+|+|.+++|.+|+.+|.++++
T Consensus        15 ~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~   71 (73)
T 2axy_A           15 EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLE   71 (73)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HeeeEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEeCHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999999997643 8999999999999999999998854

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.33  E-value=7.6e-13  Score=104.47  Aligned_cols=69  Identities=26%  Similarity=0.356  Sum_probs=60.1

Q ss_pred             CCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-----CCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263          82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGNFPEGPGFES-HHGQKIV  151 (329)
Q Consensus        82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-----~e~~i~ItG~~pe~veie~-~i~d~~~  151 (329)
                      .|++.+.++.||.+++|+||||+|++||+|+++|||+|+|+++.     .+++|+|+| ++++|+.+. +|.+++.
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~   85 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKVQQAKEMVLELIR   85 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEE-CTTTHHHHHHHHHHHHC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999999998753     578899999 999994444 7777664

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.32  E-value=6e-13  Score=99.74  Aligned_cols=55  Identities=25%  Similarity=0.417  Sum_probs=50.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +||.||||||.+||+|+++|||+|++|.+++ ++.|+|+|..+++++|+++|.+++
T Consensus        15 ~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A           15 FHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             HHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             HhhhhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999997664 678999999999999999998863

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.31  E-value=1.6e-12  Score=99.95  Aligned_cols=56  Identities=20%  Similarity=0.299  Sum_probs=50.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC---CcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~---~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++...   .++.|+|+|++++|++|+.+|.+++.
T Consensus        17 ~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   75 (82)
T 1zzk_A           17 LAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK   75 (82)
T ss_dssp             TGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             hcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999998542   37899999999999999999999864

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.31  E-value=3e-13  Score=101.94  Aligned_cols=65  Identities=20%  Similarity=0.304  Sum_probs=56.2

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      +.+.++.||.+.+|.||||||++||+|+++|||+|+++++. .+|+|+|+| .++++ ....+|.+.+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l   70 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAG-PTNAIFKAFAMIIDKL   70 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEe-CHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999998764 678999999 89998 3333666544

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.31  E-value=1.9e-12  Score=102.86  Aligned_cols=56  Identities=20%  Similarity=0.339  Sum_probs=51.6

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC----cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~----ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||||++||+|+++|||+|+||.+++    ++.|+|+|+++++++|+.+|..++.
T Consensus        27 ~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~   86 (97)
T 2ctl_A           27 YHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVG   86 (97)
T ss_dssp             THHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            5889999999999999999999999997763    5799999999999999999999864

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.30  E-value=2e-12  Score=100.49  Aligned_cols=63  Identities=17%  Similarity=0.162  Sum_probs=54.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC------CcceEEEecCHHHHHHHHHHHHHHhhhhhHhhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADHFSALRA   66 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~------~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~   66 (329)
                      +||.||||||++||+|+++|||+|+++.++      .++.|+|+|+++++++|+.+|.+++.....-++
T Consensus        13 ~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~r~   81 (87)
T 1ec6_A           13 LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVRA   81 (87)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccccc
Confidence            579999999999999999999999999653      368999999999999999999998764443333

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=99.30  E-value=5.6e-13  Score=102.49  Aligned_cols=68  Identities=18%  Similarity=0.327  Sum_probs=57.8

Q ss_pred             CCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcch-hhhhhhhhh
Q psy3263          83 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGF-ESHHGQKIV  151 (329)
Q Consensus        83 ~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~vei-e~~i~d~~~  151 (329)
                      ..+.+.++.||.+++|.||||||++||+|+++|||+|+++...   .++.|+|+| .+++++. ..+|.+++.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~   74 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG-SAASISLAQYLINARLS   74 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEE-CHHHHHHHHHHHHHHTC
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHH
Confidence            3458899999999999999999999999999999999998642   588999999 9999943 337766654

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.29  E-value=1.6e-12  Score=98.51  Aligned_cols=56  Identities=20%  Similarity=0.195  Sum_probs=50.5

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC---CcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~---~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||||++||+||++|||+|+++...   .++.|+|+|++++|++|+.+|.++++
T Consensus        15 ~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   73 (76)
T 2p2r_A           15 LIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLS   73 (76)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             HcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHH
Confidence            579999999999999999999999998532   38999999999999999999998853

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=99.29  E-value=1.5e-12  Score=100.10  Aligned_cols=56  Identities=18%  Similarity=0.175  Sum_probs=50.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC---CcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~---~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||||++||+||++|||+|+++...   .++.|+|+|++++|++|+.+|.+++.
T Consensus        16 ~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   74 (82)
T 1wvn_A           16 LIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLS   74 (82)
T ss_dssp             GHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC
T ss_pred             hccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHH
Confidence            579999999999999999999999998532   38999999999999999999999864

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.29  E-value=1.9e-12  Score=97.90  Aligned_cols=55  Identities=16%  Similarity=0.164  Sum_probs=50.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC------CcceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~------~ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +||.||||||++||+||++|||+|+++.++      .++.|+|+|+++++++|+.+|.+++
T Consensus        13 ~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i   73 (76)
T 1dtj_A           13 LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (76)
T ss_dssp             THHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             HcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHH
Confidence            579999999999999999999999999653      2689999999999999999999875

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.29  E-value=2e-12  Score=101.69  Aligned_cols=56  Identities=23%  Similarity=0.233  Sum_probs=51.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC---CcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~---~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++.+.   .++.|+|+|++++|++|+.+|.++++
T Consensus        25 ~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~   83 (92)
T 1x4n_A           25 MVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVE   83 (92)
T ss_dssp             HHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            579999999999999999999999999653   27899999999999999999999864

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.28  E-value=1e-12  Score=103.34  Aligned_cols=70  Identities=27%  Similarity=0.321  Sum_probs=59.6

Q ss_pred             CCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcch-hhhhhhhhhhh
Q psy3263          83 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGF-ESHHGQKIVFI  153 (329)
Q Consensus        83 ~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~vei-e~~i~d~~~~~  153 (329)
                      ....+.++.||.+++|.||||+|++||+|+++|||+|+|+.+.   .++.|+|+| ++++|+. ..+|.+++...
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G-~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTG-TPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEE-CHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHHhc
Confidence            4458899999999999999999999999999999999998753   468999999 8999944 44777776543

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.28  E-value=1.4e-12  Score=100.29  Aligned_cols=66  Identities=20%  Similarity=0.338  Sum_probs=57.0

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcchh-hhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGFE-SHHGQKIV  151 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~veie-~~i~d~~~  151 (329)
                      ..+.++.||.+++|.||||+|++||+|+++|||+|+++...   .++.|+|+| ++++|+.+ .+|.+++.
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~   75 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLLQNSVK   75 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHHH
Confidence            48899999999999999999999999999999999998642   568999999 99999443 37766655

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.28  E-value=7.6e-13  Score=100.07  Aligned_cols=64  Identities=23%  Similarity=0.376  Sum_probs=54.7

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC------CCCeEEEECCCCCCcchhh-hhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNFPEGPGFES-HHGQKI  150 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------~e~~i~ItG~~pe~veie~-~i~d~~  150 (329)
                      .+.++.||.+.+|.||||||++||+|+++|||+|++++++      .++.|+|+| ++++++.+. +|.+++
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i   73 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG-SPAATQAAQYLISQRV   73 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEE-SHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEe-CHHHHHHHHHHHHHHH
Confidence            6789999999999999999999999999999999999752      468899999 899984333 665544

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.28  E-value=4.7e-14  Score=113.23  Aligned_cols=85  Identities=19%  Similarity=0.257  Sum_probs=68.0

Q ss_pred             EEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCCCceEEEEEecCcccceeecCCCchHHHHHHh-cCc
Q psy3263          39 VVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQ-TNT  117 (329)
Q Consensus        39 ~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~-tga  117 (329)
                      .|+|++++|++|+.+|+++++                        ...|.+|.||..+|+.|||++|++||+|+++ +++
T Consensus         4 ~i~G~~~~V~~A~~~i~~~~~------------------------~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v   59 (102)
T 2ctf_A            4 GSSGEPEKLGQALTEVYAKAN------------------------SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKV   59 (102)
T ss_dssp             CCCCCCCCCCCSCCCCCCCCC------------------------CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSS
T ss_pred             ccCcCHHHHHHHHHHHHHHhc------------------------CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCc
Confidence            367888888888888865532                        2278999999999999999999999999997 599


Q ss_pred             eEEcCCCCCCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263         118 YIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus       118 ~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      +|+||.  +++.|+|+| .++.| .+..+|.+++
T Consensus        60 ~I~fp~--~~~~ItI~G-~~~~V~~a~~~I~~~v   90 (102)
T 2ctf_A           60 HIEFTE--GEDKITLEG-PTEDVSVAQEQIEGMV   90 (102)
T ss_dssp             EEEECS--SSCEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             EEEeCC--CCCEEEEEC-CHHHHHHHHHHHHHHH
Confidence            999998  467899999 99999 3333444333

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.27  E-value=3.4e-12  Score=101.04  Aligned_cols=58  Identities=24%  Similarity=0.322  Sum_probs=52.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC--cceEEEecCHHHHHHHHHHHHHHhhhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAADHF   61 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--ervi~ItG~~e~v~~A~~~I~~i~e~~   61 (329)
                      ++|.||||||.+||+|+++|||+|++|.+++  ++.|+|+|.+++|++|+.+|.++++.+
T Consensus        27 ~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           27 VHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             THHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999997764  678999999999999999999987533

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.27  E-value=2e-12  Score=102.02  Aligned_cols=70  Identities=20%  Similarity=0.271  Sum_probs=59.2

Q ss_pred             CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263          81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQKIV  151 (329)
Q Consensus        81 ~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~~~  151 (329)
                      .+..+.+.++.||.+++|+|||+||++||+|+++|||+|+||+.+ .++.|+|+| .++++ ....+|.+.+.
T Consensus        12 ~l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G-~~e~v~~A~~~I~~i~~   83 (94)
T 2cte_A           12 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITG-TKEGIEKARHEVLLISA   83 (94)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             HhCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEE-CHHHHHHHHHHHHHHhh
Confidence            445678999999999999999999999999999999999999755 468999999 79998 33336666554

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.27  E-value=2.3e-12  Score=96.54  Aligned_cols=64  Identities=22%  Similarity=0.331  Sum_probs=54.4

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQK  149 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~  149 (329)
                      ..+.++.||.+++|.|||+||++||+|+++|||+|+||++. +++.|+|+| .++++ +...+|.++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G-~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEG-DPQGVQQAKRELLEL   69 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEE-SSHHHHHHHHHHHHT
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEc-CHHHHHHHHHHHHHH
Confidence            47889999999999999999999999999999999999765 567899999 78888 333355543

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.27  E-value=3.3e-12  Score=98.89  Aligned_cols=55  Identities=16%  Similarity=0.132  Sum_probs=50.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-----cceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-----EPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-----ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +||.||||+|++||+|+++|||+|+++.++.     +|.|+|+|+++++++|+.+|.+++
T Consensus        24 ~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~   83 (85)
T 2opv_A           24 KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL   83 (85)
T ss_dssp             THHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             heeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHh
Confidence            5799999999999999999999999986443     678999999999999999999875

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.26  E-value=3e-12  Score=101.35  Aligned_cols=70  Identities=21%  Similarity=0.276  Sum_probs=58.7

Q ss_pred             CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC--CCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263          81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--KEPVFEVTGNFPEGPGFES-HHGQKIV  151 (329)
Q Consensus        81 ~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~--~e~~i~ItG~~pe~veie~-~i~d~~~  151 (329)
                      .+..+.+.++.||.+++|.|||+||++||+|+++|||+|+||.+.  +++.|+|+| .+++|+.+. +|.+++.
T Consensus        12 ~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G-~~e~v~~A~~~I~~i~~   84 (95)
T 2ctm_A           12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTG-LPENVEEAIDHILNLEE   84 (95)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEES-CHHHHHHHHHHHHHHHH
T ss_pred             hhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Confidence            456678999999999999999999999999999999999999765  467899999 899993333 5555443

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=99.26  E-value=2.4e-12  Score=100.54  Aligned_cols=56  Identities=20%  Similarity=0.328  Sum_probs=50.7

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCC---CCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVR---GEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~---~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++..   ..++.|+|+|++++|++|+.+|.+++.
T Consensus        24 ~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~   82 (89)
T 1j5k_A           24 LAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK   82 (89)
T ss_dssp             HHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             hcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999853   237999999999999999999999864

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.25  E-value=8.5e-13  Score=99.99  Aligned_cols=65  Identities=17%  Similarity=0.340  Sum_probs=56.0

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcchh-hhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGFE-SHHGQKI  150 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~veie-~~i~d~~  150 (329)
                      ..+.++.||.+++|.||||||++||+|+++|||+|+++...   .++.|+|+| .+++++.+ .+|.+++
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i   72 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITG-SAASISLAQYLINVRL   72 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEe-CHHHHHHHHHHHHHHH
Confidence            47889999999999999999999999999999999998733   588999999 89999433 3666654

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.25  E-value=4.1e-12  Score=102.59  Aligned_cols=56  Identities=20%  Similarity=0.148  Sum_probs=50.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+|+++|+|+|+|+.+.+   +|+|+|+|++|+|++|+++|.++++
T Consensus        21 ~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~   79 (106)
T 2hh3_A           21 SVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQ   79 (106)
T ss_dssp             THHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHh
Confidence            5799999999999999999999999985442   6899999999999999999999864

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=99.25  E-value=1.1e-12  Score=96.18  Aligned_cols=56  Identities=25%  Similarity=0.689  Sum_probs=50.7

Q ss_pred             CCCcccccccccCcccEEe--CCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~l--pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      +++..|.||++.+.+++++  ||||.+||.+|+.++......||+||+++...+++|+
T Consensus         6 ~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i~i~~   63 (64)
T 2vje_A            6 NAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYF   63 (64)
T ss_dssp             GGGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCCEEEEEEC
T ss_pred             CCcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchhceEeeec
Confidence            4667999999999999988  9999989999999998888899999999998888765

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.25  E-value=4.8e-12  Score=101.66  Aligned_cols=62  Identities=23%  Similarity=0.230  Sum_probs=53.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC-----CcceEEEecCHHHHHHHHHHHHHHhhhhhHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHFSALR   65 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-----~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~   65 (329)
                      +||.||||+|++||+|+++|||+|+++...     +++.|+|+|+.++|++|+.+|.+++......+
T Consensus        25 ~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~~~~   91 (104)
T 1we8_A           25 SVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELR   91 (104)
T ss_dssp             THHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             heeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhChHHH
Confidence            579999999999999999999999998643     37899999999999999999999875444333

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.25  E-value=3.2e-12  Score=100.93  Aligned_cols=56  Identities=29%  Similarity=0.359  Sum_probs=51.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||||++||+|+++|||+|++|..++ ++.|+|+|.+++|++|+.+|.++++
T Consensus        27 ~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~~e~v~~A~~~I~~i~~   83 (94)
T 2cte_A           27 HHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISA   83 (94)
T ss_dssp             THHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HeeeeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEECHHHHHHHHHHHHHHhh
Confidence            5789999999999999999999999996544 5889999999999999999999864

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.25  E-value=4.9e-12  Score=102.19  Aligned_cols=56  Identities=18%  Similarity=0.263  Sum_probs=51.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC------CcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~------~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+|+.+.      .+++|+|+|++++|++|+.+|.++++
T Consensus        17 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~   78 (107)
T 2hh2_A           17 KCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIE   78 (107)
T ss_dssp             GTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSC
T ss_pred             HcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHh
Confidence            589999999999999999999999998653      26999999999999999999999864

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.24  E-value=2.8e-12  Score=101.20  Aligned_cols=56  Identities=21%  Similarity=0.193  Sum_probs=51.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC-----CcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-----~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++.++     .+|+|+|+|++++|++|+.+|.++++
T Consensus        25 ~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   85 (94)
T 1x4m_A           25 KAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIR   85 (94)
T ss_dssp             HHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHC
T ss_pred             hcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHh
Confidence            579999999999999999999999998654     37899999999999999999999863

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=5e-12  Score=93.90  Aligned_cols=53  Identities=30%  Similarity=0.794  Sum_probs=48.0

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN  307 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~  307 (329)
                      .+...|.||++.+.+++++||||.+||..|+.+.    ..||+||+.+...+++|.+
T Consensus        13 ~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~CR~~i~~~~~i~~~   65 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYF----QQCPMCRQFVQESFALSGP   65 (68)
T ss_dssp             CCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHHC----SSCTTTCCCCCCEECCCSS
T ss_pred             CCCCCCCCcCcCCCCEEEECCCChhhhHHHHhcC----CCCCCCCcchhceEEeecC
Confidence            4578999999999999999999999999999975    7899999999998888765

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.23  E-value=7.3e-12  Score=100.73  Aligned_cols=60  Identities=20%  Similarity=0.289  Sum_probs=53.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhhhhhH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFSA   63 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e~~~~   63 (329)
                      +||.||||||++||+|+++|||+|++|.+++ ++.|+|+|..+++++|+.+|.++++....
T Consensus        27 ~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e~   87 (104)
T 2ctk_A           27 LHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQA   87 (104)
T ss_dssp             HHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             HccceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhHHH
Confidence            5789999999999999999999999997664 45899999999999999999998765443

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=7.4e-12  Score=93.05  Aligned_cols=52  Identities=23%  Similarity=0.622  Sum_probs=46.7

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ....+...|+||++.+.+++.++|||. ||..|+.+|+.....||+||+.+..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           10 APSLTVPECAICLQTCVHPVSLPCKHV-FCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             CSSSSCCBCSSSSSBCSSEEEETTTEE-EEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             ccCCCCCCCccCCcccCCCEEccCCCH-HHHHHHHHHHHCCCcCcCcCchhCH
Confidence            344667899999999999999999999 9999999999888899999998864

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=99.23  E-value=1.4e-12  Score=101.88  Aligned_cols=69  Identities=19%  Similarity=0.304  Sum_probs=58.1

Q ss_pred             CCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcch-hhhhhhhhhh
Q psy3263          83 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGF-ESHHGQKIVF  152 (329)
Q Consensus        83 ~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~vei-e~~i~d~~~~  152 (329)
                      ....+.++.||.+++|.||||+|++||+|+++|||+|+++...   .++.|+|+| ++++++. ..+|.+++..
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G-~~e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEE-EHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEc-CHHHHHHHHHHHHHHHHh
Confidence            3458889999999999999999999999999999999998642   578999999 8999943 3477666553

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.22  E-value=3.6e-12  Score=98.65  Aligned_cols=65  Identities=20%  Similarity=0.280  Sum_probs=55.1

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-----CCCeEEEECCCCCCcchhh-hhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGNFPEGPGFES-HHGQKI  150 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-----~e~~i~ItG~~pe~veie~-~i~d~~  150 (329)
                      ..+.++.||.+++|.||||||++||+|+++|||+|.++.+.     .++.|+|+| .+++++.+. +|.+++
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~i~   83 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMDIL   83 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHh
Confidence            37889999999999999999999999999999999998643     467799999 999994443 665543

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=99.22  E-value=1.9e-12  Score=94.69  Aligned_cols=56  Identities=25%  Similarity=0.632  Sum_probs=50.0

Q ss_pred             CCCcccccccccCcccEEe--CCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~l--pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      +....|.||++.+.+++++  ||||.+||.+|+.++++....||+||+++...+++|.
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i~i~~   62 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVFI   62 (63)
T ss_dssp             GGGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCCEEEEEEE
T ss_pred             CcCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhhceEEEec
Confidence            3457899999999999888  9999989999999998777899999999998888764

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.22  E-value=3.5e-12  Score=103.07  Aligned_cols=64  Identities=23%  Similarity=0.402  Sum_probs=55.8

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC------CCCeEEEECCCCCCcchh-hhhhhhhh
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNFPEGPGFE-SHHGQKIV  151 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------~e~~i~ItG~~pe~veie-~~i~d~~~  151 (329)
                      +.++.||.++||.||||+|++||+|+++|||+|+|..+.      .+++|+|+| ++++|+.+ .+|.+++.
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G-~~e~v~~A~~~I~~~i~   78 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRG-SPQQIDHAKQLIEEKIE   78 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEES-CHHHHHHHHHHHHHHSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEEC-CHHHHHHHHHHHHHHHh
Confidence            789999999999999999999999999999999998763      468999999 99999444 47777654

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.21  E-value=6.9e-12  Score=94.12  Aligned_cols=57  Identities=28%  Similarity=0.686  Sum_probs=48.7

Q ss_pred             CCCCCCCCCCCcccccccccCcccEEeC-CCChhccHhhHHhhcCC--CCCCccccccccc
Q psy3263         243 STSPSGSISGSRQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF--DRTCPMCRVPVNQ  300 (329)
Q Consensus       243 p~~~~~~l~~~~~C~IC~e~~~~~~~lp-CgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~  300 (329)
                      ++...+.+.++..|+||++.+.+++.++ |||. ||..|+.+|+..  ...||+||+.+..
T Consensus         5 ~~~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A            5 SSGEDDPIPDELLCLICKDIMTDAVVIPCCGNS-YCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CCSCCCCSCGGGSCSSSCCCCTTCEECSSSCCE-ECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             cccccccCCCCCCCcCCChHHhCCeEcCCCCCH-HHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            3344556788899999999999999999 9999 999999999876  3799999997543

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.21  E-value=2.5e-12  Score=108.01  Aligned_cols=61  Identities=21%  Similarity=0.544  Sum_probs=49.7

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhhhhhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFG  312 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~~~~~~  312 (329)
                      ++++.|+||++.+.+++++||||. ||..|+..|+.....||+||+++......+..+..+.
T Consensus        51 ~~~~~C~iC~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~i~  111 (138)
T 4ayc_A           51 ENELQCIICSEYFIEAVTLNCAHS-FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCIN  111 (138)
T ss_dssp             HHHSBCTTTCSBCSSEEEETTSCE-EEHHHHHHHTTTCSBCTTTCCBCCCEEECHHHHHHHH
T ss_pred             cccCCCcccCcccCCceECCCCCC-ccHHHHHHHHHcCCcCCCCCCcCCCCCCccchhHHHH
Confidence            456789999999999999999999 9999999999988999999999865443333333333

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.20  E-value=2.2e-12  Score=100.25  Aligned_cols=65  Identities=23%  Similarity=0.378  Sum_probs=55.8

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC------CCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNFPEGPGFES-HHGQKIV  151 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------~e~~i~ItG~~pe~veie~-~i~d~~~  151 (329)
                      .+.++.||.+.+|.||||||++||+|+++|||+|++++++      .++.|+|+| ++++++.+. +|.+++.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G-~~~~v~~A~~~I~~~i~   74 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG-SPAATQAAQYLISQRVT   74 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEES-SHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999999752      468899999 899994333 6666654

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.19  E-value=8.3e-12  Score=99.15  Aligned_cols=66  Identities=21%  Similarity=0.310  Sum_probs=55.3

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----CCCeEEEECCCCCCcchh-hhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNFPEGPGFE-SHHGQKIV  151 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~e~~i~ItG~~pe~veie-~~i~d~~~  151 (329)
                      ..+.++.||.++||.||||||++||+|+++|||+|+||++.    .++.|+|+| .+++++.+ .+|.+++.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G-~~e~v~~A~~~I~~iv~   86 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITG-YEKNTEAARDAILRIVG   86 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEES-CHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHH
Confidence            36889999999999999999999999999999999999765    467999999 89888333 35554443

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.18  E-value=9.9e-12  Score=93.69  Aligned_cols=53  Identities=23%  Similarity=0.644  Sum_probs=47.1

Q ss_pred             CCCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-------CCCCccccccccc
Q psy3263         247 SGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-------DRTCPMCRVPVNQ  300 (329)
Q Consensus       247 ~~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-------~~~CP~Cr~~i~~  300 (329)
                      .+.++++..|+||++.+.+++.++|||. ||..|+.+|+..       ...||+||..+..
T Consensus         6 ~~~~~~~~~C~IC~~~~~~p~~l~CgH~-fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A            6 SGNVQEEVTCPICLELLTEPLSLDCGHS-LCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             SCCCCCCCEETTTTEECSSCCCCSSSCC-CCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             HhhcccCCCCcCCCcccCCeeECCCCCH-HHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            3456788999999999999999999999 999999999876       6799999998864

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.18  E-value=1.2e-11  Score=94.10  Aligned_cols=51  Identities=22%  Similarity=0.567  Sum_probs=46.6

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      +..+....|+||++.+.++++++|||. ||..|+.+|+.....||+||+.+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           10 EEEEIPFRCFICRQAFQNPVVTKCRHY-FCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SCCCCCSBCSSSCSBCCSEEECTTSCE-EEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             ccCCCCCCCcCCCchhcCeeEccCCCH-hHHHHHHHHHHCCCcCCCcCcccc
Confidence            445677899999999999999999999 999999999987889999999986

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.18  E-value=4.6e-12  Score=102.27  Aligned_cols=68  Identities=26%  Similarity=0.356  Sum_probs=57.0

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcc-hhhhhhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPG-FESHHGQKIVFI  153 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~ve-ie~~i~d~~~~~  153 (329)
                      ..+++|.||.++||.||||+|++||+|+++|+|+|+|++++   .+++|+|+| ++++++ +..+|.+++...
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G-~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG-PPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEES-SHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEe-CHHHHHHHHHHHHHHHhcc
Confidence            36789999999999999999999999999999999998654   467899999 899994 444777776643

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=1.1e-11  Score=90.88  Aligned_cols=54  Identities=33%  Similarity=0.692  Sum_probs=46.9

Q ss_pred             CCCCCCCCcccccccccCccc-------EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         246 PSGSISGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       246 ~~~~l~~~~~C~IC~e~~~~~-------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ..+.+.+...|+||++.+.++       ++++|||. ||..|+.+|+.....||+||+.+..
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A            8 TGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCE-EEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cccCCCCCCCCcccCccccccccccCCeEeCCCCCh-hcHHHHHHHHHcCCCCCCCCCccCc
Confidence            344567789999999998877       88999999 9999999998888899999998754

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=1.9e-11  Score=91.09  Aligned_cols=55  Identities=25%  Similarity=0.643  Sum_probs=48.3

Q ss_pred             CCCCCCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263         246 PSGSISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  301 (329)
Q Consensus       246 ~~~~l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~  301 (329)
                      ..+.+++...|+||++.+.+++.+ +|||. ||..|+.+|+.....||+||+.+...
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A            8 NLSELTPYILCSICKGYLIDATTITECLHT-FCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             CCCCCCGGGSCTTTSSCCSSCEECSSSCCE-ECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             hHhhcCCCCCCCCCChHHHCcCEECCCCCH-HHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            345567889999999999999987 99999 99999999997788999999988653

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.16  E-value=6.9e-12  Score=100.75  Aligned_cols=66  Identities=20%  Similarity=0.297  Sum_probs=56.5

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-----CCCeEEEECCCCCCcc-hhhhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGNFPEGPG-FESHHGQKIV  151 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-----~e~~i~ItG~~pe~ve-ie~~i~d~~~  151 (329)
                      ..+.++.||.+++|.||||||++||+|+++|||+|+|++..     .++.|+|+| .+++++ ...+|.+++.
T Consensus        14 p~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G-~~~~v~~A~~~I~~~i~   85 (104)
T 1we8_A           14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISG-TQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEE-EHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEc-CHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999998754     478999999 888883 3336666655

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.15  E-value=4.4e-12  Score=95.46  Aligned_cols=53  Identities=32%  Similarity=0.884  Sum_probs=47.8

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      ++++..|+||++.+.+++++||||.+||..|+.+|    ..||+||+.+...+++|+
T Consensus        21 ~~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~~   73 (74)
T 4ic3_A           21 LQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKILM   73 (74)
T ss_dssp             HHHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSEEEECBC
T ss_pred             CccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----ccCCCcCcCccCcEEEee
Confidence            35568999999999999999999999999999988    799999999988877765

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.15  E-value=2.6e-11  Score=93.09  Aligned_cols=54  Identities=22%  Similarity=0.589  Sum_probs=47.2

Q ss_pred             CCCCCCCCcccccccccCcc----cEEeCCCChhccHhhHHhhcCCC---CCCccccccccc
Q psy3263         246 PSGSISGSRQCYLCNDREVT----HALIPCGHNFFCSECAERTCDFD---RTCPMCRVPVNQ  300 (329)
Q Consensus       246 ~~~~l~~~~~C~IC~e~~~~----~~~lpCgH~~fC~~Cl~~~~~~~---~~CP~Cr~~i~~  300 (329)
                      ..+.+++...|+||++.+.+    ++.++|||. ||..|+.+|+...   ..||+||+.+..
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~-fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   68 (88)
T 2ct2_A            8 NLDALREVLECPICMESFTEEQLRPKLLHCGHT-ICRQCLEKLLASSINGVRCPFCSKITRI   68 (88)
T ss_dssp             SCCCCCSCCBCTTTCCBCCTTSSCEEECSSSCE-EEHHHHHHHHHHCSSCBCCTTTCCCBCC
T ss_pred             ChhhccCCCCCccCCccccccCCCeEECCCCCh-hhHHHHHHHHHcCCCCcCCCCCCCcccc
Confidence            44567888999999999998    999999999 9999999998764   799999998744

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.13  E-value=3.4e-11  Score=91.54  Aligned_cols=53  Identities=26%  Similarity=0.610  Sum_probs=47.0

Q ss_pred             CCCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC------CCCCccccccccc
Q psy3263         247 SGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQ  300 (329)
Q Consensus       247 ~~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~------~~~CP~Cr~~i~~  300 (329)
                      .+.+.+...|+||++.+.+++.++|||. ||..|+..|+..      ...||+||..+..
T Consensus        13 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           13 LEMIKEEVTCPICLELLKEPVSADCNHS-FCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             CCCCCTTTSCTTTCSCCSSCEECTTSCC-BCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             HHhCccCCCCcCCChhhCcceeCCCCCH-HHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            3456788999999999999999999999 999999998876      6799999998854

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.13  E-value=2.7e-11  Score=91.37  Aligned_cols=51  Identities=12%  Similarity=0.274  Sum_probs=46.7

Q ss_pred             CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      .+.+++.|+||++.+.+|+.++|||. ||..|+.+|+.. ...||+||+.+..
T Consensus         4 ~~~~~~~C~IC~~~~~~Pv~~~CgH~-fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            4 EFPEYFRCPISLELMKDPVIVSTGQT-YERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEE-EEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CCcccCCCCCccccccCCEEcCCCCe-ecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            45678999999999999999999999 999999999987 8899999998854

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=8.5e-11  Score=87.28  Aligned_cols=52  Identities=29%  Similarity=0.689  Sum_probs=46.2

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC---CCCCccccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVNQ  300 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~~  300 (329)
                      +.+++...|+||++.+.+++.++|||. ||..|+..|++.   ...||+||+.+..
T Consensus        15 ~~~~~~~~C~IC~~~~~~~~~~~CgH~-fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   69 (73)
T 2ysl_A           15 NKLQEEVICPICLDILQKPVTIDCGHN-FCLKCITQIGETSCGFFKCPLCKTSVRK   69 (73)
T ss_dssp             CCCCCCCBCTTTCSBCSSEEECTTCCE-EEHHHHHHHCSSSCSCCCCSSSCCCCCC
T ss_pred             HhCccCCEeccCCcccCCeEEcCCCCh-hhHHHHHHHHHcCCCCCCCCCCCCcCCc
Confidence            456778999999999999999999999 999999999873   6799999998754

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.12  E-value=3.9e-11  Score=87.76  Aligned_cols=52  Identities=19%  Similarity=0.542  Sum_probs=46.2

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +.+++...|+||++.+.+++.++|||. ||..|+.+|+.. ...||+||+.+..
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (66)
T 2ecy_A           10 KTVEDKYKCEKCHLVLCSPKQTECGHR-FCESCMAALLSSSSPKCTACQESIVK   62 (66)
T ss_dssp             CSCCCCEECTTTCCEESSCCCCSSSCC-CCHHHHHHHHTTSSCCCTTTCCCCCT
T ss_pred             hcCCcCCCCCCCChHhcCeeECCCCCH-HHHHHHHHHHHhCcCCCCCCCcCCCh
Confidence            456778999999999999999999999 999999999954 7899999998754

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.11  E-value=3.3e-11  Score=93.72  Aligned_cols=52  Identities=29%  Similarity=0.727  Sum_probs=46.1

Q ss_pred             CCCCCCCcccccccccCcccEEeC-CCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263         247 SGSISGSRQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF--DRTCPMCRVPVN  299 (329)
Q Consensus       247 ~~~l~~~~~C~IC~e~~~~~~~lp-CgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~  299 (329)
                      .+.+.+++.|+||++.+.+|+.++ |||. ||..|+..|+..  ...||+||..+.
T Consensus         7 ~~~~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A            7 DDPIPDELLCLICKDIMTDAVVIPCCGNS-YCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCCCCTTTEETTTTEECSSCEECTTTCCE-ECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             cccCCcCCCCCCCChhhcCceECCCCCCH-HHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            345678899999999999999999 9999 999999999864  479999999873

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.11  E-value=2.1e-11  Score=97.99  Aligned_cols=54  Identities=30%  Similarity=0.592  Sum_probs=50.0

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v  140 (329)
                      .+.++.||.++||.|||+||++||+|+++|||+|+||.+. +.+.|+|+| .++++
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~~~~V~I~G-~~e~v   71 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITG-LAANL   71 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEE-CHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEc-CHHHH
Confidence            8899999999999999999999999999999999999765 445899999 88888

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=4.3e-11  Score=90.95  Aligned_cols=52  Identities=23%  Similarity=0.685  Sum_probs=46.5

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC------CCCCccccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQ  300 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~------~~~CP~Cr~~i~~  300 (329)
                      +.+.+...|+||++.+.+++.++|||. ||..|+..|+..      ...||+||..+..
T Consensus        14 ~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           14 VNVKEEVTCPICLELLTQPLSLDCGHS-FCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCCCCTTTCSCCSSCBCCSSSCC-BCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             HHccCCCCCCCCCcccCCceeCCCCCH-HHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            456778999999999999999999999 999999998765      7899999998864

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=8.9e-12  Score=93.90  Aligned_cols=52  Identities=33%  Similarity=0.871  Sum_probs=46.5

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      ++...|+||++.+.+++++||||.+||..|+.++    ..||+||.++...+++|+
T Consensus        23 ~~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~~   74 (75)
T 2ecg_A           23 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKIFM   74 (75)
T ss_dssp             HHHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHHC----SBCTTTCCBCCCCCBCCC
T ss_pred             CCCCCCCcCCCCCCCEEEecCCCHHHHHHHhhCC----CCCccCCceecCcEEEec
Confidence            4567899999999999999999998999999875    789999999988877764

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=99.08  E-value=1.5e-11  Score=93.97  Aligned_cols=53  Identities=28%  Similarity=0.853  Sum_probs=47.7

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhhh
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN  307 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~  307 (329)
                      +++..|.||++.+.+++++||||.+||..|+.++    ..||+||..+...+++|.+
T Consensus        16 ~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~~p   68 (79)
T 2yho_A           16 KEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHVQHVYLP   68 (79)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCEEEECBCT
T ss_pred             CCCCEeEEeCcccCcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhCeEEEEeC
Confidence            4567899999999999999999999999999987    5999999999998887754

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.08  E-value=9.8e-11  Score=88.24  Aligned_cols=55  Identities=20%  Similarity=0.567  Sum_probs=45.8

Q ss_pred             CCCCCCCCcccccccccCccc---EEeCCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263         246 PSGSISGSRQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  301 (329)
Q Consensus       246 ~~~~l~~~~~C~IC~e~~~~~---~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~  301 (329)
                      ..+.+.+...|+||++.+.++   ..++|+|. ||..|+.+|++....||+||+.+...
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A            8 TEEHVGSGLECPVCKEDYALGESVRQLPCNHL-FHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             CCTTSSSSCCCTTTTSCCCTTSCEEECTTSCE-EETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             CcccCCCCCCCeeCCccccCCCCEEEeCCCCe-ecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            344567788999999988644   46799999 99999999998888999999988653

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=6.1e-11  Score=87.52  Aligned_cols=53  Identities=30%  Similarity=0.917  Sum_probs=46.8

Q ss_pred             CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchh
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR  303 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~  303 (329)
                      .+.+...|+||++.+.+ +.++|||. ||..|+.+|+.....||+||+.+.....
T Consensus        11 ~~~~~~~C~IC~~~~~~-~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           11 QLTDEEECCICMDGRAD-LILPCAHS-FCQKCIDKWSDRHRNCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCCCSSSCCSCCS-EEETTTEE-ECHHHHHHSSCCCSSCHHHHHCTTCCCC
T ss_pred             cCCCCCCCeeCCcCccC-cccCCCCc-ccHHHHHHHHHCcCcCCCcCCcccCCCc
Confidence            45677899999999999 88999999 9999999999888999999998865443

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=99.07  E-value=1.5e-11  Score=97.67  Aligned_cols=51  Identities=27%  Similarity=0.650  Sum_probs=45.8

Q ss_pred             CCCCCcccccccccCcccEE-eCCCChhccHhhHHhhcCCC-CCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~~-~~CP~Cr~~i~~  300 (329)
                      .++++..|+||++.+.+++. ++|||. ||..|+.+|+... ..||+||..+..
T Consensus        18 ~l~~~~~C~IC~~~~~~p~~~~~CgH~-FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           18 SIAEVFRCFICMEKLRDARLCPHCSKL-CCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHHHHTBCTTTCSBCSSEEECTTTCCE-EEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cCCCCCCCccCCccccCccccCCCCCh-hhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            35677899999999999999 999999 9999999999885 799999999843

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.07  E-value=1.2e-10  Score=92.11  Aligned_cols=56  Identities=27%  Similarity=0.425  Sum_probs=50.9

Q ss_pred             eeeeeecCCChHHHHHHHHh-CCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKT-NTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +++.|||+||.+||+|+++| |++|++|.++. .+.|+|+|+.++|++|+++|.++++
T Consensus        27 ~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           27 LHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAE   84 (95)
T ss_dssp             HHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            57889999999999999999 99999997664 5688999999999999999999864

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.05  E-value=1.3e-10  Score=93.18  Aligned_cols=54  Identities=19%  Similarity=0.193  Sum_probs=49.7

Q ss_pred             eeeeeecCCChHHHHHHHH-hCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAK-TNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~-Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      |++.||||+|++||+|+++ ++++|+||.  +++.|+|+|+++.|++|+.+|..+++
T Consensus        37 ~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~--~~~~ItI~G~~~~V~~a~~~I~~~v~   91 (102)
T 2ctf_A           37 LHRFIIGKKGQNLAKITQQMPKVHIEFTE--GEDKITLEGPTEDVSVAQEQIEGMVK   91 (102)
T ss_dssp             THHHHHTTTTCHHHHHHHHCSSSEEEECS--SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHhhhcCCCCccHHHHHHHcCCcEEEeCC--CCCEEEEECCHHHHHHHHHHHHHHHH
Confidence            6789999999999999998 599999996  56789999999999999999999865

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}

Probab=99.04  E-value=5.7e-11  Score=96.33  Aligned_cols=52  Identities=29%  Similarity=0.654  Sum_probs=46.7

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      ..+.+++.|+||++.+.+++.++|||. ||..|+.+|+.. ...||+||..+..
T Consensus        10 ~~~~~~~~C~iC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           10 IPSLSECQCGICMEILVEPVTLPCNHT-LCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CCCHHHHBCTTTCSBCSSCEECTTSCE-ECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             cCCCCCCCCccCCcccCceeEcCCCCH-HhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            345677999999999999999999999 999999999987 7899999999864

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.04  E-value=4.3e-11  Score=88.31  Aligned_cols=50  Identities=36%  Similarity=0.774  Sum_probs=44.7

Q ss_pred             CCCCcccccccccCccc-------EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~-------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ..++..|+||++.+.++       +.++|||. ||..|+.+|+.....||+||+.+..
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINH   63 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCE-EEHHHHHHHHHHCSBCTTTCCBCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCCh-HhHHHHHHHHHcCCCCCCCCCccCh
Confidence            35678999999999887       88999999 9999999999888899999998853

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=99.03  E-value=5.4e-11  Score=87.25  Aligned_cols=55  Identities=31%  Similarity=0.734  Sum_probs=47.0

Q ss_pred             CCCcccccccccCccc-EEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         251 SGSRQCYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~-~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      +.+..|+||++.+.++ +.++|||. ||..|+.+|+.....||+||+.+...++.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~C~H~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   58 (68)
T 1chc_A            3 TVAERCPICLEDPSNYSMALPCLHA-FCYVCITRWIRQNPTCPLCKVPVESVVHTIE   58 (68)
T ss_dssp             CCCCCCSSCCSCCCSCEEETTTTEE-ESTTHHHHHHHHSCSTTTTCCCCCCEECCCC
T ss_pred             CCCCCCeeCCccccCCcEecCCCCe-eHHHHHHHHHhCcCcCcCCChhhHhhhhccc
Confidence            4567999999999986 68899999 9999999998878899999999876554443

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=99.02  E-value=1.5e-10  Score=88.26  Aligned_cols=53  Identities=26%  Similarity=0.610  Sum_probs=44.1

Q ss_pred             CCCCCCcccccccccCc--ccEEeC--CCChhccHhhHHhhcCC-CCCCcccccccccc
Q psy3263         248 GSISGSRQCYLCNDREV--THALIP--CGHNFFCSECAERTCDF-DRTCPMCRVPVNQA  301 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~--~~~~lp--CgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~  301 (329)
                      ..++++..|+||++.+.  +++++|  |||+ ||..|+.+++.. ...||+||+++...
T Consensus         6 ~~~~~~~~CpICle~~~~~d~~~~p~~CGH~-fC~~Cl~~~~~~~~~~CP~CR~~~~~~   63 (78)
T 1e4u_A            6 DAKEDPVECPLCMEPLEIDDINFFPCTCGYQ-ICRFCWHRIRTDENGLCPACRKPYPED   63 (78)
T ss_dssp             CCCCCCCBCTTTCCBCCTTTTTCCSSTTSCC-CCHHHHHHHTTSSCSBCTTTCCBCSSC
T ss_pred             cccccCCcCCccCccCccccccccccCCCCC-cCHHHHHHHHhcCCCCCCCCCCccCCC
Confidence            34678899999999773  455666  9999 999999999865 78999999998764

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=99.02  E-value=2e-10  Score=80.63  Aligned_cols=49  Identities=31%  Similarity=0.768  Sum_probs=42.9

Q ss_pred             CCCCcccccccccCcc---cEEeC-CCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         250 ISGSRQCYLCNDREVT---HALIP-CGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~---~~~lp-CgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      ++++..|+||++.+.+   ++.++ |||. ||..|+.+|++....||+||+.+.
T Consensus         2 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            2 MDDGVECAVCLAELEDGEEARFLPRCGHG-FHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCE-ECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCcCccCCccccCCCceEECCCCCCc-ccHHHHHHHHHcCCcCcCCCCEeE
Confidence            4567899999999877   67777 9999 999999999988899999998763

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=99.02  E-value=8.9e-11  Score=92.66  Aligned_cols=50  Identities=30%  Similarity=0.736  Sum_probs=45.4

Q ss_pred             CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +++...|+||++.+.+++.+ +|||. ||..|+.+|+.....||+||..+..
T Consensus        19 ~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           19 IDDLLRCGICFEYFNIAMIIPQCSHN-YCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTTCCE-EEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCCCcccCChhhCCcCEECCCCCH-hhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            35668999999999999988 99999 9999999999988899999998864

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=99.01  E-value=5.5e-11  Score=97.77  Aligned_cols=50  Identities=26%  Similarity=0.669  Sum_probs=44.9

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +++...|+||++.+.+++.++|||. ||..|+..|+.. ...||+||..+..
T Consensus        49 ~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           49 VEETFQCICCQELVFRPITTVCQHN-VCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCE-EEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CccCCCCCcCChHHcCcEEeeCCCc-ccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            3556899999999999999999999 999999999876 5699999999865

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=99.01  E-value=2.4e-10  Score=97.84  Aligned_cols=56  Identities=20%  Similarity=0.148  Sum_probs=51.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++...+   ++.|+|+|++++|++|+.+|.++++
T Consensus       101 ~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~  159 (164)
T 2jvz_A          101 SVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQ  159 (164)
T ss_dssp             THHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             hccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHh
Confidence            5899999999999999999999999986543   7899999999999999999999865

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.01  E-value=3.1e-10  Score=82.03  Aligned_cols=46  Identities=30%  Similarity=0.696  Sum_probs=41.6

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcC---CCCCCccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD---FDRTCPMC  294 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~---~~~~CP~C  294 (329)
                      +.++++..|+||++.+.+++.++|||. ||..|+.+|++   ....||+|
T Consensus        15 ~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           15 NKLQEEVICPICLDILQKPVTIDCGHN-FCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCCBCTTTCSBCSSCEECTTSSE-ECHHHHHHHHHHCSSCCCCSCC
T ss_pred             HhCccCCCCCcCCchhCCeEEeCCCCc-chHHHHHHHHHcCCCCCcCcCC
Confidence            456788999999999999999999999 99999999987   36789998

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.00  E-value=4.7e-10  Score=89.10  Aligned_cols=51  Identities=14%  Similarity=0.100  Sum_probs=47.0

Q ss_pred             CCCCCcccccccccCcccEEeCCC-ChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCG-HNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCg-H~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .+.+++.|+||++.+.+|+.++|| |. ||+.|+.+|+.....||+||.++..
T Consensus        18 ~~p~~~~CpI~~~~m~dPV~~~cG~ht-f~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           18 DACDEFLDPIMSTLMCDPVVLPSSRVT-VDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEEECTTTCCE-EEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cCcHhcCCcCccccccCCeECCCCCeE-ECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            456789999999999999999999 99 9999999999888899999999864

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.00  E-value=3.4e-10  Score=80.14  Aligned_cols=46  Identities=33%  Similarity=0.809  Sum_probs=40.8

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcC---CCCCCccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD---FDRTCPMC  294 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~---~~~~CP~C  294 (329)
                      +.+++...|+||++.+.+++.++|||. ||..|+.+|+.   ....||+|
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           10 ENLQVEASCSVCLEYLKEPVIIECGHN-FCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCSCCCCBCSSSCCBCSSCCCCSSCCC-CCHHHHHHHTTSSCCSCCCSCC
T ss_pred             hccccCCCCccCCcccCccEeCCCCCc-cCHHHHHHHHHhcCCCCCCCCC
Confidence            456778999999999999999999999 99999999954   37899998

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A

Probab=98.99  E-value=1.6e-10  Score=92.77  Aligned_cols=50  Identities=30%  Similarity=0.740  Sum_probs=46.0

Q ss_pred             CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ++++..|+||++.+.+++.+ +|||. ||..|+..|+.....||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFIDATTIIECLHS-FCKTCIVRYLETSKYCPICDVQVHK   62 (108)
T ss_dssp             HGGGTBCTTTSSBCSSEEEETTTCCE-EEHHHHHHHHTSCSBCTTTCCBSCS
T ss_pred             cCCcCCCccCChHHhCcCEeCCCCCh-hhHHHHHHHHHhCCcCcCCCccccc
Confidence            46778999999999999987 99999 9999999999888999999999864

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=98.98  E-value=7.4e-11  Score=102.81  Aligned_cols=68  Identities=24%  Similarity=0.332  Sum_probs=57.1

Q ss_pred             CCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC------CCCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~------~~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      ++++.+.++.||.+.+|.||||||++||+|+++|||+|+++..      ..+|+|+|+| .+++| .+..+|.+.+
T Consensus         2 l~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~~   76 (178)
T 2anr_A            2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG-TIEALNAVHGFIAEKI   76 (178)
T ss_dssp             -CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEe-CHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999864      2578899999 88888 3333555544

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=98.98  E-value=2.6e-10  Score=90.95  Aligned_cols=51  Identities=14%  Similarity=0.051  Sum_probs=46.9

Q ss_pred             CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .+.+.+.|+||++.+.+|+.++|||+ ||..|+.+|+.....||+|+.++..
T Consensus        25 ~~p~~~~CpI~~~~m~dPV~~~cGht-f~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           25 DAPDEFRDPLMDTLMTDPVRLPSGTI-MDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             SCSTTTBCTTTCSBCSSEEEETTTEE-EEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             cCcHhhCCcCccCcccCCeECCCCCE-EchHHHHHHHHcCCCCCCCCCCCCh
Confidence            34678999999999999999999999 9999999999888899999999864

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=98.97  E-value=1e-10  Score=84.27  Aligned_cols=48  Identities=33%  Similarity=0.746  Sum_probs=43.0

Q ss_pred             CCcccccccccCccc-------EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         252 GSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~-------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ++..|+||++.+.++       +.++|||. ||..|+.+|+.....||+||+.+..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   56 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINH   56 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCE-EEHHHHHHHHHHCSBCTTTCCBCTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCc-hhHHHHHHHHHcCCCCCCCCccCCc
Confidence            467999999998876       78999999 9999999999888899999998854

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=98.96  E-value=3.5e-10  Score=97.07  Aligned_cols=56  Identities=16%  Similarity=0.118  Sum_probs=50.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-----cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-----EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-----ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+|+++|||+|+++.++.     ++.|+|+|++++|++|+.+|.++++
T Consensus        95 ~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~  155 (163)
T 3krm_A           95 AAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILA  155 (163)
T ss_dssp             THHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             heeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999986532     4589999999999999999999865

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.96  E-value=1.5e-10  Score=91.62  Aligned_cols=69  Identities=17%  Similarity=0.236  Sum_probs=56.5

Q ss_pred             CCCCceEEEEEecCcccceeecCCCchHHHHHHhc-CceEEcCCCC-CCCeEEEECCCCCCcc-hhhhhhhhh
Q psy3263          81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT-NTYIVTPSRD-KEPVFEVTGNFPEGPG-FESHHGQKI  150 (329)
Q Consensus        81 ~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~t-ga~I~ip~~~-~e~~i~ItG~~pe~ve-ie~~i~d~~  150 (329)
                      .+....+.++.||.++++.|||+||++||+|+++| ||+|.||.+. ....|+|+| ..+.|+ +..+|.+++
T Consensus        12 e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G-~~~~v~~A~~~I~~iv   83 (95)
T 2ctj_A           12 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRG-PSSDVEKAKKQLLHLA   83 (95)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEES-CHHHHHHHHHHHHHHH
T ss_pred             HHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEc-CHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999999999999 9999999765 566899999 777772 223555443

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.95  E-value=2.9e-10  Score=84.77  Aligned_cols=53  Identities=25%  Similarity=0.639  Sum_probs=44.4

Q ss_pred             CCCCCcccccccccCcccE---EeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263         249 SISGSRQCYLCNDREVTHA---LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  302 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~---~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~  302 (329)
                      .+..+..|.||++.+.++.   .++|+|. ||..|+.+|++....||+||+.+....
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           11 ELNLHELCAVCLEDFKPRDELGICPCKHA-FHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCCCSCBCSSSCCBCCSSSCEEEETTTEE-EEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             cCCCCCCCcCCCcccCCCCcEEEcCCCCE-ecHHHHHHHHHcCCcCCCcCccccccc
Confidence            4566789999999986543   4599999 999999999988889999999886543

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=98.95  E-value=2.2e-10  Score=88.47  Aligned_cols=51  Identities=14%  Similarity=0.038  Sum_probs=46.6

Q ss_pred             CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .+.+.+.|+||++.+.+|+.++|||+ ||..|+.+|+.....||+|+.++..
T Consensus        10 ~~p~~~~CpI~~~~m~dPV~~~cGht-f~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           10 DAPDEFRDPLMDTLMTDPVRLPSGTV-MDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             TCCTTTBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             cCchheECcccCchhcCCeECCCCCE-ECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            34678999999999999999999999 9999999999888899999998864

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=98.95  E-value=3.8e-10  Score=97.96  Aligned_cols=54  Identities=17%  Similarity=0.182  Sum_probs=49.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCC------CCcceEEEecCHHHHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVR------GEEPVFVVTGRKEDVARAKREILSA   57 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~------~~ervi~ItG~~e~v~~A~~~I~~i   57 (329)
                      +||.||||+|++||+||++|||+|+++..      ..++.|+|+|++++|++|+.+|.++
T Consensus       114 ~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~  173 (174)
T 1j4w_A          114 KTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK  173 (174)
T ss_dssp             THHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             HcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHh
Confidence            57999999999999999999999999864      2368999999999999999999876

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}

Probab=98.94  E-value=5.2e-10  Score=82.23  Aligned_cols=52  Identities=23%  Similarity=0.563  Sum_probs=43.7

Q ss_pred             CCCCCcccccccccCc---ccEEeCCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263         249 SISGSRQCYLCNDREV---THALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  301 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~---~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~  301 (329)
                      .......|+||++.+.   .++.++|||. ||..|+.+|+.....||+||+.+...
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLPCMHL-FHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECTTSCE-EEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeCCCCH-HHHHHHHHHHHcCCCCcCcCccccCc
Confidence            3456789999988774   4568899999 99999999998888899999988653

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=98.94  E-value=3.6e-10  Score=88.17  Aligned_cols=50  Identities=26%  Similarity=0.575  Sum_probs=44.0

Q ss_pred             CCCCcccccccccCcc---cEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~---~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ..++..|+||++.+..   +..+||||. ||..|+..|+.....||+||+.+..
T Consensus        37 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           37 VGQEMCCPICCSEYVKGDVATELPCHHY-FHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSSCSEETTTTEECCTTCEEEEETTTEE-EEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             cCCCCCCcccChhhcCCCcEEecCCCCh-HHHHHHHHHHHcCCcCcCcCccCCC
Confidence            4567899999998876   677899999 9999999999988899999998754

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=98.93  E-value=2.9e-10  Score=79.70  Aligned_cols=47  Identities=32%  Similarity=0.730  Sum_probs=41.5

Q ss_pred             CCcccccccccCcc----cEEeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         252 GSRQCYLCNDREVT----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       252 ~~~~C~IC~e~~~~----~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      ++..|+||++.+.+    ++.++|||. ||..|+.+|+.....||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHL-LHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCE-EETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCc-ccHHHHHHHHHcCCcCCCCCCcCC
Confidence            45789999998865    678999999 999999999888899999998764

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=98.92  E-value=4.6e-10  Score=96.00  Aligned_cols=55  Identities=20%  Similarity=0.308  Sum_probs=49.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCC----CCcceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVR----GEEPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~----~~ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +||.||||+|++||+||++|||+|+++.+    .+++.|+|+|++++|++|+.+|.+++
T Consensus        99 ~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  157 (160)
T 2jzx_A           99 QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVM  157 (160)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             heeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999852    24799999999999999999998874

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.92  E-value=4.3e-10  Score=84.18  Aligned_cols=50  Identities=28%  Similarity=0.711  Sum_probs=43.5

Q ss_pred             CCCCcccccccccCccc---EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~---~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ..+...|+||++.+...   +.++|+|. ||..|+.+|++....||+||+.+..
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHE-FHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEE-EETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCH-hHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            45678999999988766   67899999 9999999999888899999998753

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}

Probab=98.91  E-value=4.5e-10  Score=95.82  Aligned_cols=51  Identities=27%  Similarity=0.610  Sum_probs=45.4

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQA  301 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~  301 (329)
                      +++.+.|+||++.+.+++.++|||. ||..|+.+|+.. ...||+||..+...
T Consensus        75 l~~~~~C~IC~~~~~~pv~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           75 LEQSFMCVCCQELVYQPVTTECFHN-VCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCE-EEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CccCCEeecCChhhcCCEEcCCCCc-hhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            3456899999999999999999999 999999999987 45899999998654

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.90  E-value=4.1e-10  Score=81.99  Aligned_cols=48  Identities=23%  Similarity=0.652  Sum_probs=40.8

Q ss_pred             CCcccccccc-cCccc----EEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         252 GSRQCYLCND-REVTH----ALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       252 ~~~~C~IC~e-~~~~~----~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      ++..|+||++ .+.++    ++++|||. ||..|+.+|+.. ...||+||+.+..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   55 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHT-LCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCC-EEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCH-hHHHHHHHHHHcCCCcCCCCCCcccc
Confidence            4578999999 77776    57899999 999999999665 6789999998854

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=98.87  E-value=7.4e-10  Score=90.30  Aligned_cols=52  Identities=21%  Similarity=0.526  Sum_probs=46.6

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +.+++.+.|+||++.+.+++.++|||. ||..|+..|+.. ...||+||..+..
T Consensus        13 ~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           13 PPLESKYECPICLMALREAVQTPCGHR-FCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             SCCCGGGBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             cCCCCCCCCCcCChhhcCeEECCcCCh-hhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            356778999999999999999999999 999999999887 4599999999865

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=98.85  E-value=6.2e-10  Score=95.82  Aligned_cols=51  Identities=25%  Similarity=0.615  Sum_probs=45.7

Q ss_pred             CCCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      .+.+...|+||++.+.+++.+ +|||. ||..|+..|+.. ...||+||..+..
T Consensus        50 ~~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           50 SLHSELMCPICLDMLKNTMTTKECLHR-FCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             CCHHHHBCTTTSSBCSSEEEETTTCCE-EEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             hCCCCCCCcccChHhhCcCEeCCCCCh-hHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            456678999999999999987 99999 999999999987 8899999998853

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.84  E-value=6.9e-10  Score=88.96  Aligned_cols=49  Identities=20%  Similarity=0.571  Sum_probs=43.3

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCC---CCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFD---RTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~---~~CP~Cr~~i~~  300 (329)
                      .+...|+||++.+.+++.++|||. ||..|+..|+...   ..||+||..+..
T Consensus        19 ~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           19 QKILECPICLELIKEPVSTKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCC-CCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCCCCCcccChhhcCeEECCCCCH-HHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            446789999999999999999999 9999999998763   589999998854

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.84  E-value=7.4e-10  Score=78.68  Aligned_cols=46  Identities=30%  Similarity=0.745  Sum_probs=40.4

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .+.+.|+||++.+.+++.++|||. ||..|+..+   ...||+||+.+..
T Consensus         4 ~~~~~C~IC~~~~~~p~~l~CgH~-fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCBCCSCSTTSCC-SBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             ccCCCceEeCCccCCeEEcCCCCc-ccHHHHccC---CCCCCcCCcEeec
Confidence            456899999999999999999999 999999773   5689999998753

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.83  E-value=5.5e-10  Score=107.51  Aligned_cols=53  Identities=40%  Similarity=0.959  Sum_probs=47.8

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF  306 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~  306 (329)
                      ++++..|+||++.+.+++++||||.+||..|+.++    ..||+||.++...+++|+
T Consensus       292 l~~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~~~~i~~  344 (345)
T 3t6p_A          292 LQEERTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGTVRTFL  344 (345)
T ss_dssp             HHTTCBCTTTSSSBCCEEEETTCCEEECTTTGGGC----SBCTTTCCBCCEEEECC-
T ss_pred             CcCCCCCCccCCcCCceEEcCCCChhHhHHHHhcC----CcCCCCCCCccCeEEeec
Confidence            45678999999999999999999999999999988    789999999998887764

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.83  E-value=3.8e-10  Score=91.87  Aligned_cols=47  Identities=26%  Similarity=0.644  Sum_probs=43.0

Q ss_pred             CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      +++.+.|+||++.+.+|+.+ +|||. ||..|+..|+.  ..||+||..+.
T Consensus        19 l~~~~~C~IC~~~~~~pv~~~~CgH~-fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           19 LEKLLRCSRCTNILREPVCLGGCEHI-FCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             HHHTTSCSSSCSCCSSCBCCCSSSCC-BCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             chhCCCCCCCChHhhCccEeCCCCCH-HHHHHHHHHhc--CCCcCCCCcCc
Confidence            45678999999999999998 99999 99999999987  78999999884

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=98.82  E-value=1.5e-09  Score=91.97  Aligned_cols=57  Identities=23%  Similarity=0.255  Sum_probs=48.7

Q ss_pred             eeeeeecCCChHHHHHHHHhCC-eEEecCCCC------cc--eEEEecCHHHHHHHHHHHHHHhhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNT-YIKTPVRGE------EP--VFVVTGRKEDVARAKREILSAADH   60 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga-~I~ip~~~~------er--vi~ItG~~e~v~~A~~~I~~i~e~   60 (329)
                      .+|++|||+|++||.+++.||+ +|+++...+      ++  .|+|+|++++|++|+.+|.+.+.+
T Consensus        77 ~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           77 LVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             GHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             HcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4689999999999999999997 999985332      23  489999999999999999998753

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=98.79  E-value=2.7e-09  Score=86.01  Aligned_cols=48  Identities=23%  Similarity=0.571  Sum_probs=40.1

Q ss_pred             CcccccccccCcccE------------------EeCCCChhccHhhHHhhc-----CCCCCCcccccccccc
Q psy3263         253 SRQCYLCNDREVTHA------------------LIPCGHNFFCSECAERTC-----DFDRTCPMCRVPVNQA  301 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~------------------~lpCgH~~fC~~Cl~~~~-----~~~~~CP~Cr~~i~~~  301 (329)
                      +..|+||++.+.++.                  +++|+|. ||..|+..|+     .....||+||+.+...
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~-Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHA-FHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCE-ECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCc-ccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            469999999986543                  7899999 9999999998     4477999999987543

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=98.78  E-value=9.2e-10  Score=92.96  Aligned_cols=50  Identities=20%  Similarity=0.466  Sum_probs=45.1

Q ss_pred             CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263         248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPV  298 (329)
Q Consensus       248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i  298 (329)
                      +.+++++.|+||++.+.+|+.++|||. ||..|+.+|+.. ...||+||.++
T Consensus        26 ~~l~~~~~C~IC~~~~~~pv~~~CgH~-FC~~Ci~~~~~~~~~~CP~Cr~~~   76 (141)
T 3knv_A           26 TKLEAKYLCSACRNVLRRPFQAQCGHR-YCSFCLASILSSGPQNCAACVHEG   76 (141)
T ss_dssp             GGCCGGGBCTTTCSBCSSEEECTTSCE-EEHHHHHHHGGGSCEECHHHHHTT
T ss_pred             ccCCcCcCCCCCChhhcCcEECCCCCc-cCHHHHHHHHhcCCCCCCCCCCcc
Confidence            356788999999999999999999999 999999999886 45999999975

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=98.78  E-value=1.2e-09  Score=105.81  Aligned_cols=66  Identities=21%  Similarity=0.304  Sum_probs=57.0

Q ss_pred             CCceEEEEEecCcccceeecCCC--chHHHHHHhcCceEEcCCCC--------CCCeEEEECCCCCCcchhh-hhhhh
Q psy3263          83 PGHVTIEVRVPYKVVGLVVGPKG--ATIKRIQHQTNTYIVTPSRD--------KEPVFEVTGNFPEGPGFES-HHGQK  149 (329)
Q Consensus        83 ~g~~t~~i~VP~~~vG~IIGkgG--~tIk~Iq~~tga~I~ip~~~--------~e~~i~ItG~~pe~veie~-~i~d~  149 (329)
                      +..+|+++.||+.+|++||||||  ++|++|+++|||+|+||.++        +...|+|+| .+++||.+. .|.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG-~~enVE~AR~~I~~l  103 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITG-YFGDVDRARMLMRRN  103 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEE-EHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEc-CHHHHHHHHHHHHhc
Confidence            46799999999999999999999  99999999999999999765        345699999 999994444 66654

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.77  E-value=2.3e-09  Score=87.80  Aligned_cols=49  Identities=37%  Similarity=0.807  Sum_probs=44.8

Q ss_pred             CCCcccccccccCccc-------EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~-------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .++..|+||++.+.++       +.++|||. ||..|+.+|++....||+||+.+..
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   60 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINH   60 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCE-EEHHHHHHHHTTCSBCTTTCCBCTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCCh-hhHHHHHHHHHhCCCCCCCCCcCcc
Confidence            4678999999999888       89999999 9999999999998899999998853

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=4.6e-09  Score=86.27  Aligned_cols=58  Identities=16%  Similarity=0.125  Sum_probs=48.4

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCC-------------CcceEEEe-cCHHHHHHHHHHHHHHhh
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRG-------------EEPVFVVT-GRKEDVARAKREILSAAD   59 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-------------~ervi~It-G~~e~v~~A~~~I~~i~e   59 (329)
                      |.|+|.|||++|.+||+|+++|||+|.|-.++             ++-.|.|+ .+.+++++|+.+|.+++.
T Consensus        27 fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~~Ie~Ll~   98 (119)
T 2yqr_A           27 FNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKKLCENLLQ   98 (119)
T ss_dssp             TCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHHHHHHHhh
Confidence            88999999999999999999999999996332             22245565 569999999999999864

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*

Probab=98.75  E-value=2.9e-09  Score=103.64  Aligned_cols=54  Identities=26%  Similarity=0.706  Sum_probs=47.0

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcC-CCCCCcccccccccchhhh
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQAMRII  305 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~-~~~~CP~Cr~~i~~~~~i~  305 (329)
                      +....|+||++.+.+++.+||||. ||..|+..|.. ....||+||+.+.....+.
T Consensus       330 ~~~~~C~ICle~~~~pv~lpCGH~-FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~i~  384 (389)
T 2y1n_A          330 STFQLCKICAENDKDVKIEPCGHL-MCTSCLTSWQESEGQGCPFCRCEIKGTEPIV  384 (389)
T ss_dssp             TSSSBCTTTSSSBCCEEEETTCCE-ECHHHHHHHHHHTCSBCTTTCCBCCEEEECS
T ss_pred             CCCCCCCccCcCCCCeEEeCCCCh-hhHHHHHHHHhcCCCCCCCCCCccCCceeEe
Confidence            445799999999999999999999 99999999988 5789999999987654443

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.74  E-value=4.7e-09  Score=82.40  Aligned_cols=47  Identities=19%  Similarity=0.395  Sum_probs=41.6

Q ss_pred             CCCCcccccccccCcccEEeC-CCChhccHhhHHhhcCC------CCCCcc--cccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF------DRTCPM--CRVP  297 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lp-CgH~~fC~~Cl~~~~~~------~~~CP~--Cr~~  297 (329)
                      ...++.|+||++.+.+|+.++ |||. ||..|+..|+..      ...||+  |++.
T Consensus         4 ~~~~~~CPI~~~~~~dPV~~~~cGh~-f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            4 GSSGFTCPITKEEMKKPVKNKVCGHT-YEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             CSSCCBCTTTCSBCSSEEEESSSCCE-EEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CCcEeECcCcCchhcCCEEcCCCCCe-ecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            356789999999999999996 9999 999999999875      358999  9876

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=98.73  E-value=3.5e-09  Score=85.79  Aligned_cols=50  Identities=28%  Similarity=0.604  Sum_probs=45.3

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +.++..|+||++.+.+++.++|||. ||..|+.+|+.. ...||+||..+..
T Consensus        20 ~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           20 FVKSISCQICEHILADPVETSCKHL-FCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             ccCCCCCCCCCcHhcCcEEcCCCCc-ccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            4567899999999999999999999 999999999887 7899999999854

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.70  E-value=6e-09  Score=95.71  Aligned_cols=49  Identities=14%  Similarity=0.144  Sum_probs=43.9

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      ...+.|+||++.+.+|++++|||+ ||..|+.+|+.. ...||+||.++..
T Consensus       206 ~~~~~c~i~~~~~~dPv~~~~gh~-f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          206 PDYLCGKISFELMREPCITPSGIT-YDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CSTTBCTTTCSBCSSEEECSSCCE-EETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CcccCCcCcCCHhcCCeECCCCCE-ECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            467899999999999999999999 999999999876 4459999999854

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.69  E-value=2e-09  Score=84.25  Aligned_cols=54  Identities=19%  Similarity=0.262  Sum_probs=47.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCe-EEecCCCCcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTY-IKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~-I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~e   59 (329)
                      ++|.+||+||.+||+|+++||++ |++.  +++..|+|.| ..+++++|+.+|..+.+
T Consensus        25 kIg~vIG~gGk~Ik~I~e~tGv~~IdI~--eddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           25 LMGLAIGTHGSNIQQARKVPGVTAIELD--EDTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             HHHHHHTTTTHHHHHHHTSTTEEEEEEE--TTTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             HhhhhcCCCcHHHHHHHHHhCCeEEEEE--cCCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            36889999999999999999998 9995  3457889999 89999999999976643

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.68  E-value=1.1e-08  Score=78.02  Aligned_cols=46  Identities=20%  Similarity=0.510  Sum_probs=37.6

Q ss_pred             CcccccccccCcc--------------cE-EeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         253 SRQCYLCNDREVT--------------HA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       253 ~~~C~IC~e~~~~--------------~~-~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      +..|.||++.+.+              .+ +.+|+|. |+..|+.+|+.....||+||+.+.
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~   75 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHS-FHNCCMSLWVKQNNRCPLCQQDWV   75 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCE-EEHHHHHHHTTTCCBCTTTCCBCC
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCc-cChHHHHHHHHhCCCCCCcCCCcc
Confidence            4568888877754              33 4469999 999999999999889999999874

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.65  E-value=1.3e-08  Score=84.98  Aligned_cols=58  Identities=28%  Similarity=0.299  Sum_probs=49.2

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCC-------------------CcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRG-------------------EEPVFVVTG-RKEDVARAKREILSAAD   59 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-------------------~ervi~ItG-~~e~v~~A~~~I~~i~e   59 (329)
                      |+|||.|||.+|.+||+|+++|||+|.|-.++                   ++-.|.|++ ..+.+++|+.+|..++.
T Consensus        21 ~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~~~A~~~I~~ll~   98 (131)
T 1k1g_A           21 INFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILK   98 (131)
T ss_dssp             HHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHHHT
T ss_pred             cceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHHHHHHHHHHHHHh
Confidence            78999999999999999999999999996422                   133567888 68899999999999864

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=98.59  E-value=1.6e-08  Score=87.20  Aligned_cols=51  Identities=22%  Similarity=0.547  Sum_probs=46.2

Q ss_pred             CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      .+++.+.|+||++.+.+|+.++|||. ||..|+.+|+.. ...||+||..+..
T Consensus        14 ~~~~~~~C~IC~~~~~~pv~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (170)
T 3hcs_A           14 PLESKYECPICLMALREAVQTPCGHR-FCKACIIKSIRDAGHKCPVDNEILLE   65 (170)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCCChhhcCcEECCCCCH-HHHHHHHHHHHhCCCCCCCCccCcch
Confidence            46788999999999999999999999 999999999876 5699999998855

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.58  E-value=1.8e-08  Score=88.39  Aligned_cols=51  Identities=16%  Similarity=0.156  Sum_probs=45.2

Q ss_pred             CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      .+.+.+.|+||++.+.+|+.+||||+ ||..|+..|+.. ...||+|+.++..
T Consensus       102 ~ip~~f~CPI~~elm~DPV~~~~Ght-fer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          102 EIPDYLCGKISFELMREPCITPSGIT-YDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCcHhhcccCccccCCCCeECCCCCE-ECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            34567999999999999999999999 999999999976 4479999998864

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.58  E-value=1.1e-08  Score=79.96  Aligned_cols=57  Identities=18%  Similarity=0.327  Sum_probs=49.4

Q ss_pred             CCCceEEEEEecCcccceeecCCCchHHHHHHhcCce-EEcCCCCCCCeEEEECCCCCCc
Q psy3263          82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY-IVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~-I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      +......++.||.+++|.+||+||++||+|+++||++ |.+.  +++..|+|.|+..+.+
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~--eddG~V~I~g~~~ea~   68 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD--EDTGTFRIYGESADAV   68 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE--TTTTEEEEEESSHHHH
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE--cCCCEEEEEECCHHHH
Confidence            3455889999999999999999999999999999998 9994  3458899999666666

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.56  E-value=1.2e-08  Score=83.45  Aligned_cols=49  Identities=37%  Similarity=0.807  Sum_probs=44.0

Q ss_pred             CCCcccccccccCccc-------EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~-------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      ++...|+||++.+.++       +.++|||. ||..|+.+|++....||+||..+..
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~  125 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINH  125 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBE-EEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCCh-hhHHHHHHHHHcCCCCCCCCCcCCh
Confidence            4568999999988876       88999999 9999999999888999999998854

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.52  E-value=4.7e-08  Score=88.34  Aligned_cols=52  Identities=13%  Similarity=0.077  Sum_probs=48.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      .+|+||||+|.|||.|++.|||+|.++    ++.|.|.|..++++.|+++|.++++
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~----~~~v~i~G~~~~i~~A~~~i~~li~  190 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVY----GKTVAIIGNPIQIEIAKTAIEKLAR  190 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEE----TTEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             hhheeECCCchHHHHHHHHhCceEEEC----CeEEEEEeCHHHHHHHHHHHHHHHc
Confidence            478899999999999999999999997    4678999999999999999999874

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.51  E-value=2.9e-08  Score=83.62  Aligned_cols=58  Identities=28%  Similarity=0.310  Sum_probs=48.1

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC--------------------cc-eEEEecC-HH-----HHHHHHHHH
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE--------------------EP-VFVVTGR-KE-----DVARAKREI   54 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--------------------er-vi~ItG~-~e-----~v~~A~~~I   54 (329)
                      |+|||+|||.+|.++|+|+++|||+|.|-.++.                    |+ -|.|++. .+     .+++|+.+|
T Consensus        16 ~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I   95 (140)
T 2bl5_A           16 FNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEV   95 (140)
T ss_dssp             SCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHH
T ss_pred             CCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHH
Confidence            899999999999999999999999999976552                    11 5678874 33     789999999


Q ss_pred             HHHhh
Q psy3263          55 LSAAD   59 (329)
Q Consensus        55 ~~i~e   59 (329)
                      ..++.
T Consensus        96 ~~lL~  100 (140)
T 2bl5_A           96 KKLLV  100 (140)
T ss_dssp             HHHSS
T ss_pred             HHHCC
Confidence            98863

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=98.50  E-value=6.8e-08  Score=77.70  Aligned_cols=46  Identities=22%  Similarity=0.437  Sum_probs=39.5

Q ss_pred             CCcccccccccCccc------------------EEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         252 GSRQCYLCNDREVTH------------------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~------------------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      ++..|.||++.+.++                  ++++|+|. |+..|+..|+.....||+||+.+
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~-FH~~Ci~~Wl~~~~~CP~Cr~~~   99 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHA-FHFHCISRWLKTRQVCPLDNREW   99 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCE-EEHHHHHHHHTTCSBCSSSCSBC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcE-ECHHHHHHHHHcCCcCcCCCCcc
Confidence            356799999887644                  46899999 99999999999989999999985

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.45  E-value=6.2e-08  Score=80.84  Aligned_cols=68  Identities=29%  Similarity=0.423  Sum_probs=51.0

Q ss_pred             CceEEEEEecCc------ccceeecCCCchHHHHHHhcCceEEcCCCC------------------CCC-eEEEECCCCC
Q psy3263          84 GHVTIEVRVPYK------VVGLVVGPKGATIKRIQHQTNTYIVTPSRD------------------KEP-VFEVTGNFPE  138 (329)
Q Consensus        84 g~~t~~i~VP~~------~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------------------~e~-~i~ItG~~pe  138 (329)
                      ...+..|.||.+      ++|.|||++|.|||+|+++|||+|.|-.+.                  +++ .|.|++..++
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            347788999977      899999999999999999999999995421                  223 3889996666


Q ss_pred             Cc-chhhhhhhhhh
Q psy3263         139 GP-GFESHHGQKIV  151 (329)
Q Consensus       139 ~v-eie~~i~d~~~  151 (329)
                      .+ ...++|.+++.
T Consensus        85 ~~~~A~~~I~~ll~   98 (131)
T 1k1g_A           85 NVKKAVEQIRNILK   98 (131)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence            66 22225555543

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=98.39  E-value=9.4e-08  Score=88.18  Aligned_cols=50  Identities=18%  Similarity=0.264  Sum_probs=44.0

Q ss_pred             CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCC--CCCCcc--ccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF--DRTCPM--CRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~--~~~CP~--Cr~~i~~  300 (329)
                      ...++.|+||++.+.+|+.. .|||+ ||..|+.+++..  ...||+  |++.+..
T Consensus       178 ~~~el~CPIcl~~f~DPVts~~CGHs-FcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          178 GKIELTCPITCKPYEAPLISRKCNHV-FDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             SBCCSBCTTTSSBCSSEEEESSSCCE-EEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             CceeeECcCccCcccCCeeeCCCCCc-ccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            46678999999999999975 99999 999999999986  468999  9997743

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.23  E-value=2.9e-07  Score=71.73  Aligned_cols=45  Identities=27%  Similarity=0.672  Sum_probs=37.1

Q ss_pred             CCcccccccccCcccEEe---CCCChhccHhhHHhhcCC--------CCCCcc--cccc
Q psy3263         252 GSRQCYLCNDREVTHALI---PCGHNFFCSECAERTCDF--------DRTCPM--CRVP  297 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~~~l---pCgH~~fC~~Cl~~~~~~--------~~~CP~--Cr~~  297 (329)
                      +...|.||++.+..+..+   +|||. ||.+|+..++..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~-FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCI-FCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEE-EEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCc-ccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            467899999998776533   79999 999999988753        258999  9998

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=98.23  E-value=5.4e-07  Score=79.70  Aligned_cols=52  Identities=25%  Similarity=0.228  Sum_probs=47.7

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      ++|+||||+|.|||.|++.|||+|.+.    ++.+.|.|..++++.|+..|..+++
T Consensus       108 ~~GrIIGk~G~tik~iE~~Tg~~I~v~----~~~v~i~G~~~~i~~Ar~~i~~li~  159 (191)
T 1tua_A          108 IKGRIIGEGGRARRTIEEMTDTYINVG----EYEVAIIGDYERAMAAKQAIEMLAE  159 (191)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC----SSEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HhhheeCCCccHHHHHHHHHCceEEEc----CCEEEEEeChHHHHHHHHHHHHHHc
Confidence            469999999999999999999999998    4578999999999999999998864

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=98.18  E-value=2.4e-07  Score=75.77  Aligned_cols=45  Identities=22%  Similarity=0.471  Sum_probs=0.4

Q ss_pred             CcccccccccCccc------------------EEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         253 SRQCYLCNDREVTH------------------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       253 ~~~C~IC~e~~~~~------------------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      +..|.||++.+.++                  +.++|+|. |+..|+.+|+.....||+||+.+
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~-FH~~CI~~Wl~~~~~CP~Cr~~~  110 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHA-FHFHCISRWLKTRQVCPLDNREW  110 (117)
T ss_dssp             C---------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCce-EcHHHHHHHHHcCCcCCCCCCee
Confidence            35899999887653                  23599999 99999999999888999999975

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.16  E-value=1.6e-06  Score=66.11  Aligned_cols=49  Identities=20%  Similarity=0.510  Sum_probs=40.5

Q ss_pred             CCCcccccccccC--cccEEeCCC-----ChhccHhhHHhhcCC--CCCCccccccccc
Q psy3263         251 SGSRQCYLCNDRE--VTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~--~~~~~lpCg-----H~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~  300 (329)
                      .+...|.||++.+  .+++++||.     |. |...|+.+|+..  ...||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~-fH~~Cl~~Wl~~~~~~~CplCr~~~~~   70 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLITPCHCTGSLHF-VHQACLQQWIKSSDTRCCELCKYEFIM   70 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEECSSSCCSSSCC-EETTHHHHHHHHHCCSBCSSSCCBCCC
T ss_pred             CCCCCCeEcCccccCCCeeEeccccCCcCCe-eCHHHHHHHHhhCCCCCCCCCCCeeec
Confidence            4567999999766  356778996     98 999999999887  3699999998743

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.14  E-value=6.4e-07  Score=73.45  Aligned_cols=66  Identities=21%  Similarity=0.226  Sum_probs=48.9

Q ss_pred             eEEEEEecC-------cccceeecCCCchHHHHHHhcCceEEcCCCC------------CCC-eEEEECCCCCCc-chhh
Q psy3263          86 VTIEVRVPY-------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------------KEP-VFEVTGNFPEGP-GFES  144 (329)
Q Consensus        86 ~t~~i~VP~-------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------------~e~-~i~ItG~~pe~v-eie~  144 (329)
                      .+..|.||-       +++|.|||++|.+||+|+++|||+|.|-.+.            +++ .|.|++..++++ ++..
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            455666664       4889999999999999999999999996331            133 488998678887 3333


Q ss_pred             hhhhhhh
Q psy3263         145 HHGQKIV  151 (329)
Q Consensus       145 ~i~d~~~  151 (329)
                      +|.+++.
T Consensus        92 ~Ie~Ll~   98 (119)
T 2yqr_A           92 LCENLLQ   98 (119)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhh
Confidence            6666655

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.04  E-value=2.2e-06  Score=72.09  Aligned_cols=37  Identities=30%  Similarity=0.555  Sum_probs=31.9

Q ss_pred             EEEEEecC------cccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          87 TIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        87 t~~i~VP~------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      +..|.||.      +++|.|||++|.|+|+|+++|||+|.|-.
T Consensus         3 ~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrG   45 (140)
T 2bl5_A            3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRG   45 (140)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEES
T ss_pred             eeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEec
Confidence            45666664      56999999999999999999999999964

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=97.97  E-value=1.9e-06  Score=62.23  Aligned_cols=47  Identities=13%  Similarity=0.109  Sum_probs=42.1

Q ss_pred             CcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         253 SRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .+.|+||++.+.+|+.. +|||. ||+.|+.+|+.....||+++.++..
T Consensus         3 ~~~CpIs~~~m~dPV~~~~sG~~-yer~~I~~~l~~~~~cP~t~~~L~~   50 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLSPKSRTI-FEKSLLEQYVKDTGNDPITNEPLSI   50 (61)
T ss_dssp             -CCCTTTCSCCSSEEEETTTTEE-EEHHHHHHHHHHHSBCTTTCCBCCG
T ss_pred             eEEecCCCCCCCCCEEeCCCCcE-EcHHHHHHHHHhCCCCcCCcCCCCh
Confidence            46899999999999999 99999 9999999999886679999998854

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.87  E-value=1.1e-05  Score=83.06  Aligned_cols=52  Identities=31%  Similarity=0.420  Sum_probs=45.7

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ...++.||.+++|.|||+||++||+|+++|||+|.|-   ++-.|.|.|+.++.+
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~---d~G~V~I~~~~~~~~  618 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV---DEETFSVFAPTPSAM  618 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC---SSSEEEEEESSHHHH
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc---CCcEEEEEeCCHHHH
Confidence            6789999999999999999999999999999999996   357899999445555

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.82  E-value=1.7e-05  Score=65.97  Aligned_cols=60  Identities=17%  Similarity=0.104  Sum_probs=51.9

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCC--CcceEEEecCHHHHHHHHHHHHHHhhhhhH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG--EEPVFVVTGRKEDVARAKREILSAADHFSA   63 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~--~ervi~ItG~~e~v~~A~~~I~~i~e~~~~   63 (329)
                      +|+.|+|++|+.|+.|+..|+|.|++-.-+  .+.-|+|.|++..=.+|+.+|.++++.+.+
T Consensus        66 lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~hr~  127 (140)
T 3v69_A           66 LLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPPPFRRDVDRMLTDLAHYCRM  127 (140)
T ss_dssp             GHHHHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEECCHHHHHHHHHHHHHHHHHHHH
Confidence            478899999999999999999999996433  366789999999999999999999875543

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.67  E-value=1.2e-05  Score=68.00  Aligned_cols=92  Identities=16%  Similarity=0.100  Sum_probs=65.3

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPG   84 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~g   84 (329)
                      ||..||++|++|+.|+++.|-+|++-...++              ....|..++.        +.......  .. ..++
T Consensus        47 vGa~IG~~G~ri~~i~~elgekIdIV~~s~d--------------~~~fI~naLs--------PA~V~~V~--i~-~~~~  101 (144)
T 2cxc_A           47 AGRAIGRGGRLIKLLREALGKNIEVVEYSSD--------------LERIVKNLFP--------GVKIESIN--VR-ERNG  101 (144)
T ss_dssp             HHHHHCGGGHHHHHHHHHHSSEEEEEECCSS--------------HHHHHHHHST--------TSCEEEEE--EE-EETT
T ss_pred             ccccCccCchHHHHHHHHhCCeeEEEEcCCC--------------HHHHHHHhcC--------CceEEEEE--Ee-ecCC
Confidence            6999999999999999999999988644443              1233433321        00000000  00 0135


Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  121 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i  121 (329)
                      .....+.||.+..++.|||+|.+++-..+-||.+|.|
T Consensus       102 ~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI  138 (144)
T 2cxc_A          102 VKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGV  138 (144)
T ss_dssp             EEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCE
T ss_pred             cEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCc
Confidence            5778899999999999999999999999999988765

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.66  E-value=1.8e-05  Score=62.38  Aligned_cols=49  Identities=33%  Similarity=0.662  Sum_probs=38.4

Q ss_pred             ccccccccCcccE-EeCCCChhccHhhHHhhcCC-CCCCcccccccccchhh
Q psy3263         255 QCYLCNDREVTHA-LIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRI  304 (329)
Q Consensus       255 ~C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~~i  304 (329)
                      -|.+|--...... .+||.|. ||.+|+..+.++ ...||.|+.++...-+.
T Consensus         3 fC~~C~~Pi~iygRmIPCkHv-FCydCa~~~~~~~~k~Cp~C~~~V~rVe~~   53 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHV-FCYDCAILHEKKGDKMCPGCSDPVQRIEQC   53 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCE-EEHHHHHHHHHTTCCBCTTTCCBCSEEEEE
T ss_pred             ecCccCCCeEEEeeecccccc-HHHHHHHHHHhccCCCCcCcCCeeeeeEEe
Confidence            4777765555443 7899998 999999998766 89999999998665444

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.39  E-value=0.00034  Score=52.39  Aligned_cols=49  Identities=16%  Similarity=0.445  Sum_probs=40.2

Q ss_pred             CCCcccccccccCcccE-EeCCCChhccHhhHHhhcCCC--CCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDFD--RTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~~~--~~CP~Cr~~i~~  300 (329)
                      +....|.||++.+.... -..|+|. |-..|+.+|++..  ..||+||+....
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~~C~h~-fH~~Ci~kWl~~~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCETCGIR-MHLPCVAKYFQSNAEPRCPHCNDYWPH   64 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECSSSCCE-ECHHHHHHHSTTCSSCCCTTTCSCCCS
T ss_pred             CCCCcCcchhhHcccCCccCCCCch-hhHHHHHHHHHhcCCCCCCCCcCcCCC
Confidence            44579999999887544 2389999 9999999999885  899999987643

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.21  E-value=0.00013  Score=76.10  Aligned_cols=52  Identities=17%  Similarity=0.229  Sum_probs=5.3

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ...++.||.+++|.|||+||.+||+|+++||++|.+-   ++..|.|.+...+.+
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~---ddG~v~I~~~~~~~~  621 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN---DDGVVKVSASDGAKI  621 (726)
T ss_dssp             C----------------------------------------------CCSCHHHH
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE---CCceEEEEeCCHHHH
Confidence            5678899999999999999999999999999999885   345678888445555

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=97.07  E-value=0.0002  Score=51.36  Aligned_cols=48  Identities=23%  Similarity=0.589  Sum_probs=38.7

Q ss_pred             CCCcccccccccCcccEEeCCCC-----hhccHhhHHhhcCC--CCCCcccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGH-----NFFCSECAERTCDF--DRTCPMCRVPVN  299 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH-----~~fC~~Cl~~~~~~--~~~CP~Cr~~i~  299 (329)
                      ++...|.||++...++...||.+     . |-..|+.+|+..  ...||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~~l~~PC~C~gs~~~-~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGNERFRACGCTGELEN-VHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGS-CCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCCCceecCcCCCCchhh-hHHHHHHHHHHhCCCCccCCCCCeee
Confidence            35578999998776666789764     4 888999999875  689999998764

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=96.83  E-value=0.00028  Score=67.46  Aligned_cols=52  Identities=15%  Similarity=0.398  Sum_probs=40.2

Q ss_pred             CCCcccccccccCcccE--------EeCCCChhccHhhHHhhcCC-----------CCCCcccccccccchh
Q psy3263         251 SGSRQCYLCNDREVTHA--------LIPCGHNFFCSECAERTCDF-----------DRTCPMCRVPVNQAMR  303 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~--------~lpCgH~~fC~~Cl~~~~~~-----------~~~CP~Cr~~i~~~~~  303 (329)
                      +...+|.||++...+.-        ...|+|. |-..|+.+|++.           ...||.||+++.....
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~-FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf~  376 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLK-CHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFA  376 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCC-BCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCc-cchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccHH
Confidence            45689999998776511        2379999 999999999865           1579999999865433

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=96.73  E-value=0.00097  Score=61.02  Aligned_cols=93  Identities=16%  Similarity=0.140  Sum_probs=65.3

Q ss_pred             eeeeecCCChHHHHH-HHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKAL-RAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~L-r~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||++|.+|+.| ++-.|-+|++-...+++              ...|...+.        +.......  .  .-+
T Consensus       128 vGacIG~~G~rI~~i~~eL~gekIDIi~~s~dp--------------~~fi~nals--------PA~V~~V~--i--~~~  181 (251)
T 2asb_A          128 KGACIGPMGQRVRNVMSELSGEKIDIIDYDDDP--------------ARFVANALS--------PAKVVSVS--V--IDQ  181 (251)
T ss_dssp             HHHHHCGGGHHHHHHHHHTTTCEEEEEECCSSH--------------HHHHHHHTT--------TSCCSEEE--E--EET
T ss_pred             HHHHhCCCchHHHHHHHHhCCCeEEEEEecCCH--------------HHHHHhccC--------CcceEEEE--E--EcC
Confidence            688899999999999 77789999986555442              233333311        00000000  0  001


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      ...+..+.||.+..++-|||+|.+|+--.+-||-+|.|-.
T Consensus       182 ~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  221 (251)
T 2asb_A          182 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  221 (251)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceE
Confidence            2357889999999999999999999999999999999854

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=96.62  E-value=0.00085  Score=55.74  Aligned_cols=52  Identities=15%  Similarity=0.214  Sum_probs=43.9

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC--CCCeEEEECCCCCC
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--KEPVFEVTGNFPEG  139 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~--~e~~i~ItG~~pe~  139 (329)
                      -..+.|....++.|||++|+.|+.|++.|+|.|++-.-+  ++-.|+|.| .+..
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG-~~~~  110 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFG-PPPF  110 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEES-CHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEEC-CHHH
Confidence            367889999999999999999999999999999996544  455599999 5443

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=96.55  E-value=0.0015  Score=62.84  Aligned_cols=94  Identities=16%  Similarity=0.138  Sum_probs=66.8

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||++|.+|+.|.++. |-+|++-...+++              ...|..++.        +.......  .  -.+
T Consensus       251 vGacIG~~G~rI~~i~~eL~gekIDIi~~s~dp--------------~~fi~nals--------PA~V~~V~--~--~~~  304 (366)
T 1k0r_A          251 KGACIGPMGQRVRNVMSELSGEKIDIIDYDDDP--------------ARFVANALS--------PAKVVSVS--V--IDQ  304 (366)
T ss_dssp             HHHHHCGGGHHHHHHHHHTTTCEEEEEECCSSH--------------HHHHHHHTT--------TSCCSEEE--E--EET
T ss_pred             cccccCCcchHHHHHHHHhCCCeEEEEEcCCCH--------------HHHHHHhcC--------CcceeEEE--E--EcC
Confidence            6889999999999999999 8889886444431              233333321        00000000  0  012


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  124 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~  124 (329)
                      ...+..+.||.+..++.|||+|.+++-..+-||.+|.|-..
T Consensus       305 ~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          305 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             CCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            24678999999999999999999999999999999998543

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.45  E-value=0.0006  Score=71.17  Aligned_cols=52  Identities=19%  Similarity=0.128  Sum_probs=11.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~   58 (329)
                      .+|.+||+||.+||+|+++||++|++-  ++..+ .|.+ ..+++++|+..|..++
T Consensus       580 ki~~vig~gg~~i~~i~~~tg~~idi~--ddG~v-~I~~~~~~~~~~A~~~i~~i~  632 (726)
T 4aid_A          580 KIREVIGSGGKVIREIVATTGAKVDIN--DDGVV-KVSASDGAKIKAAIDWIKSIT  632 (726)
T ss_dssp             -------------------------------------CCSCHHHHHHHHHC-----
T ss_pred             HHHhhcCCCchhHHHHHHHHCCceeEE--CCceE-EEEeCCHHHHHHHHHHHHHHh
Confidence            468899999999999999999999986  33344 5555 5999999999998874

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=95.64  E-value=0.0063  Score=58.16  Aligned_cols=93  Identities=16%  Similarity=0.109  Sum_probs=65.4

Q ss_pred             eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263           5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   83 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~   83 (329)
                      ||..||.+|.+|+.+.++. |-+|++-...+++.              ..|...+.        +.......  .  .-+
T Consensus       247 vGacvg~~G~ri~~i~~el~ge~Idii~~s~d~~--------------~fi~nal~--------Pa~v~~v~--~--~d~  300 (344)
T 1hh2_P          247 IGACIGEGGSRIAAILKELKGEKLDVLKWSDDPK--------------QLIANALA--------PATVIEVE--I--LDK  300 (344)
T ss_dssp             HHHHHCTTSTTHHHHHHHTTTCEEEEEECCSSHH--------------HHHHHHTC--------SSCCSEEE--E--EET
T ss_pred             cceeeccCCcEeHHHHHHhCCCeeeEEecCCCHH--------------HHHHHhcC--------ccEEEEEE--E--EcC
Confidence            6889999999999999998 78888764444332              23333210        00000000  0  012


Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      +..+..+.||.+..++-|||+|.+++--.+-||-+|.|-+
T Consensus       301 ~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          301 ENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             TTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            3467899999999999999999999999999999998843

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=94.94  E-value=0.012  Score=61.60  Aligned_cols=52  Identities=15%  Similarity=0.231  Sum_probs=0.0

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ...++.||.+++|-+||+||.+|++|.++||+.|.+-.   +..|.|.+...+.+
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---dg~v~I~~~~~~~~  611 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---DGTVKIAATDGEKA  611 (723)
T ss_dssp             -------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC---CccEEEecCCHHHH
Confidence            56778899999999999999999999999999998753   45566776334443

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.52  E-value=0.014  Score=45.22  Aligned_cols=32  Identities=22%  Similarity=0.671  Sum_probs=27.0

Q ss_pred             CCccccccccc-CcccEE--eCCCChhccHhhHHhh
Q psy3263         252 GSRQCYLCNDR-EVTHAL--IPCGHNFFCSECAERT  284 (329)
Q Consensus       252 ~~~~C~IC~e~-~~~~~~--lpCgH~~fC~~Cl~~~  284 (329)
                      ++..|.+|.+. +..++.  +.|+|+ ||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~-~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVS-YCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEE-ECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChH-HhHHHCHHH
Confidence            45789999975 667776  899999 999999983

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=94.07  E-value=0.013  Score=61.58  Aligned_cols=46  Identities=28%  Similarity=0.473  Sum_probs=16.5

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG  134 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG  134 (329)
                      ....+.||.+.+|-+||+||.+||+|+++||+.|.+-.   +..|.|++
T Consensus       598 ~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~---dG~v~Is~  643 (757)
T 1e3p_A          598 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---DGTIYIGA  643 (757)
T ss_dssp             BCCCC------------------CTTCCCCCSCC-----------CCCB
T ss_pred             eeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC---CceEEEec
Confidence            44568899999999999999999999999999998863   45666776

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=92.47  E-value=0.064  Score=40.42  Aligned_cols=36  Identities=28%  Similarity=0.760  Sum_probs=29.7

Q ss_pred             CCCcccccccccCcccEEeCC----CChhccHhhHHhhcCC
Q psy3263         251 SGSRQCYLCNDREVTHALIPC----GHNFFCSECAERTCDF  287 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpC----gH~~fC~~Cl~~~~~~  287 (329)
                      ...+.|.+|.+++.+.-++.|    .|. ||..|.+...+.
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~Hk-FCFpCsr~sIk~   52 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHK-FCFPCSRESIKA   52 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCE-ECHHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCe-eeccccHHHHHh
Confidence            345799999999999988877    688 999999876543

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=91.46  E-value=0.14  Score=46.21  Aligned_cols=47  Identities=17%  Similarity=0.456  Sum_probs=37.7

Q ss_pred             CcccccccccCcccEE-eCCCChhccHhhHHhhcCC--CCCCccccccccc
Q psy3263         253 SRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQ  300 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~  300 (329)
                      -..|.+|.+....... -.|+|. |-..|+.+|++.  ...||.|+.....
T Consensus       180 i~~C~iC~~iv~~g~~C~~C~~~-~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSCETCGIR-MHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             CCBCTTTCSBCSSCEECSSSCCE-ECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCcCcchhhHHhCCcccCccChH-HHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            5689999998875543 249998 999999999876  5699999987543

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=90.57  E-value=0.048  Score=56.96  Aligned_cols=50  Identities=24%  Similarity=0.234  Sum_probs=0.0

Q ss_pred             eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHH
Q psy3263           5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSA   57 (329)
Q Consensus         5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i   57 (329)
                      ++.+||+||.+||+|.++||+.|++-.  + ..+.|.+ ..+..++|++.|..+
T Consensus       571 i~~~ig~gGk~I~~I~~~~G~~IdI~~--d-g~v~I~~~~~~~~~~a~~~i~~i  621 (723)
T 3cdi_A          571 IKDVIGKGGSVIRALTEETGTTIEIED--D-GTVKIAATDGEKAKHAIRRIEEI  621 (723)
T ss_dssp             ------------------------------------------------------
T ss_pred             hcccccccceeeeeeehhhCceEEecC--C-ccEEEecCCHHHHHHHHHHHHHH
Confidence            578999999999999999999998863  3 3445554 566778888877665

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=89.51  E-value=0.15  Score=42.74  Aligned_cols=37  Identities=19%  Similarity=0.167  Sum_probs=34.2

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcC
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP  122 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip  122 (329)
                      ..+.+.|+...+|..||++|++|+.|+++.|-+|.+-
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV   72 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVV   72 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEE
Confidence            5678899999999999999999999999999999874

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=83.46  E-value=0.059  Score=56.56  Aligned_cols=52  Identities=15%  Similarity=0.114  Sum_probs=18.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~   58 (329)
                      .+|.+||++|.+||+|+++||+.|++-.   +..+.|++ ..+..++|++.|..+.
T Consensus       608 ki~~vIG~gGk~Ik~I~~~~G~~IdI~~---dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          608 KIGEVIGPKRQMINQIQEDTGAEITIED---DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             -------------CTTCCCCCSCC-----------CCCBSSHHHHCC---------
T ss_pred             HeehcccccceeeehhhHhhCCEEEecC---CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3688999999999999999999999873   34456665 4667777777776653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	329
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-12
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-11
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	9e-10
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	9e-07
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	9e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-05
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	6e-04
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-09
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-09
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	9e-06
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	8e-09
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	0.001
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	2e-08
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-04
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	5e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	8e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-05
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-07
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	8e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-07
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-04
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-06
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-06
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	8e-06
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-05
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-05
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	8e-05
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-04
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	3e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	4e-04
d1k1ga_	122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	5e-04
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	0.002
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	0.004

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (142), Expect = 6e-12
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGN 135
            +  V +P +    V+G  G  ++ ++ +T T I  P   D     ++TG 
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT 60

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFS 62
          I   G K++ L  KT T I+ P   +      +TG KE + +A+ E+L  +    
Sbjct: 25 IGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQD 79

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.0 bits (135), Expect = 7e-11
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 8/65 (12%)

Query: 72  ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVF 130
           AL  L P       VTIEV VP+ +   V+G KG+ I+++  +    I V     +  + 
Sbjct: 3   ALEALVP-------VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDII 55

Query: 131 EVTGN 135
            +TG 
Sbjct: 56  AITGL 60

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (127), Expect = 6e-10
 Identities = 12/52 (23%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGNF 136
           +TI + +  K VG ++G KG ++K+++ ++   I ++     E +  + G  
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPT 55

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (92), Expect = 3e-05
 Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 56
          I   G  +K +R ++   I        E +  + G    + +A   I+ 
Sbjct: 19 IGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIID 67

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (125), Expect = 9e-10
 Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGN 135
             +E+ + +K    ++G  GA I RI+ Q    +  P   +K  +  + G+
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGD 55

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (103), Expect = 9e-07
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 56
          I   G  I  ++ +    ++ P   E   +  + G  + V +AKRE+L 
Sbjct: 20 IGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLE 68

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.1 bits (125), Expect = 9e-10
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 3/53 (5%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGN 135
           +T E +VP  +VG ++G  G  I RIQ ++   I          E    +TG 
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT 60

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 9/62 (14%)

Query: 4  FVVPS------INPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREI 54
          + VP       I   G +I  ++ ++   I+         E   ++TG  E V  AKR +
Sbjct: 12 YKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLL 71

Query: 55 LS 56
            
Sbjct: 72 DQ 73

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 1e-09
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 84  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGN 135
           G   I+V +P   VG+V+G  G  IK+IQ+     I     D    E + ++TG 
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP 55

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (82), Expect = 6e-04
 Identities = 10/50 (20%), Positives = 16/50 (32%), Gaps = 3/50 (6%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVR---GEEPVFVVTGRKEDVARAKREIL 55
          I   G  IK ++      I+         E +  +TG  +    A   I 
Sbjct: 18 IGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIIT 67

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (123), Expect = 2e-09
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRIIFNQF 309
           C +C + +    + PCGH   C+ C     + + + CP CR  +     I+ + F
Sbjct: 26  CKICAENDKDVKIEPCGHLM-CTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPF 79

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.0 bits (122), Expect = 3e-09
 Identities = 10/47 (21%), Positives = 21/47 (44%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEV 132
           V+ +V + ++V   ++G +G  I++I  +    I  P         V
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCV 56

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 9e-06
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGEEP--VFVVTGRKEDVARAKREILSAADHF 61
          I   G  I+ +  +    I+ P  G        VTG  E+V  A   IL+  + +
Sbjct: 25 IGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.6 bits (118), Expect = 8e-09
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 5/59 (8%)

Query: 83  PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-----VFEVTGNF 136
           PG+   E+ +P    GLV+G  G TIK++Q +    +V      +         +TG+ 
Sbjct: 5   PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDP 63

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 5/53 (9%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGEEP-----VFVVTGRKEDVARAKREILS 56
          I   G  IK L+ +    +     G +         +TG    V +AK  +L 
Sbjct: 23 IGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLE 75

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 14/98 (14%), Positives = 29/98 (29%), Gaps = 26/98 (26%)

Query: 42  GRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVV 101
           G  E + +A  E+ + A+ F                            V  P  +   ++
Sbjct: 1   GEPEKLGQALTEVYAKANSF------------------------TVSSVAAPSWLHRFII 36

Query: 102 GPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEG 139
           G KG  + +I  Q     +  +  ++ +        E 
Sbjct: 37  GKKGQNLAKITQQMPKVHIEFTEGEDKI--TLEGPTED 72

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (115), Expect = 2e-08
 Identities = 8/50 (16%), Positives = 17/50 (34%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGN 135
              E  V   ++GL +G  G+ I++ +       +    D         +
Sbjct: 8   FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGES 57

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 4e-08
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV---TPSRDKEPVFEVTGN 135
           +T +V +P  + G ++G  G  IK+I+H++   I         ++ +  +TG 
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT 56

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 3e-04
 Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAADHFS 62
          I   G +IK +R ++   IK     E   + +  +TG ++ +  A+  + ++   +S
Sbjct: 19 IGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS 75

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 5e-08
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNF 136
            T E+ +P  ++G ++G +GA I  I+  +   I   +           +TG+ 
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA 55

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 8e-08
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNF 136
             + V V  K    ++G KGA I +I+ + +  I  P +D     +    +TG  
Sbjct: 10  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYE 64

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (92), Expect = 4e-05
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 9  INPFGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILS 56
          I   G  I  +R + +  I+ P + +    +    +TG +++   A+  IL 
Sbjct: 25 IGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILR 76

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 6/56 (10%)

Query: 87  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNF 136
            +E+ VP  +VG ++G  G T+   Q  T   I    +       +     +TG+ 
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSP 59

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 11/63 (17%), Positives = 18/63 (28%), Gaps = 12/63 (19%)

Query: 4  FVVPS------INPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAK 51
            VP       +   G  +   +  T   I+   +GE           +TG       A+
Sbjct: 7  MAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQ 66

Query: 52 REI 54
            I
Sbjct: 67 YLI 69

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 45.9 bits (109), Expect = 2e-07
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 88  IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKE 127
           I V+V  + +G V+GP+G     I  +T T I   + +  
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSM 44

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 3e-07
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 12/75 (16%)

Query: 66  ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-----V 120
           +S  SG L+  +P       V  ++ VP + VG ++G  G TI+ I   +   I      
Sbjct: 2   SSGSSGILTENTP-------VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES 54

Query: 121 TPSRDKEPVFEVTGN 135
             +     + +++G 
Sbjct: 55  EGTLLLSRLIKISGT 69

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (83), Expect = 8e-04
 Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 5/74 (6%)

Query: 9   INPFGCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSA 63
           I   G  I+++   +   I              +  ++G +++VA AK  IL        
Sbjct: 30  IGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE 89

Query: 64  LRASRKSGALSPLS 77
           LR      A  P S
Sbjct: 90  LRKRIAHSASGPSS 103

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 1/55 (1%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQ-TNTYIVTPSRDKEPVFEVTGNFPEG 139
             +EV +P K+   ++G KG  I+ I  +    +I  P         V       
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSD 64

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 255 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFN 307
           +C +C +        +PC H F C  C  R    + TCP+C+VPV   +  I +
Sbjct: 7   RCPICLEDPSNYSMALPCLHAF-CYVCITRWIRQNPTCPLCKVPVESVVHTIES 59

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 1e-06
 Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 6/55 (10%)

Query: 87  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGN 135
                VP    GL++G  G TIK I  Q+   I               +F + G 
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT 56

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 12/66 (18%)

Query: 2  FIFVVPS------INPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVAR 49
          F F+VP+      I   G  IK++  ++   I+              +F + G  + +  
Sbjct: 3  FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDY 62

Query: 50 AKREIL 55
          A++ I 
Sbjct: 63 ARQLIE 68

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 14/50 (28%), Positives = 15/50 (30%), Gaps = 2/50 (4%)

Query: 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQA 301
           S  C +C           C H  FC  C  R        CP CR P    
Sbjct: 23  SISCQICEHILADPVETSCKHL-FCRICILRCLKVMGSYCPSCRYPCFPT 71

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (99), Expect = 2e-06
 Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 4/43 (9%)

Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
           C  C        L+PC H   CS C E +      CP+C+ P 
Sbjct: 9   CQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPW 47

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 40.9 bits (96), Expect = 8e-06
 Identities = 5/50 (10%), Positives = 13/50 (26%), Gaps = 3/50 (6%)

Query: 90  VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEG 139
           + +    V  V+G   +  + +  ++   I             T      
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFV---ANNGRIWATCPSRFS 51

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 90  VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGN 135
           V +    V  V+G KG+ IK ++ + +  IV     +  +  V G+
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVV---GQNGLIWVNGD 47

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 249 SISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
           ++    +C +C     D E    L  CGH F  +EC +       TCP+CR+ V
Sbjct: 1   AMDDGVECAVCLAELEDGEEARFLPRCGHGF-HAECVDMWLGSHSTCPLCRLTV 53

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 8e-05
 Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 4/50 (8%)

Query: 255 QCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
           +C LC       ++      CG+            D +  CP CR P  +
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 4/49 (8%)

Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDR---TCPMCRVPVNQ 300
           +C +C +         C H  FC  C  +  +  +    CP+C+  + +
Sbjct: 23  ECPICLELIKEPVSTKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDITK 70

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 36.2 bits (84), Expect = 2e-04
 Identities = 13/34 (38%), Positives = 18/34 (52%)

Query: 86  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
             I V++P   +G V+GPK   I +IQ  T   I
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEI 36

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 4/75 (5%)

Query: 94  YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE--VTGNFPEGPGFESHHGQKIV 151
           +  VG ++GP+G T K+++ +T   I+   R K  + +          P +E  +    V
Sbjct: 16  FNFVGRILGPRGLTAKQLEAETGCKIMV--RGKGSMRDKKKEEQNRGKPNWEHLNEDLHV 73

Query: 152 FILTSNLYSFFDCRI 166
            I   +  +  + ++
Sbjct: 74  LITVEDAQNRAELKL 88

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 8/31 (25%), Positives = 15/31 (48%)

Query: 90  VRVPYKVVGLVVGPKGATIKRIQHQTNTYIV 120
           V +    V  V+G K + +K ++ +T   I 
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIF 35

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (86), Expect = 5e-04
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 86  VTIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEG 139
           V+ +V +P         VGL++GP+G T+K I+ + N  I+   R K  V E      +G
Sbjct: 3   VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMI--RGKGSVKEGKVGRKDG 60

Query: 140 PGFESHHGQKIVFI 153
                        +
Sbjct: 61  QMLPGEDEPLHALV 74

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 8/26 (30%), Positives = 15/26 (57%)

Query: 95  KVVGLVVGPKGATIKRIQHQTNTYIV 120
           ++ G ++G  G   + I+  T+TYI 
Sbjct: 22  RIKGRIIGEGGRARRTIEEMTDTYIN 47

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.0 bits (77), Expect = 0.004
 Identities = 8/31 (25%), Positives = 10/31 (32%), Gaps = 1/31 (3%)

Query: 267 ALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297
           A   C H F    C  R     + CP+    
Sbjct: 53  AWGVCNHAF-HFHCISRWLKTRQVCPLDNRE 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	329
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.43
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.4
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.4
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.39
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.39
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.39
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.38
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.38
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.37
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.36
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.36
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.36
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.35
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.34
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.34
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.32
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.31
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.3
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.29
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.28
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.24
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.2
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.17
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.16
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.13
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.1
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.05
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.05
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.98
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.98
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.96
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.95
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.95
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.94
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.93
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.91
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.91
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.9
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.85
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.83
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.76
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.73
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.72
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.71
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.7
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.66
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.58
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.56
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.56
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.43
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.41
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.32
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.23
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.22
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	97.98
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.72
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.53
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.49
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.45
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.18
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.79
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	88.48
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	82.27
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	80.97
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	80.89
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	80.5
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	80.19
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	80.17

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=3.3e-14  Score=105.69  Aligned_cols=59  Identities=20%  Similarity=0.332  Sum_probs=53.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHHhhhhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAADHFS   62 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i~e~~~   62 (329)
                      +||.||||+|++||+||++|||+|+++...+   +++|+|+|++++|++|+.+|.++++.|+
T Consensus        14 ~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~S   75 (75)
T d1zzka1          14 LAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS   75 (75)
T ss_dssp             TGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhcC
Confidence            6899999999999999999999999974433   7899999999999999999999987664

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=3.5e-14  Score=107.33  Aligned_cols=58  Identities=24%  Similarity=0.322  Sum_probs=53.3

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC--cceEEEecCHHHHHHHHHHHHHHhhhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAADHF   61 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--ervi~ItG~~e~v~~A~~~I~~i~e~~   61 (329)
                      +||.||||+|++|++|+++|||+|++|..++  ++.|+|+|++++|++|+++|++++++|
T Consensus        20 ~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1          20 VHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             THHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999997665  578999999999999999999998755

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=3.1e-14  Score=107.56  Aligned_cols=69  Identities=26%  Similarity=0.374  Sum_probs=59.7

Q ss_pred             CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-----CCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        81 ~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-----~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      +.+++.+.+|.||..++|+||||+|++||+|+++|||+|+|++++     .+|+|+|+| ++++| ....+|.+.+
T Consensus         3 ~~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i   77 (81)
T d1x4ma1           3 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKVQQAKEMVLELI   77 (81)
T ss_dssp             CCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEE-CTTTHHHHHHHHHHHH
T ss_pred             CCCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHH
Confidence            457889999999999999999999999999999999999997643     578899999 99999 4444666654

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=6.3e-14  Score=103.26  Aligned_cols=54  Identities=17%  Similarity=0.173  Sum_probs=49.0

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSA   57 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i   57 (329)
                      +||.||||+|++||+||++|||+|+++.+.+      +|+|+|+|++++|++|+++|.++
T Consensus        11 ~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~   70 (71)
T d1j4wa2          11 KTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK   70 (71)
T ss_dssp             THHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             hcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhh
Confidence            6899999999999999999999999974332      68999999999999999999875

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=1.5e-14  Score=107.43  Aligned_cols=67  Identities=28%  Similarity=0.442  Sum_probs=57.6

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcch-hhhhhhhhh
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGF-ESHHGQKIV  151 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~vei-e~~i~d~~~  151 (329)
                      |..++++.||.+++|+||||+|++||+|+++|||+|+++..+   .+++|+|+| ++++|+. ..+|.+++.
T Consensus         1 G~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~   71 (74)
T d1j4wa1           1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG-PPDRAQHAAEIITDLLR   71 (74)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEe-CHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999998655   467899999 9999943 447777654

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=8.1e-14  Score=102.68  Aligned_cols=56  Identities=18%  Similarity=0.224  Sum_probs=51.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++..+. +|+|+|+|++++|.+|+.+|.++++
T Consensus        14 ~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~   70 (71)
T d2axya1          14 EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLE   70 (71)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HcCeEECCCChhHHHHHHHhCCEEEEcCCCCCcceEEEEECHHHHHHHHHHHHHHhc
Confidence            4799999999999999999999999986554 8999999999999999999998854

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=8.6e-14  Score=103.24  Aligned_cols=56  Identities=20%  Similarity=0.139  Sum_probs=51.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++...+   +++|+|+|++++|++|+.+|.++++
T Consensus        13 ~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   71 (74)
T d1j4wa1          13 AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLR   71 (74)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999985443   7899999999999999999999865

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=3e-14  Score=104.80  Aligned_cols=64  Identities=19%  Similarity=0.336  Sum_probs=54.7

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcchh-hhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGFE-SHHGQK  149 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~veie-~~i~d~  149 (329)
                      +.|.++.||.++||+||||+|++||+|+++|||+|.++...   ++++|+|+| .+++|+.+ .+|.+.
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~   68 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG-SAASISLAQYLINAR   68 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEE-CHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEe-CHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999997644   577899999 99999333 355443

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=5.8e-14  Score=104.34  Aligned_cols=66  Identities=20%  Similarity=0.357  Sum_probs=56.4

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGP-GFESHHGQKIV  151 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~v-eie~~i~d~~~  151 (329)
                      ..|.+|.||.++||+|||++|++||+|+++|||+|+++..+   ++++|+|+| .+++| .+..+|.+++.
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G-~~~~v~~A~~~I~~~i~   72 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLLQNSVK   72 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEe-CHHHHHHHHHHHHHHHH
Confidence            37889999999999999999999999999999999997644   577899999 99999 33446666554

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=2.8e-14  Score=105.19  Aligned_cols=65  Identities=20%  Similarity=0.304  Sum_probs=56.5

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      ..|+++.||++.+|.||||||++||+|+++|||+|++++.. .+|+|+|+| ++++| ....+|.+.+
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l   69 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAG-PTNAIFKAFAMIIDKL   69 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCCCCcceEEEEE-CHHHHHHHHHHHHHHh
Confidence            37899999999999999999999999999999999998755 678999999 99999 4444665544

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=1.5e-13  Score=101.96  Aligned_cols=55  Identities=18%  Similarity=0.183  Sum_probs=49.9

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      +||.||||+|++||+|+++|||+|+++.+++      +|+|+|+|++++|++|+.+|.+.+
T Consensus        13 ~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_          13 LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             THHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             HcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            6899999999999999999999999985443      789999999999999999998763

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=1.1e-13  Score=102.04  Aligned_cols=55  Identities=25%  Similarity=0.417  Sum_probs=50.7

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~   58 (329)
                      |+|.||||+|++|++|+++|||+|++|..++ ++.|+|+|++++|++|+++|++++
T Consensus        15 ~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_          15 FHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             HHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             HhcccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            6799999999999999999999999997655 688999999999999999999874

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=6.8e-14  Score=103.89  Aligned_cols=64  Identities=23%  Similarity=0.365  Sum_probs=54.4

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC------CCCeEEEECCCCCCcchh-hhhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNFPEGPGFE-SHHGQKI  150 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------~e~~i~ItG~~pe~veie-~~i~d~~  150 (329)
                      .++++.||.++||.||||+|++||+|+++|||+|++++++      ++++|+|+| ++++|+.+ .+|.+.+
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG-SPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEE-SHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHc
Confidence            5689999999999999999999999999999999998644      467899999 99999433 3665543

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=3.2e-13  Score=102.53  Aligned_cols=56  Identities=20%  Similarity=0.339  Sum_probs=51.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC----cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~----ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+|+++|||+|++|..+.    ++.|+|+|++++|++|+.+|.++++
T Consensus        20 ~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~   79 (84)
T d2ctla1          20 YHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVG   79 (84)
T ss_dssp             THHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999985443    6789999999999999999999865

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=1.7e-13  Score=103.46  Aligned_cols=56  Identities=29%  Similarity=0.359  Sum_probs=52.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++|++|+++|||+|++|..++ ++.|+|+|++++|++|+.+|+++++
T Consensus        20 ~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~~v~~A~~~I~~iv~   76 (81)
T d2ctea1          20 HHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISA   76 (81)
T ss_dssp             THHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHhhccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEeCHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999997655 7899999999999999999999875

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=1.4e-13  Score=103.98  Aligned_cols=67  Identities=22%  Similarity=0.321  Sum_probs=56.1

Q ss_pred             CCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC--CCCeEEEECCCCCCc-chhhhhhhh
Q psy3263          82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--KEPVFEVTGNFPEGP-GFESHHGQK  149 (329)
Q Consensus        82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~--~e~~i~ItG~~pe~v-eie~~i~d~  149 (329)
                      +....+.++.||.++||.|||++|++|++|+++|||+|+||.++  +++.|+|+| ++++| .+..+|.++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G-~~~~V~~A~~~I~~i   75 (81)
T d2ctma1           6 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTG-LPENVEEAIDHILNL   75 (81)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEES-CHHHHHHHHHHHHHH
T ss_pred             hhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeC-CHHHHHHHHHHHHHH
Confidence            34557889999999999999999999999999999999999865  467899999 99999 223344443

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=6.3e-14  Score=103.25  Aligned_cols=62  Identities=26%  Similarity=0.359  Sum_probs=52.8

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC------CCCeEEEECCCCCCc-chhhhhhhh
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNFPEGP-GFESHHGQK  149 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------~e~~i~ItG~~pe~v-eie~~i~d~  149 (329)
                      +.++.||+.+||.||||+|++||+|+++|||+|+++.+.      ++|.|+|+| ++++| ....+|.|.
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~e~   70 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQIDYARQLIEEK   70 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEEC-CHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEe-CHHHHHHHHHHHHhh
Confidence            468899999999999999999999999999999997543      467899999 99999 444466654

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=1.9e-13  Score=100.65  Aligned_cols=66  Identities=21%  Similarity=0.312  Sum_probs=56.7

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      ...++++.||.++||+|||++|++|++|+++|||+|+||.++ +++.|+|+| .+++| .+..+|.+..
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G-~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEG-DPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEE-SSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEEC-CHHHHHHHHHHHHHHh
Confidence            346789999999999999999999999999999999999766 677899999 99999 4444666543

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.34  E-value=3.8e-13  Score=106.17  Aligned_cols=64  Identities=23%  Similarity=0.253  Sum_probs=55.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhc
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-----EPVFVVTGRKEDVARAKREILSAADHFSALRAS   67 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~   67 (329)
                      +||.||||+|.+||+||++|||+|+|+..++     +|+|+|+|++++|++|+.+|.+++++....+..
T Consensus        25 ~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~~~~   93 (104)
T d1we8a_          25 SVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKR   93 (104)
T ss_dssp             THHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcHHHHHH
Confidence            6899999999999999999999999975443     689999999999999999999998655544443

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=2.8e-13  Score=99.51  Aligned_cols=54  Identities=20%  Similarity=0.206  Sum_probs=49.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSA   57 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i   57 (329)
                      +||.||||+|.+||+|+++|||+|+++...+   +|+|+|+|++++|++|+.+|.+.
T Consensus        12 ~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~   68 (70)
T d1wvna1          12 LIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINAR   68 (70)
T ss_dssp             GHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             hcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHH
Confidence            6899999999999999999999999974433   78999999999999999999875

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.32  E-value=5.2e-13  Score=100.11  Aligned_cols=56  Identities=23%  Similarity=0.231  Sum_probs=50.9

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++|++|+++|||+|++++..+   ++.|+|+|++++|++|+.+|.++++
T Consensus        18 ~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   76 (79)
T d1x4na1          18 MVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVE   76 (79)
T ss_dssp             HHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             hhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999985433   7899999999999999999999864

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=6.9e-13  Score=102.17  Aligned_cols=62  Identities=19%  Similarity=0.273  Sum_probs=55.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhhhhhHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFSALR   65 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~   65 (329)
                      +||.||||+|.+|++|+++|||+|.+|..++ ++.|+|+|++++|++|+.+|.+++.++....
T Consensus        20 ~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~~~~~   82 (91)
T d2ctka1          20 LHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQAEQ   82 (91)
T ss_dssp             HHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhHhcCCCchhHHHHHHHhCCEEEECCCCCCcceEEEECCHHHHHHHHHHHHHHHHHHHHHh
Confidence            6899999999999999999999999997665 7889999999999999999999886554443

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=3.6e-13  Score=101.58  Aligned_cols=56  Identities=21%  Similarity=0.190  Sum_probs=50.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCC-----cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-----EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-----ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+||++|||+|+++.+.+     +|+|+|+|++++|++|+.+|.+++.
T Consensus        18 ~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   78 (81)
T d1x4ma1          18 KAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIR   78 (81)
T ss_dssp             HHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHC
T ss_pred             HcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999974332     7899999999999999999999853

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=8.4e-13  Score=99.70  Aligned_cols=56  Identities=27%  Similarity=0.421  Sum_probs=51.2

Q ss_pred             eeeeeecCCChHHHHHHHH-hCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAK-TNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~-Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++|++|+++ ++++|++|..++ ++.|+|+|++++|++|+++|+++++
T Consensus        20 ~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~v~   77 (82)
T d2ctja1          20 LHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAE   77 (82)
T ss_dssp             HHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCCCceEEEeCCHHHHHHHHHHHHHHHh
Confidence            6899999999999999988 599999997654 7899999999999999999999865

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=2.7e-13  Score=101.75  Aligned_cols=68  Identities=28%  Similarity=0.377  Sum_probs=58.8

Q ss_pred             CCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263          83 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGP-GFESHHGQKIV  151 (329)
Q Consensus        83 ~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~v-eie~~i~d~~~  151 (329)
                      +...|.+|.||..++|+|||++|++|++|+++|||+|.+++.+   +++.|+|+| ++++| ....+|.+++.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~   76 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTG-TPESVQSAKRLLDQIVE   76 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHHH
Confidence            3458899999999999999999999999999999999998644   577899999 99999 44457777664

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=4.3e-13  Score=101.23  Aligned_cols=69  Identities=20%  Similarity=0.275  Sum_probs=59.2

Q ss_pred             CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        81 ~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      .+..+.|.++.||..+||+|||++|++|++|+++|||+|.+|..+ .++.|+|+| .+++| +...+|.+++
T Consensus         5 ~~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G-~~~~v~~A~~~I~~iv   75 (81)
T d2ctea1           5 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITG-TKEGIEKARHEVLLIS   75 (81)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             HhcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEe-CHHHHHHHHHHHHHHH
Confidence            345668999999999999999999999999999999999998755 788899999 99999 4444665544

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=3.5e-14  Score=109.60  Aligned_cols=55  Identities=20%  Similarity=0.273  Sum_probs=50.0

Q ss_pred             CCceEEEEEecCcccceeecCCCchHHHHHHhc-CceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          83 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT-NTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        83 ~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~t-ga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ....|..|.||.++|++|||+||++|++|++++ +++|.+|.+  +..|+|+| ++++|
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~--~~~v~i~G-~~~~v   73 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--EDKITLEG-PTEDV   73 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS--SCEEEEEE-CHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC--CceEEEeC-CHHHH
Confidence            456899999999999999999999999999995 899999864  56799999 99999

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=1.4e-12  Score=98.86  Aligned_cols=65  Identities=22%  Similarity=0.312  Sum_probs=55.3

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----CCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNFPEGPGFES-HHGQKIV  151 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~e~~i~ItG~~pe~veie~-~i~d~~~  151 (329)
                      .++++.||..+||+|||++|++||+|+++|||+|+||+.+    +++.|+|+| .+++|+.+. +|.+++.
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G-~~e~v~~A~~~I~~~i~   79 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITG-YEKNTEAARDAILRIVG   79 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEES-CHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEEC-CHHHHHHHHHHHHHHHH
Confidence            6789999999999999999999999999999999998654    577899999 999993333 6655544

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.24  E-value=1.4e-12  Score=102.78  Aligned_cols=67  Identities=19%  Similarity=0.287  Sum_probs=57.6

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-----CCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGNFPEGP-GFESHHGQKIV  151 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-----~e~~i~ItG~~pe~v-eie~~i~d~~~  151 (329)
                      ...+.+|.||..+||+||||+|.+||+|+++|||+|.|++.+     .+|+|+|+| ++++| ....+|.+++.
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~   85 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISG-TQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEE-EHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Confidence            447889999999999999999999999999999999997644     467899999 99999 44447777665

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=2.2e-12  Score=97.35  Aligned_cols=68  Identities=18%  Similarity=0.234  Sum_probs=56.8

Q ss_pred             CCCceEEEEEecCcccceeecCCCchHHHHHHh-cCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263          82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQ-TNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQKI  150 (329)
Q Consensus        82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~-tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~~  150 (329)
                      .....|.++.||.++||+||||+|++|++|+++ ++++|.+|..+ +++.|+|+| .+++| ....+|.+.+
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~v   76 (82)
T d2ctja1           6 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRG-PSSDVEKAKKQLLHLA   76 (82)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEES-CHHHHHHHHHHHHHHH
T ss_pred             hcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCCCceEEEeC-CHHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999987 69999999865 788999999 99999 3333555443

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=3.3e-12  Score=98.25  Aligned_cols=65  Identities=25%  Similarity=0.478  Sum_probs=55.9

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP-GFESHHGQKIV  151 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v-eie~~i~d~~~  151 (329)
                      .+.++.||..+||.|||++|++|++|+++|||+|.||+.+ +++.|+|+| .+++| .+..+|.+++.
T Consensus        10 vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G-~~~~V~~A~~~I~~~v~   76 (91)
T d2ctka1          10 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITG-LAANLDRAKAGLLERVK   76 (91)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEE-CHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCCCCcceEEEEC-CHHHHHHHHHHHHHHHH
Confidence            7899999999999999999999999999999999999866 678899999 99999 33335554443

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=5.3e-12  Score=94.71  Aligned_cols=52  Identities=25%  Similarity=0.733  Sum_probs=45.4

Q ss_pred             CcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccchhhh
Q psy3263         253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRII  305 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~~i~  305 (329)
                      ...|+||++.+.++++++|||. ||.+|+.+|+.. ...||+||..+.....+.
T Consensus        23 ~~~C~IC~~~~~~~~~~~CgH~-fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i~   75 (79)
T d1fbva4          23 FQLCKICAENDKDVKIEPCGHL-MCTSCLTSWQESEGQGCPFCRCEIKGTEPIV   75 (79)
T ss_dssp             TTBCTTTSSSBCCEECSSSCCE-ECHHHHHHHHHTTCCSCTTTCCCCCCCCCSS
T ss_pred             CCCCccCCCcCCCeEEeCCCCe-eeHHHHHHHHHHCcCcCCCCCcCccCCceee
Confidence            3579999999999999999999 999999999875 678999999997655443

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.14  E-value=1.5e-11  Score=94.48  Aligned_cols=54  Identities=19%  Similarity=0.193  Sum_probs=49.2

Q ss_pred             eeeeeecCCChHHHHHHHH-hCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAK-TNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~-Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      ||+.|||+||++|++|+++ +|++|++|.  ++..|+|+|++++|++|+++|.++++
T Consensus        31 ~h~~iIG~~G~~I~~i~~~~~~v~I~~~~--~~~~v~i~G~~~~ve~Ak~~I~~iv~   85 (90)
T d2ctfa1          31 LHRFIIGKKGQNLAKITQQMPKVHIEFTE--GEDKITLEGPTEDVSVAQEQIEGMVK   85 (90)
T ss_dssp             THHHHHTTTTCHHHHHHHHCSSSEEEECS--SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHhhcCCCCchhHHHHHHHcCCcEEeeCC--CCceEEEeCCHHHHHHHHHHHHHHHH
Confidence            6889999999999999999 589999994  45779999999999999999999865

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.13  E-value=1.5e-11  Score=93.34  Aligned_cols=53  Identities=23%  Similarity=0.235  Sum_probs=48.1

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      +||.||||+|++||+|+++|||+|+++.   +..|+|+|+++++++|+.+|..+++
T Consensus        11 ~ig~IIG~gG~~I~~I~~~tg~~I~i~~---~g~v~I~G~~e~v~~A~~~I~~i~~   63 (84)
T d2ba0a3          11 RVPRVIGKKGSMIKLLKSELDVQIVVGQ---NGLIWVNGDRRKVSIAEEAIYLIEQ   63 (84)
T ss_dssp             GHHHHHCGGGHHHHHHHHHHTCEEEECT---TSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             hcceeeCCcHHHHHHHHHHHCCEEEECC---CCEEEEEeCHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999974   3568999999999999999988854

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.10  E-value=1.1e-11  Score=94.53  Aligned_cols=49  Identities=29%  Similarity=0.609  Sum_probs=43.8

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      .+.+.|+||++.+.+++.++|||. ||..|+.+|++. ...||+||.++..
T Consensus        21 ~~~l~C~IC~~~~~~pv~~~CgH~-FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          21 VKSISCQICEHILADPVETSCKHL-FCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             ccCcCCccCCcchhcceecCCCCh-hhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            355799999999999999999999 999999999865 6789999998854

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.05  E-value=1.6e-11  Score=89.40  Aligned_cols=49  Identities=33%  Similarity=0.847  Sum_probs=42.5

Q ss_pred             CcccccccccCcccE-EeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263         253 SRQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  302 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~  302 (329)
                      ...|+||++.+.+++ .++|||. ||..|+.+|++....||+||+++....
T Consensus         5 ~d~C~IC~~~~~~~~~~~~C~H~-Fc~~Ci~~w~~~~~~CP~CR~~i~~~~   54 (68)
T d1chca_           5 AERCPICLEDPSNYSMALPCLHA-FCYVCITRWIRQNPTCPLCKVPVESVV   54 (68)
T ss_dssp             CCCCSSCCSCCCSCEEETTTTEE-ESTTHHHHHHHHSCSTTTTCCCCCCEE
T ss_pred             CCCCccCCcCccCCcEEeCCCCc-CcHHHHHHHHHhCCcCCCCCcchHhhc
Confidence            357999999997765 5799999 999999999988899999999886543

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1e-11  Score=93.01  Aligned_cols=62  Identities=15%  Similarity=0.243  Sum_probs=51.8

Q ss_pred             CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hh
Q psy3263          84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HH  146 (329)
Q Consensus        84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i  146 (329)
                      ...+.++.||.+++|+|||+||++||+||++|||+|.+..+ ++..|+|+|++++.|+-+. +|
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-~~g~v~I~g~~~eav~~A~~~I   68 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-DTGTFRIYGESADAVKKARGFL   68 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-TTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-CCceEEEEECCHHHHHHHHHHH
Confidence            34788999999999999999999999999999999998653 4568999996688884443 44

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=5.1e-11  Score=93.37  Aligned_cols=48  Identities=21%  Similarity=0.564  Sum_probs=42.7

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC---CCCCcccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN  299 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~  299 (329)
                      ++.+.|+||++.+.+|+.++|||. ||..|+.+|+..   ...||+||..+.
T Consensus        19 ~~~l~CpIC~~~~~~pv~~~CgH~-fC~~Ci~~~~~~~~~~~~CP~Cr~~~~   69 (103)
T d1jm7a_          19 QKILECPICLELIKEPVSTKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDIT   69 (103)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCC-CCSHHHHHHHHSSSSSCCCTTTSCCCC
T ss_pred             ccCcCCCccCchhCCeEEcCCCCc-hhhHHHHHHHHHCCCCCcCcCCCCcCC
Confidence            455789999999999999999999 999999999865   358999999884

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.98  E-value=1.6e-10  Score=85.98  Aligned_cols=50  Identities=12%  Similarity=0.278  Sum_probs=45.4

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +.+++.|+||++.+.+|+.++|||. ||..|+.+|+.. ...||.|+.++..
T Consensus         5 iP~~l~CpIc~~~m~dPV~~~cgh~-fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDPVIVSTGQT-YERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEE-EEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CCccCCCcCcCchhhCceEccCCCc-chHHHHHHHHHHCCCCCCcccccCCc
Confidence            4578999999999999999999999 999999999987 6789999998854

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=98.96  E-value=1.7e-10  Score=80.48  Aligned_cols=48  Identities=29%  Similarity=0.740  Sum_probs=40.7

Q ss_pred             CCCCcccccccccCcc---cEEe-CCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263         250 ISGSRQCYLCNDREVT---HALI-PCGHNFFCSECAERTCDFDRTCPMCRVPV  298 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~---~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i  298 (329)
                      ++++.+|+||++.+.+   ...+ +|+|. ||..|+.+|++....||+||+++
T Consensus         2 ~ed~~~C~ICl~~~~~~~~~~~l~~C~H~-Fh~~Ci~~Wl~~~~~CP~CR~~i   53 (55)
T d1iyma_           2 MDDGVECAVCLAELEDGEEARFLPRCGHG-FHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCE-ECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCCCCCeEECccccCCCEEEEeCCCCCc-ccHHHHHHHHHhCCcCCCCCCEe
Confidence            4677899999998864   3344 69999 99999999999989999999875

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.95  E-value=1.2e-10  Score=87.12  Aligned_cols=50  Identities=16%  Similarity=0.167  Sum_probs=44.8

Q ss_pred             CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      +.+++.|+||++.+.+|+.++|||. ||..|+.+++.. ...||+||.++..
T Consensus         4 iP~~l~CpIc~~l~~dPv~~~cGht-fc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           4 IPDYLCGKISFELMREPCITPSGIT-YDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CCSTTBCTTTCSBCSSEEECSSCCE-EETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCccccCcCcCchhhhhcccCCcCe-ecHHHHHHHHhcCCccCCCccccccc
Confidence            3577899999999999999999999 999999999876 6789999998854

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.95  E-value=6.3e-11  Score=83.04  Aligned_cols=44  Identities=32%  Similarity=0.812  Sum_probs=39.1

Q ss_pred             CCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         252 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      +.++|+||++.+.+++++||||. ||..|+.++   ...||+||+++.
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~-fC~~Ci~~~---~~~CP~Cr~~~~   48 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPWP   48 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCC-SBTTTCSSS---SSSCSSCCSSSS
T ss_pred             CCCCCcccCcccCCCEEecCCCH-HhHHHHHcC---CCcCcCCCCccc
Confidence            34799999999999999999999 999998764   678999999874

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.94  E-value=1e-10  Score=88.57  Aligned_cols=57  Identities=23%  Similarity=0.128  Sum_probs=48.3

Q ss_pred             EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-chhhhhhh
Q psy3263          88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQ  148 (329)
Q Consensus        88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d  148 (329)
                      ..+.||.+.+|.|||+||++||+|+++|||+|+++.   +..|+|+| .++++ ++..+|.+
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~---~g~v~I~G-~~e~v~~A~~~I~~   60 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---NGLIWVNG-DRRKVSIAEEAIYL   60 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT---TSEEEEES-CHHHHHHHHHHHHH
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC---CCEEEEEe-CHHHHHHHHHHHHH
Confidence            458899999999999999999999999999999964   46799999 99999 33335543

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=1.2e-10  Score=87.01  Aligned_cols=53  Identities=15%  Similarity=0.174  Sum_probs=46.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHH
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSA   57 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i   57 (329)
                      +||+||||||++||+||++|||+|.+..+ ++..|+|.| ++++|++|+++|..+
T Consensus        18 ~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1          18 LMGLAIGTHGSNIQQARKVPGVTAIELDE-DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             HHHHHHTTTTHHHHHHHTSTTEEEEEEET-TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             HHHHHcCCChHHHHHHHHhcCcEEEEecC-CCceEEEEECCHHHHHHHHHHHHHh
Confidence            68999999999999999999999998743 346788999 699999999999655

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.91  E-value=2e-10  Score=79.05  Aligned_cols=46  Identities=28%  Similarity=0.602  Sum_probs=38.0

Q ss_pred             cccccccccCcc----cEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         254 RQCYLCNDREVT----HALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       254 ~~C~IC~e~~~~----~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      ++|+||++.+..    ...++|||. ||..|+.+|.+. ...||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~-~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQ-ICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCC-CCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCc-cchHHHHHHHhhcCCCCCccCCcCCC
Confidence            479999997643    234589999 999999999987 6789999998753

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.91  E-value=1.3e-10  Score=81.31  Aligned_cols=46  Identities=13%  Similarity=0.112  Sum_probs=41.9

Q ss_pred             cccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         254 RQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       254 ~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +.|+||++.+.+|+.+ .|||. ||.+|+.+|++....||+||+++..
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~-fc~~cI~~~l~~~~~CP~c~~~l~~   47 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTI-FEKSLLEQYVKDTGNDPITNEPLSI   47 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEE-EEHHHHHHHHHHHSBCTTTCCBCCG
T ss_pred             CCCccCCchHHhcCccCCCCCc-ccHHHHHHHHhhccCCCccCCcCCH
Confidence            4799999999999987 49999 9999999999998899999998754

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=1.8e-10  Score=82.91  Aligned_cols=48  Identities=23%  Similarity=0.657  Sum_probs=38.6

Q ss_pred             CCcccccccccCc-----ccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263         252 GSRQCYLCNDREV-----THALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  300 (329)
Q Consensus       252 ~~~~C~IC~e~~~-----~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~  300 (329)
                      ++..|+||++...     ..++.+|||. ||.+|+.+|+.. ...||+||+++..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~-fc~~Ci~~~~~~~~~~CP~CR~~i~~   55 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHT-LCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCC-EEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChH-hhHHHHHHHhCcCcCCCCCCCcCccc
Confidence            4679999998642     2246699999 999999999865 6789999998854

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=1.3e-10  Score=89.99  Aligned_cols=48  Identities=25%  Similarity=0.618  Sum_probs=41.3

Q ss_pred             CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      +++.+.|+||++.+.+|+.+ +|||. ||..|+.+|+.  ..||.||.++..
T Consensus        19 l~~~l~C~IC~~~~~~pv~~~~CgH~-fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          19 LEKLLRCSRCTNILREPVCLGGCEHI-FCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             HHHTTSCSSSCSCCSSCBCCCSSSCC-BCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hhhcCCCccCCchhhcCceeCCCCCc-hhHHHHHHHHh--ccccccCCcCch
Confidence            45678999999999999865 89999 99999999975  469999988743

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.83  E-value=3.2e-10  Score=82.72  Aligned_cols=57  Identities=9%  Similarity=-0.004  Sum_probs=40.1

Q ss_pred             EEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcc-hhhhhhh
Q psy3263          89 EVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPG-FESHHGQ  148 (329)
Q Consensus        89 ~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~ve-ie~~i~d  148 (329)
                      .+.||.+.+|.||||+|++||+|+++|||+|.+..   +..|+|+|..+++++ +..+|.+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~---~g~v~I~g~~~~~v~~A~~~I~~   61 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN---NGRIWATCPSRFSEEILIEAIRK   61 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT---TSEEEC-----CTTCCTHHHHTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC---CCEEEEEeCCHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999953   457999995578883 3335543

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.76  E-value=1.9e-09  Score=81.47  Aligned_cols=62  Identities=23%  Similarity=0.317  Sum_probs=45.6

Q ss_pred             EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263          88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQKIV  151 (329)
Q Consensus        88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~~~  151 (329)
                      +++.||.+.+|+||||||++||+||++|||+|+|..++  ..+.+.+...+....+. ++.|++.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~--g~v~i~~~~~~~~~~a~~~a~~iI~   67 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN--SMVIVEPEAEGIPPVNLMKAAEVVK   67 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT--TEEEEEESSTTSCHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC--CeEEEecCCccccHHHHHHHHHHHH
Confidence            46899999999999999999999999999999996544  45666662333332222 4445554

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.73  E-value=2.4e-09  Score=83.89  Aligned_cols=52  Identities=25%  Similarity=0.228  Sum_probs=45.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   59 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e   59 (329)
                      ++|+||||||.+||.|++.|||+|.+.    +..+.|.|.+++++.|+++|..+++
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~----d~~v~iig~~e~i~~A~~~Ie~li~   74 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG----EYEVAIIGDYERAMAAKQAIEMLAE   74 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC----SSEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe----CCeEEEEECchhHHHHHHHHHHHHc
Confidence            478999999999999999999999995    2345677999999999999999864

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.72  E-value=8.8e-09  Score=79.83  Aligned_cols=50  Identities=14%  Similarity=0.089  Sum_probs=44.5

Q ss_pred             CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  300 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~  300 (329)
                      .+++.|+||.+.+.+||.++|+|..||..|+.+|+.....||+|+.++..
T Consensus        20 P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            45799999999999999999876339999999999888899999999854

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.71  E-value=1.4e-10  Score=84.67  Aligned_cols=52  Identities=13%  Similarity=-0.056  Sum_probs=39.2

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I~~i~   58 (329)
                      +||.||||+|++||+|+++|||+|++..   +..|+|+|. ++++++|+.+|.++.
T Consensus        11 ~ig~iIGkgG~~Ik~i~~~tg~~I~i~~---~g~v~I~g~~~~~v~~A~~~I~~i~   63 (69)
T d2je6i3          11 KVPRVIGKNKSMYETLTSKSGCSIFVAN---NGRIWATCPSRFSEEILIEAIRKIE   63 (69)
T ss_dssp             GHHHHHCGGGHHHHHHHTTC---CEECT---TSEEEC-----CTTCCTHHHHTTTT
T ss_pred             hccceECCchhHHHHHHHHHCCEEEEcC---CCEEEEEeCCHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999963   345799995 789999999998764

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.70  E-value=1.2e-09  Score=82.59  Aligned_cols=53  Identities=15%  Similarity=0.145  Sum_probs=43.8

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEE-----ecCHHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVV-----TGRKEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~I-----tG~~e~v~~A~~~I~~i~   58 (329)
                      .||.||||||++||+||++|||+|++..++.  .+.+     +|.+.++++|++.|.++.
T Consensus        13 ~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g--~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1          13 RLGAVIGPRGEVKAEIMRRTGTVITVDTENS--MVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             GHHHHHCGGGHHHHHHHHHHTEEEEEETTTT--EEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             HcCeeecCCchhHHHHHHHHCCEEEEEcCCC--eEEEecCCccccHHHHHHHHHHHHHHh
Confidence            5799999999999999999999999974333  2333     567899999999998874

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.66  E-value=9.8e-10  Score=76.15  Aligned_cols=46  Identities=28%  Similarity=0.473  Sum_probs=14.8

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG  134 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG  134 (329)
                      ...++.||.+.+|.|||+||.+||+|+++|||+|.+.   ++..|+|+|
T Consensus         3 ~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~---ddg~v~I~a   48 (54)
T d1e3ha4           3 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE---DDGTIYIGA   48 (54)
T ss_dssp             BCC---------------------CHHHHSCCCC-----------CCCC
T ss_pred             eEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe---CCeEEEEEe
Confidence            3457899999999999999999999999999999995   457788888

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.58  E-value=2.6e-08  Score=75.41  Aligned_cols=52  Identities=19%  Similarity=-0.021  Sum_probs=45.7

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHHHHHh
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREILSAA   58 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I~~i~   58 (329)
                      .+|.|||+||++||+|+++|||+|++..+   -.|.|.|. .+.+++|+.+|..+.
T Consensus        11 ki~~vIG~gG~~ik~i~~~t~~~I~I~d~---G~V~I~g~~~~~~~~A~~~I~~I~   63 (87)
T d2z0sa2          11 KVPRVIGRKMSMLKTLEEKTECKIFVARN---GRIHLECPNEDLEAIAVMAIKIID   63 (87)
T ss_dssp             GSGGGTCGGGHHHHHHHHHHCCEEEEETT---TEEEEECSCHHHHHHHHHHHHHHH
T ss_pred             hcceeECCCCcHHHHHHHHHCCEEEECCC---cEEEEEeCCHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999633   35799995 899999999998874

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.56  E-value=1e-08  Score=81.10  Aligned_cols=46  Identities=22%  Similarity=0.528  Sum_probs=37.2

Q ss_pred             CcccccccccCcc------------------cEEeCCCChhccHhhHHhhcCC-----CCCCcccccccc
Q psy3263         253 SRQCYLCNDREVT------------------HALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVN  299 (329)
Q Consensus       253 ~~~C~IC~e~~~~------------------~~~lpCgH~~fC~~Cl~~~~~~-----~~~CP~Cr~~i~  299 (329)
                      +..|.||++.+..                  ..+++|+|. ||.+|+..|++.     ...||+||+.+.
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~-FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~   93 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHA-FHLLCLLAMYCNGNKDGSLQCPSCKTIYG   93 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCE-ECHHHHHHHHHHTCCSSCCBCTTTCCBSS
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCCh-hhHHHHHHHHHhcCcCCCCccccccchhc
Confidence            4589999987643                  246899999 999999999864     347999998773

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.56  E-value=1.8e-08  Score=76.33  Aligned_cols=33  Identities=24%  Similarity=0.397  Sum_probs=29.8

Q ss_pred             cEEeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263         266 HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  299 (329)
Q Consensus       266 ~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~  299 (329)
                      .+.++|||. ||..|+.+|++....||+||+++.
T Consensus        52 ~~~~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          52 VAWGVCNHA-FHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             EEEETTSCE-EEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             eEEccccCc-ccHHHHHHHHHHCCcCCCCCCccc
Confidence            356899999 999999999999999999999864

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.43  E-value=3.9e-08  Score=74.43  Aligned_cols=50  Identities=16%  Similarity=0.143  Sum_probs=43.1

Q ss_pred             EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263          88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP  140 (329)
Q Consensus        88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v  140 (329)
                      ..+.||.+.+|.|||+||++||+|+++|||+|.+.   ++-.|.|.|+.++.+
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~---d~G~V~I~g~~~~~~   52 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA---RNGRIHLECPNEDLE   52 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEE---TTTEEEEECSCHHHH
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEEC---CCcEEEEEeCCHHHH
Confidence            35789999999999999999999999999999994   345799999445666

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.41  E-value=6.9e-08  Score=77.60  Aligned_cols=58  Identities=29%  Similarity=0.360  Sum_probs=47.6

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC------------------cc-eEEEec-CHHHHHHHHHHHHHHhh
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE------------------EP-VFVVTG-RKEDVARAKREILSAAD   59 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------------------er-vi~ItG-~~e~v~~A~~~I~~i~e   59 (329)
                      |+|||+|||.+|.++|+|+++|||+|.|-.++.                  ++ -|.|++ ..+.+++|+.+|..++.
T Consensus        17 fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~~~A~~~i~~ll~   94 (122)
T d1k1ga_          17 INFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILK   94 (122)
T ss_dssp             HHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHHHT
T ss_pred             CCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhHHHHHHHHHHHHH
Confidence            899999999999999999999999999943221                  22 356777 47799999999999863

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=98.32  E-value=6.8e-08  Score=67.79  Aligned_cols=48  Identities=23%  Similarity=0.601  Sum_probs=40.2

Q ss_pred             CCCcccccccccCcccEEeCCC-----ChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263         251 SGSRQCYLCNDREVTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCRVPVN  299 (329)
Q Consensus       251 ~~~~~C~IC~e~~~~~~~lpCg-----H~~fC~~Cl~~~~~~--~~~CP~Cr~~i~  299 (329)
                      ++...|.||++...+....||.     |. |+..|+.+|+..  ...||+||+++.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~-~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELEN-VHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGS-CCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCE-EcHHHHHHHHhhCCCCCCcccCCeee
Confidence            4567899999988777767765     88 999999999865  679999999874

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.23  E-value=5.1e-08  Score=67.26  Aligned_cols=37  Identities=14%  Similarity=0.161  Sum_probs=13.4

Q ss_pred             eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC
Q psy3263           4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR   43 (329)
Q Consensus         4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~   43 (329)
                      .+|.|||+||.+||+|+++||++|++-   ++..|.|.|.
T Consensus        13 kig~vIG~GG~~Ik~I~~~tga~I~i~---ddg~v~I~a~   49 (54)
T d1e3ha4          13 KIGEVIGPKRQMINQIQEDTGAEITIE---DDGTIYIGAA   49 (54)
T ss_dssp             --------------CHHHHSCCCC-----------CCCCB
T ss_pred             HeeEEECCccHHHHHHHHHHCCEEEEe---CCeEEEEEec
Confidence            589999999999999999999999995   3466777774

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.22  E-value=2.3e-07  Score=75.45  Aligned_cols=57  Identities=28%  Similarity=0.311  Sum_probs=45.9

Q ss_pred             ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC--------------------cc-eEEEecCH------HHHHHHHHHH
Q psy3263           2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE--------------------EP-VFVVTGRK------EDVARAKREI   54 (329)
Q Consensus         2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--------------------er-vi~ItG~~------e~v~~A~~~I   54 (329)
                      |+|||+|||.+|.++|+|+++|||+|.|=.++.                    |+ -|.|++..      ..+++|..+|
T Consensus        16 ~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~~a~~kl~~A~~~I   95 (134)
T d2bl5a1          16 FNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEV   95 (134)
T ss_dssp             SCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHH
T ss_pred             CCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999964432                    23 35677642      3588899999


Q ss_pred             HHHh
Q psy3263          55 LSAA   58 (329)
Q Consensus        55 ~~i~   58 (329)
                      ..++
T Consensus        96 ~~lL   99 (134)
T d2bl5a1          96 KKLL   99 (134)
T ss_dssp             HHHS
T ss_pred             HHHc
Confidence            8875

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.98  E-value=3.8e-07  Score=71.07  Aligned_cols=50  Identities=20%  Similarity=0.227  Sum_probs=39.2

Q ss_pred             cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhh
Q psy3263          95 KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQK  149 (329)
Q Consensus        95 ~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~  149 (329)
                      +..|.||||||.|||.|++.|||+|.|-.    ..+.|.| .+++++.+. +|.++
T Consensus        22 R~~GrIIG~gGktik~Ie~~Tg~~I~I~d----~~v~iig-~~e~i~~A~~~Ie~l   72 (104)
T d1tuaa2          22 RIKGRIIGEGGRARRTIEEMTDTYINVGE----YEVAIIG-DYERAMAAKQAIEML   72 (104)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECS----SEEEEEE-EHHHHHHHHHHHHHH
T ss_pred             HHhcceeCCCcHHHHHHHHHHCCeEEEeC----CeEEEEE-CchhHHHHHHHHHHH
Confidence            45899999999999999999999999942    3577889 999983333 44433

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=3.4e-06  Score=63.80  Aligned_cols=43  Identities=26%  Similarity=0.634  Sum_probs=32.7

Q ss_pred             CCcccccccccCcc---cEEeCCCChhccHhhHHhhcCC--------CCCCcccc
Q psy3263         252 GSRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDF--------DRTCPMCR  295 (329)
Q Consensus       252 ~~~~C~IC~e~~~~---~~~lpCgH~~fC~~Cl~~~~~~--------~~~CP~Cr  295 (329)
                      ....|+||++....   +.+.+|+|. ||.+|+..+++.        ...||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCI-FCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEE-EEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECCCCCE-eCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            34689999987642   345689999 999999987753        23699864

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.53  E-value=1.7e-05  Score=63.21  Aligned_cols=55  Identities=36%  Similarity=0.611  Sum_probs=42.0

Q ss_pred             eEEEEEecC------cccceeecCCCchHHHHHHhcCceEEcCCC----C--------------CCCe-EEEECCCCCCc
Q psy3263          86 VTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSR----D--------------KEPV-FEVTGNFPEGP  140 (329)
Q Consensus        86 ~t~~i~VP~------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~----~--------------~e~~-i~ItG~~pe~v  140 (329)
                      .+..|.||-      ++||.|||++|+|+|+|+++|||+|.|=.+    +              ++|. |-|++..++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            456677776      459999999999999999999999999321    1              3455 77888555555

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.49  E-value=1.5e-05  Score=64.52  Aligned_cols=54  Identities=24%  Similarity=0.417  Sum_probs=41.3

Q ss_pred             EEEEEecC------cccceeecCCCchHHHHHHhcCceEEcCCCC--------------------CCCe-EEEECCCCCC
Q psy3263          87 TIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--------------------KEPV-FEVTGNFPEG  139 (329)
Q Consensus        87 t~~i~VP~------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~--------------------~e~~-i~ItG~~pe~  139 (329)
                      +..|.||.      +++|+|||++|.|+|+|+++|||+|.|=.+.                    +|+. |-|++..++.
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~   82 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHH
Confidence            34566663      6899999999999999999999999995321                    3555 8888855665


Q ss_pred             c
Q psy3263         140 P  140 (329)
Q Consensus       140 v  140 (329)
                      .
T Consensus        83 ~   83 (134)
T d2bl5a1          83 R   83 (134)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.45  E-value=0.0084  Score=42.25  Aligned_cols=39  Identities=21%  Similarity=0.206  Sum_probs=35.4

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      .....+.||.+..++.|||+|.+||-..+-||-+|.|-.
T Consensus        26 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          26 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            356889999999999999999999999999999999854

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.18  E-value=0.0099  Score=41.76  Aligned_cols=39  Identities=21%  Similarity=0.181  Sum_probs=35.5

Q ss_pred             ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263          85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  123 (329)
Q Consensus        85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~  123 (329)
                      .....+.||.+...+.|||+|.++|-..+-||-+|.|-.
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            357889999999999999999999999999999999843

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.79  E-value=0.032  Score=39.21  Aligned_cols=34  Identities=24%  Similarity=0.719  Sum_probs=28.6

Q ss_pred             CcccccccccCcccEEeCC----CChhccHhhHHhhcCC
Q psy3263         253 SRQCYLCNDREVTHALIPC----GHNFFCSECAERTCDF  287 (329)
Q Consensus       253 ~~~C~IC~e~~~~~~~lpC----gH~~fC~~Cl~~~~~~  287 (329)
                      .+.|.+|.+.+.+.-++.|    +|. ||..|.+...+.
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~Hk-FCFpCsr~sik~   45 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHK-FCFPCSRESIKA   45 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCE-ECHHHHHHHHHH
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCc-eeccccHHHHHh
Confidence            4789999999999988877    688 999999776543

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.48  E-value=0.031  Score=41.50  Aligned_cols=37  Identities=19%  Similarity=0.238  Sum_probs=29.4

Q ss_pred             eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcC
Q psy3263          86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP  122 (329)
Q Consensus        86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip  122 (329)
                      ..++|.|....-|+|||++|++|++|++.-.....++
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~~   71 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFP   71 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCCC
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHHHHHHCCC
Confidence            3467888888999999999999999988765544443

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.27  E-value=0.18  Score=38.55  Aligned_cols=30  Identities=30%  Similarity=0.338  Sum_probs=23.9

Q ss_pred             eEEEEEecC-cccceeecCCCchHHHHHHhc
Q psy3263          86 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQT  115 (329)
Q Consensus        86 ~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~t  115 (329)
                      ....+.|+. .+-+.|||++|++||+|..++
T Consensus        49 I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          49 INGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             EEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            455678887 455899999999999997664

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.97  E-value=0.15  Score=37.57  Aligned_cols=25  Identities=20%  Similarity=0.250  Sum_probs=20.2

Q ss_pred             eeeecCCChHHHHHHHHhCCeEEec
Q psy3263           6 VPSINPFGCKIKALRAKTNTYIKTP   30 (329)
Q Consensus         6 G~IIGkgG~~Ik~Lr~~Tga~I~ip   30 (329)
                      |.||||+|++|++|+++-..+..++
T Consensus        47 GivIGrkG~~I~~L~~~l~k~~~~~   71 (92)
T d1wh9a_          47 QNVLGEKGRRIRELTAVVQKRFGFP   71 (92)
T ss_dssp             HHHHCGGGHHHHHHHHHHHHHHCCC
T ss_pred             ceeeccCchhHHHHHHHHHHHHCCC
Confidence            6799999999999998876555444

>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=80.89  E-value=0.17  Score=38.20  Aligned_cols=29  Identities=24%  Similarity=0.458  Sum_probs=24.9

Q ss_pred             EEEEEecCcccceeecCCCchHHHHHHhc
Q psy3263          87 TIEVRVPYKVVGLVVGPKGATIKRIQHQT  115 (329)
Q Consensus        87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~t  115 (329)
                      .++|.|....-|+|||++|+.|++|+++-
T Consensus        62 ~i~I~I~tarPG~iIGkkG~~i~~L~~~l   90 (105)
T d2uubc1          62 NVAVTVHVAKPGVVIGRGGERIRVLREEL   90 (105)
T ss_dssp             CEECCEEESCHHHHHCSTTSHHHHHHHHH
T ss_pred             cEEEEEEECCCceEEcCCchhHHHHHHHH
Confidence            46777788899999999999999998764

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=80.50  E-value=0.39  Score=33.30  Aligned_cols=25  Identities=16%  Similarity=-0.019  Sum_probs=22.5

Q ss_pred             eeeecCCChHHHHHHHHhCCeEEec
Q psy3263           6 VPSINPFGCKIKALRAKTNTYIKTP   30 (329)
Q Consensus         6 G~IIGkgG~~Ik~Lr~~Tga~I~ip   30 (329)
                      +.-|||+|.+||-...-||-+|++-
T Consensus        39 s~AIGk~G~NvrLas~Ltg~~idI~   63 (68)
T d1hh2p3          39 SLAIGKGGQNARLAAKLTGWKIDIK   63 (68)
T ss_dssp             HHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             cccccCCcchHHHHHHHHCCEEeeE
Confidence            4679999999999999999999985

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.19  E-value=0.97  Score=30.25  Aligned_cols=42  Identities=31%  Similarity=0.740  Sum_probs=33.0

Q ss_pred             CCcccccccccCcccEEe---CCCChhccHhhHHhhcCCCCCCccc
Q psy3263         252 GSRQCYLCNDREVTHALI---PCGHNFFCSECAERTCDFDRTCPMC  294 (329)
Q Consensus       252 ~~~~C~IC~e~~~~~~~l---pCgH~~fC~~Cl~~~~~~~~~CP~C  294 (329)
                      ....|.-|+..+.+....   .|.+. ||.+|-.=+-+....||-|
T Consensus        14 ~~~~C~gC~~~l~~~~~y~C~~C~~~-FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQHVYVCAVCQNV-FCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTSEEECCTTTTCC-BCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCCceEECcCCCCc-cccccchhhhhhhcCCCCC
Confidence            456899999887766544   67888 9999987776668899988

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=80.17  E-value=0.39  Score=33.21  Aligned_cols=27  Identities=15%  Similarity=-0.048  Sum_probs=23.1

Q ss_pred             eeeecCCChHHHHHHHHhCCeEEecCC
Q psy3263           6 VPSINPFGCKIKALRAKTNTYIKTPVR   32 (329)
Q Consensus         6 G~IIGkgG~~Ik~Lr~~Tga~I~ip~~   32 (329)
                      +.-|||+|.|||-..+-||-+|++-.+
T Consensus        38 s~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          38 SLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             HHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            456999999999999999999998633