Psyllid ID: psy4141

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350---
Protein Sequence
MKKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS
Secondary Structure (PSIPRED)
cEEEccccHHHHHHHHHHccEEEcccccccccEEEcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEEccccccEEEccccHHHHHHHHHccEEEEcccccccccEEEccccHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccEEEEccccccccHHHHHHHcccccccccccHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEHHHHHHccccEEEccccccccEEEEcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEEcEEEEEEEEcccccHHHHHHHccccEEEccccccccEEEEcccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccEEEEEEcccccHHHHHHHHHHHcccccccccccHHHHHEEEcc
Coil and Loop (DISEMBL)
mkkisrsgckIKALRAKTntyiktpvrgeepvfvvTGRKEDVARAKREILSAADHFSALRAsrksgalsplspptgvpghvtieVRVPYKVVGLvvgpkgatiKRIQHQtntyivtpsrdkepvfevtgapdsVEIARQEIESHIIrrtgscvtpaeavlngddNSADLLASLCNSGLGSLGTILnyvngtsgpasdsygagpgefnfnmplsssqmnhhvfsgssgcssasssssssacaphsstqldlgsiwsgmssldkdeglgdspsfdaspvnpssiwsyppvsstspsgsisgsrqcylcndrevthalipcghnffcsecaertcdfdrtcpmcrvpvnqamriis
Flexible Loop (DISEMBL)
mkkisrsgckikalraktntyiktpvrgeepvfvvtgrkedVARAKREILSAADHFSALRASRksgalsplspptgvpghvTIEVRVPYKVVGLVVgpkgatikriqhqtntyivtpsrdkepvfevtgapdsveIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFdrtcpmcrvpvnqamriis
Low Complexity Region (SEG)
MKKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFsgssgcssasssssssacaphssTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWsyppvsstspsgsisgsRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS
Disordered region (IsUnstruct)
*********KIKALRAKTNTYIKTPVRGEEPVFVVTGRKE*V**********************************VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS****PVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNG***************************************************************************************************************QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA*****
Disordered Region (DISOPRED)
MKKISRSGCKIKALRAKTNTYIKTP*RG*E***VVTGRKEDVARAKREI**********************************EVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT***********TGAPDSVEIARQEIESHII**********EAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS
Disordered Region (DISEMBL)
MKKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHH**************************QLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSY***************RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS
Disordered Region (DISPRO)
*****RSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR************GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSG************************************************************************SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS
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	353	2.2.26 [Sep-21-2011]
Q05A36	652	RNA-binding E3 ubiquitin-	yes	N/A	0.779	0.421	0.496	4e-61
Q5U5Q3	659	RNA-binding E3 ubiquitin-	yes	N/A	0.787	0.421	0.482	5e-61
A1L3F4	507	RNA-binding protein MEX3B	N/A	N/A	0.589	0.410	0.585	1e-60
Q6ZN04	569	RNA-binding protein MEX3B	no	N/A	0.470	0.291	0.695	9e-59
A1L020	520	RNA-binding protein MEX3A	no	N/A	0.447	0.303	0.686	3e-58
Q69Z36	601	RNA-binding protein MEX3B	no	N/A	0.458	0.269	0.706	9e-58
Q86XN8	651	RNA-binding protein MEX3D	no	N/A	0.478	0.259	0.660	6e-57
Q3UE17	643	RNA-binding protein MEX3D	no	N/A	0.475	0.261	0.666	2e-56
Q8JHV9	401	Baculoviral IAP repeat-co	N/A	N/A	0.184	0.162	0.333	8e-06
A9ULZ2	345	Baculoviral IAP repeat-co	N/A	N/A	0.178	0.182	0.328	1e-05

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

 Score =  235 bits (599), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 155/312 (49%), Positives = 198/312 (63%), Gaps = 37/312 (11%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR
Sbjct: 241 VGRQGCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASR 300

Query: 64  -KSG-ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
            K+G AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct: 301 NKNGPALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 360

Query: 122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSL 181
           EPVFEVTG P++V+ AR+EIE HI  RTG+ +      LN +++                
Sbjct: 361 EPVFEVTGMPENVDRAREEIEMHIAMRTGNYIE-----LNEEND------------FHYN 403

Query: 182 GTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSS--SSSA 239
           GT +++  GT G A  S    P       P  +  M+++    SS   S S+ S   S+ 
Sbjct: 404 GTDVSFEGGTLGSAWLSSNPVP-------PSRARMMSNYRNDSSSSLGSGSTDSYFGSNR 456

Query: 240 CAPHSSTQ-LDLGSIWSG--MSSLDKDEGLGDSPSFDASPVNPSSIWS-YPPVSSTS--- 292
            A  S T     G+ W G  + S+  ++   DSP+FD+ P +  +IW+ + PV+  S   
Sbjct: 457 LADFSPTSPFSTGNFWFGDTLPSVGSEDLTVDSPAFDSLPTSAQTIWTPFEPVNPLSGFG 516

Query: 293 --PSGSISGSRQ 302
             PSG++   R+
Sbjct: 517 SDPSGNMKTQRR 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 =  234 bits (598), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 149/309 (48%), Positives = 194/309 (62%), Gaps = 31/309 (10%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR
Sbjct: 248 VGRQGCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASR 307

Query: 64  -KSG-ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
            K+G AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct: 308 NKNGPALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 367

Query: 122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSL 181
           EPVFEVTG P++V+ AR+EIE HI  RTG+ +      LN ++N      +  +   G+L
Sbjct: 368 EPVFEVTGMPENVDRAREEIEMHIAMRTGNYIE-----LN-EENDFHYNGTDVSFEGGTL 421

Query: 182 GTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACA 241
           G+       +S P   S       +  +   S    +   + GS+  +  S +S  S   
Sbjct: 422 GSAWL----SSNPVPPSRARMISNYRNDSSSSLGSGSTDSYFGSNRLADFSPTSPFST-- 475

Query: 242 PHSSTQLDLGSIWSG--MSSLDKDEGLGDSPSFDASPVNPSSIWS-YPPVSSTS-----P 293
                    G+ W G  + S+  ++   DSP+FD+ P +  +IW+ + PV+  S     P
Sbjct: 476 ---------GNFWFGDTLPSVGSEDLAVDSPAFDSLPTSAQTIWTPFEPVNPLSGFGSDP 526

Query: 294 SGSISGSRQ 302
           SG++   R+
Sbjct: 527 SGNMKTQRR 535

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

Homo sapiens (taxid: 9606)

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

 Score =  234 bits (596), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 130/222 (58%), Positives = 154/222 (69%), Gaps = 14/222 (6%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR
Sbjct: 75  VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVALARREIISAAEHFSMIRASR 134

Query: 64  KSGALS----PLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
              A +     +  P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSR
Sbjct: 135 NKNAAALNGGSVPAPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSR 194

Query: 120 DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSADLLASLC-- 174
           DKEPVFEVTG P++V+ AR+EIE+HI  RTG  +  A+      NG D   DL  SL   
Sbjct: 195 DKEPVFEVTGMPENVDRAREEIEAHIAVRTGGLIEVADENDFHANGTDVGFDLHGSLWSK 254

Query: 175 -NSGLGSLGTILNYVNG----TSGPASDSYGAGPGEFNFNMP 211
            N   GS   + NY N         ++DSY  G    +++ P
Sbjct: 255 SNQSSGSRKALSNYRNDSSSSLGSASTDSYFGGTRMADYSPP 296

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 =  227 bits (579), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 119/171 (69%), Positives = 137/171 (80%), Gaps = 5/171 (2%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR
Sbjct: 82  VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASR 141

Query: 64  -KSGALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
            K+ AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct: 142 NKNTALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 201

Query: 122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEA---VLNGDDNSADL 169
           EPVFEVTG P++V+ AR+EIE+HI  RTG  +   +      NG D   DL
Sbjct: 202 EPVFEVTGMPENVDRAREEIEAHIALRTGGIIELTDENDFHANGTDVGFDL 252

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 =  225 bits (574), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 116/169 (68%), Positives = 136/169 (80%), Gaps = 11/169 (6%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVF+VTGR+EDVA A+REI+SAA+HFS +RASR
Sbjct: 148 VGRQGCKIKALRAKTNTYIKTPVRGEEPVFMVTGRREDVATARREIISAAEHFSMIRASR 207

Query: 64  -KSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKE 122
            KSGA   ++P   +PG VTI VRVPY+VVGLVVGPKGATIKRIQ QTNTYI+TPSRD++
Sbjct: 208 NKSGAAFGVAP--ALPGQVTIRVRVPYRVVGLVVGPKGATIKRIQQQTNTYIITPSRDRD 265

Query: 123 PVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLA 171
           PVFE+TGAP +VE AR+EIE+HI  RTG  +          +N  D LA
Sbjct: 266 PVFEITGAPGNVERAREEIETHIAVRTGKILE--------YNNENDFLA 306

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 =  224 bits (570), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 118/167 (70%), Positives = 135/167 (80%), Gaps = 5/167 (2%)

Query: 8   GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 66
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR K+ 
Sbjct: 118 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASRNKNT 177

Query: 67  ALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 125
           AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct: 178 ALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 237

Query: 126 EVTGAPDSVEIARQEIESHIIRRTGSCVTPAEA---VLNGDDNSADL 169
           EVTG P++V+ AR+EIE+HI  RTG  +   +      NG D   DL
Sbjct: 238 EVTGMPENVDRAREEIEAHIALRTGGIIELTDENDFHANGTDVGFDL 284

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

Mus musculus (taxid: 10090)

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

 Score =  221 bits (563), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 115/174 (66%), Positives = 136/174 (78%), Gaps = 5/174 (2%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVF+VTGRKEDV  AKREILSAA+HFS +RA+R
Sbjct: 195 VGRQGCKIKALRAKTNTYIKTPVRGEEPVFIVTGRKEDVEMAKREILSAAEHFSIIRATR 254

Query: 64  -KSGALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
            K+G L   +  P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDK
Sbjct: 255 SKAGGLPGAAQGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK 314

Query: 122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTP---AEAVLNGDDNSADLLAS 172
           EPVF VTG P++V+ AR+EIE+HI  RTG+       ++   NG D   DLL +
Sbjct: 315 EPVFAVTGMPENVDRAREEIEAHITLRTGAFTDAGPDSDFHANGTDVCLDLLGA 368

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 =  219 bits (559), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 116/174 (66%), Positives = 137/174 (78%), Gaps = 6/174 (3%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVF+VTGRKEDV  AKREILSA +HFS +RA+R
Sbjct: 176 VGRQGCKIKALRAKTNTYIKTPVRGEEPVFIVTGRKEDVEMAKREILSA-EHFSLIRATR 234

Query: 64  -KSGALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
            K+G LS  +P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDK
Sbjct: 235 SKAGGLSGATPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK 294

Query: 122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCV---TPAEAVLNGDDNSADLLAS 172
           EPVF VTG P++V+ AR+EIE+HI  RTG+       ++   NG D   DLL +
Sbjct: 295 EPVFAVTGMPENVDRAREEIEAHITLRTGAFTDSGPDSDFHANGTDVCLDLLGA 348

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 = 51.6 bits (122), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 284 SYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 343
           S PP+S+      +   R C +C D++V+   +PCGH   C+ECA       R CP+CR 
Sbjct: 335 SAPPLSTEEQLRRLKEERMCKVCMDKDVSMLFVPCGHLVVCTECAPNL----RHCPICRA 390

Query: 344 PVNQAMRII 352
            +  ++R  
Sbjct: 391 AIRGSVRAF 399

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 = 50.8 bits (120), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 286 PPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
           PP+S+      +   R C +C D++V+   +PCGH   C+ECA       R CP+CR  +
Sbjct: 281 PPLSTEEQLQRLKEERMCKVCMDKDVSMLFVPCGHLVVCTECAPNL----RHCPICRAAI 336

Query: 346 NQAMRII 352
             ++R  
Sbjct: 337 RGSVRAF 343

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	353
219522040	428	mex-3 protein [Tribolium castaneum] gi|2	0.872	0.719	0.582	2e-96
270002843	410	hypothetical protein TcasGA2_TC001207 [T	0.872	0.751	0.582	4e-96
345483953	444	PREDICTED: RNA-binding protein MEX3B-lik	0.883	0.702	0.525	3e-85
332022800	422	RNA-binding protein MEX3A [Acromyrmex ec	0.841	0.703	0.533	7e-85
383860805	418	PREDICTED: RNA-binding protein MEX3B-lik	0.895	0.755	0.530	5e-83
322797035	326	hypothetical protein SINV_16493 [Solenop	0.869	0.941	0.524	3e-82
242017160	389	conserved hypothetical protein [Pediculu	0.920	0.835	0.497	4e-82
66510891	425	PREDICTED: RNA-binding protein MEX3B-lik	0.869	0.722	0.521	8e-82
340715365	425	PREDICTED: RNA-binding protein MEX3B-lik	0.869	0.722	0.521	1e-81
350414446	425	PREDICTED: RNA-binding protein MEX3B-lik	0.869	0.722	0.518	1e-81

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

 Score =  358 bits (920), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 212/364 (58%), Positives = 251/364 (68%), Gaps = 56/364 (15%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA+AKREILSAA+HFS +RASR
Sbjct: 104 VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAKAKREILSAAEHFSQIRASR 163

Query: 64  K-------SGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116
           K       SGA +P  PP  +PGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVT
Sbjct: 164 KNNLAGLGSGASTPPGPPANIPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVT 223

Query: 117 PSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNS 176
           PSRDKEPVFEVTG P+SVE AR+EIE+HI  RTG+      ++  G  +  DL +SL  S
Sbjct: 224 PSRDKEPVFEVTGLPESVESARREIEAHIAMRTGN----GASMGLGGLDDGDLFSSLYKS 279

Query: 177 GLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSS 236
           GL S   ILNY+              P +F    P++               SS  SSS 
Sbjct: 280 GLSS---ILNYIE-------------PEQF----PMTG--------------SSTFSSSG 305

Query: 237 SSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVS------S 290
           S + +  SS   DLG+IW   SS ++DEGLGDSPSFD+S    SSIWSYPPV+      S
Sbjct: 306 SCSSSSSSSGGRDLGAIW---SSSERDEGLGDSPSFDSS-TALSSIWSYPPVAPSRPSNS 361

Query: 291 TSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQAM 349
           TSP+ S+ GS +C +C + +VTHAL+PCGHNFFC ECA R CD  +  CP+C +P  QA+
Sbjct: 362 TSPADSLLGSAKCLVCGEAKVTHALVPCGHNFFCMECANRVCDGTEAQCPVCSLPAIQAI 421

Query: 350 RIIS 353
           RI S
Sbjct: 422 RIYS 425

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 =  357 bits (917), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 212/364 (58%), Positives = 251/364 (68%), Gaps = 56/364 (15%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA+AKREILSAA+HFS +RASR
Sbjct: 86  VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAKAKREILSAAEHFSQIRASR 145

Query: 64  K-------SGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116
           K       SGA +P  PP  +PGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVT
Sbjct: 146 KNNLAGLGSGASTPPGPPANIPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVT 205

Query: 117 PSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNS 176
           PSRDKEPVFEVTG P+SVE AR+EIE+HI  RTG+      ++  G  +  DL +SL  S
Sbjct: 206 PSRDKEPVFEVTGLPESVESARREIEAHIAMRTGN----GASMGLGGLDDGDLFSSLYKS 261

Query: 177 GLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSS 236
           GL S   ILNY+              P +F    P++               SS  SSS 
Sbjct: 262 GLSS---ILNYIE-------------PEQF----PMTG--------------SSTFSSSG 287

Query: 237 SSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVS------S 290
           S + +  SS   DLG+IW   SS ++DEGLGDSPSFD+S    SSIWSYPPV+      S
Sbjct: 288 SCSSSSSSSGGRDLGAIW---SSSERDEGLGDSPSFDSS-TALSSIWSYPPVAPSRPSNS 343

Query: 291 TSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQAM 349
           TSP+ S+ GS +C +C + +VTHAL+PCGHNFFC ECA R CD  +  CP+C +P  QA+
Sbjct: 344 TSPADSLLGSAKCLVCGEAKVTHALVPCGHNFFCMECANRVCDGTEAQCPVCSLPAIQAI 403

Query: 350 RIIS 353
           RI S
Sbjct: 404 RIYS 407

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  321 bits (823), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 197/375 (52%), Positives = 235/375 (62%), Gaps = 63/375 (16%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASR
Sbjct: 106 VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASR 165

Query: 64  KS--GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
           KS  GAL  +P  PP  VPGH+TI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSR
Sbjct: 166 KSSLGALLGAPPGPPASVPGHITIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSR 225

Query: 120 DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLG 179
           DKEPVFEVTG P+SV  AR EI++HI +RTG  V P            DLL  LC  GLG
Sbjct: 226 DKEPVFEVTGLPESVAAARTEIQAHITQRTG--VLPLCM-----HEEKDLLEVLCRGGLG 278

Query: 180 SLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSA 239
           S+   L+   G  G    S                          +   S + SSSSSS 
Sbjct: 279 SILGCLDPPGGAKGSNGSSG-------------------------AFSSSGSCSSSSSST 313

Query: 240 CAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVS---------- 289
            AP  +   DL +IW   + +++DEG+G+SPSF++   + SSIWS+P V+          
Sbjct: 314 GAPGLN---DLVAIWG--AGMERDEGIGESPSFESQTASASSIWSFPGVALPSRPSPPAS 368

Query: 290 -----------STSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTC-DFDRT 337
                       T      +G R+C +C D++VT AL+PCGH  FC EC  R C   + T
Sbjct: 369 ASPASPTDSLLGTGSGNGSTGVRECVVCGDKDVTTALVPCGHKHFCLECGHRICMSSEPT 428

Query: 338 CPMCRVPVNQAMRII 352
           CP+C  PV QA+RII
Sbjct: 429 CPVCSKPVLQALRII 443

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  320 bits (820), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 189/354 (53%), Positives = 234/354 (66%), Gaps = 57/354 (16%)

Query: 5   SRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK 64
           +R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRK
Sbjct: 42  TRPGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRK 101

Query: 65  S--GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 120
           S  GAL  +P  PP  VPGH+TI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRD
Sbjct: 102 SSLGALLGAPPGPPATVPGHITIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRD 161

Query: 121 KEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGS 180
           KEPVFEVTG P+SVE AR+EI++HI  RTG+    A  V+  DD   DLL  LC  GLGS
Sbjct: 162 KEPVFEVTGLPESVEAARREIQAHITLRTGT----APGVV--DDT--DLLGVLCRGGLGS 213

Query: 181 LGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSAC 240
           +                              L    M+    + SS  + A SSS+S + 
Sbjct: 214 V------------------------------LGIQSMDQPGSNSSSSSNGAFSSSASCSS 243

Query: 241 APHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPV------------ 288
           +  S+  + +  + +  + +++DEG+G+SPSF++ P + SSIWS+P V            
Sbjct: 244 SSSSTGGIGMNDLVAIWNGIERDEGIGESPSFESQPTSTSSIWSFPSVALPSRPSPPATA 303

Query: 289 SSTSPSGSISGS--RQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCP 339
           S  SP+ S+ G   R C +C ++EVT AL+PCGHN FC +C  R C+  D +CP
Sbjct: 304 SPASPTDSLLGGARRDCVVCGEKEVTAALVPCGHNLFCMDCGNRVCENQDPSCP 357

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  314 bits (804), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 189/356 (53%), Positives = 229/356 (64%), Gaps = 40/356 (11%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASR
Sbjct: 97  VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASR 156

Query: 64  KS--GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
           KS  GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSR
Sbjct: 157 KSSLGALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSR 216

Query: 120 DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLG 179
           DKEPVFEVTG P+SVE AR+EIE+HI  RTG+             + ++LL+ LC  GLG
Sbjct: 217 DKEPVFEVTGLPESVEAARREIEAHIALRTGT---------GPSLDDSELLSVLCRGGLG 267

Query: 180 S-LGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSS 238
           S LG +    +  S  ++ ++ +     + +    +  +N  V    +G     S   S 
Sbjct: 268 SILGCLDPPGSNGSNGSNGAFSSSGSCSSSSSSSGAPGLNDIVAIWGAGVERDESLGESP 327

Query: 239 ACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSIS 298
           +    S       SIWS              P   A P  PS   S P    TSP+ S+ 
Sbjct: 328 SFESAS-------SIWS-------------FPGV-ALPSRPSPPGSIP----TSPTDSLL 362

Query: 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQAMRIIS 353
           G R+C +C D+EVT AL+PCGHN FC +C+ R C+  D +CP+C  PV QA+RI S
Sbjct: 363 GRRECVVCGDKEVTSALVPCGHNHFCLDCSNRVCESSDPSCPVCSRPVLQALRIFS 418

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  311 bits (797), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 191/364 (52%), Positives = 239/364 (65%), Gaps = 57/364 (15%)

Query: 8   GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKS-- 65
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASRKS  
Sbjct: 1   GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASRKSSL 60

Query: 66  GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 123
           GAL  +P  PPT +PGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSRDKEP
Sbjct: 61  GALLGAPPGPPTTMPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSRDKEP 120

Query: 124 VFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGT 183
           VFEVTG P+SVE AR+EI++HI  RTG+          G  + +DLL +LC  GL S+  
Sbjct: 121 VFEVTGLPESVEAARREIQAHITLRTGTA--------PGVVDESDLLGALCRGGLSSV-- 170

Query: 184 ILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPH 243
                                       ++   ++    + SS  + A SSS+S + +  
Sbjct: 171 ----------------------------IAIQSIDQPGSNSSSSSNGAFSSSASCSSSSS 202

Query: 244 SSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPV------------SST 291
           S+  + +  + +    +++DEGLG+SPSF++ P + SSIWS+P V            S  
Sbjct: 203 STGGMGMNDLVAIWGGMERDEGLGESPSFESQPTSTSSIWSFPSVTLPSRPSPPATASPA 262

Query: 292 SPSGSISGS--RQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQA 348
           SP+ S+ G+  R C +C D+EVT AL+PCGHN FC +C  R CD  D +CP+C   V Q 
Sbjct: 263 SPTDSLLGNARRDCVVCGDKEVTAALVPCGHNLFCMDCGNRVCDSQDPSCPVCSRRVLQV 322

Query: 349 MRII 352
           +RI 
Sbjct: 323 LRIF 326

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242017160|ref|XP_002429060.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212513915|gb|EEB16322.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  311 bits (796), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 192/386 (49%), Positives = 244/386 (63%), Gaps = 61/386 (15%)

Query: 8   GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGA 67
           GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA+AKREILSAA+HFS +RASRK+  
Sbjct: 25  GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAKAKREILSAAEHFSQIRASRKTNL 84

Query: 68  LSPLSPPT------GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
              L   +       +PG VTI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct: 85  GGLLGGLSPPGPPANIPGQVTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 144

Query: 122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNG------------DDNSADL 169
           EPVFEV+G P++V++A++EIE+HI  RTG+        LNG            +DNS +L
Sbjct: 145 EPVFEVSGLPENVQVAKREIEAHIAMRTGA------GTLNGTNMADLLGAPLIEDNS-EL 197

Query: 170 LASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCS 229
           LASL  +GLGSL + L          SD+          NM   +S  +       S   
Sbjct: 198 LASLYKTGLGSLFSCLE--------PSDTNSTTLNSDALNMFHPTSLTSSASSGAFSSSG 249

Query: 230 SASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYP--- 286
           S SS+SSSS+         DL SIW+  SSL++DEG+G+SP F+ +  + S+IWS+P   
Sbjct: 250 SLSSNSSSSSNGGRIG---DLVSIWN--SSLERDEGIGESPGFETTTTS-SNIWSFPSSA 303

Query: 287 ----------PVSSTSPSGSISG--------SRQCYLCNDREVTHALIPCGHNFFCSECA 328
                     P +S SP+ S++          R C +C ++E+  AL+PCGHN FC +CA
Sbjct: 304 STTGITTRPSPTASASPTDSLASITGMSLGTKRDCLVCAEKEINAALVPCGHNLFCLDCA 363

Query: 329 ERTCD-FDRTCPMCRVPVNQAMRIIS 353
            R C+  +  CP+C   V QA+RI+S
Sbjct: 364 TRLCEGTEPACPICSRTVCQAIRILS 389

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  310 bits (793), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 194/372 (52%), Positives = 233/372 (62%), Gaps = 65/372 (17%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASR
Sbjct: 97  VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASR 156

Query: 64  KS--GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
           KS  GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSR
Sbjct: 157 KSSLGALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSR 216

Query: 120 DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLG 179
           DKEPVFEVTG P+SVE AR+EIE+HI  RTG+  T          + ++LL+ LC  GLG
Sbjct: 217 DKEPVFEVTGLPESVEAARREIEAHIALRTGTGTT---------LDDSELLSVLCRGGLG 267

Query: 180 SLGTILN-------------YVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSS 226
           S+   L+             + +  S  +S S    PG  N  + +  + M      G S
Sbjct: 268 SILGCLDPPGSNGSNGSSGAFSSSGSCSSSSSSSGAPG-LNDLVAIWGAGMERDEGLGES 326

Query: 227 GCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYP 286
               + ++S+S              SIWS              P   A P  PS     P
Sbjct: 327 PSFESQTASAS--------------SIWS-------------FPGV-ALPSRPS-----P 353

Query: 287 PVSS--TSPSGSI--SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMC 341
           P S+  TSP+ S+   G R+C +C D+EVT AL+PCGHN FC +C  R C+  D +CP+C
Sbjct: 354 PASASPTSPTDSLLGGGRRECVVCGDKEVTAALVPCGHNHFCLDCGNRVCESSDPSCPVC 413

Query: 342 RVPVNQAMRIIS 353
             PV QA+RI S
Sbjct: 414 SRPVLQALRIFS 425

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

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 =  309 bits (792), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 194/372 (52%), Positives = 233/372 (62%), Gaps = 65/372 (17%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASR
Sbjct: 97  VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASR 156

Query: 64  KS--GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
           KS  GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSR
Sbjct: 157 KSSLGALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSR 216

Query: 120 DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLG 179
           DKEPVFEVTG P+SVE AR+EIE+HI  RTG+  T          + ++LL+ LC  GLG
Sbjct: 217 DKEPVFEVTGLPESVEAARREIEAHIALRTGTGAT---------LDDSELLSVLCRGGLG 267

Query: 180 SLGTILN-------------YVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSS 226
           S+   L+             + +  S  +S S    PG  N  + +  + M      G S
Sbjct: 268 SILGCLDPPGSNGSNGSSGAFSSSGSCSSSSSSSGAPG-INDLVAIWGAGMERDEGLGES 326

Query: 227 GCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYP 286
               + ++S+S              SIWS              P   A P  PS     P
Sbjct: 327 PSFESQTASAS--------------SIWS-------------FPGV-ALPSRPS-----P 353

Query: 287 PVSS--TSPSGSI--SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMC 341
           P S+  TSP+ S+   G R+C +C D+EVT AL+PCGHN FC +C  R C+  D +CP+C
Sbjct: 354 PASASPTSPTDSLLGGGRRECVVCGDKEVTAALVPCGHNHFCLDCGNRVCESSDPSCPIC 413

Query: 342 RVPVNQAMRIIS 353
             PV QA+RI S
Sbjct: 414 SRPVLQALRIFS 425

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

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 =  309 bits (792), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 193/372 (51%), Positives = 233/372 (62%), Gaps = 65/372 (17%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA+HFS +RASR
Sbjct: 97  VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAEHFSQIRASR 156

Query: 64  KS--GAL--SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
           KS  GAL  +P  PP  VPGHVTI+VRVPY+VVGLVVGPKGATIKRIQHQT+TYIVTPSR
Sbjct: 157 KSSLGALLGAPPGPPASVPGHVTIQVRVPYRVVGLVVGPKGATIKRIQHQTHTYIVTPSR 216

Query: 120 DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLG 179
           DKEPVFEVTG P+SVE AR+EIE+HI  RTG+  T          + ++LL+ LC  GLG
Sbjct: 217 DKEPVFEVTGLPESVEAARREIEAHIALRTGTGTT---------LDDSELLSVLCRGGLG 267

Query: 180 SLGTILN-------------YVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSS 226
           S+   L+             + +  S  +S S    PG  N  + +  + M      G S
Sbjct: 268 SILGCLDPPGSNGSNGSSGAFSSSGSCSSSSSSSGAPG-LNDLVAIWGAGMERDEGLGES 326

Query: 227 GCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYP 286
               + ++S+S              SIW                SF   P+ PS     P
Sbjct: 327 PSFESQTASAS--------------SIW----------------SFPGVPL-PSR--PSP 353

Query: 287 PVSS--TSPSGSI--SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMC 341
           P S+  TSP+ S+   G R+C +C D+EVT AL+PCGHN FC +C  R C+  D +CP+C
Sbjct: 354 PASASPTSPTDSLLGGGRRECVVCGDKEVTAALVPCGHNHFCLDCGNRVCESSDPSCPIC 413

Query: 342 RVPVNQAMRIIS 353
             PV QA+RI S
Sbjct: 414 SRPVLQALRIFS 425

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

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	353
UNIPROTKB|F1N0W7	516	MEX3C "Uncharacterized protein	0.597	0.408	0.600	2.4e-75
MGI|MGI:2652843	652	Mex3c "mex3 homolog C (C. eleg	0.424	0.230	0.756	3e-75
RGD|1309023	511	Mex3c "mex-3 homolog C (C. ele	0.424	0.293	0.756	3e-75
UNIPROTKB|D4A2R5	464	Mex3c "Protein Mex3c" [Rattus	0.424	0.323	0.756	3e-75
MGI|MGI:1918252	601	Mex3b "mex3 homolog B (C. eleg	0.492	0.289	0.687	7.9e-75
UNIPROTKB|F1PM07	567	MEX3B "Uncharacterized protein	0.504	0.313	0.677	1e-74
UNIPROTKB|J9JHU9	580	MEX3B "Uncharacterized protein	0.504	0.306	0.677	1e-74
RGD|1306790	601	Mex3b "mex3 homolog B (C. eleg	0.492	0.289	0.687	2.1e-74
UNIPROTKB|E1BM86	468	E1BM86 "Uncharacterized protei	0.492	0.371	0.687	2.6e-74
UNIPROTKB|I3LE70	387	MEX3C "Uncharacterized protein	0.586	0.534	0.607	3.3e-74

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

 Score = 577 (208.2 bits), Expect = 2.4e-75, Sum P(3) = 2.4e-75
 Identities = 137/228 (60%), Positives = 162/228 (71%)

Query:     4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
             + R GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR
Sbjct:   105 VGRQGCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASR 164

Query:    64 -KSG-ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
              K+G AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct:   165 NKNGPALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 224

Query:   122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSAD--LLAS--LC 174
             EPVFEVTG P++V+ AR+EIE HI  RTG+ +   E      NG D S +   L S  L 
Sbjct:   225 EPVFEVTGMPENVDRAREEIEMHIAMRTGNYIELNEENDFHYNGTDVSFEGGTLGSAWLS 284

Query:   175 NSGL--GSLGTILNYVNGTS---GPAS-DSY-GAGP-GEFNFNMPLSS 214
             ++ +       I NY N +S   G  S DSY G+    +F+   P S+
Sbjct:   285 SNPVPPSRARMISNYRNDSSSSLGSGSTDSYFGSNRLADFSPTSPFST 332

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 576 (207.8 bits), Expect = 3.0e-75, Sum P(3) = 3.0e-75
 Identities = 115/152 (75%), Positives = 131/152 (86%)

Query:     4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
             + R GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR
Sbjct:   241 VGRQGCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASR 300

Query:    64 -KSG-ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
              K+G AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct:   301 NKNGPALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 360

Query:   122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCV 153
             EPVFEVTG P++V+ AR+EIE HI  RTG+ +
Sbjct:   361 EPVFEVTGMPENVDRAREEIEMHIAMRTGNYI 392

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 = 576 (207.8 bits), Expect = 3.0e-75, Sum P(3) = 3.0e-75
 Identities = 115/152 (75%), Positives = 131/152 (86%)

Query:     4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
             + R GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR
Sbjct:   100 VGRQGCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASR 159

Query:    64 -KSG-ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
              K+G AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct:   160 NKNGPALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 219

Query:   122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCV 153
             EPVFEVTG P++V+ AR+EIE HI  RTG+ +
Sbjct:   220 EPVFEVTGMPENVDRAREEIEMHIAMRTGNYI 251

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 = 576 (207.8 bits), Expect = 3.0e-75, Sum P(3) = 3.0e-75
 Identities = 115/152 (75%), Positives = 131/152 (86%)

Query:     4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
             + R GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR
Sbjct:    53 VGRQGCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASR 112

Query:    64 -KSG-ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
              K+G AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct:   113 NKNGPALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 172

Query:   122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCV 153
             EPVFEVTG P++V+ AR+EIE HI  RTG+ +
Sbjct:   173 EPVFEVTGMPENVDRAREEIEMHIAMRTGNYI 204

GO:0003723 "RNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 579 (208.9 bits), Expect = 7.9e-75, Sum P(3) = 7.9e-75
 Identities = 123/179 (68%), Positives = 140/179 (78%)

Query:     8 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 66
             GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR K+ 
Sbjct:   118 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASRNKNT 177

Query:    67 ALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 125
             AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   178 ALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 237

Query:   126 EVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSADLLASLCNSGLGSL 181
             EVTG P++V+ AR+EIE+HI  RTG  +   +      NG D   DL      SG GSL
Sbjct:   238 EVTGMPENVDRAREEIEAHIALRTGGIIELTDENDFHANGTDVGFDLHHGSGGSGPGSL 296

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

UNIPROTKB|F1PM07 MEX3B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 587 (211.7 bits), Expect = 1.0e-74, Sum P(3) = 1.0e-74
 Identities = 124/183 (67%), Positives = 142/183 (77%)

Query:     4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
             + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR
Sbjct:    82 VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASR 141

Query:    64 -KSGALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
              K+ AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct:   142 NKNTALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 201

Query:   122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSADLLASLCNSGL 178
             EPVFEVTG P++V+ AR+EIE+HI  RTG  +   +      NG D   DL      SG 
Sbjct:   202 EPVFEVTGMPENVDRAREEIEAHIALRTGGIIELTDENDFHANGTDVGFDLHHGSGGSGP 261

Query:   179 GSL 181
             GSL
Sbjct:   262 GSL 264

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|J9JHU9 MEX3B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 587 (211.7 bits), Expect = 1.0e-74, Sum P(3) = 1.0e-74
 Identities = 124/183 (67%), Positives = 142/183 (77%)

Query:     4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
             + R GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR
Sbjct:    95 VGRQGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASR 154

Query:    64 -KSGALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 121
              K+ AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDK
Sbjct:   155 NKNTALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK 214

Query:   122 EPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSADLLASLCNSGL 178
             EPVFEVTG P++V+ AR+EIE+HI  RTG  +   +      NG D   DL      SG 
Sbjct:   215 EPVFEVTGMPENVDRAREEIEAHIALRTGGIIELTDENDFHANGTDVGFDLHHGSGGSGP 274

Query:   179 GSL 181
             GSL
Sbjct:   275 GSL 277

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

RGD|1306790 Mex3b "mex3 homolog B (C. elegans)" [Rattus norvegicus (taxid:10116)]

 Score = 579 (208.9 bits), Expect = 2.1e-74, Sum P(3) = 2.1e-74
 Identities = 123/179 (68%), Positives = 140/179 (78%)

Query:     8 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 66
             GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR K+ 
Sbjct:   118 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASRNKNT 177

Query:    67 ALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 125
             AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:   178 ALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 237

Query:   126 EVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSADLLASLCNSGLGSL 181
             EVTG P++V+ AR+EIE+HI  RTG  +   +      NG D   DL      SG GSL
Sbjct:   238 EVTGMPENVDRAREEIEAHIALRTGGIIELTDENDFHANGTDVGFDLHHGSGGSGPGSL 296

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|E1BM86 E1BM86 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 579 (208.9 bits), Expect = 2.6e-74, Sum P(3) = 2.6e-74
 Identities = 123/179 (68%), Positives = 140/179 (78%)

Query:     8 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 66
             GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVA A+REI+SAA+HFS +RASR K+ 
Sbjct:     4 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVAMARREIISAAEHFSMIRASRNKNT 63

Query:    67 ALSPLSP-PTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 125
             AL+   P P  +PG  TI+VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:    64 ALNGAVPGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 123

Query:   126 EVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSADLLASLCNSGLGSL 181
             EVTG P++V+ AR+EIE+HI  RTG  +   +      NG D   DL      SG GSL
Sbjct:   124 EVTGMPENVDRAREEIEAHIALRTGGIIELTDENDFHANGTDVGFDLHHGSGGSGPGSL 182

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 569 (205.4 bits), Expect = 3.3e-74, Sum P(3) = 3.3e-74
 Identities = 136/224 (60%), Positives = 160/224 (71%)

Query:     8 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR-KSG 66
             GCKIKALRAKTNTYIKTPVRGEEP+FVVTGRKEDVA AKREILSAA+HFS +RASR K+G
Sbjct:     1 GCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRASRNKNG 60

Query:    67 -ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 125
              AL  LS    +PG  T++VRVPY+VVGLVVGPKGATIKRIQ QT+TYIVTPSRDKEPVF
Sbjct:    61 PALGGLSCSPNLPGQTTVQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDKEPVF 120

Query:   126 EVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAV---LNGDDNSAD--LLAS--LCNSGL 178
             EVTG P++V+ AR+EIE HI  RTG+ +   E      NG D S +   L S  L ++ +
Sbjct:   121 EVTGMPENVDRAREEIEMHIAMRTGNYIELNEENDFHYNGTDVSFEGGTLGSAWLSSNPV 180

Query:   179 --GSLGTILNYVNGTS---GPAS-DSY-GAGP-GEFNFNMPLSS 214
                    I NY N +S   G  S DSY G+    +F+   P S+
Sbjct:   181 PPSRARMISNYRNDSSSSLGSGSTDSYFGSNRLADFSPTSPFST 224

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA 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	353
smart00322	68	smart00322, KH, K homology RNA-binding domain	9e-16
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	9e-15
pfam00013	59	pfam00013, KH_1, KH domain	3e-14
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	2e-11
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	9e-11
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	4e-07
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	5e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-06
pfam00013	59	pfam00013, KH_1, KH domain	1e-05
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	2e-05
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	3e-05
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-05
pfam13014	42	pfam13014, KH_3, KH domain	4e-05
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-04
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	0.001
smart00184	40	smart00184, RING, Ring finger	0.002

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

 Score = 70.8 bits (174), Expect = 9e-16
 Identities = 27/66 (40%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQ 139
           VTIEV +P   VGL++G  G+TIK+I+ +T   I +     +E V E+TG P++VE A +
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAE 62

Query: 140 EIESHI 145
            I   +
Sbjct: 63  LILEIL 68

Length = 68

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

 Score = 68.0 bits (167), Expect = 9e-15
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIAR 138
           T  V VP  +VG ++G  G+TIK I+ +T   I  P      +E +  +TG P++VE A+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 139 QEIE 142
           + I 
Sbjct: 61  ELIL 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|215657 pfam00013, KH_1, KH domain

 Score = 66.0 bits (162), Expect = 3e-14
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141
           T  + +P   VG ++G  G+ IK I+ +T   I  P  D++    ++G P+ VE A++ I
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP-DDRDDTVTISGTPEQVEKAKELI 59

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

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

 Score = 58.2 bits (141), Expect = 2e-11
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
              C +C +R      +PCGH   C ECA+R     + CP+CR P+  
Sbjct: 2   DDLCVICLERPRNVVFLPCGHLCLCEECAKR-LRSKKKCPICRQPIES 48

Length = 49

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

 Score = 56.4 bits (137), Expect = 9e-11
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQE 140
           T EV +P K+   ++G KG+ I++I  +T   I       K     +TG  ++VE A++E
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEE 60

Query: 141 IE 142
           I 
Sbjct: 61  IL 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|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 46.0 bits (109), Expect = 4e-07
 Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 300 SRQCYLCNDREV-THALIPCGHNFFCSECAERTCDFDRTCPMCR 342
             +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 = 46.0 bits (110), Expect = 5e-07
 Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREIL 50
          I + G  IK +R +T   IK P  G   EE +  +TG  E V +AK  IL
Sbjct: 15 IGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 51
          I + G  IK +  +T   I  P  G  E V  +TG  E+V +A   IL 
Sbjct: 18 IGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILE 66

Length = 68

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI 49
          I + G  IK +R +T   I+ P    +    ++G  E V +AK  I
Sbjct: 15 IGKGGSNIKEIREETGVKIRIP-DDRDDTVTISGTPEQVEKAKELI 59

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

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

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 301 RQCYLCNDREVTHALI---PCGHNFFCSECAERTCDFDRTCPMCRVP 344
            +C +C D       +   PCGH  F  EC ++      TCP+CR P
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGH-VFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREIL 50
          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|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 = 40.1 bits (94), Expect = 4e-05
 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

Query: 302 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPV 345
           +C +C +       L+PCGH F C  C ++       TCP+CR P+
Sbjct: 1   ECPICLEEFREPVVLLPCGHVF-CRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 39.8 bits (94), Expect = 4e-05
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)

Query: 92  VGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTG 129
           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|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 38.2 bits (90), Expect = 3e-04
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 87  VPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK----EPVFEVTGAPDSVEIARQEI 141
           VP    G ++G  G+TIK I+ +T   I           E V  ++G P +V+ A   I
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
           + 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|214546 smart00184, RING, Ring finger

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 303 CYLCNDREVTHA-LIPCGHNFFCSECAERTCDFD-RTCPMC 341
           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	353
KOG2113|consensus	394		99.96
KOG2191|consensus	402		99.83
KOG1676|consensus	600		99.82
KOG1676|consensus	600		99.78
KOG2190|consensus	485		99.69
KOG2193|consensus	584		99.68
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.67
KOG2192|consensus	390		99.63
KOG2193|consensus	584		99.61
PRK13763	180	putative RNA-processing protein; Provisional	99.61
KOG2192|consensus	390		99.61
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.37
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.37
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.36
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.36
KOG2113|consensus	394		99.29
KOG2190|consensus	485		99.27
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.26
KOG4172|consensus	62		99.2
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.17
smart00322	69	KH K homology RNA-binding domain.	99.07
KOG4265|consensus	349		99.0
PF13014	43	KH_3: KH domain	98.89
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.83
KOG2191|consensus	402		98.81
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	98.78
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.77
KOG0317|consensus	293		98.77
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	98.75
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.7
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.7
PHA02929	238	N1R/p28-like protein; Provisional	98.69
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.66
KOG0823|consensus	230		98.65
KOG0320|consensus	187		98.64
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.63
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.63
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.6
PRK13763	180	putative RNA-processing protein; Provisional	98.56
KOG2279|consensus	608		98.56
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.55
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.53
KOG4275|consensus	350		98.51
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.49
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.47
KOG1571|consensus	355		98.42
KOG2208|consensus	753		98.42
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.42
PF13014	43	KH_3: KH domain	98.41
KOG0287|consensus	442		98.41
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.4
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.4
PHA02926	242	zinc finger-like protein; Provisional	98.39
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.35
PF14634	44	zf-RING_5: zinc-RING finger domain	98.33
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.3
smart00322	69	KH K homology RNA-binding domain.	98.28
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.25
KOG2164|consensus	513		98.16
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.15
KOG2177|consensus	386		98.13
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.12
KOG0119|consensus	554		98.08
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.03
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.02
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.01
KOG0978|consensus	698		97.98
KOG2208|consensus	753		97.97
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.94
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	97.87
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	97.85
KOG1100|consensus	207		97.85
KOG0336|consensus	629		97.76
KOG1588|consensus	259		97.74
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.72
KOG1785|consensus	563		97.7
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	97.66
KOG4628|consensus	348		97.65
KOG0802|consensus	543		97.61
KOG4159|consensus	398		97.5
PRK08406	140	transcription elongation factor NusA-like protein;	97.48
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.4
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	97.39
KOG4692|consensus	489		97.38
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.36
KOG2814|consensus	345		97.36
KOG2279|consensus	608		97.33
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.17
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	97.17
PRK12704	520	phosphodiesterase; Provisional	97.12
PRK00106	535	hypothetical protein; Provisional	97.12
KOG0311|consensus	381		97.09
KOG2879|consensus	298		97.05
COG5152	259	Uncharacterized conserved protein, contains RING a	97.04
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	96.86
COG1094	194	Predicted RNA-binding protein (contains KH domains	96.84
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.83
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.8
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	96.77
KOG1039|consensus	344		96.72
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.72
KOG1067|consensus	760		96.62
KOG0828|consensus	636		96.59
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.42
KOG2660|consensus	331		96.36
KOG1813|consensus	313		96.27
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	96.23
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.22
KOG0297|consensus	391		96.19
PRK12705	508	hypothetical protein; Provisional	96.18
KOG2814|consensus	345		96.08
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.0
KOG1002|consensus	791		95.97
KOG0804|consensus	493		95.93
PRK00468	75	hypothetical protein; Provisional	95.78
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	95.77
KOG0336|consensus	629		95.67
PRK02821	77	hypothetical protein; Provisional	95.66
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.48
KOG0825|consensus	1134		95.42
KOG1734|consensus	328		95.38
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.37
KOG0119|consensus	554		95.26
KOG0826|consensus	357		95.26
TIGR01953	341	NusA transcription termination factor NusA. This m	95.24
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.04
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	94.77
PRK01064	78	hypothetical protein; Provisional	94.67
KOG1001|consensus	674		94.53
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.52
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.49
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	94.32
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.13
KOG3273|consensus	252		94.1
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	94.08
KOG3002|consensus	299		94.07
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	94.0
KOG0824|consensus	324		93.85
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	93.63
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	93.61
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	93.59
PRK12704	520	phosphodiesterase; Provisional	93.55
KOG3039|consensus	303		93.52
PRK00106	535	hypothetical protein; Provisional	93.47
COG5175	480	MOT2 Transcriptional repressor [Transcription]	93.4
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	93.28
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.19
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	93.09
COG5219	1525	Uncharacterized conserved protein, contains RING Z	93.0
KOG4369|consensus	2131		92.96
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	92.7
KOG2874|consensus	356		92.63
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	92.59
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	92.53
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	92.14
KOG1814|consensus	445		92.01
KOG1588|consensus	259		92.0
PRK08406	140	transcription elongation factor NusA-like protein;	91.98
KOG1493|consensus	84		91.98
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	91.97
COG1855	604	ATPase (PilT family) [General function prediction	91.95
KOG2932|consensus	389		91.57
PF04641	260	Rtf2: Rtf2 RING-finger	91.24
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	90.37
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	90.35
PHA02825	162	LAP/PHD finger-like protein; Provisional	90.13
COG5166	657	Uncharacterized conserved protein [Function unknow	90.09
COG1782	637	Predicted metal-dependent RNase, consists of a met	89.51
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	89.45
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	89.39
KOG2874|consensus	356		89.25
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	89.13
PRK13764	602	ATPase; Provisional	89.06
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	88.71
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	88.7
KOG3273|consensus	252		87.67
KOG1941|consensus	518		87.59
KOG4362|consensus	684		87.39
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	87.3
KOG1428|consensus	3738		86.47
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	86.16
TIGR03802	562	Asp_Ala_antiprt aspartate-alanine antiporter. All	86.16
PRK12705	508	hypothetical protein; Provisional	85.99
COG5176	269	MSL5 Splicing factor (branch point binding protein	85.73
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	85.4
PHA02862	156	5L protein; Provisional	85.03
KOG2930|consensus	114		84.68
PRK00468	75	hypothetical protein; Provisional	84.21
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	84.14
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	84.08
PF04710	416	Pellino: Pellino; InterPro: IPR006800 Pellino is i	83.91
KOG3579|consensus	352		83.83
KOG3842|consensus	429		83.56
PRK02821	77	hypothetical protein; Provisional	83.5
KOG4445|consensus	368		83.31
COG1837	76	Predicted RNA-binding protein (contains KH domain)	83.13
PHA03096	284	p28-like protein; Provisional	82.76
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	82.44
KOG0827|consensus	465		82.18
PRK03818	552	putative transporter; Validated	81.67
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	80.83
KOG0825|consensus	1134		80.24

>KOG2113|consensus

Probab=99.96  E-value=6.7e-30  Score=236.98  Aligned_cols=317  Identities=35%  Similarity=0.404  Sum_probs=232.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcce
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHV   81 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~   81 (353)
                      -|+|++|++||.|+.||+++|+.|.++++++|.++|.+++|++|+++|....+|+..+++.+.+....+.   ...+++.
T Consensus        39 ~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~s~Sgg~~~---~s~s~qt  115 (394)
T KOG2113|consen   39 EIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASRSFSGGTNG---ASASGQT  115 (394)
T ss_pred             eecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCccccceeeeeeecccccCCCcc---ccccCCC
Confidence            3789999999999999999999999999999999999999999999999999999887777765433222   1245678


Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHH-HHHHH-HHHHHHHHhhhCCCCc-cCcc
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDS-VEIAR-QEIESHIIRRTGSCVT-PAEA  158 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~-V~~A~-~~I~~~i~~r~g~~~~-~~d~  158 (353)
                      +.++.+|.+++|.|+|.+|++|++||+.++.+|..+.+..++++.++|.+++ +++|. .+|++.+..|.+...+ .+||
T Consensus       116 ~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta~~ra~~i~d~dndf  195 (394)
T KOG2113|consen  116 TSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTAVTRAGQIHDTDNDF  195 (394)
T ss_pred             ceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhhhhhhhccccCCccc
Confidence            9999999999999999999999999999999999999999999999999998 88898 8999999999999888 4799


Q ss_pred             ccCCCCccchHHHhhhhCCCCCccccccccCCCCCCCCCCCCCCCCCcccCCCCCccccCccccc--CCCCCCCCCCCCC
Q psy4141         159 VLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFS--GSSGCSSASSSSS  236 (353)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~  236 (353)
                      +.+..+++.+++.+.-..      ..++...+    .+..|.                   .+|.  ....|+.++|+++
T Consensus       196 ~~~la~v~l~v~~~~~a~------~~~~~~~~----~s~f~~-------------------~~~~n~~~~~~~~~sss~~  246 (394)
T KOG2113|consen  196 AGQLAGVSLMVQKQQQAQ------QQMQEAQQ----QSMFYR-------------------RAFGNSNPFNQKEMSSSPF  246 (394)
T ss_pred             cccccccchhhhhHHHHH------HHHhhcCc----cchHHH-------------------hcccCCCccchhhccCCCc
Confidence            999999988765421000      00111111    122221                   1222  1123455555555


Q ss_pred             CCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCCCCCC------CCCCCCCC----------------------
Q psy4141         237 SSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPS------SIWSYPPV----------------------  288 (353)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~------~~~~~p~~----------------------  288 (353)
                      +..+.....+.......|...+..+.+++.|.+++....+...-      --|+..+.                      
T Consensus       247 ~~~s~~~~~~~~~~~~~~~ss~t~~~~~g~g~s~~~~~~~~~~~~~~~~~~~~~~~~s~~~i~~~e~~s~~~~~~~a~~~  326 (394)
T KOG2113|consen  247 GMESSLGLDALLRSFPSMRSSLTPESLSGTGLSRPSLGGGQSAKQDLPTYDYWGTNNSLNDIMENEILSRKYDALSAWSS  326 (394)
T ss_pred             ccccccccccchhhhhhhhccCCcccccccCCCccccCCccccccCCCcCCccccCcchhhhhhhhhhhhhcchhhcccc
Confidence            44443333344555667776555556677777766555433211      11111100                      


Q ss_pred             -----CCCCCCCCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         289 -----SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       289 -----~~~~~~~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                           --.++...+...++|.+|-+.....++.+|+|++||++|+..  .-...||+|......+++|.
T Consensus       327 ~~l~~~~~~~~~~~~s~~~~~~~~~~~~st~~~~~~~n~~~~~~a~~--s~~~~~~~c~~~~~~~~~i~  393 (394)
T KOG2113|consen  327 MGLEKREESPTNGLMSSLKGTSAGFGLLSTIWSGGNMNLSPGSLASA--SASPTSSTCDHNDHTLVPIN  393 (394)
T ss_pred             ccchhccccccccchhhcccccccCceeeeEeecCCcccChhhhhhc--ccCCccccccccceeeeecC
Confidence                 011233344557999999999999999999999999999983  23789999999888888774

>KOG2191|consensus

Probab=99.83  E-value=7.8e-20  Score=171.41  Aligned_cols=148  Identities=26%  Similarity=0.316  Sum_probs=119.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPT   75 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~   75 (353)
                      +||||+|++|.+|+++||++|++....      .|||+.|+|+.+++......|++.+++..+....    +.....+. 
T Consensus        52 sIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~k----~v~~~~pq-  126 (402)
T KOG2191|consen   52 SIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVAK----PVDILQPQ-  126 (402)
T ss_pred             ceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcC----CccccCCC-
Confidence            599999999999999999999998664      3799999999999999999999999987653222    11111111 


Q ss_pred             CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcC-CCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          76 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP-SRD-----KEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        76 ~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip-~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      .......+++.||+...|.||||+|++||.|++++|+.|++. ...     ++|+|++.|++|+..+|..+|+++|.+..
T Consensus       127 t~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDp  206 (402)
T KOG2191|consen  127 TPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDP  206 (402)
T ss_pred             CccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCC
Confidence            011125589999999999999999999999999999999886 432     47899999999999999999999999844


Q ss_pred             CCCCc
Q psy4141         150 GSCVT  154 (353)
Q Consensus       150 g~~~~  154 (353)
                      .....
T Consensus       207 qs~sc  211 (402)
T KOG2191|consen  207 QSGSC  211 (402)
T ss_pred             cccce
Confidence            43333

>KOG1676|consensus

Probab=99.82  E-value=1.2e-19  Score=181.94  Aligned_cols=140  Identities=25%  Similarity=0.356  Sum_probs=114.9

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-----CcCeEEEecCHHHHHHHHHHHHHHHhhhhh-h-hhccCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHFSA-L-RASRKSGALSPLSPP   74 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~-~-~~~~~~g~~~~~~~~   74 (353)
                      -||||+|++||.|++++|+++.+-.++     ..+.+.|+|+++.|+.|+.+|.++|++... . +.....|.       
T Consensus       152 lIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~~~g~-------  224 (600)
T KOG1676|consen  152 LIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGGHAGV-------  224 (600)
T ss_pred             eEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccccccCc-------
Confidence            489999999999999999999976554     246799999999999999999999996322 1 11111110       


Q ss_pred             CCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC----CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          75 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        75 ~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~----~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                       ..-+..+.+|.||...||.||||+|++||+|+-+|||+|+|-.++    .||.+.|.|+++.|+.|.++|.++|+..+
T Consensus       225 -~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~  302 (600)
T KOG1676|consen  225 -RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAE  302 (600)
T ss_pred             -CccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHh
Confidence             112235899999999999999999999999999999999886553    47999999999999999999999999843

>KOG1676|consensus

Probab=99.78  E-value=8.2e-19  Score=175.85  Aligned_cols=136  Identities=25%  Similarity=0.311  Sum_probs=112.4

Q ss_pred             eecCCCchHHHHHHHcCceEEecCC-C---CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCC
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVR-G---EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   78 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~-~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~   78 (353)
                      ||||+|++||+|+.+||++|+|-.. +   .+|.+.|.|+++.|+.|.++|.+|+++....     .+.....+    .|
T Consensus       244 IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~-----~~~~~~~G----~P  314 (600)
T KOG1676|consen  244 IIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG-----AGGGMGGG----AP  314 (600)
T ss_pred             EEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc-----CCCCcCCC----Cc
Confidence            8999999999999999999997533 3   4799999999999999999999999876331     11111111    12


Q ss_pred             c-ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC-----CCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          79 G-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-----DKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        79 ~-~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-----~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      . ...+.|.||.+.+|+||||+|+|||.|.+++|+++.++..     ..+++|+|.|.+.+|+.|+.||.+++..
T Consensus       315 ~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~  389 (600)
T KOG1676|consen  315 GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD  389 (600)
T ss_pred             cceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence            1 1378899999999999999999999999999999976554     2478999999999999999999998875

>KOG2190|consensus

Probab=99.69  E-value=2.4e-16  Score=159.30  Aligned_cols=137  Identities=27%  Similarity=0.426  Sum_probs=112.5

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCC--C-CcCeEEEec---------CHHHHHHHHHHHHHHHhhhhhhhhccCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVR--G-EEPVFVVTG---------RKEDVARAKREILSAADHFSALRASRKSGALS   69 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~--~-e~~vv~I~G---------~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~   69 (353)
                      +||||+|..||+||++|.++|++-..  + .+|+++|+|         ..+++.+|.++|...+++...  +....+   
T Consensus        56 ~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~--~~~d~~---  130 (485)
T KOG2190|consen   56 SIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE--AAEDNG---  130 (485)
T ss_pred             eEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc--ccccCC---
Confidence            69999999999999988888887543  2 579999999         999999999999888663311  111111   


Q ss_pred             CCCCCCCCCc-ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHHHHH
Q psy4141          70 PLSPPTGVPG-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEIESH  144 (353)
Q Consensus        70 ~~~~~~~~~~-~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I~~~  144 (353)
                           ..... .++++|.||..++|.||||+|+.||+|+++|||+|++.++    ..++.|+|.|.+++|.+|...|...
T Consensus       131 -----~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~  205 (485)
T KOG2190|consen  131 -----EDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSR  205 (485)
T ss_pred             -----ccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHH
Confidence                 01111 3899999999999999999999999999999999987665    3578899999999999999999999


Q ss_pred             HHhh
Q psy4141         145 IIRR  148 (353)
Q Consensus       145 i~~r  148 (353)
                      |.+.
T Consensus       206 L~~~  209 (485)
T KOG2190|consen  206 LLEN  209 (485)
T ss_pred             HHhc
Confidence            8884

>KOG2193|consensus

Probab=99.68  E-value=1.3e-16  Score=153.77  Aligned_cols=148  Identities=24%  Similarity=0.317  Sum_probs=117.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCC------CCcCeEEEecCHHHHHHHHHHHHHHHhhh-hh-hhhccCC--------
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVR------GEEPVFVVTGRKEDVARAKREILSAADHF-SA-LRASRKS--------   65 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~------~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~-~~-~~~~~~~--------   65 (353)
                      ++|||.|.+||+|+.+||++|.+...      +.||.+++.|+.|+|.+|..+|++.+++. .+ +.+-...        
T Consensus       293 RLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~  372 (584)
T KOG2193|consen  293 RLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLN  372 (584)
T ss_pred             hhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccC
Confidence            68999999999999999999997643      45899999999999999999999998863 22 3221110        


Q ss_pred             --------------CCCCCCCC------CC---CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---
Q psy4141          66 --------------GALSPLSP------PT---GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---  119 (353)
Q Consensus        66 --------------g~~~~~~~------~~---~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---  119 (353)
                                    .+++++.+      +.   ..+....++|.||...||.|||++|++||.|...+|+.|+|...   
T Consensus       373 ~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~p  452 (584)
T KOG2193|consen  373 LPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIP  452 (584)
T ss_pred             ccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCC
Confidence                          01111100      00   11356778999999999999999999999999999999987554   


Q ss_pred             -CCCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141         120 -DKEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus       120 -~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                       -.+|.|+|+|+|++.-+|+-.|..+|++..
T Consensus       453 dvseRMViItGppeaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  453 DVSERMVIITGPPEAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             CcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence             247899999999999999999999998843

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.67  E-value=6.4e-16  Score=137.16  Aligned_cols=129  Identities=19%  Similarity=0.260  Sum_probs=100.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEE---ecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVV---TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP   78 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I---~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~   78 (353)
                      .|||++|++||.|+++||++|++...  +..+.|   +++++++.+|+..|..+...+.--.|-+..+            
T Consensus        11 ~vIG~gG~~Ik~I~~~tgv~I~Id~~--~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~g------------   76 (172)
T TIGR03665        11 VLIGKGGETKKEIEERTGVKLDIDSE--TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD------------   76 (172)
T ss_pred             hHhCCchhHHHHHHHHhCcEEEEEcC--CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcC------------
Confidence            37999999999999999999999854  244666   8999999999999999877432100000001            


Q ss_pred             cceEE-EEEecC---------CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          79 GHVTI-EVRVPY---------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        79 ~~~t~-~v~VP~---------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ..+.. -+.|+.         +.+|+|||++|++++.||..|||+|.++.    ..|.|.|.+++++.|+++|+++++.+
T Consensus        77 d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665        77 DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence            11122 233433         47999999999999999999999999874    57999999999999999999999654

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.

>KOG2192|consensus

Probab=99.63  E-value=1.1e-15  Score=140.07  Aligned_cols=149  Identities=18%  Similarity=0.255  Sum_probs=120.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcc
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGH   80 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~   80 (353)
                      .||||+|++||+|+.++++.|.+|+.+ .+++++|+.+.+-|-...+.|+-.+++-.                  .++.-
T Consensus        61 avigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f------------------~~~~p  122 (390)
T KOG2192|consen   61 AVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGF------------------QLPSP  122 (390)
T ss_pred             ceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCC------------------CCCCc
Confidence            389999999999999999999999875 78999999999988887777777777531                  12333


Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCCCCccC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPA  156 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~~~~~~  156 (353)
                      ..++|+|+..+.|.|||++|.+||+|+++..++++|-..    ..+|+|.|.|.+.+|-.+.+.|+++|.+.-=+... -
T Consensus       123 ce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa-~  201 (390)
T KOG2192|consen  123 CELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSA-Q  201 (390)
T ss_pred             hhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcC-C
Confidence            788999999999999999999999999999999976543    57889999999999999999999999984322221 1


Q ss_pred             ccccCCCCccchH
Q psy4141         157 EAVLNGDDNSADL  169 (353)
Q Consensus       157 d~~~~~~~~~~~~  169 (353)
                      .+..|++|+.+|+
T Consensus       202 py~p~fyd~t~dy  214 (390)
T KOG2192|consen  202 PYDPNFYDETYDY  214 (390)
T ss_pred             cCCccccCccccc
Confidence            2334556776665

>KOG2193|consensus

Probab=99.61  E-value=8.1e-16  Score=148.44  Aligned_cols=131  Identities=21%  Similarity=0.340  Sum_probs=113.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   77 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~   77 (353)
                      -||||.|.+||.|-+.|.++|++-...    .+++++|-+++|...+|.++|++++.....               ...+
T Consensus       212 aIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~---------------~~k~  276 (584)
T KOG2193|consen  212 AIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAV---------------DDKV  276 (584)
T ss_pred             EEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhh---------------ccch
Confidence            389999999999999999999986432    578999999999999999999999886422               1122


Q ss_pred             CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        78 ~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ...+.+++...+.+||++|||.|.+||+|+++||++|.|.+-      ..||+|+|.|+-|+|.+|..+|..+|++
T Consensus       277 ~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre  352 (584)
T KOG2193|consen  277 AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE  352 (584)
T ss_pred             hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence            345778889999999999999999999999999999977542      4589999999999999999999999987

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.61  E-value=6.7e-15  Score=131.50  Aligned_cols=128  Identities=22%  Similarity=0.300  Sum_probs=97.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEE----ecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVV----TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   77 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I----~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~   77 (353)
                      .|||++|.+||.|+++||++|++...  +..|.|    +++++++.+|+..|..++..+..-.+-+..+           
T Consensus        16 ~iIG~gGk~Ik~I~e~tg~~I~i~~~--~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g-----------   82 (180)
T PRK13763         16 VLIGKKGETKKEIEERTGVKLEIDSE--TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD-----------   82 (180)
T ss_pred             hHhccchhHHHHHHHHHCcEEEEECC--CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC-----------
Confidence            37999999999999999999999854  244555    5899999999999999987432111100011           


Q ss_pred             CcceEEE-EEec---------CCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          78 PGHVTIE-VRVP---------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        78 ~~~~t~~-v~VP---------~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                       ..+..+ +.|.         .+.+|+|||++|++++.||+.|||+|.++.    ..|.|.|.+++++.|++.|+++++.
T Consensus        83 -d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763         83 -DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIGDPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             -CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence             011111 1111         247999999999999999999999999874    3599999999999999999998854

>KOG2192|consensus

Probab=99.61  E-value=7.9e-15  Score=134.54  Aligned_cols=145  Identities=22%  Similarity=0.372  Sum_probs=112.1

Q ss_pred             eecCCCchHHHHHHHcCceEEecC----CCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccC--------------
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPV----RGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK--------------   64 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~----~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~--------------   64 (353)
                      ||||+|++||+||++..+++++-.    ...+||+++.|.+.+|....+.|++++.+..--.....              
T Consensus       137 iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dygg  216 (390)
T KOG2192|consen  137 IIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGG  216 (390)
T ss_pred             eecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCC
Confidence            899999999999999999999632    12479999999999999999999999887542100000              


Q ss_pred             -----------CCC------CCCC--------------------------------------------------------
Q psy4141          65 -----------SGA------LSPL--------------------------------------------------------   71 (353)
Q Consensus        65 -----------~g~------~~~~--------------------------------------------------------   71 (353)
                                 .++      ..|+                                                        
T Consensus       217 f~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~y  296 (390)
T KOG2192|consen  217 FTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGY  296 (390)
T ss_pred             ceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCC
Confidence                       000      0000                                                        


Q ss_pred             --------CCCCCC-CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHH
Q psy4141          72 --------SPPTGV-PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQ  139 (353)
Q Consensus        72 --------~~~~~~-~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~  139 (353)
                              +.+..+ -...+.+|.||.++-|.||||+|+.|++|++++|+.|.+...   ..++.++|+|+.++++.|+.
T Consensus       297 dysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQY  376 (390)
T KOG2192|consen  297 DYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQY  376 (390)
T ss_pred             CccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHH
Confidence                    000000 025778999999999999999999999999999999988653   35789999999999999999


Q ss_pred             HHHHHHHh
Q psy4141         140 EIESHIIR  147 (353)
Q Consensus       140 ~I~~~i~~  147 (353)
                      ++++.|+.
T Consensus       377 LlQn~Vkq  384 (390)
T KOG2192|consen  377 LLQNSVKQ  384 (390)
T ss_pred             HHHHHHHh
Confidence            99998885

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.37  E-value=1.3e-12  Score=97.53  Aligned_cols=60  Identities=32%  Similarity=0.486  Sum_probs=55.0

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHH
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEI  141 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I  141 (353)
                      +++|.||...+|.|||++|++|++|+++|||+|.+.+.    +.++.|+|+|++++|++|+.||
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            36899999999999999999999999999999988764    3468999999999999999998

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=99.37  E-value=9.2e-13  Score=97.12  Aligned_cols=60  Identities=33%  Similarity=0.550  Sum_probs=55.3

Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHH
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIE  142 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~  142 (353)
                      .+|.||.+++|+|||++|++|++|+++|||+|.+|..+ .++.|+|+|++++|..|+++|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999763 4679999999999999999873

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=99.36  E-value=5.2e-13  Score=97.81  Aligned_cols=60  Identities=35%  Similarity=0.650  Sum_probs=55.0

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHH
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI  141 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I  141 (353)
                      |.+|.||.+++|+|||++|.+|++|+++|||+|.++.++.+..|+|+|++++|++|+++|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence            678999999999999999999999999999999998765234899999999999999987

; 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 ....

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

Probab=99.36  E-value=2.3e-12  Score=95.08  Aligned_cols=59  Identities=25%  Similarity=0.385  Sum_probs=54.4

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIE  142 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~  142 (353)
                      ....+.||.+++|+|||++|++||+|+++|||+|.++.   ++.|.|+|+ +++|++|+++|+
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHhC
Confidence            56789999999999999999999999999999999886   468999998 999999999884

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.

>KOG2113|consensus

Probab=99.29  E-value=1.6e-12  Score=121.79  Aligned_cols=67  Identities=46%  Similarity=0.692  Sum_probs=63.6

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHH
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIES  143 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~  143 (353)
                      .++++++.+.||+++|+.|+|++|.+||.|+.+|.+||+.|.++++++|.++|.+++|++|++.|..
T Consensus        22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCcc
Confidence            4567999999999999999999999999999999999999999999999999999999999999864

>KOG2190|consensus

Probab=99.27  E-value=2.8e-11  Score=122.78  Aligned_cols=144  Identities=24%  Similarity=0.340  Sum_probs=108.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhh---h--------hh--ccC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSA---L--------RA--SRK   64 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~---~--------~~--~~~   64 (353)
                      .||||+|++||+|+++|||+|++....    .++.|+|.|.+++|.+|...|...|.+...   .        +.  .+.
T Consensus       151 slIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~  230 (485)
T KOG2190|consen  151 SLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQG  230 (485)
T ss_pred             eeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCccccc
Confidence            589999999999999999999976442    467899999999999999999999887421   1        00  000


Q ss_pred             C------CCCC---------------------C-------------------------------C-C-----CCCCC---
Q psy4141          65 S------GALS---------------------P-------------------------------L-S-----PPTGV---   77 (353)
Q Consensus        65 ~------g~~~---------------------~-------------------------------~-~-----~~~~~---   77 (353)
                      .      +...                     +                               . .     .....   
T Consensus       231 ~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~  310 (485)
T KOG2190|consen  231 GPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISARENPED  310 (485)
T ss_pred             CccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeeccccCccc
Confidence            0      0000                     0                               0 0     00000   


Q ss_pred             ------------------------CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEE
Q psy4141          78 ------------------------PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVT  128 (353)
Q Consensus        78 ------------------------~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~  128 (353)
                                              ...++.++.||.+++|.||||+|++|.+|++.||+.|.+...+     .++.++|+
T Consensus       311 ~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~  390 (485)
T KOG2190|consen  311 RYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQIT  390 (485)
T ss_pred             ccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEec
Confidence                                    1126788999999999999999999999999999999886654     36799999


Q ss_pred             cCHHHHHHHHHHHHHHH
Q psy4141         129 GAPDSVEIARQEIESHI  145 (353)
Q Consensus       129 G~~e~V~~A~~~I~~~i  145 (353)
                      |...+...|+.+|...+
T Consensus       391 ~~~~~~~~~~~~~~~~~  407 (485)
T KOG2190|consen  391 GMLREDLLAQYLIRARL  407 (485)
T ss_pred             chhHHHHhhhhhccccc
Confidence            99999999998885433

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

Probab=99.26  E-value=1.4e-11  Score=90.78  Aligned_cols=60  Identities=37%  Similarity=0.595  Sum_probs=54.9

Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHHHHH
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQEIE  142 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~~I~  142 (353)
                      .+|.||.+++|+|||++|++|++|+++|||+|.++..   ..++.|.|.|+.++|+.|+.+|+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence            5799999999999999999999999999999999875   34679999999999999999873

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.

>KOG4172|consensus

Probab=99.20  E-value=1.6e-12  Score=91.28  Aligned_cols=53  Identities=28%  Similarity=0.797  Sum_probs=49.8

Q ss_pred             cccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCcccccccceeccC
Q psy4141         301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRIIS  353 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~~~ri~~  353 (353)
                      .+|.||++..++.++.-|||.|+|.+|..++|.. ...||+||+++..+||.|.
T Consensus         8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~   61 (62)
T KOG4172|consen    8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYR   61 (62)
T ss_pred             cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhc
Confidence            7899999999999999999999999999999986 8899999999999998773

>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=99.17  E-value=1.2e-11  Score=87.40  Aligned_cols=50  Identities=38%  Similarity=0.967  Sum_probs=43.9

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      ++..|.||++...+++++||||.+||..|+.+++.....||+||+++.++
T Consensus         1 ~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~V   50 (50)
T PF13920_consen    1 EDEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIESV   50 (50)
T ss_dssp             -HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SEE
T ss_pred             CcCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcCC
Confidence            35789999999999999999999999999999999899999999998753

...

>smart00322 KH K homology RNA-binding domain

Probab=99.07  E-value=9e-10  Score=80.97  Aligned_cols=65  Identities=43%  Similarity=0.648  Sum_probs=59.3

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHI  145 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i  145 (353)
                      .+.+|.||.+.+|++||++|++|++|++.||++|.++... ....++|.|.+++++.|+.+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            6789999999999999999999999999999999887653 4568999999999999999998876

>KOG4265|consensus

Probab=99.00  E-value=2e-10  Score=110.20  Aligned_cols=55  Identities=27%  Similarity=0.773  Sum_probs=51.1

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      +...+|+||+...++.+++||+|.|+|..|++.+.-+...||+||+++.+.+.|+
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~  342 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIY  342 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhhheec
Confidence            4458999999999999999999999999999999877899999999999998875

>PF13014 KH_3: KH domain

Probab=98.89  E-value=2.5e-09  Score=73.08  Aligned_cols=39  Identities=38%  Similarity=0.647  Sum_probs=35.0

Q ss_pred             CccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEc
Q psy4141          91 VVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTG  129 (353)
Q Consensus        91 ~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G  129 (353)
                      +||+|||++|++|++|+++|||+|.|+++    +.++.|+|+|
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            58999999999999999999999999982    3567999987

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

Probab=98.83  E-value=2e-09  Score=73.32  Aligned_cols=38  Identities=39%  Similarity=0.944  Sum_probs=31.1

Q ss_pred             cccccccccccEEeCCCCHhhhHHhHHHHhcc-C---CCCCCc
Q psy4141         303 CYLCNDREVTHALIPCGHNFFCSECAERTCDF-D---RTCPMC  341 (353)
Q Consensus       303 C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~---~~CP~C  341 (353)
                      |+||++.+.+++.++|||+ ||..|+.++|.. .   ..||.|
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 999999999998 2   469987

>KOG2191|consensus

Probab=98.81  E-value=1.8e-08  Score=95.49  Aligned_cols=70  Identities=23%  Similarity=0.386  Sum_probs=64.5

Q ss_pred             cceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      +...++|+||...+|.||||||++|.++|++|||+|+..+.      ..||++.|+|+-+++-...+.|.++|++.
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~  112 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREK  112 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHh
Confidence            34889999999999999999999999999999999987654      46899999999999999999999999993

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=98.78  E-value=1.1e-08  Score=75.15  Aligned_cols=49  Identities=35%  Similarity=0.540  Sum_probs=44.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREIL   50 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~   50 (353)
                      .|||++|++|++|+++|||+|.+|..+ .++.|+|+|++++|..|+.+|+
T Consensus        13 ~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394          13 FIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             hccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHhC
Confidence            589999999999999999999999754 4588999999999999999874

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.

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.77  E-value=6.2e-09  Score=92.96  Aligned_cols=54  Identities=28%  Similarity=0.666  Sum_probs=45.2

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc----------------CCCCCCccccccc--ceecc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF----------------DRTCPMCRVPVNQ--AMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~----------------~~~CP~Cr~~i~~--~~ri~  352 (353)
                      .++.+|.||++...++++++|||. ||..|+.+|+..                ...||+||.++..  ++.+|
T Consensus        16 ~~~~~CpICld~~~dPVvT~CGH~-FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy   87 (193)
T PLN03208         16 GGDFDCNICLDQVRDPVVTLCGHL-FCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIY   87 (193)
T ss_pred             CCccCCccCCCcCCCcEEcCCCch-hHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEee
Confidence            456899999999999999999999 999999998642                3589999999965  44444

>KOG0317|consensus

Probab=98.77  E-value=4.3e-09  Score=98.34  Aligned_cols=48  Identities=33%  Similarity=0.865  Sum_probs=44.5

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ....|.+|++...++...||||. ||..|+..|+.....||+||..+..
T Consensus       238 a~~kC~LCLe~~~~pSaTpCGHi-FCWsCI~~w~~ek~eCPlCR~~~~p  285 (293)
T KOG0317|consen  238 ATRKCSLCLENRSNPSATPCGHI-FCWSCILEWCSEKAECPLCREKFQP  285 (293)
T ss_pred             CCCceEEEecCCCCCCcCcCcch-HHHHHHHHHHccccCCCcccccCCC
Confidence            35789999999999999999999 9999999999999999999998853

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=98.75  E-value=2.1e-08  Score=74.67  Aligned_cols=48  Identities=27%  Similarity=0.390  Sum_probs=43.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREI   49 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I   49 (353)
                      +||||+|.+|++|+++|||+|+++...    .+++++|.|+++++.+|+.+|
T Consensus        13 ~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396          13 SIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             eeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            589999999999999999999998653    458999999999999999987

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=98.70  E-value=1e-08  Score=74.86  Aligned_cols=48  Identities=29%  Similarity=0.521  Sum_probs=43.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI   49 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I   49 (353)
                      .|||++|.+|++|+++|||.|+++..+++..+.|.|++++|++|+++|
T Consensus        13 ~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen   13 RIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             HHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred             EEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence            479999999999999999999999765335899999999999999986

; 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 ....

>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=98.70  E-value=7.8e-09  Score=69.15  Aligned_cols=38  Identities=39%  Similarity=1.065  Sum_probs=33.8

Q ss_pred             ccccccccccc-EEeCCCCHhhhHHhHHHHhccCCCCCCc
Q psy4141         303 CYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMC  341 (353)
Q Consensus       303 C~IC~~~~~~~-~llpCgH~~fC~~C~~~~~~~~~~CP~C  341 (353)
                      |.||++...++ ++++|||. ||.+|+.++.+....||+|
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 68999999 9999999999988899998

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.69  E-value=1.2e-08  Score=94.67  Aligned_cols=51  Identities=29%  Similarity=0.749  Sum_probs=43.2

Q ss_pred             CCcccccccccccc--------cEEeCCCCHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141         299 GSRQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR  350 (353)
Q Consensus       299 ~~~~C~IC~~~~~~--------~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r  350 (353)
                      .+.+|.||++....        +++.+|+|. ||..|+.+|......||+||.++..+++
T Consensus       173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~-FC~~CI~~Wl~~~~tCPlCR~~~~~v~~  231 (238)
T PHA02929        173 KDKECAICMEKVYDKEIKNMYFGILSNCNHV-FCIECIDIWKKEKNTCPVCRTPFISVIK  231 (238)
T ss_pred             CCCCCccCCcccccCccccccceecCCCCCc-ccHHHHHHHHhcCCCCCCCCCEeeEEee
Confidence            35789999997543        356789999 9999999998888999999999987754

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

Probab=98.66  E-value=5.4e-08  Score=71.70  Aligned_cols=45  Identities=24%  Similarity=0.298  Sum_probs=41.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecC-HHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREI   49 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~-~e~v~~Ak~~I   49 (353)
                      +||||+|++||+|+++|||+|+++.   +..|.|.|. ++++++|+.+|
T Consensus        15 ~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393          15 DVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHh
Confidence            5899999999999999999999996   467999998 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.

>KOG0823|consensus

Probab=98.65  E-value=1.1e-08  Score=93.08  Aligned_cols=54  Identities=26%  Similarity=0.639  Sum_probs=46.5

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCccccccc--ceecc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVNQ--AMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~~--~~ri~  352 (353)
                      ....+|.||+|...++++..|||. ||..|+-+|+..   ...||+|+..++.  ++-||
T Consensus        45 ~~~FdCNICLd~akdPVvTlCGHL-FCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlY  103 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDPVVTLCGHL-FCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLY  103 (230)
T ss_pred             CCceeeeeeccccCCCEEeecccc-eehHHHHHHHhhcCCCeeCCccccccccceEEeee
Confidence            346899999999999999999999 999999999987   5679999998863  44444

>KOG0320|consensus

Probab=98.64  E-value=1.4e-08  Score=88.81  Aligned_cols=53  Identities=34%  Similarity=0.769  Sum_probs=45.4

Q ss_pred             CCcccccccccccccE--EeCCCCHhhhHHhHHHHhccCCCCCCcccccc--cceecc
Q psy4141         299 GSRQCYLCNDREVTHA--LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN--QAMRII  352 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~--llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~--~~~ri~  352 (353)
                      ....|+|||+.+...+  ...|||. ||..|++........||+||..|+  ++++||
T Consensus       130 ~~~~CPiCl~~~sek~~vsTkCGHv-FC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~  186 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKVPVSTKCGHV-FCSQCIKDALKNTNKCPTCRKKITHKQFHRIY  186 (187)
T ss_pred             cccCCCceecchhhccccccccchh-HHHHHHHHHHHhCCCCCCcccccchhhheecc
Confidence            3478999999876554  4799999 999999999988999999998775  678887

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

Probab=98.63  E-value=8.1e-08  Score=80.29  Aligned_cols=58  Identities=26%  Similarity=0.491  Sum_probs=50.3

Q ss_pred             CCCccceeccCChHHHHHHHHhCceEEcCCCC--------------------CCCeEEEEcC---HHHHHHHHHHHHHHH
Q psy4141          89 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--------------------KEPVFEVTGA---PDSVEIARQEIESHI  145 (353)
Q Consensus        89 ~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~--------------------~e~~v~I~G~---~e~V~~A~~~I~~~i  145 (353)
                      .+++|.|||++|.|||+|+++|||+|.|-.+.                    +.-.|.|++.   .+++++|+++|+.++
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            48899999999999999999999999887651                    1247999995   489999999999988


Q ss_pred             H
Q psy4141         146 I  146 (353)
Q Consensus       146 ~  146 (353)
                      .
T Consensus        94 ~   94 (120)
T cd02395          94 K   94 (120)
T ss_pred             c
Confidence            8

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.

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

Probab=98.63  E-value=5.4e-07  Score=80.41  Aligned_cols=127  Identities=20%  Similarity=0.285  Sum_probs=94.0

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEe-----cCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVT-----GRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   77 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~-----G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~   77 (353)
                      +||+.|+..+.|++.++++|.+...  +..|.|.     .++-.+.+|+..|..+-.-|+--.|-+-..           
T Consensus        22 lig~~g~v~k~ie~~~~~~~~iD~~--~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~-----------   88 (194)
T COG1094          22 LIGKWGEVKKAIEEKTGVKLRIDSK--TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLE-----------   88 (194)
T ss_pred             eecccccchHHHHhhcCeEEEEECC--CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhc-----------
Confidence            7999999999999999999998854  3444443     268889999999988855443211111100           


Q ss_pred             CcceEEE-EEe----------cCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHH
Q psy4141          78 PGHVTIE-VRV----------PYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHII  146 (353)
Q Consensus        78 ~~~~t~~-v~V----------P~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~  146 (353)
                       ....+. +.+          -.+..|+|||++|.|.+.|++.|||+|.+.    ...|.|.|.+++|+.|++.|++++.
T Consensus        89 -d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~----g~tVaiiG~~~~v~iAr~AVemli~  163 (194)
T COG1094          89 -DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY----GKTVAIIGGFEQVEIAREAVEMLIN  163 (194)
T ss_pred             -CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe----CcEEEEecChhhhHHHHHHHHHHHc
Confidence             001111 111          135679999999999999999999999866    3479999999999999999999987


Q ss_pred             h
Q psy4141         147 R  147 (353)
Q Consensus       147 ~  147 (353)
                      .
T Consensus       164 G  164 (194)
T COG1094         164 G  164 (194)
T ss_pred             C
Confidence            5

>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=1.5e-08  Score=69.48  Aligned_cols=40  Identities=30%  Similarity=0.819  Sum_probs=35.1

Q ss_pred             ccccccccc---cccEEeCCCCHhhhHHhHHHHhccCCCCCCcc
Q psy4141         302 QCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDRTCPMCR  342 (353)
Q Consensus       302 ~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr  342 (353)
                      .|.||++.+   ...+.++|+|. ||..|+..|......||+||
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            699999987   35667899999 99999999999889999997

...

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.56  E-value=1.2e-07  Score=84.82  Aligned_cols=64  Identities=23%  Similarity=0.294  Sum_probs=57.6

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEE----cCHHHHHHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT----GAPDSVEIARQEIESHII  146 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~----G~~e~V~~A~~~I~~~i~  146 (353)
                      ....+.||.+.+|.|||++|++||.|+++||++|.+..+  +..|.|.    ++++++++|+++|.+++.
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--~g~V~I~~~~~~d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--TGEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            567899999999999999999999999999999988753  3578885    789999999999999877

>KOG2279|consensus

Probab=98.56  E-value=2.6e-08  Score=99.97  Aligned_cols=124  Identities=27%  Similarity=0.432  Sum_probs=105.0

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCC--CCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCc
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVR--GEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPG   79 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~--~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~   79 (353)
                      .|+||+|.+||.|+++|+++|.+-..  +++++.++.|-+.++..|+.+++.++.+-                    .+ 
T Consensus        81 li~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~--------------------~p-  139 (608)
T KOG2279|consen   81 LIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTEN--------------------TP-  139 (608)
T ss_pred             eeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhcC--------------------Cc-
Confidence            47999999999999999999998755  36788888889999999999999887643                    12 


Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCC---CCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK---EPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~---e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                       +..++.+|.+.++.|+|++|.+++.|...++++|.+....+   .+...|.|...-++.|+.++.+.+.+
T Consensus       140 -vk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~e  209 (608)
T KOG2279|consen  140 -VSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSE  209 (608)
T ss_pred             -ccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccc
Confidence             67788899999999999999999999999999997665432   45677777788888999999888776

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.55  E-value=7.3e-08  Score=85.64  Aligned_cols=60  Identities=23%  Similarity=0.344  Sum_probs=53.7

Q ss_pred             EEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEE---EcCHHHHHHHHHHHHHHHH
Q psy4141          85 VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEV---TGAPDSVEIARQEIESHII  146 (353)
Q Consensus        85 v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I---~G~~e~V~~A~~~I~~~i~  146 (353)
                      |.||.+.+|.|||+||++||+|+++||++|.+..+  +..|.|   +++++++.+|+++|.++..
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--~g~V~I~~~t~d~~~i~kA~~~I~~i~~   64 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--TGEVKIEEEDEDPLAVMKAREVVKAIGR   64 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--CceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence            67899999999999999999999999999988753  356888   7889999999999998766

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.

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

Probab=98.53  E-value=2.3e-07  Score=68.06  Aligned_cols=48  Identities=40%  Similarity=0.607  Sum_probs=43.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREI   49 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I   49 (353)
                      +|||++|.+|++|+++||+.|.++...   .++.+.|.|+.+++..|+.+|
T Consensus        13 ~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105          13 RIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             eeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence            589999999999999999999999764   368899999999999999887

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.

>KOG4275|consensus

Probab=98.51  E-value=8.4e-09  Score=96.21  Aligned_cols=51  Identities=31%  Similarity=0.825  Sum_probs=48.1

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceeccC
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS  353 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~~  353 (353)
                      ....|.|||+...+.++|+|||.+-|..|-+++    ..||+||+.+..+.|||.
T Consensus       299 ~~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~rvvrif~  349 (350)
T KOG4275|consen  299 TRRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYIVRVVRIFR  349 (350)
T ss_pred             HHHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHHHHHHhhhc
Confidence            378999999999999999999999999999997    699999999999999984

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.49  E-value=7.4e-08  Score=95.44  Aligned_cols=52  Identities=31%  Similarity=0.685  Sum_probs=46.9

Q ss_pred             CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ..++....|.||++.+..+++++|||. ||..|+..++.....||+||..+..
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            456778999999999999999999999 9999999998887789999998753

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

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.47  E-value=7.9e-07  Score=93.81  Aligned_cols=67  Identities=31%  Similarity=0.422  Sum_probs=59.7

Q ss_pred             CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141          76 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus        76 ~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                      ..|  ....+.||.+.+|.|||+||++||+|+++||++|.+..   +..|.|.+. .+.+++|+++|+.++..
T Consensus       575 ~aP--~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       575 YAP--RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CCC--eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            445  77889999999999999999999999999999998763   468999985 88999999999999884

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.

>KOG1571|consensus

Probab=98.42  E-value=6.7e-08  Score=93.02  Aligned_cols=54  Identities=24%  Similarity=0.709  Sum_probs=47.9

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceeccC
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS  353 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~~  353 (353)
                      .+.....|.||.+.+.+.+++||||.|.|-.|.+.+    ..||+||..|...+++|.
T Consensus       301 ~~~~p~lcVVcl~e~~~~~fvpcGh~ccct~cs~~l----~~CPvCR~rI~~~~k~y~  354 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKSAVFVPCGHVCCCTLCSKHL----PQCPVCRQRIRLVRKRYR  354 (355)
T ss_pred             ccCCCCceEEecCCccceeeecCCcEEEchHHHhhC----CCCchhHHHHHHHHHHhc
Confidence            344567899999999999999999999999999886    779999999999998873

>KOG2208|consensus

Probab=98.42  E-value=6.6e-07  Score=95.83  Aligned_cols=125  Identities=21%  Similarity=0.317  Sum_probs=105.6

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcce
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHV   81 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~   81 (353)
                      |+||+|.+|.+|++++++.|.++..+ ++..++++|...++.+|+..|..+..++.+                 .   ..
T Consensus       361 v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-----------------~---~~  420 (753)
T KOG2208|consen  361 VIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIAEILN-----------------S---IV  420 (753)
T ss_pred             hcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHHhhhc-----------------c---cc
Confidence            79999999999999999999999865 457899999999999999999999988743                 0   25


Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhC-ceEEcCCCCC-CCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTN-TYIVTPSRDK-EPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg-a~I~ip~~~~-e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ...+.||...+.+|||.+|..|..|..+++ ++|.++.... ...+++.|.-..|.+++.++..+...
T Consensus       421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~  488 (753)
T KOG2208|consen  421 KEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALKAD  488 (753)
T ss_pred             cceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccceEeccccccchhHHHHHhhhhh
Confidence            677999999999999999999999999999 8888887643 34688888877777776666655554

>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=98.42  E-value=1.3e-07  Score=63.60  Aligned_cols=38  Identities=34%  Similarity=1.009  Sum_probs=35.2

Q ss_pred             cccccccccccE-EeCCCCHhhhHHhHHHHhcc--CCCCCCc
Q psy4141         303 CYLCNDREVTHA-LIPCGHNFFCSECAERTCDF--DRTCPMC  341 (353)
Q Consensus       303 C~IC~~~~~~~~-llpCgH~~fC~~C~~~~~~~--~~~CP~C  341 (353)
                      |.||++....+. +++|||. ||..|+.+++..  ...||+|
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            889999999999 8999999 999999999993  7789988

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 ....

>PF13014 KH_3: KH domain

Probab=98.41  E-value=4e-07  Score=62.13  Aligned_cols=36  Identities=36%  Similarity=0.629  Sum_probs=31.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecC---CC-CcCeEEEec
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPV---RG-EEPVFVVTG   37 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~---~~-e~~vv~I~G   37 (353)
                      .||||+|++|++|+++|+|+|++|.   .+ .+++|+|+|
T Consensus         4 ~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    4 RIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             eEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999998   22 468899887

>KOG0287|consensus

Probab=98.41  E-value=9.4e-08  Score=90.92  Aligned_cols=51  Identities=27%  Similarity=0.729  Sum_probs=46.6

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      .+..-+.|.||++.+..+++.||+|+ ||..|+..++...+.||.|+.+++.
T Consensus        19 ~lD~lLRC~IC~eyf~ip~itpCsHt-fCSlCIR~~L~~~p~CP~C~~~~~E   69 (442)
T KOG0287|consen   19 TLDDLLRCGICFEYFNIPMITPCSHT-FCSLCIRKFLSYKPQCPTCCVTVTE   69 (442)
T ss_pred             hhHHHHHHhHHHHHhcCceeccccch-HHHHHHHHHhccCCCCCceecccch
Confidence            34556899999999999999999999 9999999999999999999998864

>smart00504 Ubox Modified RING finger domain

Probab=98.40  E-value=2.1e-07  Score=68.34  Aligned_cols=45  Identities=16%  Similarity=0.242  Sum_probs=42.1

Q ss_pred             cccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      ..|+||.+...+++.++|||. ||..|+.+|+.....||+|+.+++
T Consensus         2 ~~Cpi~~~~~~~Pv~~~~G~v-~~~~~i~~~~~~~~~cP~~~~~~~   46 (63)
T smart00504        2 FLCPISLEVMKDPVILPSGQT-YERRAIEKWLLSHGTDPVTGQPLT   46 (63)
T ss_pred             cCCcCCCCcCCCCEECCCCCE-EeHHHHHHHHHHCCCCCCCcCCCC
Confidence            579999999999999999999 999999999988889999999874

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

>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=98.40  E-value=2.5e-07  Score=62.34  Aligned_cols=43  Identities=35%  Similarity=1.015  Sum_probs=36.3

Q ss_pred             ccccccccccccEEe-CCCCHhhhHHhHHHHhcc-CCCCCCccccc
Q psy4141         302 QCYLCNDREVTHALI-PCGHNFFCSECAERTCDF-DRTCPMCRVPV  345 (353)
Q Consensus       302 ~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i  345 (353)
                      .|.||++.....+.+ +|+|. ||..|+..|... ...||+||..+
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            489999998655555 49999 999999999887 77899998753

>PHA02926 zinc finger-like protein; Provisional

Probab=98.39  E-value=1.8e-07  Score=84.75  Aligned_cols=49  Identities=24%  Similarity=0.605  Sum_probs=39.6

Q ss_pred             CCccccccccccc---------ccEEeCCCCHhhhHHhHHHHhcc------CCCCCCcccccccc
Q psy4141         299 GSRQCYLCNDREV---------THALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQA  348 (353)
Q Consensus       299 ~~~~C~IC~~~~~---------~~~llpCgH~~fC~~C~~~~~~~------~~~CP~Cr~~i~~~  348 (353)
                      ++.+|.||++...         -.++.+|+|. ||..|+..|...      ...||+||..+..+
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHs-FCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I  232 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHI-FCITCINIWHRTRRETGASDNCPICRTRFRNI  232 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCch-HHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence            4589999999742         2467799999 999999999874      24599999988754

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

Probab=98.35  E-value=1.9e-07  Score=87.21  Aligned_cols=48  Identities=31%  Similarity=0.703  Sum_probs=44.3

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      ..-..|.||.+++..+++.+|||. ||..|+.+++...+.||+||.+..
T Consensus        23 Ds~lrC~IC~~~i~ip~~TtCgHt-FCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          23 DSMLRCRICDCRISIPCETTCGHT-FCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             hhHHHhhhhhheeecceecccccc-hhHHHHHHHhcCCCCCccccccHH
Confidence            345899999999999999999999 999999999999999999999864

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.33  E-value=5e-07  Score=62.04  Aligned_cols=41  Identities=32%  Similarity=0.877  Sum_probs=35.1

Q ss_pred             ccccccccc---cccEEeCCCCHhhhHHhHHHHhccCCCCCCccc
Q psy4141         302 QCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDRTCPMCRV  343 (353)
Q Consensus       302 ~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~  343 (353)
                      .|.+|++.+   ..+.+++|||. ||..|+..+......||+||+
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            488999988   45778999999 999999999744789999984

>smart00184 RING Ring finger

Probab=98.30  E-value=7.2e-07  Score=57.94  Aligned_cols=38  Identities=34%  Similarity=1.027  Sum_probs=34.5

Q ss_pred             cccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCc
Q psy4141         303 CYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMC  341 (353)
Q Consensus       303 C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~C  341 (353)
                      |.||++....+++++|+|. ||..|+..|... ...||+|
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            7899999999999999999 999999999874 6779987

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)

>smart00322 KH K homology RNA-binding domain

Probab=98.28  E-value=3.1e-06  Score=61.85  Aligned_cols=52  Identities=35%  Similarity=0.477  Sum_probs=46.6

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAA   53 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~   53 (353)
                      .+||++|.+|++|++++|++|.++... ...++.|.|..+++..|+..|.+.+
T Consensus        16 ~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322       16 LIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            589999999999999999999998654 3578999999999999999998875

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.25  E-value=3.7e-06  Score=89.56  Aligned_cols=96  Identities=18%  Similarity=0.265  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHHHHhhhhh-hhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          40 EDVARAKREILSAADHFSA-LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        40 e~v~~Ak~~I~~i~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      +.++.|+.....+++.+.. +...+..       .....|  ...++.||.+.+|.|||+||++||+|+++|||+|.+..
T Consensus       518 ~al~~a~~~~~~I~~~m~~~l~~~~~~-------~~~~~p--~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d  588 (684)
T TIGR03591       518 QALEQAKEGRLHILGEMNKVISEPRAE-------LSPYAP--RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED  588 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcc-------ccccCC--eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec
Confidence            4455565555555554433 2222211       122345  77889999999999999999999999999999998763


Q ss_pred             CCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141         119 RDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus       119 ~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                         +..|.|.+. .+.+++|+++|..+...
T Consensus       589 ---dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       589 ---DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             ---CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence               467888874 78999999999988664

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).

>KOG2164|consensus

Probab=98.16  E-value=8.3e-07  Score=88.98  Aligned_cols=47  Identities=28%  Similarity=0.764  Sum_probs=43.1

Q ss_pred             CcccccccccccccEEeCCCCHhhhHHhHHHHhcc-----CCCCCCccccccc
Q psy4141         300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVNQ  347 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-----~~~CP~Cr~~i~~  347 (353)
                      +..|+||++....++.+.|||. ||..|+-++|..     -..||+||..|..
T Consensus       186 ~~~CPICL~~~~~p~~t~CGHi-FC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRTNCGHI-FCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcccccccCce-eeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            6899999999999999999999 999999999987     3589999998875

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

Probab=98.15  E-value=7.7e-07  Score=60.83  Aligned_cols=30  Identities=33%  Similarity=0.978  Sum_probs=21.3

Q ss_pred             cccccccccc----cEEeCCCCHhhhHHhHHHHhcc
Q psy4141         303 CYLCNDREVT----HALIPCGHNFFCSECAERTCDF  334 (353)
Q Consensus       303 C~IC~~~~~~----~~llpCgH~~fC~~C~~~~~~~  334 (353)
                      |+||++ +.+    ++.|+|||. ||.+|++++...
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 777    899999999 999999999885

>KOG2177|consensus

Probab=98.13  E-value=8.9e-07  Score=82.71  Aligned_cols=48  Identities=33%  Similarity=0.827  Sum_probs=42.7

Q ss_pred             CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV  343 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~  343 (353)
                      ....+...|.||++.+..+.++||+|+ ||..|+..++.....||.||.
T Consensus         8 ~~~~~~~~C~iC~~~~~~p~~l~C~H~-~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    8 EVLQEELTCPICLEYFREPVLLPCGHN-FCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hhccccccChhhHHHhhcCccccccch-HhHHHHHHhcCCCcCCcccCC
Confidence            345678999999999999999999999 999999999875678999993

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.12  E-value=6.4e-06  Score=88.81  Aligned_cols=96  Identities=20%  Similarity=0.220  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHHHHHhhhhhh-hhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCce-EEcC
Q psy4141          40 EDVARAKREILSAADHFSAL-RASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY-IVTP  117 (353)
Q Consensus        40 e~v~~Ak~~I~~i~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~-I~ip  117 (353)
                      ++++.|++.+..+++.+... .+.+..       .+...|  ....+.||.+.+|.|||+||.+||+|+++||+. |.+.
T Consensus       652 eAL~~A~~g~~~Il~~M~~~i~~pr~~-------~s~~aP--~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~  722 (891)
T PLN00207        652 RALLQAKDGRKHILAEMSKCSPPPSKR-------LSKYAP--LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ  722 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhh-------hcccCC--eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC
Confidence            55667777777777666552 222221       123445  778899999999999999999999999999999 7654


Q ss_pred             CCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141         118 SRDKEPVFEVTG-APDSVEIARQEIESHIIR  147 (353)
Q Consensus       118 ~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~  147 (353)
                      .   +..|.|.+ ..+.+++|+++|++++.+
T Consensus       723 d---dg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        723 D---DGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             C---CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            2   45788888 588999999999998764

>KOG0119|consensus

Probab=98.08  E-value=3.1e-05  Score=77.32  Aligned_cols=68  Identities=25%  Similarity=0.434  Sum_probs=54.8

Q ss_pred             ceEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCC-------------------CCCCeEEEEcC-HHH
Q psy4141          80 HVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSR-------------------DKEPVFEVTGA-PDS  133 (353)
Q Consensus        80 ~~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-------------------~~e~~v~I~G~-~e~  133 (353)
                      ..+.+|.||.      ++||+|||..|.|.|+|+++|||+|.|-..                   +++--+.|++. .|.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            4566677654      789999999999999999999999987541                   01125778884 789


Q ss_pred             HHHHHHHHHHHHHh
Q psy4141         134 VEIARQEIESHIIR  147 (353)
Q Consensus       134 V~~A~~~I~~~i~~  147 (353)
                      |++|.++|+.+|..
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999986

>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=98.03  E-value=3.6e-06  Score=64.25  Aligned_cols=41  Identities=32%  Similarity=0.786  Sum_probs=33.3

Q ss_pred             cccccccccc-------------cccEEeCCCCHhhhHHhHHHHhccCCCCCCcc
Q psy4141         301 RQCYLCNDRE-------------VTHALIPCGHNFFCSECAERTCDFDRTCPMCR  342 (353)
Q Consensus       301 ~~C~IC~~~~-------------~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr  342 (353)
                      ..|.||++.+             ...++.+|||. |...|+.+|......||+||
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            3499999877             23355799999 99999999999888999997

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 ....

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

Probab=98.02  E-value=2.6e-06  Score=78.98  Aligned_cols=47  Identities=32%  Similarity=0.766  Sum_probs=40.7

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHH-HhccCC-CCCCcccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAER-TCDFDR-TCPMCRVPVN  346 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~-~~~~~~-~CP~Cr~~i~  346 (353)
                      .+..|.||++....++..+|||. ||..|+-. |..+.. .||+||+.+.
T Consensus       214 ~d~kC~lC~e~~~~ps~t~CgHl-FC~~Cl~~~~t~~k~~~CplCRak~~  262 (271)
T COG5574         214 ADYKCFLCLEEPEVPSCTPCGHL-FCLSCLLISWTKKKYEFCPLCRAKVY  262 (271)
T ss_pred             cccceeeeecccCCcccccccch-hhHHHHHHHHHhhccccCchhhhhcc
Confidence            46899999999999999999999 99999999 555544 4999999763

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

Probab=98.01  E-value=2.6e-06  Score=82.13  Aligned_cols=47  Identities=36%  Similarity=0.854  Sum_probs=40.8

Q ss_pred             CCCcccccccccc-------------cccEEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141         298 SGSRQCYLCNDRE-------------VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  345 (353)
Q Consensus       298 ~~~~~C~IC~~~~-------------~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i  345 (353)
                      .+++.|.||+|..             ..+-.+||||- +...|++.|++....||+||.++
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            4679999999972             23456899998 99999999999999999999984

>KOG0978|consensus

Probab=97.98  E-value=1.9e-06  Score=90.18  Aligned_cols=54  Identities=31%  Similarity=0.748  Sum_probs=48.2

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc--ceecc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ--AMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~--~~ri~  352 (353)
                      ..-..|++|.++..++++..|+|. ||..|++..+.. .+.||.|.+.|..  +.+||
T Consensus       641 K~~LkCs~Cn~R~Kd~vI~kC~H~-FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~  697 (698)
T KOG0978|consen  641 KELLKCSVCNTRWKDAVITKCGHV-FCEECVQTRYETRQRKCPKCNAAFGANDVHRIH  697 (698)
T ss_pred             HhceeCCCccCchhhHHHHhcchH-HHHHHHHHHHHHhcCCCCCCCCCCCcccccccC
Confidence            455899999999999999999998 999999999888 8999999999854  66665

>KOG2208|consensus

Probab=97.97  E-value=1.6e-05  Score=85.35  Aligned_cols=72  Identities=22%  Similarity=0.332  Sum_probs=64.3

Q ss_pred             cceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC-CCCCeEEEEcCHHHHHHHHHHHHHHHHhhhC
Q psy4141          79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQEIESHIIRRTG  150 (353)
Q Consensus        79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g  150 (353)
                      ....+.+.|-...+..|+||+|.+|.+|++++.+.|.++.. +....+.++|...++++|.+.++..+.+-..
T Consensus       345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n  417 (753)
T KOG2208|consen  345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIAEILN  417 (753)
T ss_pred             cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence            34778899999999999999999999999999999999984 4567899999999999999999988887555

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

Probab=97.94  E-value=3.2e-05  Score=80.42  Aligned_cols=96  Identities=21%  Similarity=0.266  Sum_probs=72.6

Q ss_pred             HHHHHHHHHHHHHHhhhhh-hhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          40 EDVARAKREILSAADHFSA-LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        40 e~v~~Ak~~I~~i~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      +++.+|+..-+.++..+.+ +...+..-       ....|  ...++.|+.+.++-|||+||++|++|.++||++|.+. 
T Consensus       519 ~AL~QAk~aRlhIL~~M~~ai~~pr~el-------s~~aP--ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-  588 (692)
T COG1185         519 KALEQAKGARLHILIVMNEAISEPRKEL-------SPYAP--RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-  588 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhh-------hccCC--ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-
Confidence            4556677666666666554 33332111       11223  6678999999999999999999999999999999887 


Q ss_pred             CCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141         119 RDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus       119 ~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                        ++..|.|.+. .+.+++|++.|.+++++
T Consensus       589 --ddGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         589 --DDGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             --CCCcEEEEecchHHHHHHHHHHHHHHhh
Confidence              3457999997 48999999999999876

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

Probab=97.87  E-value=1.1e-05  Score=61.55  Aligned_cols=48  Identities=21%  Similarity=0.390  Sum_probs=40.2

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      +...|+||.+...+++++||||. |++.|+.+|... ...||+|+.++..
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            46899999999999999999999 999999999999 8999999998865

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 ....

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

Probab=97.85  E-value=3.9e-05  Score=64.21  Aligned_cols=55  Identities=22%  Similarity=0.238  Sum_probs=45.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC--------------------CcCeEEEec-C--HHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG--------------------EEPVFVVTG-R--KEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~--------------------e~~vv~I~G-~--~e~v~~Ak~~I~~i~~~~   56 (353)
                      +|||.+|.+||+|+++|||+|.|..++                    +.-.|.|++ +  .+.+++|+.+|..++...
T Consensus        19 ~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~~   96 (120)
T cd02395          19 LILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKPA   96 (120)
T ss_pred             EEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhccC
Confidence            589999999999999999999998663                    113466666 4  699999999999998743

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.

>KOG1100|consensus

Probab=97.85  E-value=3.9e-06  Score=76.61  Aligned_cols=47  Identities=38%  Similarity=0.940  Sum_probs=42.2

Q ss_pred             ccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       302 ~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      .|..|.+....++++||.|.++|..|....    ..||+|+.+....+.+|
T Consensus       160 ~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~----~~CPiC~~~~~s~~~v~  206 (207)
T KOG1100|consen  160 SCRKCGEREATVLLLPCRHLCLCGICDESL----RICPICRSPKTSSVEVN  206 (207)
T ss_pred             cceecCcCCceEEeecccceEecccccccC----ccCCCCcChhhceeecc
Confidence            399999999999999999999999998752    67999999998887775

>KOG0336|consensus

Probab=97.76  E-value=3e-05  Score=76.40  Aligned_cols=69  Identities=29%  Similarity=0.358  Sum_probs=61.7

Q ss_pred             cceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      +....-+.|-.++||.|||++|.+||+||..|+++|++.+.+.+-.|+|.|..+.-.+|+..|...+..
T Consensus        45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            456778889999999999999999999999999999999888888999999999888888888776655

>KOG1588|consensus

Probab=97.74  E-value=0.00038  Score=64.94  Aligned_cols=42  Identities=36%  Similarity=0.666  Sum_probs=35.7

Q ss_pred             CcceEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          78 PGHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        78 ~~~~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      +-+.+.+|.||-      ++||+|+|++|.++|+|+++|||+|.|-.+
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            445777788875      689999999999999999999999988543

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.72  E-value=6.1e-05  Score=80.48  Aligned_cols=96  Identities=21%  Similarity=0.329  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHHHHHhhhhh-hhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          40 EDVARAKREILSAADHFSA-LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        40 e~v~~Ak~~I~~i~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      +.++.|+.....+++.+.. +...+..-       ....|  ....+.||.+.++.+||+||.+||+|+++||+.|.+. 
T Consensus       521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~-------~~~ap--~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-  590 (693)
T PRK11824        521 EALEQAKEGRLHILGKMNEAISEPRAEL-------SPYAP--RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-  590 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCChhhh-------cccCc--hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-
Confidence            4455566665555555433 22222211       12234  5567778999999999999999999999999988753 


Q ss_pred             CCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141         119 RDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus       119 ~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                        ++..|.|.+. .+.+++|+++|+.++.+
T Consensus       591 --d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        591 --DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             --CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence              3467888884 88999999999988864

>KOG1785|consensus

Probab=97.70  E-value=1.6e-05  Score=77.36  Aligned_cols=47  Identities=30%  Similarity=0.833  Sum_probs=43.1

Q ss_pred             cccccccccccccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccccc
Q psy4141         301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQA  348 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~~~  348 (353)
                      ..|.||-++.++.-.-||||. +|..|+..|...  ...||+||..|...
T Consensus       370 eLCKICaendKdvkIEPCGHL-lCt~CLa~WQ~sd~gq~CPFCRcEIKGt  418 (563)
T KOG1785|consen  370 ELCKICAENDKDVKIEPCGHL-LCTSCLAAWQDSDEGQTCPFCRCEIKGT  418 (563)
T ss_pred             HHHHHhhccCCCcccccccch-HHHHHHHhhcccCCCCCCCceeeEeccc
Confidence            689999999999999999999 999999999865  67999999999765

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

Probab=97.66  E-value=2.2e-05  Score=74.09  Aligned_cols=47  Identities=23%  Similarity=0.673  Sum_probs=40.0

Q ss_pred             CCccccccccccc---ccEEeCCCCHhhhHHhHHHHhcc-CCCCCCcccccc
Q psy4141         299 GSRQCYLCNDREV---THALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN  346 (353)
Q Consensus       299 ~~~~C~IC~~~~~---~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~  346 (353)
                      ...+|.||++.+.   ..+.+||.|. |...|+.+|... ...||+||.++.
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            3489999999874   2456899999 999999999986 889999999874

>KOG4628|consensus

Probab=97.65  E-value=2.1e-05  Score=76.55  Aligned_cols=46  Identities=22%  Similarity=0.665  Sum_probs=38.8

Q ss_pred             ccccccccccccc---EEeCCCCHhhhHHhHHHHhccC-CCCCCccccccc
Q psy4141         301 RQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQ  347 (353)
Q Consensus       301 ~~C~IC~~~~~~~---~llpCgH~~fC~~C~~~~~~~~-~~CP~Cr~~i~~  347 (353)
                      ..|.||+|.+...   ..|||.|. |...|+..|..+. ..||+|+..+..
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~-FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHK-FHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCc-hhhccchhhHhhcCccCCCCCCcCCC
Confidence            5999999998643   34899999 9999999999995 569999987654

>KOG0802|consensus

Probab=97.61  E-value=2.2e-05  Score=81.76  Aligned_cols=47  Identities=28%  Similarity=0.704  Sum_probs=42.7

Q ss_pred             CCCcccccccccccc-----cEEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141         298 SGSRQCYLCNDREVT-----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  345 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~-----~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i  345 (353)
                      .....|.||.|....     +..+||+|. ||..|++.|.++...||+||..+
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            446899999999888     788999999 99999999999999999999944

>KOG4159|consensus

Probab=97.50  E-value=4.7e-05  Score=75.76  Aligned_cols=51  Identities=33%  Similarity=0.879  Sum_probs=45.9

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ....+..|.||+..+..++.+||||. ||..|+.+...+...||.||.++..
T Consensus        80 ~~~sef~c~vc~~~l~~pv~tpcghs-~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   80 EIRSEFECCVCSRALYPPVVTPCGHS-FCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cccchhhhhhhHhhcCCCcccccccc-ccHHHHHHHhccCCCCccccccccc
Confidence            34667999999999999999999999 9999999987778999999998764

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.48  E-value=0.00027  Score=60.74  Aligned_cols=89  Identities=17%  Similarity=0.169  Sum_probs=57.7

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT   82 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t   82 (353)
                      .||++|++|+.|++..|-+|++-..        +..      ++..|..++....-      .....     ....+...
T Consensus        46 ~IG~~G~rI~~i~e~lgekIdVve~--------s~d------~~~fI~n~l~Pa~V------~~v~I-----~~~~~~~~  100 (140)
T PRK08406         46 AIGKGGENVKRLEEKLGKDIELVEY--------SDD------PEEFIKNIFAPAAV------RSVTI-----KKKNGDKV  100 (140)
T ss_pred             cCCcCchHHHHHHHHhCCceEEEEc--------CCC------HHHHHHHHcCCCEE------EEEEE-----EecCCcEE
Confidence            5899999999999998877764322        122      22333333221100      00000     00011356


Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      ..+.|+.+..|..|||+|++|+.+++.++-++.+
T Consensus       101 ~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406        101 AYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            7788999999999999999999999999988854

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

Probab=97.40  E-value=0.00015  Score=69.56  Aligned_cols=57  Identities=28%  Similarity=0.720  Sum_probs=47.9

Q ss_pred             CCCCCCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccccc
Q psy4141         291 TSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQA  348 (353)
Q Consensus       291 ~~~~~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~~~  348 (353)
                      ++..+..++...|.||-+...-..++||+|. .|--|+-++...  .+.|++||.....+
T Consensus        52 sSaddtDEen~~C~ICA~~~TYs~~~PC~H~-~CH~Ca~RlRALY~~K~C~~CrTE~e~V  110 (493)
T COG5236          52 SSADDTDEENMNCQICAGSTTYSARYPCGHQ-ICHACAVRLRALYMQKGCPLCRTETEAV  110 (493)
T ss_pred             ccccccccccceeEEecCCceEEEeccCCch-HHHHHHHHHHHHHhccCCCccccccceE
Confidence            3445566788999999999988899999999 999999998666  78999999876544

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

Probab=97.39  E-value=0.00017  Score=56.29  Aligned_cols=31  Identities=35%  Similarity=0.730  Sum_probs=26.8

Q ss_pred             EeCCCCHhhhHHhHHHHhcc---CCCCCCcccccc
Q psy4141         315 LIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN  346 (353)
Q Consensus       315 llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~  346 (353)
                      +-.|+|. |.+.|+.+|.+.   ...||+||++..
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 999999999997   578999999763

>KOG4692|consensus

Probab=97.38  E-value=7.6e-05  Score=71.81  Aligned_cols=49  Identities=22%  Similarity=0.576  Sum_probs=44.8

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      .++..|+||+-.+.++++.||+|. -|..|+.++....+.|-.|+..+..
T Consensus       420 sEd~lCpICyA~pi~Avf~PC~H~-SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAGPINAVFAPCSHR-SCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceecccchhhccCCCCc-hHHHHHHHHHhcCCeeeEecceeee
Confidence            356899999999999999999999 9999999998889999999987764

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

Probab=97.36  E-value=4.5e-05  Score=56.15  Aligned_cols=46  Identities=30%  Similarity=0.672  Sum_probs=25.7

Q ss_pred             CCCcccccccccccccE-EeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~-llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      ++-+.|.+|.+....++ +-.|.|+ ||..|+....  ...||+|+.+..
T Consensus         5 e~lLrCs~C~~~l~~pv~l~~CeH~-fCs~Ci~~~~--~~~CPvC~~Paw   51 (65)
T PF14835_consen    5 EELLRCSICFDILKEPVCLGGCEHI-FCSSCIRDCI--GSECPVCHTPAW   51 (65)
T ss_dssp             HHTTS-SSS-S--SS-B---SSS---B-TTTGGGGT--TTB-SSS--B-S
T ss_pred             HHhcCCcHHHHHhcCCceeccCccH-HHHHHhHHhc--CCCCCCcCChHH
Confidence            34578999999999996 5799999 9999997743  456999999874

>KOG2814|consensus

Probab=97.36  E-value=0.00027  Score=67.77  Aligned_cols=67  Identities=22%  Similarity=0.371  Sum_probs=59.2

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTG-APDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G-~~e~V~~A~~~I~~~i~~  147 (353)
                      ....+.|+..++|.|||++|.|.++|+++|+++|.+|... +...|+|+| ..+.|.+|.+.|.-+|..
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids  125 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDS  125 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence            5567889999999999999999999999999999999875 455677777 588999999999988887

>KOG2279|consensus

Probab=97.33  E-value=0.00036  Score=70.71  Aligned_cols=142  Identities=18%  Similarity=0.241  Sum_probs=102.5

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhhhhh----------hhccCC---
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFSAL----------RASRKS---   65 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~----------~~~~~~---   65 (353)
                      +|+||+|+++..|+.-++++|.+.+.+   ..+...|.+...-++.|+.++.+.+++....          +..+..   
T Consensus       153 ~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n  232 (608)
T KOG2279|consen  153 RIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPIN  232 (608)
T ss_pred             cccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCcc
Confidence            689999999999999999999988776   3477888888888889999998887765432          111110   


Q ss_pred             ----C-----CCCC------------CC-C---CCCC-----------------------CcceEEEEEecCCCccceec
Q psy4141          66 ----G-----ALSP------------LS-P---PTGV-----------------------PGHVTIEVRVPYKVVGLVVG   97 (353)
Q Consensus        66 ----g-----~~~~------------~~-~---~~~~-----------------------~~~~t~~v~VP~~~vG~IIG   97 (353)
                          +     ....            ++ +   .+..                       ......+|.||..++|.|||
T Consensus       233 ~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig  312 (608)
T KOG2279|consen  233 VRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIG  312 (608)
T ss_pred             ccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhh
Confidence                0     0000            00 0   0000                       11234579999999999999


Q ss_pred             cCChHHHHHHHHhCceEEcCCC---CCC---CeEEEEcCHHHHHHHHHHHHH
Q psy4141          98 PKGATIKRIQHQTNTYIVTPSR---DKE---PVFEVTGAPDSVEIARQEIES  143 (353)
Q Consensus        98 kgG~tIk~Iq~~Tga~I~ip~~---~~e---~~v~I~G~~e~V~~A~~~I~~  143 (353)
                      +.|++|+.+...+++.+.|-..   ++-   .++.+.|+..-+..+..||..
T Consensus       313 ~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~  364 (608)
T KOG2279|consen  313 HAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTV  364 (608)
T ss_pred             hhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHHHHHHHhhhhc
Confidence            9999999999999999865432   111   468899999999999888864

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.17  E-value=0.002  Score=66.73  Aligned_cols=66  Identities=24%  Similarity=0.404  Sum_probs=53.1

Q ss_pred             ceEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~  147 (353)
                      .....|.+|+ ++-|+|||+.|.|||-++..|||.|+|.  |+...|+|+| .|---+.|+.-++.+|.+
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc--CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            3556688999 7789999999999999999999999887  4444788888 476667777777776664

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=97.17  E-value=0.0081  Score=54.75  Aligned_cols=116  Identities=16%  Similarity=0.149  Sum_probs=87.6

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT   82 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t   82 (353)
                      |...+|..++.|....|++|.+...  +..+.|+|++..++.+...|.+++...                        .+
T Consensus        40 Ll~~~~~~L~~l~~~~~~~I~~~~~--~~~i~I~g~k~~~~~i~~~i~~~l~~i------------------------~~   93 (210)
T PF14611_consen   40 LLTGNGRILENLAARNGAKIEVSRS--ENRIRITGTKSTAEYIEASINEILSNI------------------------RT   93 (210)
T ss_pred             eecCCchHHHHHHHhcCceEEEecC--CcEEEEEccHHHHHHHHHHHHHHHhhc------------------------EE
Confidence            5577888899998889999998643  567999999999999999999998865                        56


Q ss_pred             EEEEecCCCccceec----cCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-----CHHHHHHHHHHHHHHHH
Q psy4141          83 IEVRVPYKVVGLVVG----PKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-----APDSVEIARQEIESHII  146 (353)
Q Consensus        83 ~~v~VP~~~vG~IIG----kgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-----~~e~V~~A~~~I~~~i~  146 (353)
                      .+|.++.-.--+..+    .....++.|++.|+++|....++.  .+.|..     ....++.|++++...+.
T Consensus        94 ~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~~--~~~i~~~~~~~~~~~~~~a~RlL~~a~~  164 (210)
T PF14611_consen   94 EEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDGN--KLKISWLASPENEKRADRAKRLLLWALD  164 (210)
T ss_pred             EEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCCC--eEEEEEEeeccccchHHHHHHHHHHhcc
Confidence            666666432222221    246789999999999997665433  355554     57899999999987775

>PRK12704 phosphodiesterase; Provisional

Probab=97.12  E-value=0.0023  Score=66.30  Aligned_cols=65  Identities=23%  Similarity=0.399  Sum_probs=52.2

Q ss_pred             eEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~  147 (353)
                      .+..|.+|+ ++-|+|||+-|.|||.++..||+.|+|.  |+..+|.|+| .|---+.|+.-++.++..
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc--CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            556688898 7889999999999999999999999887  4445788999 466656677777666553

>PRK00106 hypothetical protein; Provisional

Probab=97.12  E-value=0.0027  Score=65.76  Aligned_cols=66  Identities=27%  Similarity=0.442  Sum_probs=53.7

Q ss_pred             ceEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~  147 (353)
                      .....|.+|+ ++-|+|||+-|.||+-++..||+.|+|.  |+...|+|+| .|---+.|+.-++.+|.+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID--DTPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc--CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            3556688999 7889999999999999999999999887  4445788998 577777777777776664

>KOG0311|consensus

Probab=97.09  E-value=8.2e-05  Score=71.71  Aligned_cols=51  Identities=22%  Similarity=0.472  Sum_probs=42.6

Q ss_pred             CCCCCcccccccccccccEE-eCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+..+..|.||++....... .-|.|. ||..|+..-... ...||-||+.+..
T Consensus        39 ~~~~~v~c~icl~llk~tmttkeClhr-fc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   39 MFDIQVICPICLSLLKKTMTTKECLHR-FCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             HhhhhhccHHHHHHHHhhcccHHHHHH-HHHHHHHHHHHhcCCCCchHHhhccc
Confidence            34567899999999876665 469999 999999998777 7899999998754

>KOG2879|consensus

Probab=97.05  E-value=0.00059  Score=63.83  Aligned_cols=49  Identities=27%  Similarity=0.722  Sum_probs=41.1

Q ss_pred             CCCcccccccccccccEEe-CCCCHhhhHHhHHHHhcc--CCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF--DRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~~  347 (353)
                      ..+.+|++|-+.+..+... +|+|. +|..|+..-...  .-.||.|-.++..
T Consensus       237 t~~~~C~~Cg~~PtiP~~~~~C~Hi-yCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIPHVIGKCGHI-YCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             cCCceeeccCCCCCCCeeeccccce-eehhhhhhhhcchhhcccCccCCCCcc
Confidence            3457999999999998876 59999 999999987665  4689999887753

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

Probab=97.04  E-value=0.00026  Score=63.14  Aligned_cols=49  Identities=27%  Similarity=0.612  Sum_probs=43.7

Q ss_pred             CcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccce
Q psy4141         300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  349 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~  349 (353)
                      ...|.||...+..++...|||. ||..|+.+-+.....|-+|.+......
T Consensus       196 PF~C~iCKkdy~spvvt~CGH~-FC~~Cai~~y~kg~~C~~Cgk~t~G~f  244 (259)
T COG5152         196 PFLCGICKKDYESPVVTECGHS-FCSLCAIRKYQKGDECGVCGKATYGRF  244 (259)
T ss_pred             ceeehhchhhccchhhhhcchh-HHHHHHHHHhccCCcceecchhhccce
Confidence            3789999999999999999999 999999998888999999988765443

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=96.86  E-value=0.00065  Score=65.26  Aligned_cols=30  Identities=30%  Similarity=0.901  Sum_probs=26.6

Q ss_pred             CCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         317 PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       317 pCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      +|||. ||..|+.+++.. ...||.|+.++..
T Consensus        25 ~CGH~-~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570        25 VCGHT-LCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             CCCCc-ccHHHHHHHhcCCCCCCCCCCCccch
Confidence            79999 999999999877 6789999998764

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).

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

Probab=96.84  E-value=0.0027  Score=56.98  Aligned_cols=49  Identities=22%  Similarity=0.294  Sum_probs=45.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~   54 (353)
                      +|||++|.+-+.|++-|+++|.+-    +..|.|-|..++|+.|+++|..+++
T Consensus       115 RIIG~~GkTr~~IE~lt~~~I~V~----g~tVaiiG~~~~v~iAr~AVemli~  163 (194)
T COG1094         115 RIIGREGKTRRAIEELTGVYISVY----GKTVAIIGGFEQVEIAREAVEMLIN  163 (194)
T ss_pred             eeeCCCchHHHHHHHHhCCeEEEe----CcEEEEecChhhhHHHHHHHHHHHc
Confidence            699999999999999999999988    5678888999999999999999987

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

Probab=96.83  E-value=0.0017  Score=58.55  Aligned_cols=42  Identities=26%  Similarity=0.616  Sum_probs=34.3

Q ss_pred             CcceEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          78 PGHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        78 ~~~~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      |...+-++.||-      ++||+|||+.|.|+|++++.|+|+|.|-..
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            334556666653      789999999999999999999999988654

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.80  E-value=0.0026  Score=59.36  Aligned_cols=63  Identities=22%  Similarity=0.248  Sum_probs=54.2

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                      -..+.||..+++.+||++|.+|+.|.+.+++.|.+-   .+..|-|.+. .+++++|+++|+++-++
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig---~NG~VwI~~~~~~~~~~a~~~I~~~e~~  209 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG---QNGRIWIKGPDEEDEEIAIEAIKKIERE  209 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc---CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence            366899999999999999999999999999999764   3467999996 66999999999876554

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=96.77  E-value=0.0039  Score=53.62  Aligned_cols=89  Identities=16%  Similarity=0.179  Sum_probs=57.2

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT   82 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t   82 (353)
                      .||++|.+|+.|++..|-+|++=        .-+.+++..-      ..++.      +.+-.....     ...++...
T Consensus        47 ~IG~~G~rIk~i~el~gekIdVV--------eys~D~~~fI------~N~l~------PA~V~~V~i-----~~~~~~~~  101 (141)
T TIGR01952        47 AIGKGGENVKRLEELIGKSIELI--------EYSENLEEFV------ANKLA------PAEVKNVTV-----SEFNGKKV  101 (141)
T ss_pred             cCCCCchHHHHHHHhcCCeeEEE--------EcCCCHHHHH------HHcCC------CceEEEEEE-----EcCCCCEE
Confidence            58999999999998888777643        2333333321      11111      000000000     00122366


Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      ..+.||.+..++.|||+|.+|+...+.++-++.+
T Consensus       102 a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952       102 AYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI  135 (141)
T ss_pred             EEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence            7899999999999999999999999999888754

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.

>KOG1039|consensus

Probab=96.72  E-value=0.00082  Score=65.75  Aligned_cols=50  Identities=30%  Similarity=0.791  Sum_probs=41.1

Q ss_pred             CCCcccccccccccccE-----E---eCCCCHhhhHHhHHHHhcc-------CCCCCCcccccccc
Q psy4141         298 SGSRQCYLCNDREVTHA-----L---IPCGHNFFCSECAERTCDF-------DRTCPMCRVPVNQA  348 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~-----l---lpCgH~~fC~~C~~~~~~~-------~~~CP~Cr~~i~~~  348 (353)
                      ..+..|-||++.....+     +   .+|.|. ||..|+..|...       .+.||.||.....+
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~-~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHS-FCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchh-hhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            34689999999977766     4   679999 999999999843       47899999876654

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

Probab=96.72  E-value=0.0026  Score=46.72  Aligned_cols=36  Identities=22%  Similarity=0.308  Sum_probs=33.4

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      ....+.|+.+.+|..|||+|.+|+.+++.+|-+|.+
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            678899999999999999999999999999988854

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.

>KOG1067|consensus

Probab=96.62  E-value=0.0041  Score=63.59  Aligned_cols=63  Identities=22%  Similarity=0.298  Sum_probs=53.6

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                      +...+.|+.+.+..+||++|...|+|+.+||+.-.+    ++..+.|... +...++|++.|..++..
T Consensus       597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----De~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----DEGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             eeeEEeecchhhheeecCccceeeeEeeeccceeee----cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            788999999999999999999999999999944442    3457888885 78889999999988765

>KOG0828|consensus

Probab=96.59  E-value=0.0011  Score=66.60  Aligned_cols=50  Identities=28%  Similarity=0.671  Sum_probs=40.3

Q ss_pred             CCCCcccccccccc-----------------cccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         297 ISGSRQCYLCNDRE-----------------VTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~-----------------~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+....|.||+...                 .+..+.||.|. |...|+.+|... .-.||+||.++..
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~Hi-fH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHI-FHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHH-HHHHHHHHHHhhhcccCCccCCCCCC
Confidence            34568899999852                 24556799999 999999999986 6699999998753

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.42  E-value=0.004  Score=56.18  Aligned_cols=90  Identities=17%  Similarity=0.163  Sum_probs=57.2

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT   82 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t   82 (353)
                      .||++|.+|+.|.++.|-+|++-          .-+.+-..-++..+. -.+         ..+...    . . .+...
T Consensus        90 ~iG~~G~rvk~i~~eLgekIdVV----------e~s~d~~~fI~nal~-Pa~---------v~~V~~----~-~-~d~~~  143 (190)
T COG0195          90 CIGKRGSRVKAVSEELGEKIDVV----------EWSEDPAEFIKNALA-PAE---------VLSVNI----K-E-DDGHV  143 (190)
T ss_pred             hccCCChHHHHHHHHhCCceEEE----------EeCCCHHHHHHHhcC-cce---------EeEEEE----E-e-CCCcE
Confidence            58999999999999998555532          222111111111111 000         000000    0 0 01136


Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ..+.||.+..+.+|||+|.+++.+.+.||-+|.+-.
T Consensus       144 ~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         144 AIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            788899999999999999999999999999997653

>KOG2660|consensus

Probab=96.36  E-value=0.0012  Score=63.46  Aligned_cols=51  Identities=24%  Similarity=0.678  Sum_probs=44.8

Q ss_pred             CCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      .....+|.+|...+.++..+ -|-|. ||..|+.+++.....||.|...+.+.
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            44568999999999998875 69999 99999999999999999999887654

>KOG1813|consensus

Probab=96.27  E-value=0.0013  Score=62.22  Aligned_cols=47  Identities=23%  Similarity=0.671  Sum_probs=42.4

Q ss_pred             cccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      ..|.||...+.++|...|+|. ||..|+..-+.....|++|.+.+...
T Consensus       242 f~c~icr~~f~~pVvt~c~h~-fc~~ca~~~~qk~~~c~vC~~~t~g~  288 (313)
T KOG1813|consen  242 FKCFICRKYFYRPVVTKCGHY-FCEVCALKPYQKGEKCYVCSQQTHGS  288 (313)
T ss_pred             ccccccccccccchhhcCCce-eehhhhccccccCCcceecccccccc
Confidence            579999999999999999999 99999999888789999998876554

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=96.23  E-value=0.0084  Score=63.91  Aligned_cols=52  Identities=17%  Similarity=0.194  Sum_probs=43.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .|||.+|.+||.|.++||++|++.+.  ..|.+..-+.+.+++|+..|..+...
T Consensus       591 ~vIG~gGk~I~~i~~~tg~~Idi~d~--G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       591 EVIGPKGKMINQIQDETGAEISIEDD--GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             heeCCCcHhHHHHHHHHCCEEEEecC--cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            48999999999999999999999853  34444445889999999999999773

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.

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.22  E-value=0.0016  Score=46.46  Aligned_cols=45  Identities=27%  Similarity=0.770  Sum_probs=37.2

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      ....|..|.......+++||||. .|..|..-.  .-..||+|..++.
T Consensus         6 ~~~~~~~~~~~~~~~~~~pCgH~-I~~~~f~~~--rYngCPfC~~~~~   50 (55)
T PF14447_consen    6 PEQPCVFCGFVGTKGTVLPCGHL-ICDNCFPGE--RYNGCPFCGTPFE   50 (55)
T ss_pred             cceeEEEccccccccccccccce-eeccccChh--hccCCCCCCCccc
Confidence            34679999999888999999999 999997653  2468999999875

>KOG0297|consensus

Probab=96.19  E-value=0.0021  Score=64.38  Aligned_cols=52  Identities=27%  Similarity=0.651  Sum_probs=46.4

Q ss_pred             CCCCcccccccccccccEE-eCCCCHhhhHHhHHHHhccCCCCCCcccccccce
Q psy4141         297 ISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  349 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~  349 (353)
                      +.++..|.+|.....+++. ..|||. ||..|+..+......||.|+..+.+..
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~-fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHR-FCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCc-ccccccchhhccCcCCcccccccchhh
Confidence            5677999999999999999 599999 999999999888899999998877653

>PRK12705 hypothetical protein; Provisional

Probab=96.18  E-value=0.013  Score=60.37  Aligned_cols=64  Identities=20%  Similarity=0.326  Sum_probs=46.5

Q ss_pred             eEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHH
Q psy4141          81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHII  146 (353)
Q Consensus        81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~  146 (353)
                      ....|.+|+ ++-|+|||+-|.+||.++..||+.|+|..  ....|+|.+. |.--+.|+..+..+|.
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--TPEAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--CccchhhcccCccchHHHHHHHHHHHh
Confidence            455678888 77899999999999999999999998873  3334666663 4444555555555444

>KOG2814|consensus

Probab=96.08  E-value=0.011  Score=56.92  Aligned_cols=56  Identities=23%  Similarity=0.180  Sum_probs=48.6

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC--cCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e--~~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .|||++|.+-|+|+++|+++|.+|.+++  +.+.++.+..+.|-+|.+.|..+++.+.
T Consensus        70 ~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   70 WLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             hhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            4899999999999999999999998873  3555566789999999999999998763

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=96.00  E-value=0.0091  Score=63.94  Aligned_cols=52  Identities=17%  Similarity=0.159  Sum_probs=44.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .|||++|.+||.|+++||++|++.+.  ..+.+.....+.+.+|++.|..+...
T Consensus       564 ~vIG~gGk~Ik~I~~~tg~~I~i~dd--G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       564 DVIGPGGKVIREITEETGAKIDIEDD--GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             hhcCCCcHHHHHHHHHHCCEEEEecC--eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            48999999999999999999999864  45556667889999999999888653

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).

>KOG1002|consensus

Probab=95.97  E-value=0.0031  Score=63.87  Aligned_cols=48  Identities=29%  Similarity=0.749  Sum_probs=41.9

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-----CCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-----~~~CP~Cr~~i~  346 (353)
                      .++.+|.+|.+.-.+++...|.|. ||+.|+..+...     ...||+|...+.
T Consensus       534 k~~~~C~lc~d~aed~i~s~ChH~-FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDYIESSCHHK-FCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             cCceeecccCChhhhhHhhhhhHH-HHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            456899999999999999999999 999999888775     568999987754

>KOG0804|consensus

Probab=95.93  E-value=0.0043  Score=61.81  Aligned_cols=45  Identities=29%  Similarity=0.647  Sum_probs=35.3

Q ss_pred             CCccccccccccccc----EEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         299 GSRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~----~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      +--+|+||+++.-.-    +.+.|.|. |...|+..|+.  ..||+||--..
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~c~Hs-fh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTILCNHS-FHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeeecccc-cchHHHhhccc--CcChhhhhhcC
Confidence            446899999986432    34789999 99999999975  78999986443

>PRK00468 hypothetical protein; Provisional

Probab=95.78  E-value=0.011  Score=45.40  Aligned_cols=31  Identities=29%  Similarity=0.468  Sum_probs=27.7

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQT  110 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T  110 (353)
                      ....++.|..+.+|+||||+|.+|+.|+.--
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3678899999999999999999999998654

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

Probab=95.77  E-value=0.011  Score=41.56  Aligned_cols=40  Identities=33%  Similarity=0.775  Sum_probs=32.2

Q ss_pred             ccccccc--cccccEEeCCC-----CHhhhHHhHHHHhcc--CCCCCCcc
Q psy4141         302 QCYLCND--REVTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCR  342 (353)
Q Consensus       302 ~C~IC~~--~~~~~~llpCg-----H~~fC~~C~~~~~~~--~~~CP~Cr  342 (353)
                      .|.||++  ...++...||.     |. +...|+.+|...  ...||+|+
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  45566778995     66 999999999976  55899995

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

>KOG0336|consensus

Probab=95.67  E-value=0.017  Score=57.44  Aligned_cols=57  Identities=30%  Similarity=0.260  Sum_probs=49.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSA   58 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~   58 (353)
                      .+||++|++||.|+..|+++|++-....+-.++|-|..+--.+|+..|...++....
T Consensus        60 ~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~k~e~  116 (629)
T KOG0336|consen   60 KVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQDKDER  116 (629)
T ss_pred             eeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhhhhhh
Confidence            589999999999999999999998777677788999998888999988887765543

>PRK02821 hypothetical protein; Provisional

Probab=95.66  E-value=0.011  Score=45.48  Aligned_cols=33  Identities=30%  Similarity=0.383  Sum_probs=29.1

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCc
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT  112 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga  112 (353)
                      ...+.+.|..+.+|+||||+|.+|+.|+.--.+
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            367889999999999999999999999877644

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

Probab=95.48  E-value=0.017  Score=44.32  Aligned_cols=32  Identities=41%  Similarity=0.556  Sum_probs=28.2

Q ss_pred             cceEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141          79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT  110 (353)
Q Consensus        79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T  110 (353)
                      .....++.|....+|.||||+|.+|+.|+.--
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            34778899999999999999999999998654

>KOG0825|consensus

Probab=95.42  E-value=0.0035  Score=66.01  Aligned_cols=50  Identities=24%  Similarity=0.394  Sum_probs=41.9

Q ss_pred             CCcccccccccccccEE---eCCCCHhhhHHhHHHHhccCCCCCCcccccccce
Q psy4141         299 GSRQCYLCNDREVTHAL---IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM  349 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~l---lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~  349 (353)
                      ....|++|+....+...   .+|+|- ||..|+..|+.-...||+||..|.+++
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~-FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKHTAHY-FCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccccccc-cHHHHhhhhhhhcccCchhhhhhheee
Confidence            45789999987655433   589999 999999999988999999999988764

>KOG1734|consensus

Probab=95.38  E-value=0.0095  Score=55.79  Aligned_cols=47  Identities=26%  Similarity=0.641  Sum_probs=38.7

Q ss_pred             CCcccccccccccc----------cEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         299 GSRQCYLCNDREVT----------HALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       299 ~~~~C~IC~~~~~~----------~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      ++..|.||-...-.          .-.+.|+|. |...|++-|+.-  .+.||.|+..+.
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHv-FHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHV-FHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeeecccc-hHHHhhhhheeecCCCCCchHHHHhh
Confidence            45789999876533          335899999 999999999987  779999998774

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.37  E-value=0.042  Score=54.43  Aligned_cols=38  Identities=16%  Similarity=0.064  Sum_probs=34.8

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ....+.||.++.++.|||+|.+++-..+.||.+|.|-+
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            56789999999999999999999999999999997643

>KOG0119|consensus

Probab=95.26  E-value=0.041  Score=55.57  Aligned_cols=53  Identities=21%  Similarity=0.223  Sum_probs=42.0

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCC-------------------CcCeEEEe-cCHHHHHHHHHHHHHHHhh
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRG-------------------EEPVFVVT-GRKEDVARAKREILSAADH   55 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~-------------------e~~vv~I~-G~~e~v~~Ak~~I~~i~~~   55 (353)
                      |||.+|.+.|+|+++|||+|.|-..+                   |+--+.|+ -+.|.|.+|.+.|..+|++
T Consensus       158 iiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  158 IIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             EecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence            89999999999999999999975311                   12234444 5778999999999999885

>KOG0826|consensus

Probab=95.26  E-value=0.0095  Score=57.23  Aligned_cols=55  Identities=18%  Similarity=0.451  Sum_probs=43.9

Q ss_pred             CCCcccccccccccccEEeCC-CCHhhhHHhHHHHhccCCCCCCcc--cccccceeccC
Q psy4141         298 SGSRQCYLCNDREVTHALIPC-GHNFFCSECAERTCDFDRTCPMCR--VPVNQAMRIIS  353 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpC-gH~~fC~~C~~~~~~~~~~CP~Cr--~~i~~~~ri~~  353 (353)
                      .+...|+||+...+++..+-- |-. ||..|+-.+......||+=.  ..+.+++|+|+
T Consensus       298 ~~~~~CpvClk~r~Nptvl~vSGyV-fCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~  355 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEVSGYV-FCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFN  355 (357)
T ss_pred             CccccChhHHhccCCCceEEecceE-EeHHHHHHHHHhcCCCCccCCcchHHHHHHHhc
Confidence            456789999999988776654 777 99999999998899999744  44567777764

>TIGR01953 NusA transcription termination factor NusA

Probab=95.24  E-value=0.005  Score=60.49  Aligned_cols=38  Identities=24%  Similarity=0.301  Sum_probs=35.2

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ....+.||.+..+..|||+|.+++-..+.||.+|.+-+
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            57889999999999999999999999999999997754

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.04  E-value=0.063  Score=53.20  Aligned_cols=39  Identities=23%  Similarity=0.220  Sum_probs=35.5

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      ....+.||.+..++.|||+|.+++-..+.||.+|.+-..
T Consensus       303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            568899999999999999999999999999999976543

>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=94.77  E-value=0.023  Score=49.33  Aligned_cols=53  Identities=25%  Similarity=0.575  Sum_probs=38.6

Q ss_pred             CCcccccccccccccEEeCCC-CHhhh-----------HHhHHHHhcc-------------------------------C
Q psy4141         299 GSRQCYLCNDREVTHALIPCG-HNFFC-----------SECAERTCDF-------------------------------D  335 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCg-H~~fC-----------~~C~~~~~~~-------------------------------~  335 (353)
                      ++..|+|||+.+-++|||-|. |.-.|           .-|+.++...                               .
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE   80 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence            357899999999999998764 22233           3677776542                               2


Q ss_pred             CCCCCcccccccceec
Q psy4141         336 RTCPMCRVPVNQAMRI  351 (353)
Q Consensus       336 ~~CP~Cr~~i~~~~ri  351 (353)
                      ..||+||-.|..+..|
T Consensus        81 L~CPLCRG~V~GWtvv   96 (162)
T PF07800_consen   81 LACPLCRGEVKGWTVV   96 (162)
T ss_pred             ccCccccCceeceEEc
Confidence            2599999999877654

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.

>PRK01064 hypothetical protein; Provisional

Probab=94.67  E-value=0.038  Score=42.65  Aligned_cols=32  Identities=28%  Similarity=0.428  Sum_probs=28.2

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhC
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTN  111 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg  111 (353)
                      ....++.|.....|.+|||+|.+|+.|+.-..
T Consensus        29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~   60 (78)
T PRK01064         29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV   60 (78)
T ss_pred             EEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence            46788999999999999999999999987643

>KOG1001|consensus

Probab=94.53  E-value=0.016  Score=61.72  Aligned_cols=44  Identities=32%  Similarity=0.892  Sum_probs=39.2

Q ss_pred             cccccccccccccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      ..|.+|.+ ...++..+|+|. ||.+|+......  ...||.||..+.
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~-~c~~c~~~~i~~~~~~~~~~cr~~l~  500 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHD-FCVECLKKSIQQSENAPCPLCRNVLK  500 (674)
T ss_pred             cccccccc-cccceeecccch-HHHHHHHhccccccCCCCcHHHHHHH
Confidence            78999999 788888999999 999999999888  457999998764

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.52  E-value=0.089  Score=53.09  Aligned_cols=38  Identities=21%  Similarity=0.249  Sum_probs=34.9

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ....+.||.+..++.|||+|.+++-..+.||-+|.|-.
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            46789999999999999999999999999999997664

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.49  E-value=0.0067  Score=62.06  Aligned_cols=38  Identities=21%  Similarity=0.282  Sum_probs=34.8

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ....+.||.+..+..|||+|.+|+...+.||.+|.+-.
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            47889999999999999999999999999999997654

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

Probab=94.32  E-value=0.08  Score=55.77  Aligned_cols=52  Identities=23%  Similarity=0.245  Sum_probs=42.7

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      +||++|.+|++|.++||++|++.+.  ..+.+..-..+.+.+|+..|..+.++.
T Consensus       566 vIG~gGk~I~~I~eetg~~Idiedd--Gtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         566 VIGPGGKTIKAITEETGVKIDIEDD--GTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             ccCCcccchhhhhhhhCcEEEecCC--CcEEEEecchHHHHHHHHHHHHHHhhc
Confidence            7999999999999999999999833  244444445688999999999998765

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

Probab=94.13  E-value=0.028  Score=53.43  Aligned_cols=42  Identities=36%  Similarity=0.739  Sum_probs=36.8

Q ss_pred             cccccccccccccEEeC-CCCHhhhHHhHHHHhcc-CCCCCCccc
Q psy4141         301 RQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF-DRTCPMCRV  343 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llp-CgH~~fC~~C~~~~~~~-~~~CP~Cr~  343 (353)
                      +.|+.|.....+++..| |+|. ||.+|+...+.. ...||.|..
T Consensus       275 LkCplc~~Llrnp~kT~cC~~~-fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPMKTPCCGHT-FCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcccCccccch-HHHHHHhhhhhhccccCCCccc
Confidence            78999999999999885 7788 999999976665 889999977

>KOG3273|consensus

Probab=94.10  E-value=0.035  Score=49.98  Aligned_cols=125  Identities=18%  Similarity=0.168  Sum_probs=75.8

Q ss_pred             HHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhc---cCCCCCCCCCCCCCCCcceEEEEEec
Q psy4141          15 RAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFSALRAS---RKSGALSPLSPPTGVPGHVTIEVRVP   88 (353)
Q Consensus        15 ~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~---~~~g~~~~~~~~~~~~~~~t~~v~VP   88 (353)
                      -+..+.+|.+--..   +-|...-+-++.+++++...|...+-.|.--.+-   +....   .-...++....+++=.=-
T Consensus       100 ve~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALlrlddl---flesFEi~dVKtL~GdHl  176 (252)
T KOG3273|consen  100 VEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALLRLDDL---FLESFEIKDVKTLKGDHL  176 (252)
T ss_pred             HHhhhheeEeecccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHHhhhhh---hheeeeecccccccchhH
Confidence            34445555543222   2244444567788888888887664433210000   00000   000001111112222223


Q ss_pred             CCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHH
Q psy4141          89 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHII  146 (353)
Q Consensus        89 ~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~  146 (353)
                      .+.+|+|+||+|+|--.|...|.++|++.    +..|.|-|..+++..|+..|..+|.
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec----CceEEEeecchhhHHHHHhhHhhhc
Confidence            57799999999999999999999999865    3469999999999999999988775

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

Probab=94.08  E-value=0.038  Score=46.60  Aligned_cols=47  Identities=21%  Similarity=0.784  Sum_probs=40.5

Q ss_pred             cccccccccccccEEeC----CCCHhhhHHhHHHHhcc---CCCCCCcccccccc
Q psy4141         301 RQCYLCNDREVTHALIP----CGHNFFCSECAERTCDF---DRTCPMCRVPVNQA  348 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llp----CgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~~~  348 (353)
                      -+|.||.|...+.-++.    ||-+ .|..|-..+|..   .+.||+|+..+...
T Consensus        81 YeCnIC~etS~ee~FLKPneCCgY~-iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   81 YECNICKETSAEERFLKPNECCGYS-ICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             eeccCcccccchhhcCCcccccchH-HHHHHHHHHHHHcccCCCCCccccccccc
Confidence            57999999988877763    9999 999999999998   78999999988653

>KOG3002|consensus

Probab=94.07  E-value=0.027  Score=54.30  Aligned_cols=47  Identities=28%  Similarity=0.711  Sum_probs=38.8

Q ss_pred             CCCCCcccccccccccccEEeCC--CCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPC--GHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpC--gH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ...+-++|+||++....+++ .|  ||. .|..|-.++   ...||.||.++..
T Consensus        44 ~~~~lleCPvC~~~l~~Pi~-QC~nGHl-aCssC~~~~---~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   44 LDLDLLDCPVCFNPLSPPIF-QCDNGHL-ACSSCRTKV---SNKCPTCRLPIGN   92 (299)
T ss_pred             cchhhccCchhhccCcccce-ecCCCcE-ehhhhhhhh---cccCCcccccccc
Confidence            34456899999999988876 66  799 999999765   6799999999873

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

Probab=94.00  E-value=0.018  Score=43.52  Aligned_cols=46  Identities=22%  Similarity=0.577  Sum_probs=23.1

Q ss_pred             Cccccccccccc-c---cEE----eCCCCHhhhHHhHHHHhcc---C--------CCCCCcccccc
Q psy4141         300 SRQCYLCNDREV-T---HAL----IPCGHNFFCSECAERTCDF---D--------RTCPMCRVPVN  346 (353)
Q Consensus       300 ~~~C~IC~~~~~-~---~~l----lpCgH~~fC~~C~~~~~~~---~--------~~CP~Cr~~i~  346 (353)
                      +.+|.||+.... .   +.+    -.|++. |...|+.+|...   .        ..||.|+.+|+
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            478999998754 1   111    268888 999999999875   1        15999999875

>KOG0824|consensus

Probab=93.85  E-value=0.032  Score=53.19  Aligned_cols=50  Identities=20%  Similarity=0.505  Sum_probs=33.7

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      ...+|.||+.....++.++|+|..+---=--.++..+..|++||.+|..-
T Consensus         6 ~~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    6 KKKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             cCCcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            35789999999999999999999000000000111177799999999764

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=93.63  E-value=0.14  Score=53.10  Aligned_cols=52  Identities=17%  Similarity=0.201  Sum_probs=41.5

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~~   55 (353)
                      +||||.|.||+.++.-||+.|-|.+.  ..+|+|++ +|-.-+-|+..|..++.+
T Consensus       218 riigreGrnir~~e~~tgvd~iiddt--p~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       218 RIIGREGRNIRALETLTGVDLIIDDT--PEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             cccCCCcchHHHHHHHhCceEEEcCC--CCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            69999999999999999999998754  35667776 666667777777777653

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

Probab=93.61  E-value=0.048  Score=39.54  Aligned_cols=41  Identities=22%  Similarity=0.344  Sum_probs=29.5

Q ss_pred             CCcccccccccccccEE-eCCCCHhhhHHhHHHHhcc--CCCCCC
Q psy4141         299 GSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF--DRTCPM  340 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~--~~~CP~  340 (353)
                      -...|+|.+..+.+++. ..|+|. |..+.+..+...  ...||+
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            35889999999999988 499999 999999999944  678998

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

Probab=93.59  E-value=0.055  Score=37.75  Aligned_cols=42  Identities=29%  Similarity=0.768  Sum_probs=21.1

Q ss_pred             cccccccc--cccEEe--CCCCHhhhHHhHHHHhcc-CCCCCCccccc
Q psy4141         303 CYLCNDRE--VTHALI--PCGHNFFCSECAERTCDF-DRTCPMCRVPV  345 (353)
Q Consensus       303 C~IC~~~~--~~~~ll--pCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i  345 (353)
                      |++|.+..  .+..+.  +||+. .|..|..++.+. ...||-||.+.
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            55666654  222334  58899 999999999875 88999999875

>PRK12704 phosphodiesterase; Provisional

Probab=93.55  E-value=0.16  Score=52.89  Aligned_cols=53  Identities=17%  Similarity=0.162  Sum_probs=43.0

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~~~   56 (353)
                      +||||.|.||+.|+.-||+.|-|.+.  ..+|+++| ++-.-+-|+..+..++.+.
T Consensus       224 riigreGrnir~~e~~tgvd~iiddt--p~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        224 RIIGREGRNIRALETLTGVDLIIDDT--PEAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             ceeCCCcchHHHHHHHhCCeEEEcCC--CCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            69999999999999999999998854  35677887 5656567888888887654

>KOG3039|consensus

Probab=93.52  E-value=0.047  Score=50.65  Aligned_cols=48  Identities=25%  Similarity=0.414  Sum_probs=41.1

Q ss_pred             CCccccccccccccc----EEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         299 GSRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~----~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ..-.|+||.+...+.    +|-||||. ||++|++++......||+|-.++..
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            457899999987654    46799999 9999999999888899999988764

>PRK00106 hypothetical protein; Provisional

Probab=93.47  E-value=0.17  Score=52.56  Aligned_cols=52  Identities=21%  Similarity=0.218  Sum_probs=42.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~~   55 (353)
                      +||||.|.||+.|+.-||+.|-|.+.  ...|+|++ +|-.-+-|+..+..++.+
T Consensus       239 riIGreGrNir~~E~~tGvdliiddt--p~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        239 RIIGREGRNIRTLESLTGIDVIIDDT--PEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             ceeCCCcchHHHHHHHhCceEEEcCC--CCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            69999999999999999999998754  34566777 777777788888777663

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=93.40  E-value=0.051  Score=52.54  Aligned_cols=48  Identities=25%  Similarity=0.626  Sum_probs=37.2

Q ss_pred             CCccccccccccc--ccEE--eCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         299 GSRQCYLCNDREV--THAL--IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~~--~~~l--lpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      ++..|+.|++..-  +.-+  -|||.. .|..|...+.+. ...||.||...+.
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            4456999999642  2223  478999 999999999887 7899999987653

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

Probab=93.28  E-value=0.14  Score=44.01  Aligned_cols=35  Identities=31%  Similarity=0.336  Sum_probs=30.8

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEE
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV  115 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~  115 (353)
                      .+-+|.|-.+.-|.+||++|.++++|.++||=.-.
T Consensus        76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~  110 (145)
T cd02410          76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPK  110 (145)
T ss_pred             CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeE
Confidence            45688888899999999999999999999996654

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.19  E-value=0.048  Score=41.19  Aligned_cols=35  Identities=26%  Similarity=0.302  Sum_probs=30.6

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceE
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI  114 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I  114 (353)
                      .....+.+..+..|.||||+|+|++.||.-.+..+
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            36788999999999999999999999998876555

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=93.09  E-value=0.11  Score=56.95  Aligned_cols=51  Identities=22%  Similarity=0.180  Sum_probs=42.5

Q ss_pred             eeecCCCchHHHHHHHcCce-EEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTY-IKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~-I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~   54 (353)
                      .|||.+|.+||.|.++||+. |++.+.  ..+.+..-+.+.+++|+..|..+..
T Consensus       698 ~vIG~GGktIk~I~eetg~~~Idi~dd--g~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        698 MIIGSGGKKVKSIIEETGVEAIDTQDD--GTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             HHhcCCchhHHHHHHHHCCCccCcCCC--eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            37999999999999999999 887753  3555555688999999999988865

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

Probab=93.00  E-value=0.038  Score=59.72  Aligned_cols=49  Identities=22%  Similarity=0.608  Sum_probs=38.2

Q ss_pred             CCCCccccccccccc--ccE-----EeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         297 ISGSRQCYLCNDREV--THA-----LIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~--~~~-----llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      .....+|.||+....  +..     .--|.|. |...|+-+|...  ...||+||..++
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            346789999998643  111     2349999 999999999988  678999998775

>KOG4369|consensus

Probab=92.96  E-value=0.2  Score=55.50  Aligned_cols=67  Identities=21%  Similarity=0.196  Sum_probs=57.0

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC----CCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~----~~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ....+.+|-....+|||++|.+|+.++.-||+.|.+.+    ...||.+.+.|.|+.+..|...|.-.|.+
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence            34568889999999999999999999999999997654    13478999999999999999988766654

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

Probab=92.70  E-value=0.19  Score=36.41  Aligned_cols=34  Identities=29%  Similarity=0.481  Sum_probs=27.8

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceE
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI  114 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I  114 (353)
                      ....+.+.....|.+||++|++|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4555666666789999999999999999998555

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.

>KOG2874|consensus

Probab=92.63  E-value=0.21  Score=47.26  Aligned_cols=51  Identities=24%  Similarity=0.434  Sum_probs=45.3

Q ss_pred             cceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          93 GLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        93 G~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      -++||++|.|+|.|+-.|.|+|.+..    .+|.+.|....++.++..+++-+.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG----~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG----NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC----cEEEeecCcchHHHHHHHHHHHHhc
Confidence            47999999999999999999998653    4799999999999999999887765

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

Probab=92.59  E-value=0.14  Score=39.43  Aligned_cols=30  Identities=30%  Similarity=0.499  Sum_probs=27.0

Q ss_pred             eCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         316 IPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       316 lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      --|.|. |...|+.+|+.....||++|++..
T Consensus        52 G~CnHa-FH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          52 GVCNHA-FHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             EecchH-HHHHHHHHHHhhCCCCCCCCceeE
Confidence            469999 999999999999999999998753

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=92.53  E-value=0.26  Score=45.96  Aligned_cols=52  Identities=19%  Similarity=0.225  Sum_probs=42.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      ++||++|.+|+.|.+++++.|.+-..  .++-+-.-+.+++.+|++.|..+-++
T Consensus       158 ~lig~~g~~i~~l~~~~~~~I~ig~N--G~VwI~~~~~~~~~~a~~~I~~~e~~  209 (235)
T PRK04163        158 RVIGKKGSMINMLKEETGCDIIVGQN--GRIWIKGPDEEDEEIAIEAIKKIERE  209 (235)
T ss_pred             hhcCCCChhHhhhhhhhCcEEEEcCC--cEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence            47999999999999999999998654  35555556777999999999887654

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=92.14  E-value=0.16  Score=54.65  Aligned_cols=52  Identities=19%  Similarity=0.195  Sum_probs=41.9

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .+||.+|.+||.|.++||+.|++.+.  ..+.+..-..+.+++|++.|..+..+
T Consensus       567 ~vIG~gg~~ik~I~~~~~~~idi~d~--G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        567 DVIGPGGKTIREITEETGAKIDIEDD--GTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             HHhcCCchhHHHHHHHHCCccccCCC--ceEEEEcccHHHHHHHHHHHHHhccc
Confidence            47999999999999999999887543  34444445789999999999888753

>KOG1814|consensus

Probab=92.01  E-value=0.081  Score=52.44  Aligned_cols=34  Identities=24%  Similarity=0.774  Sum_probs=28.7

Q ss_pred             Ccccccccccccc---cEEeCCCCHhhhHHhHHHHhcc
Q psy4141         300 SRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDF  334 (353)
Q Consensus       300 ~~~C~IC~~~~~~---~~llpCgH~~fC~~C~~~~~~~  334 (353)
                      ...|.||++...-   ..++||+|. ||..|+..+..-
T Consensus       184 lf~C~ICf~e~~G~~c~~~lpC~Hv-~Ck~C~kdY~~~  220 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHCFKFLPCSHV-FCKSCLKDYFTI  220 (445)
T ss_pred             cccceeeehhhcCcceeeecccchH-HHHHHHHHHHHH
Confidence            4789999998754   567999999 999999998764

>KOG1588|consensus

Probab=92.00  E-value=0.28  Score=46.11  Aligned_cols=26  Identities=23%  Similarity=0.276  Sum_probs=23.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVR   27 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~   27 (353)
                      +|+|.+|.++|+|+++|+|+|-|-.+
T Consensus       111 RILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen  111 RILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             ccccCCcchHHHHHHHHCCeEEEecC
Confidence            69999999999999999999998644

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=91.98  E-value=0.21  Score=42.96  Aligned_cols=36  Identities=25%  Similarity=0.320  Sum_probs=32.2

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      ..+-+.|+...+|..||++|++|+.|++..|-+|.+
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdV   67 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIEL   67 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEE
Confidence            567788899999999999999999999999988854

>KOG1493|consensus

Probab=91.98  E-value=0.074  Score=40.55  Aligned_cols=29  Identities=31%  Similarity=0.675  Sum_probs=25.2

Q ss_pred             CCCCHhhhHHhHHHHhcc---CCCCCCcccccc
Q psy4141         317 PCGHNFFCSECAERTCDF---DRTCPMCRVPVN  346 (353)
Q Consensus       317 pCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~  346 (353)
                      -|.|. |-..|+.+|...   ...||+||+.+.
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            69999 999999999887   568999998653

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=91.97  E-value=1.1  Score=40.66  Aligned_cols=71  Identities=11%  Similarity=0.182  Sum_probs=57.8

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCCCCc
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVT  154 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~~~~  154 (353)
                      ...+.++....-++...+|..++.|....|++|.+..+.  ..|.|+|+...++.+...|.+++..-.-.-++
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~--~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~   97 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRSE--NRIRITGTKSTAEYIEASINEILSNIRTEEID   97 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecCC--cEEEEEccHHHHHHHHHHHHHHHhhcEEEEEe
Confidence            445666788889999999999999989999999876544  37999999999999999999988874333333

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

Probab=91.95  E-value=0.23  Score=50.38  Aligned_cols=67  Identities=24%  Similarity=0.252  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          41 DVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        41 ~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      ....|..+|.+.++.+-.            ....-.+.+.....+.||...++.+|||+|.+|++|.++.|-+|.+-..
T Consensus       458 ~~~~a~~~i~~~i~r~~p------------~~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         458 ALKLAEEEIEREIKRYLP------------GDVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             hhHHHHHHHHHHHHHhCC------------CCceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            355677777777765510            0000011223557789999999999999999999999999999966443

>KOG2932|consensus

Probab=91.57  E-value=0.056  Score=51.68  Aligned_cols=45  Identities=36%  Similarity=0.803  Sum_probs=30.7

Q ss_pred             cccccccccccc-cEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         301 RQCYLCNDREVT-HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       301 ~~C~IC~~~~~~-~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      ..|.-|--.... .-++||.|. ||.+|+..-  ..+.||.|-.+|..+
T Consensus        91 HfCd~Cd~PI~IYGRmIPCkHv-FCl~CAr~~--~dK~Cp~C~d~VqrI  136 (389)
T KOG2932|consen   91 HFCDRCDFPIAIYGRMIPCKHV-FCLECARSD--SDKICPLCDDRVQRI  136 (389)
T ss_pred             EeecccCCcceeeecccccchh-hhhhhhhcC--ccccCcCcccHHHHH
Confidence            456556433222 224799999 999998874  257999998776543

>PF04641 Rtf2: Rtf2 RING-finger

Probab=91.24  E-value=0.19  Score=47.51  Aligned_cols=48  Identities=23%  Similarity=0.480  Sum_probs=38.2

Q ss_pred             CCCcccccccccc----cccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~----~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      .....|+|....+    .-+++.||||. |+..++..+. ....||+|-.++..
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V-~s~~alke~k-~~~~Cp~c~~~f~~  162 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCV-FSEKALKELK-KSKKCPVCGKPFTE  162 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCE-eeHHHHHhhc-ccccccccCCcccc
Confidence            4567899988765    33456799998 9999999994 35679999999875

>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=90.37  E-value=0.11  Score=36.07  Aligned_cols=47  Identities=26%  Similarity=0.693  Sum_probs=27.6

Q ss_pred             ccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141         302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR  350 (353)
Q Consensus       302 ~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r  350 (353)
                      -|.-|.-...  -++.|.....|..|+..+......||+|..++...+|
T Consensus         4 nCKsCWf~~k--~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtkir   50 (50)
T PF03854_consen    4 NCKSCWFANK--GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTKIR   50 (50)
T ss_dssp             ---SS-S--S--SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----S-
T ss_pred             cChhhhhcCC--CeeeecchhHHHHHHHHHhccccCCCcccCcCccccC
Confidence            4666765443  4677985559999999999889999999998876554

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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=90.35  E-value=0.24  Score=37.85  Aligned_cols=35  Identities=29%  Similarity=0.478  Sum_probs=29.6

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEE
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV  115 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~  115 (353)
                      ..+.+.|..+..|.+|||+|++++.||--++..+.
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            34667888899999999999999999988876654

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.

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=90.13  E-value=0.29  Score=42.66  Aligned_cols=48  Identities=23%  Similarity=0.567  Sum_probs=36.5

Q ss_pred             CCCcccccccccccccEEeCCCCH----hhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHN----FFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~----~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      ..+..|.||++.... ...||.-.    ....+|+++|...  ...|++|+.++.
T Consensus         6 ~~~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~   59 (162)
T PHA02825          6 LMDKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN   59 (162)
T ss_pred             CCCCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence            456899999998653 34587743    1467999999988  678999998763

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=90.09  E-value=0.34  Score=49.52  Aligned_cols=119  Identities=9%  Similarity=0.017  Sum_probs=78.1

Q ss_pred             eecCCCchHHHHHHHcCceEEe--cCCCCcCeE-EEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCc
Q psy4141           3 KISRSGCKIKALRAKTNTYIKT--PVRGEEPVF-VVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPG   79 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~i--p~~~e~~vv-~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~   79 (353)
                      |-||+.-++.+|++...+-+.+  -......+. .+.|..-+..++...+   .                     .+-| 
T Consensus       394 l~gkkngK~TrIm~~v~c~~~~~i~~~~gs~~~~~~~g~~~~F~k~~~~~---~---------------------~EFp-  448 (657)
T COG5166         394 LRGKKNGKATRIMKGVSCSELSSIVSSTGSIVETNGIGEKMSFSKKLSIP---P---------------------TEFP-  448 (657)
T ss_pred             hccccCcchhhhhhhcccceeeEEEecCCcEEEEeccCcchhhHHHhcCC---c---------------------ccCc-
Confidence            3477777788999888887553  222222322 2335554444322221   1                     1123 


Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHH---HHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPD---SVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e---~V~~A~~~I~~~i~~  147 (353)
                       ..+.+.||...|..|||-||..|++++...++.|++...      ...+-|.|.-+..   ++.-++.-+.++|.+
T Consensus       449 -ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~  524 (657)
T COG5166         449 -AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ  524 (657)
T ss_pred             -hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence             567889999999999999999999999999999987543      1123477777644   455577777788875

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

Probab=89.51  E-value=0.43  Score=48.87  Aligned_cols=33  Identities=36%  Similarity=0.405  Sum_probs=29.6

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCce
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY  113 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~  113 (353)
                      .+-+|.|-.+.=|+||||+|++.++|.++||-.
T Consensus        99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~  131 (637)
T COG1782          99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWA  131 (637)
T ss_pred             CCceEEEEecCCceEEecCchHHHHHHHHhCCc
Confidence            556888999999999999999999999999844

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=89.45  E-value=0.22  Score=37.87  Aligned_cols=34  Identities=26%  Similarity=0.458  Sum_probs=28.8

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceE
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI  114 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I  114 (353)
                      ....+.+....-|.|||++|++|++|.+..+-.+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            4467788889999999999999999988876555

; 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 ....

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=89.39  E-value=0.19  Score=42.66  Aligned_cols=33  Identities=27%  Similarity=0.637  Sum_probs=26.7

Q ss_pred             Ccccccccccccc---cEEeCCC------CHhhhHHhHHHHhc
Q psy4141         300 SRQCYLCNDREVT---HALIPCG------HNFFCSECAERTCD  333 (353)
Q Consensus       300 ~~~C~IC~~~~~~---~~llpCg------H~~fC~~C~~~~~~  333 (353)
                      ..+|.||++...+   .+.++|+      |. ||..|+++|..
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkm-fc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKM-FCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHH-HHHHHHHHHHh
Confidence            4789999998765   5557888      66 99999999943

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

>KOG2874|consensus

Probab=89.25  E-value=0.65  Score=44.01  Aligned_cols=51  Identities=20%  Similarity=0.296  Sum_probs=45.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      ++||.+|.++|+|+--|+|+|-+.    ...|.+.|.-..+..+++-+.+.+...
T Consensus       162 RLiGpng~TLKAlelLT~CYilVq----G~TVsaiGpfkGlkevr~IV~DcM~Ni  212 (356)
T KOG2874|consen  162 RLIGPNGSTLKALELLTNCYILVQ----GNTVSAIGPFKGLKEVRKIVEDCMKNI  212 (356)
T ss_pred             HhcCCCchhHHHHHHHhhcEEEee----CcEEEeecCcchHHHHHHHHHHHHhcc
Confidence            689999999999999999999987    456778899999999999999987754

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

Probab=89.13  E-value=0.34  Score=35.39  Aligned_cols=23  Identities=13%  Similarity=0.169  Sum_probs=20.5

Q ss_pred             eeecCCCchHHHHHHHcCceEEe
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKT   24 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~i   24 (353)
                      ..|||+|.+|+.+++-++-+|++
T Consensus        38 ~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          38 LAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             eeECCCCHHHHHHHHHHCCCeEE
Confidence            47999999999999999988764

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.

>PRK13764 ATPase; Provisional

Probab=89.06  E-value=0.43  Score=50.47  Aligned_cols=67  Identities=24%  Similarity=0.233  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          41 DVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        41 ~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      .-..|.++|.+.++.+-.       +.     ..-.+.......|.||.+.++.+|||+|.+|++|.++.|..|.+-..
T Consensus       453 ~~~~~~~~~~~~~~~~~~-------~~-----~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        453 VWRLAEKEIEREIKRYLP-------GP-----VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             HHHHHHHHHHHHHHHhcC-------Cc-----eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            345577777777776521       00     00011234667899999999999999999999999999999976443

>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=88.71  E-value=0.16  Score=47.07  Aligned_cols=46  Identities=26%  Similarity=0.704  Sum_probs=34.4

Q ss_pred             CCccccccccc-cc--ccEE--eC-CCCHhhhHHhHHHHhcc-CCCCC--Cccccc
Q psy4141         299 GSRQCYLCNDR-EV--THAL--IP-CGHNFFCSECAERTCDF-DRTCP--MCRVPV  345 (353)
Q Consensus       299 ~~~~C~IC~~~-~~--~~~l--lp-CgH~~fC~~C~~~~~~~-~~~CP--~Cr~~i  345 (353)
                      .++.|+||... +-  +..+  -| |-|. +|..|..++... ...||  -|..-+
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            45799999864 22  2222  25 9999 999999999888 77899  786543

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

Probab=88.70  E-value=0.33  Score=36.54  Aligned_cols=35  Identities=31%  Similarity=0.378  Sum_probs=27.2

Q ss_pred             EEEEEecCCC-----ccceeccCChHHHHHHHHh-CceEEc
Q psy4141          82 TIEVRVPYKV-----VGLVVGPKGATIKRIQHQT-NTYIVT  116 (353)
Q Consensus        82 t~~v~VP~~~-----vG~IIGkgG~tIk~Iq~~T-ga~I~i  116 (353)
                      ...+.|-...     +|..||++|..||.|.++. |-+|.+
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv   44 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDV   44 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence            3456666666     9999999999999999999 888854

>KOG3273|consensus

Probab=87.67  E-value=0.37  Score=43.54  Aligned_cols=49  Identities=16%  Similarity=0.150  Sum_probs=44.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~   54 (353)
                      +|+||+|.+--.|+.-|.++|.+.    +.-+.|-|.-+++..|+..|..++-
T Consensus       182 RiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  182 RIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HhhcCCCcceeeeeccceeEEEec----CceEEEeecchhhHHHHHhhHhhhc
Confidence            589999999999999999999988    4457888999999999999999865

>KOG1941|consensus

Probab=87.59  E-value=0.22  Score=49.10  Aligned_cols=46  Identities=28%  Similarity=0.626  Sum_probs=36.5

Q ss_pred             Cccccccccccc----ccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         300 SRQCYLCNDREV----THALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       300 ~~~C~IC~~~~~----~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      +.-|-.|-+..-    .--.+||.|. |...|+..+.++  .+.||-||+-..
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHI-fH~rCl~e~L~~n~~rsCP~CrklrS  416 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHI-FHLRCLQEILENNGTRSCPNCRKLRS  416 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHH-HHHHHHHHHHHhCCCCCCccHHHHHh
Confidence            578999988642    2224899999 999999999988  789999995433

>KOG4362|consensus

Probab=87.39  E-value=0.17  Score=53.62  Aligned_cols=49  Identities=18%  Similarity=0.586  Sum_probs=41.8

Q ss_pred             CCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCcccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN  346 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~  346 (353)
                      +....+|.||+.....++++.|-|. ||..|+......   ...||+|+..+.
T Consensus        18 ~~k~lEc~ic~~~~~~p~~~kc~~~-~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   18 MQKILECPICLEHVKEPSLLKCDHI-FLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             HhhhccCCceeEEeeccchhhhhHH-HHhhhhhceeeccCccccchhhhhhhh
Confidence            3456899999999999999999999 999999987776   457999996654

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=87.30  E-value=0.66  Score=39.92  Aligned_cols=35  Identities=20%  Similarity=0.302  Sum_probs=31.0

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      .+-+.|....+|..||++|.+|+.|++..|-+|.+
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV   68 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL   68 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence            66678889999999999999999999999988853

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.

>KOG1428|consensus

Probab=86.47  E-value=0.46  Score=53.87  Aligned_cols=48  Identities=23%  Similarity=0.681  Sum_probs=38.1

Q ss_pred             CCcccccccccc---cccEEeCCCCHhhhHHhHHHHhccCC----------CCCCccccccc
Q psy4141         299 GSRQCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDR----------TCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~~~----------~CP~Cr~~i~~  347 (353)
                      .+..|+||+...   .-+..+.|+|. |...|..++++..+          .||+|..+|..
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~C~Hi-FHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHI-FHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecCCccc-hhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            458899999864   33456899999 99999999888622          69999988765

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=86.16  E-value=1.6  Score=40.67  Aligned_cols=56  Identities=27%  Similarity=0.368  Sum_probs=42.7

Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHH-HHHHHHHH
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDS-VEIARQEI  141 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~-V~~A~~~I  141 (353)
                      .-+.|+...|.++||++|..++-|.+.|+|.|.+-.   ...|=|.|..+. ...|.+.|
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---NG~IWV~~~~~~~e~~~~~aI  204 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---NGRIWVDGENESLEELAIEAI  204 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---CCEEEecCCCcchHHHHHHHH
Confidence            558899999999999999999999999999998653   345777776553 33333333

>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter

Probab=86.16  E-value=5.5  Score=41.94  Aligned_cols=111  Identities=23%  Similarity=0.315  Sum_probs=67.0

Q ss_pred             CchHHHHHHHcC--ceEE---------ecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCC
Q psy4141           8 GCKIKALRAKTN--TYIK---------TPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS   72 (353)
Q Consensus         8 G~~Ik~I~~~Tg--a~I~---------ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~   72 (353)
                      |.+|+++.....  +.|.         .|..+    +.+++.+.|++++++++.+.+-..+.+.        .       
T Consensus       232 GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~~~~--------~-------  296 (562)
T TIGR03802       232 GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEVQEV--------E-------  296 (562)
T ss_pred             CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCccCCc--------c-------
Confidence            778888876553  3332         12222    3478899999999987766543221110        0       


Q ss_pred             CCCCCCcceEEEEEecCCCccceeccCChHHHHHH------HHhCceEE-cCCCC------------CCCeEEEEcCHHH
Q psy4141          73 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQ------HQTNTYIV-TPSRD------------KEPVFEVTGAPDS  133 (353)
Q Consensus        73 ~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq------~~Tga~I~-ip~~~------------~e~~v~I~G~~e~  133 (353)
                       ..+.+ ....++.+|++   .++||   +|+++.      ++.|+.|. +...+            ..+.+.+.|++++
T Consensus       297 -~~~~~-~~~e~VV~~~S---~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~  368 (562)
T TIGR03802       297 -GLDVP-METKDVVLTNK---EYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQD  368 (562)
T ss_pred             -ccCCc-eEEEEEEECCc---ccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHH
Confidence             00111 12445556654   66766   888886      36788883 32211            2368999999999


Q ss_pred             HHHHHHHH
Q psy4141         134 VEIARQEI  141 (353)
Q Consensus       134 V~~A~~~I  141 (353)
                      ++++.+.+
T Consensus       369 l~~~~~~l  376 (562)
T TIGR03802       369 VDRAAKQL  376 (562)
T ss_pred             HHHHHHHc
Confidence            99987764

All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).

>PRK12705 hypothetical protein; Provisional

Probab=85.99  E-value=0.8  Score=47.45  Aligned_cols=51  Identities=16%  Similarity=0.099  Sum_probs=36.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEe-cCHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVT-GRKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~-G~~e~v~~Ak~~I~~i~~   54 (353)
                      +||||.|.||+.++..||+.|-|.+..  .+|++. =.+..-+.|+..+..++.
T Consensus       212 riIGreGrNir~~E~~tGvdliiddtp--~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        212 RIIGREGRNIRAFEGLTGVDLIIDDTP--EAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             cccCccchhHHHHHHhhCCceEecCCc--cchhhcccCccchHHHHHHHHHHHh
Confidence            699999999999999999999987553  333444 345555556666655544

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

Probab=85.73  E-value=1.2  Score=40.68  Aligned_cols=27  Identities=22%  Similarity=0.263  Sum_probs=24.2

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCC
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGE   29 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e   29 (353)
                      |||..|.+.|+|++.++|+|-|-..+.
T Consensus       168 liGPRG~Tlk~le~~s~akIaIRG~gs  194 (269)
T COG5176         168 LIGPRGSTLKQLERISRAKIAIRGSGS  194 (269)
T ss_pred             EecCCcchHHHHHHHhCCeEEEecccc
Confidence            799999999999999999999875553

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

Probab=85.40  E-value=1  Score=34.95  Aligned_cols=36  Identities=17%  Similarity=0.202  Sum_probs=29.2

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      ..++|.|-...-|.|||++|++|++|++.-.-...+
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            347788888899999999999999998876544433

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.

>PHA02862 5L protein; Provisional

Probab=85.03  E-value=0.87  Score=39.12  Aligned_cols=45  Identities=24%  Similarity=0.622  Sum_probs=35.0

Q ss_pred             cccccccccccccEEeCCCCH----hhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         301 RQCYLCNDREVTHALIPCGHN----FFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpCgH~----~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      ..|-||++...+. .-||.-.    ....+|+.+|...  ...|++|+.++.
T Consensus         3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~   53 (156)
T PHA02862          3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN   53 (156)
T ss_pred             CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence            5799999987554 4688742    2567999999987  678999998764

>KOG2930|consensus

Probab=84.68  E-value=0.7  Score=37.35  Aligned_cols=28  Identities=25%  Similarity=0.481  Sum_probs=25.6

Q ss_pred             eCCCCHhhhHHhHHHHhccCCCCCCcccc
Q psy4141         316 IPCGHNFFCSECAERTCDFDRTCPMCRVP  344 (353)
Q Consensus       316 lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~  344 (353)
                      --|.|. |..-|+.+|......||+|.+.
T Consensus        79 G~CNHa-FH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   79 GVCNHA-FHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             eecchH-HHHHHHHHHHhhcCcCCCcCcc
Confidence            479999 9999999999999999999765

>PRK00468 hypothetical protein; Provisional

Probab=84.21  E-value=0.65  Score=35.59  Aligned_cols=16  Identities=38%  Similarity=0.466  Sum_probs=14.3

Q ss_pred             eeecCCCchHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAK   17 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~   17 (353)
                      +||||+|.+|++||.-
T Consensus        43 rVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         43 KVIGKQGRIAKAIRTV   58 (75)
T ss_pred             ceecCCChhHHHHHHH
Confidence            6999999999999953

>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=84.14  E-value=0.35  Score=38.68  Aligned_cols=33  Identities=30%  Similarity=0.723  Sum_probs=26.0

Q ss_pred             CCCCcccccccccccccEE--eCCCCHhhhHHhHHH
Q psy4141         297 ISGSRQCYLCNDREVTHAL--IPCGHNFFCSECAER  330 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~l--lpCgH~~fC~~C~~~  330 (353)
                      +.+...|.+|.....+.++  .||||. |+..|+++
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            3456789999999876554  699998 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 [].

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

Probab=84.08  E-value=1.1  Score=44.27  Aligned_cols=48  Identities=23%  Similarity=0.526  Sum_probs=32.7

Q ss_pred             CCcccccccccccccEEe-CC---------------------CCHhhhHHhHHHHhcc-------------CCCCCCccc
Q psy4141         299 GSRQCYLCNDREVTHALI-PC---------------------GHNFFCSECAERTCDF-------------DRTCPMCRV  343 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~ll-pC---------------------gH~~fC~~C~~~~~~~-------------~~~CP~Cr~  343 (353)
                      +...|.-|+....+..+. .|                     .-+ -|.+|+-+|...             ...||.||+
T Consensus       270 e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPm-WC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa  348 (358)
T PF10272_consen  270 ELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPM-WCLECMGKWFASRQDQQHPETWLSGKCPCPTCRA  348 (358)
T ss_pred             ccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccch-HHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcc
Confidence            446677787777666654 23                     222 478999998764             336999999


Q ss_pred             cccc
Q psy4141         344 PVNQ  347 (353)
Q Consensus       344 ~i~~  347 (353)
                      .+.-
T Consensus       349 ~FCi  352 (358)
T PF10272_consen  349 KFCI  352 (358)
T ss_pred             ccee
Confidence            8753

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

>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ]

Probab=83.91  E-value=0.33  Score=48.14  Aligned_cols=46  Identities=41%  Similarity=0.889  Sum_probs=0.0

Q ss_pred             Cccccccccc-------------------ccccEEeCCCCHhhhHHhHHHHhcc----------CCCCCCccccccc
Q psy4141         300 SRQCYLCNDR-------------------EVTHALIPCGHNFFCSECAERTCDF----------DRTCPMCRVPVNQ  347 (353)
Q Consensus       300 ~~~C~IC~~~-------------------~~~~~llpCgH~~fC~~C~~~~~~~----------~~~CP~Cr~~i~~  347 (353)
                      .++|++|+..                   ..+.++.||||.  |.+=..++|.+          ...||+|-.++..
T Consensus       328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv--~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g  402 (416)
T PF04710_consen  328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHV--CSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDG  402 (416)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             cccCCCccccCCceeEeeccccceeecCCCCceeecccccc--cchhhhhhhhcCCCCCCcccccccCCcccCcccC
Confidence            6899999863                   245567899996  55544555554          2479999888864

; PDB: 3EGB_B 3EGA_A.

>KOG3579|consensus

Probab=83.83  E-value=0.8  Score=43.51  Aligned_cols=34  Identities=26%  Similarity=0.708  Sum_probs=29.6

Q ss_pred             CcccccccccccccEEeCCC----CHhhhHHhHHHHhcc
Q psy4141         300 SRQCYLCNDREVTHALIPCG----HNFFCSECAERTCDF  334 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~llpCg----H~~fC~~C~~~~~~~  334 (353)
                      .+.|.+|.++..+.-++.|-    |. ||..|-.....+
T Consensus       268 pLcCTLC~ERLEDTHFVQCPSVp~HK-FCFPCSResIK~  305 (352)
T KOG3579|consen  268 PLCCTLCHERLEDTHFVQCPSVPSHK-FCFPCSRESIKQ  305 (352)
T ss_pred             ceeehhhhhhhccCceeecCCCcccc-eecccCHHHHHh
Confidence            48999999999999999995    88 999998876554

>KOG3842|consensus

Probab=83.56  E-value=0.8  Score=44.10  Aligned_cols=46  Identities=35%  Similarity=0.777  Sum_probs=33.9

Q ss_pred             CCcccccccccc-------------------cccEEeCCCCHhhhHHhHHHHhcc----------CCCCCCcccccc
Q psy4141         299 GSRQCYLCNDRE-------------------VTHALIPCGHNFFCSECAERTCDF----------DRTCPMCRVPVN  346 (353)
Q Consensus       299 ~~~~C~IC~~~~-------------------~~~~llpCgH~~fC~~C~~~~~~~----------~~~CP~Cr~~i~  346 (353)
                      .+++|++|+..-                   .+.++-||||  +|.+=-..+|.+          ...||+|-..+.
T Consensus       340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGH--v~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~  414 (429)
T KOG3842|consen  340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGH--VCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA  414 (429)
T ss_pred             ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCccc--ccchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence            468999998742                   3445679999  577777777776          346999987764

>PRK02821 hypothetical protein; Provisional

Probab=83.50  E-value=0.73  Score=35.49  Aligned_cols=19  Identities=37%  Similarity=0.441  Sum_probs=16.0

Q ss_pred             eeecCCCchHHHHHHHcCc
Q psy4141           2 KKISRSGCKIKALRAKTNT   20 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga   20 (353)
                      +||||+|.+|++||.--.+
T Consensus        44 rVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         44 KVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             ceeCCCCchHHHHHHHHHH
Confidence            6999999999999965444

>KOG4445|consensus

Probab=83.31  E-value=0.46  Score=45.42  Aligned_cols=45  Identities=24%  Similarity=0.599  Sum_probs=33.8

Q ss_pred             cccccccccccc---cEEeCCCCHhhhHHhHHHHhcc-----------------------CCCCCCcccccc
Q psy4141         301 RQCYLCNDREVT---HALIPCGHNFFCSECAERTCDF-----------------------DRTCPMCRVPVN  346 (353)
Q Consensus       301 ~~C~IC~~~~~~---~~llpCgH~~fC~~C~~~~~~~-----------------------~~~CP~Cr~~i~  346 (353)
                      ..|+||+--+.+   ....+|-|. |...|+.+++..                       ...||+||.+|.
T Consensus       116 gqCvICLygfa~~~~ft~T~C~Hy-~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~  186 (368)
T KOG4445|consen  116 GQCVICLYGFASSPAFTVTACDHY-MHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK  186 (368)
T ss_pred             CceEEEEEeecCCCceeeehhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence            568888876654   335799999 999999887651                       236999999874

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

Probab=83.13  E-value=0.72  Score=35.42  Aligned_cols=16  Identities=38%  Similarity=0.567  Sum_probs=14.4

Q ss_pred             eeecCCCchHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAK   17 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~   17 (353)
                      +||||+|.+|++||.-
T Consensus        43 kvIGk~GRti~AIRTl   58 (76)
T COG1837          43 KVIGKQGRTIQAIRTL   58 (76)
T ss_pred             ceecCCChhHHHHHHH
Confidence            6999999999999954

>PHA03096 p28-like protein; Provisional

Probab=82.76  E-value=0.75  Score=44.17  Aligned_cols=43  Identities=14%  Similarity=0.125  Sum_probs=30.8

Q ss_pred             cccccccccccc--------cEEeCCCCHhhhHHhHHHHhcc---C---CCCCCcccc
Q psy4141         301 RQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDF---D---RTCPMCRVP  344 (353)
Q Consensus       301 ~~C~IC~~~~~~--------~~llpCgH~~fC~~C~~~~~~~---~---~~CP~Cr~~  344 (353)
                      ..|-||++....        ..+-.|-|. ||..|+..|...   .   +.||.|+..
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~-fc~~ci~~wr~~~~~~e~~~~c~~~~~~  235 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHE-FNIFCIKIWMTESLYKETEPENRRLNTV  235 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcH-HHHHHHHHHHHhhhhcccCccccchhhH
Confidence            689999997532        234579999 999999988765   3   345555443

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=82.44  E-value=3.4  Score=44.09  Aligned_cols=36  Identities=33%  Similarity=0.374  Sum_probs=31.5

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      .+-+|.|-.+.-|.||||+|.++++|-++||=.-.+
T Consensus        93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~  128 (630)
T TIGR03675        93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKV  128 (630)
T ss_pred             CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeE
Confidence            557888989999999999999999999999966543

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.

>KOG0827|consensus

Probab=82.18  E-value=0.78  Score=45.37  Aligned_cols=28  Identities=32%  Similarity=0.929  Sum_probs=24.1

Q ss_pred             CCCCHhhhHHhHHHHhcc---CCCCCCccccc
Q psy4141         317 PCGHNFFCSECAERTCDF---DRTCPMCRVPV  345 (353)
Q Consensus       317 pCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i  345 (353)
                      .|||. |...|+.+|.+.   .+.||+|+..+
T Consensus        25 ~cGhi-fh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen   25 TCGHI-FHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             chhhH-HHHHHHHHHHccCCccCCCCceeecc
Confidence            59999 999999999998   35899999443

>PRK03818 putative transporter; Validated

Probab=81.67  E-value=9.8  Score=40.01  Aligned_cols=111  Identities=17%  Similarity=0.254  Sum_probs=67.8

Q ss_pred             CchHHHHHHHcCceEEe-----------cCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCC
Q psy4141           8 GCKIKALRAKTNTYIKT-----------PVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS   72 (353)
Q Consensus         8 G~~Ik~I~~~Tga~I~i-----------p~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~   72 (353)
                      |.++++++......+.+           |..+    +.+++.+.|++++++++...+-...+..            .   
T Consensus       218 GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~~~------------~---  282 (552)
T PRK03818        218 GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVDTS------------L---  282 (552)
T ss_pred             CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccCcc------------c---
Confidence            77899988876654442           2221    3478999999999877765543211100            0   


Q ss_pred             CCCCCCcceEEEEEecCCCccceeccCChHHHHH--HHHhCceEE-cCCC--------C----CCCeEEEEcCHHHHHHH
Q psy4141          73 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRI--QHQTNTYIV-TPSR--------D----KEPVFEVTGAPDSVEIA  137 (353)
Q Consensus        73 ~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~I--q~~Tga~I~-ip~~--------~----~e~~v~I~G~~e~V~~A  137 (353)
                      ...+ .......+.+|..   .++||   +|+++  +++.|+.|. +...        +    ..+.+.+.|+++++++.
T Consensus       283 ~~~~-~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l  355 (552)
T PRK03818        283 STRG-TDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAV  355 (552)
T ss_pred             cccC-cceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHH
Confidence            0000 1124455555554   67766   77877  577888873 3211        1    13589999999999997


Q ss_pred             HHH
Q psy4141         138 RQE  140 (353)
Q Consensus       138 ~~~  140 (353)
                      .+.
T Consensus       356 ~~~  358 (552)
T PRK03818        356 ANV  358 (552)
T ss_pred             HHH
Confidence            774

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

Probab=80.83  E-value=1.6  Score=35.64  Aligned_cols=31  Identities=26%  Similarity=0.563  Sum_probs=25.8

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCc
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNT  112 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga  112 (353)
                      .++|.|-...-|.|||++|++|++|++....
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~   92 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK   92 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence            3677777888999999999999999877643

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.

>KOG0825|consensus

Probab=80.24  E-value=1.7  Score=46.58  Aligned_cols=51  Identities=20%  Similarity=0.333  Sum_probs=34.5

Q ss_pred             Ccccccccccccc----cEEeC---CCCHhhhHHhHHHHhcc------CCCCCCcccccccceec
Q psy4141         300 SRQCYLCNDREVT----HALIP---CGHNFFCSECAERTCDF------DRTCPMCRVPVNQAMRI  351 (353)
Q Consensus       300 ~~~C~IC~~~~~~----~~llp---CgH~~fC~~C~~~~~~~------~~~CP~Cr~~i~~~~ri  351 (353)
                      ...|.+|...+..    .-..|   |+|. +|..|+..|..+      ...|++|..-|..+-|+
T Consensus        96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~-~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~  159 (1134)
T KOG0825|consen   96 SDTSPVCEKEHSPDVDSSNICPVQTHVEN-QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC  159 (1134)
T ss_pred             ccccchhheecCCcccccCcCchhhhhhh-hhhHHHHHHHHHhhccccccccccHHHHhhhhhhh
Confidence            3556666555544    11234   9999 999999999876      34688888766655443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	353
2dgr_A	83	Solution Structure Of The Second Kh Domain In Ring		3e-24
3t6p_A	345	Iap Antagonist-Induced Conformational Change In Cia		2e-05
3eb5_A	74	Structure Of The Ciap2 Ring Domain Length = 74		1e-04
2ecg_A	75	Solution Structure Of The Ring Domain Of The Baculo		4e-04
4ic3_A	74	Crystal Structure Of The F495l Mutant Xiap Ring Dom		5e-04
4ic2_A	74	Crystal Structure Of The Xiap Ring Domain Length =		8e-04
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		8e-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 =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/69 (75%), Positives = 62/69 (89%)
Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141
           TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF VTG P++V+ AR+EI
Sbjct: 11  TIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEI 70
Query: 142 ESHIIRRTG 150
           E+HI  R+G
Sbjct: 71  EAHITLRSG 79

>pdb|3T6P|A Chain A, Iap Antagonist-Induced Conformational Change In Ciap1 Promotes E3 Ligase Activation Via Dimerization Length = 345

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCR 342
           R C +C D+EV+   IPCGH   C ECA       R CP+CR
Sbjct: 296 RTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICR 333

>pdb|3EB5|A Chain A, Structure Of The Ciap2 Ring Domain Length = 74

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR 350
           R C +C D+EV+   IPCGH   C +CA       R CP+CR  +   +R
Sbjct: 25  RTCKVCMDKEVSIVFIPCGHLVVCKDCAPSL----RKCPICRSTIKGTVR 70

>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 = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
           C +C DR +    +PCGH   C +CAE        CPMC   +    +I
Sbjct: 28  CKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKI 72

>pdb|4IC3|A Chain A, Crystal Structure Of The F495l Mutant Xiap Ring Domain Length = 74

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 352
           C +C DR +    +PCGH   C +CAE        CPMC   +    +I+
Sbjct: 27  CKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKIL 72

>pdb|4IC2|A Chain A, Crystal Structure Of The Xiap Ring Domain Length = 74

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
           C +C DR +    +PCGH   C +CAE        CPMC   +    +I
Sbjct: 27  CKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKI 71

>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp Length = 89

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 46/89 (51%), Gaps = 5/89 (5%)
Query: 65  SGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP 123
           S  L P+ PP      +T E RVP  +VGL++G  G  I +IQ  +   + ++P     P
Sbjct: 2   SSQLGPIHPPPRT--SMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP 59
Query: 124 VFEV--TGAPDSVEIARQEIESHIIRRTG 150
              V  TGAP+SV+ A+  ++  + R  G
Sbjct: 60  ERSVSLTGAPESVQKAKMMLDDIVSRGRG 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	353
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	2e-34
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	3e-12
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-29
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-12
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-27
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-11
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-25
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-12
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-25
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	9e-13
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-18
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-10
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-17
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	5e-17
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-16
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	3e-04
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-16
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	4e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	7e-16
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-08
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	4e-15
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	3e-06
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-14
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	3e-04
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	6e-14
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	9e-08
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	4e-13
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	5e-13
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-12
2ea5_A	68	Cell growth regulator with ring finger domain prot	8e-12
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	1e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-11
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-11
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	2e-11
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-11
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	8e-11
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	8e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-10
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-10
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	8e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-10
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	3e-10
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	6e-10
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	4e-09
1we8_A	104	Tudor and KH domain containing protein; structural	2e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-08
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	3e-08
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	4e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	8e-08
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	2e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-07
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-07
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	4e-07
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	6e-07
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	3e-06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	4e-06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	5e-04
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	4e-06
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	4e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	1e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-05
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-05
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	6e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-04
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-04
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	2e-04
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-04
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	3e-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
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	6e-04
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	7e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	9e-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 =  120 bits (302), Expect = 2e-34
 Identities = 53/80 (66%), Positives = 63/80 (78%)

Query: 73  PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPD 132
                 G  TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF VTG P+
Sbjct: 2   SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPE 61

Query: 133 SVEIARQEIESHIIRRTGSC 152
           +V+ AR+EIE+HI  R+G  
Sbjct: 62  NVDRAREEIEAHITLRSGPS 81

>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 = 60.7 bits (147), Expect = 3e-12
 Identities = 27/63 (42%), Positives = 37/63 (58%), Gaps = 4/63 (6%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
          +   G  IK ++ +T+TYI TP R +EPVF VTG  E+V RA+ EI    +    LR+  
Sbjct: 25 VGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEI----EAHITLRSGP 80

Query: 64 KSG 66
           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 =  110 bits (276), Expect = 3e-29
 Identities = 31/153 (20%), Positives = 53/153 (34%), Gaps = 11/153 (7%)

Query: 4   ISRSGCKIKALRAKTNTYIK------TPVRGEEPVFVVTGRKEDVARAKREILSAADHFS 57
           I + G  I  L+ +T   IK            E V ++ G  E +      I        
Sbjct: 21  IGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMP 80

Query: 58  ALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP 117
              A  +  ++              +++ VP    GL++G  GAT+K I  Q+  ++   
Sbjct: 81  QNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLS 140

Query: 118 SRDKEP-----VFEVTGAPDSVEIARQEIESHI 145
            +         V  V+G P+    A + I   I
Sbjct: 141 QKPDGINLQNRVVTVSGEPEQNRKAVELIIQKI 173

>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 = 64.1 bits (156), Expect = 2e-12
 Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 6/98 (6%)

Query: 77  VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGA 130
           +     ++V +P    G ++G  G TI ++Q +T   I ++ S+D  P     V  + G 
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 131 PDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSAD 168
            +++      I   I     +        +     + +
Sbjct: 62  IEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVN 99

>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 =  104 bits (261), Expect = 3e-27
 Identities = 32/150 (21%), Positives = 50/150 (33%), Gaps = 16/150 (10%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEP-----VFVVTGRKEDVARAKREILSAADHFSA 58
           I + G  IK L+ +    +     G +         + G    V +A   ++        
Sbjct: 17  IGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ 76

Query: 59  LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118
                            G      I+V VP   VG+V+G  G  IK+IQ+     I    
Sbjct: 77  --------GGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQ 128

Query: 119 RD---KEPVFEVTGAPDSVEIARQEIESHI 145
            D    E +  + G PD  E A + I   +
Sbjct: 129 DDGTGPEKIAHIMGPPDRCEHAARIINDLL 158

>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 = 60.2 bits (146), Expect = 3e-11
 Identities = 20/119 (16%), Positives = 41/119 (34%), Gaps = 7/119 (5%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-----VFEVTGAPDSVEI 136
             E+ +P    GLV+G  G TIK++Q +    ++      +         + G P  V+ 
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 137 ARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLL--ASLCNSGLGSLGTILNYVNGTSG 193
           A + +   +  R            +      D+          +G  G ++  +   +G
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAG 121

>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 =  100 bits (251), Expect = 1e-25
 Identities = 36/157 (22%), Positives = 51/157 (32%), Gaps = 15/157 (9%)

Query: 4   ISRSGCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREILS------AAD 54
           I R+G  IK ++      I+         E +  +TG  +    A   I        A +
Sbjct: 18  IGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGN 77

Query: 55  HFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
                   R  G            G       VP    GL++G  G TIK I  Q+   I
Sbjct: 78  PGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARI 137

Query: 115 VTPSR------DKEPVFEVTGAPDSVEIARQEIESHI 145
                          +F + G P  ++ ARQ IE  I
Sbjct: 138 ELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>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 = 63.0 bits (153), Expect = 4e-12
 Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 3/93 (3%)

Query: 79  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGAPDSVE 135
           G   I+V +P   VG+V+G  G  IK+IQ+     I   P     P  + ++TG PD  +
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQ 60

Query: 136 IARQEIESHIIRRTGSCVTPAEAVLNGDDNSAD 168
            A + I   +                G      
Sbjct: 61  HAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQG 93

>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 = 98.3 bits (245), Expect = 5e-25
 Identities = 26/148 (17%), Positives = 52/148 (35%), Gaps = 14/148 (9%)

Query: 4   ISRSGCKIKALRAKTNTYIK-TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRAS 62
           I + G  +K +R ++   I  +     E +  + G    + +A   I+            
Sbjct: 20  IGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKL--------- 70

Query: 63  RKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK- 121
            +  + S  +        VT+ + VP    G ++G  G  IK I+  T   +        
Sbjct: 71  EEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP 130

Query: 122 ---EPVFEVTGAPDSVEIARQEIESHII 146
              E    + G P S+    ++I   ++
Sbjct: 131 NSTERAITIAGIPQSIIECVKQICVVML 158

>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 = 64.4 bits (157), Expect = 9e-13
 Identities = 23/116 (19%), Positives = 51/116 (43%), Gaps = 4/116 (3%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQ 139
           +TI + +  K VG ++G KG ++K+++ ++   I ++     E +  + G  +++  A  
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFA 64

Query: 140 EIESHIIRRTGSCVTPAEAVLNGDDNSADLL--ASLCNSGLGSLGTILNYVNGTSG 193
            I    +    S         +    +  L+  AS C S +G  G  +  +  ++G
Sbjct: 65  MIID-KLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTG 119

>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 = 80.2 bits (198), Expect = 3e-18
 Identities = 30/151 (19%), Positives = 58/151 (38%), Gaps = 23/151 (15%)

Query: 4   ISRSGCKIKALRAKTNTYIK----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSAL 59
           I + G  IK L    +  IK         +  + ++TG  E   +A+  I         L
Sbjct: 18  IGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGK------L 71

Query: 60  RASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV---- 115
           +     G              +   +RVP    G V+G  G T+  +Q+ T   +V    
Sbjct: 72  KEENFFGP--------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRD 123

Query: 116 -TPSRDKEPVFEVTGAPDSVEIARQEIESHI 145
            TP  + + + ++ G   + ++A+++I   +
Sbjct: 124 QTPDENDQVIVKIIGHFYASQMAQRKIRDIL 154

>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 = 58.6 bits (142), Expect = 1e-10
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 80  HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD---KEPVFEVTGAPDSVE 135
              ++V +P + VG ++G KG  IK++    +  I + P      K  +  +TG P++  
Sbjct: 2   QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQF 61

Query: 136 IARQEIESHIIRR 148
            A+  I   +   
Sbjct: 62  KAQGRIYGKLKEE 74

>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 = 75.6 bits (186), Expect = 3e-17
 Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-VFEVTGAPDSVEIARQ 139
           VTIEV VP+ +   V+G KG+ I+++  +    I  P+ + +  +  +TG   +++ A+ 
Sbjct: 17  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKA 76

Query: 140 EIESHI 145
            +   +
Sbjct: 77  GLLERV 82

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREILSAADHFSALRAS 62
          I + G  I+ +  +    I  P    +  +  +TG   ++ RAK  +L       A +  
Sbjct: 32 IGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQAEQED 91

Query: 63 RK 64
          R 
Sbjct: 92 RA 93

>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 = 74.4 bits (183), Expect = 5e-17
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQ 139
            +  V +P +    V+G  G  ++ ++ +T T I  P   D     ++TG  + +E AR 
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARH 76

Query: 140 EIESHI 145
           E+    
Sbjct: 77  EVLLIS 82

>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 = 50.1 bits (120), Expect = 2e-08
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEPVFV-VTGRKEDVARAKREILSAADHFSALRAS 62
          I ++G K++ L  KT T I+ P   +    + +TG KE + +A+ E+L  +      R+ 
Sbjct: 32 IGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQDK-RSG 90

Query: 63 RKSG 66
            SG
Sbjct: 91 PSSG 94

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 73.2 bits (180), Expect = 1e-16
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 5/79 (6%)

Query: 72  SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 126
               G       E+ +P    GLV+G  G TIK++Q +    ++     + + + +    
Sbjct: 5   DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR 64

Query: 127 VTGAPDSVEIARQEIESHI 145
           + G P  V+ A + +   +
Sbjct: 65  IIGDPYKVQQACEMVMDIL 83

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 8/53 (15%), Positives = 18/53 (33%), Gaps = 5/53 (9%)

Query: 4  ISRSGCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILS 51
          I + G  IK L+ +    +      +     +    + G    V +A   ++ 
Sbjct: 29 IGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMD 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 = 72.4 bits (178), Expect = 3e-16
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 72  SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 126
           S     PG+   E+ +P    GLV+G  G TIK++Q +    +V       +   +    
Sbjct: 6   SGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR 65

Query: 127 VTGAPDSVEIARQEIESHI 145
           +TG P  V+ A++ +   I
Sbjct: 66  ITGDPYKVQQAKEMVLELI 84

>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 = 38.2 bits (89), Expect = 4e-04
 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 5/52 (9%)

Query: 4  ISRSGCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREIL 50
          I + G  IK L+ +    +          G +    +TG    V +AK  +L
Sbjct: 30 IGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVL 81

>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 = 71.3 bits (175), Expect = 7e-16
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP--VFEVTGAPDSVEIAR 138
           V+ +V + ++V   ++G +G  I++I  +    I  P           VTG P++VE A 
Sbjct: 17  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAI 76

Query: 139 QEIES 143
             I +
Sbjct: 77  DHILN 81

>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 = 51.3 bits (123), Expect = 1e-08
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEP--VFVVTGRKEDVARAKREILSAADHF 56
          I   G  I+ +  +    I+ P  G        VTG  E+V  A   IL+  + +
Sbjct: 32 IGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY 86

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 68.5 bits (168), Expect = 4e-15
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQ 139
             +E+ + +K    ++G  GA I RI+ Q    +  P   +K  +  + G P  V+ A++
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKR 64

Query: 140 EIES 143
           E+  
Sbjct: 65  ELLE 68

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 51
          I +SG  I  ++ +    ++ P   E   +  + G  + V +AKRE+L 
Sbjct: 20 IGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLE 68

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 67.5 bits (165), Expect = 2e-14
 Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 72  SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVT 128
           +  TG      I+V VP   VG+V+G  G  IK+IQ+     I         P  +  + 
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61

Query: 129 GAPDSVEIARQEIESHI 145
           G PD  E A + I   +
Sbjct: 62  GPPDRCEHAARIINDLL 78

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 16/79 (20%), Positives = 23/79 (29%), Gaps = 3/79 (3%)

Query: 4   ISRSGCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALR 60
           I RSG  IK ++      I+       G E +  + G  +    A R I        +  
Sbjct: 26  IGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGP 85

Query: 61  ASRKSGALSPLSPPTGVPG 79
                G   P        G
Sbjct: 86  PGPPGGPGMPPGGRGRGRG 104

>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 = 66.0 bits (161), Expect = 6e-14
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE----VTGAPDSVEI 136
             + V V  K    ++G KGA I +I+ + +  I  P +D     +    +TG   + E 
Sbjct: 17  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEA 76

Query: 137 ARQEIESHI 145
           AR  I   +
Sbjct: 77  ARDAILRIV 85

>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 = 48.7 bits (116), Expect = 9e-08
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEP----VFVVTGRKEDVARAKREILS 51
          I R G  I  +R + +  I+ P + +         +TG +++   A+  IL 
Sbjct: 32 IGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILR 83

>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 = 4e-13
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
           +  C +C + E+     PCGH   C  CA +     ++CP+CR  V     +
Sbjct: 18  AMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHVQHV 65

>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 = 63.2 bits (154), Expect = 5e-13
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 69  SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VF 125
           S  S        +T E +VP  +VG ++G  G  I RIQ ++   I + P     P    
Sbjct: 3   SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62

Query: 126 EVTGAPDSVEIARQEIESHI 145
            +TG P+SV+ A++ ++  +
Sbjct: 63  MLTGTPESVQSAKRLLDQIV 82

>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 = 60.4 bits (147), Expect = 4e-12
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGAPDSV 134
             +E+ VP  +VG ++G  G T+   Q  T   I ++   +  P        +TG+P + 
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 135 EIARQEIESHI 145
           + A+  I   +
Sbjct: 63  QAAQYLISQRV 73

>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 = 59.0 bits (143), Expect = 8e-12
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 289 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 348
            S+    S   S+ C +C +  V   L+PC H   C  C +      + CPMCR  V ++
Sbjct: 4   GSSGVEPSEENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYF----QQCPMCRQFVQES 59

Query: 349 MRI 351
             +
Sbjct: 60  FAL 62

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 59.0 bits (143), Expect = 1e-11
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
            + C +C DR +    +PCGH   C +CAE        CPMC   +    +I
Sbjct: 25  EKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKI 72

>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 = 59.3 bits (144), Expect = 1e-11
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGAPDSV 134
             +E+ VP  +VG ++G  G T+   Q  T   I ++   +  P        +TG+P + 
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 135 EIARQEIESHI 145
           + A+  I   +
Sbjct: 63  QAAQYLISQRV 73

>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 = 58.4 bits (142), Expect = 1e-11
 Identities = 14/68 (20%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 79  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIA 137
             +TI + +  K VG ++G KG ++K+++ ++   I ++     E +  + G  +++  A
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKA 62

Query: 138 RQEIESHI 145
              I   +
Sbjct: 63  FAMIIDKL 70

>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 = 63.5 bits (152), Expect = 2e-11
 Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 4/50 (8%)

Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
            C +C D+EV+   IPCGH   C ECA       R CP+CR  +   +R 
Sbjct: 297 TCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGTVRT 342

>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 = 58.1 bits (141), Expect = 3e-11
 Identities = 16/78 (20%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Query: 76  GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGAPD 132
            +   +T +V +P  + G ++G  G  IK+I+H++   I +    +  ++ +  +TG  D
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 61

Query: 133 SVEIARQEIESHIIRRTG 150
            ++ A+  +++ + + +G
Sbjct: 62  QIQNAQYLLQNSVKQYSG 79

>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 = 57.3 bits (139), Expect = 6e-11
 Identities = 16/73 (21%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGAPDSVEIA 137
           +T +V +P  + G ++G  G  IK+I+H++   I +    +  ++ +  +TG  D ++ A
Sbjct: 14  ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 73

Query: 138 RQEIESHIIRRTG 150
           +  +++ + + +G
Sbjct: 74  QYLLQNSVKQYSG 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 = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 301 RQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
           + C LC  R     +I    GH   C  CA R      +CP+C+  +   +++
Sbjct: 8   KPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKV 60

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 56.5 bits (137), Expect = 8e-11
 Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGAPDSVEIA 137
            + E+ +P  ++G ++G +GA I  I+  +   I +    +        +TG+  S+ +A
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLA 64

Query: 138 RQEIESHIIRRT 149
           +  I   +   T
Sbjct: 65  QYLINVRLSSET 76

>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 = 56.5 bits (137), Expect = 1e-10
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 77  VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGAPDS 133
           +    T E+ +P  ++G ++G +GA I  I+  +   I +    +        +TG+  S
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 61

Query: 134 VEIARQEIESHI 145
           + +A+  I + +
Sbjct: 62  ISLAQYLINARL 73

>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 = 57.7 bits (139), Expect = 2e-10
 Identities = 27/151 (17%), Positives = 46/151 (30%), Gaps = 38/151 (25%)

Query: 4   ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
           I   G  I+  R          +  +   F + G  +D  +  R  L  A+         
Sbjct: 19  IGTHGANIQQARKVPGV-TAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDV------- 70

Query: 64  KSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 123
                                ++VP  +VG V+G  G  I+ I  ++    V    + E 
Sbjct: 71  ---------------------IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEK 109

Query: 124 ---------VFEVTGAPDSVEIARQEIESHI 145
                     F   G  DS+  A   ++ H+
Sbjct: 110 NVPQEEGMVPFVFVGTKDSIANATVLLDYHL 140

>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 = 53.1 bits (127), Expect = 8e-09
 Identities = 13/61 (21%), Positives = 24/61 (39%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141
             +  V   ++GL +G  GA I++ +       +    D           D+V+ AR  +
Sbjct: 5   HEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFL 64

Query: 142 E 142
           E
Sbjct: 65  E 65

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 79  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-------VFEVTGAP 131
               +   +P    GLV+G  G  +K I  QT  ++   SR   P       +F + G+P
Sbjct: 5   PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFV-EISRQLPPNGDPNFKLFIIRGSP 63

Query: 132 DSVEIARQEIESHI 145
             ++ A+Q IE  I
Sbjct: 64  QQIDHAKQLIEEKI 77

>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 = 54.8 bits (132), Expect = 3e-10
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 294 SGSISGSRQCYLCNDREVTHALIP--CGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
           S  ++    C +C  R     ++    GH   C  CA++    ++ CP+CR P+   +  
Sbjct: 2   SLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLT 61

>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 = 57.8 bits (139), Expect = 6e-10
 Identities = 33/145 (22%), Positives = 53/145 (36%), Gaps = 7/145 (4%)

Query: 4   ISRSGCKIKALRAKTNTYIK-TPVRGEEPVFVV--TGRKEDVARAKREILSAADHFSALR 60
           I + G   K +  +T T I      GE  +     T     V +A+  +L+    FS  R
Sbjct: 49  IGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPER 108

Query: 61  ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 120
           A R       L         +  E     +V G ++G KG T + I+  +   +    + 
Sbjct: 109 AFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGK- 167

Query: 121 KEPVFEVTGAPDSVEIARQEIESHI 145
                 + G P  +EIA+  IE   
Sbjct: 168 ---TVAIIGNPIQIEIAKTAIEKLA 189

>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 = 52.5 bits (126), Expect = 4e-09
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT--GAPDSVEIAR 138
             +EV +P K+   ++G KG  I+ I  +     +    +      V   G    VE A+
Sbjct: 17  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAK 76

Query: 139 QEIESHI 145
           +++    
Sbjct: 77  KQLLHLA 83

>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 = 50.6 bits (121), Expect = 2e-08
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 12/90 (13%)

Query: 61  ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-----V 115
           +S  SG L+  +P       V  ++ VP + VG ++G  G TI+ I   +   I      
Sbjct: 2   SSGSSGILTENTP-------VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES 54

Query: 116 TPSRDKEPVFEVTGAPDSVEIARQEIESHI 145
             +     + +++G    V  A+  I   +
Sbjct: 55  EGTLLLSRLIKISGTQKEVAAAKHLILEKV 84

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 51.2 bits (122), Expect = 3e-08
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
           QC +C++  +    + C H+F CS C          CP+CR  +  
Sbjct: 66  QCIICSEYFIEAVTLNCAHSF-CSYCINEWMKRKIECPICRKDIKS 110

>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 Length = 102

 Score = 49.9 bits (119), Expect = 3e-08
 Identities = 12/65 (18%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQE 140
               V  P  +   ++G KG  + +I  Q     +  +  ++ +  + G  + V +A+++
Sbjct: 27  TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKIT-LEGPTEDVSVAQEQ 85

Query: 141 IESHI 145
           IE  +
Sbjct: 86  IEGMV 90

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 49.1 bits (117), Expect = 4e-08
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 289 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346
            S+  +       +C +C    V    +PC H F C  C +      + C +CR  + 
Sbjct: 4   GSSGNTAPSLTVPECAICLQTCVHPVSLPCKHVF-CYLCVKGASWLGKRCALCRQEIP 60

>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 = 52.5 bits (125), Expect = 8e-08
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRII 352
           S  + C +C + +    + PCGH   C+ C     + + + CP CR  +     I+
Sbjct: 330 STFQLCKICAENDKDVKIEPCGHLM-CTSCLTSWQESEGQGCPFCRCEIKGTEPIV 384

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 1/45 (2%)

Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346
           +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 = 46.7 bits (111), Expect = 2e-07
 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 2/47 (4%)

Query: 302 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
            C +C         +  C H F C  C  R   +   CP C + V+Q
Sbjct: 17  LCSICKGYLIDATTITECLHTF-CKSCIVRHFYYSNRCPKCNIVVHQ 62

>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 = 47.5 bits (113), Expect = 3e-07
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 6/49 (12%)

Query: 302 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
            C LC        T  +I C H+F C  C  R  +  + CP+C V V++
Sbjct: 17  MCVLCGGYFIDATT--IIECLHSF-CKTCIVRYLETSKYCPICDVQVHK 62

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 46.4 bits (110), Expect = 3e-07
 Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 8/66 (12%)

Query: 289 SSTSPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMC 341
            S+      SG+  C +C D                CGH F CS+C   +     TCP C
Sbjct: 4   GSSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTC 62

Query: 342 RVPVNQ 347
           R  +N 
Sbjct: 63  RKKINH 68

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 45.9 bits (109), Expect = 4e-07
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 298 SGSRQCYLC-NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS 353
           + + +C +C  D       +PC H F C  C  R    + TCP+C+VPV   +  I 
Sbjct: 3   TVAERCPICLEDPSNYSMALPCLHAF-CYVCITRWIRQNPTCPLCKVPVESVVHTIE 58

>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 = 45.6 bits (108), Expect = 6e-07
 Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 292 SPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 344
           +     SG+  C +C D                CGH F CS+C   +     TCP CR  
Sbjct: 2   TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTCRKK 60

Query: 345 VNQ 347
           +N 
Sbjct: 61  INH 63

>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 = 3e-06
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 302 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
           +C +C +   +   +  C HN+ CS C  +   +   CP C V V +
Sbjct: 24  RCGICFEYFNIAMIIPQCSHNY-CSLCIRKFLSYKTQCPTCCVTVTE 69

>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 Length = 191

 Score = 46.2 bits (109), Expect = 4e-06
 Identities = 26/146 (17%), Positives = 49/146 (33%), Gaps = 14/146 (9%)

Query: 1   MKKIS-RSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSAL 59
             +I  R+G  I      +   ++    G  PV ++  +  +V +A          F  L
Sbjct: 26  KAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLM--KAAEVVKAISLGFPPEKAFRLL 83

Query: 60  RASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
              +    +           H+        ++ G ++G  G   + I+  T+TYI     
Sbjct: 84  EEDQILVVVDLKQVVGDSQNHLK-------RIKGRIIGEGGRARRTIEEMTDTYINV--- 133

Query: 120 DKEPVFEVTGAPDSVEIARQEIESHI 145
             E    + G  +    A+Q IE   
Sbjct: 134 -GEYEVAIIGDYERAMAAKQAIEMLA 158

>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 Length = 191

 Score = 39.6 bits (92), Expect = 5e-04
 Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141
            I V+V  + +G V+GP+G     I  +T T I   + +      V    + +       
Sbjct: 5   RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSM--VIVEPEAEGIPPVNLMK 62

Query: 142 ESHIIRRTGSCVTPAEAV-LNGDDNSAD 168
            + +++       P +A  L  +D    
Sbjct: 63  AAEVVKAISLGFPPEKAFRLLEEDQILV 90

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 47.2 bits (111), Expect = 4e-06
 Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 10/73 (13%)

Query: 80  HVTIEVRVPYKVVGLVVGPKG--ATIKRIQHQTNTYIVTPSRDKEPVFE--------VTG 129
            VT+ +    +   L+    G    +  I  +TNT I  P R               +TG
Sbjct: 29  RVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITG 88

Query: 130 APDSVEIARQEIE 142
               V+ AR  + 
Sbjct: 89  YFGDVDRARMLMR 101

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 43.8 bits (102), Expect = 4e-05
 Identities = 19/122 (15%), Positives = 37/122 (30%), Gaps = 23/122 (18%)

Query: 31  PVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYK 90
               +T R+++            +       + ++                T+   +   
Sbjct: 150 TYLRITAREKNQHELIEAAKRLNEILFRESPAPENN--------------FTLHFTLSTY 195

Query: 91  VVGLVVGPKGA--TIKRIQHQTNTYIVTP-------SRDKEPVFEVTGAPDSVEIARQEI 141
            V  V+G       +  I+ +T T I  P       +R      +V G  D+V  AR+ I
Sbjct: 196 YVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYI 255

Query: 142 ES 143
             
Sbjct: 256 MD 257

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 4/44 (9%)

Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
           +C  C        L+PC H   CS C E +      CP+C+ P 
Sbjct: 8   RCQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPW 47

>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 = 42.6 bits (100), Expect = 2e-05
 Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 2/37 (5%)

Query: 316 IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRI 351
           +PC H   C  C + T +     CP CR  V+   R 
Sbjct: 31  LPCNHTL-CKPCFQSTVEKASLCCPFCRRRVSSWTRY 66

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64

 Score = 40.1 bits (94), Expect = 4e-05
 Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)

Query: 317 PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
            CGH F CS+C   +     TCP CR  +N 
Sbjct: 27  ECGHVF-CSQCLRDSLKNANTCPTCRKKINH 56

>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 = 40.6 bits (95), Expect = 6e-05
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 302 QCYLCNDREVTHALIP-CGHNFFCSECAER-TCDFDRTCPMCRVPVNQAM 349
           +C++C ++     L P C     C  C  R   +    CP CR P+    
Sbjct: 24  RCFICMEKLRDARLCPHCSKLC-CFSCIRRWLTEQRAQCPHCRAPLQLRE 72

>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 = 41.1 bits (96), Expect = 1e-04
 Identities = 25/128 (19%), Positives = 38/128 (29%), Gaps = 8/128 (6%)

Query: 224 GSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIW 283
           GSS      SS      +P +S           + +             D          
Sbjct: 2   GSSHHHHHHSSGLVPRGSPSASKVYKASDSAEAIEAFQLTPQQQHLIREDCQNQKLWDEV 61

Query: 284 SYPPVSSTSPSGSISGSRQCYLCND---REVTHALIPCGHNFFCSECAERTCDFD-RTCP 339
               V   +    +  S  C  C +   + VT     C HN  C +C +R+      +CP
Sbjct: 62  LSHLVEGPNFLKKLEQSFMCVCCQELVYQPVT---TECFHN-VCKDCLQRSFKAQVFSCP 117

Query: 340 MCRVPVNQ 347
            CR  + Q
Sbjct: 118 ACRHDLGQ 125

>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 = 39.7 bits (93), Expect = 2e-04
 Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 4/35 (11%)

Query: 316 IPCGHNFFCSECAERTCDFDR---TCPMCRVPVNQ 347
             C H  FC  C  +  +  +    CP+C+  + +
Sbjct: 37  TKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDITK 70

>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 = 40.0 bits (93), Expect = 2e-04
 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 9/67 (13%)

Query: 287 PVSSTSPSGSISGSR---QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDR---TCPM 340
           P S +     +S      QC  C +         C HN  C +C +R+  F     +CP 
Sbjct: 36  PASGSPFQLFLSKVEETFQCICCQELVFRPITTVCQHN-VCKDCLDRS--FRAQVFSCPA 92

Query: 341 CRVPVNQ 347
           CR  + +
Sbjct: 93  CRYDLGR 99

>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: 316 IPCGHNFFCSECAERTCDFDRT---CPMCRVPVNQ 347
           I CGHN FC +C  +  +       CP+C+  V +
Sbjct: 36  IDCGHN-FCLKCITQIGETSCGFFKCPLCKTSVRK 69

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
           +C +C D      L PC H  FC +C ++  D  R CP+CR+ +
Sbjct: 17  ECCICMDGRADLIL-PCAH-SFCQKCIDKWSDRHRNCPICRLQM 58

>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 = 39.5 bits (92), Expect = 3e-04
 Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 26/93 (27%)

Query: 76  GVPGHVTIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYIV-------------- 115
            +   V+ +V +P         VGL++GP+G T+K I+ + N  I+              
Sbjct: 2   AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGR 61

Query: 116 ----TPSRDKEPVF-EVTG-APDSVEIARQEIE 142
                   + EP+   VT    ++V+ A ++I 
Sbjct: 62  KDGQMLPGEDEPLHALVTANTMENVKKAVEQIR 94

>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: 316 IPCGHNFFCSECAERTCDFDRT-------CPMCRVPVNQ 347
           + 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: 316 IPCGHNFFCSECAERTCDFDRT------CPMCRVPVNQ 347
             C H+ FC  C     + +R       CP+CRVP   
Sbjct: 35  ADCNHS-FCRACITLNYESNRNTDGKGNCPVCRVPYPF 71

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 7/38 (18%)

Query: 316 IPCGHNFFCSECAERTCD------FDRTCPMCRVPVNQ 347
           + CGH+ FC  C             + +CP+CR+    
Sbjct: 35  LDCGHS-FCQACLTANHKKSMLDKGESSCPVCRISYQP 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 = 38.0 bits (88), Expect = 7e-04
 Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 8/47 (17%)

Query: 302 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
           +C  C +     V   L  C H F CS C          CP+C  P 
Sbjct: 24  RCSRCTNILREPVC--LGGCEHIF-CSNCVSDC--IGTGCPVCYTPA 65

>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 = 9e-04
 Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 4/35 (11%)

Query: 315 LIPCGHNFFCSECAERTCDFDR---TCPMCRVPVN 346
           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	353
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.9
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.9
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.89
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
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.74
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.74
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.74
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.62
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.58
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.54
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.53
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.53
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.53
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.52
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.52
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.51
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.51
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.51
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.51
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.5
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.49
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.48
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.48
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.48
1we8_A	104	Tudor and KH domain containing protein; structural	99.47
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.47
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.46
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.42
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.36
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.34
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.34
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.31
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.23
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.22
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.21
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.21
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.19
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.16
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.16
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.16
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.14
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.13
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.12
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.12
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.09
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.08
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.08
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.07
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.07
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.07
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.04
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.04
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.04
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.03
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.03
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.03
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.01
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.01
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.0
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.0
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.0
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.0
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	98.99
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	98.99
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.99
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.98
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.97
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	98.96
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.94
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.94
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	98.93
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	98.92
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.91
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.91
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	98.91
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.9
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	98.9
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.89
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.89
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	98.89
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.89
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	98.89
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.89
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	98.88
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.88
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	98.88
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	98.88
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	98.88
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	98.87
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	98.87
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.86
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.86
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.85
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.85
1we8_A	104	Tudor and KH domain containing protein; structural	98.85
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.84
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.84
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	98.83
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.81
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.81
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.78
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.77
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.76
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.76
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.74
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.74
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.71
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.7
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.7
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.68
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.67
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.65
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.59
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.56
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.56
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.56
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.54
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.53
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.5
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.48
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.48
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.46
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.36
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.21
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.19
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.16
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.15
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.13
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.09
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.07
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.03
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.98
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	97.89
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	97.76
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.55
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	97.41
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.32
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.25
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.03
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.01
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	96.85
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.72
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.7
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.69
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.62
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	95.27
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	94.53
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.17
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.09
3nw0_A	238	Non-structural maintenance of chromosomes element	92.02
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	89.41
2cxc_A	144	NUSA; transcription termination, RNA binding prote	88.79
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	85.03
3gku_A	225	Probable RNA-binding protein; APC21302, clostridiu	84.63
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	81.06

>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=3.2e-24  Score=189.54  Aligned_cols=146  Identities=21%  Similarity=0.291  Sum_probs=113.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPT   75 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~   75 (353)
                      .||||+|++||+|+++|||+|+++..+      .+++++|+|++++|.+|+.+|.+++.+...-.+........++....
T Consensus        19 ~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (178)
T 2anr_A           19 SIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTV   98 (178)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCCC----------------
T ss_pred             eeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCCccccCCcccccCCccCC
Confidence            479999999999999999999998643      35899999999999999999999988653210000000000010011


Q ss_pred             CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          76 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        76 ~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      +.....+.+|.||.+++|+||||+|++||+|+++|||+|.++...     .++.|+|+|++++|++|+++|.++|.+
T Consensus        99 ~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A           99 NPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE  175 (178)
T ss_dssp             -CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHS
T ss_pred             CCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            112347899999999999999999999999999999999998753     357999999999999999999999876

>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=1.7e-23  Score=182.07  Aligned_cols=139  Identities=24%  Similarity=0.286  Sum_probs=113.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTG   76 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~   76 (353)
                      .||||+|++||+|+++||++|+++..+     .+++++|+|++++|.+|+.+|++++++...    .  +  +.+.....
T Consensus        15 ~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~----~--~--~~~~~~~~   86 (164)
T 2jvz_A           15 LVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ----G--G--FGDRNEYG   86 (164)
T ss_dssp             HHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSS----C--C--CSSCSSCT
T ss_pred             EEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccC----C--C--CCCccccC
Confidence            479999999999999999999997543     357999999999999999999999886521    0  0  00000001


Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCC---CCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK---EPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~---e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .....+.+|.||.+++|+||||+|++||+|+++|||+|.++..+.   ++.|+|+|++++|++|+++|++++++-
T Consensus        87 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A           87 SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             TSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            111256889999999999999999999999999999999987532   579999999999999999999999873

>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=99.89  E-value=4.9e-23  Score=179.33  Aligned_cols=133  Identities=21%  Similarity=0.325  Sum_probs=113.0

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   77 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~   77 (353)
                      .||||+|++||+|+++|||+|+++..+    .+++++|+|+++++.+|+.+|++++.+...      .      .+..  
T Consensus        16 ~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~------~------~~~~--   81 (163)
T 3krm_A           16 AIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENF------F------GPKE--   81 (163)
T ss_dssp             HHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTS------S------CSSC--
T ss_pred             eeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccc------c------cccc--
Confidence            379999999999999999999998753    468999999999999999999999876411      0      1111  


Q ss_pred             CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC----CC-CeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KE-PVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        78 ~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~----~e-~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ....+.+|.||.+++|+||||+|++|++|+++|||+|.++.+.    .+ +.|+|+|++++|++|+++|++++++-
T Consensus        82 ~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  157 (163)
T 3krm_A           82 EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQV  157 (163)
T ss_dssp             CCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            1237789999999999999999999999999999999998652    12 37999999999999999999999873

>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-23  Score=180.56  Aligned_cols=137  Identities=20%  Similarity=0.304  Sum_probs=113.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcc
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGH   80 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~   80 (353)
                      .||||+|++||+|+++||++|+++..+ .+++++|+|++++|.+|+.+|++++.+...  ...  .    .. .......
T Consensus        18 ~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~--~~~--~----~~-~~~~~~~   88 (160)
T 2jzx_A           18 SIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEEDIS--SSM--T----NS-TAASRPP   88 (160)
T ss_dssp             HHHCGGGHHHHHHHHHHCSEEEEECCTTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHT--SCC--C----SS-SCCCCCS
T ss_pred             eeECCCcHHHHHHHHHHCCEEEEcCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhhcc--ccC--C----CC-ccCCCCC
Confidence            479999999999999999999999764 468999999999999999999998876421  100  0    00 0000113


Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|.++.+    ..++.|+|+|++++|++|+++|.+++.+
T Consensus        89 ~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            789999999999999999999999999999999998753    3468999999999999999999999876

>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=3.9e-23  Score=182.00  Aligned_cols=140  Identities=26%  Similarity=0.327  Sum_probs=109.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCC------
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS------   72 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~------   72 (353)
                      .||||+|++||+|+++|||+|+++...   .++++.|+|++++|.+|+.+|.+++++...-    .++...+.+      
T Consensus        16 ~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~----~~~~~~p~~~~~~~~   91 (174)
T 1j4w_A           16 IVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAG----NPGGPGPGGRGRGRG   91 (174)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred             eeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccC----CCCCCCCCCCCCCCC
Confidence            479999999999999999999997432   3589999999999999999999999876320    000000000      


Q ss_pred             --CC--CCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHHHHHHHHHHHH
Q psy4141          73 --PP--TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPDSVEIARQEIE  142 (353)
Q Consensus        73 --~~--~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e~V~~A~~~I~  142 (353)
                        ..  .......+.+|.||.+++|+||||+|++||+|+++|||+|.++.+      ..++.|+|+|++++|++|+++|+
T Consensus        92 ~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~  171 (174)
T 1j4w_A           92 QGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIE  171 (174)
T ss_dssp             ------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHH
T ss_pred             CCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHH
Confidence              00  000124688999999999999999999999999999999998764      23579999999999999999999


Q ss_pred             HHH
Q psy4141         143 SHI  145 (353)
Q Consensus       143 ~~i  145 (353)
                      ++|
T Consensus       172 ~~i  174 (174)
T 1j4w_A          172 EKI  174 (174)
T ss_dssp             HHC
T ss_pred             HhC
Confidence            875

>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=99.74  E-value=1.3e-18  Score=135.10  Aligned_cols=78  Identities=68%  Similarity=1.072  Sum_probs=73.4

Q ss_pred             CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCCCC
Q psy4141          76 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCV  153 (353)
Q Consensus        76 ~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~~~  153 (353)
                      +.+++.+.+|.||.+++|+||||+|++||+||++|||+|+++.+++++.|+|+|++++|++|+++|++++..|+|+++
T Consensus         5 ~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~~~~~v~ItG~~e~v~~A~~~I~~~i~~r~~~~~   82 (83)
T 2dgr_A            5 SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEIEAHITLRSGPSS   82 (83)
T ss_dssp             CSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSSSCCEEEEEECTTTHHHHHHHHHHHHHSCCSCCC
T ss_pred             CCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCCCCCeEEEEcCHHHHHHHHHHHHHHHhcccCCCC
Confidence            456779999999999999999999999999999999999999877789999999999999999999999999999875

>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=99.74  E-value=2e-18  Score=147.71  Aligned_cols=116  Identities=20%  Similarity=0.306  Sum_probs=92.6

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT   82 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t   82 (353)
                      +||++|++|++|++++|+.|.....+.+.++...+++++|.+|+.++    + +                        ..
T Consensus        18 ~IG~~G~~I~~i~~e~gI~ii~~~~~~~~~i~~~~~p~~v~~~~~~l----~-~------------------------~e   68 (144)
T 2qnd_A           18 AIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFL----E-F------------------------AE   68 (144)
T ss_dssp             HHCGGGHHHHHHHTSTTEEEEEEETTTTEEEEEESSHHHHHHHHHHH----C-E------------------------EE
T ss_pred             EECCChhHHHHHHHHHCCeEeccCCCchheeeccCCHHHHHHHHHhh----h-c------------------------ce
Confidence            69999999999999999544433333344444456799999887633    1 1                        23


Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCc-eEEcCCCCC------CC--eEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNT-YIVTPSRDK------EP--VFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga-~I~ip~~~~------e~--~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      .+|.||.+++|++|||+|++||.|++.||+ +|.|+.+++      ++  .|+|+|++++|++|+++|+++|..
T Consensus        69 ~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           69 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             EEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            789999999999999999999999999997 998876421      23  489999999999999999999874

>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=5.6e-18  Score=164.70  Aligned_cols=145  Identities=22%  Similarity=0.219  Sum_probs=106.8

Q ss_pred             eeecCCC--chHHHHHHHcCceEEecCCC--------CcCeEEEecCHHHHHHHHHHHHHHHh-----hh----------
Q psy4141           2 KKISRSG--CKIKALRAKTNTYIKTPVRG--------EEPVFVVTGRKEDVARAKREILSAAD-----HF----------   56 (353)
Q Consensus         2 ~IIGk~G--~~Ik~I~~~Tga~I~ip~~~--------e~~vv~I~G~~e~v~~Ak~~I~~i~~-----~~----------   56 (353)
                      +||||+|  ++|++|+++|||+|++|+.+        ....|+|+|.+++|++|+.+|++++.     +.          
T Consensus        43 ~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~Pl~i~~elp~~~i~~~~l  122 (376)
T 3n89_A           43 LMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCHFTVFMALSKMKMPLHEL  122 (376)
T ss_dssp             HHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCEEEEEEECTTCSSCHHHH
T ss_pred             hhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCCceEEEEccccccCcchh
Confidence            5899999  99999999999999999875        12689999999999999999988410     00          


Q ss_pred             -hhhhhccCCCCC--CCC---------------CCC---------------------CCCCcceEEEEEecCCCccceec
Q psy4141          57 -SALRASRKSGAL--SPL---------------SPP---------------------TGVPGHVTIEVRVPYKVVGLVVG   97 (353)
Q Consensus        57 -~~~~~~~~~g~~--~~~---------------~~~---------------------~~~~~~~t~~v~VP~~~vG~IIG   97 (353)
                       .-+......+..  ++.               |+.                     ......++.+|.|+..+|.+|||
T Consensus       123 ~~~I~qq~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e~~~~~~~s~~v~V~~~~H~~IIG  202 (376)
T 3n89_A          123 QAHVRQNPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLSTYYVDQVLG  202 (376)
T ss_dssp             HHHHHHCCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--CCCSSCEEEEEEEEGGGHHHHTC
T ss_pred             hhhhccceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhhcccccceEEEEEeCHHHHHHhhc
Confidence             011111111110  000               100                     00113478899999999999999


Q ss_pred             cCC--hHHHHHHHHhCceEEcCCCCC-------CCeEEEEcCHHHHHHHHHHHHHHHH
Q psy4141          98 PKG--ATIKRIQHQTNTYIVTPSRDK-------EPVFEVTGAPDSVEIARQEIESHII  146 (353)
Q Consensus        98 kgG--~tIk~Iq~~Tga~I~ip~~~~-------e~~v~I~G~~e~V~~A~~~I~~~i~  146 (353)
                      ++|  ..|++|+++|||+|.||..+.       ...|+|+|+.++|++|+++|+++|=
T Consensus       203 k~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLP  260 (376)
T 3n89_A          203 SSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLLP  260 (376)
T ss_dssp             CTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTSE
T ss_pred             CCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhCC
Confidence            998  677999999999999997532       2479999999999999999987654

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.62  E-value=1.2e-15  Score=138.92  Aligned_cols=128  Identities=23%  Similarity=0.273  Sum_probs=97.1

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecC-----HHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-----KEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   77 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~-----~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~   77 (353)
                      |||++|.+|+.|+++||++|++...  +..+.|.+.     ++++++|+..|..++..+.--.+....        .++ 
T Consensus        48 lIG~gGk~Ik~I~e~tgvkI~I~~~--~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~g~~ll--------~dd-  116 (219)
T 2e3u_A           48 LIGKKGQTKKEIEKRTKTKITIDSE--TGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLL--------NEG-  116 (219)
T ss_dssp             HHCGGGHHHHHHHHHHTEEEEECTT--TCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHHHGGGG--------STT-
T ss_pred             hhcccHHHHHHHHHHHCcEEEEEcC--CCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCccccceec--------cCC-
Confidence            7999999999999999999999833  455677664     799999999999998432111111000        000 


Q ss_pred             CcceEEEEEec-----------CCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHH
Q psy4141          78 PGHVTIEVRVP-----------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHII  146 (353)
Q Consensus        78 ~~~~t~~v~VP-----------~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~  146 (353)
                        .....+.|+           .+.+|+||||+|+|||.|++.|||+|+++.    +.|.|.|++++|+.|+++|+++|.
T Consensus       117 --~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~----~~v~i~G~~~~i~~A~~~i~~li~  190 (219)
T 2e3u_A          117 --EYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG----KTVAIIGNPIQIEIAKTAIEKLAR  190 (219)
T ss_dssp             --CEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET----TEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             --ccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC----eEEEEEeCHHHHHHHHHHHHHHHc
Confidence              011223333           236899999999999999999999999863    579999999999999999999995


Q ss_pred             h
Q psy4141         147 R  147 (353)
Q Consensus       147 ~  147 (353)
                      .
T Consensus       191 g  191 (219)
T 2e3u_A          191 G  191 (219)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.58  E-value=4.8e-15  Score=114.63  Aligned_cols=72  Identities=22%  Similarity=0.481  Sum_probs=65.9

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCC
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQEIESHIIRRTGS  151 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~  151 (353)
                      ..+.+|.||.+++|.||||+|++||+|+++|||+|.++..   ..++.|+|+|++++|++|+++|++++.+..|.
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~g~   80 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYSGK   80 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHHHSS
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccCC
Confidence            4889999999999999999999999999999999998864   23579999999999999999999999987765

>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=99.54  E-value=6.7e-15  Score=112.00  Aligned_cols=68  Identities=24%  Similarity=0.398  Sum_probs=61.4

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC------CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~------~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      +.+.+|.||.+++|.||||+|++||+|+++|||+|.++.++      .++.|+|+|++++|++|+++|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            36889999999999999999999999999999999998752      357999999999999999999998865

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.53  E-value=5.4e-15  Score=112.63  Aligned_cols=69  Identities=20%  Similarity=0.425  Sum_probs=63.1

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ..+.+|.||.+++|.||||+|++|++|+++|||+|.++..   ..++.|+|+|++++|++|+++|.+++.+.
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4889999999999999999999999999999999998763   24689999999999999999999998764

>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=99.53  E-value=2.4e-14  Score=113.78  Aligned_cols=78  Identities=22%  Similarity=0.281  Sum_probs=69.0

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC--CCCeEEEEcCHHHHHHHHHHHHHHHHhhhCCCCc
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--KEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVT  154 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~--~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~~~~  154 (353)
                      +...++.+|.||.+++|.|||++|++||+|+++|||+|.||.+.  .++.|+|+|.+++|++|+++|++++++......+
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~~~~~   92 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEYLADSGP   92 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHHHTSCCC
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            34468999999999999999999999999999999999999764  3568999999999999999999999986664443

>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=99.53  E-value=7.6e-15  Score=111.06  Aligned_cols=68  Identities=21%  Similarity=0.353  Sum_probs=63.0

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ..+.+|.||.+.+|.||||+|++||+|+++|||+|.++.++ .++.|+|+|++++|.+|+++|.++|++
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            38899999999999999999999999999999999998763 467999999999999999999999875

>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=99.52  E-value=1e-14  Score=112.76  Aligned_cols=69  Identities=22%  Similarity=0.434  Sum_probs=62.3

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ..+.+|.||.+++|.||||+|++||+|+++|||+|.++..   ..++.|+|+|++++|++|+++|.+++.+.
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4889999999999999999999999999999999998763   24679999999999999999999998875

>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=99.52  E-value=5.6e-16  Score=124.83  Aligned_cols=90  Identities=21%  Similarity=0.361  Sum_probs=76.0

Q ss_pred             EecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHH-hCce
Q psy4141          35 VTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQ-TNTY  113 (353)
Q Consensus        35 I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~-Tga~  113 (353)
                      |+|++++|.+|+.+|+++++.                        .++.+|.||..+|++|||++|++||+|+++ ++++
T Consensus         5 i~G~~~~V~~A~~~i~~~~~~------------------------~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~   60 (102)
T 2ctf_A            5 SSGEPEKLGQALTEVYAKANS------------------------FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVH   60 (102)
T ss_dssp             CCCCCCCCCCSCCCCCCCCCC------------------------CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSE
T ss_pred             cCcCHHHHHHHHHHHHHHhcC------------------------eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcE
Confidence            467777777777776544332                        278999999999999999999999999997 5999


Q ss_pred             EEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhhhC
Q psy4141         114 IVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTG  150 (353)
Q Consensus       114 I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g  150 (353)
                      |.||.  .++.|+|.|++++|++|+.+|++++++...
T Consensus        61 I~fp~--~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           61 IEFTE--GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             EEECS--SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEeCC--CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            99997  456899999999999999999999988544

>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=99.51  E-value=3.1e-14  Score=112.96  Aligned_cols=74  Identities=22%  Similarity=0.367  Sum_probs=66.4

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHHHhhhC
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIRRTG  150 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g  150 (353)
                      +..+++.+|.||.+++|.|||+||++||+|+++|||+|.|+..+ .++.|+|+|++++|++|+++|++++.+..-
T Consensus        13 l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~   87 (94)
T 2cte_A           13 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQDK   87 (94)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             hCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEECHHHHHHHHHHHHHHhhcccc
Confidence            34468999999999999999999999999999999999999754 357999999999999999999999987443

>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=99.51  E-value=3.3e-14  Score=112.32  Aligned_cols=71  Identities=28%  Similarity=0.463  Sum_probs=64.5

Q ss_pred             cceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC---CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~---~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      ..++.+|.||.+++|+||||+|++||+|+++|||+|.++.+.   .++.|+|+|++++|++|+++|++++++..
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            358899999999999999999999999999999999998752   35799999999999999999999998743

>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=99.51  E-value=8.7e-15  Score=114.94  Aligned_cols=72  Identities=22%  Similarity=0.481  Sum_probs=64.6

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCC
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQEIESHIIRRTGS  151 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~  151 (353)
                      ..+.+|.||.+++|.||||+|++||+|+++|||+|.++..   ..++.|+|+|++++|++|+++|++++.+..|.
T Consensus        13 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~~g~   87 (89)
T 1j5k_A           13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYSGK   87 (89)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHC--
T ss_pred             eEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhhhcC
Confidence            5889999999999999999999999999999999999764   24689999999999999999999999987554

>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=99.51  E-value=1.1e-14  Score=115.62  Aligned_cols=72  Identities=28%  Similarity=0.462  Sum_probs=65.7

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .|+..+.+|.||.+++|+||||+|++||+|+++|||+|.++.+.     .++.|+|+|++++|++|+++|++++.+.
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            35679999999999999999999999999999999999988653     4688999999999999999999999863

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.50  E-value=3.8e-14  Score=110.32  Aligned_cols=68  Identities=22%  Similarity=0.361  Sum_probs=61.5

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ..+.+|.||.+.+|.||||+|++||+|+++|||+|.++.+.     .++.|+|+|++++|++|+++|++++++
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            37889999999999999999999999999999999988653     256799999999999999999998864

>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=99.49  E-value=5.5e-14  Score=112.16  Aligned_cols=70  Identities=26%  Similarity=0.337  Sum_probs=64.3

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC----CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~----~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      ..+.+|.||.++||.|||+||++|++|+++|||+|.|+.+.    .++.|+|+|++++|++|+++|++++.+-.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e   89 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELE   89 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999765    35799999999999999999999988743

>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=99.48  E-value=2.5e-14  Score=111.80  Aligned_cols=68  Identities=24%  Similarity=0.404  Sum_probs=62.5

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC------CCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~------~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .+.+|.||.+.+|+||||+|++|++|+++|||+|.++.++      .++.|+|+|++++|++|+++|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            6889999999999999999999999999999999998642      3579999999999999999999999873

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.48  E-value=3e-14  Score=107.19  Aligned_cols=66  Identities=24%  Similarity=0.414  Sum_probs=60.5

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHI  145 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i  145 (353)
                      ..+.+|.||.+++|.|||+||++|++|+++|||+|.|+.+. .++.|+|+|++++|++|+++|++++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            37889999999999999999999999999999999999764 4569999999999999999998864

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=3.6e-14  Score=115.25  Aligned_cols=68  Identities=26%  Similarity=0.465  Sum_probs=62.0

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC------CCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~------~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .+.+|.||.++||+||||+|++||+|+++|||+|+|..+.      .++.|+|+|++++|++|+++|+++|.+.
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            4789999999999999999999999999999999988752      3479999999999999999999998763

>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=99.47  E-value=8.8e-14  Score=112.34  Aligned_cols=67  Identities=22%  Similarity=0.382  Sum_probs=62.4

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      .+.+|.||.+++|.||||+|++||+|+++|||+|.++...     .++.|+|+|++++|++|+++|++++.+
T Consensus        15 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             EEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            7899999999999999999999999999999999998753     368999999999999999999999976

>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=99.47  E-value=1.3e-13  Score=122.69  Aligned_cols=128  Identities=19%  Similarity=0.224  Sum_probs=101.3

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEe-----cCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVT-----GRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV   77 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~-----G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~   77 (353)
                      |||++|++++.|+++++++|++...  ++.+.|.     |++.++.+|+..|..+...|+.-.+.+...           
T Consensus        18 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           18 VIGPRGEVKAEIMRRTGTVITVDTE--NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAFRLLE-----------   84 (191)
T ss_dssp             HHCGGGHHHHHHHHHHTEEEEEETT--TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHHHGGGGS-----------
T ss_pred             HHhcCHhHHHHHHHHHCcEEEEEcC--CCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHHHhhhccc-----------
Confidence            6999999999999999999999743  5666777     999999999999999988664322221110           


Q ss_pred             CcceEEEEEec----------CCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          78 PGHVTIEVRVP----------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        78 ~~~~t~~v~VP----------~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      .+.....+.++          .+.+|+||||+|.||+.|+..|||+|++..    ..|.|.|++++++.|+..|+++|..
T Consensus        85 Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~----~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A           85 EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE----YEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS----SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC----CEEEEEeChHHHHHHHHHHHHHHcC
Confidence            01122234444          246899999999999999999999999863    3899999999999999999999963

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.46  E-value=6.6e-14  Score=113.45  Aligned_cols=71  Identities=31%  Similarity=0.450  Sum_probs=62.5

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC---CCCeEEEEcCHHHHHHHHHHHHHHHHhhhCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIARQEIESHIIRRTGS  151 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~---~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~  151 (353)
                      .+++|.||.+++|.||||+|++||+|+++|||+|+|+.++   .++.|+|+|++++|++|+++|++++.+..-.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~g   84 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSG   84 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC--
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhccccC
Confidence            5789999999999999999999999999999999998653   3568999999999999999999999885443

>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=99.42  E-value=2.6e-13  Score=109.54  Aligned_cols=69  Identities=25%  Similarity=0.491  Sum_probs=63.4

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      .+.+|.||.++||.|||+||++||+|+++|||+|.|+.+. ..+.|+|+|++++|++|+++|++++++-.
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            8899999999999999999999999999999999999764 34599999999999999999999988733

>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=99.36  E-value=1.1e-12  Score=104.16  Aligned_cols=73  Identities=21%  Similarity=0.340  Sum_probs=65.9

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHh-CceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT-NTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T-ga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      +...++..|.||.++++.|||++|++||+|+++| ||+|.||.+. ..+.|+|.|+.++|++|+++|++++.+..
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e   87 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            4556899999999999999999999999999999 9999999764 34689999999999999999999998743

>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=99.34  E-value=2.4e-13  Score=99.78  Aligned_cols=54  Identities=26%  Similarity=0.644  Sum_probs=50.2

Q ss_pred             CCcccccccccccccEEe--CCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         299 GSRQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~ll--pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      ....|.||++.+.+++++  ||||.+||..|+.+++.....||+||+++..+++||
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i~i~   61 (63)
T 2vje_B            6 LLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVF   61 (63)
T ss_dssp             GGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCCEEEEEE
T ss_pred             cCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhhceEEEe
Confidence            457899999999999888  999998999999999887889999999999999998

>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=99.34  E-value=2.8e-13  Score=99.75  Aligned_cols=55  Identities=24%  Similarity=0.660  Sum_probs=50.9

Q ss_pred             CCCcccccccccccccEEe--CCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         298 SGSRQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~ll--pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      .++..|.||++.+.+++++  ||||.+||..|+.+|+.....||+||+++.+++++|
T Consensus         6 ~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i~i~   62 (64)
T 2vje_A            6 NAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTY   62 (64)
T ss_dssp             GGGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCCEEEEEE
T ss_pred             CCcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchhceEeee
Confidence            3567899999999999988  999998999999999988889999999999999997

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=9.6e-13  Score=98.06  Aligned_cols=53  Identities=30%  Similarity=0.818  Sum_probs=48.4

Q ss_pred             CCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceeccC
Q psy4141         297 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS  353 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~~  353 (353)
                      ..+...|.||++.+.+++++||||.+||..|+..+    ..||+||.++...+++|.
T Consensus        12 ~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~CR~~i~~~~~i~~   64 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYF----QQCPMCRQFVQESFALSG   64 (68)
T ss_dssp             CCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHHC----SSCTTTCCCCCCEECCCS
T ss_pred             CCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhcC----CCCCCCCcchhceEEeec
Confidence            34568999999999999999999999999999974    899999999999999983

>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=99.23  E-value=6.1e-12  Score=110.57  Aligned_cols=71  Identities=21%  Similarity=0.305  Sum_probs=64.0

Q ss_pred             CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        78 ~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ++.++.+|.||.+++|.||||+|++||+|+++|||+|.++..      ..++.|+|+|++++|++|+.+|.+++.+.
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~   79 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREM   79 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            456899999999999999999999999999999999998764      23578999999999999999999998763

>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=99.22  E-value=1.2e-11  Score=106.97  Aligned_cols=69  Identities=23%  Similarity=0.385  Sum_probs=62.3

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      .+.+|.||.+++|.||||+|++||+|+++|||+|.++.+.     .++.|+|+|++++|++|+.+|.+++.+..
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~   75 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhcc
Confidence            6789999999999999999999999999999999886542     35799999999999999999999988744

>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=99.21  E-value=1.3e-11  Score=106.87  Aligned_cols=68  Identities=24%  Similarity=0.382  Sum_probs=62.9

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .+++|.||.+.+|.||||+|++||+|+++|||+|.++.+    ..++.|+|+|+++++.+|+.+|.+++.+.
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~   74 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEE   74 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            688999999999999999999999999999999999874    24678999999999999999999999875

>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=99.21  E-value=9.1e-12  Score=109.12  Aligned_cols=70  Identities=29%  Similarity=0.439  Sum_probs=63.2

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      ..+.+|.||.+++|.||||+|++||+|+++|||+|.+...   ..++.|+|+|++++|++|+.+|.+++.+..
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~   74 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQ   74 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            4788999999999999999999999999999999998753   235789999999999999999999998753

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.19  E-value=3.3e-12  Score=96.55  Aligned_cols=52  Identities=33%  Similarity=0.890  Sum_probs=48.3

Q ss_pred             CCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         297 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      +.++..|.||++.+.+++++||||.+||..|+.+|    ..||+||.++...+++|
T Consensus        21 ~~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~   72 (74)
T 4ic3_A           21 LQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKIL   72 (74)
T ss_dssp             HHHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSEEEECB
T ss_pred             CccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----ccCCCcCcCccCcEEEe
Confidence            34568999999999999999999999999999997    89999999999999987

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=2.4e-11  Score=90.74  Aligned_cols=50  Identities=24%  Similarity=0.641  Sum_probs=45.4

Q ss_pred             CCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ..+...|.||++.+.+++.++|||. ||..|+.+|......||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           12 SLTVPECAICLQTCVHPVSLPCKHV-FCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSSCCBCSSSSSBCSSEEEETTTEE-EEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCCccCCcccCCCEEccCCCH-HHHHHHHHHHHCCCcCcCcCchhCH
Confidence            3456899999999999999999999 9999999998888899999999864

>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=99.16  E-value=5.9e-12  Score=96.51  Aligned_cols=51  Identities=29%  Similarity=0.879  Sum_probs=47.3

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      .++..|.||++.+.+++++||||.+||..|+..+    ..||+||.++...+++|
T Consensus        16 ~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~   66 (79)
T 2yho_A           16 KEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHVQHVY   66 (79)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCEEEECB
T ss_pred             CCCCEeEEeCcccCcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhCeEEEE
Confidence            4567899999999999999999999999999987    59999999999999987

>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=99.16  E-value=2e-11  Score=105.32  Aligned_cols=69  Identities=20%  Similarity=0.319  Sum_probs=63.6

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC-CCCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      .+.+|.||.+.+|.||||+|++||+|+++|||+|.++.. ..++.|+|+|++++|++|+.+|.+++.+..
T Consensus         5 ~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTTTEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhhc
Confidence            789999999999999999999999999999999999875 346799999999999999999999988753

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.14  E-value=6.4e-12  Score=95.09  Aligned_cols=51  Identities=33%  Similarity=0.878  Sum_probs=47.0

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      .++..|.||++.+.+++++||||.+||..|+.++    ..||+||.++...++||
T Consensus        23 ~~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~   73 (75)
T 2ecg_A           23 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKIF   73 (75)
T ss_dssp             HHHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHHC----SBCTTTCCBCCCCCBCC
T ss_pred             CCCCCCCcCCCCCCCEEEecCCCHHHHHHHhhCC----CCCccCCceecCcEEEe
Confidence            4567899999999999999999999999999874    89999999999999987

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=4.5e-11  Score=91.44  Aligned_cols=53  Identities=21%  Similarity=0.534  Sum_probs=46.9

Q ss_pred             CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      +...+...|.||++.+.++++++|||. ||..|+.+|+.....||+||.++...
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (81)
T 2csy_A           10 EEEEIPFRCFICRQAFQNPVVTKCRHY-FCESCALEHFRATPRCYICDQPTGGI   62 (81)
T ss_dssp             SCCCCCSBCSSSCSBCCSEEECTTSCE-EEHHHHHHHHHHCSBCSSSCCBCCSC
T ss_pred             ccCCCCCCCcCCCchhcCeeEccCCCH-hHHHHHHHHHHCCCcCCCcCcccccc
Confidence            344567899999999999999999999 99999999998888999999998643

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=2.8e-11  Score=89.20  Aligned_cols=52  Identities=35%  Similarity=0.715  Sum_probs=45.8

Q ss_pred             CCCCCCccccccccccccc-------EEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         295 GSISGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~-------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ....+...|.||++.+.++       ++++|||. ||..|+.+|+.....||+||.++..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           10 LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCE-EEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCCCcccCccccccccccCCeEeCCCCCh-hcHHHHHHHHHcCCCCCCCCCccCc
Confidence            3456678999999998876       88999998 9999999999888899999998864

>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=99.12  E-value=4e-11  Score=92.76  Aligned_cols=53  Identities=43%  Similarity=0.654  Sum_probs=49.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~   54 (353)
                      .||||+|++||+|+++|||+|+++..+++++++|+|+++++++|+.+|.+++.
T Consensus        23 ~IIGkgG~tIk~Iqe~Tga~I~I~~~~~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A           23 LVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             HHHTTTTSSHHHHHHHTTCEEECCCSSSCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             eeECCCchHHHHHHHHhCCeEEecCCCCCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            37999999999999999999999987778999999999999999999999755

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.12  E-value=4.8e-11  Score=89.31  Aligned_cols=54  Identities=26%  Similarity=0.661  Sum_probs=48.0

Q ss_pred             CCCCCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         294 SGSISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       294 ~~~~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      .+.+.+...|.||++.+.+++.+ +|||. ||..|+.+|+.....||+||.++...
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A            9 LSELTPYILCSICKGYLIDATTITECLHT-FCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             CCCCCGGGSCTTTSSCCSSCEECSSSCCE-ECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             HhhcCCCCCCCCCChHHHCcCEECCCCCH-HHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            34567789999999999999987 99999 99999999998888999999998653

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=1.4e-10  Score=86.52  Aligned_cols=52  Identities=29%  Similarity=0.689  Sum_probs=46.0

Q ss_pred             CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCccccccc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVNQ  347 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~~  347 (353)
                      +.+.+...|.||++.+.+++.++|||. ||..|+..|+..   ...||+||.++..
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            456677999999999999999999999 999999999863   6689999998864

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.08  E-value=1.1e-10  Score=89.40  Aligned_cols=54  Identities=26%  Similarity=0.588  Sum_probs=47.5

Q ss_pred             CCCCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc------CCCCCCccccccc
Q psy4141         293 PSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQ  347 (353)
Q Consensus       293 ~~~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~------~~~CP~Cr~~i~~  347 (353)
                      ..+.+.+...|.||++.+.++++++|||. ||..|+..|+..      ...||+||..+..
T Consensus        12 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           12 VLEMIKEEVTCPICLELLKEPVSADCNHS-FCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             CCCCCCTTTSCTTTCSCCSSCEECTTSCC-BCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             HHHhCccCCCCcCCChhhCcceeCCCCCH-HHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            34456678999999999999999999999 999999999887      6789999999863

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=4.6e-11  Score=88.68  Aligned_cols=55  Identities=29%  Similarity=0.862  Sum_probs=48.3

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      .+.+...|.||++.+.+ +++||||. ||..|+.+|......||+||.++.....+|
T Consensus        11 ~~~~~~~C~IC~~~~~~-~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   65 (70)
T 2ecn_A           11 QLTDEEECCICMDGRAD-LILPCAHS-FCQKCIDKWSDRHRNCPICRLQMTGANESS   65 (70)
T ss_dssp             CCCCCCCCSSSCCSCCS-EEETTTEE-ECHHHHHHSSCCCSSCHHHHHCTTCCCCCC
T ss_pred             cCCCCCCCeeCCcCccC-cccCCCCc-ccHHHHHHHHHCcCcCCCcCCcccCCCccc
Confidence            44567899999999999 88999999 999999999888899999999998765554

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.07  E-value=4.5e-11  Score=88.74  Aligned_cols=54  Identities=35%  Similarity=0.726  Sum_probs=46.7

Q ss_pred             CCCccccccccccccc-------EEeCCCCHhhhHHhHHHHhccCCCCCCccccccc--ceecc
Q psy4141         298 SGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ--AMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~-------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~--~~ri~  352 (353)
                      .++..|.||++.+.++       ++++|||. ||..|+.+|+.....||+||.++..  +.++|
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   70 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINHKRYHPIY   70 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCE-EEHHHHHHHHHHCSBCTTTCCBCCCCSCCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCCh-HhHHHHHHHHHcCCCCCCCCCccChhheeecc
Confidence            4568999999998887       88999999 9999999999888899999999863  45554

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.07  E-value=9.7e-11  Score=113.89  Aligned_cols=67  Identities=25%  Similarity=0.358  Sum_probs=61.4

Q ss_pred             CcceEEEEEecCCCccceeccCC--hHHHHHHHHhCceEEcCCCC--------CCCeEEEEcCHHHHHHHHHHHHHH
Q psy4141          78 PGHVTIEVRVPYKVVGLVVGPKG--ATIKRIQHQTNTYIVTPSRD--------KEPVFEVTGAPDSVEIARQEIESH  144 (353)
Q Consensus        78 ~~~~t~~v~VP~~~vG~IIGkgG--~tIk~Iq~~Tga~I~ip~~~--------~e~~v~I~G~~e~V~~A~~~I~~~  144 (353)
                      ...+|.++.||..+|++||||||  ++|++|+++|||+|.||.++        ....|+|+|.+++|++|+++|.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            45799999999999999999999  99999999999999999764        235899999999999999999874

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.07  E-value=6.2e-11  Score=89.27  Aligned_cols=53  Identities=28%  Similarity=0.701  Sum_probs=46.5

Q ss_pred             CCCCCCCcccccccccccccEEeC-CCCHhhhHHhHHHHhccC--CCCCCccccccc
Q psy4141         294 SGSISGSRQCYLCNDREVTHALIP-CGHNFFCSECAERTCDFD--RTCPMCRVPVNQ  347 (353)
Q Consensus       294 ~~~~~~~~~C~IC~~~~~~~~llp-CgH~~fC~~C~~~~~~~~--~~CP~Cr~~i~~  347 (353)
                      .+.+.++..|.||++.+.+++.++ |||. ||..|+.+|+...  ..||+||.++..
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A            9 DDPIPDELLCLICKDIMTDAVVIPCCGNS-YCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CCCSCGGGSCSSSCCCCTTCEECSSSCCE-ECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             cccCCCCCCCcCCChHHhCCeEcCCCCCH-HHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            345667899999999999999999 9999 9999999999863  789999998654

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.04  E-value=5.3e-11  Score=90.24  Aligned_cols=53  Identities=23%  Similarity=0.644  Sum_probs=46.7

Q ss_pred             CCCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-------CCCCCCccccccc
Q psy4141         294 SGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-------DRTCPMCRVPVNQ  347 (353)
Q Consensus       294 ~~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-------~~~CP~Cr~~i~~  347 (353)
                      .+.+.++..|.||++.+.+++.++|||. ||..|+.+|+..       ...||+||.++..
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            4456778999999999999999999999 999999999876       5689999998853

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.04  E-value=6.5e-11  Score=99.93  Aligned_cols=49  Identities=27%  Similarity=0.720  Sum_probs=44.9

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      ++..|.||++.+.+++.+||||. ||..|+..|+.....||+||.++...
T Consensus        52 ~~~~C~iC~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           52 NELQCIICSEYFIEAVTLNCAHS-FCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHSBCTTTCSBCSSEEEETTSCE-EEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             ccCCCcccCcccCCceECCCCCC-ccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            45789999999999999999998 99999999998889999999998653

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=1.6e-10  Score=89.32  Aligned_cols=52  Identities=23%  Similarity=0.630  Sum_probs=45.8

Q ss_pred             CCCCCCCcccccccccccc----cEEeCCCCHhhhHHhHHHHhccC---CCCCCcccccc
Q psy4141         294 SGSISGSRQCYLCNDREVT----HALIPCGHNFFCSECAERTCDFD---RTCPMCRVPVN  346 (353)
Q Consensus       294 ~~~~~~~~~C~IC~~~~~~----~~llpCgH~~fC~~C~~~~~~~~---~~CP~Cr~~i~  346 (353)
                      .+.+.+...|.||++.+.+    +++++|||. ||..|+.+|+...   ..||+||.++.
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~-fC~~Ci~~~~~~~~~~~~CP~Cr~~~~   67 (88)
T 2ct2_A            9 LDALREVLECPICMESFTEEQLRPKLLHCGHT-ICRQCLEKLLASSINGVRCPFCSKITR   67 (88)
T ss_dssp             CCCCCSCCBCTTTCCBCCTTSSCEEECSSSCE-EEHHHHHHHHHHCSSCBCCTTTCCCBC
T ss_pred             hhhccCCCCCccCCccccccCCCeEECCCCCh-hhHHHHHHHHHcCCCCcCCCCCCCccc
Confidence            3456677999999999998    999999999 9999999998874   78999999874

>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=99.04  E-value=1.4e-10  Score=87.40  Aligned_cols=54  Identities=17%  Similarity=0.311  Sum_probs=49.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .||||+|++||+|+++|||+|++++.+ .++++.|+|+++++.+|+.+|.+++++
T Consensus        18 ~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A           18 SIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999999775 468999999999999999999999875

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=99.03  E-value=1e-10  Score=91.74  Aligned_cols=51  Identities=25%  Similarity=0.570  Sum_probs=44.6

Q ss_pred             CCCCCcccccccccccc---cEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~---~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ...++..|.||++.+..   +..+||+|. ||..|+..|+.....||+||..+..
T Consensus        36 ~~~~~~~C~IC~~~~~~~~~~~~l~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           36 AVGQEMCCPICCSEYVKGDVATELPCHHY-FHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSSSCSEETTTTEECCTTCEEEEETTTEE-EEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             ccCCCCCCcccChhhcCCCcEEecCCCCh-HHHHHHHHHHHcCCcCcCcCccCCC
Confidence            44567899999998776   777899999 9999999999888899999998764

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.03  E-value=1.3e-10  Score=85.34  Aligned_cols=51  Identities=20%  Similarity=0.559  Sum_probs=45.3

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+.++..|.||++.+.+++.++|||. ||..|+.+|+.. ...||+||.++..
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (66)
T 2ecy_A           11 TVEDKYKCEKCHLVLCSPKQTECGHR-FCESCMAALLSSSSPKCTACQESIVK   62 (66)
T ss_dssp             SCCCCEECTTTCCEESSCCCCSSSCC-CCHHHHHHHHTTSSCCCTTTCCCCCT
T ss_pred             cCCcCCCCCCCChHhcCeeECCCCCH-HHHHHHHHHHHhCcCCCCCCCcCCCh
Confidence            45567899999999999999999999 999999999954 7789999998864

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=99.03  E-value=8.6e-11  Score=85.23  Aligned_cols=53  Identities=32%  Similarity=0.671  Sum_probs=46.2

Q ss_pred             CCccccccccccccc-------EEeCCCCHhhhHHhHHHHhccCCCCCCcccccc--cceecc
Q psy4141         299 GSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN--QAMRII  352 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~-------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~--~~~ri~  352 (353)
                      ++..|.||++.+.++       ++++|||. ||..|+.+|......||+||.++.  .+.++|
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   63 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINHKRYHPIY   63 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCE-EEHHHHHHHHHHCSBCTTTCCBCTTTCEEECC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCc-hhHHHHHHHHHcCCCCCCCCccCCccceeeee
Confidence            457899999998776       78999999 999999999988889999999987  456655

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.01  E-value=1.6e-10  Score=87.50  Aligned_cols=54  Identities=20%  Similarity=0.577  Sum_probs=44.9

Q ss_pred             CCCCCCCccccccccccccc---EEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141         294 SGSISGSRQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA  348 (353)
Q Consensus       294 ~~~~~~~~~C~IC~~~~~~~---~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~  348 (353)
                      .+...+...|.||++.+...   ..++|+|. ||..|+.+|+.....||+||..+...
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A            9 EEHVGSGLECPVCKEDYALGESVRQLPCNHL-FHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             CTTSSSSCCCTTTTSCCCTTSCEEECTTSCE-EETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             cccCCCCCCCeeCCccccCCCCEEEeCCCCe-ecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            34456678999999887543   56799999 99999999998888999999998753

>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=99.01  E-value=5.3e-10  Score=88.96  Aligned_cols=57  Identities=23%  Similarity=0.413  Sum_probs=51.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC----cCeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILSAADHFSA   58 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e----~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~   58 (353)
                      .||||+|.+|++|+++|||+|+||+.++    ++.|+|+|.++++++|+.+|..++.+...
T Consensus        30 ~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~   90 (97)
T 2ctl_A           30 KIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELEQ   90 (97)
T ss_dssp             HHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHh
Confidence            4899999999999999999999998763    47899999999999999999999987654

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.00  E-value=1.9e-10  Score=89.89  Aligned_cols=52  Identities=29%  Similarity=0.727  Sum_probs=45.8

Q ss_pred             CCCCCCCcccccccccccccEEeC-CCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         294 SGSISGSRQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       294 ~~~~~~~~~C~IC~~~~~~~~llp-CgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      .+.+.++..|.||++.+.+++.+| |||. ||..|+..|+..  ...||+||.++.
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            345667899999999999999999 9999 999999999875  469999999873

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=99.00  E-value=1.8e-10  Score=88.02  Aligned_cols=55  Identities=25%  Similarity=0.570  Sum_probs=44.8

Q ss_pred             CCCCCCccccccccccc--ccEEeC--CCCHhhhHHhHHHHhcc-CCCCCCccccccccee
Q psy4141         295 GSISGSRQCYLCNDREV--THALIP--CGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMR  350 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~--~~~llp--CgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~~~r  350 (353)
                      ..++++..|+||++...  +.+++|  |||+ ||..|+.++|.. ...||+||.++.....
T Consensus         6 ~~~~~~~~CpICle~~~~~d~~~~p~~CGH~-fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            6 DAKEDPVECPLCMEPLEIDDINFFPCTCGYQ-ICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCCCCBCTTTCCBCCTTTTTCCSSTTSCC-CCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             cccccCCcCCccCccCccccccccccCCCCC-cCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            45677899999999773  455666  9999 999999999866 6789999999876433

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.00  E-value=2.5e-10  Score=86.46  Aligned_cols=51  Identities=12%  Similarity=0.274  Sum_probs=46.3

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+.++..|.||++.+.+++.++|||. ||..|+.+|+.. ...||+||.++..
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            45667999999999999999999999 999999999987 7899999998853

>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=99.00  E-value=1.8e-10  Score=90.18  Aligned_cols=64  Identities=23%  Similarity=0.363  Sum_probs=57.1

Q ss_pred             CcceEEEEEecCCCccceeccCChHHHHHHHHhCce-EEcCCCCCCCeEEEEc-CHHHHHHHHHHHHH
Q psy4141          78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY-IVTPSRDKEPVFEVTG-APDSVEIARQEIES  143 (353)
Q Consensus        78 ~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~-I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~  143 (353)
                      ...+..+|.||.+++|.|||++|++||+|+++||++ |.+.  +++..|+|.| +.+++++|+++|+.
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~--eddG~V~I~g~~~ea~~~A~~~I~~   77 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD--EDTGTFRIYGESADAVKKARGFLEF   77 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE--TTTTEEEEEESSHHHHHHHHHHHSC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE--cCCCEEEEEECCHHHHHHHHHHHHh
Confidence            345889999999999999999999999999999998 9885  3347899999 79999999999964

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.99  E-value=1.8e-10  Score=88.08  Aligned_cols=52  Identities=23%  Similarity=0.685  Sum_probs=46.4

Q ss_pred             CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc------CCCCCCccccccc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQ  347 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~------~~~CP~Cr~~i~~  347 (353)
                      ..+.+...|.||++.+.+++.++|||. ||..|+..|+..      ...||+||..+..
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            455677899999999999999999999 999999999876      7899999998863

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=98.99  E-value=1.3e-10  Score=85.62  Aligned_cols=52  Identities=31%  Similarity=0.766  Sum_probs=46.2

Q ss_pred             CCccccccccccccc-EEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceec
Q psy4141         299 GSRQCYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI  351 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~-~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri  351 (353)
                      +...|.||++.+.++ +.+||||. ||..|+.+|......||+||.++...++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~C~H~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   56 (68)
T 1chc_A            4 VAERCPICLEDPSNYSMALPCLHA-FCYVCITRWIRQNPTCPLCKVPVESVVHT   56 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEE-ESTTHHHHHHHHSCSTTTTCCCCCCEECC
T ss_pred             CCCCCeeCCccccCCcEecCCCCe-eHHHHHHHHHhCcCcCcCCChhhHhhhhc
Confidence            457899999999885 78999999 99999999988889999999999877654

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.99  E-value=2.2e-10  Score=85.94  Aligned_cols=56  Identities=23%  Similarity=0.614  Sum_probs=46.2

Q ss_pred             CCCCCCcccccccccccc---cEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceec
Q psy4141         295 GSISGSRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI  351 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~---~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri  351 (353)
                      ..+.++..|.||++.+..   ...+||+|. ||..|+.+|+.....||+||.++..+.++
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   68 (74)
T 2ep4_A           10 KELNLHELCAVCLEDFKPRDELGICPCKHA-FHRKCLIKWLEVRKVCPLCNMPVLQLAQL   68 (74)
T ss_dssp             CCCCCSCBCSSSCCBCCSSSCEEEETTTEE-EEHHHHHHHHHHCSBCTTTCCBCSSCCSC
T ss_pred             ccCCCCCCCcCCCcccCCCCcEEEcCCCCE-ecHHHHHHHHHcCCcCCCcCccccccccc
Confidence            345567899999999754   344599999 99999999998888999999999876554

>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=98.98  E-value=4.7e-10  Score=82.91  Aligned_cols=54  Identities=22%  Similarity=0.554  Sum_probs=45.1

Q ss_pred             CCCCCcccccccccc---cccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141         296 SISGSRQCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR  350 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r  350 (353)
                      ...+...|.||++.+   ..++.+||+|. ||..|+.+|+.....||+||..+...+.
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLPCMHL-FHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECTTSCE-EEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeCCCCH-HHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            345568899998876   35677999999 9999999999888899999999876553

>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=98.97  E-value=8.3e-10  Score=87.49  Aligned_cols=57  Identities=26%  Similarity=0.371  Sum_probs=51.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC--cCeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAADHFSA   58 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e--~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~   58 (353)
                      .|||++|.+||+|+++|||+|++|+.++  ++.|.|+|.++++++|+.+|..+++++.+
T Consensus        30 ~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           30 RIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             HHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            4799999999999999999999998763  46899999999999999999999988754

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.96  E-value=6.4e-10  Score=80.75  Aligned_cols=46  Identities=30%  Similarity=0.718  Sum_probs=41.3

Q ss_pred             CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMC  341 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~C  341 (353)
                      +.+.++..|.||++.+.+++.++|||. ||..|+.+|+..   ...||+|
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            456678999999999999999999999 999999999973   5689998

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.94  E-value=3.4e-10  Score=85.22  Aligned_cols=51  Identities=27%  Similarity=0.696  Sum_probs=43.7

Q ss_pred             CCCCCccccccccccccc---EEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~---~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ...+...|.||++.+...   ..+||+|. ||..|+.+|+.....||+||+.+..
T Consensus        19 ~~~~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           19 HQSEQTLCVVCMCDFESRQLLRVLPCNHE-FHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             CSSSCCEETTTTEECCBTCEEEEETTTEE-EETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             ccCCCCCCeECCcccCCCCeEEEECCCCH-hHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            345668999999987665   77899999 9999999999888899999998754

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=98.94  E-value=3.9e-10  Score=79.51  Aligned_cols=48  Identities=31%  Similarity=0.767  Sum_probs=42.2

Q ss_pred             CCCcccccccccccc---cEEeC-CCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVT---HALIP-CGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~---~~llp-CgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      ++...|.||++.+..   +..++ |+|. ||..|+.+|......||+||.++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHG-FHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCE-ECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCc-ccHHHHHHHHHcCCcCcCCCCEeE
Confidence            456889999999877   67777 9999 999999999988889999998763

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=98.93  E-value=5.4e-10  Score=83.76  Aligned_cols=52  Identities=25%  Similarity=0.471  Sum_probs=47.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAA   53 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~   53 (353)
                      .|||++|.+|++|+++|||+|++|+.+ .++.|.|+|..+++++|+.+|.+++
T Consensus        18 ~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A           18 HLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             HHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             hhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            489999999999999999999999876 3468999999999999999998764

>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=98.92  E-value=9.4e-10  Score=84.69  Aligned_cols=55  Identities=20%  Similarity=0.400  Sum_probs=49.9

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|++++..   .+++++|+|+++++++|+.+|.+++++.
T Consensus        20 ~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A           20 SIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             GGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            489999999999999999999998642   3589999999999999999999999875

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.91  E-value=8e-10  Score=78.58  Aligned_cols=46  Identities=33%  Similarity=0.809  Sum_probs=40.3

Q ss_pred             CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhc---cCCCCCCc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCD---FDRTCPMC  341 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~---~~~~CP~C  341 (353)
                      +.+.+...|.||++.+.+++.++|||. ||..|+.+|+.   ....||+|
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            445667899999999999999999999 99999999955   36789998

>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=98.91  E-value=4e-10  Score=79.38  Aligned_cols=47  Identities=32%  Similarity=0.730  Sum_probs=41.8

Q ss_pred             CCcccccccccccc----cEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         299 GSRQCYLCNDREVT----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       299 ~~~~C~IC~~~~~~----~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      ++..|.||++.+.+    +++++|+|. ||..|+.+|......||+||.++.
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            45789999998855    788999998 999999999988899999999875

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=98.91  E-value=1.2e-09  Score=84.70  Aligned_cols=53  Identities=17%  Similarity=0.229  Sum_probs=47.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC-----cCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE-----EPVFVVTGRKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e-----~~vv~I~G~~e~v~~Ak~~I~~i~~   54 (353)
                      .||||+|++||+|+++|||+|+++..+.     +++|.|+|+++++++|+.+|.+++.
T Consensus        27 ~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           27 LVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             HHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             eeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            4899999999999999999999987542     5779999999999999999999875

>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=98.90  E-value=4.3e-10  Score=92.95  Aligned_cols=49  Identities=27%  Similarity=0.661  Sum_probs=44.5

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+...|.||++.+.+++.+||||. ||..|+..|+.. ...||+||.++..
T Consensus        50 ~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVFRPITTVCQHN-VCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCSSEEECTTSCE-EEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHcCcEEeeCCCc-ccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            456889999999999999999999 999999999986 5699999999865

>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=98.90  E-value=1.6e-09  Score=85.23  Aligned_cols=55  Identities=24%  Similarity=0.268  Sum_probs=50.0

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|+++...   .+++|+|+|++++|++|+.+|.+++++.
T Consensus        28 ~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           28 FIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             HHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             eeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999999753   3589999999999999999999999875

>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=98.89  E-value=1.9e-09  Score=90.38  Aligned_cols=69  Identities=29%  Similarity=0.469  Sum_probs=59.1

Q ss_pred             cceEEEEEecCC------CccceeccCChHHHHHHHHhCceEEcCCC-------------------CCCCeEEEEc-CHH
Q psy4141          79 GHVTIEVRVPYK------VVGLVVGPKGATIKRIQHQTNTYIVTPSR-------------------DKEPVFEVTG-APD  132 (353)
Q Consensus        79 ~~~t~~v~VP~~------~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-------------------~~e~~v~I~G-~~e  132 (353)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|..+                   +.+-.|.|++ +.+
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            358899999987      88999999999999999999999988542                   1134788999 489


Q ss_pred             HHHHHHHHHHHHHHh
Q psy4141         133 SVEIARQEIESHIIR  147 (353)
Q Consensus       133 ~V~~A~~~I~~~i~~  147 (353)
                      .+++|+++|++++..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999875

>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=98.89  E-value=2.1e-09  Score=85.55  Aligned_cols=52  Identities=13%  Similarity=0.101  Sum_probs=47.1

Q ss_pred             CCCCCCcccccccccccccEEeCCC-CHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         295 GSISGSRQCYLCNDREVTHALIPCG-HNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~llpCg-H~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ..+.++..|+||++...++|.++|| |. ||+.|+.+|+.....||+||.++..
T Consensus        17 ~~~p~~~~CpI~~~~m~dPV~~~cG~ht-f~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           17 ADACDEFLDPIMSTLMCDPVVLPSSRVT-VDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CSCCTTTBCTTTCSBCSSEEECTTTCCE-EEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             hcCcHhcCCcCccccccCCeECCCCCeE-ECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            3456679999999999999999999 99 9999999999888899999999864

>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=98.89  E-value=1.1e-09  Score=82.82  Aligned_cols=54  Identities=15%  Similarity=0.189  Sum_probs=47.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .||||+|++||+|+++|||+|+++..+      .++.|.|+|+++++.+|+.+|.+++.+
T Consensus        16 ~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A           16 AILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             HHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999998752      358999999999999999999998753

>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=98.89  E-value=3.7e-10  Score=90.05  Aligned_cols=50  Identities=26%  Similarity=0.648  Sum_probs=45.4

Q ss_pred             CCCCcccccccccccccEE-eCCCCHhhhHHhHHHHhccC-CCCCCccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~~-~~CP~Cr~~i~~  347 (353)
                      +.++..|.||++.+.+++. ++|||. ||..|+.+|+... ..||+||.++..
T Consensus        19 l~~~~~C~IC~~~~~~p~~~~~CgH~-FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           19 IAEVFRCFICMEKLRDARLCPHCSKL-CCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTTCCE-EEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCCccCCccccCccccCCCCCh-hhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            4567899999999999999 999999 9999999999885 799999999853

>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=98.89  E-value=9.3e-10  Score=86.97  Aligned_cols=55  Identities=22%  Similarity=0.273  Sum_probs=49.9

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-----CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|++++.+     .+++|+|+|++++|++|+.+|.+++++.
T Consensus        28 ~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           28 LVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             HHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             eEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            489999999999999999999998754     3688999999999999999999998764

>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=98.89  E-value=3.5e-10  Score=92.20  Aligned_cols=51  Identities=29%  Similarity=0.696  Sum_probs=45.8

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      ...++..|.||++.+.+++.++|||. ||..|+.+|+.. ...||+||..+..
T Consensus        11 ~~~~~~~C~iC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           11 PSLSECQCGICMEILVEPVTLPCNHT-LCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CCHHHHBCTTTCSBCSSCEECTTSCE-ECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCCCccCCcccCceeEcCCCCH-HhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            44567999999999999999999999 999999999877 7799999998763

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=98.88  E-value=1.8e-09  Score=87.41  Aligned_cols=55  Identities=20%  Similarity=0.341  Sum_probs=49.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|+|.+..      .+++|+|+|++++|++|+.+|.+++++.
T Consensus        20 ~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A           20 LVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             TTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             ccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            489999999999999999999998753      2489999999999999999999998864

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.88  E-value=6.1e-10  Score=81.45  Aligned_cols=48  Identities=23%  Similarity=0.652  Sum_probs=40.6

Q ss_pred             CCcccccccc-ccccc----EEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         299 GSRQCYLCND-REVTH----ALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~-~~~~~----~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      ++..|.||++ .+.++    ++++|||. ||..|+.+|+.. ...||+||.++..
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            3578999999 66666    57899999 999999999766 6789999999864

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=98.88  E-value=1.4e-09  Score=82.36  Aligned_cols=54  Identities=22%  Similarity=0.242  Sum_probs=48.6

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .||||+|++|++|+++|||+|++++..   .+++|.|+|+++++.+|+.+|.+++++
T Consensus        18 ~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A           18 CIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             eEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            479999999999999999999998632   368999999999999999999999864

>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=98.88  E-value=1.2e-09  Score=85.50  Aligned_cols=55  Identities=20%  Similarity=0.400  Sum_probs=49.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|+++...   .+++|+|+|+++++++|+.+|.+++++.
T Consensus        27 ~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           27 SIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             HHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             eeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            479999999999999999999998642   3689999999999999999999999875

>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=98.88  E-value=2.1e-09  Score=83.60  Aligned_cols=59  Identities=15%  Similarity=0.192  Sum_probs=51.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADHFSALR   60 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~   60 (353)
                      .||||+|.+|++|+++|||+|+++..+      .++.|+|+|+++++.+|+.+|.+++.+....+
T Consensus        16 ~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~r   80 (87)
T 1ec6_A           16 AILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVR   80 (87)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccccc
Confidence            479999999999999999999999753      35899999999999999999999988765433

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=98.87  E-value=2.1e-09  Score=86.84  Aligned_cols=56  Identities=21%  Similarity=0.234  Sum_probs=50.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .||||+|++||+|+++|+|+|+|+...   .+++|+|+|+++++++|+.+|.+++++..
T Consensus        24 ~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           24 VVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             HHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             ccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            479999999999999999999998543   35789999999999999999999998753

>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=98.87  E-value=1.9e-09  Score=85.14  Aligned_cols=56  Identities=29%  Similarity=0.415  Sum_probs=50.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC-cCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e-~~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .||||+|.+||+|+++|||+|++|..++ ++.|+|+|.++++++|+.+|.+++++..
T Consensus        30 ~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           30 FVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             HHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             eeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            3799999999999999999999997543 5789999999999999999999988753

>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=98.86  E-value=3e-09  Score=85.62  Aligned_cols=57  Identities=21%  Similarity=0.356  Sum_probs=51.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCc-CeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEE-PVFVVTGRKEDVARAKREILSAADHFSA   58 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~-~vv~I~G~~e~v~~Ak~~I~~i~~~~~~   58 (353)
                      .|||++|.+||+|+++|||+|++|+.+++ +.|+|+|..+++++|+.+|..++++...
T Consensus        30 ~IIG~gG~~Ir~I~eetg~~I~I~~~g~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e~   87 (104)
T 2ctk_A           30 YVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQA   87 (104)
T ss_dssp             HHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhHHH
Confidence            48999999999999999999999987633 5899999999999999999999887654

>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=98.86  E-value=9e-10  Score=88.80  Aligned_cols=50  Identities=30%  Similarity=0.740  Sum_probs=45.9

Q ss_pred             CCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      +.++..|.||++.+.+++.+ +|||. ||..|+..|+.....||+||..+..
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            45678999999999999998 99999 9999999999888999999999864

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.85  E-value=5.9e-09  Score=85.79  Aligned_cols=68  Identities=18%  Similarity=0.215  Sum_probs=56.2

Q ss_pred             ceEEEEEecCC-------CccceeccCChHHHHHHHHhCceEEcCCCC-------------CCCeEEEEc-CHHHHHHHH
Q psy4141          80 HVTIEVRVPYK-------VVGLVVGPKGATIKRIQHQTNTYIVTPSRD-------------KEPVFEVTG-APDSVEIAR  138 (353)
Q Consensus        80 ~~t~~v~VP~~-------~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-------------~e~~v~I~G-~~e~V~~A~  138 (353)
                      ..+.+|.||-+       ++|.|||++|.+||+|+++|||+|.|-.+.             ++-.|.|.+ +++++++|+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~   90 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAK   90 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHH
Confidence            36677777654       789999999999999999999999885331             224788887 599999999


Q ss_pred             HHHHHHHHh
Q psy4141         139 QEIESHIIR  147 (353)
Q Consensus       139 ~~I~~~i~~  147 (353)
                      ++|++++..
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999999886

>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=98.85  E-value=4.1e-10  Score=109.01  Aligned_cols=52  Identities=40%  Similarity=0.965  Sum_probs=48.6

Q ss_pred             CCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141         297 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII  352 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~  352 (353)
                      +.++..|.||++.+.+++++||||.+||..|+..+    ..||+||.++...+++|
T Consensus       292 l~~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~~~~i~  343 (345)
T 3t6p_A          292 LQEERTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGTVRTF  343 (345)
T ss_dssp             HHTTCBCTTTSSSBCCEEEETTCCEEECTTTGGGC----SBCTTTCCBCCEEEECC
T ss_pred             CcCCCCCCccCCcCCceEEcCCCChhHhHHHHhcC----CcCCCCCCCccCeEEee
Confidence            45678999999999999999999999999999987    79999999999999997

>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=98.85  E-value=2.3e-09  Score=86.25  Aligned_cols=58  Identities=22%  Similarity=0.317  Sum_probs=51.6

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHFSAL   59 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~   59 (353)
                      .||||+|++||+|+++|||+|+++...     ++++|+|+|+.+++++|+.+|.+++++...+
T Consensus        28 ~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~~~   90 (104)
T 1we8_A           28 RIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEEL   90 (104)
T ss_dssp             HHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhChHH
Confidence            489999999999999999999998654     3689999999999999999999999866553

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=98.84  E-value=2.5e-09  Score=82.89  Aligned_cols=51  Identities=14%  Similarity=0.038  Sum_probs=46.5

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      .+.++..|+||++...+++.++|||+ ||+.|+.+|+.....||+||.++..
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            34567999999999999999999999 9999999999888899999998864

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=98.84  E-value=9.9e-10  Score=87.11  Aligned_cols=50  Identities=30%  Similarity=0.736  Sum_probs=45.3

Q ss_pred             CCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      +.+...|.||++.+.+++.+ +|||. ||..|+.+|+.....||+||..+..
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            45568999999999999988 99999 9999999999888899999998864

>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=98.83  E-value=2.1e-09  Score=82.64  Aligned_cols=55  Identities=20%  Similarity=0.193  Sum_probs=48.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|++++..   .+++|.|+|+++++++|+.+|.+++.+.
T Consensus        19 ~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A           19 CIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             ceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            379999999999999999999998632   3689999999999999999999998764

>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=98.81  E-value=2.4e-09  Score=85.61  Aligned_cols=51  Identities=14%  Similarity=0.051  Sum_probs=46.5

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      .+.++..|+||++...+++.++|||+ ||+.|+.+|+.....||+||.++..
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            34567999999999999999999999 9999999999888899999999864

>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=98.81  E-value=1.4e-09  Score=93.29  Aligned_cols=49  Identities=29%  Similarity=0.617  Sum_probs=44.4

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+...|.||++.+.+++.+||||. ||..|+..|+.. ...||+||.++..
T Consensus        76 ~~~~~C~IC~~~~~~pv~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~  125 (150)
T 1z6u_A           76 EQSFMCVCCQELVYQPVTTECFHN-VCKDCLQRSFKAQVFSCPACRHDLGQ  125 (150)
T ss_dssp             HHHTBCTTTSSBCSSEEECTTSCE-EEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCEeecCChhhcCCEEcCCCCc-hhHHHHHHHHHhCCCcCCCCCccCCC
Confidence            456899999999999999999999 999999999987 4589999999875

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.78  E-value=5.7e-10  Score=79.52  Aligned_cols=46  Identities=30%  Similarity=0.745  Sum_probs=40.7

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      .+...|.||++.+.+++.+||||. ||..|+..+   ...||+||..+..
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            456889999999999999999999 999998873   5789999998764

>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=98.77  E-value=3.1e-09  Score=87.08  Aligned_cols=51  Identities=22%  Similarity=0.547  Sum_probs=45.9

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+.+...|.||++.+.+++.++|||. ||..|+..|+.. ...||+||.++..
T Consensus        14 ~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           14 PLESKYECPICLMALREAVQTPCGHR-FCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCcCChhhcCeEECCcCCh-hhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            45677899999999999999999999 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=98.76  E-value=2.1e-09  Score=93.22  Aligned_cols=52  Identities=25%  Similarity=0.597  Sum_probs=45.7

Q ss_pred             CCCCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         295 GSISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       295 ~~~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      ..+.+...|.||++.+.+++.+ +|||. ||..|+..|+.. ...||+||.++..
T Consensus        49 ~~~~~~~~C~IC~~~~~~p~~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           49 RSLHSELMCPICLDMLKNTMTTKECLHR-FCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             -CCHHHHBCTTTSSBCSSEEEETTTCCE-EEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             hhCCCCCCCcccChHhhCcCEeCCCCCh-hHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            3456678999999999999987 99999 999999999987 7889999998853

>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=98.76  E-value=1.1e-08  Score=81.98  Aligned_cols=55  Identities=18%  Similarity=0.245  Sum_probs=50.0

Q ss_pred             eeecCCCchHHHHHHH-cCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141           2 KKISRSGCKIKALRAK-TNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSA   58 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~-Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~   58 (353)
                      +|||++|++||+|+++ ++++|++|+  ++++|+|.|+++.|++|+.+|..+++++..
T Consensus        40 ~IIG~~G~~Ik~i~~~~~~v~I~fp~--~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           40 FIIGKKGQNLAKITQQMPKVHIEFTE--GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             HHHTTTTCHHHHHHHHCSSSEEEECS--SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhcCCCCccHHHHHHHcCCcEEEeCC--CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            4899999999999997 599999997  467899999999999999999999988754

>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=98.74  E-value=4e-09  Score=85.59  Aligned_cols=47  Identities=21%  Similarity=0.530  Sum_probs=39.2

Q ss_pred             CcccccccccccccE------------------EeCCCCHhhhHHhHHHHhc-----cCCCCCCccccccc
Q psy4141         300 SRQCYLCNDREVTHA------------------LIPCGHNFFCSECAERTCD-----FDRTCPMCRVPVNQ  347 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~------------------llpCgH~~fC~~C~~~~~~-----~~~~CP~Cr~~i~~  347 (353)
                      +..|.||++.+..+.                  +++|+|. ||..|+..|+.     ....||+||+.+..
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~-Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHA-FHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCE-ECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCc-ccHHHHHHHHHcccCCCCCcCCCCCCccCC
Confidence            468999999985533                  7899999 99999999984     36799999998754

>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=98.74  E-value=1.7e-09  Score=87.28  Aligned_cols=49  Identities=20%  Similarity=0.571  Sum_probs=43.3

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccC---CCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFD---RTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~---~~CP~Cr~~i~~  347 (353)
                      .+...|.||++.+.+++.++|||. ||..|+..|+...   ..||+||.++..
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            345789999999999999999999 9999999999863   489999998864

>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=98.71  E-value=6.5e-09  Score=101.56  Aligned_cols=51  Identities=25%  Similarity=0.720  Sum_probs=45.8

Q ss_pred             CcccccccccccccEEeCCCCHhhhHHhHHHHhc-cCCCCCCcccccccceec
Q psy4141         300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQAMRI  351 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~-~~~~CP~Cr~~i~~~~ri  351 (353)
                      ...|.||++...+++++||||. ||..|+..|.. ....||+||.++.....+
T Consensus       332 ~~~C~ICle~~~~pv~lpCGH~-FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~i  383 (389)
T 2y1n_A          332 FQLCKICAENDKDVKIEPCGHL-MCTSCLTSWQESEGQGCPFCRCEIKGTEPI  383 (389)
T ss_dssp             SSBCTTTSSSBCCEEEETTCCE-ECHHHHHHHHHHTCSBCTTTCCBCCEEEEC
T ss_pred             CCCCCccCcCCCCeEEeCCCCh-hhHHHHHHHHhcCCCCCCCCCCccCCceeE
Confidence            4799999999999999999999 99999999988 488999999999876544

>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=98.70  E-value=1.9e-08  Score=79.56  Aligned_cols=55  Identities=27%  Similarity=0.445  Sum_probs=50.1

Q ss_pred             eeecCCCchHHHHHHHc-CceEEecCCCC-cCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKT-NTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~T-ga~I~ip~~~e-~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .|||++|.+|++|+++| |++|++|+.++ .+.|+|.|..++|++|+++|..++++.
T Consensus        30 ~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A           30 SLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             HHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            47999999999999999 99999998763 368999999999999999999999875

>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=98.70  E-value=2.2e-09  Score=91.08  Aligned_cols=49  Identities=20%  Similarity=0.482  Sum_probs=44.2

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPV  345 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i  345 (353)
                      .+.++..|.||++.+.+++.++|||. ||..|+.+|+.. ...||+||.++
T Consensus        27 ~l~~~~~C~IC~~~~~~pv~~~CgH~-FC~~Ci~~~~~~~~~~CP~Cr~~~   76 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRRPFQAQCGHR-YCSFCLASILSSGPQNCAACVHEG   76 (141)
T ss_dssp             GCCGGGBCTTTCSBCSSEEECTTSCE-EEHHHHHHHGGGSCEECHHHHHTT
T ss_pred             cCCcCcCCCCCChhhcCcEECCCCCc-cCHHHHHHHHhcCCCCCCCCCCcc
Confidence            45678999999999999999999999 999999999887 45899999965

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.68  E-value=6.4e-09  Score=85.91  Aligned_cols=49  Identities=37%  Similarity=0.807  Sum_probs=44.4

Q ss_pred             CCCccccccccccccc-------EEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~-------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      .++..|.||++.+.++       +.++|||. ||..|+.+|+.....||+||..+..
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            3568999999999887       89999999 9999999999888899999999864

>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=98.67  E-value=6.1e-09  Score=84.89  Aligned_cols=51  Identities=27%  Similarity=0.591  Sum_probs=45.8

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+.++..|.||++.+.+++.++|||. ||..|+.+|+.. ...||+||.++..
T Consensus        19 ~~~~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           19 HFVKSISCQICEHILADPVETSCKHL-FCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHHHHTBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             hccCCCCCCCCCcHhcCcEEcCCCCc-ccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            34567899999999999999999999 999999999987 7899999999864

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.65  E-value=1.3e-08  Score=77.86  Aligned_cols=46  Identities=20%  Similarity=0.510  Sum_probs=38.1

Q ss_pred             Ccccccccccccc--------------c-EEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         300 SRQCYLCNDREVT--------------H-ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       300 ~~~C~IC~~~~~~--------------~-~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      +..|.||++.+..              . ++.+|+|. ||..|+.+|+.....||+||+++.
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            4668888887754              3 44469999 999999999998889999999875

>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=98.59  E-value=5.4e-09  Score=85.54  Aligned_cols=47  Identities=26%  Similarity=0.644  Sum_probs=42.9

Q ss_pred             CCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      +.+...|.||++.+.+++.+ +|||. ||..|+..|+.  ..||+||.++.
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            45678999999999999999 99999 99999999976  78999999884

>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=98.56  E-value=2.3e-08  Score=92.72  Aligned_cols=48  Identities=15%  Similarity=0.144  Sum_probs=43.5

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      +...|+||++...++|.+||||+ ||..|+.+|+.. ...||+||.++..
T Consensus       207 ~~~~c~i~~~~~~dPv~~~~gh~-f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMREPCITPSGIT-YDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCSSEEECSSCCE-EETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhcCCeECCCCCE-ECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            46899999999999999999999 999999999987 4459999999864

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.56  E-value=2.1e-08  Score=82.75  Aligned_cols=54  Identities=35%  Similarity=0.728  Sum_probs=46.6

Q ss_pred             CCCccccccccccccc-------EEeCCCCHhhhHHhHHHHhccCCCCCCcccccc--cceecc
Q psy4141         298 SGSRQCYLCNDREVTH-------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN--QAMRII  352 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~-------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~--~~~ri~  352 (353)
                      .+...|.||++.+..+       +.++|||. ||..|+.+|+.....||+||..+.  ++.++|
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  132 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHV-FCSQCLRDSLKNANTCPTCRKKINHKRYHPIY  132 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBE-EEHHHHHHHHHHCSBCTTTCCBCCGGGEEEEC
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCCh-hhHHHHHHHHHcCCCCCCCCCcCChhcceeee
Confidence            4568899999998775       88999999 999999999988999999999986  355555

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.56  E-value=8.3e-08  Score=99.44  Aligned_cols=92  Identities=25%  Similarity=0.321  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHHhhhhh-hhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC
Q psy4141          42 VARAKREILSAADHFSA-LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD  120 (353)
Q Consensus        42 v~~Ak~~I~~i~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~  120 (353)
                      ++.|++....+++.+.. +...+..       .....|  ....|.||.+.+|.|||+||++||+|+++|||+|.|.   
T Consensus       536 L~~A~~g~~~I~~~m~~al~~~~~~-------~~~~ap--~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~---  603 (630)
T 3u1k_A          536 IQQASVAKKEILQIMNKTISKPRAS-------RKENGP--VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV---  603 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSCCSS-------CCTTCC--EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh-------hcccCC--eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc---
Confidence            45566666666555443 2222111       122345  7889999999999999999999999999999999876   


Q ss_pred             CCCeEEEEcC-HHHHHHHHHHHHHHH
Q psy4141         121 KEPVFEVTGA-PDSVEIARQEIESHI  145 (353)
Q Consensus       121 ~e~~v~I~G~-~e~V~~A~~~I~~~i  145 (353)
                      ++..|.|.|+ .+.+++|+++|++++
T Consensus       604 d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          604 DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            3468999996 689999999998765

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.54  E-value=6.9e-08  Score=87.65  Aligned_cols=64  Identities=27%  Similarity=0.267  Sum_probs=57.7

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-----HHHHHHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-----PDSVEIARQEIESHII  146 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-----~e~V~~A~~~I~~~i~  146 (353)
                      ...+|.||.+.+|.|||++|++|+.|+++||++|.+..+  ++.|+|.|+     ++++++|+++|.+++.
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~--~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE--TGEVWITSTKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT--TCEEEEEECTTCCSHHHHHHHHHHHHHHHT
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC--CCEEEEecCCCCCCHHHHHHHHHHHHHHhc
Confidence            567999999999999999999999999999999998743  567999886     6999999999999873

>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=98.53  E-value=4e-08  Score=77.38  Aligned_cols=47  Identities=19%  Similarity=0.390  Sum_probs=41.5

Q ss_pred             CCCCcccccccccccccEEeC-CCCHhhhHHhHHHHhccC------CCCCC--cccc
Q psy4141         297 ISGSRQCYLCNDREVTHALIP-CGHNFFCSECAERTCDFD------RTCPM--CRVP  344 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~llp-CgH~~fC~~C~~~~~~~~------~~CP~--Cr~~  344 (353)
                      ..++..|+||++.+.+++.++ |||+ ||..|+.+|+...      ..||+  |+..
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 9999999999863      58999  9865

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.50  E-value=9.8e-08  Score=80.50  Aligned_cols=66  Identities=23%  Similarity=0.414  Sum_probs=52.2

Q ss_pred             eEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCCC--------------------CC-CeEEEEcC-HH
Q psy4141          81 VTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--------------------KE-PVFEVTGA-PD  132 (353)
Q Consensus        81 ~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~--------------------~e-~~v~I~G~-~e  132 (353)
                      .+.+|.||.      +++|+|||++|.++|+|+++|||+|.|-.+.                    .+ --|.|++. ++
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            456677774      5599999999999999999999999886542                    11 26889984 43


Q ss_pred             -----HHHHHHHHHHHHHH
Q psy4141         133 -----SVEIARQEIESHII  146 (353)
Q Consensus       133 -----~V~~A~~~I~~~i~  146 (353)
                           .+++|+++|++++.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                 78999999998875

>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=98.48  E-value=7.5e-08  Score=77.67  Aligned_cols=45  Identities=22%  Similarity=0.471  Sum_probs=38.7

Q ss_pred             Cccccccccccccc------------------EEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141         300 SRQCYLCNDREVTH------------------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  345 (353)
Q Consensus       300 ~~~C~IC~~~~~~~------------------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i  345 (353)
                      +..|.||++.+...                  ++++|+|. ||..|+..|+.....||+||+.+
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~-FH~~Ci~~Wl~~~~~CP~Cr~~~   99 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHA-FHFHCISRWLKTRQVCPLDNREW   99 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCE-EEHHHHHHHHTTCSBCSSSCSBC
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecccCcE-ECHHHHHHHHHcCCcCcCCCCcc
Confidence            46799998876543                  56899999 99999999998889999999985

>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=98.48  E-value=5.7e-08  Score=84.36  Aligned_cols=51  Identities=22%  Similarity=0.547  Sum_probs=45.9

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+.+...|.||++.+.+++.++|||. ||..|+.+|+.. ...||+||.++..
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            45677999999999999999999999 999999999877 5599999998865

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.46  E-value=7.1e-08  Score=84.84  Aligned_cols=49  Identities=14%  Similarity=0.134  Sum_probs=44.2

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+...|+||++...+||.+||||+ ||..|+..|+.. ...||+|+.++..
T Consensus       104 p~~f~CPI~~elm~DPV~~~~Ght-fer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          104 PDYLCGKISFELMREPCITPSGIT-YDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CGGGBCTTTCSBCSSEEECTTSCE-EEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cHhhcccCccccCCCCeECCCCCE-ECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            456899999999999999999999 999999999987 4579999998864

>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=98.36  E-value=1.9e-07  Score=79.27  Aligned_cols=60  Identities=23%  Similarity=0.380  Sum_probs=48.9

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEI  141 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I  141 (353)
                      ++.++.||.+.+|.+||++|++|++|++++|+.|...+++.+ .+.+.| +|+.|.+|+.++
T Consensus         4 ~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~~~~-~~i~~~~~p~~v~~~~~~l   64 (144)
T 2qnd_A            4 FHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTC-TFHIYGEDQDAVKKARSFL   64 (144)
T ss_dssp             CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEETTTT-EEEEEESSHHHHHHHHHHH
T ss_pred             eEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCCCch-heeeccCCHHHHHHHHHhh
Confidence            688999999999999999999999999999966655544444 455555 699999998754

>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=98.21  E-value=5.4e-07  Score=83.35  Aligned_cols=50  Identities=18%  Similarity=0.264  Sum_probs=43.7

Q ss_pred             CCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhcc--CCCCCC--ccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF--DRTCPM--CRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~--~~~CP~--Cr~~i~~  347 (353)
                      ...+..|+||++.+.++|.. .|||+ ||..|+.+||..  ...||+  ||..+..
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            35678999999999999985 99999 999999999986  358999  9997753

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.19  E-value=1e-06  Score=67.38  Aligned_cols=49  Identities=20%  Similarity=0.510  Sum_probs=40.4

Q ss_pred             CCCcccccccccc--cccEEeCCC-----CHhhhHHhHHHHhcc--CCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDRE--VTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~--~~~~llpCg-----H~~fC~~C~~~~~~~--~~~CP~Cr~~i~~  347 (353)
                      .++..|.||++.+  .+.+++||.     |. |+..|+.+|...  ...||+||..+.-
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            3457899999765  356778996     99 999999999887  3699999998854

>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=98.16  E-value=2.3e-06  Score=75.90  Aligned_cols=64  Identities=23%  Similarity=0.331  Sum_probs=57.4

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEE-----cCHHHHHHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT-----GAPDSVEIARQEIESHII  146 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~-----G~~e~V~~A~~~I~~~i~  146 (353)
                      ...++.||.+.+|.|||++|++++.|++++|++|.+..  .++.|+|.     |+|.++.+|+++|.++..
T Consensus         4 ~~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~--~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~r   72 (191)
T 1tua_A            4 PRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT--ENSMVIVEPEAEGIPPVNLMKAAEVVKAISL   72 (191)
T ss_dssp             CCEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET--TTTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             cceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc--CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Confidence            34689999999999999999999999999999998864  46678888     999999999999988765

>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=98.15  E-value=2.9e-07  Score=75.51  Aligned_cols=44  Identities=23%  Similarity=0.489  Sum_probs=0.0

Q ss_pred             ccccccccccccc------------------EEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141         301 RQCYLCNDREVTH------------------ALIPCGHNFFCSECAERTCDFDRTCPMCRVPV  345 (353)
Q Consensus       301 ~~C~IC~~~~~~~------------------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i  345 (353)
                      ..|.||++.+...                  ++++|+|. ||..|+.+|......||+||+++
T Consensus        49 d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~-FH~~CI~~Wl~~~~~CP~Cr~~~  110 (117)
T 4a0k_B           49 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHA-FHFHCISRWLKTRQVCPLDNREW  110 (117)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             CcCeECChhhcCcChhhhcccccccccccccccCCcCce-EcHHHHHHHHHcCCcCCCCCCee
Confidence            5799999887542                  23599999 99999999998888999999985

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.13  E-value=2.1e-06  Score=70.44  Aligned_cols=56  Identities=14%  Similarity=0.159  Sum_probs=45.9

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-------------Cc-CeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-------------EE-PVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-------------e~-~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .|||++|.+||+|+++|||+|.|-.++             ++ .+.+...+.+++++|+++|.+++....
T Consensus        32 ~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~~Ie~Ll~~v~  101 (119)
T 2yqr_A           32 KVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKKLCENLLQTVH  101 (119)
T ss_dssp             HHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             eEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHHHHHHHhhchH
Confidence            489999999999999999999996442             22 455555789999999999999987543

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=98.09  E-value=1.8e-06  Score=90.59  Aligned_cols=64  Identities=19%  Similarity=0.236  Sum_probs=12.3

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                      ....+.||.+.+|.|||+||++||+|+++||++|.+.   ++..|.|.+. .+.+++|+++|..++.+
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~---ddG~v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN---DDGVVKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             C----------------------------------------------CCSCHHHHHHHHHC-------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE---CCceEEEEeCCHHHHHHHHHHHHHHhhh
Confidence            5678999999999999999999999999999999875   2456888885 88999999999988765

>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=98.07  E-value=1e-06  Score=69.00  Aligned_cols=45  Identities=27%  Similarity=0.671  Sum_probs=36.7

Q ss_pred             CCcccccccccccccEE---eCCCCHhhhHHhHHHHhcc--------CCCCCC--cccc
Q psy4141         299 GSRQCYLCNDREVTHAL---IPCGHNFFCSECAERTCDF--------DRTCPM--CRVP  344 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~l---lpCgH~~fC~~C~~~~~~~--------~~~CP~--Cr~~  344 (353)
                      +..+|.||++.+.....   .+|||. ||..|+..++..        ...||.  |+..
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            45789999998766543   379999 999999999874        247999  9987

>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=98.03  E-value=1.2e-06  Score=68.44  Aligned_cols=50  Identities=20%  Similarity=0.276  Sum_probs=43.0

Q ss_pred             eecCCCchHHHHHHHcCce-EEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHh
Q psy4141           3 KISRSGCKIKALRAKTNTY-IKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD   54 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~-I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~   54 (353)
                      +||++|.+||+|+++||++ |++.+  ++..|.|.| +.+++++|+.+|..+.+
T Consensus        29 vIG~gGk~Ik~I~e~tGv~~IdI~e--ddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           29 AIGTHGSNIQQARKVPGVTAIELDE--DTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             HHTTTTHHHHHHHTSTTEEEEEEET--TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             hcCCCcHHHHHHHHHhCCeEEEEEc--CCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            7999999999999999998 99973  347788888 89999999999965544

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.98  E-value=9.5e-06  Score=67.40  Aligned_cols=68  Identities=12%  Similarity=0.107  Sum_probs=60.0

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCC--CCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK--EPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~--e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ....+.|...+++.|||++|+.|+.|++.|++.|.+..-+.  +-.|+|.|++..-.+|+.+|..+..-.
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            45778999999999999999999999999999998765443  568999999999999999999887763

>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=97.89  E-value=1.2e-05  Score=67.10  Aligned_cols=54  Identities=24%  Similarity=0.263  Sum_probs=44.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-------------------CcCeEEEec-CHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-------------------EEPVFVVTG-RKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-------------------e~~vv~I~G-~~e~v~~Ak~~I~~i~~~   55 (353)
                      +|||.+|.+||+|+++|||+|.|..++                   ++-.|.|++ +.+.+++|+++|..++..
T Consensus        26 ~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           26 LLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHHHTT
T ss_pred             eEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHHHHHHHHHHHHHhc
Confidence            489999999999999999999996532                   122345555 789999999999999875

>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=97.76  E-value=8.8e-06  Score=58.80  Aligned_cols=47  Identities=13%  Similarity=0.109  Sum_probs=42.2

Q ss_pred             CcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         300 SRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ...|+||++...+++.. +|||. ||+.|+.+|......||+++.++..
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            36899999999999999 99999 9999999999876679999999854

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.55  E-value=4.4e-05  Score=60.12  Aligned_cols=48  Identities=33%  Similarity=0.676  Sum_probs=37.6

Q ss_pred             cccccccccccc-EEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccccee
Q psy4141         302 QCYLCNDREVTH-ALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMR  350 (353)
Q Consensus       302 ~C~IC~~~~~~~-~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~~~r  350 (353)
                      -|.+|--..... -.+||.|. ||.+|+..|..+ ...||.|+.++..+-+
T Consensus         3 fC~~C~~Pi~iygRmIPCkHv-FCydCa~~~~~~~~k~Cp~C~~~V~rVe~   52 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHV-FCYDCAILHEKKGDKMCPGCSDPVQRIEQ   52 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCE-EEHHHHHHHHHTTCCBCTTTCCBCSEEEE
T ss_pred             ecCccCCCeEEEeeecccccc-HHHHHHHHHHhccCCCCcCcCCeeeeeEE
Confidence            366776665543 35899998 999999999866 8899999999876533

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.41  E-value=0.00024  Score=53.24  Aligned_cols=48  Identities=17%  Similarity=0.442  Sum_probs=39.7

Q ss_pred             CCCcccccccccccccEE-eCCCCHhhhHHhHHHHhccC--CCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDFD--RTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~~--~~CP~Cr~~i~  346 (353)
                      +....|.||++....... ..|+|. |...|+.+|+...  ..||+||..+.
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~~C~h~-fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCETCGIR-MHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECSSSCCE-ECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             CCCCcCcchhhHcccCCccCCCCch-hhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            345889999998865443 389999 9999999999875  89999998865

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=97.32  E-value=9.6e-05  Score=53.12  Aligned_cols=49  Identities=20%  Similarity=0.533  Sum_probs=38.9

Q ss_pred             CCCcccccccccccccEEeCCCCH----hhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHN----FFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~----~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      ++...|.||++...+..+.||.+.    .|...|+.+|...  ...||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCCCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            356789999987766667897641    2999999999876  678999998764

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.25  E-value=0.00013  Score=61.38  Aligned_cols=53  Identities=23%  Similarity=0.212  Sum_probs=42.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC--------------------c-CeEEEec-CH-----HHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE--------------------E-PVFVVTG-RK-----EDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e--------------------~-~vv~I~G-~~-----e~v~~Ak~~I~~i~~   54 (353)
                      +|||.+|.++|+|+++|||+|.|-.++.                    + --|.|++ +.     +.+++|+.+|.+++.
T Consensus        21 ~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           21 RILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHHHHSS
T ss_pred             EEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHHHHHCC
Confidence            5899999999999999999999876541                    1 1456666 33     379999999999976

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=97.03  E-value=0.00024  Score=74.76  Aligned_cols=64  Identities=16%  Similarity=0.241  Sum_probs=0.0

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                      ....+.||.+.++.|||+||++|++|.++||+.|.+..   +..|.|.+. .+.+++|+++|+.++.+
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---DGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC---CccEEEecCCHHHHHHHHHHHHHHhhh
Confidence            66788999999999999999999999999999997663   456777775 67888899988877644

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.01  E-value=0.0003  Score=59.50  Aligned_cols=89  Identities=18%  Similarity=0.173  Sum_probs=58.6

Q ss_pred             eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141           3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT   82 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t   82 (353)
                      .||++|++|+.|+++.|-+|++-...++        ++.      .|...+.-      .+-.+...     ....+...
T Consensus        50 ~IG~~G~ri~~i~~elgekIdIV~~s~d--------~~~------fI~naLsP------A~V~~V~i-----~~~~~~~~  104 (144)
T 2cxc_A           50 AIGRGGRLIKLLREALGKNIEVVEYSSD--------LER------IVKNLFPG------VKIESINV-----RERNGVKQ  104 (144)
T ss_dssp             HHCGGGHHHHHHHHHHSSEEEEEECCSS--------HHH------HHHHHSTT------SCEEEEEE-----EEETTEEE
T ss_pred             cCccCchHHHHHHHHhCCeeEEEEcCCC--------HHH------HHHHhcCC------ceEEEEEE-----eecCCcEE
Confidence            4899999999999999988885433322        221      22222110      00000000     00023467


Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      ..+.||.+..++.|||+|.+++-..+.||.+|.|
T Consensus       105 ~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI  138 (144)
T 2cxc_A          105 VVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGV  138 (144)
T ss_dssp             EEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCE
T ss_pred             EEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCc
Confidence            8899999999999999999999999999988754

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=96.85  E-value=0.0017  Score=53.97  Aligned_cols=56  Identities=18%  Similarity=0.151  Sum_probs=48.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC--cCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e--~~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .|+|++|++|+.|+..+++.|++..-..  ..-|+|.|++..-.+|+.+|..+++...
T Consensus        69 ~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~hr  126 (140)
T 3v69_A           69 IMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPPPFRRDVDRMLTDLAHYCR  126 (140)
T ss_dssp             HHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            3799999999999999999999875432  4568889999999999999999987553

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=96.72  E-value=0.00032  Score=67.13  Aligned_cols=50  Identities=18%  Similarity=0.470  Sum_probs=39.4

Q ss_pred             CCCcccccccccccccEE--------eCCCCHhhhHHhHHHHhcc--C---------CCCCCcccccccc
Q psy4141         298 SGSRQCYLCNDREVTHAL--------IPCGHNFFCSECAERTCDF--D---------RTCPMCRVPVNQA  348 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~l--------lpCgH~~fC~~C~~~~~~~--~---------~~CP~Cr~~i~~~  348 (353)
                      ....+|.||++.....-.        ..|+|. |...|+.+|...  .         ..||+||.+++.-
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~-FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLK-CHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCC-BCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCc-cchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            456899999998765111        379999 999999999875  1         3699999998753

>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=96.70  E-value=0.00016  Score=76.35  Aligned_cols=94  Identities=23%  Similarity=0.327  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          40 EDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        40 e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      +.++.|+.....+++.+...-....       .-....|  ....|.||.+.+|.|||++|++||+|+++||+.|.+.. 
T Consensus       566 ~aL~~A~~~~~~I~~~m~~al~~~~-------~~~~~ap--~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-  635 (757)
T 1e3p_A          566 AALKQARDARLHILDVMMEAIDTPD-------EMSPNAP--RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-  635 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSCC-------CCCTTSC--BCCCC------------------CTTCCCCCSCC-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccc-------cccccCc--eeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-
Confidence            4455666666666555433211111       1112344  44578899999999999999999999999999998763 


Q ss_pred             CCCCeEEEEcC-HHHHHHHHHHHHHHH
Q psy4141         120 DKEPVFEVTGA-PDSVEIARQEIESHI  145 (353)
Q Consensus       120 ~~e~~v~I~G~-~e~V~~A~~~I~~~i  145 (353)
                        +..|.|.+. .+..++|+++|..+.
T Consensus       636 --dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          636 --DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             ------CCCBSSHHHHCC---------
T ss_pred             --CceEEEecCCHHHHHHHHHHHHHhc
Confidence              457888875 677788888887665

>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=95.69  E-value=0.013  Score=53.70  Aligned_cols=91  Identities=14%  Similarity=0.119  Sum_probs=58.4

Q ss_pred             eecCCCchHHHH-HHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcce
Q psy4141           3 KISRSGCKIKAL-RAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHV   81 (353)
Q Consensus         3 IIGk~G~~Ik~I-~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~   81 (353)
                      .||++|.+|+.| ++-.|-+|++-...++        ++      ..|...+.-      ..-.....    . + ....
T Consensus       131 cIG~~G~rI~~i~~eL~gekIDIi~~s~d--------p~------~fi~nalsP------A~V~~V~i----~-~-~~~~  184 (251)
T 2asb_A          131 CIGPMGQRVRNVMSELSGEKIDIIDYDDD--------PA------RFVANALSP------AKVVSVSV----I-D-QTAR  184 (251)
T ss_dssp             HHCGGGHHHHHHHHHTTTCEEEEEECCSS--------HH------HHHHHHTTT------SCCSEEEE----E-E-TTTT
T ss_pred             HhCCCchHHHHHHHHhCCCeEEEEEecCC--------HH------HHHHhccCC------cceEEEEE----E-c-CCCc
Confidence            489999999999 6777777775433322        11      112122110      00000000    0 0 1125


Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      ...+.||.++.++-|||+|.+|+-..+.||-+|.|...
T Consensus       185 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          185 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             EEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            68899999999999999999999999999999977543

>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=95.62  E-value=0.015  Score=56.17  Aligned_cols=91  Identities=14%  Similarity=0.107  Sum_probs=60.0

Q ss_pred             eecCCCchHHHHHHHc-CceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcce
Q psy4141           3 KISRSGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHV   81 (353)
Q Consensus         3 IIGk~G~~Ik~I~~~T-ga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~   81 (353)
                      .||++|.+|+.|.++. |-+|++-...++        ++      ..|...+.      ..+......      -.+...
T Consensus       254 cIG~~G~rI~~i~~eL~gekIDIi~~s~d--------p~------~fi~nals------PA~V~~V~~------~~~~~~  307 (366)
T 1k0r_A          254 CIGPMGQRVRNVMSELSGEKIDIIDYDDD--------PA------RFVANALS------PAKVVSVSV------IDQTAR  307 (366)
T ss_dssp             HHCGGGHHHHHHHHHTTTCEEEEEECCSS--------HH------HHHHHHTT------TSCCSEEEE------EETTTT
T ss_pred             ccCCcchHHHHHHHHhCCCeEEEEEcCCC--------HH------HHHHHhcC------CcceeEEEE------EcCCCc
Confidence            4899999999999998 777775433222        11      12222211      000000000      001235


Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR  119 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~  119 (353)
                      ...+.||.+..++.|||+|.+++-..+.||.+|.|-..
T Consensus       308 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          308 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             EEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            78899999999999999999999999999999977544

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=95.27  E-value=0.004  Score=65.36  Aligned_cols=53  Identities=21%  Similarity=0.134  Sum_probs=12.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .|||++|.+||.|.++||++|++.+.  ..+.+...+.+.+++|+..|..++.+.
T Consensus       583 ~vig~gg~~i~~i~~~tg~~idi~dd--G~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          583 EVIGSGGKVIREIVATTGAKVDINDD--GVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             ---------------------------------CCSCHHHHHHHHHC--------
T ss_pred             hhcCCCchhHHHHHHHHCCceeEECC--ceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            48999999999999999999998743  355555567999999999998887644

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.17  E-value=0.016  Score=45.24  Aligned_cols=33  Identities=21%  Similarity=0.638  Sum_probs=27.2

Q ss_pred             CCccccccccc-ccccEE--eCCCCHhhhHHhHHHHh
Q psy4141         299 GSRQCYLCNDR-EVTHAL--IPCGHNFFCSECAERTC  332 (353)
Q Consensus       299 ~~~~C~IC~~~-~~~~~l--lpCgH~~fC~~C~~~~~  332 (353)
                      ++..|.||.+. +..++.  +.|+|+ ||..|+..++
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~-~C~~Cl~~~h   37 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVS-YCDECLKATH   37 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEE-ECHHHHHHHS
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChH-HhHHHCHHHh
Confidence            45789999975 566666  899999 9999999843

>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=93.09  E-value=0.16  Score=48.74  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=35.0

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ....+.||.++.++-|||+|.+++--.+.||-+|.+-+
T Consensus       303 ~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          303 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            57889999999999999999999999999999997653

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=92.02  E-value=0.1  Score=47.41  Aligned_cols=46  Identities=17%  Similarity=0.469  Sum_probs=37.1

Q ss_pred             CcccccccccccccEEe-CCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         300 SRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      -..|.+|.+.......= .|+|. |...|+.+|+..  ...||.|+....
T Consensus       180 i~~C~iC~~iv~~g~~C~~C~~~-~H~~C~~~~~~~~~~~~CP~C~~~W~  228 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSCETCGIR-MHLPCVAKYFQSNAEPRCPHCNDYWP  228 (238)
T ss_dssp             CCBCTTTCSBCSSCEECSSSCCE-ECHHHHHHHTTTCSSCBCTTTCCBCC
T ss_pred             CCcCcchhhHHhCCcccCccChH-HHHHHHHHHHHhCCCCCCCCCCCCCC
Confidence            46799999987655442 38998 999999999876  459999998764

>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=89.41  E-value=0.15  Score=38.23  Aligned_cols=34  Identities=24%  Similarity=0.719  Sum_probs=29.4

Q ss_pred             CcccccccccccccEEeCC----CCHhhhHHhHHHHhcc
Q psy4141         300 SRQCYLCNDREVTHALIPC----GHNFFCSECAERTCDF  334 (353)
Q Consensus       300 ~~~C~IC~~~~~~~~llpC----gH~~fC~~C~~~~~~~  334 (353)
                      .+.|.+|.++..+.-++.|    .|. ||..|.+...+.
T Consensus        15 ~l~CtlC~erLEdtHFVQCPsv~~Hk-FCFpCsr~sIk~   52 (93)
T 2cs3_A           15 PLCCTICHERLEDTHFVQCPSVPSHK-FCFPCSRESIKA   52 (93)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCE-ECHHHHHHHHHH
T ss_pred             eeEeecchhhhccCceeeCCCccCCe-eeccccHHHHHh
Confidence            4789999999999888888    488 999999887664

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=88.79  E-value=0.25  Score=41.46  Aligned_cols=36  Identities=19%  Similarity=0.188  Sum_probs=33.2

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT  116 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i  116 (353)
                      ....+.|+...+|..||++|++|+.|+++.|-+|.+
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdI   71 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEV   71 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEE
Confidence            567899999999999999999999999999999954

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=85.03  E-value=0.17  Score=53.10  Aligned_cols=51  Identities=25%  Similarity=0.271  Sum_probs=0.0

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~   54 (353)
                      .+||++|.+|+.|.++||+.|++...  ..+.+...+.+.+.+|++.|..++.
T Consensus       573 ~~ig~gGk~I~~I~~~~G~~IdI~~d--g~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          573 DVIGKGGSVIRALTEETGTTIEIEDD--GTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             -----------------------------------------------------
T ss_pred             ccccccceeeeeeehhhCceEEecCC--ccEEEecCCHHHHHHHHHHHHHHhh
Confidence            47999999999999999999988743  3555544566777888777766654

>3gku_A Probable RNA-binding protein; APC21302, clostridium symbiosum ATCC 14 structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940}

Probab=84.63  E-value=0.61  Score=41.96  Aligned_cols=112  Identities=13%  Similarity=0.152  Sum_probs=65.0

Q ss_pred             eEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC-CcceEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141          32 VFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV-PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT  110 (353)
Q Consensus        32 vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T  110 (353)
                      +|.++=..+..+.|+..|.++++.+.-         ..  .-.... .....+.|.|..+..|.|||+.|++++.||..+
T Consensus        53 ~V~v~~~~~~~~~a~~~L~~ll~~m~~---------~~--~i~~~~~~~~~~i~i~i~g~d~g~LIGk~G~tLdALQyL~  121 (225)
T 3gku_A           53 IIRAKRKETLQDKAIEFLEQVFDAMNM---------AV--DISVEYNETEKEMNVNLKGDDMGILIGKRGQTLDSLQYLV  121 (225)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHHHHTTC---------CC--EEEEEEETTTTEEEEEEECHHHHHCSTTHHHHHHHHHHHH
T ss_pred             EEEEEeccchHHHHHHHHHHHHHHcCC---------Ce--EEEEEEecCCCEEEEEEcCCccceeecCCCeEhHHHHHHH
Confidence            344433334456788888888876521         00  000000 011345677777889999999999999999999


Q ss_pred             CceEEcCCCCCCC-eEEEEcCHHHHHHHHHHHHHHHHh---hhCCCCc
Q psy4141         111 NTYIVTPSRDKEP-VFEVTGAPDSVEIARQEIESHIIR---RTGSCVT  154 (353)
Q Consensus       111 ga~I~ip~~~~e~-~v~I~G~~e~V~~A~~~I~~~i~~---r~g~~~~  154 (353)
                      ...+.-...+..+ .+-|-|-.+.-+.....+...+.+   ++|..+.
T Consensus       122 ~~~vn~~~~~~~rv~LDi~~YR~rR~e~L~~lA~~~A~kV~~tg~~v~  169 (225)
T 3gku_A          122 SLVVNKSSSDYIRVKLDTENYRERRKETLETLAKNIAYKVKRTKRSVS  169 (225)
T ss_dssp             HHHHHHTCSSCCEEEEESTTHHHHHHHHHHHHHHHHHHHHHHHCSCEE
T ss_pred             HHHHHhcCCCceEEEEecchHHHHHHHHHHHHHHHHHHHHHHhCCEEE
Confidence            8666433222222 344445555555555555544444   6787765

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=81.06  E-value=0.39  Score=40.58  Aligned_cols=72  Identities=14%  Similarity=0.122  Sum_probs=48.1

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh---hhCCCCc
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR---RTGSCVT  154 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~---r~g~~~~  154 (353)
                      ++.+.+..+..|.||||.|.|++.||--+.-.+.-.. +..=.+-|.|-.+.-+...+.+...+.+   ++|+.+.
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~~~~vn~~~-~~~V~LDve~YRerReetL~~lA~~~A~kV~~tgk~v~  108 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHPTY-GYSIRLEISTFLQNQEKVMDTQLQSVIMTVHEVGKGQM  108 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHHHHH-SCEEEEEETTHHHHHHHHHHHHHHHHHHHHHHTSCEEE
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHHHHHhhhcC-CceEEEEhHHhHHHHHHHHHHHHHHHHHHHHHHCCcCC
Confidence            4667788899999999999999999977744432111 1111244445567777776666666665   6777765

---

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	353
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	8e-17
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-09
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-16
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	6e-15
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-05
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	8e-15
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-07
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-14
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-04
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	9e-14
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-06
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-13
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	0.002
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-13
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	8e-04
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-13
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	7e-13
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-12
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-04
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-12
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-05
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	2e-12
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-12
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-11
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-11
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	0.002
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-10
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	6e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	3e-08
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	3e-08
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-07
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	8e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-06
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-06
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	7e-06
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-05
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	4e-05
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	1e-04
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	5e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	6e-04
d1k1ga_	122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	7e-04
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	0.002

>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 = 72.0 bits (177), Expect = 8e-17
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQ 139
            +  V +P +    V+G  G  ++ ++ +T T I  P   D     ++TG  + +E AR 
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARH 69

Query: 140 EIES 143
           E+  
Sbjct: 70  EVLL 73

>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 = 50.1 bits (120), Expect = 7e-09
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFS 57
          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 = 69.8 bits (171), Expect = 7e-16
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 67  ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVF 125
           AL  L P       VTIEV VP+ +   V+G KG+ I+++  +    I V     +  + 
Sbjct: 3   ALEALVP-------VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDII 55

Query: 126 EVTGAPDSVEIARQEIESHI 145
            +TG   +++ A+  +   +
Sbjct: 56  AITGLAANLDRAKAGLLERV 75

>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 = 67.2 bits (164), Expect = 6e-15
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIA 137
           +T E +VP  +VG ++G  G  I RIQ ++   I          E    +TG P+SV+ A
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSA 67

Query: 138 RQEIESHI 145
           ++ ++  +
Sbjct: 68  KRLLDQIV 75

>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 = 40.6 bits (95), Expect = 1e-05
 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 3/51 (5%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILS 51
          I R G +I  ++ ++   I+         E   ++TG  E V  AKR +  
Sbjct: 23 IGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQ 73

>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 = 66.7 bits (163), Expect = 6e-15
 Identities = 14/66 (21%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQ 139
           +TI + +  K VG ++G KG ++K+++ ++   I ++     E +  + G  +++  A  
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFA 63

Query: 140 EIESHI 145
            I   +
Sbjct: 64  MIIDKL 69

>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 = 41.7 bits (98), Expect = 6e-06
 Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 1/49 (2%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 51
          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 = 66.3 bits (162), Expect = 8e-15
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQ 139
             +E+ + +K    ++G  GA I RI+ Q    +  P   +K  +  + G P  V+ A++
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKR 64

Query: 140 EIES 143
           E+  
Sbjct: 65  ELLE 68

>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 = 45.1 bits (107), Expect = 3e-07
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 51
          I +SG  I  ++ +    ++ P   E   +  + G  + V +AKRE+L 
Sbjct: 20 IGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLE 68

>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 = 66.0 bits (161), Expect = 1e-14
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 79  GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVE 135
           G   I+V +P   VG+V+G  G  IK+IQ+     I     D    E + ++TG PD  +
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQ 60

Query: 136 IARQEIESHI 145
            A + I   +
Sbjct: 61  HAAEIITDLL 70

>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 = 37.5 bits (87), Expect = 2e-04
 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 3/50 (6%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVR---GEEPVFVVTGRKEDVARAKREIL 50
          I R+G  IK ++      I+         E +  +TG  +    A   I 
Sbjct: 18 IGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIIT 67

>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 = 63.7 bits (155), Expect = 9e-14
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP--VFEVTGAPDSVEIAR 138
           V+ +V + ++V   ++G +G  I++I  +    I  P           VTG P++VE A 
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAI 69

Query: 139 QEIESHI 145
             I +  
Sbjct: 70  DHILNLE 76

>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 = 42.9 bits (101), Expect = 3e-06
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEP--VFVVTGRKEDVARAKREILSAADHF 56
          I   G  I+ +  +    I+ P  G        VTG  E+V  A   IL+  + +
Sbjct: 25 IGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY 79

>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 = 63.3 bits (154), Expect = 1e-13
 Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIA 137
            T E+ +P  ++G ++G +GA I  I+  +   I   +           +TG+  S+ +A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 138 RQEIESHI 145
           +  I + +
Sbjct: 62  QYLINARL 69

>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 = 34.4 bits (79), Expect = 0.002
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 3/51 (5%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILS 51
          I R G  I  +R  +   IK     E        +TG    ++ A+  I +
Sbjct: 17 IGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 67

>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 = 63.4 bits (154), Expect = 1e-13
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 78  PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-----VFEVTGAPD 132
           PG+   E+ +P    GLV+G  G TIK++Q +    +V      +         +TG P 
Sbjct: 5   PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPY 64

Query: 133 SVEIARQEIESHI 145
            V+ A++ +   I
Sbjct: 65  KVQQAKEMVLELI 77

>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 = 35.7 bits (82), Expect = 8e-04
 Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 5/53 (9%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEP-----VFVVTGRKEDVARAKREILS 51
          I + G  IK L+ +    +     G +         +TG    V +AK  +L 
Sbjct: 23 IGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLE 75

>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 = 62.2 bits (151), Expect = 3e-13
 Identities = 15/68 (22%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV---TPSRDKEPVFEVTGAPDSVEIA 137
           +T +V +P  + G ++G  G  IK+I+H++   I         ++ +  +TG  D ++ A
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 63

Query: 138 RQEIESHI 145
           +  +++ +
Sbjct: 64  QYLLQNSV 71

>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 = 37.5 bits (87), Expect = 2e-04
 Identities = 12/57 (21%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAADHFS 57
          I + G +IK +R ++   IK     E   + +  +TG ++ +  A+  + ++   +S
Sbjct: 19 IGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS 75

>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 = 61.4 bits (149), Expect = 7e-13
 Identities = 13/63 (20%), Positives = 25/63 (39%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQE 140
              E  V   ++GL +G  G+ I++ +       +    D         + D+V+ AR  
Sbjct: 8   FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGF 67

Query: 141 IES 143
           +E 
Sbjct: 68  LEF 70

>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 = 60.6 bits (147), Expect = 1e-12
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 6/70 (8%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVE 135
            +E+ VP  +VG ++G  G T+   Q  T   I    +       +     +TG+P + +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 136 IARQEIESHI 145
            A+  I   +
Sbjct: 64  AAQYLISQRV 73

>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 = 37.5 bits (87), Expect = 2e-04
 Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 6/52 (11%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREI 49
          + + G  +   +  T   I+   +GE           +TG       A+  I
Sbjct: 18 LGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLI 69

>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 = 60.6 bits (147), Expect = 1e-12
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGAPDSVEI 136
             + V V  K    ++G KGA I +I+ + +  I  P +D     +    +TG   + E 
Sbjct: 10  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEA 69

Query: 137 ARQEIESHI 145
           AR  I   +
Sbjct: 70  ARDAILRIV 78

>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 = 40.6 bits (95), Expect = 2e-05
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILS 51
          I R G  I  +R + +  I+ P + +    +    +TG +++   A+  IL 
Sbjct: 25 IGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILR 76

>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 = 60.2 bits (146), Expect = 2e-12
 Identities = 19/109 (17%), Positives = 38/109 (34%), Gaps = 25/109 (22%)

Query: 37  GRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVV 96
           G  E + +A  E+ + A+ F                            V  P  +   ++
Sbjct: 1   GEPEKLGQALTEVYAKANSF------------------------TVSSVAAPSWLHRFII 36

Query: 97  GPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHI 145
           G KG  + +I  Q     +  +   E    + G  + V +A+++IE  +
Sbjct: 37  GKKGQNLAKITQQMPKVHIEFTEG-EDKITLEGPTEDVSVAQEQIEGMV 84

>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 = 58.8 bits (142), Expect = 4e-12
 Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 82  TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVE 135
                VP    GL++G  G TIK I  Q+   I               +F + G P  ++
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 136 IARQEIESHI 145
            ARQ IE  I
Sbjct: 62  YARQLIEEKI 71

>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 = 37.2 bits (86), Expect = 2e-04
 Identities = 9/53 (16%), Positives = 21/53 (39%), Gaps = 6/53 (11%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREIL 50
          I + G  IK++  ++   I+              +F + G  + +  A++ I 
Sbjct: 16 IGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIE 68

>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 = 57.9 bits (140), Expect = 1e-11
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQ-TNTYI-VTPSRDKEPVFEVTGAPDSVEIAR 138
             +EV +P K+   ++G KG  I+ I  +    +I             + G    VE A+
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAK 69

Query: 139 QEIE 142
           +++ 
Sbjct: 70  KQLL 73

>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 = 57.3 bits (138), Expect = 3e-11
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 12/90 (13%)

Query: 61  ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-----V 115
           +S  SG L+  +P       V  ++ VP + VG ++G  G TI+ I   +   I      
Sbjct: 2   SSGSSGILTENTP-------VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES 54

Query: 116 TPSRDKEPVFEVTGAPDSVEIARQEIESHI 145
             +     + +++G    V  A+  I   +
Sbjct: 55  EGTLLLSRLIKISGTQKEVAAAKHLILEKV 84

>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 = 34.9 bits (80), Expect = 0.002
 Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 5/74 (6%)

Query: 4   ISRSGCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSA 58
           I R G  I+++   +   I              +  ++G +++VA AK  IL        
Sbjct: 30  IGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE 89

Query: 59  LRASRKSGALSPLS 72
           LR      A  P S
Sbjct: 90  LRKRIAHSASGPSS 103

>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 = 54.4 bits (131), Expect = 2e-10
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 85  VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIES 143
           V +    V  V+G KG+ IK ++ + +  IV     +  +  V G    V IA + I  
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVV---GQNGLIWVNGDRRKVSIAEEAIYL 60

>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 = 36.3 bits (84), Expect = 6e-04
 Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 4  ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI 49
          I + G  IK L+++ +  I     G+  +  V G +  V+ A+  I
Sbjct: 16 IGKKGSMIKLLKSELDVQIVV---GQNGLIWVNGDRRKVSIAEEAI 58

>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 = 51.3 bits (123), Expect = 2e-09
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 2/82 (2%)

Query: 83  IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIE 142
           I V+V  + +G V+GP+G     I  +T T I   + +   V     A     +   +  
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSM-VIVEPEAEGIPPVNLMKAA 63

Query: 143 SHIIRRTGSCVTPAEAVLNGDD 164
             +++       P +A    ++
Sbjct: 64  E-VVKAISLGFPPEKAFRLLEE 84

>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 = 48.5 bits (115), Expect = 3e-08
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRII 352
           C +C + +    + PCGH   C+ C     + + + CP CR  +     I+
Sbjct: 26  CKICAENDKDVKIEPCGHLM-CTSCLTSWQESEGQGCPFCRCEIKGTEPIV 75

>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 = 47.8 bits (114), Expect = 3e-08
 Identities = 13/67 (19%), Positives = 22/67 (32%), Gaps = 9/67 (13%)

Query: 85  VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEI-- 141
           + +    V  V+G   +  + +  ++   I             T     S EI  + I  
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFV---ANNGRIWATCPSRFSEEILIEAIRK 61

Query: 142 ---ESHI 145
              ESHI
Sbjct: 62  IENESHI 68

>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 = 46.2 bits (110), Expect = 2e-07
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 90  KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIES 143
           ++ G ++G  G   + I+  T+TYI      +  V  + G  +    A+Q IE 
Sbjct: 22  RIKGRIIGEGGRARRTIEEMTDTYINV---GEYEVA-IIGDYERAMAAKQAIEM 71

>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 = 43.8 bits (103), Expect = 8e-07
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 302 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 352
           +C +C +        +PC H F C  C  R    + TCP+C+VPV   +  I
Sbjct: 7   RCPICLEDPSNYSMALPCLHAF-CYVCITRWIRQNPTCPLCKVPVESVVHTI 57

>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 = 44.1 bits (104), Expect = 1e-06
 Identities = 14/50 (28%), Positives = 15/50 (30%), Gaps = 2/50 (4%)

Query: 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQA 348
           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 = 42.6 bits (100), Expect = 1e-06
 Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 4/43 (9%)

Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
           C  C        L+PC H   CS C E +      CP+C+ P 
Sbjct: 9   CQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPW 47

>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 = 41.6 bits (98), Expect = 7e-06
 Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 4/60 (6%)

Query: 85  VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIES 143
           V +    V  V+G K + +K ++ +T   I      +     +     D   IA   I+ 
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFV---ARNGRIHLECPNEDLEAIAVMAIKI 61

>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 = 39.9 bits (93), Expect = 1e-05
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 296 SISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
           ++    +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 = 38.5 bits (89), Expect = 4e-05
 Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 4/50 (8%)

Query: 302 QCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
           +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 = 38.5 bits (89), Expect = 1e-04
 Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 4/49 (8%)

Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDR---TCPMCRVPVNQ 347
           +C +C +         C H  FC  C  +  +  +    CP+C+  + +
Sbjct: 23  ECPICLELIKEPVSTKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDITK 70

>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 = 37.5 bits (87), Expect = 5e-04
 Identities = 9/26 (34%), Positives = 17/26 (65%)

Query: 89  YKVVGLVVGPKGATIKRIQHQTNTYI 114
           +  VG ++GP+G T K+++ +T   I
Sbjct: 16  FNFVGRILGPRGLTAKQLEAETGCKI 41

>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 = 35.4 bits (82), Expect = 6e-04
 Identities = 13/34 (38%), Positives = 18/34 (52%)

Query: 81  VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
             I V++P   +G V+GPK   I +IQ  T   I
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEI 36

>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 = 36.7 bits (85), Expect = 7e-04
 Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 6/40 (15%)

Query: 81  VTIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYI 114
           V+ +V +P         VGL++GP+G T+K I+ + N  I
Sbjct: 3   VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKI 42

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 8/31 (25%), Positives = 10/31 (32%), Gaps = 1/31 (3%)

Query: 314 ALIPCGHNFFCSECAERTCDFDRTCPMCRVP 344
           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	353
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.59
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.59
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.58
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.58
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.56
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.56
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.56
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.55
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.51
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.49
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.35
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.34
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.15
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.11
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.1
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.09
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.07
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.06
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.02
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.02
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.01
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.0
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.0
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.0
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.0
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	98.98
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	98.97
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.96
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	98.96
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	98.94
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	98.94
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.94
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	98.91
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.91
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.9
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.88
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.88
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.85
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.84
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.84
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.83
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.81
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.81
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.77
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.59
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.59
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.57
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.52
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.51
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.45
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.43
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.32
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.28
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.19
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.1
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.07
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.02
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.55
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	97.26
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.02
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	96.34
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.91
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.54
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	88.27
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	85.37
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	84.26
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	82.64

>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=99.60  E-value=9.5e-16  Score=114.69  Aligned_cols=69  Identities=22%  Similarity=0.441  Sum_probs=63.1

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC---CCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~---~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .++.+|.||.+++|+|||++|++|++|+++|||+|.++...   .++.|+|+|++++|++|+++|.++|++.
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            37899999999999999999999999999999999987542   3578999999999999999999999875

>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=99.59  E-value=4.5e-16  Score=116.30  Aligned_cols=68  Identities=31%  Similarity=0.484  Sum_probs=62.4

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC---CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~---~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ..+++|.||.+++|+||||+|++||+|+++|||+|.++..+   .++.|+|+|++++|++|+++|.++|++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999987653   346899999999999999999999986

>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=99.59  E-value=5.2e-16  Score=115.09  Aligned_cols=67  Identities=21%  Similarity=0.360  Sum_probs=62.5

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ++++|.||.+++|.|||++|++|++|+++|||+|.++... .+++|+|+|++++|++|+.+|.++|++
T Consensus         4 vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           4 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             EEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCCCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            7899999999999999999999999999999999988753 468999999999999999999999875

>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=99.58  E-value=7.2e-16  Score=114.01  Aligned_cols=65  Identities=23%  Similarity=0.445  Sum_probs=59.8

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC---CCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIARQEIESHI  145 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~---~e~~v~I~G~~e~V~~A~~~I~~~i  145 (353)
                      .|.+|.||.+++|+||||+|.+|++|+++|||+|.++...   .++.|+|+|++++|++|+++|+++|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            6889999999999999999999999999999999987642   3568999999999999999999876

>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=99.58  E-value=4.9e-16  Score=118.12  Aligned_cols=72  Identities=28%  Similarity=0.462  Sum_probs=65.0

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC-----CCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-----DKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-----~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .+++.+.+|.||..++|+||||+|++||+|+++|||+|.|+++     +.++.|+|+|++++|++|+++|+++|.++
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3567999999999999999999999999999999999998654     24678999999999999999999999764

>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=99.56  E-value=1.3e-15  Score=112.80  Aligned_cols=64  Identities=33%  Similarity=0.535  Sum_probs=57.6

Q ss_pred             EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC------CCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141          82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVEIARQEIESHI  145 (353)
Q Consensus        82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~------~e~~v~I~G~~e~V~~A~~~I~~~i  145 (353)
                      +.+|.||..++|+||||+|++||+|+++|||+|.++.+.      .++.|+|+|++++|++|+++|+++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            468999999999999999999999999999999986542      3468999999999999999999875

>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=99.56  E-value=3.5e-15  Score=113.33  Aligned_cols=71  Identities=24%  Similarity=0.311  Sum_probs=64.6

Q ss_pred             CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCC--CCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK--EPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        78 ~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~--e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ...++.+|.||.++||+|||++|.+|++|+++|||+|.||..+.  .+.|+|+|++++|++|+++|++++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            34578999999999999999999999999999999999998643  468999999999999999999998863

>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=99.56  E-value=3.3e-15  Score=113.52  Aligned_cols=73  Identities=22%  Similarity=0.377  Sum_probs=66.5

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC-CCCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQEIESHIIRRT  149 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~  149 (353)
                      +....+.+|.||..++|+|||++|.+|++|+++|||+|.||.. +.++.|+|+|++++|++|+++|++++++..
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            3445899999999999999999999999999999999999876 456799999999999999999999998854

>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=99.55  E-value=2.8e-15  Score=111.95  Aligned_cols=65  Identities=25%  Similarity=0.425  Sum_probs=59.2

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC------CCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVEIARQEIESHI  145 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~------~e~~v~I~G~~e~V~~A~~~I~~~i  145 (353)
                      ..++|.||.+++|+||||+|++||+|+++|||+|+++.++      .++.|+|+|++++|++|+++|.++|
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            5689999999999999999999999999999999987642      3568999999999999999999876

>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=99.53  E-value=7.1e-15  Score=111.82  Aligned_cols=74  Identities=20%  Similarity=0.328  Sum_probs=66.0

Q ss_pred             CCcceEEEEEecCCCccceeccCChHHHHHHHH-hCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHHHhhhC
Q psy4141          77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQ-TNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIRRTG  150 (353)
Q Consensus        77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~-Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g  150 (353)
                      +...++.+|.||.++||+|||++|++|++|+++ ++++|.+|..+ .++.|+|+|++++|++|+++|++++++...
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~~   81 (82)
T d2ctja1           6 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   81 (82)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             hcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCCCceEEEeCCHHHHHHHHHHHHHHHhhhhc
Confidence            344588999999999999999999999999987 59999999864 568999999999999999999999998643

>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=99.52  E-value=3e-16  Score=121.75  Aligned_cols=68  Identities=21%  Similarity=0.346  Sum_probs=62.4

Q ss_pred             cceEEEEEecCCCccceeccCChHHHHHHHHh-CceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT-NTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T-ga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ...+.+|.||..+|++|||++|++|++|++++ |++|.+|.+  ++.|+|+|++++|++|+++|++++++.
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~--~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--EDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS--SCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC--CceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            45899999999999999999999999999995 899999854  468999999999999999999999874

>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=99.52  E-value=6.3e-15  Score=109.13  Aligned_cols=66  Identities=24%  Similarity=0.414  Sum_probs=60.6

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHI  145 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i  145 (353)
                      ....+|.||.+++++|||++|++|++|+++|||+|.||.++ .++.|+|+|++++|++|+++|++++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            36789999999999999999999999999999999999764 4578999999999999999999864

>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=99.51  E-value=8.2e-15  Score=110.65  Aligned_cols=68  Identities=29%  Similarity=0.487  Sum_probs=62.6

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC---CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~---~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      .++.+|.||..++|+|||++|.+|++|+++|||+|.++..+   .++.|+|+|++++|++|+.+|.++|.+
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            58899999999999999999999999999999999987643   356899999999999999999999986

>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=99.50  E-value=2.1e-14  Score=109.65  Aligned_cols=67  Identities=27%  Similarity=0.365  Sum_probs=62.1

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC----CCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~----~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      .+.+|.||..++|+|||++|++|++|+++|||+|.||..+    .++.|+|+|++++|++|+.+|++++.+
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            7789999999999999999999999999999999998652    357899999999999999999999986

>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=99.49  E-value=1.5e-14  Score=114.93  Aligned_cols=69  Identities=22%  Similarity=0.364  Sum_probs=62.8

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      .++.+|.||..++|+||||+|.+||+|+++|||+|.|+..+     .++.|+|+|++++|++|+++|+++|++.
T Consensus        14 ~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            38899999999999999999999999999999999997642     3568999999999999999999999874

>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=99.46  E-value=3.7e-14  Score=109.93  Aligned_cols=68  Identities=25%  Similarity=0.498  Sum_probs=63.7

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIRR  148 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i~~r  148 (353)
                      ++.+|.||..+||+|||++|.+|++|+++|||+|.||..+ .++.|+|+|++++|++|+++|++++.+.
T Consensus        10 vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1          10 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCCCCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999999864 4678999999999999999999999863

>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=99.35  E-value=1.5e-13  Score=103.41  Aligned_cols=64  Identities=22%  Similarity=0.338  Sum_probs=57.2

Q ss_pred             ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHHHHH
Q psy4141          80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEIESH  144 (353)
Q Consensus        80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~~  144 (353)
                      ..+.+|.||.+++|+|||+||++||+||++|||+|++..+ +++.|+|.| ++++|++|++||+.+
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-CCceEEEEECCHHHHHHHHHHHHHh
Confidence            4889999999999999999999999999999999987643 446899999 699999999999643

>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=99.34  E-value=5.5e-13  Score=101.59  Aligned_cols=62  Identities=26%  Similarity=0.242  Sum_probs=57.5

Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ..+.||.+++|+|||++|++|++|+++|||+|+++.   +..|+|+|++++|++|+++|+.++++
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~---~g~v~I~G~~e~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---NGLIWVNGDRRKVSIAEEAIYLIEQE   64 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT---TSEEEEESCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC---CCEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            468899999999999999999999999999999974   45899999999999999999998887

>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=99.15  E-value=2.5e-11  Score=91.61  Aligned_cols=55  Identities=25%  Similarity=0.383  Sum_probs=50.9

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC--cCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e--~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|.+|++|+++|||+|++|..++  .++|+|+|++++|++|+++|+++++++
T Consensus        23 ~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1          23 RIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             HHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999998764  468999999999999999999999987

>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=99.11  E-value=2.3e-11  Score=89.53  Aligned_cols=54  Identities=17%  Similarity=0.311  Sum_probs=49.6

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .||||+|.+|++|+++|||+|++++.+ .++++.|+|++++|.+|+.+|.+++++
T Consensus        17 ~IIGk~G~~I~~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1          17 SIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEECCCChhHHHHHHHhCCEEEEcCCCCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            479999999999999999999998765 468999999999999999999999874

>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=99.10  E-value=1.9e-11  Score=91.83  Aligned_cols=50  Identities=26%  Similarity=0.760  Sum_probs=44.6

Q ss_pred             cccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCcccccccceec
Q psy4141         301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRI  351 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~~~ri  351 (353)
                      ..|.||++...+++++||||. ||..|+.+|... ...||+||..+.....|
T Consensus        24 ~~C~IC~~~~~~~~~~~CgH~-fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i   74 (79)
T d1fbva4          24 QLCKICAENDKDVKIEPCGHL-MCTSCLTSWQESEGQGCPFCRCEIKGTEPI   74 (79)
T ss_dssp             TBCTTTSSSBCCEECSSSCCE-ECHHHHHHHHHTTCCSCTTTCCCCCCCCCS
T ss_pred             CCCccCCCcCCCeEEeCCCCe-eeHHHHHHHHHHCcCcCCCCCcCccCCcee
Confidence            579999999999999999999 999999999875 67899999999875444

>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=99.09  E-value=7.3e-11  Score=89.51  Aligned_cols=57  Identities=23%  Similarity=0.394  Sum_probs=51.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSA   58 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~   58 (353)
                      +||||+|++|++|+++|||+|++|..+    .++++.|+|++++|++|+.+|+++++++..
T Consensus        23 ~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~e~   83 (84)
T d2ctla1          23 KIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELEQ   83 (84)
T ss_dssp             HHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhHhc
Confidence            489999999999999999999998654    357899999999999999999999998743

>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=99.07  E-value=5.6e-11  Score=88.11  Aligned_cols=56  Identities=21%  Similarity=0.406  Sum_probs=50.5

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .||||+|++|++|+++|||+|++++..   .+++++|+|++++|++|+.+|.+++++++
T Consensus        17 ~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~S   75 (75)
T d1zzka1          17 SIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS   75 (75)
T ss_dssp             GGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             eeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhcC
Confidence            489999999999999999999997543   35799999999999999999999999873

>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=99.06  E-value=6.5e-11  Score=89.25  Aligned_cols=56  Identities=29%  Similarity=0.396  Sum_probs=51.2

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .|||++|.+|++|+++|||+|++|..+ .+++++|+|++++|++|+.+|++++++..
T Consensus        23 ~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1          23 FVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             HHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             hccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            489999999999999999999999766 45899999999999999999999998763

>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=99.02  E-value=7.4e-11  Score=86.70  Aligned_cols=52  Identities=25%  Similarity=0.471  Sum_probs=47.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAA   53 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~   53 (353)
                      .|||++|++|++|+++|||+|++|..+ +++.++|+|++++|++|+.+|++++
T Consensus        18 ~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_          18 HLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             HHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            489999999999999999999999776 3578999999999999999999874

>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=99.02  E-value=4e-12  Score=93.17  Aligned_cols=61  Identities=15%  Similarity=0.053  Sum_probs=47.9

Q ss_pred             EEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141          84 EVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus        84 ~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                      -+.||.+.+|.||||+|++||+|+++|||+|.+..   +..|+|+|. ++++++|+++|+.+.++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~---~g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN---NGRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT---TSEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC---CCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999863   457999996 78999999999876655

>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=99.01  E-value=3.9e-11  Score=87.45  Aligned_cols=49  Identities=33%  Similarity=0.832  Sum_probs=42.9

Q ss_pred             ccccccccccccc-EEeCCCCHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141         301 RQCYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR  350 (353)
Q Consensus       301 ~~C~IC~~~~~~~-~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r  350 (353)
                      ..|.||++.+.+. +.+||||. ||..|+.+|+.....||+||.++..+..
T Consensus         6 d~C~IC~~~~~~~~~~~~C~H~-Fc~~Ci~~w~~~~~~CP~CR~~i~~~~~   55 (68)
T d1chca_           6 ERCPICLEDPSNYSMALPCLHA-FCYVCITRWIRQNPTCPLCKVPVESVVH   55 (68)
T ss_dssp             CCCSSCCSCCCSCEEETTTTEE-ESTTHHHHHHHHSCSTTTTCCCCCCEEC
T ss_pred             CCCccCCcCccCCcEEeCCCCc-CcHHHHHHHHHhCCcCCCCCcchHhhcc
Confidence            5699999998765 45799999 9999999999989999999999877654

>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=99.00  E-value=4.4e-11  Score=91.24  Aligned_cols=49  Identities=29%  Similarity=0.609  Sum_probs=43.9

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      .+...|.||++.+.+++.++|||. ||..|+.+|++. ...||+||.++..
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            355789999999999999999999 999999999875 6789999998763

>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=99.00  E-value=1.3e-10  Score=85.85  Aligned_cols=55  Identities=20%  Similarity=0.213  Sum_probs=49.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|+++...   .+++++|+|++++|++|+.+|.+++++.
T Consensus        16 ~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1          16 IVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999998654   3579999999999999999999998853

>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=99.00  E-value=1.2e-10  Score=88.24  Aligned_cols=61  Identities=25%  Similarity=0.346  Sum_probs=51.0

Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEE-----cCHHHHHHHHHHHHHHH
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT-----GAPDSVEIARQEIESHI  145 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~-----G~~e~V~~A~~~I~~~i  145 (353)
                      +.|.||.+.+|.|||++|++||+||++|||+|++..++  ..+.+.     |.+.++++|+++|.++.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~--g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN--SMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT--TEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC--CeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999987543  345554     46788888988887753

>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=99.00  E-value=2.3e-10  Score=87.97  Aligned_cols=57  Identities=21%  Similarity=0.347  Sum_probs=51.8

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCC-cCeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFSA   58 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e-~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~   58 (353)
                      .|||++|.+|++|+++|||+|.+|..++ +++|+|+|++++|++|+.+|+++++++..
T Consensus        23 ~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~~~   80 (91)
T d2ctka1          23 YVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQA   80 (91)
T ss_dssp             HHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhcCCCchhHHHHHHHhCCEEEECCCCCCcceEEEECCHHHHHHHHHHHHHHHHHHHH
Confidence            4799999999999999999999998763 57899999999999999999999987654

>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=98.98  E-value=2.4e-10  Score=90.07  Aligned_cols=58  Identities=22%  Similarity=0.317  Sum_probs=51.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHFSAL   59 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~   59 (353)
                      .||||+|.+||+|+++|||+|+|+...     .+++|+|+|++++|.+|+.+|.+++++....
T Consensus        28 ~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~   90 (104)
T d1we8a_          28 RIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEEL   90 (104)
T ss_dssp             HHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcHHH
Confidence            489999999999999999999997653     2579999999999999999999999876554

>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=98.97  E-value=1.6e-10  Score=84.86  Aligned_cols=52  Identities=17%  Similarity=0.282  Sum_probs=46.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAA   53 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~   53 (353)
                      .||||+|++||+|+++|||+|+++...      .+++++|+|++++|++|+++|.+++
T Consensus        14 ~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2          14 LIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             eEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            489999999999999999999997543      2479999999999999999998863

>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=98.96  E-value=5.7e-10  Score=84.85  Aligned_cols=62  Identities=19%  Similarity=0.146  Sum_probs=55.5

Q ss_pred             EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141          83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR  147 (353)
Q Consensus        83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~  147 (353)
                      ..+.||.+.+|.|||++|++||.|+++|||+|.+.   ++..|.|.|. .+.+..|+++|+.+.++
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~---d~G~V~I~g~~~~~~~~A~~~I~~I~~e   65 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA---RNGRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEE---TTTEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEEC---CCcEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            45889999999999999999999999999999885   3458999995 88999999999988765

>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=98.96  E-value=3.4e-10  Score=84.66  Aligned_cols=55  Identities=24%  Similarity=0.268  Sum_probs=49.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .|||++|.+|++|+++|||+|+++...   .+++++|+|++++|++|+.+|.+++++.
T Consensus        21 ~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1          21 FIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             HHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             ceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            479999999999999999999998654   3578999999999999999999999863

>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=98.94  E-value=2.3e-10  Score=86.12  Aligned_cols=54  Identities=22%  Similarity=0.294  Sum_probs=48.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC-----CcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      .||||+|++||+|+++|||+|+++...     .+++++|+|++++|++|+.+|.+++++
T Consensus        21 ~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1          21 LVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             HHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             eeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            489999999999999999999997542     358999999999999999999999864

>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=98.94  E-value=3.2e-10  Score=83.85  Aligned_cols=52  Identities=15%  Similarity=0.210  Sum_probs=46.5

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAA   53 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~   53 (353)
                      .||||+|++||+|+++|||+|+++..+      .+++++|+|++++|++|+.+|.+++
T Consensus        16 ~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_          16 AILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             HHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             eeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            479999999999999999999997643      2579999999999999999998864

>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=98.94  E-value=6.3e-10  Score=83.82  Aligned_cols=55  Identities=27%  Similarity=0.436  Sum_probs=49.9

Q ss_pred             eeecCCCchHHHHHHH-cCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAK-TNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~-Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++|++|+++ ++++|++|..+ .+++|+|+|++++|++|+++|++++++.
T Consensus        23 ~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1          23 SLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             HHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCCCCccHHHHHHHcCCcEEEEeCCCCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            4899999999999987 69999999876 4589999999999999999999999875

>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=98.91  E-value=4e-10  Score=82.44  Aligned_cols=52  Identities=21%  Similarity=0.227  Sum_probs=46.4

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAA   53 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~   53 (353)
                      .||||+|.+|++|+++|||+|+++...   .++++.|+|++++|++|+.+|.+.+
T Consensus        15 ~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1          15 CIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            479999999999999999999997543   3579999999999999999998764

>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=98.91  E-value=2.5e-10  Score=79.62  Aligned_cols=48  Identities=29%  Similarity=0.740  Sum_probs=40.2

Q ss_pred             CCCCcccccccccccc---cEEe-CCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141         297 ISGSRQCYLCNDREVT---HALI-PCGHNFFCSECAERTCDFDRTCPMCRVPV  345 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~---~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i  345 (353)
                      +++..+|.||++.+..   ...+ +|+|. ||..|+.+|......||+||.++
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            4566789999998753   3344 69999 99999999999888999999876

>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=98.90  E-value=5.7e-11  Score=83.31  Aligned_cols=45  Identities=31%  Similarity=0.782  Sum_probs=39.8

Q ss_pred             CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      +.++|.||++.+.+++++||||. ||..|+.++   ...||+||.++..
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~-fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCC-SBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             CCCCCcccCcccCCCEEecCCCH-HhHHHHHcC---CCcCcCCCCcccC
Confidence            34799999999999999999998 999998765   6789999998853

>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=98.88  E-value=5.6e-10  Score=83.24  Aligned_cols=51  Identities=12%  Similarity=0.274  Sum_probs=45.9

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      +..++..|+||++...+++.++|||. ||+.|+.+|+.. ...||.|+.++..
T Consensus         4 eiP~~l~CpIc~~~m~dPV~~~cgh~-fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKDPVIVSTGQT-YERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEE-EEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CCCccCCCcCcCchhhCceEccCCCc-chHHHHHHHHHHCCCCCCcccccCCc
Confidence            35577999999999999999999999 999999999987 6789999998864

>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=98.88  E-value=3.7e-10  Score=81.45  Aligned_cols=48  Identities=23%  Similarity=0.677  Sum_probs=39.1

Q ss_pred             CCcccccccccc-----cccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         299 GSRQCYLCNDRE-----VTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       299 ~~~~C~IC~~~~-----~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      ++..|+||++..     ...++.+|||. ||..|+.+|+.. ...||+||+++..
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            468999999853     22355799999 999999999866 6689999999864

>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=98.85  E-value=3e-10  Score=89.31  Aligned_cols=48  Identities=21%  Similarity=0.564  Sum_probs=42.6

Q ss_pred             CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~  346 (353)
                      .+...|+||++.+.+++.++|||. ||..|+.+|+..   ...||+||.++.
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            345789999999999999999999 999999999876   358999999875

>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=98.84  E-value=4e-10  Score=77.65  Aligned_cols=45  Identities=29%  Similarity=0.603  Sum_probs=37.2

Q ss_pred             cccccccccccc----cEEeCCCCHhhhHHhHHHHhcc-CCCCCCcccccc
Q psy4141         301 RQCYLCNDREVT----HALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN  346 (353)
Q Consensus       301 ~~C~IC~~~~~~----~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~  346 (353)
                      .+|+||++.+..    ..+++|||. ||..|+.+|... ...||+||+++.
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~-~c~~C~~~w~~~~~~~CP~CR~~~~   50 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQ-ICRFCWHRIRTDENGLCPACRKPYP   50 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCC-CCHHHHHHHTTTSCCBCTTTCCBCS
T ss_pred             CCCcCCChhhhCCCceEEecCCCCc-cchHHHHHHHhhcCCCCCccCCcCC
Confidence            479999997632    334689999 999999999987 668999999875

>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=98.84  E-value=5.3e-10  Score=83.82  Aligned_cols=51  Identities=16%  Similarity=0.167  Sum_probs=45.5

Q ss_pred             CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141         296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ  347 (353)
Q Consensus       296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~  347 (353)
                      +..++..|+||++...+++.++|||. ||..|+.+|+.. ...||+||.++..
T Consensus         3 eiP~~l~CpIc~~l~~dPv~~~cGht-fc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           3 DIPDYLCGKISFELMREPCITPSGIT-YDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CCCSTTBCTTTCSBCSSEEECSSCCE-EETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCCccccCcCcCchhhhhcccCCcCe-ecHHHHHHHHhcCCccCCCccccccc
Confidence            34577999999999999999999999 999999999876 6689999998864

>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=98.83  E-value=4.1e-10  Score=78.76  Aligned_cols=46  Identities=15%  Similarity=0.171  Sum_probs=42.1

Q ss_pred             cccccccccccccEEeC-CCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         301 RQCYLCNDREVTHALIP-CGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llp-CgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      +.|.||++...+++.++ |||. ||.+|+.+|......||+||.++..
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            46999999999999885 9999 9999999999998899999999863

>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=98.81  E-value=1.1e-09  Score=86.01  Aligned_cols=54  Identities=26%  Similarity=0.362  Sum_probs=48.7

Q ss_pred             CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141          90 KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR  147 (353)
Q Consensus        90 ~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~  147 (353)
                      ++.|+|||++|++||.|++.|||+|.+.    +..|.|.|.+++++.|+++|++++..
T Consensus        22 R~~GrIIG~gGktik~Ie~~Tg~~I~I~----d~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          22 RIKGRIIGEGGRARRTIEEMTDTYINVG----EYEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEEC----SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HHhcceeCCCcHHHHHHHHHHCCeEEEe----CCeEEEEECchhHHHHHHHHHHHHcC
Confidence            5689999999999999999999999885    23688899999999999999999975

>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=98.81  E-value=3e-09  Score=81.53  Aligned_cols=54  Identities=19%  Similarity=0.246  Sum_probs=49.0

Q ss_pred             eeecCCCchHHHHHHHc-CceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141           2 KKISRSGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFS   57 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~T-ga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~   57 (353)
                      .|||++|++|++|++++ +++|.+|..  +.+++|+|++++|++|+++|.++++++.
T Consensus        34 ~iIG~~G~~I~~i~~~~~~v~I~~~~~--~~~v~i~G~~~~ve~Ak~~I~~iv~el~   88 (90)
T d2ctfa1          34 FIIGKKGQNLAKITQQMPKVHIEFTEG--EDKITLEGPTEDVSVAQEQIEGMVKDLI   88 (90)
T ss_dssp             HHHTTTTCHHHHHHHHCSSSEEEECSS--SCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCCCchhHHHHHHHcCCcEEeeCCC--CceEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            48999999999999995 899999954  5789999999999999999999999874

>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=98.77  E-value=2.6e-09  Score=80.80  Aligned_cols=51  Identities=22%  Similarity=0.320  Sum_probs=46.6

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      +||||+|++|++|+++|||+|++++   +..+.|.|+++++++|+.+|..++++
T Consensus        14 ~IIG~gG~~I~~I~~~tg~~I~i~~---~g~v~I~G~~e~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3          14 RVIGKKGSMIKLLKSELDVQIVVGQ---NGLIWVNGDRRKVSIAEEAIYLIEQE   64 (84)
T ss_dssp             HHHCGGGHHHHHHHHHHTCEEEECT---TSEEEEESCHHHHHHHHHHHHHHHHC
T ss_pred             eeeCCcHHHHHHHHHHHCCEEEECC---CCEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4899999999999999999999984   35789999999999999999999875

>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=98.59  E-value=2.5e-09  Score=82.92  Aligned_cols=48  Identities=25%  Similarity=0.618  Sum_probs=40.9

Q ss_pred             CCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      +.+...|.||++.+.+++.+ +|||. ||..|+.+|..  ..||.||.++..
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            45668999999999999865 89999 99999999864  469999988753

>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=98.59  E-value=1.4e-09  Score=75.24  Aligned_cols=47  Identities=30%  Similarity=0.480  Sum_probs=15.0

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA  130 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~  130 (353)
                      ...+|.||.+.+|.|||+||++||+|+++|||+|.+.   ++..|.|.|.
T Consensus         3 ~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~---ddg~v~I~a~   49 (54)
T d1e3ha4           3 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE---DDGTIYIGAA   49 (54)
T ss_dssp             BCC---------------------CHHHHSCCCC-----------CCCCB
T ss_pred             eEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe---CCeEEEEEec
Confidence            4567899999999999999999999999999999875   3457877775

>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=98.57  E-value=1.1e-08  Score=81.25  Aligned_cols=46  Identities=22%  Similarity=0.528  Sum_probs=37.0

Q ss_pred             Ccccccccccccc------------------cEEeCCCCHhhhHHhHHHHhcc-----CCCCCCcccccc
Q psy4141         300 SRQCYLCNDREVT------------------HALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVN  346 (353)
Q Consensus       300 ~~~C~IC~~~~~~------------------~~llpCgH~~fC~~C~~~~~~~-----~~~CP~Cr~~i~  346 (353)
                      +..|.||++.+..                  ..+++|+|. ||..|+..|+..     ...||+||+.+.
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            3579999987532                  457899999 999999999875     247999998774

>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=98.52  E-value=5.8e-08  Score=75.29  Aligned_cols=51  Identities=14%  Similarity=0.082  Sum_probs=44.8

Q ss_pred             CCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141         297 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ  347 (353)
Q Consensus       297 ~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~  347 (353)
                      ..++..|+||++...++|.++|+|..||+.|+.+|+.....||+||.++..
T Consensus        19 ~P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             CcHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            345799999999999999999886339999999999888899999999864

>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=98.51  E-value=2.9e-08  Score=75.48  Aligned_cols=33  Identities=24%  Similarity=0.397  Sum_probs=30.0

Q ss_pred             cEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141         313 HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN  346 (353)
Q Consensus       313 ~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~  346 (353)
                      .++++|+|. ||..|+.+|+.....||+||+++.
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            567899999 999999999999999999999864

>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=98.45  E-value=4.9e-08  Score=72.58  Aligned_cols=52  Identities=17%  Similarity=0.178  Sum_probs=43.6

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~   54 (353)
                      .|||++|++|++|+++||++|.+.+.. +..|.|.| ++++|++|+++|..+.+
T Consensus        21 ~vIG~gG~~I~~I~~~tGa~i~i~~~~-~g~v~I~g~~~eav~~A~~~Ie~~~~   73 (78)
T d2cpqa1          21 LAIGTHGSNIQQARKVPGVTAIELDED-TGTFRIYGESADAVKKARGFLEFVED   73 (78)
T ss_dssp             HHHTTTTHHHHHHHTSTTEEEEEEETT-TTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             HHcCCChHHHHHHHHhcCcEEEEecCC-CceEEEEECCHHHHHHHHHHHHHhhe
Confidence            479999999999999999999987643 45678887 79999999999955443

>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=98.43  E-value=2.8e-07  Score=74.08  Aligned_cols=68  Identities=31%  Similarity=0.519  Sum_probs=55.1

Q ss_pred             ceEEEEEecCC------CccceeccCChHHHHHHHHhCceEEcCCCC------------------CCC-eEEEEcC-HHH
Q psy4141          80 HVTIEVRVPYK------VVGLVVGPKGATIKRIQHQTNTYIVTPSRD------------------KEP-VFEVTGA-PDS  133 (353)
Q Consensus        80 ~~t~~v~VP~~------~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~------------------~e~-~v~I~G~-~e~  133 (353)
                      +.+.+|.||-+      ++|+|||++|.++|+|+++|||+|.|-.+.                  .++ -|.|++. ++.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            36777888765      499999999999999999999999874320                  122 5778885 789


Q ss_pred             HHHHHHHHHHHHHh
Q psy4141         134 VEIARQEIESHIIR  147 (353)
Q Consensus       134 V~~A~~~I~~~i~~  147 (353)
                      +++|+.+|+.+|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999975

>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=8.7e-08  Score=67.39  Aligned_cols=48  Identities=23%  Similarity=0.601  Sum_probs=40.4

Q ss_pred             CCCcccccccccccccEEeCCC-----CHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141         298 SGSRQCYLCNDREVTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCRVPVN  346 (353)
Q Consensus       298 ~~~~~C~IC~~~~~~~~llpCg-----H~~fC~~C~~~~~~~--~~~CP~Cr~~i~  346 (353)
                      ++...|.||++...+....||.     |. ||..|+.+|...  ...||+||+++.
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            4568899999988777777775     88 999999999865  668999999875

>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=98.28  E-value=2.2e-07  Score=72.54  Aligned_cols=50  Identities=24%  Similarity=0.283  Sum_probs=43.9

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      +|||++|.+|+.|++.|||+|.+.+    ..+.|.|++++++.|+.+|..+++.
T Consensus        26 rIIG~gGktik~Ie~~Tg~~I~I~d----~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          26 RIIGEGGRARRTIEEMTDTYINVGE----YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHCGGGHHHHHHHHHHTCEEEECS----SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             ceeCCCcHHHHHHHHHHCCeEEEeC----CeEEEEECchhHHHHHHHHHHHHcC
Confidence            5899999999999999999999963    3355669999999999999999874

>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=98.19  E-value=2.1e-08  Score=72.88  Aligned_cols=51  Identities=12%  Similarity=0.033  Sum_probs=37.5

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecC-HHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~-~e~v~~Ak~~I~~i~~~   55 (353)
                      +||||+|++||+|+++|||+|++++.   ..+.|.|. ++++++|+.+|..+.++
T Consensus        14 ~iIGkgG~~Ik~i~~~tg~~I~i~~~---g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3          14 RVIGKNKSMYETLTSKSGCSIFVANN---GRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             HHHCGGGHHHHHHHTTC---CEECTT---SEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             ceECCchhHHHHHHHHHCCEEEEcCC---CEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            48999999999999999999999743   45788884 78999999999877654

>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=98.10  E-value=1.6e-06  Score=65.33  Aligned_cols=51  Identities=20%  Similarity=0.095  Sum_probs=44.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~~   55 (353)
                      +|||++|.+||.|+++|||+|.+.+.   -.|.|.| +.+.+.+|+.+|..+.++
T Consensus        14 ~vIG~gG~~ik~i~~~t~~~I~I~d~---G~V~I~g~~~~~~~~A~~~I~~I~~e   65 (87)
T d2z0sa2          14 RVIGRKMSMLKTLEEKTECKIFVARN---GRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             GGTCGGGHHHHHHHHHHCCEEEEETT---TEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             eeECCCCcHHHHHHHHHCCEEEECCC---cEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            58999999999999999999999744   4578888 589999999999888664

>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=98.07  E-value=2e-06  Score=69.89  Aligned_cols=66  Identities=21%  Similarity=0.387  Sum_probs=50.3

Q ss_pred             eEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCCC---------------------CCCeEEEEcC-H-
Q psy4141          81 VTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---------------------KEPVFEVTGA-P-  131 (353)
Q Consensus        81 ~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~---------------------~e~~v~I~G~-~-  131 (353)
                      .+.+|.||.      +++|+|||++|.|+|+|+++|||+|.|-.+.                     .+--|.|++. + 
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            455666663      6899999999999999999999999885431                     1225788875 2 


Q ss_pred             ----HHHHHHHHHHHHHHH
Q psy4141         132 ----DSVEIARQEIESHII  146 (353)
Q Consensus       132 ----e~V~~A~~~I~~~i~  146 (353)
                          ..+++|.++|+.+|.
T Consensus        82 ~~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHcC
Confidence                358889999988773

>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=98.02  E-value=1.9e-06  Score=64.59  Aligned_cols=53  Identities=15%  Similarity=0.143  Sum_probs=42.3

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEE-----ecCHHHHHHHHHHHHHHHhhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVV-----TGRKEDVARAKREILSAADHF   56 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I-----~G~~e~v~~Ak~~I~~i~~~~   56 (353)
                      .||||+|++||+|+++|||+|++...+  ..+.+     .+.+.++++|+..|.++...|
T Consensus        16 ~vIG~gG~~Ik~i~~~tg~~I~Id~d~--g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1          16 AVIGPRGEVKAEIMRRTGTVITVDTEN--SMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             HHHCGGGHHHHHHHHHHTEEEEEETTT--TEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             eeecCCchhHHHHHHHHCCEEEEEcCC--CeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            379999999999999999999997432  22333     457889999999998886655

>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=97.55  E-value=1.3e-05  Score=60.78  Aligned_cols=43  Identities=23%  Similarity=0.583  Sum_probs=32.9

Q ss_pred             Cccccccccccc--c-cEEeCCCCHhhhHHhHHHHhcc--------CCCCCCccc
Q psy4141         300 SRQCYLCNDREV--T-HALIPCGHNFFCSECAERTCDF--------DRTCPMCRV  343 (353)
Q Consensus       300 ~~~C~IC~~~~~--~-~~llpCgH~~fC~~C~~~~~~~--------~~~CP~Cr~  343 (353)
                      ...|.||++...  + +.+++|+|. ||..|+..++..        ...||.|+-
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCI-FCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEE-EEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECCCCCE-eCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            468999999763  2 445689999 999999998864        125998643

>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=97.26  E-value=1.4e-05  Score=54.63  Aligned_cols=34  Identities=12%  Similarity=0.115  Sum_probs=12.7

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecC
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR   38 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~   38 (353)
                      .|||++|.+||.|+++||++|++.+   +..|.|.|.
T Consensus        16 ~vIG~GG~~Ik~I~~~tga~I~i~d---dg~v~I~a~   49 (54)
T d1e3ha4          16 EVIGPKRQMINQIQEDTGAEITIED---DGTIYIGAA   49 (54)
T ss_dssp             -----------CHHHHSCCCC-----------CCCCB
T ss_pred             EEECCccHHHHHHHHHHCCEEEEeC---CeEEEEEec
Confidence            4899999999999999999999873   355666553

>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=97.02  E-value=0.00038  Score=55.27  Aligned_cols=54  Identities=22%  Similarity=0.306  Sum_probs=43.1

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC------------------Cc--CeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG------------------EE--PVFVVTGRKEDVARAKREILSAADH   55 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------------------e~--~vv~I~G~~e~v~~Ak~~I~~i~~~   55 (353)
                      +|||.+|.++|+|+++|||+|.|-.++                  ++  .+++..-+.+.+++|+.+|..++..
T Consensus        22 ~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          22 LLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHHHTT
T ss_pred             eEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhHHHHHHHHHHHHHh
Confidence            589999999999999999999974321                  12  3444456788999999999999874

>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=96.34  E-value=0.0015  Score=52.48  Aligned_cols=53  Identities=23%  Similarity=0.244  Sum_probs=40.0

Q ss_pred             eeecCCCchHHHHHHHcCceEEecCCC---------------------CcCeEEEecC--H----HHHHHHHHHHHHHHh
Q psy4141           2 KKISRSGCKIKALRAKTNTYIKTPVRG---------------------EEPVFVVTGR--K----EDVARAKREILSAAD   54 (353)
Q Consensus         2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---------------------e~~vv~I~G~--~----e~v~~Ak~~I~~i~~   54 (353)
                      +|||.+|.++|+|+++|||+|.|-.++                     ++--|.|++.  +    ..+++|+.+|..++.
T Consensus        21 ~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          21 RILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHHHHSS
T ss_pred             EEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHHHHHHHHHHHHHHHHHHcC
Confidence            589999999999999999999986443                     1223555553  1    358889999988874

>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=94.91  E-value=0.0081  Score=42.31  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=34.8

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ....+.||.+..+..|||+|.+||-..+.||.+|.+-.
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            46889999999999999999999999999999997653

>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=94.54  E-value=0.0096  Score=41.79  Aligned_cols=38  Identities=21%  Similarity=0.193  Sum_probs=34.9

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS  118 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~  118 (353)
                      ....+.||.+.....|||+|.++|-..+.||-+|.+-.
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            56889999999999999999999999999999997654

>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=88.27  E-value=0.06  Score=37.63  Aligned_cols=33  Identities=24%  Similarity=0.736  Sum_probs=28.8

Q ss_pred             cccccccccccccEEeCC----CCHhhhHHhHHHHhcc
Q psy4141         301 RQCYLCNDREVTHALIPC----GHNFFCSECAERTCDF  334 (353)
Q Consensus       301 ~~C~IC~~~~~~~~llpC----gH~~fC~~C~~~~~~~  334 (353)
                      ..|.+|.++..+.-++.|    +|. ||..|.+...+.
T Consensus         9 l~CtlC~erLEdtHFVQCPsv~~Hk-FCFpCsr~sik~   45 (80)
T d2cs3a1           9 LCCTICHERLEDTHFVQCPSVPSHK-FCFPCSRESIKA   45 (80)
T ss_dssp             CCCSSSCSCCSSTTSEECSSCSSCE-ECHHHHHHHHHH
T ss_pred             eeeeeehhhhcCCceEeCCCCcCCc-eeccccHHHHHh
Confidence            789999999999888888    488 999999887664

>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=85.37  E-value=0.14  Score=37.78  Aligned_cols=31  Identities=19%  Similarity=0.268  Sum_probs=26.5

Q ss_pred             eEEEEEecCCCccceeccCChHHHHHHHHhC
Q psy4141          81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTN  111 (353)
Q Consensus        81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg  111 (353)
                      ..++|.|....-|.|||++|+.|++|++.-.
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l~   65 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVVQ   65 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHHH
Confidence            3467889999999999999999999976654

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

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: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=84.26  E-value=0.39  Score=34.71  Aligned_cols=57  Identities=9%  Similarity=-0.034  Sum_probs=45.2

Q ss_pred             EEEecCCCccceeccCCh-HHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHH
Q psy4141          84 EVRVPYKVVGLVVGPKGA-TIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIES  143 (353)
Q Consensus        84 ~v~VP~~~vG~IIGkgG~-tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~  143 (353)
                      -+.|+..++..|||+++. .|+.|.+.+++.|.+-   ....|-|.|. ++....+.+.|..
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG---~NGrIWi~~~~~~~~i~i~~aI~~   62 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG---LNGKIWVKCEELSNTLACYRTIME   62 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE---TTTEEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe---cCcEEEEECCCHHHHHHHHHHHHH
Confidence            467899999999999998 8999999999999764   4457999995 6666655555543

>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=82.64  E-value=0.19  Score=38.38  Aligned_cols=30  Identities=30%  Similarity=0.338  Sum_probs=25.1

Q ss_pred             eEEEEEecC-CCccceeccCChHHHHHHHHh
Q psy4141          81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQT  110 (353)
Q Consensus        81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~T  110 (353)
                      +...+.|+. .+-+.|||++|++||+|..+.
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            666788888 667899999999999997655