Psyllid ID: psy11278

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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-------24
Protein Sequence
MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIKS
Secondary Structure (PSIPRED)
cEEEEcccccccEEccccHHHHHHHHHHccEEEccccccccccccccEEEEEccHHHHHHHHHHHHccccEEEEEEccccccccccccHHHHHHHHHcccEEEEEccccccccEEEEEccHHHHHHHHHHHHHHHHHHHccccccccEEEEEEccccccccccccccccHHHHHHHcccEEEcccccccccccccccEEEEEccHHHHHHHHHHHHHccccccEEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccEEccHHHccEEEccccccHHHHHHHcccEEEEcccccccccccccEEEEEccHHHHHHHHHHHHHHcccEEEEcccccccccccccHHHHHHHHHccEEEEEcccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEcHHHccEEEccccccHHHHHHHcccEEEcccccccccccccccEEEEEccHHHHHHHHHHHHHccccccccEEEEEEcHHHHcc
Coil and Loop (DISEMBL)
mkldvsytdhshiigrGGLTIKKVMeetgchvhfpdsnrsvnaeksnQVSIAGSLLGLERARYRVRELTPlifcfeyplmgstpnanspFVQIIQEAYNVQVmfrnrpklqptlVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMeispqhhpimegpnainLKTIMAQTGaqivfpeandpiipvlkkssvtvsgniDSVYLARQMLVVSSVRPRRRLLLITipndiiks
Flexible Loop (DISEMBL)
mkldvsytdhshiigrgGLTIKKVMEETGCHvhfpdsnrsvnaeksNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFrnrpklqptlvmvkGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMlvvssvrprrrlllitipndiiks
Low Complexity Region (SEG)
MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMlvvssvrprrrlllITIPNDIIKS
Disordered region (IsUnstruct)
******YTDHSHIIGRGGLTIKKVMEETGCHVHF**************VSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDI***
Disordered Region (DISOPRED)
MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNR***AEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYP***********************VMFRN*PKLQPTLVMVKGCEKDVERVKEATTKL****************MMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN*****VLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPND****
Disordered Region (DISEMBL)
MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIKS
Disordered Region (DISPRO)
MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRS***EKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPND****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIKS
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	238	2.2.26 [Sep-21-2011]
Q24009	905	Protein bicaudal C OS=Dro	yes	N/A	0.907	0.238	0.547	8e-64
Q5U4T7	970	Protein bicaudal C homolo	N/A	N/A	0.890	0.218	0.525	2e-60
Q9IA00	963	Protein bicaudal C homolo	N/A	N/A	0.890	0.220	0.525	6e-60
Q9H694	974	Protein bicaudal C homolo	yes	N/A	0.890	0.217	0.515	3e-59
Q99MQ1	977	Protein bicaudal C homolo	yes	N/A	0.890	0.216	0.506	8e-58
Q9Z1A6	1268	Vigilin OS=Rattus norvegi	no	N/A	0.798	0.149	0.247	2e-08
Q8VDJ3	1268	Vigilin OS=Mus musculus G	no	N/A	0.798	0.149	0.247	3e-08
Q00341	1268	Vigilin OS=Homo sapiens G	no	N/A	0.798	0.149	0.242	4e-08
Q5R439	1268	Vigilin OS=Pongo abelii G	no	N/A	0.798	0.149	0.242	5e-08
P81021	1270	Vigilin OS=Gallus gallus	no	N/A	0.789	0.148	0.225	1e-05

>sp|Q24009|BICC_DROME Protein bicaudal C OS=Drosophila melanogaster GN=BicC PE=1 SV=2

 Score =  243 bits (620), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 120/219 (54%), Positives = 161/219 (73%), Gaps = 3/219 (1%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MK+DVSYTDHS+IIGRGG  IK++M++T  H+HFPDSNRS   EKSNQVS+ GSL G+ER
Sbjct: 175 MKMDVSYTDHSYIIGRGGNNIKRIMDDTHTHIHFPDSNRSNPTEKSNQVSLCGSLEGVER 234

Query: 61  ARYRVRELTPLIFCFEYPLMGST---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR  VR  TPL+  FE P+MG     P+  +P++++I+  +NVQV+F  RPKL  +LV+V
Sbjct: 235 ARALVRLSTPLLISFEMPVMGPNKPQPDHETPYIKMIETKFNVQVIFSTRPKLHTSLVLV 294

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KG EK+  +V++AT  LI   C S+A+Q  V + MEISPQHH I++G N +NL +IM +T
Sbjct: 295 KGSEKESAQVRDATQLLINFACESIASQILVNVQMEISPQHHEIVKGKNNVNLLSIMERT 354

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
             +I+FP+ +D  +  LKKS VT+SG ID VYLARQ L+
Sbjct: 355 QTKIIFPDLSDMNVKPLKKSQVTISGRIDDVYLARQQLL 393

RNA-binding protein that is involved in oogenesis. Required for correct targeting of the migrating anterior follicle cells and the establishment of anterior-posterior polarity in the oocyte. May act as translational repressor of oskar during oogenesis. Function seems to be sensitive to small changes in expression.
Drosophila melanogaster (taxid: 7227)

>sp|Q5U4T7|BIC1B_XENLA Protein bicaudal C homolog 1-B OS=Xenopus laevis GN=bicc1-b PE=2 SV=1

 Score =  232 bits (591), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 115/219 (52%), Positives = 152/219 (69%), Gaps = 7/219 (3%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct: 133 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 192

Query: 61  ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct: 193 ARVRIRELLPLVLMFELPIAGILQPIPDPNSPTIQQISQTYNITVSFKQRSRVYGATVIV 252

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct: 253 RGSQNNTSAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGCNIKHIMQRT 312

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
           GAQI FP+ N+P    LKKS+V + G I+SV LARQ L+
Sbjct: 313 GAQIHFPDPNNP----LKKSTVYLQGTIESVCLARQYLM 347

Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development. Seems to be involved in endoderm formation. Ectopic expression results in endoderm formation in the absence of mesoderm induction.

Xenopus laevis (taxid: 8355)

>sp|Q9IA00|BIC1A_XENLA Protein bicaudal C homolog 1-A OS=Xenopus laevis GN=bicc1-a PE=2 SV=1

 Score =  230 bits (587), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 115/219 (52%), Positives = 150/219 (68%), Gaps = 7/219 (3%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +K+DV +T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct: 131 LKMDVLHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 190

Query: 61  ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct: 191 ARVRIRELLPLVLMFELPIAGILQPIPDPNSPTIQQISQTYNLTVSFKQRSRVYGATVIV 250

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           +G + +   VKE T  L+EH+ GSLA    V   ++I+ QHH  M G N  N+K IM +T
Sbjct: 251 RGSQNNTSAVKEGTAMLLEHLAGSLATAIPVSTQLDIAAQHHLFMMGRNGCNIKHIMQRT 310

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
           GAQI FP+ N+P    LKKS+V + G IDSV LARQ L+
Sbjct: 311 GAQIHFPDPNNP----LKKSTVYLQGTIDSVCLARQYLM 345

Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development. Seems to be involved in endoderm formation. Ectopic expression results in endoderm formation in the absence of mesoderm induction.

Xenopus laevis (taxid: 8355)

>sp|Q9H694|BICC1_HUMAN Protein bicaudal C homolog 1 OS=Homo sapiens GN=BICC1 PE=1 SV=2

 Score =  228 bits (581), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 113/219 (51%), Positives = 151/219 (68%), Gaps = 7/219 (3%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct: 135 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 194

Query: 61  ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct: 195 ARVRIRELLPLVLMFELPIAGILQPVPDPNSPSIQHISQTYNISVSFKQRSRMYGATVIV 254

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct: 255 RGSQNNTSAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNIKHIMQRT 314

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
           GAQI FP+ ++P     KKS+V + G I+SV LARQ L+
Sbjct: 315 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQYLM 349

Putative RNA-binding protein. Acts as a negative regulator of Wnt signaling. May be involved in regulating gene expression during embryonic development.

Homo sapiens (taxid: 9606)

>sp|Q99MQ1|BICC1_MOUSE Protein bicaudal C homolog 1 OS=Mus musculus GN=Bicc1 PE=2 SV=1

 Score =  223 bits (569), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 111/219 (50%), Positives = 150/219 (68%), Gaps = 7/219 (3%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +K+DVS+T+HSH+IG+GG  IKKVME+TGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct: 137 LKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 196

Query: 61  ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR R+REL PL+  FE P+ G     P+ N+P +Q I + Y+V V F+ R ++    V V
Sbjct: 197 ARARIRELLPLVLMFELPIAGILQPVPDPNTPSIQHISQTYSVSVSFKQRSRMYGATVTV 256

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct: 257 RGSQNNTNAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNVKHIMQRT 316

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
           GAQI FP+ ++P     KKS+V + G I+SV LARQ L+
Sbjct: 317 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQYLM 351

Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.

Mus musculus (taxid: 10090)

>sp|Q9Z1A6|VIGLN_RAT Vigilin OS=Rattus norvegicus GN=Hdlbp PE=1 SV=1

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 89/214 (41%), Gaps = 24/214 (11%)

Query: 10  HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV---- 65
           H +IIG+GG  IKK+ EE+   +  P  N +     S  + I G     E AR R+    
Sbjct: 593 HKNIIGKGGANIKKIREESNTKIDLPAENSN-----SETIVITGKRANCEAARSRILSIQ 647

Query: 66  ---RELTPLIFCFEYPLMGSTPNANSPFVQ-IIQEAYNVQVMFRNRPKLQPTLVMVKGCE 121
                +  +       L  S        ++ I++E   V + F        T+V ++G  
Sbjct: 648 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVV-IRGPS 706

Query: 122 KDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQI 181
            DVE+ K+    L E          S  + +   P++H  + G     ++ +   TGA+I
Sbjct: 707 SDVEKAKKQLLHLAEE-----KQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARI 761

Query: 182 VFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
           +FP A D       +  +T+ G  D+V  A++ L
Sbjct: 762 IFPAAEDK-----DQDLITIIGKEDAVREAQKEL 790

Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

Rattus norvegicus (taxid: 10116)

>sp|Q8VDJ3|VIGLN_MOUSE Vigilin OS=Mus musculus GN=Hdlbp PE=1 SV=1

 Score = 58.9 bits (141), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 89/214 (41%), Gaps = 24/214 (11%)

Query: 10  HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV---- 65
           H +IIG+GG  IKK+ EE+   +  P  N +     S  + I G     E AR R+    
Sbjct: 593 HKNIIGKGGANIKKIREESNTKIDLPAENSN-----SETIIITGKRANCEAARSRILSIQ 647

Query: 66  ---RELTPLIFCFEYPLMGSTPNANSPFVQ-IIQEAYNVQVMFRNRPKLQPTLVMVKGCE 121
                +  +       L  S        ++ I++E   V + F        T+V ++G  
Sbjct: 648 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVV-IRGPS 706

Query: 122 KDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQI 181
            DVE+ K+    L E          S  + +   P++H  + G     ++ +   TGA+I
Sbjct: 707 SDVEKAKKQLLHLAEE-----KQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARI 761

Query: 182 VFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
           +FP A D       +  +T+ G  D+V  A++ L
Sbjct: 762 IFPAAEDK-----DQDLITIIGKEDAVREAQKEL 790

Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

Mus musculus (taxid: 10090)

>sp|Q00341|VIGLN_HUMAN Vigilin OS=Homo sapiens GN=HDLBP PE=1 SV=2

 Score = 58.5 bits (140), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 52/214 (24%), Positives = 89/214 (41%), Gaps = 24/214 (11%)

Query: 10  HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV---- 65
           H +IIG+GG  IKK+ EE+   +  P  N +     S  + I G     E AR R+    
Sbjct: 593 HKNIIGKGGANIKKIREESNTKIDLPAENSN-----SETIIITGKRANCEAARSRILSIQ 647

Query: 66  ---RELTPLIFCFEYPLMGSTPNANSPFVQ-IIQEAYNVQVMFRNRPKLQPTLVMVKGCE 121
                +  +       L  S        ++ I++E   V + F        T+V ++G  
Sbjct: 648 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVV-IRGPS 706

Query: 122 KDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQI 181
            DVE+ K+    L E          S  + +   P++H  + G     ++ +   TGA++
Sbjct: 707 SDVEKAKKQLLHLAEE-----KQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARV 761

Query: 182 VFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
           +FP A D       +  +T+ G  D+V  A++ L
Sbjct: 762 IFPAAEDK-----DQDLITIIGKEDAVREAQKEL 790

Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

Homo sapiens (taxid: 9606)

>sp|Q5R439|VIGLN_PONAB Vigilin OS=Pongo abelii GN=HDLBP PE=2 SV=1

 Score = 58.2 bits (139), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 52/214 (24%), Positives = 89/214 (41%), Gaps = 24/214 (11%)

Query: 10  HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV---- 65
           H +IIG+GG  IKK+ EE+   +  P  N +     S  + I G     E AR R+    
Sbjct: 593 HKNIIGKGGANIKKIREESNTKIDLPAENSN-----SETIIITGKRANCEAARSRILSIQ 647

Query: 66  ---RELTPLIFCFEYPLMGSTPNANSPFVQ-IIQEAYNVQVMFRNRPKLQPTLVMVKGCE 121
                +  +       L  S        ++ I++E   V + F        T+V ++G  
Sbjct: 648 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVV-IRGPS 706

Query: 122 KDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQI 181
            DVE+ K+    L E          S  + +   P++H  + G     ++ +   TGA++
Sbjct: 707 SDVEKAKKQLLHLAEE-----KQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARV 761

Query: 182 VFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
           +FP A D       +  +T+ G  D+V  A++ L
Sbjct: 762 IFPAAEDK-----DQDLITIIGKEDAVREAQKEL 790

Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

Pongo abelii (taxid: 9601)

>sp|P81021|VIGLN_CHICK Vigilin OS=Gallus gallus GN=HDLBP PE=2 SV=1

 Score = 50.4 bits (119), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/217 (22%), Positives = 92/217 (42%), Gaps = 29/217 (13%)

Query: 10  HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV---- 65
           H +IIG+GG  IKK+ EE+   +  P   ++       Q+   G    ++  R+R+    
Sbjct: 592 HKNIIGKGGANIKKIREESNTKIDLPGREQATQ----RQLLSQGREQTVKLLRHRILAIQ 647

Query: 66  REL---TPLIFCFEYPLMGSTPNANSPFVQ-IIQEAYNVQVMFRNRPKLQPTLVMVKGCE 121
           +EL   T +       L  S   A   F++ I++E   V + F        T+ +     
Sbjct: 648 KELANITEVEVSIPSKLHNSLIGAKGRFIRSIMEECGGVHIHFPTEGSGSATVTI----- 702

Query: 122 KDVERVKEATTKLIEHMCGSLANQ---TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTG 178
               R +  T +     C + A +    S  + +   P++H  + G    N++ +   TG
Sbjct: 703 ----RAQPRTWRKPRSSCCTWAEEKQTKSYTVDLRAKPEYHKFLIGKGGGNIRKVRDNTG 758

Query: 179 AQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
           A+I+FP + D       +  +T+ G  ++V  A++ L
Sbjct: 759 ARIIFPTSEDK-----DQELITIMGTEEAVKEAQKEL 790

Gallus gallus (taxid: 9031)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	238
307215504	861	Protein bicaudal C [Harpegnathos saltato	0.983	0.271	0.639	8e-81
340729029	865	PREDICTED: protein bicaudal C-like [Bomb	0.983	0.270	0.639	1e-80
350401510	865	PREDICTED: protein bicaudal C-like [Bomb	0.983	0.270	0.639	1e-80
345480322	909	PREDICTED: protein bicaudal C homolog 1-	0.915	0.239	0.649	3e-80
380030025	863	PREDICTED: protein bicaudal C-like [Apis	0.983	0.271	0.634	3e-80
328705626	712	PREDICTED: protein bicaudal C homolog 1-	0.966	0.323	0.623	5e-80
328775873	865	PREDICTED: protein bicaudal C [Apis mell	0.983	0.270	0.630	8e-80
332022439	817	Protein bicaudal C-like protein 1-B [Acr	0.915	0.266	0.669	1e-79
383865401	863	PREDICTED: protein bicaudal C-like [Mega	0.915	0.252	0.665	5e-79
307177283	729	Protein bicaudal C [Camponotus floridanu	0.983	0.320	0.626	1e-78

>gi|307215504|gb|EFN90156.1| Protein bicaudal C [Harpegnathos saltator]

 Score =  305 bits (782), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 154/241 (63%), Positives = 184/241 (76%), Gaps = 7/241 (2%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIK+VMEETGCH+HFPDSNRS + +KSNQVSIAG + G+ER
Sbjct: 142 MKLDVSYTDHSHIIGKGGLTIKRVMEETGCHIHFPDSNRSNHQDKSNQVSIAGEMEGVER 201

Query: 61  ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR RVR LTPLIF FE P+MG   STP+  SP+V  IQE YNVQVMFR RPKL  TLV+V
Sbjct: 202 ARARVRNLTPLIFSFELPIMGASQSTPDCTSPYVVKIQEKYNVQVMFRTRPKLHATLVVV 261

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI +MC +LA+Q  V M MEISPQHH I+ G  + NLK IM +T
Sbjct: 262 KGCEWEVSQVKEATVLLIRYMCKNLASQIQVQMSMEISPQHHSIVLGKQSSNLKMIMQRT 321

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIK 237
             QI+FP+A DP IP LKKS+VT++G I +VYLARQ LV S       +L+  +P D + 
Sbjct: 322 ATQIMFPDAGDPNIPSLKKSNVTITGAIHNVYLARQQLVGS----LPLVLMFDLPEDSVS 377

Query: 238 S 238
           +
Sbjct: 378 A 378

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340729029|ref|XP_003402812.1| PREDICTED: protein bicaudal C-like [Bombus terrestris]

 Score =  305 bits (781), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 154/241 (63%), Positives = 185/241 (76%), Gaps = 7/241 (2%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIK+VMEETGCH+HFPDSNRS + EKSNQVSIAG + G+ER
Sbjct: 145 MKLDVSYTDHSHIIGKGGLTIKRVMEETGCHIHFPDSNRSNHQEKSNQVSIAGEMEGVER 204

Query: 61  ARYRVRELTPLIFCFEYPLMGST---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR RVR LTPLIF FE P+M ++   P++ SP+V  IQE YNVQVMFR RPKL  TLV+V
Sbjct: 205 ARARVRNLTPLIFSFELPIMSASQTVPDSTSPYVVKIQEKYNVQVMFRTRPKLHATLVVV 264

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI +MC +LA+Q  V M MEISPQHH I+ G  + NLK IM +T
Sbjct: 265 KGCEWEVSQVKEATVLLIHYMCQNLASQIQVQMSMEISPQHHSIVLGKQSSNLKMIMQRT 324

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIK 237
           G QI+FP+A DP IP LKKS+VT++G I +VYLARQ LV S       +L+  +P D + 
Sbjct: 325 GTQIMFPDAGDPNIPSLKKSNVTITGGIHNVYLARQQLVGS----LPLVLMFDLPEDSMS 380

Query: 238 S 238
           S
Sbjct: 381 S 381

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350401510|ref|XP_003486177.1| PREDICTED: protein bicaudal C-like [Bombus impatiens]

 Score =  305 bits (780), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 154/241 (63%), Positives = 185/241 (76%), Gaps = 7/241 (2%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIK+VMEETGCH+HFPDSNRS + EKSNQVSIAG + G+ER
Sbjct: 145 MKLDVSYTDHSHIIGKGGLTIKRVMEETGCHIHFPDSNRSNHQEKSNQVSIAGEMEGVER 204

Query: 61  ARYRVRELTPLIFCFEYPLMGST---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR RVR LTPLIF FE P+M ++   P++ SP+V  IQE YNVQVMFR RPKL  TLV+V
Sbjct: 205 ARARVRNLTPLIFSFELPIMSASQTVPDSTSPYVVKIQEKYNVQVMFRTRPKLHATLVVV 264

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI +MC +LA+Q  V M MEISPQHH I+ G  + NLK IM +T
Sbjct: 265 KGCEWEVSQVKEATVLLIHYMCQNLASQIQVQMSMEISPQHHSIVLGKQSSNLKMIMQRT 324

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIK 237
           G QI+FP+A DP IP LKKS+VT++G I +VYLARQ LV S       +L+  +P D + 
Sbjct: 325 GTQIMFPDAGDPNIPSLKKSNVTITGGIHNVYLARQQLVGS----LPLVLMFDLPEDSMS 380

Query: 238 S 238
           S
Sbjct: 381 S 381

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345480322|ref|XP_001605489.2| PREDICTED: protein bicaudal C homolog 1-like [Nasonia vitripennis]

 Score =  303 bits (777), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 148/228 (64%), Positives = 177/228 (77%), Gaps = 10/228 (4%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIKKVMEET CH+HFPDSNRS + EKSNQVSIAG + G+E+
Sbjct: 132 MKLDVSYTDHSHIIGKGGLTIKKVMEETSCHIHFPDSNRSNHQEKSNQVSIAGDMEGVEK 191

Query: 61  ARYRVRELTPLIFCFEYPLMG----------STPNANSPFVQIIQEAYNVQVMFRNRPKL 110
           AR RVR LTPLIF FE P+MG          +TP + SP++  IQE YNVQVMFR RPKL
Sbjct: 192 ARARVRTLTPLIFSFELPVMGNSSQIATAANTTPFSTSPYIVKIQEKYNVQVMFRTRPKL 251

Query: 111 QPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINL 170
             TLV+VKGCE +V++VKEAT  LI HMC +LA+Q  V M MEISPQHH ++ G  + NL
Sbjct: 252 HATLVVVKGCEWEVQKVKEATVLLIHHMCETLASQIQVQMSMEISPQHHSVVLGKQSNNL 311

Query: 171 KTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218
           K+IM  T  QI+FP+A DP IP LKKS+VT++G+I +VYLARQ L+ S
Sbjct: 312 KSIMQTTATQIMFPDAGDPNIPSLKKSNVTITGSIHNVYLARQQLMGS 359

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380030025|ref|XP_003698660.1| PREDICTED: protein bicaudal C-like [Apis florea]

 Score =  303 bits (777), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 153/241 (63%), Positives = 185/241 (76%), Gaps = 7/241 (2%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIK+VMEETGCH+HFPDSNRS + EKSNQVSIAG + G+ER
Sbjct: 145 MKLDVSYTDHSHIIGKGGLTIKRVMEETGCHIHFPDSNRSNHQEKSNQVSIAGEMEGVER 204

Query: 61  ARYRVRELTPLIFCFEYPLMGST---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR RVR LTPLIF FE P+M ST   P++ +P++  IQE YNVQVMFR RPKL  TLV+V
Sbjct: 205 ARARVRNLTPLIFSFELPIMSSTQALPDSTTPYLVKIQEKYNVQVMFRTRPKLHATLVVV 264

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI +MC +LA+Q  V + MEISPQHH I+ G  + NLK IM +T
Sbjct: 265 KGCEWEVSQVKEATVLLIHYMCQNLASQIQVQISMEISPQHHSIVLGKQSSNLKMIMQRT 324

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIK 237
           G QI+FP+A DP IP LKKS+VT++G I +VYLARQ LV S       +L+  +P D + 
Sbjct: 325 GTQIMFPDAGDPNIPSLKKSNVTITGGIHNVYLARQQLVGS----LPLVLMFDLPEDSMS 380

Query: 238 S 238
           S
Sbjct: 381 S 381

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328705626|ref|XP_001944274.2| PREDICTED: protein bicaudal C homolog 1-like [Acyrthosiphon pisum]

 Score =  303 bits (775), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 149/239 (62%), Positives = 183/239 (76%), Gaps = 9/239 (3%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLD+SYTDHSHIIGRGGLTIK+VME TGCH+HFPDSNR+   EKSNQVSIAG+   +ER
Sbjct: 89  MKLDLSYTDHSHIIGRGGLTIKQVMENTGCHIHFPDSNRTSLLEKSNQVSIAGNCGAVER 148

Query: 61  ARYRVRELTPLIFCFEYPLMGST-----PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLV 115
           AR RVRELTPLIFCF++P +G+      P++  P++  IQ+ +NV VMFR RPKL  T+V
Sbjct: 149 ARARVRELTPLIFCFDWPNIGTVQNYQDPSSQFPYIGSIQDNFNVHVMFRTRPKLHSTMV 208

Query: 116 MVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMA 175
           MVKG E DV RVKEAT +LI HMCG+LANQ  ++M+MEISPQHH I+ GP    L+ I  
Sbjct: 209 MVKGHEWDVVRVKEATMQLITHMCGNLANQVLILMVMEISPQHHKIVMGPGNETLRAITR 268

Query: 176 QTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPND 234
           +TGAQI+FP+A DP IP +KKSSVT++G+I +VY ARQML+ S       LL+  IP D
Sbjct: 269 RTGAQILFPDAKDPNIPSIKKSSVTITGHIHNVYAARQMLIGS----LPLLLMFDIPQD 323

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328775873|ref|XP_396860.4| PREDICTED: protein bicaudal C [Apis mellifera]

 Score =  302 bits (773), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 152/241 (63%), Positives = 185/241 (76%), Gaps = 7/241 (2%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIK+VMEETGCH+HFPDSNRS + EKSNQVSIAG + G+ER
Sbjct: 145 MKLDVSYTDHSHIIGKGGLTIKRVMEETGCHIHFPDSNRSNHQEKSNQVSIAGEMEGVER 204

Query: 61  ARYRVRELTPLIFCFEYPLMGST---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR RVR LTPLIF FE P+M S+   P++ +P++  IQE YNVQVMFR RPKL  TLV+V
Sbjct: 205 ARARVRNLTPLIFSFELPIMSSSQALPDSTTPYLVKIQEKYNVQVMFRTRPKLHATLVVV 264

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI +MC +LA+Q  V + MEISPQHH I+ G  + NLK IM +T
Sbjct: 265 KGCEWEVSQVKEATVLLIHYMCQNLASQIQVQISMEISPQHHSIVLGKQSSNLKMIMQRT 324

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIK 237
           G QI+FP+A DP IP LKKS+VT++G I +VYLARQ LV S       +L+  +P D + 
Sbjct: 325 GTQIMFPDAGDPNIPSLKKSNVTITGGIHNVYLARQQLVGS----LPLVLMFDLPEDSMS 380

Query: 238 S 238
           S
Sbjct: 381 S 381

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022439|gb|EGI62747.1| Protein bicaudal C-like protein 1-B [Acromyrmex echinatior]

 Score =  301 bits (771), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 148/221 (66%), Positives = 175/221 (79%), Gaps = 3/221 (1%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIK+VMEETGCH+HFPDSNRS + +KSNQVSIAG +  +ER
Sbjct: 93  MKLDVSYTDHSHIIGKGGLTIKRVMEETGCHIHFPDSNRSNHQDKSNQVSIAGEMESVER 152

Query: 61  ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR RVR LTPLIF FE P+MG   S P+  SP+V  IQ+ +NVQVMFR RPKL  TLV+V
Sbjct: 153 ARARVRNLTPLIFSFELPIMGASQSMPDCTSPYVVKIQDKFNVQVMFRTRPKLHATLVVV 212

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI HMC +LA+Q  V M MEISPQHH I+ G  + NLK IM +T
Sbjct: 213 KGCEWEVSQVKEATQLLIRHMCKNLASQIQVQMSMEISPQHHSIVLGKQSSNLKMIMQRT 272

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218
             QI+FP+A DP IP LKKS+VT++G+I +VYLARQ LV S
Sbjct: 273 ATQIMFPDAGDPNIPSLKKSNVTITGDIHNVYLARQQLVGS 313

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383865401|ref|XP_003708162.1| PREDICTED: protein bicaudal C-like [Megachile rotundata]

 Score =  300 bits (767), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 147/221 (66%), Positives = 176/221 (79%), Gaps = 3/221 (1%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKL+V YTDHSHIIG+GGLTIK+VMEETGCH+HFPDSNRS + EKSNQVSIAG + G+ER
Sbjct: 144 MKLEVGYTDHSHIIGKGGLTIKRVMEETGCHIHFPDSNRSNHQEKSNQVSIAGEMEGVER 203

Query: 61  ARYRVRELTPLIFCFEYPLMGST---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR R+R LT LIF FE P+MGS+   P++ SP++  IQE YNVQVMFR RPKL  TLV+V
Sbjct: 204 ARARIRNLTALIFSFELPIMGSSQTVPDSTSPYMIKIQEKYNVQVMFRTRPKLHATLVVV 263

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI +MC +LA+Q  V M MEISPQHH I+ G  + NLK IM +T
Sbjct: 264 KGCEWEVSQVKEATVLLIHYMCQNLASQIQVQMTMEISPQHHSIVLGKQSSNLKMIMQRT 323

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218
           G QI+FP+A DP IP LKKS+VT++G I +VYLARQ LV S
Sbjct: 324 GTQIMFPDAGDPNIPSLKKSNVTITGGIHNVYLARQQLVGS 364

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307177283|gb|EFN66461.1| Protein bicaudal C [Camponotus floridanus]

 Score =  298 bits (763), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 151/241 (62%), Positives = 182/241 (75%), Gaps = 7/241 (2%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           MKLDVSYTDHSHIIG+GGLTIK+VMEET CH+HFPDSNRS + +KSNQVSIAG +  +ER
Sbjct: 14  MKLDVSYTDHSHIIGKGGLTIKRVMEETSCHIHFPDSNRSNHQDKSNQVSIAGEMESVER 73

Query: 61  ARYRVRELTPLIFCFEYPLMGS---TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
           AR RVR LTPLIF FE P+MG+   TP+ +SP+V  IQE YNVQVMFR RPKL  T V+V
Sbjct: 74  ARARVRNLTPLIFSFELPIMGASQNTPDCSSPYVVKIQEKYNVQVMFRTRPKLHATQVVV 133

Query: 118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
           KGCE +V +VKEAT  LI +MC +LA+Q  V M MEISPQHH I+ G  + NLK IM +T
Sbjct: 134 KGCEWEVSQVKEATVLLIRYMCKNLASQIQVQMSMEISPQHHSIVLGKQSSNLKMIMQRT 193

Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIPNDIIK 237
             QI+FP+A DP IP LKKS+VT++G I +VYLARQ LV S       +L+  +P D I 
Sbjct: 194 ATQIMFPDAGDPNIPSLKKSNVTITGAIHNVYLARQQLVGS----LPLVLMFDLPEDSIS 249

Query: 238 S 238
           +
Sbjct: 250 A 250

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	238
FB|FBgn0000182	905	BicC "Bicaudal C" [Drosophila	0.894	0.235	0.550	1.4e-58
UNIPROTKB|F1PUI2	872	BICC1 "Uncharacterized protein	0.878	0.239	0.518	2.4e-54
UNIPROTKB|F1PUI0	889	BICC1 "Uncharacterized protein	0.878	0.235	0.518	2.8e-54
UNIPROTKB|F1MDL5	870	BICC1 "Uncharacterized protein	0.878	0.240	0.518	3.1e-54
UNIPROTKB|Q9H694	974	BICC1 "Protein bicaudal C homo	0.878	0.214	0.518	4.8e-54
UNIPROTKB|F1RG08	894	BICC1 "Uncharacterized protein	0.878	0.233	0.513	6.3e-54
UNIPROTKB|F1NFQ2	872	BICC1 "Uncharacterized protein	0.878	0.239	0.513	3.2e-53
ZFIN|ZDB-GENE-080522-3	892	bicc1b "bicaudal C homolog 1b	0.878	0.234	0.509	1e-52
MGI|MGI:1933388	977	Bicc1 "bicaudal C homolog 1 (D	0.878	0.213	0.509	1.6e-52
RGD|1307459	898	Bicc1 "bicaudal C homolog 1 (D	0.878	0.232	0.504	1.8e-52

FB|FBgn0000182 BicC "Bicaudal C" [Drosophila melanogaster (taxid:7227)]

 Score = 605 (218.0 bits), Expect = 1.4e-58, P = 1.4e-58
 Identities = 119/216 (55%), Positives = 159/216 (73%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             MK+DVSYTDHS+IIGRGG  IK++M++T  H+HFPDSNRS   EKSNQVS+ GSL G+ER
Sbjct:   175 MKMDVSYTDHSYIIGRGGNNIKRIMDDTHTHIHFPDSNRSNPTEKSNQVSLCGSLEGVER 234

Query:    61 ARYRVRELTPLIFCFEYPLMGST---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR  VR  TPL+  FE P+MG     P+  +P++++I+  +NVQV+F  RPKL  +LV+V
Sbjct:   235 ARALVRLSTPLLISFEMPVMGPNKPQPDHETPYIKMIETKFNVQVIFSTRPKLHTSLVLV 294

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             KG EK+  +V++AT  LI   C S+A+Q  V + MEISPQHH I++G N +NL +IM +T
Sbjct:   295 KGSEKESAQVRDATQLLINFACESIASQILVNVQMEISPQHHEIVKGKNNVNLLSIMERT 354

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
               +I+FP+ +D  +  LKKS VT+SG ID VYLARQ
Sbjct:   355 QTKIIFPDLSDMNVKPLKKSQVTISGRIDDVYLARQ 390

GO:0007297 "ovarian follicle cell migration" evidence=IMP

GO:0048477 "oogenesis" evidence=NAS;IMP;TAS

GO:0007319 "negative regulation of oskar mRNA translation" evidence=TAS

GO:0003729 "mRNA binding" evidence=ISS;NAS;TAS

GO:0005887 "integral to plasma membrane" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0003723 "RNA binding" evidence=IEA

GO:0007067 "mitosis" evidence=IMP

GO:0030036 "actin cytoskeleton organization" evidence=IMP

GO:0000226 "microtubule cytoskeleton organization" evidence=IMP

UNIPROTKB|F1PUI2 BICC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 566 (204.3 bits), Expect = 2.4e-54, P = 2.4e-54
 Identities = 112/216 (51%), Positives = 149/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:    33 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 92

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct:    93 ARVRIRELLPLVLMFELPIAGILQPVPDPNSPSIQHISQTYNISVSFKQRSRMYGATVIV 152

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   153 RGSQNNTSAVKEGTATLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNIKHIMQRT 212

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   213 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 244

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1PUI0 BICC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 566 (204.3 bits), Expect = 2.8e-54, P = 2.8e-54
 Identities = 112/216 (51%), Positives = 149/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:    75 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 134

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct:   135 ARVRIRELLPLVLMFELPIAGILQPVPDPNSPSIQHISQTYNISVSFKQRSRMYGATVIV 194

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   195 RGSQNNTSAVKEGTATLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNIKHIMQRT 254

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   255 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 286

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1MDL5 BICC1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 565 (203.9 bits), Expect = 3.1e-54, P = 3.1e-54
 Identities = 112/216 (51%), Positives = 149/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:    33 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 92

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct:    93 ARVRIRELLPLVLMFELPIAGILQPVPDPNSPSIQHISQMYNISVSFKQRSRMYGATVIV 152

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   153 RGSQNNTSAVKEGTATLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNIKHIMQRT 212

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   213 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 244

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q9H694 BICC1 "Protein bicaudal C homolog 1" [Homo sapiens (taxid:9606)]

 Score = 566 (204.3 bits), Expect = 4.8e-54, P = 4.8e-54
 Identities = 112/216 (51%), Positives = 149/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:   135 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 194

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct:   195 ARVRIRELLPLVLMFELPIAGILQPVPDPNSPSIQHISQTYNISVSFKQRSRMYGATVIV 254

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   255 RGSQNNTSAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNIKHIMQRT 314

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   315 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 346

GO:0003723 "RNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IDA

UNIPROTKB|F1RG08 BICC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 563 (203.2 bits), Expect = 6.3e-54, P = 6.3e-54
 Identities = 111/216 (51%), Positives = 149/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:    55 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 114

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ NSP +Q I + YN+ V F+ R ++    V+V
Sbjct:   115 ARVRIRELLPLVLMFELPIAGILQPVPDPNSPSIQHISQTYNISVSFKQRSRMYGATVIV 174

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   +KE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   175 RGSQNNTSALKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNIKHIMQRT 234

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   235 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 266

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1NFQ2 BICC1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 556 (200.8 bits), Expect = 3.2e-53, P = 3.2e-53
 Identities = 111/216 (51%), Positives = 148/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVMEETGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:    33 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 92

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ NS  +Q I + YN+ V F+ R ++    V+V
Sbjct:    93 ARVRIRELLPLVLMFELPIAGILQPIPDPNSHTIQHISQTYNISVSFKQRSRMYGATVIV 152

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   153 RGSQNNTSAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNIKHIMQRT 212

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   213 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 244

GO:0003723 "RNA binding" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

ZFIN|ZDB-GENE-080522-3 bicc1b "bicaudal C homolog 1b (Drosophila)" [Danio rerio (taxid:7955)]

 Score = 552 (199.4 bits), Expect = 1.0e-52, P = 1.0e-52
 Identities = 109/214 (50%), Positives = 148/214 (69%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVME+TGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:    55 LKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQAEKSNQVSIAGQPGGVEA 114

Query:    61 ARYRVRELTPLIFCFEYPLMGS-TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKG 119
             AR R+REL PL+  FE P++    P+ +SP +Q I + YN+ V F+ R +L     +V+G
Sbjct:   115 ARARIRELLPLVLMFELPVIVQLNPDPSSPAIQHISQTYNISVAFKQRSRLYGATGVVRG 174

Query:   120 CEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGA 179
              + +   VK  T  L+EH+ G+LA+  ++   ++I+PQHH  M G N  N+K IM +TGA
Sbjct:   175 SQNNAAAVKRGTAVLLEHLAGNLASAITISTQLDIAPQHHLFMMGRNGSNIKHIMQRTGA 234

Query:   180 QIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             Q+ FP+ N P     KKS+V V G IDSV LARQ
Sbjct:   235 QVHFPDPNCP----QKKSTVYVQGTIDSVCLARQ 264

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1933388 Bicc1 "bicaudal C homolog 1 (Drosophila)" [Mus musculus (taxid:10090)]

 Score = 552 (199.4 bits), Expect = 1.6e-52, P = 1.6e-52
 Identities = 110/216 (50%), Positives = 148/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVME+TGCH+HFPDSNR+  AEKSNQVSIAG   G+E 
Sbjct:   137 LKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVES 196

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ N+P +Q I + Y+V V F+ R ++    V V
Sbjct:   197 ARARIRELLPLVLMFELPIAGILQPVPDPNTPSIQHISQTYSVSVSFKQRSRMYGATVTV 256

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   257 RGSQNNTNAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNVKHIMQRT 316

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   317 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 348

GO:0003723 "RNA binding" evidence=ISA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=ISO

RGD|1307459 Bicc1 "bicaudal C homolog 1 (Drosophila)" [Rattus norvegicus (taxid:10116)]

 Score = 550 (198.7 bits), Expect = 1.8e-52, P = 1.8e-52
 Identities = 109/216 (50%), Positives = 148/216 (68%)

Query:     1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             +K+DVS+T+HSH+IG+GG  IKKVME+TGCH+HFPDSNR+   EKSNQVSIAG   G+E 
Sbjct:    55 LKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQVEKSNQVSIAGQPAGVES 114

Query:    61 ARYRVRELTPLIFCFEYPLMG---STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMV 117
             AR R+REL PL+  FE P+ G     P+ N+P +Q I + Y+V V F+ R ++    V+V
Sbjct:   115 ARARIRELLPLVLMFELPIAGILQPVPDPNTPSIQHISQTYSVSVSFKQRSRMYGATVIV 174

Query:   118 KGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177
             +G + +   VKE T  L+EH+ GSLA+   V   ++I+ QHH  M G N  N+K IM +T
Sbjct:   175 RGSQNNTNAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMMGRNGSNVKHIMQRT 234

Query:   178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQ 213
             GAQI FP+ ++P     KKS+V + G I+SV LARQ
Sbjct:   235 GAQIHFPDPSNP----QKKSTVYLQGTIESVCLARQ 266

GO:0003723 "RNA binding" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA;ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q24009	BICC_DROME	No assigned EC number	0.5479	0.9075	0.2386	yes	N/A
Q99MQ1	BICC1_MOUSE	No assigned EC number	0.5068	0.8907	0.2169	yes	N/A
Q9H694	BICC1_HUMAN	No assigned EC number	0.5159	0.8907	0.2176	yes	N/A

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	238
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	3e-13
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-10
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-09
pfam00013	59	pfam00013, KH_1, KH domain	3e-08
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	1e-07
pfam13014	42	pfam13014, KH_3, KH domain	7e-07
pfam00013	59	pfam00013, KH_1, KH domain	2e-05
smart00322	68	smart00322, KH, K homology RNA-binding domain	7e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-04

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

 Score = 62.1 bits (152), Expect = 3e-13
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 5/62 (8%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           ++++    H  IIG+ G  I+K+MEETG  + FPD        KS+ ++I G    +E+
Sbjct: 2  EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKENVEK 56

Query: 61 AR 62
          A+
Sbjct: 57 AK 58

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

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           ++ V  +    IIG+GG TIK++ EETG  +  PDS    +  +   V+I G+   +E+
Sbjct: 2  ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG---SGSEERIVTITGTPEAVEK 58

Query: 61 ARYRV 65
          A+  +
Sbjct: 59 AKELI 63

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 = 51.5 bits (124), Expect = 3e-09
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          +++ +       IIG+GG TIKK+ EETG  +  P         +   V I G    +E+
Sbjct: 5  IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-----SEERVVEITGPPENVEK 59

Query: 61 ARYRVREL 68
          A   + E+
Sbjct: 60 AAELILEI 67

Length = 68

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

 Score = 48.7 bits (117), Expect = 3e-08
 Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 7/65 (10%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           ++ +       IIG+GG  IK++ EETG  +  PD       ++ + V+I+G+   +E+
Sbjct: 2  ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD-------DRDDTVTISGTPEQVEK 54

Query: 61 ARYRV 65
          A+  +
Sbjct: 55 AKELI 59

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

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

 Score = 46.7 bits (112), Expect = 1e-07
 Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 6/67 (8%)

Query: 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSV 208
              +EI  + H  + G    N++ IM +TG +I FP+         K  ++T++G  ++V
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS------KSDTITITGPKENV 54

Query: 209 YLARQML 215
             A++ +
Sbjct: 55  EKAKEEI 61

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|221895 pfam13014, KH_3, KH domain

 Score = 44.5 bits (106), Expect = 7e-07
 Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG 53
             IIG+GG TIK++ EETG  +  P             V+I G
Sbjct: 2  VGAIIGKGGETIKEIREETGAKIQIPKPE---PGSGERIVTITG 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|215657 pfam00013, KH_1, KH domain

 Score = 40.6 bits (96), Expect = 2e-05
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 8/67 (11%)

Query: 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSV 208
              + I P     + G    N+K I  +TG +I  P+  D          VT+SG  + V
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDT--------VTISGTPEQV 52

Query: 209 YLARQML 215
             A++++
Sbjct: 53  EKAKELI 59

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

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

 Score = 39.6 bits (93), Expect = 7e-05
 Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 6/70 (8%)

Query: 146 TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNI 205
             V + + I      ++ G     +K I  +TG +I  P              V ++G  
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERV------VEITGPP 54

Query: 206 DSVYLARQML 215
           ++V  A +++
Sbjct: 55  ENVEKAAELI 64

Length = 68

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

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 13/64 (20%), Positives = 31/64 (48%), Gaps = 4/64 (6%)

Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
           + +       + G     +K I  +TGA+I  P++        ++  VT++G  ++V  A
Sbjct: 4   VLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSG----SEERIVTITGTPEAVEKA 59

Query: 212 RQML 215
           ++++
Sbjct: 60  KELI 63

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	238
KOG1676|consensus	600		99.96
KOG2193|consensus	584		99.94
KOG1676|consensus	600		99.94
KOG2193|consensus	584		99.91
KOG2192|consensus	390		99.91
KOG2191|consensus	402		99.86
KOG2190|consensus	485		99.8
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.71
PRK13763	180	putative RNA-processing protein; Provisional	99.68
KOG2190|consensus	485		99.68
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.51
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.5
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.49
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.44
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.42
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.42
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.39
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.37
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.36
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.35
KOG2192|consensus	390		99.28
PF13014	43	KH_3: KH domain	99.16
KOG2208|consensus	753		99.14
KOG2208|consensus	753		99.13
smart00322	69	KH K homology RNA-binding domain.	99.13
smart00322	69	KH K homology RNA-binding domain.	99.11
PF13014	43	KH_3: KH domain	99.1
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.99
KOG2191|consensus	402		98.76
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.73
KOG2279|consensus	608		98.61
KOG2113|consensus	394		98.59
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.46
PRK13763	180	putative RNA-processing protein; Provisional	98.41
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.36
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.15
KOG2814|consensus	345		97.9
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.89
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.88
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.68
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.6
KOG0119|consensus	554		97.53
KOG2279|consensus	608		97.51
KOG2113|consensus	394		97.45
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.39
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.38
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.22
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	97.2
PRK08406	140	transcription elongation factor NusA-like protein;	97.2
KOG2814|consensus	345		97.2
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.19
KOG0336|consensus	629		97.17
KOG0336|consensus	629		97.12
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.06
PRK00106	535	hypothetical protein; Provisional	97.04
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.03
PRK00106	535	hypothetical protein; Provisional	96.96
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.95
PRK12704	520	phosphodiesterase; Provisional	96.93
PRK12704	520	phosphodiesterase; Provisional	96.93
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.92
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.9
KOG0119|consensus	554		96.73
KOG1588|consensus	259		96.68
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.65
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.64
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.41
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.16
PRK12705	508	hypothetical protein; Provisional	96.12
KOG1067|consensus	760		96.11
COG5166	657	Uncharacterized conserved protein [Function unknow	95.97
KOG1588|consensus	259		95.94
PRK12705	508	hypothetical protein; Provisional	95.92
PRK00468	75	hypothetical protein; Provisional	95.24
PRK02821	77	hypothetical protein; Provisional	95.07
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.04
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.02
PRK01064	78	hypothetical protein; Provisional	94.67
COG5176	269	MSL5 Splicing factor (branch point binding protein	94.05
KOG4369|consensus	2131		93.97
KOG2874|consensus	356		93.44
PRK00468	75	hypothetical protein; Provisional	93.34
KOG1067|consensus	760		93.32
KOG2874|consensus	356		93.31
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	93.0
PRK02821	77	hypothetical protein; Provisional	92.82
COG1837	76	Predicted RNA-binding protein (contains KH domain)	92.79
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	92.72
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	92.51
PRK01064	78	hypothetical protein; Provisional	92.48
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	92.43
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	91.78
COG1855	604	ATPase (PilT family) [General function prediction	91.33
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	91.3
COG5166	657	Uncharacterized conserved protein [Function unknow	90.92
PRK13764	602	ATPase; Provisional	90.81
KOG3273|consensus	252		90.62
PRK08406	140	transcription elongation factor NusA-like protein;	90.4
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	90.36
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	90.08
KOG4369|consensus	2131		88.7
PRK06418	166	transcription elongation factor NusA-like protein;	88.6
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	88.59
KOG3273|consensus	252		88.5
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	88.49
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	88.22
PRK12328	374	nusA transcription elongation factor NusA; Provisi	87.92
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	86.81
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	85.93
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	85.68
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	85.68
PRK09202	470	nusA transcription elongation factor NusA; Validat	85.58
COG1855	604	ATPase (PilT family) [General function prediction	85.08
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	83.93
PRK13764	602	ATPase; Provisional	83.51
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	82.91
COG1782	637	Predicted metal-dependent RNase, consists of a met	82.49
TIGR01953	341	NusA transcription termination factor NusA. This m	82.42
COG0195	190	NusA Transcription elongation factor [Transcriptio	81.87
PRK12328	374	nusA transcription elongation factor NusA; Provisi	81.31
PRK12329	449	nusA transcription elongation factor NusA; Provisi	80.63
COG0195	190	NusA Transcription elongation factor [Transcriptio	80.49
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	80.43
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	80.2

>KOG1676|consensus

Probab=99.96  E-value=3.9e-28  Score=213.97  Aligned_cols=218  Identities=17%  Similarity=0.252  Sum_probs=179.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc----------
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL----------   71 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~----------   71 (238)
                      ++.||.+.+|.||||+|.+||.|++++||++.+-..+....+ ....+.|+|+++.|+.|+.++.+++.+          
T Consensus       142 eI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~  220 (600)
T KOG1676|consen  142 EILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGG  220 (600)
T ss_pred             eeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhcccCCCcccc
Confidence            578999999999999999999999999999999776654322 457999999999999999999888762          


Q ss_pred             ----------eEEEeecC--cCCCCCCCChHHHHHHHHhCceEEeeCC--CCCCCcEEEEEccccchHHHHHHHHHHHHH
Q psy11278         72 ----------IFCFEYPL--MGSTPNANSPFVQIIQEAYNVQVMFRNR--PKLQPTLVMVKGCEKDVERVKEATTKLIEH  137 (238)
Q Consensus        72 ----------~~~~~~p~--~~~~~~~~g~~i~~i~~~~gv~I~~~~~--~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~  137 (238)
                                .+.+++|.  ++..+|++|++||+|+.++|++|+|.+.  |.+..+.+.|.|.++.+.+|.+.|.+++..
T Consensus       221 ~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~  300 (600)
T KOG1676|consen  221 HAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE  300 (600)
T ss_pred             ccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence                      13344564  3447899999999999999999999764  344579999999999999999999998886


Q ss_pred             hhccc-------cccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHH
Q psy11278        138 MCGSL-------ANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYL  210 (238)
Q Consensus       138 ~~~~~-------~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~  210 (238)
                      .....       .-..-....+.||+..++++||++|++||.|..+|||++.++... ++ ...+++.|+|+|++.+|.-
T Consensus       301 ~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~-p~-~~~~ektf~IrG~~~QIdh  378 (600)
T KOG1676|consen  301 AEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQP-PN-GNPKEKTFVIRGDKRQIDH  378 (600)
T ss_pred             HhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCC-CC-CCccceEEEEecCcccchH
Confidence            54431       000101478999999999999999999999999999999887661 11 1225899999999999999


Q ss_pred             HHHHHHhhcCCC
Q psy11278        211 ARQMLVVSSVRP  222 (238)
Q Consensus       211 A~~~I~~~l~~~  222 (238)
                      |+.+|++.+..+
T Consensus       379 Ak~LIr~kvg~~  390 (600)
T KOG1676|consen  379 AKQLIRDKVGDI  390 (600)
T ss_pred             HHHHHHHHhccc
Confidence            999999999663

>KOG2193|consensus

Probab=99.94  E-value=6.2e-27  Score=198.32  Aligned_cols=230  Identities=17%  Similarity=0.221  Sum_probs=180.0

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc-e----EEE
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL-I----FCF   75 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~-~----~~~   75 (238)
                      |+++||..++|.||||.|+||+.|.+.|.++|++.....  .+..++.++|.|.+|+..+|+++|.+++.. .    +.-
T Consensus       201 lR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k~~~  278 (584)
T KOG2193|consen  201 LRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDKVAE  278 (584)
T ss_pred             eeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchHHHHHHHHHHHHHhhhccchhh
Confidence            689999999999999999999999999999999976443  244678999999999999999999887541 1    223


Q ss_pred             eec--------CcCCCCCCCChHHHHHHHHhCceEEeeCCCCC----CCcEEEEEccccchHHHHHHHHHHHHHhhcc--
Q psy11278         76 EYP--------LMGSTPNANSPFVQIIQEAYNVQVMFRNRPKL----QPTLVMVKGCEKDVERVKEATTKLIEHMCGS--  141 (238)
Q Consensus        76 ~~p--------~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~----~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~--  141 (238)
                      ++|        +.+.++|+.|.++++|+.++|.+|.+.+..+.    ..+.++++|.-+.|..|...|+.-+....++  
T Consensus       279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl  358 (584)
T KOG2193|consen  279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDL  358 (584)
T ss_pred             hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhH
Confidence            344        24457899999999999999999998764222    3689999999888877776666555432211  


Q ss_pred             ----cc----------------cc--------------------------ceEEEEEEeCCCeeeEEecCCCchHHHHHH
Q psy11278        142 ----LA----------------NQ--------------------------TSVIMMMEISPQHHPIMEGPNAINLKTIMA  175 (238)
Q Consensus       142 ----~~----------------~~--------------------------~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~  175 (238)
                          ++                +.                          ......+.||...+|.|||++|.+|+.|.+
T Consensus       359 ~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~R  438 (584)
T KOG2193|consen  359 AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSR  438 (584)
T ss_pred             HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHH
Confidence                00                00                          012378899999999999999999999999


Q ss_pred             HhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC--------CceEEEEeecCCc
Q psy11278        176 QTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP--------RRRLLLITIPNDI  235 (238)
Q Consensus       176 ~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~--------~p~~~~~~~~~~~  235 (238)
                      .+||+|++..+.-++.   .+++|+|+|++++..+|+.+|...++.-        ..+...+.||...
T Consensus       439 fagASiKIappE~pdv---seRMViItGppeaqfKAQgrifgKikEenf~~PkeevklethirVPs~~  503 (584)
T KOG2193|consen  439 FAGASIKIAPPEIPDV---SERMVIITGPPEAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSA  503 (584)
T ss_pred             hccceeeecCCCCCCc---ceeEEEecCChHHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchh
Confidence            9999999976665543   5899999999999999999999988542        3455666666543

>KOG1676|consensus

Probab=99.94  E-value=1.3e-25  Score=198.13  Aligned_cols=214  Identities=19%  Similarity=0.290  Sum_probs=172.4

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce---------
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI---------   72 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~---------   72 (238)
                      +..||...++++|||+|+-|..|+.++||+++++......   ..|.+.+.|.+++|+.|+.+|.+.....         
T Consensus        57 ~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~---~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~  133 (600)
T KOG1676|consen   57 RYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGI---GYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDN  133 (600)
T ss_pred             ccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCc---ccccccccCCcccHHHHHHhhhhhhhccCCCCCcccc
Confidence            4579999999999999999999999999999987654322   4689999999999999999997763211         


Q ss_pred             -----EEEe--ecC--cCCCCCCCChHHHHHHHHhCceEEeeCCC---CCCCcEEEEEccccchHHHHHHHHHHHHHhhc
Q psy11278         73 -----FCFE--YPL--MGSTPNANSPFVQIIQEAYNVQVMFRNRP---KLQPTLVMVKGCEKDVERVKEATTKLIEHMCG  140 (238)
Q Consensus        73 -----~~~~--~p~--~~~~~~~~g~~i~~i~~~~gv~I~~~~~~---~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~  140 (238)
                           .+.+  +|.  .+..++++|.+|++|++.+||++.+....   ....+.+.|+|+++.++.|+..+.++|.....
T Consensus       134 q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~  213 (600)
T KOG1676|consen  134 QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDD  213 (600)
T ss_pred             CCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhccc
Confidence                 2333  343  22367899999999999999998775431   11357899999999999999888888874322


Q ss_pred             ccccc---------ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHH
Q psy11278        141 SLANQ---------TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA  211 (238)
Q Consensus       141 ~~~~~---------~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A  211 (238)
                      +....         -+.+.+|.||...||.||||+|++||+|+.+|||+|.|-.++++..   .+|.+.|.|+++.|+.|
T Consensus       214 ~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~s---peR~~~IiG~~d~ie~A  290 (600)
T KOG1676|consen  214 EVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSS---PERPAQIIGTVDQIEHA  290 (600)
T ss_pred             CCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCC---ccceeeeecCHHHHHHH
Confidence            21100         1235899999999999999999999999999999999977666532   58999999999999999


Q ss_pred             HHHHHhhcCC
Q psy11278        212 RQMLVVSSVR  221 (238)
Q Consensus       212 ~~~I~~~l~~  221 (238)
                      .++|.+++.+
T Consensus       291 a~lI~eii~~  300 (600)
T KOG1676|consen  291 AELINEIIAE  300 (600)
T ss_pred             HHHHHHHHHH
Confidence            9999999943

>KOG2193|consensus

Probab=99.91  E-value=1.6e-24  Score=183.81  Aligned_cols=214  Identities=12%  Similarity=0.197  Sum_probs=166.9

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce--------
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI--------   72 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~--------   72 (238)
                      |+++-...++|.+|||.|.+||+|+++||++|.|.+..+.+-.+.+|.|+|.|+.|+|.+|..+|++.+.++        
T Consensus       282 Lk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~  361 (584)
T KOG2193|consen  282 LKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAM  361 (584)
T ss_pred             hhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHh
Confidence            345556778999999999999999999999999988776554556899999999999999999985432210        


Q ss_pred             ---------------------------------EEEee------------------cC--cCCCCCCCChHHHHHHHHhC
Q psy11278         73 ---------------------------------FCFEY------------------PL--MGSTPNANSPFVQIIQEAYN   99 (238)
Q Consensus        73 ---------------------------------~~~~~------------------p~--~~~~~~~~g~~i~~i~~~~g   99 (238)
                                                       ++|.-                  |.  ++..+|++|.+|+.|.++.|
T Consensus       362 s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~Rfag  441 (584)
T KOG2193|consen  362 SLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAG  441 (584)
T ss_pred             hccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhcc
Confidence                                             01000                  00  11134688999999999999


Q ss_pred             ceEEeeCC--CCCCCcEEEEEccccchHHHHHHHHHHHHHhhccc----cccceEEEEEEeCCCeeeEEecCCCchHHHH
Q psy11278        100 VQVMFRNR--PKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSL----ANQTSVIMMMEISPQHHPIMEGPNAINLKTI  173 (238)
Q Consensus       100 v~I~~~~~--~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~----~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I  173 (238)
                      ++|.+.++  |+...+.|+|.|+++..-+|+.-+   ..++.++.    .+...+...+.+|+...|.+|||||.+++++
T Consensus       442 ASiKIappE~pdvseRMViItGppeaqfKAQgri---fgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnEL  518 (584)
T KOG2193|consen  442 ASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRI---FGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNEL  518 (584)
T ss_pred             ceeeecCCCCCCcceeEEEecCChHHHHhhhhhh---hhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHH
Confidence            99998764  454568999999998776666333   22222221    1234466899999999999999999999999


Q ss_pred             HHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        174 MAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       174 ~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +.-|+|.+.+|.+..++  .++.-+|.|.|..-+...|++.|.+++
T Consensus       519 Qnlt~AeV~vPrdqtpd--End~vivriiGhfyatq~aQrki~~iv  562 (584)
T KOG2193|consen  519 QNLTSAEVVVPRDQTPD--ENDQVIVRIIGHFYATQNAQRKIAHIV  562 (584)
T ss_pred             hccccceEEccccCCCC--ccceeeeeeechhhcchHHHHHHHHHH
Confidence            99999999999887664  346789999999999999999999988

>KOG2192|consensus

Probab=99.91  E-value=3e-23  Score=166.91  Aligned_cols=211  Identities=18%  Similarity=0.247  Sum_probs=162.6

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEE----Ee
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFC----FE   76 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~----~~   76 (238)
                      |++++.++-+|.||||+|+|||.|+.+++++|.+++++.     .+++++|+.+.+.|-.-.+.|.--+.+-+.    ++
T Consensus        50 ~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~-----peri~tisad~~ti~~ilk~iip~lee~f~~~~pce  124 (390)
T KOG2192|consen   50 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG-----PERILTISADIETIGEILKKIIPTLEEGFQLPSPCE  124 (390)
T ss_pred             EEEEEecccccceeccccccHHHHhhhccceeeccCCCC-----CceeEEEeccHHHHHHHHHHHhhhhhhCCCCCCchh
Confidence            578899999999999999999999999999999999876     579999999999887766655433322111    11


Q ss_pred             ec------CcCCCCCCCChHHHHHHHHhCceEEeeC--CCCCCCcEEEEEccccchHHHHHHHHHHHHHhh--c------
Q psy11278         77 YP------LMGSTPNANSPFVQIIQEAYNVQVMFRN--RPKLQPTLVMVKGCEKDVERVKEATTKLIEHMC--G------  140 (238)
Q Consensus        77 ~p------~~~~~~~~~g~~i~~i~~~~gv~I~~~~--~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~--~------  140 (238)
                      +.      ..+..++.+|+.|++|+++|.+++.+-.  .|.++.+.+.+.|.+++|-...+.+..++...-  +      
T Consensus       125 ~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~  204 (390)
T KOG2192|consen  125 LRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYD  204 (390)
T ss_pred             hhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCC
Confidence            21      2334678899999999999999887654  366677888889998888666555555443210  0      


Q ss_pred             -ccc-------------------------------------------------------------------------c--
Q psy11278        141 -SLA-------------------------------------------------------------------------N--  144 (238)
Q Consensus       141 -~~~-------------------------------------------------------------------------~--  144 (238)
                       ++.                                                                         +  
T Consensus       205 p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~Sew  284 (390)
T KOG2192|consen  205 PNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEW  284 (390)
T ss_pred             ccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCcccc
Confidence             000                                                                         0  


Q ss_pred             ---------------c------------ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278        145 ---------------Q------------TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS  197 (238)
Q Consensus       145 ---------------~------------~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~  197 (238)
                                     .            --.+++|+||+++-+.|||++|++|++|++++||.|++..+.+..    .++
T Consensus       285 qmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGs----edr  360 (390)
T KOG2192|consen  285 QMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGS----EDR  360 (390)
T ss_pred             ccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCC----Cce
Confidence                           0            023699999999999999999999999999999999997754432    369


Q ss_pred             EEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        198 SVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       198 ~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      .++|+|+.++++.|+.+++..+.
T Consensus       361 IitItGTqdQIqnAQYLlQn~Vk  383 (390)
T KOG2192|consen  361 IITITGTQDQIQNAQYLLQNSVK  383 (390)
T ss_pred             EEEEeccHHHHhhHHHHHHHHHH
Confidence            99999999999999999998873

>KOG2191|consensus

Probab=99.86  E-value=1.4e-20  Score=155.58  Aligned_cols=164  Identities=20%  Similarity=0.261  Sum_probs=127.6

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLM   80 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~   80 (238)
                      |+|+||+...|.||||+|++|.+++++|||+|++++..+..|...+|++.|+|+.+++....+.|.+.+.          
T Consensus        41 ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKir----------  110 (402)
T KOG2191|consen   41 LKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIR----------  110 (402)
T ss_pred             EEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHH----------
Confidence            6899999999999999999999999999999999999999999999999999999999999888864422          


Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                                  +.-...+-.+.+.+ |..          ++                  ..     -...+.+|....+
T Consensus       111 ------------e~p~~~~k~v~~~~-pqt----------~~------------------r~-----kqikivvPNstag  144 (402)
T KOG2191|consen  111 ------------EKPQAVAKPVDILQ-PQT----------PD------------------RI-----KQIKIVVPNSTAG  144 (402)
T ss_pred             ------------HhHHhhcCCccccC-CCC----------cc------------------cc-----ceeEEeccCCccc
Confidence                        11111111011100 000          00                  00     0167788999999


Q ss_pred             EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      .||||+|.+||.+++++||+|++.... +......++.+|+.|.+++..+|..+|.+.+..
T Consensus       145 ~iigkggAtiK~~~Eqsga~iqisPqk-pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~e  204 (402)
T KOG2191|consen  145 MIIGKGGATIKAIQEQSGAWIQISPQK-PTGISLQERVVTVSGEPEQNMKAVSLILQKIQE  204 (402)
T ss_pred             ceecCCcchHHHHHHhhCcceEecccC-CCCccceeEEEEecCCHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999986322 222344689999999999999999999999844

>KOG2190|consensus

Probab=99.80  E-value=1.3e-18  Score=155.35  Aligned_cols=214  Identities=16%  Similarity=0.231  Sum_probs=153.2

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce--------
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI--------   72 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~--------   72 (238)
                      ++++||++++|.||||+|+.||+|+++|||+|.+.+...  |...++.|+|.|.++.|.+|...|-.++-+.        
T Consensus       140 ~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~l--P~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~  217 (485)
T KOG2190|consen  140 CRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDML--PNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPL  217 (485)
T ss_pred             EEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCC--CcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCC
Confidence            479999999999999999999999999999999988643  4446788999999999999999884432110        


Q ss_pred             -EEEe-ec--------------------------------------C--cCCCCCCCChHHHHHHHHhCceEEeeCCCCC
Q psy11278         73 -FCFE-YP--------------------------------------L--MGSTPNANSPFVQIIQEAYNVQVMFRNRPKL  110 (238)
Q Consensus        73 -~~~~-~p--------------------------------------~--~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~  110 (238)
                       .+.. .|                                      .  .+...++.+..++.++..++..+.+...-. 
T Consensus       218 ~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~-  296 (485)
T KOG2190|consen  218 VSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRT-  296 (485)
T ss_pred             CCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccC-
Confidence             0000 01                                      0  001235678889999999999988865311 


Q ss_pred             CCcEEEEEccc--c-chHHHHHHHHHHHHHhhccc-cc-cceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        111 QPTLVMVKGCE--K-DVERVKEATTKLIEHMCGSL-AN-QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       111 ~~~~v~I~G~~--~-~v~~a~~ai~~~~~~~~~~~-~~-~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                       .+.+++....  + ....+++|+........+.. .+ ...++.++.+|+++++++||++|.+|.+|++.|||.|++-.
T Consensus       297 -~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~  375 (485)
T KOG2190|consen  297 -DRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILN  375 (485)
T ss_pred             -cceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEcc
Confidence             1455555443  1 11234445333222221111 11 33567999999999999999999999999999999999976


Q ss_pred             CCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        186 ANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       186 ~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      ..+.  ...++..++|+|...+...|+.++...+.
T Consensus       376 ~~~~--~~~~e~~~~I~~~~~~~~~~~~~~~~~~~  408 (485)
T KOG2190|consen  376 KEEV--SGVREALVQITGMLREDLLAQYLIRARLS  408 (485)
T ss_pred             cccc--CCcceeEEEecchhHHHHhhhhhcccccc
Confidence            5541  01257999999999999999999976663

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.71  E-value=7.3e-17  Score=126.68  Aligned_cols=147  Identities=19%  Similarity=0.298  Sum_probs=107.3

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEE---EeCHHHHHHHHHHHHhhCCceEEEeecC
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSI---AGSLLGLERARYRVRELTPLIFCFEYPL   79 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I---~G~~~~v~~A~~~I~~~~~~~~~~~~p~   79 (238)
                      +.||.+.+|.|||++|++|+.|+++||++|++.+.        +..|.|   +++++++.+|++.|..+....   + |.
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf---~-~e   69 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGF---S-PE   69 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCC---C-HH
Confidence            57999999999999999999999999999999763        357888   689999999999998763321   1 00


Q ss_pred             cCCCCCCCChHHHHHHHHhCceE-EeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCe
Q psy11278         80 MGSTPNANSPFVQIIQEAYNVQV-MFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQH  158 (238)
Q Consensus        80 ~~~~~~~~g~~i~~i~~~~gv~I-~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~  158 (238)
                               .-.+-+.+.|...+ .+.+        +  .+.+   ..        +                    ...
T Consensus        70 ---------~A~~l~gd~y~~~Vi~I~~--------~--~~~~---~~--------~--------------------~~~   99 (172)
T TIGR03665        70 ---------KALKLLDDDYMLEVIDLKE--------Y--GKSP---NA--------L--------------------RRI   99 (172)
T ss_pred             ---------HHHHhcCCcceEEEEEhhh--------c--cCCH---HH--------H--------------------HHH
Confidence                     00011222222221 1110        0  0110   00        0                    014


Q ss_pred             eeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278        159 HPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP  222 (238)
Q Consensus       159 ~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  222 (238)
                      .+.|||++|.+++.|+..|||+|.++.           ..|.|.|++++++.|+..|++++...
T Consensus       100 ~griIG~~G~t~~~ie~~t~~~i~i~~-----------~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       100 KGRIIGEGGKTRRIIEELTGVSISVYG-----------KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             HhhhcCCCcHHHHHHHHHHCCeEEEcC-----------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence            688999999999999999999999974           47999999999999999999999654

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.68  E-value=4.2e-16  Score=123.17  Aligned_cols=147  Identities=19%  Similarity=0.274  Sum_probs=108.2

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEE----eCHHHHHHHHHHHHhhCCceEEEee
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIA----GSLLGLERARYRVRELTPLIFCFEY   77 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~~~~~~~~~~   77 (238)
                      .+.||.+.++.|||++|++|+.|+++||++|++.+.        .+.|.|.    ++++++.+|++.|..+....   + 
T Consensus         6 ~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf---~-   73 (180)
T PRK13763          6 YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGF---S-   73 (180)
T ss_pred             EEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC---C-
Confidence            588999999999999999999999999999999863        3688885    79999999999998874320   1 


Q ss_pred             cCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEE--ccccchHHHHHHHHHHHHHhhccccccceEEEEEEeC
Q psy11278         78 PLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVK--GCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEIS  155 (238)
Q Consensus        78 p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~--G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~  155 (238)
                      |.         ...+-+.+.|...+            +.|.  +...          ..                    .
T Consensus        74 ~e---------~A~~l~gd~y~~~V------------i~i~~~~~~~----------~~--------------------~  102 (180)
T PRK13763         74 PE---------KALRLLDDDYVLEV------------IDLSDYGDSP----------NA--------------------L  102 (180)
T ss_pred             HH---------HHHHHhCCCceEEE------------EEhhhccCCh----------hH--------------------H
Confidence            00         00111222221111            1110  0000          00                    0


Q ss_pred             CCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278        156 PQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP  222 (238)
Q Consensus       156 ~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  222 (238)
                      ...+|.|||++|.+++.|++.|||+|.++.           ..|.|.|+++++..|+..|..++...
T Consensus       103 ~r~~griIG~~G~~~k~ie~~t~~~i~i~~-----------~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        103 RRIKGRIIGEGGKTRRIIEELTGVDISVYG-----------KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             HHHhhheeCCCcHHHHHHHHHHCcEEEEcC-----------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence            125799999999999999999999999963           34999999999999999999999654

>KOG2190|consensus

Probab=99.68  E-value=5e-16  Score=138.82  Aligned_cols=156  Identities=21%  Similarity=0.173  Sum_probs=119.2

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe---------CHHHHHHHHHHHHhhCCc
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG---------SLLGLERARYRVRELTPL   71 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G---------~~~~v~~A~~~I~~~~~~   71 (238)
                      .+++.+.+++|.||||+|..+++|+.+|+++|++.+...   ++.+|+++|+|         ..+++.+|..+|-....+
T Consensus        45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~---~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~  121 (485)
T KOG2190|consen   45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLP---GCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE  121 (485)
T ss_pred             EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCC---CCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence            378999999999999999999999999999999987643   33679999999         677777777776321110


Q ss_pred             eEEEeecCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEE
Q psy11278         72 IFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMM  151 (238)
Q Consensus        72 ~~~~~~p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~  151 (238)
                      .                         -   ....+.           |                     ...+.-.++..
T Consensus       122 d-------------------------~---~~~~d~-----------~---------------------~~~~~~~v~~R  141 (485)
T KOG2190|consen  122 D-------------------------D---EAAEDN-----------G---------------------EDASGPEVTCR  141 (485)
T ss_pred             c-------------------------c---cccccC-----------C---------------------ccccCCceEEE
Confidence            0                         0   000000           0                     00000025589


Q ss_pred             EEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278        152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP  222 (238)
Q Consensus       152 v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  222 (238)
                      +.||..++|.||||+|+.|++|+++|||+|.+-.+..|.+   .++.|+|.|.+++|.+|...|...|-..
T Consensus       142 LlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~s---ter~V~IsG~~~av~~al~~Is~~L~~~  209 (485)
T KOG2190|consen  142 LLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNS---TERAVTISGEPDAVKKALVQISSRLLEN  209 (485)
T ss_pred             EEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcc---cceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999877655554   4788999999999999999999998553

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.51  E-value=3.2e-14  Score=93.01  Aligned_cols=59  Identities=36%  Similarity=0.685  Sum_probs=54.9

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV   65 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I   65 (238)
                      ++.||.++|+.|||++|++|++|+++|||+|++++.+.     .++.|+|+|++++|..|+.+|
T Consensus         3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~-----~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           3 EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS-----KSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             EEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCC-----CCCEEEEEcCHHHHHHHHHHh
Confidence            68999999999999999999999999999999998653     568999999999999999987

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.50  E-value=6.9e-14  Score=92.29  Aligned_cols=63  Identities=30%  Similarity=0.471  Sum_probs=56.7

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV   65 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I   65 (238)
                      +++.||.+.+|.|||++|++|++|+++|||+|++++..+  +...++.|+|+|+++++..|+.+|
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhh
Confidence            479999999999999999999999999999999987654  233678999999999999999987

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=99.49  E-value=5.3e-14  Score=92.00  Aligned_cols=61  Identities=26%  Similarity=0.512  Sum_probs=55.9

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV  216 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~  216 (238)
                      ..+.||..+|++|||++|++|++|+++|||+|.+|+..++      .+.|+|+|++++|..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~------~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSK------SDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCC------CCEEEEEcCHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999987643      589999999999999998874

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.44  E-value=4.2e-13  Score=88.52  Aligned_cols=63  Identities=22%  Similarity=0.275  Sum_probs=56.3

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHH
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML  215 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I  215 (238)
                      .++.||...+++|||++|.+|++|+++|||+|.+++..+++   ..++.|+|.|+++++..|+.+|
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~---~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPG---STERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCC---CCceEEEEEeCHHHHHHHHHhh
Confidence            67899999999999999999999999999999998765421   1478999999999999999987

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=99.42  E-value=1e-13  Score=90.04  Aligned_cols=60  Identities=27%  Similarity=0.429  Sum_probs=55.0

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHH
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML  215 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I  215 (238)
                      |.+|.||..++++|||++|++|++|+++|||.|.||+.+       +...|+|+|++++|..|+++|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-------ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-------EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-------CcEEEEEEeCHHHHHHHHhhC
Confidence            478999999999999999999999999999999998762       257999999999999999886

; 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=99.42  E-value=6.5e-13  Score=86.34  Aligned_cols=55  Identities=35%  Similarity=0.527  Sum_probs=51.2

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC-HHHHHHHHHHH
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRV   65 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I   65 (238)
                      .+.||.+.++.|||++|++|++|+++|||+|++++         ++.|.|+|+ +++++.|+.+|
T Consensus         5 ~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           5 TMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             EEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeCCHHHHHHHHHHh
Confidence            57899999999999999999999999999999986         258999998 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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.39  E-value=1.9e-13  Score=88.73  Aligned_cols=59  Identities=32%  Similarity=0.560  Sum_probs=53.3

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV   65 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I   65 (238)
                      .+|.||.++++.|||++|++|++|+++|||+|++++.+      ....|+|+|++++|+.|+++|
T Consensus         2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~------~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD------ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT------EEEEEEEEESHHHHHHHHHHH
T ss_pred             EEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC------CcEEEEEEeCHHHHHHHHhhC
Confidence            37899999999999999999999999999999998751      235999999999999999886

; 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=99.37  E-value=2.9e-12  Score=83.29  Aligned_cols=58  Identities=24%  Similarity=0.419  Sum_probs=53.0

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHH
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLV  216 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~  216 (238)
                      ...+.||+.++++|||++|++|++|+++|||+|.+++.          ..|+|+|+ +++++.|+.+|+
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~----------g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD----------GTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC----------CEEEEEeCCHHHHHHHHHHhC
Confidence            36889999999999999999999999999999999862          47999998 999999998874

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.

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

Probab=99.36  E-value=3.1e-12  Score=83.97  Aligned_cols=63  Identities=21%  Similarity=0.339  Sum_probs=56.1

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV  216 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~  216 (238)
                      .++.||..++++|||++|++|++|+++|||.|.++...+..    ..+.|+|.|+.+++..|+.+|+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~----~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGS----EERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCC----CceEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999765321    4689999999999999998874

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

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

Probab=99.35  E-value=4.1e-12  Score=83.35  Aligned_cols=61  Identities=34%  Similarity=0.554  Sum_probs=54.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV   65 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I   65 (238)
                      ++.||.++++.|||++|++|++|+++|||+|.++....   ...++.|.|.|+.+++..|+.+|
T Consensus         3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           3 RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHh
Confidence            68999999999999999999999999999999988543   12467999999999999999886

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.

>KOG2192|consensus

Probab=99.28  E-value=1.8e-11  Score=99.28  Aligned_cols=133  Identities=11%  Similarity=0.134  Sum_probs=104.9

Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                      +..++++|.+|+.|+.+|++++++++.. ...+.++|+.+.+.+-.   -++.++..+.+.++-.....+.+.|..++.+
T Consensus        60 gavigkgg~nik~lr~d~na~v~vpds~-~peri~tisad~~ti~~---ilk~iip~lee~f~~~~pce~rllihqs~ag  135 (390)
T KOG2192|consen   60 GAVIGKGGKNIKALRTDYNASVSVPDSS-GPERILTISADIETIGE---ILKKIIPTLEEGFQLPSPCELRLLIHQSLAG  135 (390)
T ss_pred             cceeccccccHHHHhhhccceeeccCCC-CCceeEEEeccHHHHHH---HHHHHhhhhhhCCCCCCchhhhhhhhhhhcc
Confidence            3367899999999999999999998742 23578999988554433   4455555554444333334478899999999


Q ss_pred             EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      .|||++|++|+++++++.|++++-....|++   ..+++.+.|.+..|-.+.+.|++++.
T Consensus       136 ~iigrngskikelrekcsarlkift~c~p~s---tdrv~l~~g~~k~v~~~i~~il~~i~  192 (390)
T KOG2192|consen  136 GIIGRNGSKIKELREKCSARLKIFTECCPHS---TDRVVLIGGKPKRVVECIKIILDLIS  192 (390)
T ss_pred             ceecccchhHHHHHHhhhhhhhhhhccCCCC---cceEEEecCCcchHHHHHHHHHHHhh
Confidence            9999999999999999999998877666654   46888899999999999999999983

>PF13014 KH_3: KH domain

Probab=99.16  E-value=6e-11  Score=71.52  Aligned_cols=43  Identities=40%  Similarity=0.659  Sum_probs=36.6

Q ss_pred             ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe
Q psy11278          9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG   53 (238)
Q Consensus         9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G   53 (238)
                      +||+|||++|++|++|+++|+|+|+|++...  +...++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~--~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENE--PGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccC--CCCCceEEEEEC
Confidence            5899999999999999999999999999222  334678999987

>KOG2208|consensus

Probab=99.14  E-value=1.3e-10  Score=109.80  Aligned_cols=202  Identities=20%  Similarity=0.278  Sum_probs=148.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce------EEE
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI------FCF   75 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~------~~~   75 (238)
                      .+.|-+.++..++||+|+++.+||++++|.|.++....     ....++++|...++.+|.+.+.....+.      ..+
T Consensus       350 ~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~-----~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~~~~~~~  424 (753)
T KOG2208|consen  350 KREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGS-----NNKKVVITGVSANDEKAVEDVEKIIAEILNSIVKEEV  424 (753)
T ss_pred             EEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccC-----CCCCeEEeccccchhHHHHHHHHHHHhhhccccccee
Confidence            35677888999999999999999999999999998543     4579999999999999999987765433      336


Q ss_pred             eecCcC--CCCCCCChHHHHHHHHhC-ceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEE
Q psy11278         76 EYPLMG--STPNANSPFVQIIQEAYN-VQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMM  152 (238)
Q Consensus        76 ~~p~~~--~~~~~~g~~i~~i~~~~g-v~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v  152 (238)
                      .+|...  ...+.+|..|..|+.+++ +.+.++.. .......+++|....+..++..+..+... ..+.    .+...+
T Consensus       425 ~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-~~~~~~~~~~~~~~dv~~~~~~~~~~~~~-a~~~----~~~~~~  498 (753)
T KOG2208|consen  425 QIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-NNSSDMVTIRGISKDVEKSVSLLKALKAD-AKNL----KFRDVV  498 (753)
T ss_pred             ecCccchhhhhccccccHHHHHhhcCcEEEecCCC-CcccccceEeccccccchhHHHHHhhhhh-hhcc----hhhhhh
Confidence            667533  366788999999999998 88888753 33456788888888887755443332221 1111    111222


Q ss_pred             EeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        153 EISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       153 ~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .=...++...+|+.+.....++...+....||...+.     +...++|.|..+.|.+|+..|..+.
T Consensus       499 ~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~-----~~~~i~i~gk~~~v~~a~~~L~~~~  560 (753)
T KOG2208|consen  499 TKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDE-----DHEKITIEGKLELVLEAPAELKALI  560 (753)
T ss_pred             hccccchHHhhcccccCceeeeccCCceeeccccccc-----ccceeeecccccchhhhHHHHHhcc
Confidence            2333455666666666677778888888888876433     3689999999999999999999887

>KOG2208|consensus

Probab=99.13  E-value=2.5e-10  Score=107.78  Aligned_cols=218  Identities=23%  Similarity=0.306  Sum_probs=143.4

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCC--CCeEEEEeCHHHHHHHHHHHHh--hCCceEEEee
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEK--SNQVSIAGSLLGLERARYRVRE--LTPLIFCFEY   77 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~--~~~v~I~G~~~~v~~A~~~I~~--~~~~~~~~~~   77 (238)
                      ++.+-...|+++||++|.++..+++++.+++++|..+...+...  .+...+......+..|..+++.  ..+......+
T Consensus       204 k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~  283 (753)
T KOG2208|consen  204 KMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRL  283 (753)
T ss_pred             EeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhhccc
Confidence            56778889999999999999999999999999998876432211  1223333333344444444422  1111111111


Q ss_pred             cCcCCCCCCCChHHHHHHHHh-CceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCC
Q psy11278         78 PLMGSTPNANSPFVQIIQEAY-NVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISP  156 (238)
Q Consensus        78 p~~~~~~~~~g~~i~~i~~~~-gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~  156 (238)
                      |..  ..+..+..+..++..+ .+.+.++..| +....+.++|....+..+......++.....+     ++...+.+.+
T Consensus       284 ~~~--~~~~~~~~~~~~~~~~~~~~~i~~~~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n-----n~~i~~~i~~  355 (753)
T KOG2208|consen  284 PRF--IRGIPGEEINQLRDYMPEVDSIFQNYP-SKDDSIVLSGFEVGAVLAKRDKTLLLKNSEEN-----NENIKREIFP  355 (753)
T ss_pred             ccc--ccccccchhhHHHhhcchhhhhhcccc-ccceeEeecccccchhhhhhHHHHHHHHhhcc-----ceeeEEeecH
Confidence            111  2234466677776554 4444444422 33578899999877766554433333322222     1448899999


Q ss_pred             CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC-CC-ceEEEEeecC
Q psy11278        157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR-PR-RRLLLITIPN  233 (238)
Q Consensus       157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~-~~-p~~~~~~~~~  233 (238)
                      .++.+++|++|.++.+|++++.|.+.++...+.      ...++++|...++.+|...++..... .+ ++.-.|-+|.
T Consensus       356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~------~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~~~~~~~~iP~  428 (753)
T KOG2208|consen  356 EELKFVIGKKGANIEKIREESQVKIDLPKQGSN------NKKVVITGVSANDEKAVEDVEKIIAEILNSIVKEEVQIPT  428 (753)
T ss_pred             HhhhhhcCCCCccHHHHHHhhhhceecccccCC------CCCeEEeccccchhHHHHHHHHHHHhhhcccccceeecCc
Confidence            999999999999999999999999999996554      47899999999999999998887744 33 3444455554

>smart00322 KH K homology RNA-binding domain

Probab=99.13  E-value=2.9e-10  Score=74.92  Aligned_cols=63  Identities=32%  Similarity=0.497  Sum_probs=56.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      ++.||.+.++.+||++|++|++|+++||++|.++....     ....+.|.|+.+++..|...|.+.+
T Consensus         6 ~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-----~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        6 EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-----EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             EEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC-----CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            68899999999999999999999999999999987542     3479999999999999999998753

>smart00322 KH K homology RNA-binding domain

Probab=99.11  E-value=5.9e-10  Score=73.44  Aligned_cols=66  Identities=21%  Similarity=0.330  Sum_probs=59.3

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .+..+.||..+++++||++|++|++|++.+|++|.++.....      ...++|.|+.+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~------~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSE------ERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCC------ccEEEEEcCHHHHHHHHHHHHHHh
Confidence            347899999999999999999999999999999999875532      478999999999999999999876

>PF13014 KH_3: KH domain

Probab=99.10  E-value=1.9e-10  Score=69.32  Aligned_cols=43  Identities=30%  Similarity=0.452  Sum_probs=36.4

Q ss_pred             eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc
Q psy11278        158 HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG  203 (238)
Q Consensus       158 ~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G  203 (238)
                      +|++|||++|++|++|+++|||+|.||+...++   ..++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~---~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPG---SNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCC---CCceEEEEEC
Confidence            589999999999999999999999999932221   2579999998

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

Probab=98.99  E-value=2.3e-08  Score=78.37  Aligned_cols=152  Identities=16%  Similarity=0.232  Sum_probs=107.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-----CHHHHHHHHHHHHhhCCceEEEe
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-----SLLGLERARYRVRELTPLIFCFE   76 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-----~~~~v~~A~~~I~~~~~~~~~~~   76 (238)
                      .+.||....+.+||+.|..-+.|++.+++++.+...        +..|+|..     +|..+.+|++.++.+-.-   |+
T Consensus        11 ~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG---F~   79 (194)
T COG1094          11 AVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIGRG---FP   79 (194)
T ss_pred             eeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHhcC---CC
Confidence            378999999999999999999999999999999773        45777753     688999999999866221   00


Q ss_pred             ecCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCC
Q psy11278         77 YPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISP  156 (238)
Q Consensus        77 ~p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~  156 (238)
                      .          ..-++=++ + +..+.+-+          |              .++..    ...+  .+       .
T Consensus        80 p----------e~A~~LL~-d-~~~levId----------i--------------~~~~~----~~~~--~l-------~  110 (194)
T COG1094          80 P----------EKALKLLE-D-DYYLEVID----------L--------------KDVVT----LSGD--HL-------R  110 (194)
T ss_pred             H----------HHHHHHhc-C-CcEEEEEE----------H--------------HHhcc----Cchh--hh-------h
Confidence            0          01122222 2 32222211          0              00000    0000  00       1


Q ss_pred             CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCc
Q psy11278        157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRR  224 (238)
Q Consensus       157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p  224 (238)
                      ...|.|||++|.+-+-|++-|||.|.+-.           ..|-|.|.+++|..|++.|+.++.+..|
T Consensus       111 R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-----------~tVaiiG~~~~v~iAr~AVemli~G~~h  167 (194)
T COG1094         111 RIKGRIIGREGKTRRAIEELTGVYISVYG-----------KTVAIIGGFEQVEIAREAVEMLINGAPH  167 (194)
T ss_pred             HhhceeeCCCchHHHHHHHHhCCeEEEeC-----------cEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence            24588999999999999999999999853           6799999999999999999999976543

>KOG2191|consensus

Probab=98.76  E-value=1.8e-08  Score=84.28  Aligned_cols=69  Identities=22%  Similarity=0.301  Sum_probs=58.4

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.+|.+-.|.||||+|++||.+++++++.|+|+......-.-.+|+|+++|++++..+|..+|.+.+.
T Consensus       135 kivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~  203 (402)
T KOG2191|consen  135 KIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQ  203 (402)
T ss_pred             EEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhh
Confidence            688999999999999999999999999999999743322122367899999999999999999976544

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

Probab=98.73  E-value=5.5e-08  Score=71.61  Aligned_cols=70  Identities=21%  Similarity=0.241  Sum_probs=54.4

Q ss_pred             EEEecC------CccceeeccCCccHHHHHHHcCCEEEecCCCCCC--------------CCCCCCeEEEEeC---HHHH
Q psy11278          2 KLDVSY------TDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSV--------------NAEKSNQVSIAGS---LLGL   58 (238)
Q Consensus         2 ~i~ip~------~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~--------------~~~~~~~v~I~G~---~~~v   58 (238)
                      ++.||.      +++|.|||++|+++|+|+++|||+|.|.......              ..++...|.|+++   .+++
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~   82 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL   82 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence            456665      3569999999999999999999999998763211              0123468999995   5999


Q ss_pred             HHHHHHHHhhCCc
Q psy11278         59 ERARYRVRELTPL   71 (238)
Q Consensus        59 ~~A~~~I~~~~~~   71 (238)
                      .+|+.+|..++..
T Consensus        83 ~~A~~~I~~ll~~   95 (120)
T cd02395          83 AKAVEAIEELLKP   95 (120)
T ss_pred             HHHHHHHHHHhcc
Confidence            9999999988653

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.

>KOG2279|consensus

Probab=98.61  E-value=9.4e-08  Score=84.90  Aligned_cols=213  Identities=15%  Similarity=0.175  Sum_probs=144.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce--EEEeecC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI--FCFEYPL   79 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~--~~~~~p~   79 (238)
                      ++-+|...+..++||+|++|+.|+..|+++|.+...+..    +++.-++.|-+..+..|+..+.+..-..  +...++.
T Consensus        71 e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g----~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pvk~~lsv  146 (608)
T KOG2279|consen   71 EMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG----DERVLLISGFPVQVCKAKAAIHQILTENTPVSEQLSV  146 (608)
T ss_pred             eEeecccceeeeeccccCCcchhhcccccceecCcccCC----cccchhhccCCCCCChHHHHHHHHHhcCCcccccccc
Confidence            567899999999999999999999999999999776542    4567777778899999988886654322  2223322


Q ss_pred             ----cCCCCCCCChHHHHHHHHhCceEEeeCCCCCC-CcEEEEEccccchHHHHHHHHHHHH-------Hhhcc------
Q psy11278         80 ----MGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQ-PTLVMVKGCEKDVERVKEATTKLIE-------HMCGS------  141 (238)
Q Consensus        80 ----~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~-~~~v~I~G~~~~v~~a~~ai~~~~~-------~~~~~------  141 (238)
                          .+..++.+|..++.+.+-.+++|.+....... .+...|.|..+-.+.++..+.+-++       ...+.      
T Consensus       147 pqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvp  226 (608)
T KOG2279|consen  147 PQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVP  226 (608)
T ss_pred             hhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCC
Confidence                22356778888888888888888776542222 2455555555544454432211111       00000      


Q ss_pred             cc-----------------------------------------c----------------------cceEEEEEEeCCCe
Q psy11278        142 LA-----------------------------------------N----------------------QTSVIMMMEISPQH  158 (238)
Q Consensus       142 ~~-----------------------------------------~----------------------~~~~~~~v~i~~~~  158 (238)
                      ++                                         +                      ......+|.+|.-.
T Consensus       227 rk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~l  306 (608)
T KOG2279|consen  227 RKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEIL  306 (608)
T ss_pred             CCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCccc
Confidence            00                                         0                      00112789999999


Q ss_pred             eeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        159 HPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       159 ~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++.+||+.|..+..+...+|+.++|-....... .....++.+.|+-.-+..|..++....
T Consensus       307 sg~lig~~gey~s~yssasn~~~hi~t~pyt~~-v~~~qic~~egkqh~~n~vl~ml~~~~  366 (608)
T KOG2279|consen  307 SGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR-VLQLQICVNEGKQHYENSVLEMLTVHV  366 (608)
T ss_pred             ccchhhhhhhhhhhhhhccCccceEEeccccch-hhhhhhheecchhHHHHHHHhhhhccC
Confidence            999999999999999999999987754332110 012267899999999999999988655

>KOG2113|consensus

Probab=98.59  E-value=4.3e-08  Score=81.44  Aligned_cols=151  Identities=19%  Similarity=0.211  Sum_probs=107.9

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCcC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMG   81 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~~   81 (238)
                      .+.+|...++.+.|++|.+|+.++.+|+++|.-|...      .+.+..++|..++|+.|+.+|..-..   -|.++.  
T Consensus        29 sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saae---H~~l~~--   97 (394)
T KOG2113|consen   29 SVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAAE---HFGLIR--   97 (394)
T ss_pred             eeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCccccc---eeeeee--
Confidence            4678988889999999999999999999999998865      35799999999999999998843211   111110  


Q ss_pred             CCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeE
Q psy11278         82 STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPI  161 (238)
Q Consensus        82 ~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~  161 (238)
                                 ......|..+...           .                       .  .+  .+.++.+|-..++.
T Consensus        98 -----------~s~s~Sgg~~~~s-----------~-----------------------s--~q--t~sy~svP~rvvgl  128 (394)
T KOG2113|consen   98 -----------ASRSFSGGTNGAS-----------A-----------------------S--GQ--TTSYVSVPLRVVGL  128 (394)
T ss_pred             -----------ecccccCCCcccc-----------c-----------------------c--CC--Cceeeeccceeeee
Confidence                       0010111000000           0                       0  11  12567778889999


Q ss_pred             EecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHH-HHHHH-HHHHhhc
Q psy11278        162 MEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDS-VYLAR-QMLVVSS  219 (238)
Q Consensus       162 iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~-v~~A~-~~I~~~l  219 (238)
                      +.|.+|.+|+.|++.++..|.-|-...       +.++-++|-+.+ +++|+ ..|+.-.
T Consensus       129 vv~~~~~ti~~iqq~tnt~I~T~v~~~-------~~Vf~Vtg~~~nC~kra~s~eie~ta  181 (394)
T KOG2113|consen  129 VVGPKGATIKRIQQFTNTYIATPVRCG-------EPVFCVTGAPKNCVKRARSCEIEQTA  181 (394)
T ss_pred             ccccccCccchheecccceEeeeccCC-------CceEEEecCCcchhhhccccchhhhh
Confidence            999999999999999999998876552       579999998888 66676 4454433

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.46  E-value=2.5e-07  Score=72.68  Aligned_cols=52  Identities=29%  Similarity=0.344  Sum_probs=48.2

Q ss_pred             ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ..|.|||++|.+++.|+..|||+|.+++          ..|.|.|++++++.|+..|.++..
T Consensus        99 ~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~i~~li~  150 (172)
T TIGR03665        99 IKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAREAIEMLIE  150 (172)
T ss_pred             HHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHHHHHHHHHc
Confidence            5799999999999999999999999975          589999999999999999998854

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.41  E-value=4.7e-07  Score=71.69  Aligned_cols=63  Identities=16%  Similarity=0.218  Sum_probs=56.5

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEE----cCHHHHHHHHHHHHhhcC
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVS----GNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~l~  220 (238)
                      ...+.||++.++.|||++|++|+.|+++|||+|.+...         ...|.|.    ++++++.+|+.+|.++..
T Consensus         4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---------TGEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---------CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999999763         2567885    899999999999999884

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

Probab=98.36  E-value=2e-06  Score=63.38  Aligned_cols=65  Identities=15%  Similarity=0.132  Sum_probs=51.0

Q ss_pred             CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCC-------------CCCcceEEEEEcC---HHHHHHHHHHHHhhcC
Q psy11278        157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPII-------------PVLKKSSVTVSGN---IDSVYLARQMLVVSSV  220 (238)
Q Consensus       157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~-------------~~~~~~~v~I~G~---~~~v~~A~~~I~~~l~  220 (238)
                      +++|.|||.+|+++|+|+++|||+|.+-...+...             ...+.--|.|+++   .+++.+|..+|+.++.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            58899999999999999999999999976521100             0012367899996   5999999999999995


Q ss_pred             C
Q psy11278        221 R  221 (238)
Q Consensus       221 ~  221 (238)
                      .
T Consensus        95 ~   95 (120)
T cd02395          95 P   95 (120)
T ss_pred             c
Confidence            3

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

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.15  E-value=4.5e-06  Score=78.09  Aligned_cols=60  Identities=22%  Similarity=0.361  Sum_probs=54.8

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      .+.||.+.++.|||+||++||.|.++|||+|++.+         +..|.|.+ +.+.+++|+.+|..+..
T Consensus       581 ~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       581 TVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             EEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            57899999999999999999999999999999976         36899988 68999999999998865

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.

>KOG2814|consensus

Probab=97.90  E-value=1.2e-05  Score=67.75  Aligned_cols=64  Identities=28%  Similarity=0.338  Sum_probs=54.9

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCCc
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTPL   71 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~   71 (238)
                      +.+++++.++|||++|.|.++|+++|+++|-+|.++.     ....|+|.| ....|.+|..+|..++..
T Consensus        61 i~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~-----n~~~i~i~~~~~~~V~~a~~Ri~~~ids  125 (345)
T KOG2814|consen   61 ILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT-----NKEEIKIIGISRNCVIQALERIAKLIDS  125 (345)
T ss_pred             hhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC-----CcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999875     345677766 778999999999776543

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.89  E-value=6.2e-05  Score=70.67  Aligned_cols=87  Identities=18%  Similarity=0.292  Sum_probs=67.9

Q ss_pred             hHHHHHHHHHHHHHhhcc------ccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278        124 VERVKEATTKLIEHMCGS------LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS  197 (238)
Q Consensus       124 v~~a~~ai~~~~~~~~~~------~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~  197 (238)
                      .+.|+++...+++.+.+.      +....+....+.||++..+.+||.||.+||+|.++|||.|.+.+          ..
T Consensus       548 L~~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d----------~G  617 (719)
T TIGR02696       548 LKQARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED----------DG  617 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------Cc
Confidence            345555555566554332      22223455889999999999999999999999999999999875          25


Q ss_pred             EEEEEcC-HHHHHHHHHHHHhhcC
Q psy11278        198 SVTVSGN-IDSVYLARQMLVVSSV  220 (238)
Q Consensus       198 ~v~I~G~-~~~v~~A~~~I~~~l~  220 (238)
                      .|.|.+. .++.++|+.+|+.+..
T Consensus       618 ~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       618 TVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             EEEEEeCCHHHHHHHHHHHHHhhC
Confidence            7999985 8999999999999985

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.88  E-value=1.7e-05  Score=75.03  Aligned_cols=60  Identities=27%  Similarity=0.416  Sum_probs=53.2

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.+.++.|||++|++||.|+++|||+|++.+         +..|.|.+ +.+.+++|+..|..+..
T Consensus       554 ~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------dG~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------DGTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             EEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence            57899999999999999999999999999999975         35788876 68999999999987743

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).

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.68  E-value=0.00013  Score=69.15  Aligned_cols=86  Identities=21%  Similarity=0.308  Sum_probs=64.9

Q ss_pred             HHHHHHHHHHHHHhhcc-------ccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278        125 ERVKEATTKLIEHMCGS-------LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS  197 (238)
Q Consensus       125 ~~a~~ai~~~~~~~~~~-------~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~  197 (238)
                      ..|+++...+++.+.+.       +....+....+.||+...+.|||++|++|++|.++|||.|.+.++          .
T Consensus       521 ~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd----------G  590 (684)
T TIGR03591       521 EQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD----------G  590 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC----------e
Confidence            44455555555544322       222234557899999999999999999999999999999998652          4


Q ss_pred             EEEEEc-CHHHHHHHHHHHHhhcC
Q psy11278        198 SVTVSG-NIDSVYLARQMLVVSSV  220 (238)
Q Consensus       198 ~v~I~G-~~~~v~~A~~~I~~~l~  220 (238)
                      .|.|.+ ..+.+++|+++|..+..
T Consensus       591 ~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       591 TVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             EEEEEECcHHHHHHHHHHHHhhhc
Confidence            677777 58899999999998874

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

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

Probab=97.60  E-value=0.00015  Score=57.18  Aligned_cols=53  Identities=32%  Similarity=0.331  Sum_probs=48.2

Q ss_pred             ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278          9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL   71 (238)
Q Consensus         9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~   71 (238)
                      ..|.|||++|.+-+.|++-|+|.|.+..          ..|.|-|.+++|..|++.|..+...
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHHHHHHcC
Confidence            3589999999999999999999999976          5999999999999999999888553

>KOG0119|consensus

Probab=97.53  E-value=0.00016  Score=64.02  Aligned_cols=64  Identities=19%  Similarity=0.206  Sum_probs=49.9

Q ss_pred             CccceeeccCCccHHHHHHHcCCEEEecCCCCC----------C---CCCCCCeEEEEe-CHHHHHHHHHHHHhhCCc
Q psy11278          8 TDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRS----------V---NAEKSNQVSIAG-SLLGLERARYRVRELTPL   71 (238)
Q Consensus         8 ~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~----------~---~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~   71 (238)
                      +++|+|||..|.|.|+|+++|||+|.|-.....          .   ...++-.+.|++ +.+.|.+|...|+.++..
T Consensus       153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999762211          0   112334788888 568999999999887654

>KOG2279|consensus

Probab=97.51  E-value=9e-05  Score=66.37  Aligned_cols=126  Identities=12%  Similarity=0.205  Sum_probs=95.1

Q ss_pred             CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeEE
Q psy11278         83 TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIM  162 (238)
Q Consensus        83 ~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~i  162 (238)
                      ..+..|++++.+...+++++.+.+..-.......+.|.+..+.+++.++...+..   +    ..+..+..+|...++.|
T Consensus        82 i~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~---~----~pvk~~lsvpqr~~~~i  154 (608)
T KOG2279|consen   82 IIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE---N----TPVSEQLSVPQRSVGRI  154 (608)
T ss_pred             eeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc---C----Ccccccccchhhhcccc
Confidence            4456789999999999999998764222234455566888888888665544331   1    23557888899999999


Q ss_pred             ecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        163 EGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       163 IG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +|++|.+++.|+..++|+|.+....-.    +..+...|.|...-+..|+.++.+.+
T Consensus       155 ~grgget~~si~~ss~aki~~d~ngr~----g~~~~~~i~~qqk~~~~a~~~~~~~~  207 (608)
T KOG2279|consen  155 IGRGGETIRSICKSSGAKITCDKNGRL----GLSRLIKISGQQKEVAAAKHLILEKV  207 (608)
T ss_pred             cccchhhhcchhccccccccccccccc----ccccceecccccchHHHHHhhhhccc
Confidence            999999999999999999998765422    23567777777777778998888776

>KOG2113|consensus

Probab=97.45  E-value=0.0001  Score=61.69  Aligned_cols=63  Identities=22%  Similarity=0.320  Sum_probs=57.6

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHh
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVV  217 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~  217 (238)
                      ++..+.+|..+++.+.|++|.+|+.++.+|.++|.-|....       +..|.++|.++.|..|++.|..
T Consensus        26 vt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e-------ePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   26 VTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE-------EPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             cceeeecCcccceeecccCccccchhhhhhcceeccCCCCC-------CCcceeccCchhHHHHhhcCcc
Confidence            55889999999999999999999999999999999997653       4799999999999999999887

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.39  E-value=0.00034  Score=67.25  Aligned_cols=87  Identities=16%  Similarity=0.401  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHHHHHhhcc-------ccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCe-EEccCCCCCCCCCCc
Q psy11278        124 VERVKEATTKLIEHMCGS-------LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQ-IVFPEANDPIIPVLK  195 (238)
Q Consensus       124 v~~a~~ai~~~~~~~~~~-------~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~-I~~p~~~~~~~~~~~  195 (238)
                      ...|+++...+++.+.+.       +....+....+.||++.++.|||.||.+|++|.++||+. |.+-+          
T Consensus       654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----------  723 (891)
T PLN00207        654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----------  723 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC----------
Confidence            355556666666655432       222334568899999999999999999999999999999 77654          


Q ss_pred             ceEEEEEc-CHHHHHHHHHHHHhhcC
Q psy11278        196 KSSVTVSG-NIDSVYLARQMLVVSSV  220 (238)
Q Consensus       196 ~~~v~I~G-~~~~v~~A~~~I~~~l~  220 (238)
                      ...|.|.| ..+.+++|+.+|..+..
T Consensus       724 dg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        724 DGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            25788888 59999999999998873

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.38  E-value=0.00014  Score=69.88  Aligned_cols=60  Identities=32%  Similarity=0.494  Sum_probs=53.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCE-EEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCH-VHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~-I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      .+.||.+.++.|||.||.+|+.|.++||+. |++.+         +..|.|.+ +.+.++.|+++|..+..
T Consensus       688 ~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        688 IMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             EEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999 99865         36888888 78999999999988754

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

Probab=97.22  E-value=0.0004  Score=44.86  Aligned_cols=33  Identities=18%  Similarity=0.334  Sum_probs=30.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEe
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHF   34 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i   34 (238)
                      .+.||.+..|..|||+|.||+.+++.++-+|++
T Consensus        28 ~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          28 RVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             EEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578999999999999999999999999988876

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.

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=97.20  E-value=0.0081  Score=48.66  Aligned_cols=105  Identities=12%  Similarity=0.152  Sum_probs=79.8

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEE--EeecCc
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFC--FEYPLM   80 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~--~~~p~~   80 (238)
                      +.++......+...+|..++.|....|++|.+..        ..+.+.|+|+...++.+...|.+++....+  ++++..
T Consensus        30 v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~l~~~  101 (210)
T PF14611_consen   30 VWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNIRTEEIDLSPI  101 (210)
T ss_pred             EEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhcEEEEEecchh
Confidence            4567778889999999999999889999999977        346999999999999999999999876644  444432


Q ss_pred             CC------CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEc
Q psy11278         81 GS------TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKG  119 (238)
Q Consensus        81 ~~------~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G  119 (238)
                      ..      ........++.+++.+++.+...+.    ...+.|.+
T Consensus       102 ~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----~~~~~i~~  142 (210)
T PF14611_consen  102 ISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----GNKLKISW  142 (210)
T ss_pred             hhhhcccccccccHHHHHHHHHHHcEEEEECCC----CCeEEEEE
Confidence            21      0112467789999999999887653    23455554

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.20  E-value=0.0023  Score=48.46  Aligned_cols=34  Identities=18%  Similarity=0.283  Sum_probs=30.7

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF  183 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~  183 (238)
                      ..+.+++...+..|||+|++++.++.-+|-++.+
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            6778899999999999999999999999988755

>KOG2814|consensus

Probab=97.20  E-value=0.00033  Score=59.26  Aligned_cols=75  Identities=13%  Similarity=0.130  Sum_probs=60.6

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhcCC---CCc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSSVR---PRR  224 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~---~~p  224 (238)
                      ...+.+++.+.++|+|++|.+-++|+++|++.|.+|.+.+.      ...++|+| +.++|.+|..+|..++..   ..|
T Consensus        58 ~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n------~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p  131 (345)
T KOG2814|consen   58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN------KEEIKIIGISRNCVIQALERIAKLIDSDRKSFP  131 (345)
T ss_pred             hhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC------cceEEEeehhHHHHHHHHHHHHHHHHhhhhcCc
Confidence            35678899999999999999999999999999999998854      24555555 799999999999998843   345


Q ss_pred             eEEEE
Q psy11278        225 RLLLI  229 (238)
Q Consensus       225 ~~~~~  229 (238)
                      +.+..
T Consensus       132 ~thfl  136 (345)
T KOG2814|consen  132 ITHFL  136 (345)
T ss_pred             hhhhh
Confidence            44443

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

Probab=97.19  E-value=0.00052  Score=63.52  Aligned_cols=61  Identities=31%  Similarity=0.467  Sum_probs=54.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC-HHHHHHHHHHHHhhCCc
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELTPL   71 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~~~~   71 (238)
                      ++.|+.+.++-+||++|++|++|.++||++|++.+         +..|.|.+. .+.+.+|+..|..+..+
T Consensus       555 t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---------dGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         555 TIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---------DGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             EEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence            57789999999999999999999999999999973         368999885 58999999999998754

>KOG0336|consensus

Probab=97.17  E-value=0.00033  Score=61.28  Aligned_cols=58  Identities=21%  Similarity=0.352  Sum_probs=48.3

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHH
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVR   66 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~   66 (238)
                      +.|-++.+|.+||++|++|+.||..|+++|++.+-+      .+..|+|.|...--.+|+..|.
T Consensus        51 f~iks~mvg~vigrggskik~iq~~tnt~iqii~~~------~e~kv~ifg~~~m~~kaka~id  108 (629)
T KOG0336|consen   51 FSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD------LEVKVTIFGINHMRKKAKASID  108 (629)
T ss_pred             hhhhhhhhheeeccCcchhhhhhcccceeEEEeccC------ceeEEEEechHHHHHHHHhhHh
Confidence            456778899999999999999999999999998743      3568999998776667777663

>KOG0336|consensus

Probab=97.12  E-value=0.00037  Score=60.99  Aligned_cols=63  Identities=16%  Similarity=0.134  Sum_probs=55.5

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ..+.|.+.++|.+||++|++|++|+..|+++|++.+-..       +..|+|-|..+--.+|+..|....
T Consensus        49 lcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~-------e~kv~ifg~~~m~~kaka~id~~~  111 (629)
T KOG0336|consen   49 LCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDL-------EVKVTIFGINHMRKKAKASIDRGQ  111 (629)
T ss_pred             hhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCc-------eeEEEEechHHHHHHHHhhHhhhh
Confidence            678888899999999999999999999999999876442       578999999998888888887766

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.06  E-value=0.0011  Score=54.82  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=53.9

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCCce
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTPLI   72 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~~   72 (238)
                      .+.||.+.++.+||++|.+|+.|.++|++.|.+-.         ...|.|.| +.+++..|...|+.+..+.
T Consensus       148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        148 IVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            47899999999999999999999999999999954         36899998 5679999999998775543

>PRK00106 hypothetical protein; Provisional

Probab=97.04  E-value=0.0014  Score=60.15  Aligned_cols=60  Identities=27%  Similarity=0.390  Sum_probs=51.6

Q ss_pred             EEEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~   69 (238)
                      .|.+|++.+ |.||||.|.||+.++.-|||-+-|.+        ....|+++| +|-.-+-|+..|..+.
T Consensus       228 ~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~v~lS~fdpvRReiAr~~le~Li  289 (535)
T PRK00106        228 TVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--------TPEVVVLSGFDPIRREIARMTLESLI  289 (535)
T ss_pred             eEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--------CCCeEEEeCCChHHHHHHHHHHHHHH
Confidence            367899766 99999999999999999999999977        346899999 8888888888886654

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.03  E-value=0.0014  Score=60.18  Aligned_cols=60  Identities=25%  Similarity=0.393  Sum_probs=51.1

Q ss_pred             EEEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~   69 (238)
                      .|.+|++.+ |.||||.|-||+.++.-|||-|=|.+        ....|+|+| +|-.-+-|+..|..+.
T Consensus       207 ~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~fdp~rreia~~~l~~li  268 (514)
T TIGR03319       207 VVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPVRREIARMALEKLI  268 (514)
T ss_pred             eEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--------CCCeEEecCCchHHHHHHHHHHHHHH
Confidence            367899766 99999999999999999999999977        346899999 8888888888776654

>PRK00106 hypothetical protein; Provisional

Probab=96.96  E-value=0.0046  Score=56.76  Aligned_cols=73  Identities=16%  Similarity=0.282  Sum_probs=57.8

Q ss_pred             HhhccccccceEEEEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHH
Q psy11278        137 HMCGSLANQTSVIMMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQM  214 (238)
Q Consensus       137 ~~~~~~~~~~~~~~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~  214 (238)
                      +...+..+..++ ..|.+|++ +-|.|||+.|.+|+-+..-||+.+.+.+..         ..|+|+| .|---+.|+..
T Consensus       215 r~a~~~~~e~tv-s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp---------~~v~lS~fdpvRReiAr~~  284 (535)
T PRK00106        215 RLAGEYVTEQTI-TTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP---------EVVVLSGFDPIRREIARMT  284 (535)
T ss_pred             Hhcchhhhhhee-eeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC---------CeEEEeCCChHHHHHHHHH
Confidence            333333333343 67889985 889999999999999999999999997643         5788999 58888889999


Q ss_pred             HHhhc
Q psy11278        215 LVVSS  219 (238)
Q Consensus       215 I~~~l  219 (238)
                      |+.++
T Consensus       285 le~Li  289 (535)
T PRK00106        285 LESLI  289 (535)
T ss_pred             HHHHH
Confidence            98888

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

Probab=96.95  E-value=0.0032  Score=58.44  Aligned_cols=96  Identities=21%  Similarity=0.335  Sum_probs=72.0

Q ss_pred             EEEEEccccch-----HHHHHHHHHHHHHhhccc-------cccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeE
Q psy11278        114 LVMVKGCEKDV-----ERVKEATTKLIEHMCGSL-------ANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQI  181 (238)
Q Consensus       114 ~v~I~G~~~~v-----~~a~~ai~~~~~~~~~~~-------~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I  181 (238)
                      .+.|.|-...+     ..|+.+...+++.+.+..       ....+...++.|++...+-+||++|.+|++|.++|||.|
T Consensus       506 DiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~I  585 (692)
T COG1185         506 DIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKI  585 (692)
T ss_pred             eeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEE
Confidence            45666766432     455666666666554322       112233478899999999999999999999999999999


Q ss_pred             EccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHHhhc
Q psy11278        182 VFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLVVSS  219 (238)
Q Consensus       182 ~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l  219 (238)
                      .+.+          ...|.|.++ .+.+++|+..|..+.
T Consensus       586 died----------dGtv~i~~s~~~~~~~ak~~I~~i~  614 (692)
T COG1185         586 DIED----------DGTVKIAASDGESAKKAKERIEAIT  614 (692)
T ss_pred             EecC----------CCcEEEEecchHHHHHHHHHHHHHH
Confidence            9973          257899997 588899999999987

>PRK12704 phosphodiesterase; Provisional

Probab=96.93  E-value=0.0022  Score=58.92  Aligned_cols=60  Identities=25%  Similarity=0.403  Sum_probs=50.2

Q ss_pred             EEEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~   69 (238)
                      .|.+|++.+ |.||||.|-||+.++.-|||-|-|.+        ....|.++| +|..-+.|+..|..+.
T Consensus       213 ~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~  274 (520)
T PRK12704        213 VVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLV  274 (520)
T ss_pred             eeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHH
Confidence            367899766 99999999999999999999999977        346899999 7777777777776653

>PRK12704 phosphodiesterase; Provisional

Probab=96.93  E-value=0.0044  Score=57.00  Aligned_cols=61  Identities=16%  Similarity=0.245  Sum_probs=50.9

Q ss_pred             EEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhc
Q psy11278        150 MMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSS  219 (238)
Q Consensus       150 ~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l  219 (238)
                      ..|.+|++ +-|.|||+.|-+|+-+..-||+.|.+.+..         ..|.|+| .|---+.|+..|+.++
T Consensus       212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp---------~~v~ls~~~~~rre~a~~~l~~l~  274 (520)
T PRK12704        212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---------EAVILSGFDPIRREIARLALEKLV  274 (520)
T ss_pred             eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC---------CeEEEecCChhhHHHHHHHHHHHH
Confidence            67889885 789999999999999999999999997642         6788999 4666567888777776

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.92  E-value=0.0043  Score=56.97  Aligned_cols=61  Identities=16%  Similarity=0.249  Sum_probs=52.8

Q ss_pred             EEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhc
Q psy11278        150 MMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSS  219 (238)
Q Consensus       150 ~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l  219 (238)
                      ..|.+|++ +-|.|||+.|-+|+-+..-||+.|.+.+..         ..|+|+| .|---+.|+.-|+.++
T Consensus       206 ~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp---------~~v~ls~fdp~rreia~~~l~~li  268 (514)
T TIGR03319       206 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---------EAVILSGFDPVRREIARMALEKLI  268 (514)
T ss_pred             eeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC---------CeEEecCCchHHHHHHHHHHHHHH
Confidence            67899985 789999999999999999999999997643         5788999 5777788999998888

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.90  E-value=0.00079  Score=64.00  Aligned_cols=60  Identities=30%  Similarity=0.487  Sum_probs=52.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      .+.||.+.++.+||.||.+|++|.++||++|++.+         +..|.|.+ +.+.+++|+..|..+..
T Consensus       557 ~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---------~G~v~i~~~~~~~~~~a~~~I~~~~~  617 (693)
T PRK11824        557 TIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---------DGTVKIAATDGEAAEAAKERIEGITA  617 (693)
T ss_pred             eecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------CceEEEEcccHHHHHHHHHHHHHhcc
Confidence            46688899999999999999999999999998854         46888888 68999999999988764

>KOG0119|consensus

Probab=96.73  E-value=0.0058  Score=54.47  Aligned_cols=66  Identities=18%  Similarity=0.175  Sum_probs=48.9

Q ss_pred             CCeeeEEecCCCchHHHHHHHhCCeEEccCCC---------C-CC-CC-CCcceEEEEEc-CHHHHHHHHHHHHhhcCC
Q psy11278        156 PQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN---------D-PI-IP-VLKKSSVTVSG-NIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       156 ~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~---------~-~~-~~-~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~  221 (238)
                      -+|+|+|||..|.+.|+|+++|||+|.|=...         + .+ .. +.+.=-+.|++ +.|.|++|...|+.+|+.
T Consensus       152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence            45889999999999999999999999774311         0 00 00 11223577777 599999999999999943

>KOG1588|consensus

Probab=96.68  E-value=0.002  Score=53.05  Aligned_cols=38  Identities=29%  Similarity=0.473  Sum_probs=32.5

Q ss_pred             EEEecCC------ccceeeccCCccHHHHHHHcCCEEEecCCCC
Q psy11278          2 KLDVSYT------DHSHIIGRGGLTIKKVMEETGCHVHFPDSNR   39 (238)
Q Consensus         2 ~i~ip~~------~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~   39 (238)
                      +|.||-+      ++|.|+|.+|.++|+|+++|||+|.|-...+
T Consensus        95 Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgS  138 (259)
T KOG1588|consen   95 KVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGS  138 (259)
T ss_pred             EEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCc
Confidence            4566654      7899999999999999999999999987654

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.65  E-value=0.004  Score=59.32  Aligned_cols=87  Identities=18%  Similarity=0.320  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHHHHhhccc-------cccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278        125 ERVKEATTKLIEHMCGSL-------ANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS  197 (238)
Q Consensus       125 ~~a~~ai~~~~~~~~~~~-------~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~  197 (238)
                      +.|+++...+++.+...+       ....+....+.||+...+.+||.||.+|++|.++||+.|.+-+          ..
T Consensus       524 ~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d----------~G  593 (693)
T PRK11824        524 EQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED----------DG  593 (693)
T ss_pred             HHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC----------Cc
Confidence            455556666666554332       1122334677889999999999999999999999999877632          35


Q ss_pred             EEEEEc-CHHHHHHHHHHHHhhcCC
Q psy11278        198 SVTVSG-NIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       198 ~v~I~G-~~~~v~~A~~~I~~~l~~  221 (238)
                      .|.|.+ ..+.+++|+++|..+...
T Consensus       594 ~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        594 TVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             eEEEEcccHHHHHHHHHHHHHhccc
Confidence            788888 589999999999998843

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

Probab=96.64  E-value=0.004  Score=40.14  Aligned_cols=34  Identities=12%  Similarity=0.147  Sum_probs=31.5

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF  183 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~  183 (238)
                      ..+.+++...+..||++|.+|+.+++.+|-+|.+
T Consensus        27 ~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          27 ARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             EEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            7889999999999999999999999999987764

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.41  E-value=0.0062  Score=50.33  Aligned_cols=62  Identities=16%  Similarity=0.284  Sum_probs=53.6

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHHhhcCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLVVSSVR  221 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~  221 (238)
                      ..+.||..+++.+||++|..|+.|.+.+++.|.+-.          ...|.|.|+ .+++.+|..+|+.+-..
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~----------NG~VwI~~~~~~~~~~a~~~I~~~e~~  209 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ----------NGRIWIKGPDEEDEEIAIEAIKKIERE  209 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC----------CcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence            568889999999999999999999999999999854          257999996 66899999999887643

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.16  E-value=0.12  Score=41.88  Aligned_cols=113  Identities=12%  Similarity=0.150  Sum_probs=79.8

Q ss_pred             CCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeEEe-c
Q psy11278         86 ANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIME-G  164 (238)
Q Consensus        86 ~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~iI-G  164 (238)
                      .++..++.+...+|++|.+...    ...+.|+|++..++.+...+..++..    .     .+..|.++.-...+-- +
T Consensus        43 ~~~~~L~~l~~~~~~~I~~~~~----~~~i~I~g~k~~~~~i~~~i~~~l~~----i-----~~~~i~l~~~~~~~~~~~  109 (210)
T PF14611_consen   43 GNGRILENLAARNGAKIEVSRS----ENRIRITGTKSTAEYIEASINEILSN----I-----RTEEIDLSPIISKHSEKK  109 (210)
T ss_pred             CCchHHHHHHHhcCceEEEecC----CcEEEEEccHHHHHHHHHHHHHHHhh----c-----EEEEEecchhhhhhcccc
Confidence            4678889997788999998763    36899999988887777666666652    2     2245555533211111 1


Q ss_pred             ---CCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEE-----cCHHHHHHHHHHHHhhcC
Q psy11278        165 ---PNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVS-----GNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       165 ---~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~l~  220 (238)
                         .....++.|++.|++.|....+.         ..+.|.     -.+.....|+++|...+.
T Consensus       110 ~~~~~~~~l~~i~~~t~~~ie~~~~~---------~~~~i~~~~~~~~~~~~~~a~RlL~~a~~  164 (210)
T PF14611_consen  110 NSQFTPDLLEEIQKLTNVYIEKNPDG---------NKLKISWLASPENEKRADRAKRLLLWALD  164 (210)
T ss_pred             cccccHHHHHHHHHHHcEEEEECCCC---------CeEEEEEEeeccccchHHHHHHHHHHhcc
Confidence               13677899999999999987654         234444     468899999999999994

>PRK12705 hypothetical protein; Provisional

Probab=96.12  E-value=0.0051  Score=56.13  Aligned_cols=59  Identities=25%  Similarity=0.359  Sum_probs=46.4

Q ss_pred             EEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278          3 LDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT   69 (238)
Q Consensus         3 i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~   69 (238)
                      +.+|++.+ |.||||.|.||+.++..||+.+-|.+.        ...|++++ +|..-+.|+..++.++
T Consensus       202 v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--------p~~V~ls~fdp~rreia~~~l~~Li  262 (508)
T PRK12705        202 VPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT--------PEAVVISSFNPIRREIARLTLEKLL  262 (508)
T ss_pred             eecCChHhhccccCccchhHHHHHHhhCCceEecCC--------ccchhhcccCccchHHHHHHHHHHH
Confidence            67888766 999999999999999999999999773        34666776 5666666666665553

>KOG1067|consensus

Probab=96.11  E-value=0.018  Score=52.45  Aligned_cols=95  Identities=16%  Similarity=0.251  Sum_probs=71.4

Q ss_pred             hHHHHHHHHHHHHHhhcccc-------ccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcc
Q psy11278        124 VERVKEATTKLIEHMCGSLA-------NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKK  196 (238)
Q Consensus       124 v~~a~~ai~~~~~~~~~~~~-------~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~  196 (238)
                      ..+|+.+..++++.+..+..       .+.++...+.++++....+||.+|.+.|+|..+||+.-.+.           +
T Consensus       566 l~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e  634 (760)
T KOG1067|consen  566 LQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------E  634 (760)
T ss_pred             HHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------C
Confidence            45566677778887765432       12345688899999999999999999999999999654442           3


Q ss_pred             eEEEEEcC-HHHHHHHHHHHHhhcCCCCceEEEE
Q psy11278        197 SSVTVSGN-IDSVYLARQMLVVSSVRPRRRLLLI  229 (238)
Q Consensus       197 ~~v~I~G~-~~~v~~A~~~I~~~l~~~~p~~~~~  229 (238)
                      ..++|.-+ +++.++|+..|.+++..+.-..|.|
T Consensus       635 ~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~  668 (760)
T KOG1067|consen  635 GTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEF  668 (760)
T ss_pred             ceEEEEecCHHHHHHHHHHHHHHhcCccccceEe
Confidence            56888775 8888999999999997654444444

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=95.97  E-value=0.025  Score=50.90  Aligned_cols=113  Identities=14%  Similarity=0.127  Sum_probs=74.8

Q ss_pred             eeeccCCccHHHHHHHcCCE--EEecCCCCCCCCCCCCeEE-EEeCHHHHHHHHHHHHhhCCceEEEeecCcCC--CCCC
Q psy11278         12 HIIGRGGLTIKKVMEETGCH--VHFPDSNRSVNAEKSNQVS-IAGSLLGLERARYRVRELTPLIFCFEYPLMGS--TPNA   86 (238)
Q Consensus        12 ~IIGk~G~~I~~I~~~t~~~--I~i~~~~~~~~~~~~~~v~-I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~~~--~~~~   86 (238)
                      ++=||+.-++.+||+...|.  +.+.++++      +.+.+ +.|..-+..++.+.+..-.|+..+|-+|..++  .+|.
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~g------s~~~~~~~g~~~~F~k~~~~~~~EFpae~~f~i~e~~h~~IIgt  466 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSSTG------SIVETNGIGEKMSFSKKLSIPPTEFPAEIAFIIMESGHEMIIGT  466 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEecCC------cEEEEeccCcchhhHHHhcCCcccCchheEEEeecccceeeecc
Confidence            66788877799999999888  45555432      23222 34666666666666655555556777776654  6788


Q ss_pred             CChHHHHHHHHhCceEEeeCC---CCCC-CcEEEEEccccchHHHHHH
Q psy11278         87 NSPFVQIIQEAYNVQVMFRNR---PKLQ-PTLVMVKGCEKDVERVKEA  130 (238)
Q Consensus        87 ~g~~i~~i~~~~gv~I~~~~~---~~~~-~~~v~I~G~~~~v~~a~~a  130 (238)
                      +|..|++.+.+++|.|.|...   +.+. .+.|.|+-+.+|.+....+
T Consensus       467 gG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~  514 (657)
T COG5166         467 GGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGK  514 (657)
T ss_pred             CchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcc
Confidence            999999999999999988652   2221 2346666666655444433

>KOG1588|consensus

Probab=95.94  E-value=0.012  Score=48.59  Aligned_cols=72  Identities=17%  Similarity=0.192  Sum_probs=48.8

Q ss_pred             EEEEEEeCC------CeeeEEecCCCchHHHHHHHhCCeEEccCCC-------------CCCCCCCc---ceEEEEEcCH
Q psy11278        148 VIMMMEISP------QHHPIMEGPNAINLKTIMAQTGAQIVFPEAN-------------DPIIPVLK---KSSVTVSGNI  205 (238)
Q Consensus       148 ~~~~v~i~~------~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~-------------~~~~~~~~---~~~v~I~G~~  205 (238)
                      ++..|.||-      +|+|.|+|..|.++++++++|||+|.+=...             ++++....   .-.|...+++
T Consensus        92 ~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~  171 (259)
T KOG1588|consen   92 LTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPP  171 (259)
T ss_pred             EEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCH
Confidence            445555554      4899999999999999999999999774322             11111111   2367777776


Q ss_pred             HHHH----HHHHHHHhhc
Q psy11278        206 DSVY----LARQMLVVSS  219 (238)
Q Consensus       206 ~~v~----~A~~~I~~~l  219 (238)
                      +-+.    .|...|+.+|
T Consensus       172 ~ea~~rl~~AleeI~klL  189 (259)
T KOG1588|consen  172 AEAYARLAYALEEIKKLL  189 (259)
T ss_pred             HHHHHHHHHHHHHHHHhc
Confidence            6555    4777788777

>PRK12705 hypothetical protein; Provisional

Probab=95.92  E-value=0.02  Score=52.40  Aligned_cols=79  Identities=16%  Similarity=0.212  Sum_probs=56.6

Q ss_pred             HHHHHHhhccccccceEEEEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHH
Q psy11278        132 TKLIEHMCGSLANQTSVIMMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVY  209 (238)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~  209 (238)
                      ...+++...+..+..++ ..|.+|++ +-|.|||+.|.+|+-+...||+.+.+.+..         ..|+|.+. |.--+
T Consensus       183 ~~aiqr~a~~~~~e~tv-s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp---------~~V~ls~fdp~rre  252 (508)
T PRK12705        183 AQAMQRIASETASDLSV-SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP---------EAVVISSFNPIRRE  252 (508)
T ss_pred             HHHHHHhccchhhhhee-eeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc---------cchhhcccCccchH
Confidence            33344444444333343 57788875 779999999999999999999999997643         45777774 66666


Q ss_pred             HHHHHHHhhcC
Q psy11278        210 LARQMLVVSSV  220 (238)
Q Consensus       210 ~A~~~I~~~l~  220 (238)
                      .|+..+..++.
T Consensus       253 ia~~~l~~Li~  263 (508)
T PRK12705        253 IARLTLEKLLA  263 (508)
T ss_pred             HHHHHHHHHHh
Confidence            77877777773

>PRK00468 hypothetical protein; Provisional

Probab=95.24  E-value=0.014  Score=39.28  Aligned_cols=26  Identities=27%  Similarity=0.411  Sum_probs=23.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHH
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEE   27 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~   27 (238)
                      ++.+..+..|.+|||+|.+++.|+.-
T Consensus        33 ~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         33 ELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             EEEEChhhCcceecCCChhHHHHHHH
Confidence            57788999999999999999999853

>PRK02821 hypothetical protein; Provisional

Probab=95.07  E-value=0.015  Score=39.19  Aligned_cols=28  Identities=29%  Similarity=0.430  Sum_probs=24.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETG   29 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~   29 (238)
                      .+.+.++..|.+|||+|.+++.|+.--.
T Consensus        34 ~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         34 EVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             EEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            5778899999999999999999986543

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

Probab=95.04  E-value=0.03  Score=44.59  Aligned_cols=32  Identities=19%  Similarity=0.219  Sum_probs=28.8

Q ss_pred             CCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278          7 YTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN   38 (238)
Q Consensus         7 ~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~   38 (238)
                      .+++|.|||..|+|+++|+..|+|+|.|-...
T Consensus       162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             cceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            35789999999999999999999999997754

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

Probab=95.02  E-value=0.018  Score=38.60  Aligned_cols=25  Identities=32%  Similarity=0.525  Sum_probs=22.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHH
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVME   26 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~   26 (238)
                      ++.+.++..|.+|||+|.+++.|+-
T Consensus        33 ~l~v~~~D~GkvIGk~GRti~AIRT   57 (76)
T COG1837          33 ELRVAPEDMGKVIGKQGRTIQAIRT   57 (76)
T ss_pred             EEEECcccccceecCCChhHHHHHH
Confidence            5678889999999999999999985

>PRK01064 hypothetical protein; Provisional

Probab=94.67  E-value=0.029  Score=38.00  Aligned_cols=26  Identities=38%  Similarity=0.512  Sum_probs=23.3

Q ss_pred             EEEecCCccceeeccCCccHHHHHHH
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEE   27 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~   27 (238)
                      ++.+.++..|.+|||+|.+|+.|+.-
T Consensus        33 ~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         33 ELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             EEEECcccceEEECCCCccHHHHHHH
Confidence            57788999999999999999999874

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

Probab=94.05  E-value=0.094  Score=41.83  Aligned_cols=32  Identities=19%  Similarity=0.302  Sum_probs=28.3

Q ss_pred             CCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278        156 PQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN  187 (238)
Q Consensus       156 ~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~  187 (238)
                      .+|+|+|||..|.+.++++..|+|+|.+-...
T Consensus       162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             cceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            46999999999999999999999999875443

>KOG4369|consensus

Probab=93.97  E-value=0.022  Score=55.89  Aligned_cols=64  Identities=17%  Similarity=0.170  Sum_probs=54.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHh
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRE   67 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~   67 (238)
                      ++.+|....+.+||++|+||..++.-||+.|++.+....  +..+|.+.+.|.++.+..|...|.-
T Consensus      1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~--Nqaers~~~kg~p~~~r~a~~~I~~ 1406 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPD--NQAERSKAPKGRPPSQRVATSPIGL 1406 (2131)
T ss_pred             ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCc--cchhhhcccCCCChhhhhhhccccc
Confidence            467888889999999999999999999999999874431  2357899999999999999988843

>KOG2874|consensus

Probab=93.44  E-value=0.13  Score=42.87  Aligned_cols=52  Identities=29%  Similarity=0.402  Sum_probs=46.6

Q ss_pred             cceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278         10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL   71 (238)
Q Consensus        10 ~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~   71 (238)
                      +..+||.+|+|++.|+--|+|.|-+..          ..|.+.|...++..++..+.+++..
T Consensus       160 RqRLiGpng~TLKAlelLT~CYilVqG----------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  160 RQRLIGPNGSTLKALELLTNCYILVQG----------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHHhcCCCchhHHHHHHHhhcEEEeeC----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            457899999999999999999999965          6899999999999999999887653

>PRK00468 hypothetical protein; Provisional

Probab=93.34  E-value=0.11  Score=34.90  Aligned_cols=32  Identities=22%  Similarity=0.286  Sum_probs=27.5

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCC
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGA  179 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga  179 (238)
                      ...++.+.+.-.|.+|||+|.+|+.|+.--.+
T Consensus        30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~a   61 (75)
T PRK00468         30 VILELKVAPEDMGKVIGKQGRIAKAIRTVVKA   61 (75)
T ss_pred             EEEEEEEChhhCcceecCCChhHHHHHHHHHH
Confidence            45788999999999999999999999986443

>KOG1067|consensus

Probab=93.32  E-value=0.087  Score=48.13  Aligned_cols=59  Identities=27%  Similarity=0.374  Sum_probs=50.0

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      .+.++.+.+..+||.+|.+.|+|+.|||+.-.+          ++..++|.. ++...+.|++.|..+..
T Consensus       600 tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----------De~t~~i~A~~~~am~~Ak~~I~~i~~  659 (760)
T KOG1067|consen  600 TLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----------DEGTFSIFAPTQAAMEEAKEFIDGIIK  659 (760)
T ss_pred             EEeecchhhheeecCccceeeeEeeeccceeee----------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence            477999999999999999999999999955555          346888887 68899999999987754

>KOG2874|consensus

Probab=93.31  E-value=0.13  Score=42.91  Aligned_cols=55  Identities=18%  Similarity=0.214  Sum_probs=48.7

Q ss_pred             eEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCce
Q psy11278        160 PIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRR  225 (238)
Q Consensus       160 ~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p~  225 (238)
                      ..+||.+|++++.|+--|.|.|-+..           ..|.+.|+..++..+++.+.+.|.--+|+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG-----------~TVsaiGpfkGlkevr~IV~DcM~NiHPi  215 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG-----------NTVSAIGPFKGLKEVRKIVEDCMKNIHPI  215 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC-----------cEEEeecCcchHHHHHHHHHHHHhccchH
Confidence            46899999999999999999999863           67999999999999999999998665554

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

Probab=93.00  E-value=0.13  Score=33.13  Aligned_cols=28  Identities=18%  Similarity=0.252  Sum_probs=23.0

Q ss_pred             ecCCccceeeccCCccHHHHHHHcCCEE
Q psy11278          5 VSYTDHSHIIGRGGLTIKKVMEETGCHV   32 (238)
Q Consensus         5 ip~~~~g~IIGk~G~~I~~I~~~t~~~I   32 (238)
                      +.....|.+||++|.+++.++..++-.+
T Consensus        31 ~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          31 VARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             ECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            3444579999999999999999998554

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.

>PRK02821 hypothetical protein; Provisional

Probab=92.82  E-value=0.13  Score=34.65  Aligned_cols=33  Identities=9%  Similarity=0.110  Sum_probs=28.5

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCe
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQ  180 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~  180 (238)
                      ....+.+.+.-.|.+|||+|..|+.|+.--.+.
T Consensus        31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~   63 (77)
T PRK02821         31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI   63 (77)
T ss_pred             EEEEEEEChhhCcceeCCCCchHHHHHHHHHHh
Confidence            347888899999999999999999999885553

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

Probab=92.79  E-value=0.19  Score=33.76  Aligned_cols=31  Identities=13%  Similarity=0.281  Sum_probs=27.4

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHh
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQT  177 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~t  177 (238)
                      .+..++.+.+.-.|.+|||+|.+|+-|+.--
T Consensus        29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             eEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            4568889999999999999999999999863

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

Probab=92.72  E-value=0.094  Score=34.62  Aligned_cols=28  Identities=29%  Similarity=0.408  Sum_probs=23.0

Q ss_pred             cceeeccCCccHHHHHHHc-CCEEEecCC
Q psy11278         10 HSHIIGRGGLTIKKVMEET-GCHVHFPDS   37 (238)
Q Consensus        10 ~g~IIGk~G~~I~~I~~~t-~~~I~i~~~   37 (238)
                      +|..||++|++|+.|+++. |-+|++-.-
T Consensus        19 vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen   19 VGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             HHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             ceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            7999999999999999999 999988553

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

Probab=92.51  E-value=0.31  Score=39.95  Aligned_cols=59  Identities=19%  Similarity=0.339  Sum_probs=49.1

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHH-HHHHHHHHHHhhCC
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLL-GLERARYRVRELTP   70 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~-~v~~A~~~I~~~~~   70 (238)
                      +.||+..+..+||++|+.++.|.++|+|.|-+-.         ...|-|.|..+ ....|...|+.+..
T Consensus       150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---------NG~IWV~~~~~~~e~~~~~aI~~ie~  209 (239)
T COG1097         150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---------NGRIWVDGENESLEELAIEAIRKIER  209 (239)
T ss_pred             EEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---------CCEEEecCCCcchHHHHHHHHHHHhh
Confidence            6799999999999999999999999999999965         25888888776 46667777776644

>PRK01064 hypothetical protein; Provisional

Probab=92.48  E-value=0.26  Score=33.35  Aligned_cols=33  Identities=12%  Similarity=0.171  Sum_probs=27.9

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCC
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGA  179 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga  179 (238)
                      .+..++.+.+.-.|.+|||+|.+|+.|+.-.++
T Consensus        29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~   61 (78)
T PRK01064         29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVS   61 (78)
T ss_pred             EEEEEEEECcccceEEECCCCccHHHHHHHHHH
Confidence            345788899999999999999999999986443

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=92.43  E-value=0.035  Score=36.95  Aligned_cols=28  Identities=18%  Similarity=0.326  Sum_probs=24.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETG   29 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~   29 (238)
                      .+.+..+..|.+|||+|.+++.||--.+
T Consensus        32 ~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   32 VVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             EEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             EEEECCCccceEECCCCeeHHHHHHHHH
Confidence            4678888999999999999999997554

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=91.78  E-value=0.2  Score=38.00  Aligned_cols=34  Identities=15%  Similarity=0.207  Sum_probs=30.2

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF  183 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~  183 (238)
                      ..+.+|++..+..||++|++++..++-+|-++.+
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            6788888999999999999999999999888754

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.

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

Probab=91.33  E-value=0.11  Score=46.66  Aligned_cols=37  Identities=22%  Similarity=0.388  Sum_probs=33.4

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN   38 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~   38 (238)
                      -+.+|.+.++.+|||+|.+|++|++..|.+|.+....
T Consensus       489 vv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         489 VVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             EEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            3678999999999999999999999999999996644

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=91.30  E-value=0.19  Score=33.78  Aligned_cols=33  Identities=18%  Similarity=0.255  Sum_probs=26.9

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEe
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHF   34 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i   34 (238)
                      .+.+..+..|.+|||+|.++..||--++.-++-
T Consensus        27 ~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          27 EVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            466778889999999999999999877655443

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.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=90.92  E-value=1.2  Score=40.55  Aligned_cols=36  Identities=19%  Similarity=0.388  Sum_probs=33.0

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      ..+.||...|..|||.||..|++++.+.++.|.|..
T Consensus       451 ~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n  486 (657)
T COG5166         451 IAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKN  486 (657)
T ss_pred             eEEEeecccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence            678999999999999999999999999999987643

>PRK13764 ATPase; Provisional

Probab=90.81  E-value=0.14  Score=47.92  Aligned_cols=37  Identities=27%  Similarity=0.451  Sum_probs=33.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN   38 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~   38 (238)
                      .+.||.+.++.+|||+|.+|.+|+++.|.+|++....
T Consensus       484 ~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~  520 (602)
T PRK13764        484 VVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD  520 (602)
T ss_pred             EEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence            4679999999999999999999999999999996644

>KOG3273|consensus

Probab=90.62  E-value=0.18  Score=40.09  Aligned_cols=50  Identities=26%  Similarity=0.369  Sum_probs=45.4

Q ss_pred             ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278          9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL   68 (238)
Q Consensus         9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~   68 (238)
                      .+|.|+||+|.+--.|++-|.++|.+.+          ..|-|-|..+++..|+..+..+
T Consensus       179 AIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niriAR~avcsL  228 (252)
T KOG3273|consen  179 AIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSL  228 (252)
T ss_pred             HHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHHHHHhhHhh
Confidence            4689999999999999999999999965          5899999999999999999765

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=90.40  E-value=0.35  Score=36.64  Aligned_cols=36  Identities=17%  Similarity=0.280  Sum_probs=31.2

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      .-+-+++..+|..||++|++|+.|++..|-+|.+-.
T Consensus        34 vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve   69 (140)
T PRK08406         34 IIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE   69 (140)
T ss_pred             EEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence            566778889999999999999999999998886544

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

Probab=90.36  E-value=0.77  Score=37.69  Aligned_cols=47  Identities=21%  Similarity=0.420  Sum_probs=39.6

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHH
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID  206 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~  206 (238)
                      .-+.|++..+..+||++|+.++-+.++++|.|.+-..          ..|-+.|..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N----------G~IWV~~~~~  194 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN----------GRIWVDGENE  194 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC----------CEEEecCCCc
Confidence            5688999999999999999999999999999998653          3566666655

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=90.08  E-value=0.1  Score=35.12  Aligned_cols=31  Identities=26%  Similarity=0.401  Sum_probs=25.4

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEE
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVH   33 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~   33 (238)
                      +.+-.++-+.+||++|++|++|.++.+-.+.
T Consensus        29 i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   29 IVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             EEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             EEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            5567778899999999999999987765553

; 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 ....

>KOG4369|consensus

Probab=88.70  E-value=0.18  Score=49.91  Aligned_cols=67  Identities=15%  Similarity=0.013  Sum_probs=53.6

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ..+.+|-+...++||++|++|+.++.-|||.|.+.+-...+-   .++.+.+.|.++.+..|...|--.+
T Consensus      1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nq---aers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQ---AERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred             cccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccc---hhhhcccCCCChhhhhhhcccccee
Confidence            456777788899999999999999999999999876332221   3789999999999998886665444

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=88.60  E-value=0.47  Score=36.93  Aligned_cols=34  Identities=26%  Similarity=0.317  Sum_probs=29.0

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEEecCC
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDS   37 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~   37 (238)
                      +.|-... |.-|||+|.+++++++..|-+|.+-..
T Consensus        65 fvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         65 LLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             EEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            4455666 999999999999999999999988653

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

Probab=88.59  E-value=0.23  Score=33.91  Aligned_cols=35  Identities=17%  Similarity=0.402  Sum_probs=28.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD   36 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~   36 (238)
                      ++.|-...-|.+||++|++|++|+++..-...++.
T Consensus        33 ~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~   67 (81)
T cd02413          33 EIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE   67 (81)
T ss_pred             EEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence            46677777899999999999999998876666643

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.

>KOG3273|consensus

Probab=88.50  E-value=0.28  Score=38.98  Aligned_cols=56  Identities=16%  Similarity=0.211  Sum_probs=48.8

Q ss_pred             eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCc
Q psy11278        158 HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRR  224 (238)
Q Consensus       158 ~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p  224 (238)
                      .+|.|.|++|.+---|++.|-++|.+.+           ..|.|-|..+++..|+..+..++-+.-|
T Consensus       179 AIGRiaGk~GkTkfaIEn~trtrIVlad-----------~kIHiLG~~~niriAR~avcsLIlGspp  234 (252)
T KOG3273|consen  179 AIGRIAGKGGKTKFAIENVTRTRIVLAD-----------SKIHILGAFQNIRIARDAVCSLILGSPP  234 (252)
T ss_pred             HHHHhhcCCCcceeeeeccceeEEEecC-----------ceEEEeecchhhHHHHHhhHhhhccCCc
Confidence            4578999999999999999999999864           5799999999999999999998855443

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

Probab=88.49  E-value=0.8  Score=34.66  Aligned_cols=87  Identities=13%  Similarity=0.174  Sum_probs=53.8

Q ss_pred             CCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhcccccc--ceEEEEEEeCCCeeeEEe
Q psy11278         86 ANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQ--TSVIMMMEISPQHHPIME  163 (238)
Q Consensus        86 ~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~--~~~~~~v~i~~~~~~~iI  163 (238)
                      .++..+++|.++.--+|.+.+.|.       +.-+   -+.|.+.|.+++-.-+ ...+-  ...+-+|.|-...-|.+|
T Consensus        23 ~~~dli~~lAk~lrKRIvvR~dps-------~l~~---~e~A~~~I~~ivP~ea-~i~di~Fd~~tGEV~IeaeKPG~Vi   91 (145)
T cd02410          23 EDGDLVKDLAKDLRKRIVIRPDPS-------VLKP---PEEAIKIILEIVPEEA-GITDIYFDDDTGEVIIEAEKPGLVI   91 (145)
T ss_pred             cccHHHHHHHHHHhceEEEcCChh-------hcCC---HHHHHHHHHHhCCCcc-CceeeEecCCCcEEEEEEcCCeEEE
Confidence            356778888888776777654331       1112   2345545555442111 11110  011256777777889999


Q ss_pred             cCCCchHHHHHHHhCCeEEc
Q psy11278        164 GPNAINLKTIMAQTGAQIVF  183 (238)
Q Consensus       164 G~~G~~I~~I~~~tga~I~~  183 (238)
                      |++|..+++|..+||-+-.+
T Consensus        92 Gk~g~~~reI~~~tgW~p~v  111 (145)
T cd02410          92 GKGGSTLREITRETGWAPKV  111 (145)
T ss_pred             ecCchhHHHHHHHhCCeeEE
Confidence            99999999999999998655

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.

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

Probab=88.22  E-value=0.27  Score=32.39  Aligned_cols=37  Identities=16%  Similarity=0.186  Sum_probs=26.0

Q ss_pred             EEEeCCCe-----eeEEecCCCchHHHHHHHh-CCeEEccCCC
Q psy11278        151 MMEISPQH-----HPIMEGPNAINLKTIMAQT-GAQIVFPEAN  187 (238)
Q Consensus       151 ~v~i~~~~-----~~~iIG~~G~~I~~I~~~t-ga~I~~p~~~  187 (238)
                      .+.+.+..     +|..||++|.+|+.|+++. |-+|.+-..+
T Consensus         6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s   48 (69)
T PF13184_consen    6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS   48 (69)
T ss_dssp             EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred             EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence            44444444     7899999999999999999 8888765443

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=87.92  E-value=0.39  Score=42.22  Aligned_cols=37  Identities=19%  Similarity=0.344  Sum_probs=33.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN   38 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~   38 (238)
                      .+.||.++.+..|||+|.|++--.+-||.+|+|..-.
T Consensus       311 ~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        311 IVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             EEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            4679999999999999999999999999999996643

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

Probab=86.81  E-value=1.3  Score=28.20  Aligned_cols=32  Identities=6%  Similarity=0.228  Sum_probs=25.6

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeE
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQI  181 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I  181 (238)
                      ..+.+.....+.+||++|.+++.++..++-.+
T Consensus        27 ~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          27 IIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            44455544579999999999999999988765

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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=85.93  E-value=1.1  Score=30.12  Aligned_cols=34  Identities=12%  Similarity=0.111  Sum_probs=28.7

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF  183 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~  183 (238)
                      ..+.+.....+.+||++|++++.|+--++..++-
T Consensus        26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            5677778888999999999999999888776554

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=85.68  E-value=0.23  Score=32.98  Aligned_cols=32  Identities=13%  Similarity=0.191  Sum_probs=27.9

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeE
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQI  181 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I  181 (238)
                      ..+.+.....|.+|||+|.+++.|+.-.+..+
T Consensus        31 i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   31 IVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             EEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            67888899999999999999999998776654

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=85.68  E-value=0.85  Score=34.55  Aligned_cols=36  Identities=17%  Similarity=0.194  Sum_probs=30.9

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      .-+.+.+..+|..||++|++|+.+++..|-+|.+-.
T Consensus        35 iifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe   70 (141)
T TIGR01952        35 VVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE   70 (141)
T ss_pred             EEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence            567788889999999999999999988998876543

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=85.58  E-value=0.6  Score=42.57  Aligned_cols=36  Identities=19%  Similarity=0.278  Sum_probs=33.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDS   37 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~   37 (238)
                      .+.||.++.+.-|||+|.|++-..+-||.+|+|-..
T Consensus       305 ~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        305 DVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            477999999999999999999999999999999663

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

Probab=85.08  E-value=0.52  Score=42.45  Aligned_cols=37  Identities=16%  Similarity=0.247  Sum_probs=33.8

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEA  186 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~  186 (238)
                      +-+.+|..+.+.+|||+|.+|++|+++.|-.|.+-..
T Consensus       488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            6788999999999999999999999999999988543

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

Probab=83.93  E-value=0.75  Score=31.32  Aligned_cols=36  Identities=14%  Similarity=0.251  Sum_probs=29.7

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      .++.|-...-+.+||++|+.|++|++.-.....+++
T Consensus        32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~   67 (81)
T cd02413          32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE   67 (81)
T ss_pred             EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence            667777777799999999999999998777766644

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.

>PRK13764 ATPase; Provisional

Probab=83.51  E-value=0.78  Score=43.12  Aligned_cols=36  Identities=17%  Similarity=0.246  Sum_probs=33.5

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      +-+.+|..+.+.+|||+|.+|++|.++.|..|.+-.
T Consensus       483 ~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~  518 (602)
T PRK13764        483 AVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP  518 (602)
T ss_pred             EEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence            778999999999999999999999999999998743

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=82.91  E-value=0.31  Score=32.72  Aligned_cols=33  Identities=18%  Similarity=0.314  Sum_probs=27.9

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEE
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIV  182 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~  182 (238)
                      ..+.+...+-+.+||++|++|++|....+-.+.
T Consensus        27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   27 IIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             EEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            566777788899999999999999998877664

; 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 ....

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

Probab=82.49  E-value=10  Score=34.91  Aligned_cols=115  Identities=17%  Similarity=0.250  Sum_probs=65.6

Q ss_pred             HHHHHHHHHHhhCCc-e----EEEeecCcCC------CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchH
Q psy11278         57 GLERARYRVRELTPL-I----FCFEYPLMGS------TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVE  125 (238)
Q Consensus        57 ~v~~A~~~I~~~~~~-~----~~~~~p~~~~------~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~  125 (238)
                      ..+.-++.|.+++|. .    ..|+=|.+..      .....|..++++.++.--+|.+.+.|..       .-+   -+
T Consensus         6 ~l~ei~~~i~~~~p~~~~It~vefEGPelvvY~k~P~~~~~~~dlik~lAk~lrKRI~iR~dPsv-------l~~---~e   75 (637)
T COG1782           6 VLEEIRNKINEILPSDVKITDVEFEGPELVVYTKNPELFAKDGDLIKDLAKDLRKRIIIRPDPSV-------LKP---PE   75 (637)
T ss_pred             HHHHHHHHHHHhCCCcCceEEEEecCCeEEEEecCHHHhccchhHHHHHHHHHhhceEeccCchh-------cCC---HH
Confidence            344556677777774 2    2222243211      1224678899999888777777654421       111   23


Q ss_pred             HHHHHHHHHHHHhhcccccc--ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEE
Q psy11278        126 RVKEATTKLIEHMCGSLANQ--TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIV  182 (238)
Q Consensus       126 ~a~~ai~~~~~~~~~~~~~~--~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~  182 (238)
                      .|++-|.+++...++ ..+-  ...+-+|.|-++.=|.+||++|++.++|..+||-.-.
T Consensus        76 ~A~~~I~eivP~ea~-i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~  133 (637)
T COG1782          76 EARKIILEIVPEEAG-ITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPK  133 (637)
T ss_pred             HHHHHHHHhCccccC-ceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcce
Confidence            344333433321111 1000  0012567777777899999999999999999998643

>TIGR01953 NusA transcription termination factor NusA

Probab=82.42  E-value=1.3  Score=38.60  Aligned_cols=36  Identities=14%  Similarity=0.135  Sum_probs=33.5

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      +.+.+|....+.-||++|.+++-.++-||.+|.+-.
T Consensus       303 ~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       303 AEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            789999999999999999999999999999998754

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.

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=81.87  E-value=1.2  Score=35.55  Aligned_cols=88  Identities=13%  Similarity=0.144  Sum_probs=55.4

Q ss_pred             CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHH--HHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         83 TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATT--KLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        83 ~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~--~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                      ..|++|.+++.++++.|-+|.+-.-          +-++  ..-++.++.  .++.-...+. + .. .+.+.+|++..+
T Consensus        90 ~iG~~G~rvk~i~~eLgekIdVVe~----------s~d~--~~fI~nal~Pa~v~~V~~~~~-d-~~-~~~v~V~~~~~~  154 (190)
T COG0195          90 CIGKRGSRVKAVSEELGEKIDVVEW----------SEDP--AEFIKNALAPAEVLSVNIKED-D-GH-VAIVVVPPDQLS  154 (190)
T ss_pred             hccCCChHHHHHHHHhCCceEEEEe----------CCCH--HHHHHHhcCcceEeEEEEEeC-C-Cc-EEEEEECHHHHh
Confidence            5688999999999999865554321          0000  111111111  0000000000 0 11 377889999999


Q ss_pred             EEecCCCchHHHHHHHhCCeEEccC
Q psy11278        161 IMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      ..||++|.+++-.++-||-++.+-.
T Consensus       155 ~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         155 LAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             hccCcccHHHHHHHHHhCCEEEEEe
Confidence            9999999999999999999998754

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=81.31  E-value=1.4  Score=38.76  Aligned_cols=38  Identities=21%  Similarity=0.307  Sum_probs=34.2

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN  187 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~  187 (238)
                      +.+.+|....+.-||++|++++-.++-||.+|.+-.-.
T Consensus       310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            78899999999999999999999999999999875433

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=80.63  E-value=1.2  Score=39.92  Aligned_cols=35  Identities=23%  Similarity=0.321  Sum_probs=32.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD   36 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~   36 (238)
                      .+.||.++.+.-|||+|.|++--..-||.+|+|.+
T Consensus       338 ~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        338 HVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            46799999999999999999999999999999965

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=80.49  E-value=1.5  Score=35.00  Aligned_cols=83  Identities=16%  Similarity=0.189  Sum_probs=51.6

Q ss_pred             ecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc-------------
Q psy11278          5 VSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL-------------   71 (238)
Q Consensus         5 ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~-------------   71 (238)
                      +-.+.+|..||++|++++.|.++.|=+|++-.-++              ++  .+-.++.+.   |.             
T Consensus        82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------d~--~~fI~nal~---Pa~v~~V~~~~~d~~  142 (190)
T COG0195          82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------DP--AEFIKNALA---PAEVLSVNIKEDDGH  142 (190)
T ss_pred             cCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------CH--HHHHHHhcC---cceEeEEEEEeCCCc
Confidence            33456799999999999999999997777744221              11  111122221   21             


Q ss_pred             eEEEeecC--cCCCCCCCChHHHHHHHHhCceEEeeC
Q psy11278         72 IFCFEYPL--MGSTPNANSPFVQIIQEAYNVQVMFRN  106 (238)
Q Consensus        72 ~~~~~~p~--~~~~~~~~g~~i~~i~~~~gv~I~~~~  106 (238)
                      .....+|.  .+..+|++|.+++-..+-+|-++.+..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            11122332  233578899999988888887777654

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

Probab=80.43  E-value=1.3  Score=31.92  Aligned_cols=30  Identities=23%  Similarity=0.315  Sum_probs=24.4

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCE
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCH   31 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~   31 (238)
                      ++.|-...-|.|||++|++|++|++.....
T Consensus        64 ~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~   93 (109)
T cd02412          64 EVTIHTARPGIIIGKKGAGIEKLRKELQKL   93 (109)
T ss_pred             EEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence            466777778999999999999999876543

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.

>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein

Probab=80.20  E-value=1.6  Score=29.85  Aligned_cols=27  Identities=26%  Similarity=0.490  Sum_probs=21.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHc
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEET   28 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t   28 (238)
                      ++.|-...-|.+||++|.+|++|++..
T Consensus        41 ~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          41 QITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             EEEEEECCCCceECCCchhHHHHHHHH
Confidence            355666677999999999999988765

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	238
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	8e-56
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	5e-16
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	3e-07
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	3e-04
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	9e-18
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	8e-08
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	6e-16
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-08
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	9e-16
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-15
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	9e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-15
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-07
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	4e-14
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	8e-11
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-09
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-07
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-06
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	9e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	7e-06
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-08
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-08
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	9e-06
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	5e-08
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-08
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-06
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-07
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-06
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-06
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	2e-06
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-06
1we8_A	104	Tudor and KH domain containing protein; structural	3e-06
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-06
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	4e-05
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-05
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	9e-05
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-04
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-04

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score =  181 bits (460), Expect = 8e-56
 Identities = 45/225 (20%), Positives = 86/225 (38%), Gaps = 11/225 (4%)

Query: 1   MKLDVSYTDHSHIIGRGGLT--IKKVMEETGCHVHFPDSNRSVNAEK--SNQVSIAGSLL 56
           + ++     +S +    G    +  +M ET   +  PD +         + QV+I G   
Sbjct: 32  LNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFG 91

Query: 57  GLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPK---LQPT 113
            ++RAR  +R             M   P              NV++ F + P+   +  T
Sbjct: 92  DVDRARMLMRRNCHFTVFMALSKM-KMPLHELQAHVRQNPIQNVEMSFVDAPEKNGIVTT 150

Query: 114 LVMVKGCEKDVERVKEATTKLIEHMCG-SLANQTSVIMMMEISPQHHPIMEGPNAIN--L 170
            + +   EK+   + EA  +L E +   S A + +  +   +S  +   + G ++    +
Sbjct: 151 YLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLSTYYVDQVLGSSSTAQLM 210

Query: 171 KTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
             I  +T   I +P  N+          + V GNID+V  AR+ +
Sbjct: 211 PVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYI 255

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 75.4 bits (184), Expect = 5e-16
 Identities = 23/175 (13%), Positives = 61/175 (34%), Gaps = 17/175 (9%)

Query: 1   MKLDVSYTDHSHIIGR--GGLTIKKVMEETGCHVHFPDSN-RSVNAEKSNQVSIAGSLLG 57
           +   +S      ++G       +  +  ET   + +P  N R+       ++ + G++  
Sbjct: 188 LHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDN 247

Query: 58  LERARYRVRELTPLIFCFEYP--LMGSTPNANSPFVQIIQEAYNVQVMFRNRPK------ 109
           + +AR  + +L P+  CF      M      +   + +I +   + +             
Sbjct: 248 VLKARRYIMDLLPISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLL 307

Query: 110 ---LQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPI 161
              +      ++  E +++++  A  K++      +A         + S  HH +
Sbjct: 308 SGEVPLNCASLRSKEFNIKKLYTAYQKVLSKKFDFIA---PQPNDYDNSIWHHSL 359

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 49.6 bits (117), Expect = 3e-07
 Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 3/95 (3%)

Query: 124 VERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPN--AINLKTIMAQTGAQI 181
           + ++K     L  ++     N T V + ME   Q++ +M   N    N+ +IMA+T   I
Sbjct: 6   IHQLKAQGLPLPSNIPMIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLI 65

Query: 182 VFPEANDPIIPVLKKSS-VTVSGNIDSVYLARQML 215
             P+ +         +  VT++G    V  AR ++
Sbjct: 66  QLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLM 100

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 40.3 bits (93), Expect = 3e-04
 Identities = 19/144 (13%), Positives = 48/144 (33%), Gaps = 23/144 (15%)

Query: 85  NANSPFVQIIQEAYNVQVMF-----RNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMC 139
           ++ +  + +I+      + +     RN  +     + V G   +V + +     L+    
Sbjct: 204 SSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL---- 259

Query: 140 GSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFP----EANDPIIPVLK 195
                   + M   I           +  N+  I+ ++G  +       E  D +   + 
Sbjct: 260 -------PISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVP 312

Query: 196 KSSVTVSG---NIDSVYLARQMLV 216
            +  ++     NI  +Y A Q ++
Sbjct: 313 LNCASLRSKEFNIKKLYTAYQKVL 336

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 73.9 bits (182), Expect = 9e-18
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 5/67 (7%)

Query: 2  KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
          ++++ +  H H+IG+ G  I ++ ++    V  P  +     EKSN + I G   G+++A
Sbjct: 8  EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQA 62

Query: 62 RYRVREL 68
          +  + EL
Sbjct: 63 KRELLEL 69

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 47.3 bits (113), Expect = 8e-08
 Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 6/64 (9%)

Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
           + I  + H  + G +  N+  I  Q    +  P  ++      K + + + G+   V  A
Sbjct: 9   INIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE------KSNLIRIEGDPQGVQQA 62

Query: 212 RQML 215
           ++ L
Sbjct: 63  KREL 66

>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 = 69.8 bits (171), Expect = 6e-16
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 4/69 (5%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
            + + +  H+ IIG  G  I+K+M+E    + FP S     A   N V++ G    +E 
Sbjct: 19 EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS----GAPDPNCVTVTGLPENVEE 74

Query: 61 ARYRVRELT 69
          A   +  L 
Sbjct: 75 AIDHILNLE 83

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 50.2 bits (120), Expect = 1e-08
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 7/81 (8%)

Query: 135 IEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVL 194
              + G L    S  +   +  + H  + G     ++ IM +    I FP++  P     
Sbjct: 6   SGRIVGELEQMVSEDV--PLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP----- 58

Query: 195 KKSSVTVSGNIDSVYLARQML 215
             + VTV+G  ++V  A   +
Sbjct: 59  DPNCVTVTGLPENVEEAIDHI 79

>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 = 69.5 bits (170), Expect = 9e-16
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          + + V    H  IIGR G  I ++  E   ++ FPD +     +  +Q++I G     E 
Sbjct: 19 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG--NQPQDQITITGYEKNTEA 76

Query: 61 ARYRVREL 68
          AR  +  +
Sbjct: 77 ARDAILRI 84

>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 = 46.7 bits (111), Expect = 3e-07
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
           S  + + + P++HP + G     +  I  +    I FP+ +D       +  +T++G   
Sbjct: 16  SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD---GNQPQDQITITGYEK 72

Query: 207 SVYLARQML 215
           +   AR  +
Sbjct: 73  NTEAARDAI 81

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 69.1 bits (169), Expect = 1e-15
 Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          ++++V +  H ++IG+ G  I+K+M+E   ++H P         +S+ ++I G    L+R
Sbjct: 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDR 73

Query: 61 ARYRVREL 68
          A+  + E 
Sbjct: 74 AKAGLLER 81

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 45.2 bits (107), Expect = 9e-07
 Identities = 11/74 (14%), Positives = 26/74 (35%), Gaps = 6/74 (8%)

Query: 142 LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTV 201
           L     V + +E+    H  + G     ++ +M +    I  P          +   + +
Sbjct: 11  LEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL------QSDIIAI 64

Query: 202 SGNIDSVYLARQML 215
           +G   ++  A+  L
Sbjct: 65  TGLAANLDRAKAGL 78

>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 = 67.4 bits (165), Expect = 4e-15
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
            + +    H  +IG+ G  ++ +  +T   +  P  +     + SNQ+ I G+  G+E+
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEK 73

Query: 61 ARYRVRELTP 70
          AR+ V  ++ 
Sbjct: 74 ARHEVLLISA 83

>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 = 47.4 bits (113), Expect = 1e-07
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN 204
           QT     + I  +HH  + G N   L+ +  +T  +I  P  +DP       + + ++G 
Sbjct: 14  QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------SNQIKITGT 67

Query: 205 IDSVYLARQML 215
            + +  AR  +
Sbjct: 68  KEGIEKARHEV 78

>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 = 65.2 bits (159), Expect = 4e-14
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLE 59
          +++ +    H+ +IG  G  I+ +MEE  G H+HFP          S+ V I G    +E
Sbjct: 19 VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSDVE 73

Query: 60 RARYRVREL 68
          +A+ ++  L
Sbjct: 74 KAKKQLLHL 82

>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 = 39.0 bits (91), Expect = 1e-04
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 9/75 (12%)

Query: 142 LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQ-TGAQIVFPEANDPIIPVLKKSSVT 200
           LAN   V +   I  + H  + G     +++IM +  G  I FP             +V 
Sbjct: 13  LANIAEVEV--SIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS------GSDTVV 64

Query: 201 VSGNIDSVYLARQML 215
           + G    V  A++ L
Sbjct: 65  IRGPSSDVEKAKKQL 79

>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 = 56.4 bits (136), Expect = 8e-11
 Identities = 10/70 (14%), Positives = 28/70 (40%), Gaps = 9/70 (12%)

Query: 2  KLDVSYTDHSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +      H  IIG+ G  + K+ ++    H+ F +          +++++ G    +  
Sbjct: 30 SVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------EDKITLEGPTEDVSV 81

Query: 61 ARYRVRELTP 70
          A+ ++  +  
Sbjct: 82 AQEQIEGMVK 91

>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 = 52.1 bits (125), Expect = 8e-09
 Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 2/68 (2%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          +++ +       IIG+ G  IK++       +         +  +   V I G      +
Sbjct: 5  VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRM--VIITGPPEAQFK 62

Query: 61 ARYRVREL 68
          A+ R+   
Sbjct: 63 AQGRIYGK 70

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
             + V  +    +IG+GG T+ ++   T   V  P        ++   V I G     + 
Sbjct: 87  THIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQV-IVKIIGHFYASQM 145

Query: 61  ARYRVREL 68
           A+ ++R++
Sbjct: 146 AQRKIRDI 153

>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 = 46.3 bits (110), Expect = 1e-06
 Identities = 16/141 (11%), Positives = 53/141 (37%), Gaps = 7/141 (4%)

Query: 90  FVQIIQEAYN--VQVMFRNRPKLQPTLVMVKGCEKDVERVKEA-TTKLIEHMCGSLANQT 146
            ++ +    +  +++     P  +  +V++ G  +   + +     KL E        + 
Sbjct: 24  HIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPKEEV 83

Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
            +   + +       + G     +  +   T A++V P    P      +  V + G+  
Sbjct: 84  KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTP--DENDQVIVKIIGHFY 141

Query: 207 SVYLARQML--VVSSVRPRRR 225
           +  +A++ +  +++ V+ + +
Sbjct: 142 ASQMAQRKIRDILAQVKQQHQ 162

>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 = 51.3 bits (123), Expect = 2e-08
 Identities = 23/156 (14%), Positives = 48/156 (30%), Gaps = 22/156 (14%)

Query: 2   KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
           ++ +       +IG+GG TIK++ E  G  +       S N      + I G    +++A
Sbjct: 5   EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-SQNTNVDKPLRIIGDPYKVQQA 63

Query: 62  RYRVRELTPLIFCFEYPLMGSTPNANSPFVQI--------------------IQEAYNVQ 101
              V ++        +       +     + +                    IQ    V+
Sbjct: 64  CEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVR 123

Query: 102 VMFRNRPKLQPT-LVMVKGCEKDVERVKEATTKLIE 136
           + F+      P  +  + G     E        L++
Sbjct: 124 IQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQ 159

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 49.4 bits (118), Expect = 9e-08
 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           + + V       +IGR G  IKK+  + G  + F   + +   EK     I G     E 
Sbjct: 93  IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT-GPEKI--AHIMGPPDRCEH 149

Query: 61  ARYRVREL 68
           A   + +L
Sbjct: 150 AARIINDL 157

>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 = 44.0 bits (104), Expect = 7e-06
 Identities = 15/132 (11%), Positives = 42/132 (31%), Gaps = 14/132 (10%)

Query: 94  IQEAYNVQVMFRNRPKLQPT---LVMVKGCEKDVERVKEATTKLIEHMC-------GSLA 143
           +QE   V+++              + + G    V++  E    ++               
Sbjct: 27  LQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGFGDRNEYG 86

Query: 144 NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG 203
           ++    + + +      ++ G +   +K I    G +I F + +        +    + G
Sbjct: 87  SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT----GPEKIAHIMG 142

Query: 204 NIDSVYLARQML 215
             D    A +++
Sbjct: 143 PPDRCEHAARII 154

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFP-DSNRSVNAEKSNQVSIAGSLLGLE 59
           ++ +       +IG+GG TIK++ E  G  +    D +++ N +K   + I G    ++
Sbjct: 16 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDK--PLRIIGDPYKVQ 73

Query: 60 RARYRVREL 68
          +A   V ++
Sbjct: 74 QACEMVMDI 82

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 49.5 bits (118), Expect = 3e-08
 Identities = 15/68 (22%), Positives = 25/68 (36%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          M   +       +IGRGG  +K + ++TG  V                  I GS   ++ 
Sbjct: 9  MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDH 68

Query: 61 ARYRVREL 68
          A+  + E 
Sbjct: 69 AKQLIEEK 76

>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 = 51.0 bits (122), Expect = 3e-08
 Identities = 41/218 (18%), Positives = 67/218 (30%), Gaps = 57/218 (26%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +K+ +       IIG+GG TI ++ +ETG  +    S             I G++  L  
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67

Query: 61  ARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGC 120
               + E                          I+E             LQP        
Sbjct: 68  VHGFIAE-------------------------KIREMPQNVAKTEPVSILQP-------- 94

Query: 121 EKDVERVKEATTKLI--EHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTG 178
           +  V   +    K+I      G       +I              G     +K IM Q+G
Sbjct: 95  QTTVNPDRANQVKIIVPNSTAG------LII--------------GKGGATVKAIMEQSG 134

Query: 179 AQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
           A +    +  P    L+   VTVSG  +    A ++++
Sbjct: 135 AWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELII 170

>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 = 43.7 bits (103), Expect = 9e-06
 Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +K+ V  +    IIG+GG T+K +ME++G  V        +N +    V+++G      +
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQN-RVVTVSGEPEQNRK 164

Query: 61  ARYRVREL 68
           A   + + 
Sbjct: 165 AVELIIQK 172

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 48.6 bits (116), Expect = 5e-08
 Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 3/68 (4%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          + + V       +IGR G  IKK+  + G  + F   +     EK     I G     E 
Sbjct: 13 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQF-KQDDGTGPEK--IAHIMGPPDRCEH 69

Query: 61 ARYRVREL 68
          A   + +L
Sbjct: 70 AARIINDL 77

>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 = 50.2 bits (120), Expect = 5e-08
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           ++L V  +    +IG+GG  IK++ E TG  V         + E+   ++IAG    +  
Sbjct: 91  LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTER--AITIAGIPQSIIE 148

Query: 61  ARYRVREL 68
              ++  +
Sbjct: 149 CVKQICVV 156

>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 = 45.5 bits (108), Expect = 2e-06
 Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          ++L +   +   IIG+ G ++KK+ EE+G  ++  + N     E+   +++AG    + +
Sbjct: 7  IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---CPER--IITLAGPTNAIFK 61

Query: 61 ARYRVREL 68
          A   + + 
Sbjct: 62 AFAMIIDK 69

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 47.4 bits (113), Expect = 1e-07
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           ++ +  +    +IG+GG TIK++ E  G  +                + I G    +++
Sbjct: 17 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA-DKPLRITGDPYKVQQ 75

Query: 61 ARYRVREL 68
          A+  V EL
Sbjct: 76 AKEMVLEL 83

>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 = 46.4 bits (110), Expect = 1e-06
 Identities = 15/67 (22%), Positives = 27/67 (40%)

Query: 1   MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
               V       IIG+GG TIK + +++G  +    +            +I G+   ++ 
Sbjct: 106 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDY 165

Query: 61  ARYRVRE 67
           AR  + E
Sbjct: 166 ARQLIEE 172

>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 = 46.0 bits (109), Expect = 1e-06
 Identities = 30/203 (14%), Positives = 57/203 (28%), Gaps = 49/203 (24%)

Query: 13  IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI 72
           +IGR G  IKK+  + G  + F   + +   E+     I G     + A   + +L    
Sbjct: 17  VIGRNGEMIKKIQNDAGVRIQFKPDDGTTP-ERI--AQITGPPDRAQHAAEIITDL---- 69

Query: 73  FCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATT 132
                             ++ +Q           R + +                     
Sbjct: 70  ------------------LRSVQAGNPGGPGPGGRGRGRG-------------------- 91

Query: 133 KLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIP 192
              +                 +      ++ G     +K+I  Q+GA+I       P   
Sbjct: 92  ---QGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNAD 148

Query: 193 VLKKSSVTVSGNIDSVYLARQML 215
              K   T+ G    +  ARQ++
Sbjct: 149 PNMK-LFTIRGTPQQIDYARQLI 170

>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 = 43.8 bits (104), Expect = 1e-06
 Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          ++L +   +   IIG+ G ++KK+ EE+G  ++  + N     E+   +++AG    + +
Sbjct: 7  IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---CPER--IITLAGPTNAIFK 61

Query: 61 ARYRVREL 68
          A   + + 
Sbjct: 62 AFAMIIDK 69

>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 = 43.8 bits (103), Expect = 2e-06
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 6/68 (8%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          +++ V Y     ++G  G TIK++ + T  ++  P        +K    ++ G    ++R
Sbjct: 12 IQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR------DKEPVFAVTGMPENVDR 65

Query: 61 ARYRVREL 68
          AR  +   
Sbjct: 66 AREEIEAH 73

>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 = 43.4 bits (103), Expect = 2e-06
 Identities = 14/56 (25%), Positives = 28/56 (50%)

Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
          I+G+GG T+ +  E TG  +        +   ++ +V+I GS    + A+Y + + 
Sbjct: 17 ILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQR 72

>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 = 44.0 bits (104), Expect = 3e-06
 Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
          IIGRGG TI+ + + +G  +     +          + I+G+   +  A++ + E 
Sbjct: 29 IIGRGGETIRSICKASGAKITCDKESEGTLLLSR-LIKISGTQKEVAAAKHLILEK 83

>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 = 43.5 bits (103), Expect = 3e-06
 Identities = 15/68 (22%), Positives = 32/68 (47%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          +++ V       I+G+GG T+ +  E TG  +        +   ++ +V+I GS    + 
Sbjct: 5  VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 61 ARYRVREL 68
          A+Y + + 
Sbjct: 65 AQYLISQR 72

>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 = 40.5 bits (95), Expect = 4e-05
 Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
          IIGRGG  I ++ +E+GC +     +            + G+   ++ A+  + ++
Sbjct: 29 IIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQI 81

>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 = 40.0 bits (94), Expect = 5e-05
 Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           ++ +       IIG+GG  IK++  E+G  +     +  +   +   ++I G+   ++ 
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQN 72

Query: 61 ARYRVREL 68
          A+Y ++  
Sbjct: 73 AQYLLQNS 80

>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 = 39.2 bits (92), Expect = 9e-05
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 12 HIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
           IIGR G  I ++ + +G  +   +     +  +   V+I GS   +  A+Y +   
Sbjct: 19 CIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQ---VTITGSAASISLAQYLINAR 72

>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 = 38.8 bits (91), Expect = 1e-04
 Identities = 13/56 (23%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
          IIG+GG  IK++  E+G  +     +  +   +   ++I G+   ++ A+Y ++  
Sbjct: 21 IIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNAQYLLQNS 73

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 36.5 bits (85), Expect = 6e-04
 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 3/57 (5%)

Query: 12 HIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
           IIGR G  I ++ + +G  +   +        +   V+I GS   +  A+Y +   
Sbjct: 18 CIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQ---VTITGSAASISLAQYLINVR 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	238
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	100.0
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.92
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.92
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.91
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.91
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.91
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.76
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.67
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.6
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.58
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.56
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.54
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.54
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.54
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.54
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.52
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.52
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.52
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.52
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.51
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.51
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.51
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.51
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.51
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.5
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.5
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.5
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.5
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.5
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.49
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.49
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.48
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.48
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.46
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.45
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.45
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.44
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.44
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.44
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.44
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.43
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.43
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.43
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.42
1we8_A	104	Tudor and KH domain containing protein; structural	99.42
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.42
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.41
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.41
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.4
1we8_A	104	Tudor and KH domain containing protein; structural	99.4
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.4
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.4
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.32
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.29
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.27
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.24
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.19
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.14
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.14
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.12
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.95
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.8
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.74
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.6
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.43
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.43
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.41
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.21
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.15
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.06
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.92
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.91
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.65
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.45
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.56
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.23
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.03
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.87
2cxc_A	144	NUSA; transcription termination, RNA binding prote	92.37
2cxc_A	144	NUSA; transcription termination, RNA binding prote	85.37
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	85.12

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=100.00  E-value=1.2e-43  Score=304.51  Aligned_cols=231  Identities=20%  Similarity=0.240  Sum_probs=187.5

Q ss_pred             CEEEecCCccceeeccCC--ccHHHHHHHcCCEEEecCCC--CCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEe
Q psy11278          1 MKLDVSYTDHSHIIGRGG--LTIKKVMEETGCHVHFPDSN--RSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFE   76 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G--~~I~~I~~~t~~~I~i~~~~--~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~   76 (238)
                      ++++||+.+|++||||+|  +||++||++|||+|+||+.+  ..++...++.|+|+|.+++|++|+.+|+++.|....|+
T Consensus        32 l~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~Pl~i~~e  111 (376)
T 3n89_A           32 LNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCHFTVFMA  111 (376)
T ss_dssp             EEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCEEEEEEE
T ss_pred             EEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCCceEEEE
Confidence            478999999999999999  99999999999999999987  33344567899999999999999999999999999999


Q ss_pred             ecCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCC---CcEEEEEccccchHHHHHHHHHHHHHhhcc-ccccceEEEEE
Q psy11278         77 YPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQ---PTLVMVKGCEKDVERVKEATTKLIEHMCGS-LANQTSVIMMM  152 (238)
Q Consensus        77 ~p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~---~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~-~~~~~~~~~~v  152 (238)
                      +|.........+.+|.+ ++.|||+|.|++.++..   ++.|+|+|++++++.|++|+..+++++.+. ..+..+++.++
T Consensus       112 lp~~~i~~~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e~~~~~~~s~~v  190 (376)
T 3n89_A          112 LSKMKMPLHELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHF  190 (376)
T ss_dssp             CTTCSSCHHHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--CCCSSCEEEEE
T ss_pred             ccccccCcchhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhhcccccceEEEE
Confidence            98754321111234444 45689999998765432   578999999999999999999999887665 33334678999


Q ss_pred             EeCCCeeeEEecCCC--chHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCceEEEEe
Q psy11278        153 EISPQHHPIMEGPNA--INLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLIT  230 (238)
Q Consensus       153 ~i~~~~~~~iIG~~G--~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p~~~~~~  230 (238)
                      .|++.+|.+|||++|  ..|++|+++|||+|.||+.++++....+...|+|+|++++|..|+++|+++|    |++|.||
T Consensus       191 ~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL----Pv~l~Fd  266 (376)
T 3n89_A          191 TLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL----PISMCFN  266 (376)
T ss_dssp             EEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS----EEEEEEE
T ss_pred             EeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC----CEEEEEe
Confidence            999999999999998  5569999999999999987664332335789999999999999999999999    9999999


Q ss_pred             ecCCcc
Q psy11278        231 IPNDII  236 (238)
Q Consensus       231 ~~~~~~  236 (238)
                      +++++.
T Consensus       267 ~~~~d~  272 (376)
T 3n89_A          267 IKNTDM  272 (376)
T ss_dssp             EEGGGB
T ss_pred             cCCccc
Confidence            999865

>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=99.92  E-value=3.4e-25  Score=172.05  Aligned_cols=151  Identities=17%  Similarity=0.191  Sum_probs=121.8

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLM   80 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~   80 (238)
                      ++|.||.+.+|.||||+|++|++|+++|||+|++++...  +...++.|+|+|+++++..|+.+|.+++.+         
T Consensus         5 ~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~--~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e---------   73 (163)
T 3krm_A            5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRMVIITGPPEAQFKAQGRIYGKLKE---------   73 (163)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSS--TTCSEEEEEEEECHHHHHHHHHHHHHHHHH---------
T ss_pred             EEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhc---------
Confidence            478999999999999999999999999999999987542  334568999999999999999999655221         


Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                                       .+    +. .|.                              ..    ..++.++.||..+++
T Consensus        74 -----------------~~----~~-~~~------------------------------~~----~~~~~~i~vp~~~~g   97 (163)
T 3krm_A           74 -----------------EN----FF-GPK------------------------------EE----VKLETHIRVPASAAG   97 (163)
T ss_dssp             -----------------TT----SS-CSS------------------------------CC----CCEEEEEEEETTTHH
T ss_pred             -----------------cc----cc-ccc------------------------------cC----CceEEEEEcChhhee
Confidence                             10    00 010                              01    124478999999999


Q ss_pred             EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      +|||++|++|++|+++|||+|.+++...++.  .+.+.|+|+|++++|..|+.+|.+++.
T Consensus        98 ~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~--~~~~~v~I~G~~~~v~~A~~~I~~~i~  155 (163)
T 3krm_A           98 RVIGKGGKTVNELQNLTAAEVVVPRDQTPDE--NDQVIVKIIGHFYASQMAQRKIRDILA  155 (163)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEECCTTCCCCT--TSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             eEEcCCChHHHHHHHHhCCeEEECCCCCCCC--CCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999987654432  134589999999999999999999883

>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=99.92  E-value=3.5e-25  Score=174.44  Aligned_cols=167  Identities=21%  Similarity=0.264  Sum_probs=123.6

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLM   80 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~   80 (238)
                      +++.||.+.+|.||||+|++|++|+++|||+|++++..+..+...++.|+|+|++++|.+|+.+|.+++...     |..
T Consensus         8 ~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~-----~~~   82 (178)
T 2anr_A            8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREM-----PQN   82 (178)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCC-----CCC
T ss_pred             EEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhcc-----CCc
Confidence            478999999999999999999999999999999987654334456789999999999999999998875432     100


Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                          ....                        ..+.+.++....                +...  ..+..+.||..+++
T Consensus        83 ----~~~~------------------------~~~~~~~~~~~~----------------~~~~--~~~~~i~Vp~~~vg  116 (178)
T 2anr_A           83 ----VAKT------------------------EPVSILQPQTTV----------------NPDR--ANQVKIIVPNSTAG  116 (178)
T ss_dssp             -------------------------------------------------------------CGG--GGEEEEEEEHHHHH
T ss_pred             ----cccC------------------------CcccccCCccCC----------------CCCC--ceEEEEEEchhhee
Confidence                0000                        000000100000                0001  12378999999999


Q ss_pred             EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      +|||++|++|++|+++|||+|.++...+.  ....++.|+|+|++++|.+|+.+|.+++.
T Consensus       117 ~iIGkgG~~Ik~i~~~tga~I~i~~~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~  174 (178)
T 2anr_A          117 LIIGKGGATVKAIMEQSGAWVQLSQKPDG--INLQNRVVTVSGEPEQNRKAVELIIQKIQ  174 (178)
T ss_dssp             HHHCGGGHHHHHHHHHSSCEEEECCCC------CCEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             eeECCCcHHHHHHHHHHCCEEEEeCCCCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999875421  11246899999999999999999999984

>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=99.91  E-value=2.1e-24  Score=167.76  Aligned_cols=154  Identities=17%  Similarity=0.237  Sum_probs=120.8

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCcC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMG   81 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~~   81 (238)
                      +|.||.+++|.||||+|++|++|+++|||+|++++... .+...++.|+|+|++++|.+|+.+|.+++.+..        
T Consensus         5 ~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~--------   75 (164)
T 2jvz_A            5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDILRERD--------   75 (164)
T ss_dssp             EEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTT-SSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSS--------
T ss_pred             EEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCC-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhcc--------
Confidence            78999999999999999999999999999999976432 122356799999999999999999998865431        


Q ss_pred             CCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeE
Q psy11278         82 STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPI  161 (238)
Q Consensus        82 ~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~  161 (238)
                       .   .+               +.+.++.        |..                    .    .++..+.||..++++
T Consensus        76 -~---~~---------------~~~~~~~--------~~~--------------------~----~~~~~i~vp~~~~g~  104 (164)
T 2jvz_A           76 -Q---GG---------------FGDRNEY--------GSR--------------------I----GGGIDVPVPRHSVGV  104 (164)
T ss_dssp             -S---CC---------------CSSCSSC--------TTS--------------------C----SSSBCCEEETTTHHH
T ss_pred             -C---CC---------------CCCcccc--------CCC--------------------C----CceEEEEEChhhccc
Confidence             0   00               0000000        000                    0    012567899999999


Q ss_pred             EecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        162 MEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       162 iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      |||++|.+|++|+++|||+|.+++..+..    .++.|+|+|+++++..|+.+|.+++
T Consensus       105 iIGk~G~~I~~i~~~tg~~I~i~~~~~~~----~~~~v~I~G~~~~v~~A~~~I~~~i  158 (164)
T 2jvz_A          105 VIGRSGEMIKKIQNDAGVRIQFKQDDGTG----PEKIAHIMGPPDRCEHAARIINDLL  158 (164)
T ss_dssp             HHCSSSHHHHHHHHHTCCEEEECCCCTTS----SEEEEEEESCHHHHHHHHHHHHHHH
T ss_pred             cCCCCcHhHHHHHHHHCCeEEEeCCCCCC----CcEEEEEEcCHHHHHHHHHHHHHHH
Confidence            99999999999999999999998754321    3689999999999999999999987

>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=99.91  E-value=1.3e-24  Score=168.29  Aligned_cols=151  Identities=18%  Similarity=0.258  Sum_probs=120.2

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLM   80 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~   80 (238)
                      +++.||.+.+|.||||+|++|++|+++|||+|++++.+.     .++.|+|+|++++|.+|+.+|.+.+.+.    ++  
T Consensus         7 ~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~-----~~r~v~I~G~~~~v~~A~~~I~~~i~e~----~~--   75 (160)
T 2jzx_A            7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC-----PERIITLAGPTNAIFKAFAMIIDKLEED----IS--   75 (160)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTT-----TEEEEEEEEEHHHHHHHHHHHHHHHHHH----HT--
T ss_pred             EEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCCC-----CceEEEEEeCHHHHHHHHHHHHHHHHhh----cc--
Confidence            478999999999999999999999999999999988543     4689999999999999999997552211    00  


Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                                        .      ..+.+.        .                    .  ....++.++.||..+++
T Consensus        76 ------------------~------~~~~~~--------~--------------------~--~~~~~~~~i~vp~~~~g  101 (160)
T 2jzx_A           76 ------------------S------SMTNST--------A--------------------A--SRPPVTLRLVVPASQCG  101 (160)
T ss_dssp             ------------------S------CCCSSS--------C--------------------C--CCCSEEEEEEEEHHHHH
T ss_pred             ------------------c------cCCCCc--------c--------------------C--CCCCEEEEEEEChhhee
Confidence                              0      000000        0                    0  00124588999999999


Q ss_pred             EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +|||++|.+|++|+++|||+|.++....++   .+++.|+|+|++++|.+|+.+|.+++
T Consensus       102 ~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~---~~~~~v~I~G~~~~v~~A~~~I~~~i  157 (160)
T 2jzx_A          102 SLIGKGGCKIKEIRESTGAQVQVAGDMLPN---STERAITIAGIPQSIIECVKQICVVM  157 (160)
T ss_dssp             HHHCGGGHHHHHHHHHHSSEECCCCCCSTT---CCEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             eEECCCCHHHHHHHHHhCCeEEECCCCCCC---CCceEEEEEcCHHHHHHHHHHHHHHH
Confidence            999999999999999999999998643332   24799999999999999999999876

>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=99.91  E-value=1.2e-24  Score=170.75  Aligned_cols=170  Identities=18%  Similarity=0.249  Sum_probs=120.1

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLM   80 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~   80 (238)
                      ++|.||.+.+|.||||+|++|++|+++|||+|+|++...   ...++.|+|+|++++|.+|+.+|.+++.....-  ++ 
T Consensus         5 ~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~--~~-   78 (174)
T 1j4w_A            5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG---TTPERIAQITGPPDRAQHAAEIITDLLRSVQAG--NP-   78 (174)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT---SCSEEEEEEEECHHHHHHHHHHHHHHHHHHC-------
T ss_pred             EEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCC---CCCccEEEEEeCHHHHHHHHHHHHHHHHhcccC--CC-
Confidence            478999999999999999999999999999999976432   224689999999999999999998775432100  00 


Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                      + .++..+.       .++                  ++. .+..             ......  ..+.++.||..+++
T Consensus        79 ~-~~~p~~~-------~~~------------------~~~-~~~~-------------~~~~~~--~~~~~i~vp~~~~g  116 (174)
T 1j4w_A           79 G-GPGPGGR-------GRG------------------RGQ-GNWN-------------MGPPGG--LQEFNFIVPTGKTG  116 (174)
T ss_dssp             -------------------------------------------------------------------CEEEEEEETTTHH
T ss_pred             C-CCCCCCC-------CCC------------------CCC-Cccc-------------cCCCCC--cEEEEEEEChHHcC
Confidence            0 0000000       000                  000 0000             000001  12378999999999


Q ss_pred             EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +|||++|.+|++|+++|||+|.+++...++ ....++.|+|+|++++|..|+.+|.+++
T Consensus       117 ~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          117 LIIGKGGETIKSISQQSGARIELQRNPPPN-ADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             HHHCGGGHHHHHHHHHHCCEEEEECCCTTT-SCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             eeECCCchHHHHHHHHHCCEEEECCCCCCC-CCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            999999999999999999999998754321 1124689999999999999999999875

>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=99.76  E-value=6.1e-19  Score=133.68  Aligned_cols=131  Identities=18%  Similarity=0.209  Sum_probs=99.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTPLIFCFEYPLM   80 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~~~~~~~p~~   80 (238)
                      ++.||.+.+|.+||++|++|+.|++++|  |++...++     +...+.+.| +|+.|..|+.++.              
T Consensus         7 ~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~-----~~~~~i~~~~~p~~v~~~~~~l~--------------   65 (144)
T 2qnd_A            7 QFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDE-----DTCTFHIYGEDQDAVKKARSFLE--------------   65 (144)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEET-----TTTEEEEEESSHHHHHHHHHHHC--------------
T ss_pred             EEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCC-----CchheeeccCCHHHHHHHHHhhh--------------
Confidence            6899999999999999999999999999  55433221     223455554 5777777765330              


Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP  160 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~  160 (238)
                                             +.                                           ..++.+|.++++
T Consensus        66 -----------------------~~-------------------------------------------e~~v~Vp~~~~g   79 (144)
T 2qnd_A           66 -----------------------FA-------------------------------------------EDVIQVPRNLVG   79 (144)
T ss_dssp             -----------------------EE-------------------------------------------EEEEEEEGGGHH
T ss_pred             -----------------------cc-------------------------------------------eEEEEECHHHcC
Confidence                                   00                                           046778999999


Q ss_pred             EEecCCCchHHHHHHHhCC-eEEccCCCCCCCCCC-cceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        161 IMEGPNAINLKTIMAQTGA-QIVFPEANDPIIPVL-KKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       161 ~iIG~~G~~I~~I~~~tga-~I~~p~~~~~~~~~~-~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++|||+|.+|+.+++.||| +|.|+...+...+.. ....|+|+|++++|+.|+.+|+.+|
T Consensus        80 ~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l  140 (144)
T 2qnd_A           80 KVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHL  140 (144)
T ss_dssp             HHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred             eeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHH
Confidence            9999999999999999997 899986543321111 1246999999999999999999987

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.67  E-value=2e-16  Score=127.34  Aligned_cols=150  Identities=15%  Similarity=0.158  Sum_probs=105.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC-----HHHHHHHHHHHHhhCCceEEEe
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-----LLGLERARYRVRELTPLIFCFE   76 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~-----~~~v~~A~~~I~~~~~~~~~~~   76 (238)
                      ++.||.+.++.|||++|++|+.|+++|||+|++..        +++.|+|.|+     ++++.+|+.+|..+....   +
T Consensus        37 ~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~--------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~---~  105 (219)
T 2e3u_A           37 YVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS--------ETGEVWITSTKETEDPLAVWKARDIVLAIGRGF---S  105 (219)
T ss_dssp             EEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT--------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTC---C
T ss_pred             EEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc--------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhccC---C
Confidence            68899999999999999999999999999999975        2468999875     799999999998874210   0


Q ss_pred             ecCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCC
Q psy11278         77 YPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISP  156 (238)
Q Consensus        77 ~p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~  156 (238)
                      . ..       |..+  +.++  ...          ..+.|...   +..              ...         ...+
T Consensus       106 ~-e~-------g~~l--l~dd--~~~----------e~i~i~~~---~v~--------------~~~---------~~~~  137 (219)
T 2e3u_A          106 P-ER-------AFRL--LNEG--EYL----------EIINLTDI---IIG--------------NEK---------NALP  137 (219)
T ss_dssp             H-HH-------HGGG--GSTT--CEE----------EEEEGGGC---C-----------------------------CHH
T ss_pred             c-cc-------ccee--ccCC--ccc----------eeEEcccc---ccc--------------CCc---------hhhh
Confidence            0 00       0000  0000  000          00100000   000              000         0011


Q ss_pred             CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      ...|+|||++|.+|+.|++.|||+|.++.           +.|+|.|++++++.|+.+|.+++..
T Consensus       138 r~~GriIGk~G~tik~ie~~Tg~~I~v~~-----------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          138 RVRGRIIGRKGRTRQIIEEMSGASVSVYG-----------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHCCEEEEET-----------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             hhhheeECCCchHHHHHHHHhCceEEECC-----------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            24678999999999999999999999963           4699999999999999999999954

>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=99.60  E-value=1.4e-15  Score=102.74  Aligned_cols=70  Identities=21%  Similarity=0.380  Sum_probs=61.7

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +++.||.+.+|.||||+|++|++|+++|||+|++++.++..+...++.|+|+|+++++..|+.+|.+++.
T Consensus         5 ~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   74 (76)
T 1dtj_A            5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (76)
T ss_dssp             EEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             EEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHh
Confidence            3689999999999999999999999999999999986543344456899999999999999999998764

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.58  E-value=1.9e-15  Score=100.50  Aligned_cols=63  Identities=27%  Similarity=0.542  Sum_probs=57.8

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      ++.||.+.|+.|||++|++|++|+++|||+|+|++..+     .++.|+|+|+++++++|+.+|+++.
T Consensus         8 ~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~-----~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            8 EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-----KSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCS-----SSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCCC-----cccEEEEEcCHHHHHHHHHHHHHHh
Confidence            68899999999999999999999999999999998543     4579999999999999999998874

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.56  E-value=6e-15  Score=98.11  Aligned_cols=65  Identities=17%  Similarity=0.301  Sum_probs=60.2

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +..+.||+.+|+.|||++|++|++|+++|||+|.||++.++      .+.|+|+|+++++.+|+.+|.+++
T Consensus         6 ~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~------~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            6 YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK------SNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSS------SEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCCCc------ccEEEEEcCHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999986643      589999999999999999999876

>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=99.54  E-value=1.9e-15  Score=101.10  Aligned_cols=64  Identities=22%  Similarity=0.362  Sum_probs=58.2

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      +++.||.+.+|.||||+|++|++|+++|||+|++++.+.     .++.|+|+|+++++..|+.+|.+++
T Consensus         7 ~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~-----~er~v~I~G~~~~v~~A~~~I~~~l   70 (73)
T 2axy_A            7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC-----PERIITLAGPTNAIFKAFAMIIDKL   70 (73)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCC-----SEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCCC-----CcEEEEEEeCHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999988532     4689999999999999999998764

>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=99.54  E-value=3e-15  Score=102.35  Aligned_cols=62  Identities=23%  Similarity=0.373  Sum_probs=56.9

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      +|.||.+.+|+||||+|++|++|+++|||+|++++.+      +++.++|+|+++++++|+.+|.++.
T Consensus        13 ~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~v~~A~~~I~~~i   74 (83)
T 2dgr_A           13 QVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPENVDRAREEIEAHI   74 (83)
T ss_dssp             EEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTTHHHHHHHHHHHH
T ss_pred             EEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999998743      3579999999999999999998763

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.54  E-value=1.7e-15  Score=130.07  Aligned_cols=139  Identities=12%  Similarity=0.225  Sum_probs=102.1

Q ss_pred             CEEEecCCccceeeccCCc--cHHHHHHHcCCEEEecCCCCCC-CCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEee
Q psy11278          1 MKLDVSYTDHSHIIGRGGL--TIKKVMEETGCHVHFPDSNRSV-NAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEY   77 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~--~I~~I~~~t~~~I~i~~~~~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~   77 (238)
                      +++.||.++|+.|||++|+  .|++|+++|||+|+||+.++.. +..+...|+|+|+.++|..|++.|++++|....|++
T Consensus       188 ~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLPv~l~Fd~  267 (376)
T 3n89_A          188 LHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLLPISMCFNI  267 (376)
T ss_dssp             EEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTSEEEEEEEE
T ss_pred             EEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhCCEEEEEec
Confidence            3689999999999999995  4599999999999999865421 111346899999999999999999999999999999


Q ss_pred             cCcCC--CCCCCChHHHHHHHHhCceEEeeCCCCCC---------CcEEEEEccccchHHHHHHHHHHHHHhh
Q psy11278         78 PLMGS--TPNANSPFVQIIQEAYNVQVMFRNRPKLQ---------PTLVMVKGCEKDVERVKEATTKLIEHMC  139 (238)
Q Consensus        78 p~~~~--~~~~~g~~i~~i~~~~gv~I~~~~~~~~~---------~~~v~I~G~~~~v~~a~~ai~~~~~~~~  139 (238)
                      +....  +.......+..++++++|.+++.+.+..+         ...+++++.+.|..++.+|.+.++..-.
T Consensus       268 ~~~d~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~s~e~n~~~~y~~~~~~l~~~~  340 (376)
T 3n89_A          268 KNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVPLNCASLRSKEFNIKKLYTAYQKVLSKKF  340 (376)
T ss_dssp             EGGGBC--------CBEEEECTTSCEEEEEEEEECCSSSSCCCEEEEEEEEEEEGGGHHHHHHHHHHHBCGGG
T ss_pred             CCcccccccccchhHHHHHHHhcCeEEEEeecCCCchhhcccccccceEEEEEEeccHHHHHHHHHHHhCCcc
Confidence            85321  11111222344677889999886643222         1579999999999999999888876543

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.54  E-value=1.4e-14  Score=104.02  Aligned_cols=72  Identities=21%  Similarity=0.284  Sum_probs=62.8

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI   72 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~   72 (238)
                      ++|.||.+.++.||||+|++|++|+++|||+|+|++..+..+...++.|+|+|++++|++|+.+|.+++.+.
T Consensus         9 ~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            9 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             EEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             EEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            378999999999999999999999999999999988654222234689999999999999999999998764

>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=99.52  E-value=5.3e-15  Score=102.43  Aligned_cols=70  Identities=21%  Similarity=0.380  Sum_probs=61.3

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +++.||.+.+|.||||+|++|++|+++|||+|++++.++..++..++.|+|+|+++++..|+.+|.+++.
T Consensus         5 ~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~   74 (87)
T 1ec6_A            5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (87)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             EEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Confidence            3689999999999999999999999999999999986543344466899999999999999999987743

>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=99.52  E-value=1.8e-14  Score=101.60  Aligned_cols=68  Identities=26%  Similarity=0.449  Sum_probs=59.7

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++|.||.+.|+.|||++|++|++|+++|||+|+|++..+  +...++.|+|+|+++++++|+.+|+.+..
T Consensus        19 ~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~~~~~~V~I~G~~e~v~~A~~~I~~iv~   86 (97)
T 2ctl_A           19 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVG   86 (97)
T ss_dssp             EEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999999999998653  22246899999999999999999987743

>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=3.3e-16  Score=111.37  Aligned_cols=86  Identities=17%  Similarity=0.210  Sum_probs=70.8

Q ss_pred             EEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeEEecCCCchHHHHHHH-hCCeEEccCCCCCCCCCC
Q psy11278        116 MVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQ-TGAQIVFPEANDPIIPVL  194 (238)
Q Consensus       116 ~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~-tga~I~~p~~~~~~~~~~  194 (238)
                      .|+|+++++.+|+..+.+++        +.. ++.++.+|+.||++|||++|++|++|+++ ++++|.||+.        
T Consensus         4 ~i~G~~~~V~~A~~~i~~~~--------~~~-~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~~--------   66 (102)
T 2ctf_A            4 GSSGEPEKLGQALTEVYAKA--------NSF-TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------   66 (102)
T ss_dssp             CCCCCCCCCCCSCCCCCCCC--------CCC-EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS--------
T ss_pred             ccCcCHHHHHHHHHHHHHHh--------cCe-EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCCC--------
Confidence            36788888887764432211        111 45899999999999999999999999997 5999999982        


Q ss_pred             cceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        195 KKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       195 ~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                       ++.|+|+|++++|.+|+.+|+.++
T Consensus        67 -~~~ItI~G~~~~V~~a~~~I~~~v   90 (102)
T 2ctf_A           67 -EDKITLEGPTEDVSVAQEQIEGMV   90 (102)
T ss_dssp             -SCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             -CCEEEEECCHHHHHHHHHHHHHHH
Confidence             368999999999999999999887

>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=99.52  E-value=1.7e-14  Score=98.65  Aligned_cols=68  Identities=21%  Similarity=0.263  Sum_probs=60.9

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++.++.||..++++|||++|++|++|+++|||+|.+++....    ..++.|+|+|+++++.+|+.+|.+++
T Consensus         7 ~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~----~~~~~v~I~G~~~~v~~A~~~I~~~i   74 (82)
T 1zzk_A            7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG----SEDRIITITGTQDQIQNAQYLLQNSV   74 (82)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSC----SSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCC----CCceEEEEEeCHHHHHHHHHHHHHHH
Confidence            558999999999999999999999999999999999864321    14689999999999999999999987

>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=99.51  E-value=1.9e-14  Score=98.50  Aligned_cols=67  Identities=19%  Similarity=0.412  Sum_probs=58.9

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +++.||.+.+|.||||+|++|++|+++|||+|++++...   ...++.|+|+|++++|++|+.+|.+++.
T Consensus         9 ~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~   75 (82)
T 1zzk_A            9 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQDQIQNAQYLLQNSVK   75 (82)
T ss_dssp             EEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTS---CSSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999999999987432   2356899999999999999999987643

>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=1.3e-14  Score=101.88  Aligned_cols=64  Identities=25%  Similarity=0.489  Sum_probs=58.2

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.+.||.|||++|++|++|+++|||+|+|++.++     .++.|+|+|+++++++|+.+|++++.
T Consensus        20 ~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~-----~~~~V~I~G~~e~v~~A~~~I~~i~~   83 (94)
T 2cte_A           20 TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-----PSNQIKITGTKEGIEKARHEVLLISA   83 (94)
T ss_dssp             EEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTS-----SCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCC-----CCCeEEEEECHHHHHHHHHHHHHHhh
Confidence            68999999999999999999999999999999997543     35799999999999999999988754

>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=99.51  E-value=2.9e-14  Score=96.16  Aligned_cols=70  Identities=17%  Similarity=0.246  Sum_probs=61.2

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +.++.||..++|+|||++|++|++|+++|||+|.+++..++. +....+.|+|+|+++++..|+.+|.+++
T Consensus         4 ~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i   73 (76)
T 1dtj_A            4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL-PGTRNRRVTITGSPAATQAAQYLISQRV   73 (76)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS-TTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCC-CCCceeEEEEEeCHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999754321 1124689999999999999999999987

>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=99.51  E-value=1.5e-14  Score=99.05  Aligned_cols=69  Identities=22%  Similarity=0.352  Sum_probs=59.9

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI   72 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~   72 (238)
                      +++.||.+.+|.||||+|++|++|+++|||+|++++..+   ...++.|+|+|+++++.+|+.+|.+++.+.
T Consensus         8 ~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            8 HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCT---TCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             EEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            368999999999999999999999999999999987432   235689999999999999999999987643

>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=99.51  E-value=7.8e-15  Score=100.25  Aligned_cols=65  Identities=20%  Similarity=0.293  Sum_probs=59.8

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++.+|.||.+++++|||++|++|++|+++|||+|.+|..++       ++.|+|+|+++++++|+.+|.+++
T Consensus        10 ~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~~-------~~~v~ItG~~e~v~~A~~~I~~~i   74 (83)
T 2dgr_A           10 TTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK-------EPVFAVTGMPENVDRAREEIEAHI   74 (83)
T ss_dssp             EEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSSS-------CCEEEEEECTTTHHHHHHHHHHHH
T ss_pred             eEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCCC-------CCeEEEEcCHHHHHHHHHHHHHHH
Confidence            45899999999999999999999999999999999997543       478999999999999999999986

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.50  E-value=7.9e-15  Score=98.93  Aligned_cols=66  Identities=23%  Similarity=0.388  Sum_probs=59.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.+.+|.||||+|++|++|+++|||+|++++..   +...++.|+|+|+++++..|+.+|.+++.
T Consensus         8 ~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   73 (76)
T 2p2r_A            8 ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV---EGSTDRQVTITGSAASISLAQYLINVRLS   73 (76)
T ss_dssp             EEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             EEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCC---CCCCeEEEEEEeCHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999998743   23356899999999999999999988754

>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=99.50  E-value=9.8e-15  Score=97.61  Aligned_cols=66  Identities=17%  Similarity=0.294  Sum_probs=61.0

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++..+.||++.+|.|||++|++|++|+++|||+|.+++...      .++.|+|+|+++++.+|+.+|.++|
T Consensus         5 ~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~------~er~v~I~G~~~~v~~A~~~I~~~l   70 (73)
T 2axy_A            5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC------PERIITLAGPTNAIFKAFAMIIDKL   70 (73)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCC------SEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCCC------CcEEEEEEeCHHHHHHHHHHHHHHH
Confidence            55899999999999999999999999999999999997643      3689999999999999999999987

>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=99.50  E-value=3e-14  Score=100.44  Aligned_cols=69  Identities=19%  Similarity=0.350  Sum_probs=62.0

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++..|.||+.+|+.|||++|++|++|+++|||+|.||+..+++   ...+.|+|+|+++++.+|+.+|..++
T Consensus        17 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~---~~~~~V~I~G~~e~v~~A~~~I~~iv   85 (97)
T 2ctl_A           17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN---QPQDQITITGYEKNTEAARDAILRIV   85 (97)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCS---SCSSEEEEESCHHHHHHHHHHHHHHH
T ss_pred             eeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCC---CCccEEEEEeCHHHHHHHHHHHHHHH
Confidence            4589999999999999999999999999999999999866432   13689999999999999999999887

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.50  E-value=3.2e-14  Score=98.00  Aligned_cols=68  Identities=21%  Similarity=0.334  Sum_probs=59.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.+.+|.||||+|++|++|+++|||+|++++... .+...++.|+|+|++++++.|+.+|.+++.
T Consensus        17 ~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           17 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             EEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC-SSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             EEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999999999999987432 123356789999999999999999988753

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.50  E-value=1.3e-14  Score=97.80  Aligned_cols=68  Identities=21%  Similarity=0.261  Sum_probs=61.1

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++.++.||..++|+|||++|++|++|+++|||+|.+++....    ..++.|+|+|+++++.+|+.+|.+++
T Consensus         5 ~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~----~~~~~v~I~G~~~~v~~A~~~I~~~i   72 (76)
T 2p2r_A            5 TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEG----STDRQVTITGSAASISLAQYLINVRL   72 (76)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTT----CSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCC----CCeEEEEEEeCHHHHHHHHHHHHHHH
Confidence            558999999999999999999999999999999999874221    14799999999999999999999987

>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=99.49  E-value=2.8e-14  Score=97.66  Aligned_cols=70  Identities=20%  Similarity=0.244  Sum_probs=61.7

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      ++.+|.||.+++++|||++|++|++|+++|||+|.+++....    ..++.|+|+|+++++.+|+.+|.+++..
T Consensus         6 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~----~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (82)
T 1wvn_A            6 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEG----SSGRQVTITGSAASISLAQYLINARLSS   75 (82)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTT----CSEEEEEEEECHHHHHHHHHHHHHHTC-
T ss_pred             EEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCC----CCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            458999999999999999999999999999999999874321    1478999999999999999999999843

>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=99.49  E-value=4.4e-14  Score=99.13  Aligned_cols=65  Identities=28%  Similarity=0.443  Sum_probs=58.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.+.|+.|||++|++|++|+++|||+|+|++..+.    .++.|+|+|.+++|++|+.+|+.+..
T Consensus        20 ~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~----~~~~V~I~G~~e~v~~A~~~I~~i~~   84 (95)
T 2ctm_A           20 DVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP----DPNCVTVTGLPENVEEAIDHILNLEE   84 (95)
T ss_dssp             EEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCS----CTTEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCC----CCcEEEEEcCHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999875431    35799999999999999999988754

>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=99.48  E-value=5.2e-14  Score=98.78  Aligned_cols=67  Identities=22%  Similarity=0.314  Sum_probs=61.0

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++..+.||+.+|+.|||++|++|++|+++|||+|.||+..+.     ..+.|+|+|+++++++|+.+|..++
T Consensus        17 vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~-----~~~~V~I~G~~e~v~~A~~~I~~i~   83 (95)
T 2ctm_A           17 VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP-----DPNCVTVTGLPENVEEAIDHILNLE   83 (95)
T ss_dssp             CCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCS-----CTTEEEEESCHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCC-----CCcEEEEEcCHHHHHHHHHHHHHHH
Confidence            448999999999999999999999999999999999986543     2578999999999999999999987

>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=99.48  E-value=3.1e-14  Score=99.89  Aligned_cols=66  Identities=23%  Similarity=0.451  Sum_probs=60.8

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++..|.||+.+|++|||++|.+|++|+++|||+|.+|+..++      .+.|+|+|+++++.+|+.+|.+++
T Consensus        17 ~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~------~~~V~I~G~~e~v~~A~~~I~~i~   82 (94)
T 2cte_A           17 ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------SNQIKITGTKEGIEKARHEVLLIS   82 (94)
T ss_dssp             EEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSS------CCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCCC------CCeEEEEECHHHHHHHHHHHHHHh
Confidence            558999999999999999999999999999999999976543      378999999999999999999988

>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=99.46  E-value=5.2e-14  Score=100.42  Aligned_cols=64  Identities=28%  Similarity=0.504  Sum_probs=58.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.+.|+.|||++|++|++|+++|||+|+|++..+     .++.|+|+|+.+++++|+.+|..+..
T Consensus        20 ~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~-----~~~~V~I~G~~e~v~~A~~~I~~i~~   83 (104)
T 2ctk_A           20 EVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLAANLDRAKAGLLERVK   83 (104)
T ss_dssp             EEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT-----TCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC-----CcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            68899999999999999999999999999999998543     34699999999999999999988754

>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=99.45  E-value=5.1e-14  Score=98.40  Aligned_cols=71  Identities=14%  Similarity=0.204  Sum_probs=62.8

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      .++.+|.||..++++|||++|.+|++|+++|||+|.+++..+..    .++.|+|+|++++|.+|+.+|.+++..
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~----~~r~v~I~G~~e~v~~A~~~I~~~i~~   84 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGL----PERSCMLTGTPESVQSAKRLLDQIVEK   84 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTC----SEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCC----CccEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            35689999999999999999999999999999999998754221    478999999999999999999999843

>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=99.45  E-value=3.8e-14  Score=98.46  Aligned_cols=66  Identities=20%  Similarity=0.423  Sum_probs=58.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.+.+|.||||+|++|++|+++|||+|++++..   +...++.|+|+|++++|++|+.+|.+++.
T Consensus        17 ~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~---~~~~~~~v~I~G~~e~v~~A~~~I~~~i~   82 (89)
T 1j5k_A           17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQIQNAQYLLQNSVK   82 (89)
T ss_dssp             EEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             EEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCC---CCCCccEEEEEcCHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999998743   23356899999999999999999987743

>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=99.44  E-value=4.6e-14  Score=98.02  Aligned_cols=69  Identities=20%  Similarity=0.251  Sum_probs=61.4

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .++.++.||..+++.|||++|++|++|+++|||+|.+++....    ..++.|+|+|+++++.+|+.+|.+++
T Consensus        13 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~----~~~~~v~I~G~~e~v~~A~~~I~~~i   81 (89)
T 1j5k_A           13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG----SEDRIITITGTQDQIQNAQYLLQNSV   81 (89)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSS----SSEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCC----CCccEEEEEcCHHHHHHHHHHHHHHH
Confidence            4568999999999999999999999999999999999864211    14799999999999999999999987

>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=99.44  E-value=5.5e-14  Score=98.64  Aligned_cols=69  Identities=22%  Similarity=0.337  Sum_probs=60.4

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL   71 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~   71 (238)
                      +|.||.+.++.||||+|++|++|+++|||+|+|++..... ...++.|+|+|++++|+.|+.+|.+++.+
T Consensus        18 ~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           18 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-TGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             EEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS-SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             EEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC-CCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            6899999999999999999999999999999998754321 22568999999999999999999988654

>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=99.44  E-value=6.4e-14  Score=97.88  Aligned_cols=66  Identities=20%  Similarity=0.402  Sum_probs=58.8

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +|.||.+.+|.||||+|++|++|+++|||+|+|++..+   ...++.|+|+|++++|.+|+.+|.+++.
T Consensus        18 ~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~---g~~~r~v~I~G~~e~v~~A~~~I~~~i~   83 (92)
T 1x4n_A           18 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGTPESVQSAKRLLDQIVE   83 (92)
T ss_dssp             EEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT---TCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCC---CCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999987542   2246899999999999999999988754

>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=99.44  E-value=6.2e-14  Score=96.99  Aligned_cols=70  Identities=16%  Similarity=0.237  Sum_probs=60.9

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +.+|.||..++|+|||++|++|++|+++|||+|.+++..++. +....+.|+|+|+++++..|+.+|.+++
T Consensus         4 t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~g~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (87)
T 1ec6_A            4 LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL-PGTRNRRVTITGSPAATQAAQYLISQRV   73 (87)
T ss_dssp             EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBS-TTSCEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCC-CCCCceEEEEEcCHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999754310 1124689999999999999999999987

>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=99.43  E-value=1.1e-13  Score=98.82  Aligned_cols=68  Identities=15%  Similarity=0.232  Sum_probs=62.0

Q ss_pred             ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        146 TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       146 ~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .+++..|.||+.+|+.|||++|++|++|+++|||+|.+|+..+.      .+.|+|+|+++++.+|+.+|.+++
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~------~~~V~I~G~~e~v~~A~~~I~~i~   82 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQ------SDIIAITGLAANLDRAKAGLLERV   82 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTT------CCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCCC------cceEEEEcCHHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999999999986542      469999999999999999999987

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.43  E-value=1.1e-13  Score=99.03  Aligned_cols=68  Identities=22%  Similarity=0.344  Sum_probs=59.5

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL   71 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~   71 (238)
                      ++|.||.+.++.||||+|++|++|+++|+|+|+|++...   ...++.|+|+|++++|++|+.+|.+++.+
T Consensus        13 ~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~   80 (106)
T 2hh3_A           13 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG---TGPEKIAHIMGPPDRCEHAARIINDLLQS   80 (106)
T ss_dssp             EEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCS---SSSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCC---CCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            378999999999999999999999999999999986432   22457999999999999999999988654

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.43  E-value=2e-13  Score=97.98  Aligned_cols=72  Identities=21%  Similarity=0.216  Sum_probs=62.8

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP  222 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  222 (238)
                      .+|.||.+++++|||++|++|++|+++|||+|.+++..+++. ...++.|+|+|++++|.+|+.+|.+++...
T Consensus         9 ~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~-~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            9 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNG-DPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             EEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTC-CTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             EEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCC-CCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            789999999999999999999999999999999987653321 114689999999999999999999999654

>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=99.42  E-value=2.4e-13  Score=96.56  Aligned_cols=61  Identities=16%  Similarity=0.384  Sum_probs=55.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHc-CCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEET-GCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t-~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +|.||+.+|++|||++|++|++|++++ +++|+||+        .++.|+|+|+++.|++|+.+|..++.
T Consensus        30 ~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~--------~~~~ItI~G~~~~V~~a~~~I~~~v~   91 (102)
T 2ctf_A           30 SVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSVAQEQIEGMVK   91 (102)
T ss_dssp             EEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC--------CCCEEEEECCHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999975 99999998        24699999999999999999987743

>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=99.42  E-value=1.9e-13  Score=97.68  Aligned_cols=68  Identities=24%  Similarity=0.365  Sum_probs=59.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +|.||.+.+|.||||+|++|++|+++|||+|+|++..... ...++.|+|+|+.+++++|+.+|.+++.
T Consensus        18 ~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~   85 (104)
T 1we8_A           18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-LLLSRLIKISGTQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             EEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS-SSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             EEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC-CCCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999998754321 1246899999999999999999988753

>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=99.42  E-value=1.8e-13  Score=107.46  Aligned_cols=121  Identities=17%  Similarity=0.179  Sum_probs=101.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEE-----eCHHHHHHHHHHHHhhC-------
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIA-----GSLLGLERARYRVRELT-------   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~~-------   69 (238)
                      ++.||.+.+|.|||++|++++.|++++|++|++..        .++.|+|.     |++..+.+|++.|..+.       
T Consensus         7 ~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~--------~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~e~   78 (191)
T 1tua_A            7 YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT--------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEK   78 (191)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET--------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHH
T ss_pred             EEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc--------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHHH
Confidence            68999999999999999999999999999999965        35788998     99999999999995542       


Q ss_pred             -----Cc---eEEEeecCc------------CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHH
Q psy11278         70 -----PL---IFCFEYPLM------------GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKE  129 (238)
Q Consensus        70 -----~~---~~~~~~p~~------------~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~  129 (238)
                           ..   ...|+++..            +..+|++|.+++.|+..+|++|.++.      ..+.|.|..+++..|+.
T Consensus        79 A~~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~------~~v~i~G~~~~i~~Ar~  152 (191)
T 1tua_A           79 AFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE------YEVAIIGDYERAMAAKQ  152 (191)
T ss_dssp             HGGGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS------SEEEEEEEHHHHHHHHH
T ss_pred             hhhcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC------CEEEEEeChHHHHHHHH
Confidence                 11   245555532            22468899999999999999999974      48999999999999998


Q ss_pred             HHHHHHH
Q psy11278        130 ATTKLIE  136 (238)
Q Consensus       130 ai~~~~~  136 (238)
                      ++.+++.
T Consensus       153 ~i~~li~  159 (191)
T 1tua_A          153 AIEMLAE  159 (191)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHc
Confidence            8888774

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.41  E-value=3.5e-13  Score=92.74  Aligned_cols=70  Identities=11%  Similarity=0.178  Sum_probs=61.0

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ....|.||+..++.|||++|++|++|+++|||+|.+++.....  ...++.|+|+|+++++.+|+.+|.+++
T Consensus        14 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~--~~~er~v~I~G~~~~v~~A~~~I~~i~   83 (85)
T 2opv_A           14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN--TNVDKPLRIIGDPYKVQQACEMVMDIL   83 (85)
T ss_dssp             EEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSS--TTSCEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHh
Confidence            4478999999999999999999999999999999998754311  124678999999999999999999987

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.41  E-value=2.1e-13  Score=97.55  Aligned_cols=66  Identities=14%  Similarity=0.175  Sum_probs=59.7

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .+|.||.++++.|||++|++|++|+++|||+|.++++....    .++.|+|+|+++++++|+.+|++++
T Consensus        13 ~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~----~er~V~I~G~~e~v~~A~~~I~~ii   78 (106)
T 2hh3_A           13 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTG----PEKIAHIMGPPDRCEHAARIINDLL   78 (106)
T ss_dssp             EEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSS----SEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCC----ceeEEEEEeCHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999999999998644221    3689999999999999999999988

>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=99.40  E-value=2.1e-13  Score=95.65  Aligned_cols=72  Identities=13%  Similarity=0.205  Sum_probs=63.1

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      ++.+|.||..++++|||++|++|++|+++|||+|.+++...+.  ...++.|+|+|+++++.+|+.+|.+++..
T Consensus        15 ~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           15 AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN--TGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             EEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS--SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             EEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            5589999999999999999999999999999999998764321  11468999999999999999999999954

>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=99.40  E-value=4.8e-13  Score=95.55  Aligned_cols=73  Identities=16%  Similarity=0.295  Sum_probs=63.3

Q ss_pred             cceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       145 ~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ..+.+..|.||..+++.|||++|++|++|+++|||+|.+++..+..  ...++.|+|+|+++++.+|+.+|.+++
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~--~~~~~~V~I~G~~~~v~~A~~~I~~~i   84 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT--LLLSRLIKISGTQKEVAAAKHLILEKV   84 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS--SSSEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC--CCCcceEEEEcCHHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999999999999998754321  113689999999999999999999988

>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=99.40  E-value=2e-13  Score=95.61  Aligned_cols=71  Identities=24%  Similarity=0.363  Sum_probs=62.6

Q ss_pred             cccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHh-CCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        141 SLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQT-GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       141 ~~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~t-ga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++.+..  +..|.||+.+|+.|||++|.+|++|+++| ||+|.||++.+.      .+.|+|.|+.+++.+|+++|++++
T Consensus        12 e~~~~v--t~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~------~~~V~I~G~~~~v~~A~~~I~~iv   83 (95)
T 2ctj_A           12 DLANIA--EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSG------SDTVVIRGPSSDVEKAKKQLLHLA   83 (95)
T ss_dssp             CCCSSC--CEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTT------CCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             HHhhcE--EEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCC------cceEEEEcCHHHHHHHHHHHHHHH
Confidence            344443  48899999999999999999999999999 999999986543      579999999999999999999987

>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=99.40  E-value=2.4e-13  Score=95.23  Aligned_cols=64  Identities=31%  Similarity=0.554  Sum_probs=58.2

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHc-CCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEET-GCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t-~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      .|.||.++|+.|||++|++|++|+++| ||+|+||+...     .++.|+|.|+.++|++|+.+|+++..
T Consensus        20 ~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~-----~~~~V~I~G~~~~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           20 EVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-----GSDTVVIRGPSSDVEKAKKQLLHLAE   84 (95)
T ss_dssp             EEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTT-----TCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCC-----CcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999 99999998543     45799999999999999999988754

>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=99.32  E-value=1.8e-12  Score=99.99  Aligned_cols=84  Identities=15%  Similarity=0.166  Sum_probs=70.9

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC------
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP------  222 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~------  222 (238)
                      +..|.||..++|.|||++|++|++|+++|||+|.+++...++.   .++.|+|+|+++++.+|+.+|.+++...      
T Consensus         4 ~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~---~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~~~   80 (163)
T 3krm_A            4 MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDS---KVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPK   80 (163)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTC---SEEEEEEEECHHHHHHHHHHHHHHHHHTTSSCSS
T ss_pred             EEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCC---CceEEEEEcCHHHHHHHHHHHHHHHhcccccccc
Confidence            4789999999999999999999999999999999988643322   4789999999999999999999887432      


Q ss_pred             --CceEEEEeecCCc
Q psy11278        223 --RRRLLLITIPNDI  235 (238)
Q Consensus       223 --~p~~~~~~~~~~~  235 (238)
                        .+..+.+.+|++-
T Consensus        81 ~~~~~~~~i~vp~~~   95 (163)
T 3krm_A           81 EEVKLETHIRVPASA   95 (163)
T ss_dssp             CCCCEEEEEEEETTT
T ss_pred             cCCceEEEEEcChhh
Confidence              3456788888763

>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=99.29  E-value=2.3e-12  Score=100.53  Aligned_cols=67  Identities=22%  Similarity=0.351  Sum_probs=59.0

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL   68 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~   68 (238)
                      ++.||.+.+|.||||+|++|++|+++|||+|++++..+..+...++.|+|+|++++|..|+.+|.++
T Consensus       107 ~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~  173 (174)
T 1j4w_A          107 NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK  173 (174)
T ss_dssp             EEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             EEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHh
Confidence            6889999999999999999999999999999998864432233568999999999999999999876

>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=99.27  E-value=3.6e-12  Score=98.03  Aligned_cols=82  Identities=17%  Similarity=0.309  Sum_probs=71.2

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC-----
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR-----  221 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~-----  221 (238)
                      +++.++.||..+++.|||++|++|++|+++|||+|.+++...+      ++.|+|+|+++++.+|+.+|.+.+..     
T Consensus         4 ~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~------~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~~   77 (160)
T 2jzx_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAGPTNAIFKAFAMIIDKLEEDISSS   77 (160)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTTT------EEEEEEEEEHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             cEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCCCC------ceEEEEEeCHHHHHHHHHHHHHHHHhhcccc
Confidence            4668999999999999999999999999999999999986433      68999999999999999999877632     


Q ss_pred             --------CCceEEEEeecCC
Q psy11278        222 --------PRRRLLLITIPND  234 (238)
Q Consensus       222 --------~~p~~~~~~~~~~  234 (238)
                              +.|..+.+.+|++
T Consensus        78 ~~~~~~~~~~~~~~~i~vp~~   98 (160)
T 2jzx_A           78 MTNSTAASRPPVTLRLVVPAS   98 (160)
T ss_dssp             CCSSSCCCCCSEEEEEEEEHH
T ss_pred             CCCCccCCCCCEEEEEEEChh
Confidence                    2478888888865

>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=99.24  E-value=1.3e-11  Score=95.28  Aligned_cols=71  Identities=11%  Similarity=0.177  Sum_probs=61.1

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      +.+|.||..++++|||++|++|++|+++|||+|.++.+...  ....++.|+|+|++++|.+|+.+|.+++..
T Consensus         3 ~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e   73 (164)
T 2jvz_A            3 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ--NTNVDKPLRIIGDPYKVQQACEMVMDILRE   73 (164)
T ss_dssp             EEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTS--SSSSCEEEEEEECHHHHHHHHHHHHHHTTC
T ss_pred             EEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999764311  011367999999999999999999999964

>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=99.19  E-value=1.6e-11  Score=96.05  Aligned_cols=73  Identities=14%  Similarity=0.209  Sum_probs=62.5

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      ++.+|.||.+++|.|||++|++|++|+++|||+|.+++..+.. ....++.|+|+|+++++.+|+.+|.+++..
T Consensus         6 ~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~-~~~~er~v~I~G~~~~v~~A~~~I~~~~~~   78 (178)
T 2anr_A            6 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFY-PGTTERVCLIQGTIEALNAVHGFIAEKIRE   78 (178)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBC-TTSSEEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             EEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCC-CCCCCceEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4589999999999999999999999999999999998654210 112478999999999999999999998854

>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=99.14  E-value=1.1e-10  Score=91.69  Aligned_cols=132  Identities=12%  Similarity=0.143  Sum_probs=98.6

Q ss_pred             EEeecC--cCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEE-----ccccchHHHHHHHHHHHHHhh----cc-
Q psy11278         74 CFEYPL--MGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVK-----GCEKDVERVKEATTKLIEHMC----GS-  141 (238)
Q Consensus        74 ~~~~p~--~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~-----G~~~~v~~a~~ai~~~~~~~~----~~-  141 (238)
                      .+.+|.  ++..+++.|..++.|++.+++++.+...    .+.+.|+     |++..+.+|++.++.+..-+.    -. 
T Consensus         7 ~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~----~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~e~A~~L   82 (191)
T 1tua_A            7 YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAFRL   82 (191)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHHHGGG
T ss_pred             EEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC----CCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHHHhhhc
Confidence            344553  3335678899999999999999999753    4688888     777778888877766654221    11 


Q ss_pred             ccccceEEEEEEeCC----------CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHH
Q psy11278        142 LANQTSVIMMMEISP----------QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA  211 (238)
Q Consensus       142 ~~~~~~~~~~v~i~~----------~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A  211 (238)
                      +.++ .+...+.++.          ...|.|||++|.+++.|+..|||+|.+..           ..+.|.|++++++.|
T Consensus        83 l~Dd-~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~-----------~~v~i~G~~~~i~~A  150 (191)
T 1tua_A           83 LEED-QILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE-----------YEVAIIGDYERAMAA  150 (191)
T ss_dssp             GSTT-EEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS-----------SEEEEEEEHHHHHHH
T ss_pred             ccCc-ceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC-----------CEEEEEeChHHHHHH
Confidence            1122 1223444542          24699999999999999999999999963           479999999999999


Q ss_pred             HHHHHhhcCC
Q psy11278        212 RQMLVVSSVR  221 (238)
Q Consensus       212 ~~~I~~~l~~  221 (238)
                      +..|+.++..
T Consensus       151 r~~i~~li~g  160 (191)
T 1tua_A          151 KQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHcC
Confidence            9999999865

>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=99.14  E-value=2.6e-11  Score=91.59  Aligned_cols=68  Identities=15%  Similarity=0.255  Sum_probs=56.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCC-EEEecCCCCCCCCCCCC--eEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGC-HVHFPDSNRSVNAEKSN--QVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~-~I~i~~~~~~~~~~~~~--~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      .+.||.+++|.+|||+|.||+.+++.||+ +|+|++.++......++  .|+|+|++++|+.|+.+|...+
T Consensus        70 ~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l  140 (144)
T 2qnd_A           70 VIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHL  140 (144)
T ss_dssp             EEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHH
Confidence            68899999999999999999999999997 99998755432111223  5899999999999999998764

>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=99.12  E-value=2.6e-11  Score=83.43  Aligned_cols=61  Identities=18%  Similarity=0.214  Sum_probs=55.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCE-EEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCH-VHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~-I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      .+.||.+.++.+||++|++|++|+++||++ |++.+        +++.|+|.| +.+++++|+.+|..+..
T Consensus        18 ~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e--------ddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           18 EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             EEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             EEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc--------CCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            578999999999999999999999999998 99965        247999999 89999999999987644

>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=98.95  E-value=2.3e-10  Score=78.76  Aligned_cols=66  Identities=17%  Similarity=0.175  Sum_probs=58.5

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCe-EEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhcCC
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQ-IVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~-I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~  221 (238)
                      ++...|.||++.++.+||++|.+|++|+++|||. |.+.++         ...|+|.| +.+++++|+.+|+.+-..
T Consensus        14 ~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed---------dG~V~I~g~~~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           14 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED---------TGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             ceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC---------CCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            3568999999999999999999999999999998 999642         36899999 799999999999887744

>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=98.80  E-value=6e-09  Score=76.96  Aligned_cols=70  Identities=13%  Similarity=0.224  Sum_probs=55.9

Q ss_pred             EEEecCC------ccceeeccCCccHHHHHHHcCCEEEecCCCCCC-------------CCCCCCeEEEEe-CHHHHHHH
Q psy11278          2 KLDVSYT------DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSV-------------NAEKSNQVSIAG-SLLGLERA   61 (238)
Q Consensus         2 ~i~ip~~------~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~-------------~~~~~~~v~I~G-~~~~v~~A   61 (238)
                      +|.||.+      ++|.|||++|.+||+|+++|||+|.|.......             ..+++..|.|++ +.+.+.+|
T Consensus        10 kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~~~A   89 (131)
T 1k1g_A           10 KVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKA   89 (131)
T ss_dssp             EEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHH
T ss_pred             EEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHHHHH
Confidence            6788988      667999999999999999999999997632110             012356899999 68999999


Q ss_pred             HHHHHhhCCc
Q psy11278         62 RYRVRELTPL   71 (238)
Q Consensus        62 ~~~I~~~~~~   71 (238)
                      +++|+.++..
T Consensus        90 ~~~I~~ll~~   99 (131)
T 1k1g_A           90 VEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHhc
Confidence            9999998643

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.74  E-value=1.6e-08  Score=73.24  Aligned_cols=63  Identities=19%  Similarity=0.196  Sum_probs=49.3

Q ss_pred             CccceeeccCCccHHHHHHHcCCEEEecCCCCC------CC-CCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          8 TDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRS------VN-AEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         8 ~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~------~~-~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      +.++.|||++|.+|++|+++|||+|.|......      .. .+++..|.|++ +.+++++|+.+|++++.
T Consensus        28 n~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~~Ie~Ll~   98 (119)
T 2yqr_A           28 NVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKKLCENLLQ   98 (119)
T ss_dssp             CHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHHHHHHHhh
Confidence            367899999999999999999999999743211      00 11345888887 68999999999988754

>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=98.60  E-value=6.6e-08  Score=71.35  Aligned_cols=76  Identities=16%  Similarity=0.111  Sum_probs=58.6

Q ss_pred             EEEEEEeCCC------eeeEEecCCCchHHHHHHHhCCeEEccCCCCC------------CCCCCcceEEEEEc-CHHHH
Q psy11278        148 VIMMMEISPQ------HHPIMEGPNAINLKTIMAQTGAQIVFPEANDP------------IIPVLKKSSVTVSG-NIDSV  208 (238)
Q Consensus       148 ~~~~v~i~~~------~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~------------~~~~~~~~~v~I~G-~~~~v  208 (238)
                      ++..|.||..      ++|.|||.+|.+|++|+++|||+|.+-....-            .....+.-.|.|++ +.+.+
T Consensus         7 ~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~   86 (131)
T 1k1g_A            7 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   86 (131)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             EEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHH
Confidence            5578899888      77899999999999999999999998542110            00011246788999 59999


Q ss_pred             HHHHHHHHhhcCCCC
Q psy11278        209 YLARQMLVVSSVRPR  223 (238)
Q Consensus       209 ~~A~~~I~~~l~~~~  223 (238)
                      .+|..+|+.++....
T Consensus        87 ~~A~~~I~~ll~~~~  101 (131)
T 1k1g_A           87 KKAVEQIRNILKQGI  101 (131)
T ss_dssp             HHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHhccC
Confidence            999999999996533

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.43  E-value=1.5e-07  Score=75.50  Aligned_cols=52  Identities=29%  Similarity=0.403  Sum_probs=47.9

Q ss_pred             ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ..|.||||+|+|++.|++.|||+|.|++          +.|.|.|++++++.|+..|.+++.
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~~----------~~v~i~G~~~~i~~A~~~i~~li~  190 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVYG----------KTVAIIGNPIQIEIAKTAIEKLAR  190 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEET----------TEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             hhheeECCCchHHHHHHHHhCceEEECC----------eEEEEEeCHHHHHHHHHHHHHHHc
Confidence            5788999999999999999999999964          589999999999999999998854

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.43  E-value=2.1e-07  Score=69.05  Aligned_cols=69  Identities=29%  Similarity=0.358  Sum_probs=52.7

Q ss_pred             EEEecCCc------cceeeccCCccHHHHHHHcCCEEEecCCCCCC-----------C----CCCCCeEEEEeC-HH---
Q psy11278          2 KLDVSYTD------HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSV-----------N----AEKSNQVSIAGS-LL---   56 (238)
Q Consensus         2 ~i~ip~~~------~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~-----------~----~~~~~~v~I~G~-~~---   56 (238)
                      +|.||-+.      +|.|||++|.++|+|+++|||+|.|......-           +    .++.-.|.|++. ++   
T Consensus         5 Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~   84 (140)
T 2bl5_A            5 KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRA   84 (140)
T ss_dssp             EEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHH
T ss_pred             EEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhH
Confidence            56777655      78999999999999999999999998754211           0    112348889984 43   


Q ss_pred             --HHHHHHHHHHhhCC
Q psy11278         57 --GLERARYRVRELTP   70 (238)
Q Consensus        57 --~v~~A~~~I~~~~~   70 (238)
                        .+.+|++.|++++.
T Consensus        85 ~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           85 ELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHCC
Confidence              79999999998853

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.41  E-value=4.8e-07  Score=65.47  Aligned_cols=72  Identities=15%  Similarity=0.154  Sum_probs=52.6

Q ss_pred             EEEEEEeCCC-------eeeEEecCCCchHHHHHHHhCCeEEccCCCCC------CCCCCcceEEEEEc-CHHHHHHHHH
Q psy11278        148 VIMMMEISPQ-------HHPIMEGPNAINLKTIMAQTGAQIVFPEANDP------IIPVLKKSSVTVSG-NIDSVYLARQ  213 (238)
Q Consensus       148 ~~~~v~i~~~-------~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~------~~~~~~~~~v~I~G-~~~~v~~A~~  213 (238)
                      ++..+.||-.       +++.|||++|.+|++|+++|||+|.+-...+.      .....+.-.|.|.+ +++++++|+.
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            3455655543       67889999999999999999999999532110      00011234688887 5999999999


Q ss_pred             HHHhhc
Q psy11278        214 MLVVSS  219 (238)
Q Consensus       214 ~I~~~l  219 (238)
                      +|++++
T Consensus        92 ~Ie~Ll   97 (119)
T 2yqr_A           92 LCENLL   97 (119)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            999998

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.21  E-value=5.5e-07  Score=82.73  Aligned_cols=59  Identities=24%  Similarity=0.423  Sum_probs=51.9

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC-HHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~~   69 (238)
                      .+.||.+.++.+||++|++|+.|+++|||+|++.+         +..|.|.|. .+.+++|+++|..+.
T Consensus       570 ~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d---------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          570 TVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD---------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS---------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             EEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC---------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999974         369999985 789999999997763

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=98.15  E-value=2.8e-06  Score=61.92  Aligned_cols=68  Identities=12%  Similarity=0.041  Sum_probs=60.1

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP  222 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  222 (238)
                      ..|.+.+..++.|||++|+.|+.|+..|+|.|.+..-+..     +...|+|.|++..-..|+.+|+.+...+
T Consensus        58 lVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~-----g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           58 KRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPE-----RRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             EEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTT-----SCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCC-----CcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            6788999999999999999999999999999999765433     4789999999999999999999887443

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.06  E-value=3.7e-06  Score=77.22  Aligned_cols=85  Identities=18%  Similarity=0.297  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHHhhccc-------cccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278        125 ERVKEATTKLIEHMCGSL-------ANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS  197 (238)
Q Consensus       125 ~~a~~ai~~~~~~~~~~~-------~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~  197 (238)
                      +.|+++...+++.+.+.+       ....+....+.||+..++.+||++|++|++|.++|||.|.+.+          ..
T Consensus       537 ~~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d----------~G  606 (630)
T 3u1k_A          537 QQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD----------EE  606 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS----------SS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC----------Cc
Confidence            455555566665554322       2223456889999999999999999999999999999999863          25


Q ss_pred             EEEEEcC-HHHHHHHHHHHHhhc
Q psy11278        198 SVTVSGN-IDSVYLARQMLVVSS  219 (238)
Q Consensus       198 ~v~I~G~-~~~v~~A~~~I~~~l  219 (238)
                      .|+|.|+ .++..+|+.+|.+++
T Consensus       607 ~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          607 TFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEESSHHHHHHHHHHTTC--
T ss_pred             EEEEEeCCHHHHHHHHHHHHHHh
Confidence            8999997 788999999998765

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.92  E-value=8.1e-06  Score=60.52  Aligned_cols=71  Identities=14%  Similarity=0.104  Sum_probs=51.0

Q ss_pred             EEEEeCC------CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCC--------------CCCcceEEEEEcC-HH--
Q psy11278        150 MMMEISP------QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPII--------------PVLKKSSVTVSGN-ID--  206 (238)
Q Consensus       150 ~~v~i~~------~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~--------------~~~~~~~v~I~G~-~~--  206 (238)
                      ..|.||-      +++|.|||.+|.++|+|+++|||+|.+-...+-..              ...+.=-|.|++. ++  
T Consensus         4 ~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~   83 (140)
T 2bl5_A            4 EKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNR   83 (140)
T ss_dssp             EEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHH
T ss_pred             eEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhh
Confidence            5566654      34889999999999999999999998865432100              0001126788884 43  


Q ss_pred             ---HHHHHHHHHHhhcC
Q psy11278        207 ---SVYLARQMLVVSSV  220 (238)
Q Consensus       207 ---~v~~A~~~I~~~l~  220 (238)
                         .+.+|..+|+.+|.
T Consensus        84 ~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           84 AELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHCC
Confidence               79999999999993

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.91  E-value=1.6e-05  Score=57.90  Aligned_cols=64  Identities=14%  Similarity=0.091  Sum_probs=55.2

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      .+.+.....+.|+|++|+.|+.|+..|++.|++..-+..    ....|+|.|++..=.+|+.+|..+.
T Consensus        59 VF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~----g~tEVtIfG~~~~Q~rak~MI~sLA  122 (140)
T 3v69_A           59 RLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPE----RRAEIWIFGPPPFRRDVDRMLTDLA  122 (140)
T ss_dssp             EEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTT----SCEEEEEESCHHHHHHHHHHHHHHH
T ss_pred             EEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCC----CcEEEEEECCHHHHHHHHHHHHHHH
Confidence            467888999999999999999999999999999775321    3569999999999999999997663

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.65  E-value=8.6e-06  Score=75.75  Aligned_cols=86  Identities=20%  Similarity=0.328  Sum_probs=11.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTPLIFCFEYPLM   80 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~~~~~~~p~~   80 (238)
                      .+.||.+.++.+||+||++|+.|+++||++|++.+         +..|.|.+ +.+.+++|+..|..+....   +   .
T Consensus       573 ~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d---------dG~v~I~~~~~~~~~~A~~~i~~i~~~~---~---v  637 (726)
T 4aid_A          573 TINIPTDKIREVIGSGGKVIREIVATTGAKVDIND---------DGVVKVSASDGAKIKAAIDWIKSITDEA---E---V  637 (726)
T ss_dssp             --------------------------------------------------CCSCHHHHHHHHHC----------------
T ss_pred             EEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC---------CceEEEEeCCHHHHHHHHHHHHHHhhhh---c---C
Confidence            46799999999999999999999999999999964         35788876 5899999999998875422   1   1


Q ss_pred             CCCCCCCChHHHHHHHHhCceEEeeC
Q psy11278         81 GSTPNANSPFVQIIQEAYNVQVMFRN  106 (238)
Q Consensus        81 ~~~~~~~g~~i~~i~~~~gv~I~~~~  106 (238)
                      +-  -+.| .+..+. .||+.+.+.+
T Consensus       638 G~--v~~G-~V~~I~-~fGaFVel~~  659 (726)
T 4aid_A          638 GK--IYDG-KVVKVV-DFGAFVNFFG  659 (726)
T ss_dssp             --------------------------
T ss_pred             Cc--EEEE-EEEEEe-ccEEEEEECC
Confidence            10  0122 345554 6777777653

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.45  E-value=6.8e-05  Score=69.78  Aligned_cols=88  Identities=17%  Similarity=0.231  Sum_probs=23.7

Q ss_pred             hHHHHHHHHHHHHHhhcccc-------ccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcc
Q psy11278        124 VERVKEATTKLIEHMCGSLA-------NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKK  196 (238)
Q Consensus       124 v~~a~~ai~~~~~~~~~~~~-------~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~  196 (238)
                      .+.|+++...+++.+.+.+.       ...+....+.||+...+.+||++|.+|++|.++||+.|.+.+          .
T Consensus       539 L~~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d----------d  608 (726)
T 4aid_A          539 LAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND----------D  608 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCSSCCSSCCC------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC----------C
Confidence            34555566666665544332       122344788999999999999999999999999999998863          2


Q ss_pred             eEEEEEcC-HHHHHHHHHHHHhhcCC
Q psy11278        197 SSVTVSGN-IDSVYLARQMLVVSSVR  221 (238)
Q Consensus       197 ~~v~I~G~-~~~v~~A~~~I~~~l~~  221 (238)
                      ..|.|.++ .++.++|+.+|..++..
T Consensus       609 G~v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          609 GVVKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             -----CCSCHHHHHHHHHC-------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHhhh
Confidence            56788886 88999999999988743

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.56  E-value=0.0022  Score=59.92  Aligned_cols=59  Identities=29%  Similarity=0.463  Sum_probs=0.0

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~   69 (238)
                      .+.||.+.++.+||++|.+|+.|.++||+.|++.+         +..|.|.+ +.+.+++|++.|..+.
T Consensus       563 ~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---------dg~v~I~~~~~~~~~~a~~~i~~i~  622 (723)
T 3cdi_A          563 TIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---------DGTVKIAATDGEKAKHAIRRIEEIT  622 (723)
T ss_dssp             ---------------------------------------------------------------------
T ss_pred             EEEECHHHhcccccccceeeeeeehhhCceEEecC---------CccEEEecCCHHHHHHHHHHHHHHh
Confidence            46799999999999999999999999999998865         25677766 5678888888887664

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.23  E-value=0.0076  Score=56.29  Aligned_cols=85  Identities=14%  Similarity=0.215  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHhhcccc-------ccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278        125 ERVKEATTKLIEHMCGSLA-------NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS  197 (238)
Q Consensus       125 ~~a~~ai~~~~~~~~~~~~-------~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~  197 (238)
                      +.|+++...+++.+.+.+.       ...+....+.||+...+.+||++|.+|+.|.+++|+.|.+..          ..
T Consensus       530 ~~A~~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~----------dg  599 (723)
T 3cdi_A          530 NQAKGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED----------DG  599 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHCC-------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC----------Cc
Confidence            4455555555555443222       122344778899999999999999999999999999997764          14


Q ss_pred             EEEEEcC-HHHHHHHHHHHHhhc
Q psy11278        198 SVTVSGN-IDSVYLARQMLVVSS  219 (238)
Q Consensus       198 ~v~I~G~-~~~v~~A~~~I~~~l  219 (238)
                      .+.|.+. .+...+|+.+|..+.
T Consensus       600 ~v~I~~~~~~~~~~a~~~i~~i~  622 (723)
T 3cdi_A          600 TVKIAATDGEKAKHAIRRIEEIT  622 (723)
T ss_dssp             -----------------------
T ss_pred             cEEEecCCHHHHHHHHHHHHHHh
Confidence            5666664 667777887777665

>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=95.03  E-value=0.0011  Score=62.27  Aligned_cols=59  Identities=19%  Similarity=0.335  Sum_probs=19.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~   69 (238)
                      .+.||.+.++.+||++|++|+.|.++||+.|++.+         ++.|.|++ +....++|++.|..+.
T Consensus       601 ~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~---------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          601 TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CC------------------CTTCCCCCSCC-----------------CCCBSSHHHHCC---------
T ss_pred             EEEEChHHeehcccccceeeehhhHhhCCEEEecC---------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            46799999999999999999999999999999974         25677766 5677778887776654

>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=93.87  E-value=0.0051  Score=57.69  Aligned_cols=85  Identities=15%  Similarity=0.263  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHhhcccc------ccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceE
Q psy11278        125 ERVKEATTKLIEHMCGSLA------NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSS  198 (238)
Q Consensus       125 ~~a~~ai~~~~~~~~~~~~------~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~  198 (238)
                      +.|+++...+++.+.+.+.      ...+....+.||+...+.+||++|..|++|.+++|+.|.+..          ...
T Consensus       569 ~~A~~~~~~I~~~m~~al~~~~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~----------dG~  638 (757)
T 1e3p_A          569 KQARDARLHILDVMMEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----------DGT  638 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSCCCCCTTSCBCCCC------------------CTTCCCCCSCC-----------------
T ss_pred             HHHHHHHHHHHHHHHHHhcccccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC----------Cce
Confidence            5555555556555433221      112333678899999999999999999999999999998864          145


Q ss_pred             EEEEcC-HHHHHHHHHHHHhhc
Q psy11278        199 VTVSGN-IDSVYLARQMLVVSS  219 (238)
Q Consensus       199 v~I~G~-~~~v~~A~~~I~~~l  219 (238)
                      |.|.+. .+...+|+.+|..+.
T Consensus       639 v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          639 IYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             -CCCBSSHHHHCC---------
T ss_pred             EEEecCCHHHHHHHHHHHHHhc
Confidence            777765 566666776766654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=92.37  E-value=0.043  Score=40.65  Aligned_cols=36  Identities=31%  Similarity=0.371  Sum_probs=32.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDS   37 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~   37 (238)
                      .+.|+...+|..||++|++++.|++++|-+|++-.-
T Consensus        39 i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~   74 (144)
T 2cxc_A           39 IFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEY   74 (144)
T ss_dssp             EEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEEC
T ss_pred             EEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEc
Confidence            467888999999999999999999999999998664

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=85.37  E-value=0.33  Score=35.88  Aligned_cols=36  Identities=17%  Similarity=0.155  Sum_probs=32.4

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      +-+.+++..+|..||++|++|+.++++.|-+|.+-.
T Consensus        38 ~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~   73 (144)
T 2cxc_A           38 LIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE   73 (144)
T ss_dssp             EEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE
T ss_pred             EEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE
Confidence            678888999999999999999999999999996644

>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=85.12  E-value=0.27  Score=39.72  Aligned_cols=37  Identities=19%  Similarity=0.239  Sum_probs=33.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN   38 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~   38 (238)
                      .+.||.++.+.-|||+|.|++--.+-||.+|+|.+..
T Consensus       187 ~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          187 RVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            4678999999999999999999999999999996644

---

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	238
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-11
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-11
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-11
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-08
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-10
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	8e-10
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-07
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-04
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-08
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	9e-04
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-04
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	0.004
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-07
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	0.002
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	6e-07
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-04
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	7e-07
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	0.004
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	2e-06
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	3e-04
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-06
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	0.004
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-04
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	8e-05
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	9e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.003

>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 = 56.3 bits (136), Expect = 2e-11
 Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
            + +    H  +IG+ G  ++ +  +T   +  P  +     + SNQ+ I G+  G+E+
Sbjct: 12 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEK 66

Query: 61 ARYRVRELT 69
          AR+ V  ++
Sbjct: 67 ARHEVLLIS 75

>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 = 47.4 bits (113), Expect = 3e-08
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN 204
           QT     + I  +HH  + G N   L+ +  +T  +I  P  +DP       + + ++G 
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------SNQIKITGT 60

Query: 205 IDSVYLARQML 215
            + +  AR  +
Sbjct: 61  KEGIEKARHEV 71

>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 = 55.2 bits (133), Expect = 4e-11
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          + + V    H  IIGR G  I ++  E   ++ FPD +     +  +Q++I G     E 
Sbjct: 12 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG--NQPQDQITITGYEKNTEA 69

Query: 61 ARYRVRELT 69
          AR  +  + 
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 = 45.2 bits (107), Expect = 2e-07
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
           S  + + + P++HP + G     +  I  +    I FP+ +D   P   +  +T++G   
Sbjct: 9   SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQP---QDQITITGYEK 65

Query: 207 SVYLARQML 215
           +   AR  +
Sbjct: 66  NTEAARDAI 74

>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 = 54.8 bits (132), Expect = 7e-11
 Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          ++++V +  H ++IG+ G  I+K+M+E   ++H P         +S+ ++I G    L+R
Sbjct: 12 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDR 66

Query: 61 ARYRVRELT 69
          A+  + E  
Sbjct: 67 AKAGLLERV 75

>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 = 48.3 bits (115), Expect = 2e-08
 Identities = 11/75 (14%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 141 SLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVT 200
           +L     V + +E+    H  + G     ++ +M +    I  P              + 
Sbjct: 3   ALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQ------SDIIA 56

Query: 201 VSGNIDSVYLARQML 215
           ++G   ++  A+  L
Sbjct: 57  ITGLAANLDRAKAGL 71

>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 = 54.0 bits (130), Expect = 1e-10
 Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 2  KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
          ++++ +  H H+IG+ G  I ++ ++    V  P  +     EKSN + I G   G+++A
Sbjct: 8  EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQA 62

Query: 62 RYRVRELT 69
          +  + EL 
Sbjct: 63 KRELLELA 70

>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 = 45.5 bits (108), Expect = 1e-07
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 6/64 (9%)

Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
           + I  + H  + G +  N+  I  Q    +  P  ++        + + + G+   V  A
Sbjct: 9   INIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK------SNLIRIEGDPQGVQQA 62

Query: 212 RQML 215
           ++ L
Sbjct: 63  KREL 66

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (124), Expect = 8e-10
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
            + + +  H+ IIG  G  I+K+M+E    + FP S         N V++ G    +E 
Sbjct: 12 EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEE 67

Query: 61 ARYRVRELT 69
          A   +  L 
Sbjct: 68 AIDHILNLE 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 = 44.4 bits (105), Expect = 4e-07
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 5/71 (7%)

Query: 145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN 204
           +  V   + +  + H  + G     ++ IM +    I FP++  P       + VTV+G 
Sbjct: 7   EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP-----DPNCVTVTGL 61

Query: 205 IDSVYLARQML 215
            ++V  A   +
Sbjct: 62  PENVEEAIDHI 72

>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 = 48.3 bits (115), Expect = 1e-08
 Identities = 15/68 (22%), Positives = 32/68 (47%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          +++ V       I+G+GG T+ +  E TG  +        +   ++ +V+I GS    + 
Sbjct: 5  VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 61 ARYRVREL 68
          A+Y + + 
Sbjct: 65 AQYLISQR 72

>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 = 37.1 bits (86), Expect = 2e-04
 Identities = 12/67 (17%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSV 208
           ++ M +       + G     L      TGA+I   +  +  +P  +   VT++G+  + 
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF-LPGTRNRRVTITGSPAAT 62

Query: 209 YLARQML 215
             A+ ++
Sbjct: 63  QAAQYLI 69

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 2e-08
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +L V       IIGRGG TI+ + + +G  +     +       S  + I+G+   +  
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISGTQKEVAA 75

Query: 61 ARYRVRELT 69
          A++ + E  
Sbjct: 76 AKHLILEKV 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 = 48.4 bits (115), Expect = 3e-08
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 140 GSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSV 199
           G L   T V   + +  +    + G     +++I   +GA+I   + ++    +L    +
Sbjct: 7   GILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG--TLLLSRLI 64

Query: 200 TVSGNIDSVYLARQML 215
            +SG    V  A+ ++
Sbjct: 65  KISGTQKEVAAAKHLI 80

>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 = 47.9 bits (114), Expect = 2e-08
 Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 2  KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
          +  V       IIGRGG  I ++ +E+GC +     +            + G+   ++ A
Sbjct: 11 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG---LPERSCMLTGTPESVQSA 67

Query: 62 RYRVREL 68
          +  + ++
Sbjct: 68 KRLLDQI 74

>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 = 35.2 bits (81), Expect = 9e-04
 Identities = 11/71 (15%), Positives = 29/71 (40%), Gaps = 4/71 (5%)

Query: 145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN 204
           ++ +    ++       + G     +  I  ++G +I     +      L + S  ++G 
Sbjct: 5   RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG----LPERSCMLTGT 60

Query: 205 IDSVYLARQML 215
            +SV  A+++L
Sbjct: 61  PESVQSAKRLL 71

>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 = 47.3 bits (112), Expect = 4e-08
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           ++ +  +    +IG+GG TIK++ E  G  +         N      + I G    +++
Sbjct: 10 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG-PQNTGADKPLRITGDPYKVQQ 68

Query: 61 ARYRVRELT 69
          A+  V EL 
Sbjct: 69 AKEMVLELI 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 = 36.8 bits (85), Expect = 2e-04
 Identities = 9/69 (13%), Positives = 27/69 (39%), Gaps = 2/69 (2%)

Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
           + +  + I      ++ G     +K +  + G ++V  +             + ++G+  
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ--NTGADKPLRITGDPY 64

Query: 207 SVYLARQML 215
            V  A++M+
Sbjct: 65  KVQQAKEMV 73

>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 = 45.3 bits (107), Expect = 1e-07
 Identities = 15/68 (22%), Positives = 27/68 (39%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
              V       IIG+GG TIK + +++G  +    +            +I G+   ++ 
Sbjct: 3  FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDY 62

Query: 61 ARYRVREL 68
          AR  + E 
Sbjct: 63 ARQLIEEK 70

>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 = 32.9 bits (75), Expect = 0.004
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
             +      ++ G     +K+I  Q+GA+I       P      K   T+ G    +  A
Sbjct: 5   FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMK-LFTIRGTPQQIDYA 63

Query: 212 RQML 215
           RQ++
Sbjct: 64  RQLI 67

>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 = 44.8 bits (106), Expect = 2e-07
 Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          ++L +   +   IIG+ G ++KK+ EE+G  ++  + N          +++AG    + +
Sbjct: 6  IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNAIFK 60

Query: 61 ARYRVREL 68
          A   + + 
Sbjct: 61 AFAMIIDK 68

>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 = 33.6 bits (77), Expect = 0.002
 Identities = 12/70 (17%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
           ++ + + +  +    + G    ++K +  ++GA+I   E N P      +  +T++G  +
Sbjct: 3   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAGPTN 56

Query: 207 SVYLARQMLV 216
           +++ A  M++
Sbjct: 57  AIFKAFAMII 66

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (104), Expect = 6e-07
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLE 59
          +++ +    H+ +IG  G  I+ +MEE  G H+HFP          S+ V I G    +E
Sbjct: 12 VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-----GSDTVVIRGPSSDVE 66

Query: 60 RARYRVRELT 69
          +A+ ++  L 
Sbjct: 67 KAKKQLLHLA 76

>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 = 37.5 bits (87), Expect = 1e-04
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 9/75 (12%)

Query: 142 LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQ-TGAQIVFPEANDPIIPVLKKSSVT 200
           LAN   V +   I  + H  + G     +++IM +  G  I FP             +V 
Sbjct: 6   LANIAEVEV--SIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSG------SDTVV 57

Query: 201 VSGNIDSVYLARQML 215
           + G    V  A++ L
Sbjct: 58  IRGPSSDVEKAKKQL 72

>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 = 43.3 bits (102), Expect = 7e-07
 Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 3/68 (4%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          + + +       +IGR G  IKK+  + G  + F   + +          I G     + 
Sbjct: 5  IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERI---AQITGPPDRAQH 61

Query: 61 ARYRVREL 68
          A   + +L
Sbjct: 62 AAEIITDL 69

>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 = 32.9 bits (75), Expect = 0.004
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 4/69 (5%)

Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
           S ++ + I      I+ G N   +K I    G +I F   +        +    ++G  D
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGT----TPERIAQITGPPD 57

Query: 207 SVYLARQML 215
               A +++
Sbjct: 58  RAQHAAEII 66

>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 = 42.5 bits (100), Expect = 2e-06
 Identities = 10/69 (14%), Positives = 28/69 (40%), Gaps = 9/69 (13%)

Query: 2  KLDVSYTDHSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
           +      H  IIG+ G  + K+ ++    H+ F +          +++++ G    +  
Sbjct: 24 SVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSV 75

Query: 61 ARYRVRELT 69
          A+ ++  + 
Sbjct: 76 AQEQIEGMV 84

>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 = 36.4 bits (84), Expect = 3e-04
 Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 16/94 (17%)

Query: 123 DVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQ-TGAQI 181
           + E++ +A T++           +  +  +      H  + G    NL  I  Q     I
Sbjct: 2   EPEKLGQALTEVYAKA------NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHI 55

Query: 182 VFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
            F E  D I          + G  + V +A++ +
Sbjct: 56  EFTEGEDKIT---------LEGPTEDVSVAQEQI 80

>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 = 41.4 bits (97), Expect = 4e-06
 Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 2  KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
          +L +       IIGR G  I ++ + +G  +   +     +  +   V+I GS   +  A
Sbjct: 5  ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQ---VTITGSAASISLA 61

Query: 62 RYRVRE 67
          +Y +  
Sbjct: 62 QYLINA 67

>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 = 32.9 bits (75), Expect = 0.004
 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 4/64 (6%)

Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
           + I       + G    N+  I   +GAQI      +          VT++G+  S+ LA
Sbjct: 6   LTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEG----SSGRQVTITGSAASISLA 61

Query: 212 RQML 215
           + ++
Sbjct: 62  QYLI 65

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 8/67 (11%), Positives = 21/67 (31%), Gaps = 9/67 (13%)

Query: 3  LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERAR 62
          + ++      +IG+ G  IK +  E    +    +           + + G    +  A 
Sbjct: 5  VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGL---------IWVNGDRRKVSIAE 55

Query: 63 YRVRELT 69
            +  + 
Sbjct: 56 EAIYLIE 62

>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 = 3e-04
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 10/65 (15%)

Query: 151 MMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYL 210
           ++ I+P   P + G     +K + ++   QIV  +             + V+G+   V +
Sbjct: 4   IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ----------NGLIWVNGDRRKVSI 53

Query: 211 ARQML 215
           A + +
Sbjct: 54  AEEAI 58

>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 = 39.9 bits (93), Expect = 2e-05
 Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 2  KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
          ++ +       IIG+GG  IK++  E+G  +   +            ++I G+   ++ A
Sbjct: 7  QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE---DRIITITGTQDQIQNA 63

Query: 62 RYRVREL 68
          +Y ++  
Sbjct: 64 QYLLQNS 70

>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 = 37.8 bits (88), Expect = 8e-05
 Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 3/69 (4%)

Query: 1  MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
          + + V       +IG  G    ++M  TG  +     N  V  E     +     + L +
Sbjct: 5  IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVE---PEAEGIPPVNLMK 61

Query: 61 ARYRVRELT 69
          A   V+ ++
Sbjct: 62 AAEVVKAIS 70

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.5 bits (82), Expect = 9e-04
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 10/59 (16%)

Query: 11 SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT 69
            IIG GG   + + E T  +++  +           +V+I G       A+  +  L 
Sbjct: 25 GRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLA 73

>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 = 33.2 bits (76), Expect = 0.003
 Identities = 9/68 (13%), Positives = 24/68 (35%), Gaps = 10/68 (14%)

Query: 3  LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERA 61
          +D+       +IG+     + +  ++GC +   ++ R         +     S    E  
Sbjct: 5  IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGR---------IWATCPSRFSEEIL 55

Query: 62 RYRVRELT 69
             +R++ 
Sbjct: 56 IEAIRKIE 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	238
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.66
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.66
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.64
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.63
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.62
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.61
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.6
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.6
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.6
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.59
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.59
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.59
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.59
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.58
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.58
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.58
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.56
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.56
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.56
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.54
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.53
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.53
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.52
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.49
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.4
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.39
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.36
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.29
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.2
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.15
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	99.09
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.98
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.87
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.85
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.78
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.77
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.64
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.42
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.38
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.0
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.78
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.19
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.84
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.64
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.21
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.7
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	91.55
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	89.61
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	83.08
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	81.68
d1mlaa2	70	Probable ACP-binding domain of malonyl-CoA ACP tra	80.98

>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=99.66  E-value=5.7e-17  Score=107.27  Aligned_cols=69  Identities=22%  Similarity=0.385  Sum_probs=62.1

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      +++.||.+++|.||||+|++|++|+++|||+|++++..+..+...++.|+|+|++++|..|+.+|.+.+
T Consensus         5 i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            478999999999999999999999999999999988766555556789999999999999999998764

>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=99.66  E-value=4.7e-17  Score=106.84  Aligned_cols=67  Identities=22%  Similarity=0.351  Sum_probs=60.3

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL   68 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~   68 (238)
                      +|.||.+.+|.||||+|++|++|+++|||+|++++..+..+.+.++.|+|+|++++|..|+.+|.+.
T Consensus         4 ~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~   70 (71)
T d1j4wa2           4 NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK   70 (71)
T ss_dssp             EEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             EEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhh
Confidence            6899999999999999999999999999999998766544445668999999999999999999875

>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=99.64  E-value=1.4e-16  Score=104.44  Aligned_cols=65  Identities=17%  Similarity=0.301  Sum_probs=60.4

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ..++.||..+|++|||++|++|++|+++|||+|.||+..++      .+.|+|+|++++|..|+++|+++.
T Consensus         6 ~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~------~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           6 YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK------SNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSS------SEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCCCC------CCEEEEECCHHHHHHHHHHHHHHh
Confidence            37899999999999999999999999999999999987654      589999999999999999999986

>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=99.64  E-value=1.2e-16  Score=104.81  Aligned_cols=63  Identities=27%  Similarity=0.542  Sum_probs=58.4

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      ++.||.++|++|||++|++|++|+++|||+|+||+.++     .++.|+|+|++++|++|+++|+++.
T Consensus         8 ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~-----~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           8 EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-----KSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCS-----SSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCCC-----CCCEEEEECCHHHHHHHHHHHHHHh
Confidence            68899999999999999999999999999999988654     5679999999999999999999875

>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=99.64  E-value=1.6e-16  Score=106.86  Aligned_cols=68  Identities=22%  Similarity=0.279  Sum_probs=61.9

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      ++.++.||..+|++|||++|++|++|+++|||+|.||...+++     .+.|+|+|++++|.+|+++|+++++
T Consensus        10 ~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~-----~~~v~I~G~~~~V~~A~~~I~~i~~   77 (81)
T d2ctma1          10 VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD-----PNCVTVTGLPENVEEAIDHILNLEE   77 (81)
T ss_dssp             CCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSC-----TTEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCC-----CCEEEEeCCHHHHHHHHHHHHHHHH
Confidence            3489999999999999999999999999999999999877653     5789999999999999999998873

>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=99.63  E-value=1.7e-16  Score=104.07  Aligned_cols=69  Identities=19%  Similarity=0.250  Sum_probs=60.6

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .+|.||..++|+|||++|++|++|++.|||+|.++...++.. ...++.|+|+|++++|++|+.+|.+++
T Consensus         3 ~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~-~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           3 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA-DPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTS-CTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCC-CCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            688999999999999999999999999999999987654331 225689999999999999999999875

>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=99.62  E-value=2.1e-16  Score=103.26  Aligned_cols=67  Identities=21%  Similarity=0.262  Sum_probs=60.5

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +.+|.||..++|+|||++|.+|++|+++|||+|.+++.....    +++.|+|+|++++|..|+.+|++.|
T Consensus         3 T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~----~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           3 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGS----SGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTC----SEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             EEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCC----CcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            588999999999999999999999999999999997654332    4689999999999999999999887

>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=99.62  E-value=1.8e-16  Score=106.65  Aligned_cols=66  Identities=23%  Similarity=0.451  Sum_probs=61.9

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++.+|.||..+|++|||++|.+|++|+++|||+|.||...++      .+.|+|+|++++|.+|+.+|++++
T Consensus        10 ~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~------~~~v~I~G~~~~v~~A~~~I~~iv   75 (81)
T d2ctea1          10 ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------SNQIKITGTKEGIEKARHEVLLIS   75 (81)
T ss_dssp             EEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSS------CCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCCCC------CCEEEEEeCHHHHHHHHHHHHHHH
Confidence            458999999999999999999999999999999999987765      589999999999999999999987

>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=99.61  E-value=6.2e-16  Score=102.20  Aligned_cols=69  Identities=17%  Similarity=0.236  Sum_probs=61.2

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .++.||..++|+|||++|++|++|+++|||+|.+++..++. +...++.|+|+|++++|..|+.+|.++|
T Consensus         5 i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL-PGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS-TTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCC-CCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            78999999999999999999999999999999998765432 1225789999999999999999999987

>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=99.60  E-value=2.1e-16  Score=103.63  Aligned_cols=67  Identities=18%  Similarity=0.338  Sum_probs=62.1

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +++.++.+|.+++|+|||++|++|++|+++|||+|.+++...+      ++.|+|+|++++|.+|+.+|.++|
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~------er~v~I~G~~~~v~~A~~~I~~~l   69 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAGPTNAIFKAFAMIIDKL   69 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCS------EEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCCCC------cceEEEEECHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999999886654      689999999999999999999887

>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=99.60  E-value=1.1e-16  Score=105.02  Aligned_cols=64  Identities=22%  Similarity=0.362  Sum_probs=58.4

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      +++.||.+++|.||||+|++|++|+++|||+|++++...     .++.|+|+|++++|.+|+.+|.+++
T Consensus         6 ~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~-----~er~v~I~G~~~~v~~A~~~I~~~l   69 (71)
T d2axya1           6 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC-----PERIITLAGPTNAIFKAFAMIIDKL   69 (71)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCC-----SEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCCC-----CcceEEEEECHHHHHHHHHHHHHHh
Confidence            478999999999999999999999999999999987544     4689999999999999999998764

>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=6.2e-16  Score=102.54  Aligned_cols=69  Identities=20%  Similarity=0.253  Sum_probs=61.4

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      ++.+|.||..++++|||++|++|++|+++|||+|.++++.+..    .++.|+|+|++++|..|+.+|.+++.
T Consensus         4 ~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~----~~r~i~I~G~~~~v~~A~~~I~~~i~   72 (75)
T d1zzka1           4 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS----EDRIITITGTQDQIQNAQYLLQNSVK   72 (75)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCS----SEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCC----CceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            4589999999999999999999999999999999997654322    46899999999999999999999873

>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=99.59  E-value=7.5e-16  Score=104.34  Aligned_cols=69  Identities=19%  Similarity=0.349  Sum_probs=61.8

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++..|.||..+|++|||++|++|++|+++|||+|.||+...++.   ..+.|+|+|++++|..|+.+|.+++
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~---~~~~i~I~G~~e~v~~A~~~I~~~i   78 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQ---PQDQITITGYEKNTEAARDAILRIV   78 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSS---CSSEEEEESCHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCC---CcceEEEECCHHHHHHHHHHHHHHH
Confidence            45889999999999999999999999999999999987654432   4678999999999999999999987

>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=99.59  E-value=1e-15  Score=102.93  Aligned_cols=65  Identities=28%  Similarity=0.443  Sum_probs=58.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||..+|+.|||++|++|++|+++|||+|+||+.++.    .++.|+|+|++++|++|+++|+++..
T Consensus        13 ~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~----~~~~v~I~G~~~~V~~A~~~I~~i~~   77 (81)
T d2ctma1          13 DVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP----DPNCVTVTGLPENVEEAIDHILNLEE   77 (81)
T ss_dssp             EEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCS----CTTEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCC----CCCEEEEeCCHHHHHHHHHHHHHHHH
Confidence            588999999999999999999999999999999986542    35799999999999999999988754

>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=99.59  E-value=6.5e-16  Score=100.92  Aligned_cols=65  Identities=23%  Similarity=0.403  Sum_probs=58.0

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      +|.||.+++|+||||+|++|++|+++|||+|++++...   ...++.|+|+|++++|+.|+.+|.+.+
T Consensus         5 ~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           5 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCT---TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             EEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCC---CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            68999999999999999999999999999999977553   224579999999999999999997754

>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=3.2e-16  Score=103.63  Aligned_cols=67  Identities=18%  Similarity=0.226  Sum_probs=60.8

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ..+|.||..++++|||++|++|++|+++|||+|.++...+..    .++.|+|+|++++|..|+.+|.++|
T Consensus         4 ~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~----~~r~v~I~G~~~~v~~A~~~I~~~i   70 (74)
T d1j4wa1           4 MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTT----PERIAQITGPPDRAQHAAEIITDLL   70 (74)
T ss_dssp             EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSC----SEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCC----CeeEEEEEeCHHHHHHHHHHHHHHH
Confidence            489999999999999999999999999999999998765432    4689999999999999999999987

>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=99.58  E-value=2.5e-16  Score=104.13  Aligned_cols=66  Identities=20%  Similarity=0.341  Sum_probs=58.9

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      +++.||.+++|.||||+|++|++|+++|||+|++++.++.   ..++.|+|+|++++|.+|+.+|.+++
T Consensus         5 ~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~---~~~r~v~I~G~~~~v~~A~~~I~~~i   70 (74)
T d1j4wa1           5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGT---TPERIAQITGPPDRAQHAAEIITDLL   70 (74)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTS---CSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCC---CCeeEEEEEeCHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999876542   24579999999999999999998764

>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=99.58  E-value=6.9e-16  Score=106.10  Aligned_cols=70  Identities=14%  Similarity=0.216  Sum_probs=63.6

Q ss_pred             ccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        144 NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       144 ~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ....++.+|.||+.+|++|||++|.+|++|+++|||.|.||..++.      .+.|+|+|++++|..|+.+|++++
T Consensus         6 ~~~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~------~~~v~I~G~~~~V~~A~~~I~~~v   75 (91)
T d2ctka1           6 ALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQ------SDIIAITGLAANLDRAKAGLLERV   75 (91)
T ss_dssp             CSSCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTT------CCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             hhCCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCCCC------cceEEEECCHHHHHHHHHHHHHHH
Confidence            3345779999999999999999999999999999999999987654      578999999999999999999987

>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=99.58  E-value=1.5e-15  Score=102.87  Aligned_cols=68  Identities=26%  Similarity=0.449  Sum_probs=59.4

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +++.||.++|+.|||++|++|++|+++|||+|+||+....  ...++.|+|+|++++|.+|+.+|.+++.
T Consensus        12 ~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~--~~~~~~i~I~G~~e~v~~A~~~I~~~i~   79 (84)
T d2ctla1          12 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG--NQPQDQITITGYEKNTEAARDAILRIVG   79 (84)
T ss_dssp             EEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTC--SSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCC--CCCcceEEEECCHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999999999999875542  2246799999999999999999987743

>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=99.57  E-value=1e-15  Score=102.88  Aligned_cols=64  Identities=25%  Similarity=0.489  Sum_probs=58.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.++|++|||++|++|++|+++|||+|++|..++     .++.|+|+|++++|++|+.+|++++.
T Consensus        13 ~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-----~~~~v~I~G~~~~v~~A~~~I~~iv~   76 (81)
T d2ctea1          13 TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-----PSNQIKITGTKEGIEKARHEVLLISA   76 (81)
T ss_dssp             EEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTS-----SCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCCC-----CCCEEEEEeCHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999988654     56899999999999999999988753

>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=99.56  E-value=2.3e-15  Score=99.74  Aligned_cols=65  Identities=20%  Similarity=0.430  Sum_probs=58.0

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      ++.||.+++|.|||++|++|++|+++|||+|++++..+   ...++.|+|+|++++|+.|+.+|.+++
T Consensus         7 ~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~---~~~~r~i~I~G~~~~v~~A~~~I~~~i   71 (75)
T d1zzka1           7 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQDQIQNAQYLLQNSV   71 (75)
T ss_dssp             EEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTS---CSSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCC---CCCceEEEEEeCHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999977543   225679999999999999999998764

>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=99.56  E-value=9.5e-16  Score=103.35  Aligned_cols=65  Identities=22%  Similarity=0.345  Sum_probs=59.8

Q ss_pred             EEEEEeCCCeeeEEecCCCchHHHHHHH-hCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        149 IMMMEISPQHHPIMEGPNAINLKTIMAQ-TGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~-tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      +.+|.||+.+|++|||++|++|++|+++ ++|+|.||...++      .+.|+|+|++++|.+|+.+|++++
T Consensus        11 t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~------~~~v~I~G~~~~v~~A~~~I~~~v   76 (82)
T d2ctja1          11 EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSG------SDTVVIRGPSSDVEKAKKQLLHLA   76 (82)
T ss_dssp             CEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTT------CCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             EEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCC------CceEEEeCCHHHHHHHHHHHHHHH
Confidence            4889999999999999999999999977 6999999987654      589999999999999999999987

>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=99.56  E-value=1.2e-15  Score=102.15  Aligned_cols=70  Identities=14%  Similarity=0.194  Sum_probs=62.7

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      .++.+|.||..++++|||++|.+|++|+++|||+|.+++.....    .++.|+|+|++++|..|+.+|.++|.
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~----~~r~v~I~G~~~~v~~A~~~I~~~i~   76 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGL----PERSCMLTGTPESVQSAKRLLDQIVE   76 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTC----SEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCC----CceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            35689999999999999999999999999999999998755432    46899999999999999999999884

>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=99.54  E-value=1.4e-15  Score=102.16  Aligned_cols=69  Identities=23%  Similarity=0.381  Sum_probs=60.2

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++|.||.+++|.||||+|++|++|+++|||+|.|++..+. +...++.|+|+|++++|.+|+.+|.+++.
T Consensus        10 ~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   78 (81)
T d1x4ma1          10 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ-NTGADKPLRITGDPYKVQQAKEMVLELIR   78 (81)
T ss_dssp             EEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC-SSCSCEEEEEEECTTTHHHHHHHHHHHHC
T ss_pred             EEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCC-CCCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999999999999874432 23356899999999999999999988754

>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=99.53  E-value=2.8e-15  Score=100.72  Aligned_cols=71  Identities=13%  Similarity=0.209  Sum_probs=61.9

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV  220 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  220 (238)
                      ++.+|.||+.++++|||++|++|++|+++|||+|.+++.....  ...++.|+|+|++++|.+|+++|.++|.
T Consensus         8 ~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~   78 (81)
T d1x4ma1           8 AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN--TGADKPLRITGDPYKVQQAKEMVLELIR   78 (81)
T ss_dssp             EEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS--SCSCEEEEEEECTTTHHHHHHHHHHHHC
T ss_pred             EEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            5589999999999999999999999999999999998643211  1247899999999999999999999883

>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=99.53  E-value=3.9e-15  Score=102.23  Aligned_cols=64  Identities=28%  Similarity=0.504  Sum_probs=58.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||.++|+.|||++|++|++|+++|||+|.||+.+.     .++.|+|+|++++|++|+.+|.+++.
T Consensus        13 ~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-----~~~~v~I~G~~~~V~~A~~~I~~~v~   76 (91)
T d2ctka1          13 EVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLAANLDRAKAGLLERVK   76 (91)
T ss_dssp             EEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT-----TCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCCC-----CcceEEEECCHHHHHHHHHHHHHHHH
Confidence            58899999999999999999999999999999988654     56799999999999999999987743

>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=99.53  E-value=4.7e-16  Score=106.48  Aligned_cols=63  Identities=21%  Similarity=0.300  Sum_probs=58.2

Q ss_pred             EEEEEEeCCCeeeEEecCCCchHHHHHHH-hCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        148 VIMMMEISPQHHPIMEGPNAINLKTIMAQ-TGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~-tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ++.+|.||..+|++|||++|++|++|+++ +|++|.||..         .+.|+|+|++++|.+|+.+|++++
T Consensus        21 ~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~---------~~~v~i~G~~~~ve~Ak~~I~~iv   84 (90)
T d2ctfa1          21 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG---------EDKITLEGPTEDVSVAQEQIEGMV   84 (90)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS---------SCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC---------CceEEEeCCHHHHHHHHHHHHHHH
Confidence            56999999999999999999999999999 5899999863         368999999999999999999987

>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=99.53  E-value=3.5e-15  Score=99.79  Aligned_cols=65  Identities=20%  Similarity=0.411  Sum_probs=58.2

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~   69 (238)
                      +|.||.+++|+|||++|.+|++|+++|||+|++++...   ...++.|+|+|++++|.+|+.+|.+++
T Consensus        11 ~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i   75 (79)
T d1x4na1          11 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGTPESVQSAKRLLDQIV   75 (79)
T ss_dssp             EEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT---TCSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999987543   224579999999999999999998764

>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=99.52  E-value=9e-15  Score=102.89  Aligned_cols=72  Identities=17%  Similarity=0.296  Sum_probs=63.5

Q ss_pred             ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        146 TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       146 ~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      .+++.+|.||..++++|||++|.+|++|+++|||+|.|++..+..  ...++.|+|+|++++|..|+.+|++++
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i   84 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT--LLLSRLIKISGTQKEVAAAKHLILEKV   84 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS--SSSEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCC--CCCccEEEEEeCHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999998765432  124689999999999999999999988

>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=99.52  E-value=4.7e-15  Score=99.88  Aligned_cols=64  Identities=31%  Similarity=0.551  Sum_probs=57.9

Q ss_pred             EEEecCCccceeeccCCccHHHHHHH-cCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~-t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      ++.||..+||+|||++|++|++|+++ ++++|++|+.+.     .++.|+|+|++++|++|+.+|.+++.
T Consensus        13 ~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~-----~~~~v~I~G~~~~v~~A~~~I~~~v~   77 (82)
T d2ctja1          13 EVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-----GSDTVVIRGPSSDVEKAKKQLLHLAE   77 (82)
T ss_dssp             EEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTT-----TCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCC-----CCceEEEeCCHHHHHHHHHHHHHHHh
Confidence            68899999999999999999999988 599999998654     56899999999999999999988754

>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=1.1e-14  Score=102.51  Aligned_cols=68  Identities=24%  Similarity=0.356  Sum_probs=59.6

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      +|.||..++|.||||+|.+|++|+++|||+|.|++..+... ..++.|+|+|++++|..|+.+|.+++.
T Consensus        18 ~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~-~~~r~v~I~G~~~~v~~A~~~I~~~i~   85 (104)
T d1we8a_          18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISGTQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             EEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSS-SSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             EEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCC-CCccEEEEEeCHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999987654322 245799999999999999999988754

>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=99.46  E-value=4.4e-14  Score=96.46  Aligned_cols=61  Identities=16%  Similarity=0.384  Sum_probs=55.7

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHc-CCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEET-GCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP   70 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t-~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~   70 (238)
                      .+.||..+|++|||++|++|++|++++ +++|++++        +++.|+|+|++++|++|+.+|.+++.
T Consensus        24 ~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~--------~~~~v~i~G~~~~ve~Ak~~I~~iv~   85 (90)
T d2ctfa1          24 SVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSVAQEQIEGMVK   85 (90)
T ss_dssp             EEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC--------CCceEEEeCCHHHHHHHHHHHHHHHH
Confidence            588999999999999999999999995 89999986        34699999999999999999988754

>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=99.40  E-value=1.1e-13  Score=92.98  Aligned_cols=61  Identities=13%  Similarity=0.165  Sum_probs=55.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL   71 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~   71 (238)
                      -+.||.+.++.|||++|++|++|+++|||+|++++         ++.|+|+|+++++..|+.+|+.+..+
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~---------~g~v~I~G~~e~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRRKVSIAEEAIYLIEQE   64 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT---------TSEEEEESCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC---------CCEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            37899999999999999999999999999999975         35899999999999999999887544

>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=99.39  E-value=5.3e-14  Score=93.23  Aligned_cols=61  Identities=20%  Similarity=0.159  Sum_probs=54.8

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT   69 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~   69 (238)
                      +|.||.+.+|.|||++|++|++|+++|||+|.+.+.       +++.|+|.| ++++|++|+.+|..+.
T Consensus        11 ~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-------~~g~v~I~g~~~eav~~A~~~Ie~~~   72 (78)
T d2cpqa1          11 EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLEFVE   72 (78)
T ss_dssp             EEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             EEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-------CCceEEEEECCHHHHHHHHHHHHHhh
Confidence            588999999999999999999999999999999764       247899999 6999999999997654

>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=99.36  E-value=8.1e-14  Score=92.34  Aligned_cols=65  Identities=14%  Similarity=0.179  Sum_probs=57.7

Q ss_pred             eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhc
Q psy11278        147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSS  219 (238)
Q Consensus       147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l  219 (238)
                      .++.+|.||.+++|+|||++|++|++|++.|||+|.+.+..        ...|+|.| ++++|.+|+++|+.+.
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~~--------~g~v~I~g~~~eav~~A~~~Ie~~~   72 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED--------TGTFRIYGESADAVKKARGFLEFVE   72 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT--------TTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecCC--------CceEEEEECCHHHHHHHHHHHHHhh
Confidence            36689999999999999999999999999999999886543        36899999 6999999999998666

>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=99.29  E-value=5.5e-13  Score=89.46  Aligned_cols=62  Identities=19%  Similarity=0.307  Sum_probs=56.2

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR  221 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  221 (238)
                      .-+.||+..++.|||++|++|++|+++|||+|.+++          ...|+|+|+++++..|+.+|+.++..
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            457899999999999999999999999999999974          25799999999999999999988744

>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=99.20  E-value=4.2e-13  Score=86.68  Aligned_cols=61  Identities=11%  Similarity=0.251  Sum_probs=48.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC-HHHHHHHHHHHHhhCCc
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELTPL   71 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~~~~   71 (238)
                      -+.||.+.+|.||||+|++|++|+++|||+|++.+         +..|+|.|. +++++.|+.+|+.+..+
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            47899999999999999999999999999999964         358999995 78999999999887654

>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=99.15  E-value=1.2e-11  Score=82.53  Aligned_cols=60  Identities=18%  Similarity=0.246  Sum_probs=51.2

Q ss_pred             CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEE-----eCHHHHHHHHHHHHhh
Q psy11278          1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIA-----GSLLGLERARYRVREL   68 (238)
Q Consensus         1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~   68 (238)
                      |.+.||.+.+|.|||++|++|++|+++|||+|+|++.        ...+.+.     |.+.++.+|++.|+++
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d--------~g~v~i~~~~~~~~~~a~~~a~~iI~aI   69 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE--------NSMVIVEPEAEGIPPVNLMKAAEVVKAI   69 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT--------TTEEEEEESSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC--------CCeEEEecCCccccHHHHHHHHHHHHHH
Confidence            3688999999999999999999999999999999763        3466665     4578899999998765

>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=99.09  E-value=7.6e-11  Score=78.83  Aligned_cols=59  Identities=15%  Similarity=0.236  Sum_probs=53.3

Q ss_pred             EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278          3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP   70 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~   70 (238)
                      +.||.+.++.|||++|++|+.|+++|||+|++.+         +..|.|.| +.+.+..|+..|..+..
T Consensus         5 i~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d---------~G~V~I~g~~~~~~~~A~~~I~~I~~   64 (87)
T d2z0sa2           5 VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR---------NGRIHLECPNEDLEAIAVMAIKIIDE   64 (87)
T ss_dssp             EECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET---------TTEEEEECSCHHHHHHHHHHHHHHHH
T ss_pred             EEEChhhcceeECCCCcHHHHHHHHHCCEEEECC---------CcEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999964         35899999 58999999999987744

>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=98.98  E-value=7.7e-12  Score=80.62  Aligned_cols=61  Identities=15%  Similarity=0.172  Sum_probs=47.6

Q ss_pred             EEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHHhhcCC
Q psy11278        151 MMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLVVSSVR  221 (238)
Q Consensus       151 ~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~  221 (238)
                      -+.||+..++.|||++|++|++|+++|||+|.++++          ..|+|+|+ ++++.+|+.+|+.+...
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 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN----------GRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT----------SEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC----------CEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999999999999999642          46999996 78999999999887643

>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=98.87  E-value=8.3e-11  Score=78.41  Aligned_cols=66  Identities=21%  Similarity=0.217  Sum_probs=53.4

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEE-----EcCHHHHHHHHHHHHhhcCCCCc
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTV-----SGNIDSVYLARQMLVVSSVRPRR  224 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I-----~G~~~~v~~A~~~I~~~l~~~~p  224 (238)
                      +++.||.+.++.|||++|++|++|+++|||+|.++..+         ..+.+     .|.+.++++|+.+|.++.....|
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~---------g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf~P   75 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN---------SMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPP   75 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT---------TEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC---------CeEEEecCCccccHHHHHHHHHHHHHHhCCCCh
Confidence            56899999999999999999999999999999996543         23444     45688999999999887533333

>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=98.85  E-value=9.8e-11  Score=71.06  Aligned_cols=44  Identities=18%  Similarity=0.405  Sum_probs=13.1

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS   54 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~   54 (238)
                      ++.||.+.+|.|||++|++||.|+++|||+|++.+         ++.|+|.|.
T Consensus         6 ~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d---------dg~v~I~a~   49 (54)
T d1e3ha4           6 TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAA   49 (54)
T ss_dssp             ---------------------CHHHHSCCCC-----------------CCCCB
T ss_pred             EEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC---------CeEEEEEec
Confidence            57899999999999999999999999999999964         356777664

>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=98.78  E-value=2.8e-09  Score=71.07  Aligned_cols=62  Identities=21%  Similarity=0.252  Sum_probs=54.4

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHHhhcCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLVVSSVR  221 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~  221 (238)
                      ..+.||+..++.+||++|++|+.|+++|||+|.+.+          ...|+|.|+ .+.+..|+.+|..+...
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 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR----------NGRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET----------TTEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC----------CcEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999953          247999995 89999999999987643

>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=98.77  E-value=2.7e-09  Score=73.56  Aligned_cols=52  Identities=23%  Similarity=0.311  Sum_probs=46.5

Q ss_pred             cceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278         10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL   71 (238)
Q Consensus        10 ~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~   71 (238)
                      .|.|||++|.+|+.|++.|||.|.|.+          ..|.|.|++++++.|+.+|..+...
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d----------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeC----------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            588999999999999999999999954          4678889999999999999988643

>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=98.64  E-value=6.9e-09  Score=71.44  Aligned_cols=55  Identities=18%  Similarity=0.147  Sum_probs=48.4

Q ss_pred             eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCC
Q psy11278        158 HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPR  223 (238)
Q Consensus       158 ~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  223 (238)
                      ..|.|||++|.+|+.|++.|||.|.+..           ..+.|.|+++++..|+.+|+.++..+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d-----------~~v~iig~~e~i~~A~~~Ie~li~~~e   77 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE-----------YEVAIIGDYERAMAAKQAIEMLAEGRM   77 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-----------SEEEEEEEHHHHHHHHHHHHHHHTTCC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC-----------CeEEEEECchhHHHHHHHHHHHHcCCC
Confidence            3678999999999999999999999842           358888999999999999999997654

>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=98.42  E-value=8.3e-09  Score=62.35  Aligned_cols=45  Identities=18%  Similarity=0.347  Sum_probs=14.0

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN  204 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~  204 (238)
                      ..+.||+..++.+||++|++||+|+++|||+|.+.+          +..|+|.|+
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d----------dg~v~I~a~   49 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----------DGTIYIGAA   49 (54)
T ss_dssp             C---------------------CHHHHSCCCC------------------CCCCB
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC----------CeEEEEEec
Confidence            568899999999999999999999999999998863          256777775

>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=98.38  E-value=3.5e-07  Score=64.76  Aligned_cols=69  Identities=13%  Similarity=0.282  Sum_probs=53.0

Q ss_pred             EEEecCCc------cceeeccCCccHHHHHHHcCCEEEecCCCCC------------CCC-CCCCeEEEEe-CHHHHHHH
Q psy11278          2 KLDVSYTD------HSHIIGRGGLTIKKVMEETGCHVHFPDSNRS------------VNA-EKSNQVSIAG-SLLGLERA   61 (238)
Q Consensus         2 ~i~ip~~~------~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~------------~~~-~~~~~v~I~G-~~~~v~~A   61 (238)
                      +|.||-+.      +|.|||.+|+++|+|+++|||+|.|-.....            .+. ++.-.|.|++ +.+.+..|
T Consensus         6 Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~~~A   85 (122)
T d1k1ga_           6 KVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKA   85 (122)
T ss_dssp             EEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHH
T ss_pred             EEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhHHHH
Confidence            56777765      7999999999999999999999999653321            011 1223788888 57899999


Q ss_pred             HHHHHhhCC
Q psy11278         62 RYRVRELTP   70 (238)
Q Consensus        62 ~~~I~~~~~   70 (238)
                      +..+..++.
T Consensus        86 ~~~i~~ll~   94 (122)
T d1k1ga_          86 VEQIRNILK   94 (122)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence            999988764

>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=98.00  E-value=2.5e-06  Score=60.93  Aligned_cols=68  Identities=31%  Similarity=0.361  Sum_probs=51.5

Q ss_pred             EEEecCC------ccceeeccCCccHHHHHHHcCCEEEecCCCCCC---------------CCCCCCeEEEEeCH-----
Q psy11278          2 KLDVSYT------DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSV---------------NAEKSNQVSIAGSL-----   55 (238)
Q Consensus         2 ~i~ip~~------~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~---------------~~~~~~~v~I~G~~-----   55 (238)
                      +|.||-+      ++|.|||++|.++|+|+++|||+|.|-......               ..++.-.|.|+++-     
T Consensus         5 Kv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~~a   84 (134)
T d2bl5a1           5 KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRA   84 (134)
T ss_dssp             EEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHH
T ss_pred             EEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHHHH
Confidence            4667644      679999999999999999999999998765320               01234588888852     


Q ss_pred             -HHHHHHHHHHHhhC
Q psy11278         56 -LGLERARYRVRELT   69 (238)
Q Consensus        56 -~~v~~A~~~I~~~~   69 (238)
                       ..+..|...|+.++
T Consensus        85 ~~kl~~A~~~I~~lL   99 (134)
T d2bl5a1          85 ELKLKRAVEEVKKLL   99 (134)
T ss_dssp             HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHc
Confidence             35888999998875

>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=97.78  E-value=2.9e-05  Score=54.59  Aligned_cols=73  Identities=18%  Similarity=0.169  Sum_probs=52.3

Q ss_pred             EEEEEeCCC------eeeEEecCCCchHHHHHHHhCCeEEccCCCC--------CC---CCC-CcceEEEEEcC-HHHHH
Q psy11278        149 IMMMEISPQ------HHPIMEGPNAINLKTIMAQTGAQIVFPEAND--------PI---IPV-LKKSSVTVSGN-IDSVY  209 (238)
Q Consensus       149 ~~~v~i~~~------~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~--------~~---~~~-~~~~~v~I~G~-~~~v~  209 (238)
                      +..|.||-+      ++|.|+|.+|+++++|+++|||+|.+=...+        .+   ... ...=-|.|++. ++.+.
T Consensus         4 ~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~~   83 (122)
T d1k1ga_           4 SDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVK   83 (122)
T ss_dssp             EEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHH
T ss_pred             eEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhHH
Confidence            356666654      4799999999999999999999998732111        00   000 11235677885 88999


Q ss_pred             HHHHHHHhhcCC
Q psy11278        210 LARQMLVVSSVR  221 (238)
Q Consensus       210 ~A~~~I~~~l~~  221 (238)
                      .|..+++.+|..
T Consensus        84 ~A~~~i~~ll~~   95 (122)
T d1k1ga_          84 KAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHh
Confidence            999999999954

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.19  E-value=0.00017  Score=51.15  Aligned_cols=63  Identities=14%  Similarity=0.086  Sum_probs=45.0

Q ss_pred             CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCC--------C-----C-CCcceEEEEEcC--H----HHHHHHHHHHH
Q psy11278        157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPI--------I-----P-VLKKSSVTVSGN--I----DSVYLARQMLV  216 (238)
Q Consensus       157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~--------~-----~-~~~~~~v~I~G~--~----~~v~~A~~~I~  216 (238)
                      +++|.|||.+|.++++|+++|||+|.+=...+-.        .     . ..+.=-|.|++.  +    ..+..|..+|+
T Consensus        17 NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~~a~~kl~~A~~~I~   96 (134)
T d2bl5a1          17 NFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVK   96 (134)
T ss_dssp             CHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHH
T ss_pred             CeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHHHHHHHHHHHHHHHH
Confidence            4779999999999999999999999875432100        0     0 012235667764  2    35888999999


Q ss_pred             hhc
Q psy11278        217 VSS  219 (238)
Q Consensus       217 ~~l  219 (238)
                      .+|
T Consensus        97 ~lL   99 (134)
T d2bl5a1          97 KLL   99 (134)
T ss_dssp             HHS
T ss_pred             HHc
Confidence            998

>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=95.84  E-value=0.0014  Score=40.67  Aligned_cols=35  Identities=26%  Similarity=0.355  Sum_probs=32.5

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD   36 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~   36 (238)
                      .+.||.++.+..|||+|.|++-..+-||.+|+|..
T Consensus        30 ~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          30 RVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            46799999999999999999999999999999965

>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=95.64  E-value=0.0016  Score=40.22  Aligned_cols=36  Identities=19%  Similarity=0.248  Sum_probs=32.8

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEecCC
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDS   37 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~   37 (238)
                      .+.+|.++.+..|||+|.|++=..+-||.+|++...
T Consensus        29 ~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          29 RVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             EEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             EEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            467999999999999999999999999999999653

>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=95.21  E-value=0.0026  Score=39.21  Aligned_cols=38  Identities=13%  Similarity=0.083  Sum_probs=34.4

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN  187 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~  187 (238)
                      +.+.+|....+.-|||+|.+++-..+-||.+|.+-..+
T Consensus        28 ~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          28 ARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             EEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            77899999999999999999999999999999886544

>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=94.70  E-value=0.0054  Score=37.86  Aligned_cols=36  Identities=17%  Similarity=0.188  Sum_probs=33.4

Q ss_pred             EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278        150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE  185 (238)
Q Consensus       150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~  185 (238)
                      +.+.+|....+.-|||+|.+++-.++-||.+|.+-.
T Consensus        29 ~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          29 ARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            788999999999999999999999999999998754

>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=91.55  E-value=0.12  Score=33.05  Aligned_cols=57  Identities=12%  Similarity=0.096  Sum_probs=46.3

Q ss_pred             EEecCCccceeeccCCc-cHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhh
Q psy11278          3 LDVSYTDHSHIIGRGGL-TIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVREL   68 (238)
Q Consensus         3 i~ip~~~~g~IIGk~G~-~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~   68 (238)
                      +.||.+++..++|++++ -++.|.+.+++.|.+-.         ...|-|.| +++....+.+.|+.+
T Consensus         5 ~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~---------NGrIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           5 IDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL---------NGKIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET---------TTEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec---------CcEEEEECCCHHHHHHHHHHHHHH
Confidence            67889999999999998 68889999999999965         25899999 467766666666544

>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=89.61  E-value=0.11  Score=33.14  Aligned_cols=57  Identities=11%  Similarity=0.134  Sum_probs=44.9

Q ss_pred             EEEeCCCeeeEEecCCCc-hHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHHh
Q psy11278        151 MMEISPQHHPIMEGPNAI-NLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLVV  217 (238)
Q Consensus       151 ~v~i~~~~~~~iIG~~G~-~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~  217 (238)
                      -+.++..+++.++|++++ -++.|.+.+++.|.+-..          ..|-|.|. ++....+...|..
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N----------GrIWi~~~~~~~~i~i~~aI~~   62 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN----------GKIWVKCEELSNTLACYRTIME   62 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT----------TEEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC----------cEEEEECCCHHHHHHHHHHHHH
Confidence            467888899999999998 789999999999999653          57889995 6666655555543

>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=83.08  E-value=0.13  Score=33.28  Aligned_cols=33  Identities=15%  Similarity=0.284  Sum_probs=25.3

Q ss_pred             EEEecCCccceeeccCCccHHHHHHHcCCEEEe
Q psy11278          2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHF   34 (238)
Q Consensus         2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i   34 (238)
                      +|.|-...-|.|||++|++|++|++...-++.+
T Consensus        38 ~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~   70 (92)
T d1wh9a_          38 EIIILATRTQNVLGEKGRRIRELTAVVQKRFGF   70 (92)
T ss_dssp             EEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCC
T ss_pred             EEEEEeCCCceeeccCchhHHHHHHHHHHHHCC
Confidence            466777777999999999999998766544333

>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=81.68  E-value=0.13  Score=34.77  Aligned_cols=25  Identities=28%  Similarity=0.351  Sum_probs=18.9

Q ss_pred             EEecCCc-cceeeccCCccHHHHHHH
Q psy11278          3 LDVSYTD-HSHIIGRGGLTIKKVMEE   27 (238)
Q Consensus         3 i~ip~~~-~g~IIGk~G~~I~~I~~~   27 (238)
                      +.++.+- .+.|||++|++|++|..+
T Consensus        53 I~V~~~sqk~IiIGk~G~~ik~I~~~   78 (113)
T d1egaa2          53 ILVEREGQKKMVIGNKGAKIKTIGIE   78 (113)
T ss_dssp             EEESSHHHHHHHHCGGGHHHHHHHHH
T ss_pred             EEECCcchhhhhhcccchHHHHHHHH
Confidence            4455554 488999999999988653

>d1mlaa2 d.58.23.1 (A:128-197) Probable ACP-binding domain of malonyl-CoA ACP transacylase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Probable ACP-binding domain of malonyl-CoA ACP transacylase
family: Probable ACP-binding domain of malonyl-CoA ACP transacylase
domain: Probable ACP-binding domain of malonyl-CoA ACP transacylase
species: Escherichia coli [TaxId: 562]

Probab=80.98  E-value=0.94  Score=27.36  Aligned_cols=53  Identities=13%  Similarity=0.188  Sum_probs=40.3

Q ss_pred             eEEecCCCchHHHHHHHhC--CeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278        160 PIMEGPNAINLKTIMAQTG--AQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS  219 (238)
Q Consensus       160 ~~iIG~~G~~I~~I~~~tg--a~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  219 (238)
                      ..++|-.-..+.++.++..  -.+.+-..+.|       ..++|.|+.+++..+...+.+.=
T Consensus         6 aAVlg~~~~~v~~i~~~~~~~~~v~iAN~Nsp-------~Q~VISG~~~ai~~~~~~~k~~G   60 (70)
T d1mlaa2           6 AAIIGLDDASIAKACEEAAEGQVVSPVNFNSP-------GQVVIAGHKEAVERAGAACKAAG   60 (70)
T ss_dssp             EEEESCCHHHHHHHHHHHCTTSCEEEEEEEET-------TEEEEEEEHHHHHHHHHHHHHTT
T ss_pred             EEEeCCCHHHHHHHHHHhcCCCEEEEEecCCC-------cceeeeCCHHHHHHHHHHHHHcC
Confidence            4567888888999988753  23555555544       68999999999999999988763