Citrus Sinensis ID: 006320

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650
Protein Sequence
MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVYLR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccEEEEEcccccHHHHHHHHHHccEEEEcccccccccEEEEEEccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEEEEccccccHHcccccHHHHHHHHHccccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccEEEccccHHHHHHHHHHccEEEEccccccccccEEEEEccccccccccHHHHHHHHHHHHHccccccccccEEEEEEEEcccEEEEEcccccHHHHHHHHccEEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccEEccccccHHHHHHHHHHHHHHHHcccHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccccEcEEEcccccHHHHHHHHcccEEEEcccccccccEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccEEEEEEEEcccEEEEEcccccEHHHHHHHcccEEEEEcccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccEEEcccccHHHHHHHHcccEEEEccccccccccEEEEEccccccHHHHHHHHHHHHHHHHHHHccccccccEEEEEEEccccEEEEEcccccHHHHHHHcccEEEEEccHccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccHcccEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mdrsrskrnyyydhqdydgdtmgrtkprynhyyqpnnnyrhrgnnnnntnnimnnntsinnsnnransnpkdpslmvTTTYRILCHdmkaggvigksGSIIKSIRQHTGawinvhelipgdeeriieisdtrrrdpegrmpsfspaQEALFLIHDRilesdggggfygeeeeeygggggvggggfrgggnrVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTqirilprdhslprcvsMSEEIVQVVGDINNVKNAVAIISSRLResqhrdrshfhgrlhspdrffpdddyvphmnntarrpsmdgarfsgsnyrsnnygprpsgysieagaapmsdsvqpfygedlVFRMLcpidkvgrvigESEGIVELLQNEIgvdlkvadpvdgsdeqiitisseegpddelfpAQEALLHIQTRIVDlgadkdniittrllvpsseigclegrdgslsemrrstganiqilsreevpacvsgTDELVQIVGEIQAARDALVEVTTRLRSYLYRdffqketppsstgptgsalvveaaspiditparevqtvtdppaathqsvqipatsqpskeaagsvsetvkqneserredvptvinrvplplvtrstlevvlpdyavpklitKSKTLLTRFSEVSLLLHLINLFNFVKVYLR
Flexible Loop (DISEMBL)
mdrsrskrnyyydhqdydgdtmgrtKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSINNSnnransnpkdpSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAwinvhelipgdeeriieisdtrrrdpegrmpsFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLlgkggkiieQMRMETKtqirilprdhslprCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHrdrshfhgrlhspdrffpddDYVPHMNntarrpsmdgarfSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITIsseegpddELFPAQEALLHIQTRIVDLGADKDNIITtrllvpsseigclegrdgslsemRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFfqketppsstgptgsALVVEAASPIDITPAREVQTVTDPPAATHqsvqipatsqpskeaagsvsetvkqneserredvptvinrvplplvtrstlevvlpdyavpklitkskTLLTRFSEVSLLLHlinlfnfvkvylr
Low Complexity Region (SEG)
MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPnnnyrhrgnnnnntnnimnnntsinnsnnransnPKDPSLMVTTTYRILCHDMkaggvigksgsiiksiRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDggggfygeeeeeygggggvggggfrgggNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVYLR
Disordered region (IsUnstruct)
**************************************************************************LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERII**********************ALFLIHDRILE********************************VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIIS*****************************************************************************VQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVD*****II***********LFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLE***************NIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQ*****************************************************************************TVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVYL*
Disordered Region (DISOPRED)
*******************************************************************************TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI***********************************ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSG*SI*AGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGV*****************ISSEEGPDDELFPAQEALLH****************TTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRL***************************************************************************************************RSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVYLR
Disordered Region (DISEMBL)
********NYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSR***********FHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQK***********SALVVEAASPIDITPAREVQTVT***************************************DVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVYLR
Disordered Region (DISPRO)
******************GDTM*RTK************************************************LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGG*************************GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRD**********PDRFFPDDDYVPHMNNTARRP*****RFSGSNYRSN**************************GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKE*******************************VTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVYLR
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVYLR
Positional Conservation
no confident homologs detected

---

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	650	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.655	0.702	0.280	7e-35
O42254	576	Insulin-like growth facto	yes	no	0.538	0.607	0.242	2e-09
Q9PW80	582	Insulin-like growth facto	yes	no	0.573	0.640	0.238	8e-09
P57721	371	Poly(rC)-binding protein	no	no	0.210	0.369	0.305	2e-07
Q15366	365	Poly(rC)-binding protein	no	no	0.44	0.783	0.234	2e-07
P57722	371	Poly(rC)-binding protein	no	no	0.210	0.369	0.305	3e-07
O19048	356	Poly(rC)-binding protein	no	no	0.441	0.806	0.234	1e-06
P60335	356	Poly(rC)-binding protein	no	no	0.441	0.806	0.234	1e-06
Q15365	356	Poly(rC)-binding protein	no	no	0.441	0.806	0.234	1e-06
Q5E9A3	356	Poly(rC)-binding protein	no	no	0.441	0.806	0.234	1e-06

>sp|P58223|Y4837_ARATH KH domain-containing protein At4g18375 OS=Arabidopsis thaliana GN=At4g18375 PE=2 SV=1

 Score =  149 bits (376), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 143/509 (28%), Positives = 239/509 (46%), Gaps = 83/509 (16%)

Query: 54  NNNTSINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWIN 113
           NN+ S  N   R + +  +   +V   YRILC     GGVIGKSG +I +IR +T A I 
Sbjct: 13  NNSESNRNQKRRISHDKINRDELVV--YRILCPIDVVGGVIGKSGKVINAIRHNTKAKIK 70

Query: 114 VHELIPGDEERIIEI--SDTRRRDPEGRMPS----FSPAQEALFLIHDRILESDGGGGFY 167
           V + + G  +R+I I  S   +++  G   S       AQ+AL  ++D I+ SD      
Sbjct: 71  VFDQLHGCSQRVITIYCSVKEKQEEIGFTKSENEPLCCAQDALLKVYDAIVASD------ 124

Query: 168 GEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRI 227
               EE      V     +        R++V       L+GK G+ I+++R  T+  +++
Sbjct: 125 ----EENNTKTNVDRDDNK------ECRLLVPFSQSSSLIGKAGENIKRIRRRTRASVKV 174

Query: 228 LPRDHSLPR--CVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDR------------ 273
           + +D S P   C    + +V + G+  +VK A+  +S+ + +   R+             
Sbjct: 175 VSKDVSDPSHVCAMEYDNVVVISGEPESVKQALFAVSAIMYKINPRENIPLDSTSQDVPA 234

Query: 274 ------SHFHGRLHSPDRFFPDDDYVPHMNNTARRPS----MDGARFSGSNYRSNNYGPR 323
                 S     ++    F+ + D++  +   A  PS    +  + F G  Y      P 
Sbjct: 235 ASVIVPSDLSNSVYPQTGFYSNQDHI--LQQGAGVPSYFNALSVSDFQG--YAETAANPV 290

Query: 324 PSGYSIEAGAAPMSDSVQPFYG----EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGV 379
           P    + A + P++     F G    E+LVF++LCP+  + RVIG+    ++ ++   G 
Sbjct: 291 P----VFASSLPVT---HGFGGSSRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGS 343

Query: 380 DLKVADPVD--GSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLL 437
            ++V D     G DE +I +++ E PDD    A EA+L +Q  I D  A+    +  +LL
Sbjct: 344 CIEVNDSRTKCGDDECVIIVTATESPDDMKSMAVEAVLLLQEYINDEDAEN---VKMQLL 400

Query: 438 VPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSG--TDELVQIVGEIQAARD 494
           V S  IGC+ G+ GS ++E+R+ T ANI          C+S    D+LV++ GE+ + RD
Sbjct: 401 VSSKVIGCVIGKSGSVINEIRKRTNANI----------CISKGKKDDLVEVSGEVSSVRD 450

Query: 495 ALVEVTTRLRSYLY--RDFFQKETPPSST 521
           AL+++  RLR  +   +D      PP+ T
Sbjct: 451 ALIQIVLRLREDVLGDKDSVATRKPPART 479

Arabidopsis thaliana (taxid: 3702)

>sp|O42254|IF2B1_CHICK Insulin-like growth factor 2 mRNA-binding protein 1 OS=Gallus gallus GN=IGF2BP1 PE=1 SV=1

 Score = 65.1 bits (157), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 104/429 (24%), Positives = 178/429 (41%), Gaps = 79/429 (18%)

Query: 82  RILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH-ELIPGDEERIIEISDTRRRDPEGRM 140
           R+L      G +IGK G+ I++I + T + I+VH +   G  E+ I I  T    PEG  
Sbjct: 199 RLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKAISIHST----PEG-- 252

Query: 141 PSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSR 200
                   A  +I + I++ +       +E                     V  +++   
Sbjct: 253 -----CSAACKMILE-IMQKEAKDTKTADE---------------------VPLKILAHN 285

Query: 201 MHVGCLLGKGGKIIEQMRMETKTQIRILP-RDHSLPRCVSMSEEIVQVVGDINNVKNAVA 259
             VG L+GK G+ ++++  +T+T+I I   +D +L       E  + V G I N   A  
Sbjct: 286 NFVGRLIGKEGRNLKKVEQDTETKITISSLQDLTL----YNPERTITVKGSIENCCKAEQ 341

Query: 260 IISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNN 319
            I  ++RE+   D +    + H           +P +N  A         F  S   SN 
Sbjct: 342 EIMKKVREAYENDVAAMSLQSH----------LIPGLNLAAV------GLFPAS---SNA 382

Query: 320 YGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGV 379
             P PS  S   GAAP S  + P   E     +  P   VG +IG+    ++ L      
Sbjct: 383 VPPPPSSVS---GAAPYSSFMPP---EQETVHVFIPAQAVGAIIGKKGQHIKQLSRFASA 436

Query: 380 DLKVADP-VDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLV 438
            +K+A P    S  +++ I+   GP +  F AQ  +          G  ++  + T + V
Sbjct: 437 SIKIAPPETPDSKVRMVVIT---GPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRV 493

Query: 439 PSSEIGCLEGRDG-SLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAA----- 492
           P+S  G + G+ G +++E++  T A + ++ R++ P        +V+I+G   A+     
Sbjct: 494 PASAAGRVIGKGGKTVNELQNLTAAEV-VVPRDQTPD--ENEQVIVKIIGHFYASQMAQR 550

Query: 493 --RDALVEV 499
             RD L +V
Sbjct: 551 KIRDILAQV 559

RNA-binding factor that affects mRNA nuclear export, localization, stability and translation. Component of the coding region determinant (CRD)-mediated complex that promotes mRNA stability. May regulate mRNA stability in stress granules during the cellular stress response (By similarity). Acts as translational regulator that represses translation by blocking translation initiation. Promotes transport and localization of the beta-actin mRNA to actin-rich protrusions in primary fibroblasts and neurons. Binds to a conserved 54-nucleotide element in the 3'-UTR of the beta actin mRNA known as the 'zipcode'. Binds to the minimal 5'-ACACCC-3'sequence that is sufficient for localization of beta actin mRNA.

Gallus gallus (taxid: 9031)

>sp|Q9PW80|IF2B3_DANRE Insulin-like growth factor 2 mRNA-binding protein 3 OS=Danio rerio GN=igf2bp3 PE=1 SV=1

 Score = 62.8 bits (151), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 111/466 (23%), Positives = 196/466 (42%), Gaps = 93/466 (19%)

Query: 73  PSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH-ELIPGDEERIIEISDT 131
           P L      R+L      G +IGK G+ I++I + T + I++H +   G  E+ I +  T
Sbjct: 189 PKLQSDVPLRLLVPTQFVGAIIGKEGATIRNITKQTHSKIDIHRKENAGAAEKPITVHST 248

Query: 132 RRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNR 191
               PEG     S  +  + ++    +++        EE                     
Sbjct: 249 ----PEG---CSSACRNIMEIMQKEAIDTK-----ITEE--------------------- 275

Query: 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP-RDHSLPRCVSMSEEIVQVVGD 250
           +  +++     VG L+GK G+ ++++  +T T+I I P +D +L       E  + V G 
Sbjct: 276 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTL----YNPERTITVKGT 331

Query: 251 INNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARF 310
           ++    A   I  ++RES   D +  H  L S        + +P +N  A    +     
Sbjct: 332 LDACAKAEEEIMKKVRESYENDVAAMH--LQS--------NLIPGLNLNAL--GLFPGAA 379

Query: 311 SGSNYRSNNYGPRP---SGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESE 367
           SG    S   GP P   +GY    GA   S++V  F           P   VG +IG+  
Sbjct: 380 SGGISPSVVSGPPPGAQAGYQ-SFGAQMESETVHLF----------IPALAVGAIIGKQG 428

Query: 368 GIVELLQNEIGVDLKVADPVDGSD--EQIITISSEEGPDDELFPAQEALLHIQTRIVDLG 425
             ++ L    G  +K+A P DG D  ++++ IS   GP +  F AQ  +          G
Sbjct: 429 QHIKQLSRFAGASIKIA-PADGIDAKQRMVIIS---GPPEAQFKAQGRIFGKLKEENFFG 484

Query: 426 ADKDNIITTRLLVPSSEIGCLEGRDG-SLSEMRRSTGANIQILSREEVPACVSGTDELVQ 484
             ++  +   + VPS   G + G+ G +++E++  T A + ++ R++ P      DE  Q
Sbjct: 485 PKEEVKLEAHIKVPSFAAGRVIGKGGKTVNELQNLTSAEV-VVPRDQTP------DENDQ 537

Query: 485 IVGEI-------QAARDALVEVTTRLRSYLYRDFFQKETPPSSTGP 523
           +V +I       Q A+  + E+ +++R        Q++  PS+ GP
Sbjct: 538 VVVKITGHFYASQLAQRKIQEIISQVRR-------QQQPKPSAAGP 576

RNA-binding protein that may regulate mRNA translation and stability (By similarity). Involved in the correct neuronal crest migration.

Danio rerio (taxid: 7955)

>sp|P57721|PCBP3_HUMAN Poly(rC)-binding protein 3 OS=Homo sapiens GN=PCBP3 PE=2 SV=2

 Score = 58.2 bits (139), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/154 (30%), Positives = 80/154 (51%), Gaps = 17/154 (11%)

Query: 348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDEL 407
           L  R+L    +VG +IG+    V+ ++ E G  + +++      E+I+TI+   GP D +
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTIT---GPTDAI 100

Query: 408 FPAQEALLH-----IQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG 461
           F A   + +     I   + +  A     +T RL+VP+S+ G L G+ GS + E+R STG
Sbjct: 101 FKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTG 160

Query: 462 ANIQIL-----SREEVPACVSGT-DELVQIVGEI 489
           A +Q+      +  E    +SGT D ++Q V +I
Sbjct: 161 AQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQI 194

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

>sp|Q15366|PCBP2_HUMAN Poly(rC)-binding protein 2 OS=Homo sapiens GN=PCBP2 PE=1 SV=1

 Score = 58.2 bits (139), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 86/367 (23%), Positives = 147/367 (40%), Gaps = 81/367 (22%)

Query: 75  LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGD-EERIIEISDTRR 133
           L VT T R+L H  + G +IGK G  +K +R+ +GA IN+ E   G+  ERII ++    
Sbjct: 10  LNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE---GNCPERIITLAGPTN 66

Query: 134 RDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVA 193
                         +A  +I D+ LE D                              V 
Sbjct: 67  A-----------IFKAFAMIIDK-LEEDISSSMTNSTAASR---------------PPVT 99

Query: 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRI----LPRDHSLPRCVSMSEEIVQVVG 249
            R+VV     G L+GKGG  I+++R  T  Q+++    LP  +S  R ++++  I Q + 
Sbjct: 100 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP--NSTERAITIA-GIPQSI- 155

Query: 250 DINNVKNAVAIISSRLRES-------QHRDRSHFHGRLHS--PDRFFPDDDYV--PHMN- 297
            I  VK    ++   L +S        +R +      + +   DR+    D    PH   
Sbjct: 156 -IECVKQICVVMLETLSQSPPKGVTIPYRPKPSSSPVIFAGGQDRYSTGSDSASFPHTTP 214

Query: 298 NTARRPSMDGARFSGSNYRSNNYGPRP---------------------SGYSIEAGAAPM 336
           +    P ++G        +     P+P                     +G+S   G    
Sbjct: 215 SMCLNPDLEGPPLEAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGNTGFS---GIESS 271

Query: 337 SDSVQPFYGEDLVFR-----MLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSD 391
           S  V+ ++G D   +     +  P D +G +IG     +  ++   G  +K+A+PV+GS 
Sbjct: 272 SPEVKGYWGLDASAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGST 331

Query: 392 EQIITIS 398
           ++ +TI+
Sbjct: 332 DRQVTIT 338

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitinationa and degradation.

Homo sapiens (taxid: 9606)

>sp|P57722|PCBP3_MOUSE Poly(rC)-binding protein 3 OS=Mus musculus GN=Pcbp3 PE=2 SV=3

 Score = 57.4 bits (137), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 47/154 (30%), Positives = 80/154 (51%), Gaps = 17/154 (11%)

Query: 348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDEL 407
           L  R+L    +VG +IG+    V+ ++ E G  + +++      E+I+TI+   GP D +
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTIT---GPTDAI 100

Query: 408 FPAQEALLH-----IQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG 461
           F A   + +     I   + +  A     +T RL+VP+S+ G L G+ GS + E+R STG
Sbjct: 101 FKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTG 160

Query: 462 ANIQIL-----SREEVPACVSGT-DELVQIVGEI 489
           A +Q+      +  E    +SGT D ++Q V +I
Sbjct: 161 AQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQI 194

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Mus musculus (taxid: 10090)

>sp|O19048|PCBP1_RABIT Poly(rC)-binding protein 1 OS=Oryctolagus cuniculus GN=PCBP1 PE=2 SV=1

 Score = 55.8 bits (133), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 84/358 (23%), Positives = 140/358 (39%), Gaps = 71/358 (19%)

Query: 75  LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRR 134
           L VT T R+L H  + G +IGK G  +K IR+ +GA IN+ E      ERII ++     
Sbjct: 10  LNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLT----- 62

Query: 135 DPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVAT 194
            P   +  F    +A  +I D+ LE D                              V  
Sbjct: 63  GPTNAI--F----KAFAMIIDK-LEEDINSSMTNSTAASR---------------PPVTL 100

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R+VV     G L+GKGG  I+++R  T  Q+++      LP   + +E  + + G   +V
Sbjct: 101 RLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLP---NSTERAITIAGVPQSV 155

Query: 255 KNAVAIISSRLRESQHRDRSHFHGRLHS-PDRFFPDDDYV---------------PHMNN 298
              V  I   + E+  +      GR+ + P +  P    V               PH  +
Sbjct: 156 TECVKQICLVMLETLSQSP---QGRVMTIPYQPMPASSPVICAGGQDRCSDAAGYPHATH 212

Query: 299 TARRPSMDGARFSGSNYRS-------NNYGPRPSGYSIE------AGAAPMSDSVQPFYG 345
               P +D     G +  S       N    + S +++       AG    S  V+ ++ 
Sbjct: 213 DLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWA 272

Query: 346 E-----DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITIS 398
                      +  P + +G +IG     +  ++   G  +K+A+PV+GS  + +TI+
Sbjct: 273 SLDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 330

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Oryctolagus cuniculus (taxid: 9986)

>sp|P60335|PCBP1_MOUSE Poly(rC)-binding protein 1 OS=Mus musculus GN=Pcbp1 PE=1 SV=1

 Score = 55.8 bits (133), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 84/358 (23%), Positives = 140/358 (39%), Gaps = 71/358 (19%)

Query: 75  LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRR 134
           L VT T R+L H  + G +IGK G  +K IR+ +GA IN+ E      ERII ++     
Sbjct: 10  LNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLT----- 62

Query: 135 DPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVAT 194
            P   +  F    +A  +I D+ LE D                              V  
Sbjct: 63  GPTNAI--F----KAFAMIIDK-LEEDINSSMTNSTAASR---------------PPVTL 100

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R+VV     G L+GKGG  I+++R  T  Q+++      LP   + +E  + + G   +V
Sbjct: 101 RLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLP---NSTERAITIAGVPQSV 155

Query: 255 KNAVAIISSRLRESQHRDRSHFHGRLHS-PDRFFPDDDYV---------------PHMNN 298
              V  I   + E+  +      GR+ + P +  P    V               PH  +
Sbjct: 156 TECVKQICLVMLETLSQSP---QGRVMTIPYQPMPASSPVICAGGQDRCSDAAGYPHATH 212

Query: 299 TARRPSMDGARFSGSNYRS-------NNYGPRPSGYSIE------AGAAPMSDSVQPFYG 345
               P +D     G +  S       N    + S +++       AG    S  V+ ++ 
Sbjct: 213 DLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWA 272

Query: 346 E-----DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITIS 398
                      +  P + +G +IG     +  ++   G  +K+A+PV+GS  + +TI+
Sbjct: 273 SLDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 330

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Mus musculus (taxid: 10090)

>sp|Q15365|PCBP1_HUMAN Poly(rC)-binding protein 1 OS=Homo sapiens GN=PCBP1 PE=1 SV=2

 Score = 55.8 bits (133), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 84/358 (23%), Positives = 140/358 (39%), Gaps = 71/358 (19%)

Query: 75  LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRR 134
           L VT T R+L H  + G +IGK G  +K IR+ +GA IN+ E      ERII ++     
Sbjct: 10  LNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLT----- 62

Query: 135 DPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVAT 194
            P   +  F    +A  +I D+ LE D                              V  
Sbjct: 63  GPTNAI--F----KAFAMIIDK-LEEDINSSMTNSTAASR---------------PPVTL 100

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R+VV     G L+GKGG  I+++R  T  Q+++      LP   + +E  + + G   +V
Sbjct: 101 RLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLP---NSTERAITIAGVPQSV 155

Query: 255 KNAVAIISSRLRESQHRDRSHFHGRLHS-PDRFFPDDDYV---------------PHMNN 298
              V  I   + E+  +      GR+ + P +  P    V               PH  +
Sbjct: 156 TECVKQICLVMLETLSQSP---QGRVMTIPYQPMPASSPVICAGGQDRCSDAAGYPHATH 212

Query: 299 TARRPSMDGARFSGSNYRS-------NNYGPRPSGYSIE------AGAAPMSDSVQPFYG 345
               P +D     G +  S       N    + S +++       AG    S  V+ ++ 
Sbjct: 213 DLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWA 272

Query: 346 E-----DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITIS 398
                      +  P + +G +IG     +  ++   G  +K+A+PV+GS  + +TI+
Sbjct: 273 SLDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 330

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

>sp|Q5E9A3|PCBP1_BOVIN Poly(rC)-binding protein 1 OS=Bos taurus GN=PCBP1 PE=2 SV=1

 Score = 55.8 bits (133), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 84/358 (23%), Positives = 140/358 (39%), Gaps = 71/358 (19%)

Query: 75  LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRR 134
           L VT T R+L H  + G +IGK G  +K IR+ +GA IN+ E      ERII ++     
Sbjct: 10  LNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLT----- 62

Query: 135 DPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVAT 194
            P   +  F    +A  +I D+ LE D                              V  
Sbjct: 63  GPTNAI--F----KAFAMIIDK-LEEDINSSMTNSTAASR---------------PPVTL 100

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R+VV     G L+GKGG  I+++R  T  Q+++      LP   + +E  + + G   +V
Sbjct: 101 RLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLP---NSTERAITIAGVPQSV 155

Query: 255 KNAVAIISSRLRESQHRDRSHFHGRLHS-PDRFFPDDDYV---------------PHMNN 298
              V  I   + E+  +      GR+ + P +  P    V               PH  +
Sbjct: 156 TECVKQICLVMLETLSQSP---QGRVMTIPYQPMPASSPVICAGGQDRCSDAAGYPHATH 212

Query: 299 TARRPSMDGARFSGSNYRS-------NNYGPRPSGYSIE------AGAAPMSDSVQPFYG 345
               P +D     G +  S       N    + S +++       AG    S  V+ ++ 
Sbjct: 213 DLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWA 272

Query: 346 E-----DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITIS 398
                      +  P + +G +IG     +  ++   G  +K+A+PV+GS  + +TI+
Sbjct: 273 SLDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 330

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Bos taurus (taxid: 9913)

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	650
224135123	685	predicted protein [Populus trichocarpa]	0.943	0.894	0.717	0.0
356516077	647	PREDICTED: KH domain-containing protein	0.915	0.919	0.674	0.0
224118310	655	predicted protein [Populus trichocarpa]	0.910	0.903	0.7	0.0
225455340	661	PREDICTED: KH domain-containing protein	0.935	0.919	0.679	0.0
356509231	644	PREDICTED: KH domain-containing protein	0.910	0.919	0.668	0.0
449456987	666	PREDICTED: KH domain-containing protein	0.938	0.915	0.681	0.0
255561850	704	nucleic acid binding protein, putative [	0.852	0.786	0.723	0.0
302143921	575	unnamed protein product [Vitis vinifera]	0.803	0.907	0.700	0.0
8809595	660	RNA-binding protein-like [Arabidopsis th	0.916	0.903	0.603	0.0
30696273	652	RNA-binding KH domain-containing protein	0.916	0.914	0.603	0.0

>gi|224135123|ref|XP_002321989.1| predicted protein [Populus trichocarpa] gi|222868985|gb|EEF06116.1| predicted protein [Populus trichocarpa]

 Score =  865 bits (2235), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 473/659 (71%), Positives = 527/659 (79%), Gaps = 46/659 (6%)

Query: 1   MDRSRSKRNYYYDHQDYDGDT--------MGRTKPRYNHYYQPNNNYRHRGNNNNNTNNI 52
           M+RSRSKRNYYYDHQDYD D         M RTKPRYN+    NN YR RG   NN  N 
Sbjct: 1   MERSRSKRNYYYDHQDYDNDNLNNNNNNNMVRTKPRYNNN---NNYYRQRGQGGNNMFNN 57

Query: 53  MNNNTSINNSNNRANSNPKDPS--LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGA 110
            NN  S      +     +DPS  LMVTT+YRILCHDMKAGGVIGKSGSIIKSIRQHTGA
Sbjct: 58  NNNRFSRTQQQQQPPQQQQDPSSTLMVTTSYRILCHDMKAGGVIGKSGSIIKSIRQHTGA 117

Query: 111 WINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESD--------G 162
           WINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE+D        G
Sbjct: 118 WINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILENDLQYGVVSSG 177

Query: 163 GGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK 222
            GGF   EE+EY G GG          NRVATR+VVSRMHVGCLLGKGGKIIEQMRMETK
Sbjct: 178 AGGF---EEDEYVGRGG----------NRVATRLVVSRMHVGCLLGKGGKIIEQMRMETK 224

Query: 223 TQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHS 282
           TQIRILPRDH+LPRCVS+SEEIVQV+GD+N VKNAVAIISSRLRESQHRDRSHFHGR+ S
Sbjct: 225 TQIRILPRDHTLPRCVSVSEEIVQVIGDVNAVKNAVAIISSRLRESQHRDRSHFHGRVQS 284

Query: 283 PDRFFPDDDYVPHMNNTARRPSMDG-----ARFSGSNYRSNNYGPRPSGYSIEAGAAPMS 337
           P+RF  DDDYVPHMN   RR SMDG     +R SG NYR+NNY  R  G+ ++AGA P +
Sbjct: 285 PERFL-DDDYVPHMNT--RRSSMDGPPSFGSRLSGPNYRNNNYSSRAPGFPVDAGADPNA 341

Query: 338 DSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITI 397
           DS QPFY EDLVFR+LCPIDKV RV+GES+G+V+LLQNEIGVD+KVADPV GSDEQIITI
Sbjct: 342 DSAQPFYVEDLVFRILCPIDKVNRVVGESDGLVDLLQNEIGVDVKVADPVSGSDEQIITI 401

Query: 398 SSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMR 457
            SEEGPDDELFPAQEALLHIQTRIVDL ADKDNIITTRLLVPSSEIGCLEGRDGSLSEM 
Sbjct: 402 CSEEGPDDELFPAQEALLHIQTRIVDLVADKDNIITTRLLVPSSEIGCLEGRDGSLSEME 461

Query: 458 RSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETP 517
             TGA I+IL +E +P  +SGTDELVQI GE++AARDALVEVT+RLRSYLY+D FQK+ P
Sbjct: 462 SLTGATIEILPKEMLPTYLSGTDELVQIQGEVKAARDALVEVTSRLRSYLYKDVFQKDLP 521

Query: 518 P--SSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVS 575
           P  S+ GP G+A  ++AAS  + TPARE  +  DPP AT+Q+VQ  +T QPSK+A GS +
Sbjct: 522 PTVSAPGPAGTAGGLQAASSNNPTPAREGHSGGDPP-ATYQNVQSASTPQPSKDARGSSA 580

Query: 576 ETVKQNESERREDV-PTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
           ETVKQNESE RED+ P  +NR+P+ LVTRS LEVV+P+ AVPKLITKSK  L + SE+S
Sbjct: 581 ETVKQNESEHREDLPPPTMNRIPVTLVTRSILEVVIPEPAVPKLITKSKNKLAQISELS 639

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516077|ref|XP_003526723.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  826 bits (2133), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 431/639 (67%), Positives = 500/639 (78%), Gaps = 44/639 (6%)

Query: 1   MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSIN 60
           M+RSRSKRNYYYD QDYD +T+ RT+PRYNH+Y    N RHRG                 
Sbjct: 1   MERSRSKRNYYYD-QDYDSETLARTRPRYNHHYTTAGNQRHRGGGAA------------- 46

Query: 61  NSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG 120
               R     +D  L VTT+YRILCHD+KAGGVIGKSGSIIKSIRQHTGAWINVHEL+PG
Sbjct: 47  ----RHAKTQQDSPLTVTTSYRILCHDLKAGGVIGKSGSIIKSIRQHTGAWINVHELMPG 102

Query: 121 DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGV 180
           DEERIIEISDTRRRDPEGRMPSFSPAQEAL LIH+RILESD   G   E++EEY      
Sbjct: 103 DEERIIEISDTRRRDPEGRMPSFSPAQEALLLIHERILESDAAFGV-AEDDEEY-----G 156

Query: 181 GGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSM 240
            G G   G +RVATR+VVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDH+LPRCVSM
Sbjct: 157 AGRGGGAGRDRVATRLVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHNLPRCVSM 216

Query: 241 SEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFF-PDDDYVPHMNNT 299
           SEEIVQVVGD+N VKNA+ IISSRLRESQHRDRSHFHGR+HSP+RFF PDDDYVPH+ + 
Sbjct: 217 SEEIVQVVGDVNAVKNALVIISSRLRESQHRDRSHFHGRVHSPERFFSPDDDYVPHVTSG 276

Query: 300 ARRPSMDGARF----SGSNYRSNNYGPRPS-GYSIEAGAAPMSDSVQPFYGEDLVFRMLC 354
           +RR S+DGA F    S +N R+NN+   PS  Y++E GAAP+ D  Q FYGE+LVFR+LC
Sbjct: 277 SRRSSVDGASFGSRGSNTNSRNNNH---PSLSYAMEPGAAPVVDDAQGFYGEELVFRILC 333

Query: 355 PIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEAL 414
           P++KV  +IGES+GIVE LQ+E+GVD+KV DPV GSDEQII I+SEEGPDDELFPAQEAL
Sbjct: 334 PVEKVDLIIGESDGIVEFLQSEVGVDVKVTDPVGGSDEQIIIITSEEGPDDELFPAQEAL 393

Query: 415 LHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPA 474
           LHIQTRIVDL  DKDN ITTRL+VPSSEI CL+G+D SLSE+RR TGANIQIL R+++P 
Sbjct: 394 LHIQTRIVDLVLDKDNTITTRLVVPSSEIECLDGKDVSLSEIRRLTGANIQILPRDDLPL 453

Query: 475 CVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAAS 534
           CV+ TDELVQIVGEI+AARDA+VEVT+RLRSYLYRDFFQ++  P      G+    EA+S
Sbjct: 454 CVAKTDELVQIVGEIKAARDAVVEVTSRLRSYLYRDFFQRDPIPLPAPLPGA----EASS 509

Query: 535 PIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVIN 594
             +I P  E  T       T+Q+VQ  A + P KE  GS +E  KQ ES RR+DV + +N
Sbjct: 510 SNNIVPVAETST-------TYQNVQTVAAALPPKETGGSSTEVGKQKESGRRDDVLSGLN 562

Query: 595 RVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
           R+ +PLVTRSTLEVV+P+YAVPKLI KSK+ L + SE+S
Sbjct: 563 RIAVPLVTRSTLEVVIPEYAVPKLIAKSKSKLAQISELS 601

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118310|ref|XP_002317787.1| predicted protein [Populus trichocarpa] gi|222858460|gb|EEE96007.1| predicted protein [Populus trichocarpa]

 Score =  820 bits (2117), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 455/650 (70%), Positives = 509/650 (78%), Gaps = 58/650 (8%)

Query: 1   MDRSRSKRNYYYDHQDYDGDT-----MGRT-KPRYNHYYQPNNNYRHRGNNNNNTNNIMN 54
           MDRSRSKRNYYYDHQDYD D      M RT KPRYN+    NN YRHRG   NN  N   
Sbjct: 1   MDRSRSKRNYYYDHQDYDNDNLNNNNMTRTTKPRYNNNNN-NNYYRHRGQGGNNMFN--- 56

Query: 55  NNTSINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV 114
                                    +YRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV
Sbjct: 57  ---------------------NNNNSYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV 95

Query: 115 HELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESD-----GGGGFYGE 169
           HELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE+D        G  G 
Sbjct: 96  HELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILENDLQYGVVSSGVGGL 155

Query: 170 EEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP 229
           EE+EY G GG          NRVATR+VVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP
Sbjct: 156 EEDEYVGRGG----------NRVATRLVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP 205

Query: 230 RDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPD 289
           RDH+LPRCVSMSEEIVQVVGD++ VKNAVAIISSRLRESQHRDRSHFHGR+HSP+R F D
Sbjct: 206 RDHTLPRCVSMSEEIVQVVGDVSAVKNAVAIISSRLRESQHRDRSHFHGRVHSPERLF-D 264

Query: 290 DDYVPHMNNTARRPSMDG-----ARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFY 344
           DDY PHMN   RR SMDG     +R  GSNYR+NNY  R SG++ +AGA P++DS QPFY
Sbjct: 265 DDYAPHMNT--RRSSMDGPPSFGSRVPGSNYRNNNYSSRASGFAADAGADPIADSAQPFY 322

Query: 345 GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPD 404
            EDLVFR+LCPIDK+ RV+GES+GIV+LLQNEIGVD+KVADPV GSDEQIITI SEEGPD
Sbjct: 323 VEDLVFRILCPIDKLNRVVGESDGIVDLLQNEIGVDVKVADPVSGSDEQIITIFSEEGPD 382

Query: 405 DELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANI 464
           DELFPAQEALLHIQTRIVDL  D D+I TTRLLV SSEIGCLEGRD SLSE+ R TGA I
Sbjct: 383 DELFPAQEALLHIQTRIVDLVPDNDHITTTRLLVRSSEIGCLEGRDASLSEIERLTGATI 442

Query: 465 QILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPT 524
           +IL +E++P+ +SG DE+VQI GEI+AARDALVEVT+RLRSY+Y+D F+K+ PP  + P 
Sbjct: 443 EILPKEKLPSYLSGIDEIVQIEGEIRAARDALVEVTSRLRSYIYKDVFEKDLPPPVSAP- 501

Query: 525 GSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESE 584
           G A  ++AASP   TPARE     DPP A++Q+VQ  AT QPSK+A GS  E VKQNESE
Sbjct: 502 GLAGGMQAASP-SPTPAREGPIGGDPP-ASYQNVQSAATPQPSKDARGSSVEAVKQNESE 559

Query: 585 RREDVP-TVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
           RRE++P T +NR+P+ LVTRSTLEVV+P+ AVPKLITKSK  L + SE+S
Sbjct: 560 RREELPVTTMNRIPVTLVTRSTLEVVIPEPAVPKLITKSKNKLAQISELS 609

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455340|ref|XP_002272224.1| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  820 bits (2117), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 435/640 (67%), Positives = 508/640 (79%), Gaps = 32/640 (5%)

Query: 1   MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSIN 60
           MDRSRSKR Y+Y+ QDYD +T+GRTKPRYN+            NN+   +   N++    
Sbjct: 1   MDRSRSKRGYFYE-QDYDSETLGRTKPRYNNN-----------NNHGGHHYNTNSHHRRG 48

Query: 61  NSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG 120
            +     S  +D S+MVTT+YRILCHD+KAGGVIGKSGSIIKSIRQHTGAWINVHELIPG
Sbjct: 49  GAGAGRASKLQDSSVMVTTSYRILCHDVKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG 108

Query: 121 DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGV 180
           DEERIIEISDTRRRDPEGRMP FSPAQEALF+IHDRILESD G G       +       
Sbjct: 109 DEERIIEISDTRRRDPEGRMPQFSPAQEALFMIHDRILESDAGFGNGFGGNGDD-----D 163

Query: 181 GGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSM 240
              G RGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMR+ETKTQIRILPRDH+LPRCVSM
Sbjct: 164 DDFGPRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRIETKTQIRILPRDHNLPRCVSM 223

Query: 241 SEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHS-PDRFFPDDDYVPHMNNT 299
           SEEIVQVVGD+N VKNA+A ISSRLRESQHRDRSHFHGR+ S P+RFFP DD   HMNN 
Sbjct: 224 SEEIVQVVGDVNAVKNAIANISSRLRESQHRDRSHFHGRIQSSPERFFPPDDDYSHMNNA 283

Query: 300 ARRPSMDGARFSGS------NYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRML 353
            RR  +DG  F           RSN++  R SGY++E+GAAP++D+ Q F GED+VFR+L
Sbjct: 284 PRRMPIDGNSFGSRVSTGLVGTRSNSFASRTSGYTLESGAAPIADNAQQFLGEDIVFRIL 343

Query: 354 CPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEA 413
           CP+DKV  V+GES+GI+ELLQNEIGVD+KVAD V GS+EQII I+SEEGPDDELFPAQEA
Sbjct: 344 CPVDKVECVVGESDGIIELLQNEIGVDVKVADHVAGSNEQIIVITSEEGPDDELFPAQEA 403

Query: 414 LLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVP 473
           LLHIQTRIV+L  DK+N+ITTRLLVPSSEIGC EGRD SLSEMRR TGANIQI+ RE++P
Sbjct: 404 LLHIQTRIVNLLPDKENVITTRLLVPSSEIGCFEGRDCSLSEMRRLTGANIQIVPREQLP 463

Query: 474 ACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAA 533
           A +SGTDEL++IVGEI+AARDALVEVT+RLRSYLYR+FF K+ PP S    GS   +EA+
Sbjct: 464 AFISGTDELLEIVGEIKAARDALVEVTSRLRSYLYREFFPKDMPPPSISAPGS---LEAS 520

Query: 534 SPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVI 593
           SP +ITPARE  T +DPP   +Q+VQ  A+ QPSK++ G+  ETVKQNE+     VP+V+
Sbjct: 521 SPNNITPAREGHTASDPPTTNYQNVQAIASVQPSKDSGGTGGETVKQNET-----VPSVL 575

Query: 594 NRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
           NR+P+ LVTRSTLEVV+P++AVPKLIT+SK  L + SE S
Sbjct: 576 NRIPVTLVTRSTLEVVIPEHAVPKLITRSKNKLAQISEWS 615

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509231|ref|XP_003523354.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  815 bits (2105), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 427/639 (66%), Positives = 498/639 (77%), Gaps = 47/639 (7%)

Query: 1   MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSIN 60
           M+RSRSKRNYYYD QDYD +T+ RT+PRYNH+Y                 +   N+    
Sbjct: 1   MERSRSKRNYYYD-QDYDSETLARTRPRYNHHY-----------------STGGNHRHRG 42

Query: 61  NSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG 120
               R     +D  L VTT+YRILCHD+KAGGVIGKSGSIIKSIRQHTGAWINVHEL+PG
Sbjct: 43  GGAARHAKTQQDSPLTVTTSYRILCHDLKAGGVIGKSGSIIKSIRQHTGAWINVHELMPG 102

Query: 121 DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGV 180
           DEERIIEISDTRRRDPEGRMPSFSPAQEAL LIH+RILESD   G               
Sbjct: 103 DEERIIEISDTRRRDPEGRMPSFSPAQEALLLIHERILESDAAFGV---------AEEDE 153

Query: 181 GGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSM 240
             GG  GG +R+ATR+VVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDH+LPRCVSM
Sbjct: 154 EYGGRGGGRDRIATRLVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHNLPRCVSM 213

Query: 241 SEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFF-PDDDYVPHMNNT 299
           SEEIVQVVG++N VKNA+ IISSRLRESQHRDRSHFHGR+HSP+RFF PDDDYVPH+ + 
Sbjct: 214 SEEIVQVVGNVNAVKNALVIISSRLRESQHRDRSHFHGRVHSPERFFSPDDDYVPHVTSG 273

Query: 300 ARRPSMDGARF----SGSNYRSNNYGPRPS-GYSIEAGAAPMSDSVQPFYGEDLVFRMLC 354
           +RR S+DGA F    S +N R+NN+   PS  Y++E GAAP+ D  Q FYGE+LVFR+LC
Sbjct: 274 SRRSSVDGASFGSRGSNTNSRNNNH---PSLNYAMEPGAAPVVDDAQGFYGEELVFRILC 330

Query: 355 PIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEAL 414
           PI+KV R+IGESEGIVE LQNE+GVD+KV DPV GSDEQII I+SEEGPDDELFPAQEAL
Sbjct: 331 PIEKVDRIIGESEGIVEFLQNEVGVDVKVTDPVGGSDEQIIIITSEEGPDDELFPAQEAL 390

Query: 415 LHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPA 474
           LH+QTRIVDL  DKDN ITTRL+VPSSEI CL+G+D SLSE+RR TGANIQIL R+E+P 
Sbjct: 391 LHVQTRIVDLVLDKDNTITTRLVVPSSEIECLDGKDVSLSEIRRLTGANIQILPRDELPL 450

Query: 475 CVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAAS 534
           CV+ TDELVQIVGEI+AARDA+VEVT+RLRSYLYRDFFQ++T P      G+A    A+S
Sbjct: 451 CVAKTDELVQIVGEIKAARDAVVEVTSRLRSYLYRDFFQRDTVPLPAPLPGAA----ASS 506

Query: 535 PIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVIN 594
             +I P  E  T       T+Q++Q  A + PSKE  GS +ET KQ ES+RR+D+ + +N
Sbjct: 507 SNNIVPVTETPT-------TYQNLQTVAAALPSKETGGSSTETGKQKESDRRDDLLSGLN 559

Query: 595 RVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
           R+ +PLVTRSTLEVVLP+YAVPKL+ KSK+ L + SE+S
Sbjct: 560 RIAVPLVTRSTLEVVLPEYAVPKLVAKSKSKLAQISELS 598

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456987|ref|XP_004146230.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus] gi|449517605|ref|XP_004165836.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  814 bits (2103), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 438/643 (68%), Positives = 514/643 (79%), Gaps = 33/643 (5%)

Query: 1   MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSIN 60
           M++SRSKRNYYYDHQD+D D+MGRT+PRYN+ + PNNNYRHRGN                
Sbjct: 1   MEKSRSKRNYYYDHQDFDSDSMGRTRPRYNNNHYPNNNYRHRGNAVRP------------ 48

Query: 61  NSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG 120
                  S P+D SLMVTTTYRILCHD KAGGVIGKSGSIIKSIRQHTGAWINVHEL+PG
Sbjct: 49  -------SKPQDQSLMVTTTYRILCHDAKAGGVIGKSGSIIKSIRQHTGAWINVHELVPG 101

Query: 121 DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF----YGEEEEEYGG 176
           DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIH+RILES+   GF    YG E+EE   
Sbjct: 102 DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHERILESEMSPGFNGMGYGPEDEE-DD 160

Query: 177 GGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPR 236
            GGV GGG  G G RVATR+VVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDH+LPR
Sbjct: 161 YGGVRGGGGGGCGGRVATRLVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHNLPR 220

Query: 237 CVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFP-DDDYVPH 295
           C+SMSEEIVQ+VGD N VK A+AI+SSRLRESQHRDRSHFHGRLHSP+R FP +DDYVPH
Sbjct: 221 CISMSEEIVQIVGDTNAVKKAIAIVSSRLRESQHRDRSHFHGRLHSPERIFPPEDDYVPH 280

Query: 296 MNNTARRPSMDG----ARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFR 351
               ARR  MDG     R S SN R N+Y  R S + +E GAAP++D++ PFYGEDLVF+
Sbjct: 281 ---NARRLPMDGRPFRPRMSASNTRGNDYSSRQSNFMVEPGAAPVNDNMMPFYGEDLVFK 337

Query: 352 MLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQ 411
           +LCPI+KV  VIGES GI+ELL+N++GVD+KV+DPV GS+EQI+ ISS+EGPDDELFPAQ
Sbjct: 338 ILCPIEKVDSVIGESNGIIELLRNDVGVDIKVSDPVTGSNEQILIISSDEGPDDELFPAQ 397

Query: 412 EALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREE 471
           EALLHIQTRIVDL  DK+NI+TTRLLVPSS+IGCLEGRDGSL EM+R TGAN+ I+ RE+
Sbjct: 398 EALLHIQTRIVDLVPDKENIVTTRLLVPSSDIGCLEGRDGSLLEMKRLTGANVHIVPRED 457

Query: 472 VPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPS-STGPTGSALVV 530
           +P  VSG DELVQI+G+I+AARDALVE+T+RLR+ LY++ FQK+  P  S   T  +L +
Sbjct: 458 LPMFVSGADELVQIIGDIKAARDALVELTSRLRNCLYKEPFQKDASPQVSVQSTMVSLGL 517

Query: 531 EAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVP 590
           E +S  +   AREV +  D  +   Q+VQ   T+Q  KE  GS +ET  QNE++RRED+P
Sbjct: 518 EESSSNNNAAAREVHSGNDSASTAFQNVQPFGTAQLLKETGGSSNETGTQNENDRREDLP 577

Query: 591 TVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
           + +NR+P+PLVTRSTLEVV+P+ AVPKLITKSK  L + SE+S
Sbjct: 578 SGLNRIPVPLVTRSTLEVVIPEPAVPKLITKSKNKLAQISELS 620

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561850|ref|XP_002521934.1| nucleic acid binding protein, putative [Ricinus communis] gi|223538859|gb|EEF40458.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  791 bits (2044), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/579 (72%), Positives = 473/579 (81%), Gaps = 25/579 (4%)

Query: 1   MDRSRSKRNYYYDHQ-DYDGD-TMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTS 58
           M+RSRSKRNYYYDHQ DYD + TM RTKPRYN       N  +  NNN+   N       
Sbjct: 1   MERSRSKRNYYYDHQQDYDNEITMSRTKPRYN-------NNTNNTNNNHYFPNNNRYRGG 53

Query: 59  INNSNNRANSNPK-DPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHEL 117
            NNSNN   S P+ D SLMVTT+YRILCHDMKAGGVIGKSG+IIKSIRQHTGAWINVHEL
Sbjct: 54  SNNSNNNRPSKPQQDNSLMVTTSYRILCHDMKAGGVIGKSGTIIKSIRQHTGAWINVHEL 113

Query: 118 IPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF-YGEEEEEYGG 176
           IPGDEERIIEISDTRRRDPEGRMP+FSPAQEALFLIHDRILESDG  G  Y  EE+EYGG
Sbjct: 114 IPGDEERIIEISDTRRRDPEGRMPAFSPAQEALFLIHDRILESDGQFGMSYANEEDEYGG 173

Query: 177 GGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPR 236
            G           NRVATR+VVSRMHVGCLLGKGGKIIEQMR+ETKTQIRILPRDH+LPR
Sbjct: 174 RG------INNSNNRVATRLVVSRMHVGCLLGKGGKIIEQMRIETKTQIRILPRDHTLPR 227

Query: 237 CVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSH--FHGRLHSPDRFFPDDDYVP 294
           CVSMSEEIVQVVGD+N VKNA+AIISSRLRESQHRDRSH  FHGR+HSP+RFFPDDDYVP
Sbjct: 228 CVSMSEEIVQVVGDVNAVKNAIAIISSRLRESQHRDRSHGNFHGRMHSPERFFPDDDYVP 287

Query: 295 HMNNTARRPSMDGARF----SGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVF 350
           HMNNT RR S+DG  F    SG NYR++NY  R  GY++EAGA P++DS QPFYG+DLVF
Sbjct: 288 HMNNTGRRSSIDGPSFGSRASGPNYRNSNYSSRQYGYNVEAGA-PVADSAQPFYGDDLVF 346

Query: 351 RMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPA 410
           RMLCP DKV +V+GES+GI++LLQN+IGVD+KV+DPV GSDEQ+I ISSEEGPDDELFPA
Sbjct: 347 RMLCPADKVNKVVGESDGILDLLQNDIGVDVKVSDPVSGSDEQMIIISSEEGPDDELFPA 406

Query: 411 QEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSRE 470
           QEALLHIQT I+DL  D DNII T+L+V S EIGCLEGRDGSLSEM R TGA IQIL RE
Sbjct: 407 QEALLHIQTHIIDLVPDSDNIIKTKLIVSSGEIGCLEGRDGSLSEMERLTGAKIQILPRE 466

Query: 471 EVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGP-TGSALV 529
           ++PACVS  DELVQI GEI+AARDALVEVT+RLRSYLY+++FQK+TPP  + P TG+AL 
Sbjct: 467 KLPACVSEADELVQIEGEIKAARDALVEVTSRLRSYLYKEYFQKDTPPPISVPSTGNALG 526

Query: 530 VEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSK 568
           +EAASP +I P R+  +  +PPAA + + +  A  Q SK
Sbjct: 527 MEAASPNNINPPRDGHSGGEPPAANYHTPKTAAPIQLSK 565

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143921|emb|CBI23026.3| unnamed protein product [Vitis vinifera]

 Score =  778 bits (2009), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 396/565 (70%), Positives = 457/565 (80%), Gaps = 43/565 (7%)

Query: 76  MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRD 135
           MVTT+YRILCHD+KAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRD
Sbjct: 1   MVTTSYRILCHDVKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRD 60

Query: 136 PEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATR 195
           PEGRMP FSPAQEALF+IHDRILESD G          +G G                  
Sbjct: 61  PEGRMPQFSPAQEALFMIHDRILESDAG----------FGNG------------------ 92

Query: 196 MVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVK 255
           MVVSRMHVGCLLGKGGKIIEQMR+ETKTQIRILPRDH+LPRCVSMSEEIVQVVGD+N VK
Sbjct: 93  MVVSRMHVGCLLGKGGKIIEQMRIETKTQIRILPRDHNLPRCVSMSEEIVQVVGDVNAVK 152

Query: 256 NAVAIISSRLRESQHRDRSHFHGRLHS-PDRFFPDDDYVPHMNNTARRPSMDGARFSGS- 313
           NA+A ISSRLRESQHRDRSHFHGR+ S P+RFFP DD   HMNN  RR  +DG  F    
Sbjct: 153 NAIANISSRLRESQHRDRSHFHGRIQSSPERFFPPDDDYSHMNNAPRRMPIDGNSFGSRV 212

Query: 314 -----NYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEG 368
                  RSN++  R SGY++E+GAAP++D+ Q F GED+VFR+LCP+DKV  V+GES+G
Sbjct: 213 STGLVGTRSNSFASRTSGYTLESGAAPIADNAQQFLGEDIVFRILCPVDKVECVVGESDG 272

Query: 369 IVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADK 428
           I+ELLQNEIGVD+KVAD V GS+EQII I+SEEGPDDELFPAQEALLHIQTRIV+L  DK
Sbjct: 273 IIELLQNEIGVDVKVADHVAGSNEQIIVITSEEGPDDELFPAQEALLHIQTRIVNLLPDK 332

Query: 429 DNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE 488
           +N+ITTRLLVPSSEIGC EGRD SLSEMRR TGANIQI+ RE++PA +SGTDEL++IVGE
Sbjct: 333 ENVITTRLLVPSSEIGCFEGRDCSLSEMRRLTGANIQIVPREQLPAFISGTDELLEIVGE 392

Query: 489 IQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVT 548
           I+AARDALVEVT+RLRSYLYR+FF K+ PP S    GS   +EA+SP +ITPARE  T +
Sbjct: 393 IKAARDALVEVTSRLRSYLYREFFPKDMPPPSISAPGS---LEASSPNNITPAREGHTAS 449

Query: 549 DPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEV 608
           DPP   +Q+VQ  A+ QPSK++ G+  ETVKQNE+     VP+V+NR+P+ LVTRSTLEV
Sbjct: 450 DPPTTNYQNVQAIASVQPSKDSGGTGGETVKQNET-----VPSVLNRIPVTLVTRSTLEV 504

Query: 609 VLPDYAVPKLITKSKTLLTRFSEVS 633
           V+P++AVPKLIT+SK  L + SE S
Sbjct: 505 VIPEHAVPKLITRSKNKLAQISEWS 529

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8809595|dbj|BAA97146.1| RNA-binding protein-like [Arabidopsis thaliana]

 Score =  706 bits (1823), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/643 (60%), Positives = 475/643 (73%), Gaps = 47/643 (7%)

Query: 1   MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSIN 60
           M+RSRSKRNY+YD QDYDGD+M R+KPRYN      NNY H G      N          
Sbjct: 1   MERSRSKRNYHYD-QDYDGDSMPRSKPRYN------NNY-HFGGGGGGNNRYRGGGGGGG 52

Query: 61  NSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG 120
            +   + S+P+    M TTTYRILCHD KAGGVIGKSG+IIKSIRQHTGAWINVHEL+PG
Sbjct: 53  GNGRPSKSHPET---MATTTYRILCHDAKAGGVIGKSGTIIKSIRQHTGAWINVHELVPG 109

Query: 121 DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYG---EEEEEYGGG 177
           D ERIIEISD RRRDP+GRMPSFSPAQEALF +HDRILES+   G+ G   EEEE+YGG 
Sbjct: 110 DAERIIEISDNRRRDPDGRMPSFSPAQEALFSVHDRILESEAQFGYGGPPPEEEEDYGGV 169

Query: 178 GGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237
              G         RV TR+VVSRMHVGCLLGKGGKIIEQMR+ETKT IRILPR+ +LPRC
Sbjct: 170 RPGG--------GRVVTRLVVSRMHVGCLLGKGGKIIEQMRIETKTHIRILPRESNLPRC 221

Query: 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPD--DDYVPH 295
           VS+SEEIVQ+VG++N VKNA+AI+SSRLRESQHRDRS+F GR HSP+R F    DDY+P 
Sbjct: 222 VSLSEEIVQIVGELNAVKNALAIVSSRLRESQHRDRSNFQGRSHSPERSFAAAGDDYMPQ 281

Query: 296 MNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCP 355
           +    RR S D  RF   N+R+NN+  R S Y+ EA A P+ ++V   Y E+LVF++LCP
Sbjct: 282 L----RRQSSD--RFPRGNFRNNNFSSRQSNYAEEAPAVPVGENV---YSEELVFQILCP 332

Query: 356 IDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALL 415
            DK+ RV+GES+GI++LLQNEIGVD++V+DPV GSDEQIITISSEE PDD  FPAQEALL
Sbjct: 333 ADKIVRVVGESQGIIDLLQNEIGVDVRVSDPVAGSDEQIITISSEEAPDDPFFPAQEALL 392

Query: 416 HIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPAC 475
           HIQT+I+DL  DKDN+ITTRLLVPS +  CLEG+ GS+SE+ R TG ++QIL+REE+P C
Sbjct: 393 HIQTQIIDLIPDKDNLITTRLLVPSRDSICLEGKAGSVSEISRLTGTSVQILAREEIPRC 452

Query: 476 VSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGS----ALVVE 531
            S  D ++QI GEI+AAR+ALVE+T  LRS+++++  QKETPP+ST  TG     A V+E
Sbjct: 453 ASINDVVIQITGEIRAAREALVELTLLLRSHMFKELSQKETPPASTSTTGPLEGVAGVME 512

Query: 532 AASPIDITPAREVQTVTDPPAATHQSVQIPATSQPS-KEAAGSVSETVKQNESERREDVP 590
            AS  +   +RE       P +++ ++Q  +T  P  KE  GSV+   K  ESE RE+VP
Sbjct: 513 VASSNNTIQSRE------GPTSSNLNLQQVSTILPQFKEGFGSVA---KAGESEHREEVP 563

Query: 591 TVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
              +R+ +PLVTRSTLEVVLP+  VPKL+TKS+  L + SE S
Sbjct: 564 VTTSRMAVPLVTRSTLEVVLPEAVVPKLVTKSRNKLAQISEWS 606

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30696273|ref|NP_200118.3| RNA-binding KH domain-containing protein [Arabidopsis thaliana] gi|17065220|gb|AAL32764.1| RNA-binding protein-like [Arabidopsis thaliana] gi|30725478|gb|AAP37761.1| At5g53060 [Arabidopsis thaliana] gi|332008915|gb|AED96298.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana]

 Score =  705 bits (1819), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/643 (60%), Positives = 475/643 (73%), Gaps = 47/643 (7%)

Query: 1   MDRSRSKRNYYYDHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNTSIN 60
           M+RSRSKRNY+YD QDYDGD+M R+KPRYN      NNY H G      N          
Sbjct: 1   MERSRSKRNYHYD-QDYDGDSMPRSKPRYN------NNY-HFGGGGGGNNRYRGGGGGGG 52

Query: 61  NSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG 120
            +   + S+P+    M TTTYRILCHD KAGGVIGKSG+IIKSIRQHTGAWINVHEL+PG
Sbjct: 53  GNGRPSKSHPET---MATTTYRILCHDAKAGGVIGKSGTIIKSIRQHTGAWINVHELVPG 109

Query: 121 DEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYG---EEEEEYGGG 177
           D ERIIEISD RRRDP+GRMPSFSPAQEALF +HDRILES+   G+ G   EEEE+YGG 
Sbjct: 110 DAERIIEISDNRRRDPDGRMPSFSPAQEALFSVHDRILESEAQFGYGGPPPEEEEDYGGV 169

Query: 178 GGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237
              G         RV TR+VVSRMHVGCLLGKGGKIIEQMR+ETKT IRILPR+ +LPRC
Sbjct: 170 RPGG--------GRVVTRLVVSRMHVGCLLGKGGKIIEQMRIETKTHIRILPRESNLPRC 221

Query: 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPD--DDYVPH 295
           VS+SEEIVQ+VG++N VKNA+AI+SSRLRESQHRDRS+F GR HSP+R F    DDY+P 
Sbjct: 222 VSLSEEIVQIVGELNAVKNALAIVSSRLRESQHRDRSNFQGRSHSPERSFAAAGDDYMPQ 281

Query: 296 MNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCP 355
           +    RR S D  RF   N+R+NN+  R S Y+ EA A P+ ++V   Y E+LVF++LCP
Sbjct: 282 L----RRQSSD--RFPRGNFRNNNFSSRQSNYAEEAPAVPVGENV---YSEELVFQILCP 332

Query: 356 IDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALL 415
            DK+ RV+GES+GI++LLQNEIGVD++V+DPV GSDEQIITISSEE PDD  FPAQEALL
Sbjct: 333 ADKIVRVVGESQGIIDLLQNEIGVDVRVSDPVAGSDEQIITISSEEAPDDPFFPAQEALL 392

Query: 416 HIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPAC 475
           HIQT+I+DL  DKDN+ITTRLLVPS +  CLEG+ GS+SE+ R TG ++QIL+REE+P C
Sbjct: 393 HIQTQIIDLIPDKDNLITTRLLVPSRDSICLEGKAGSVSEISRLTGTSVQILAREEIPRC 452

Query: 476 VSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGS----ALVVE 531
            S  D ++QI GEI+AAR+ALVE+T  LRS+++++  QKETPP+ST  TG     A V+E
Sbjct: 453 ASINDVVIQITGEIRAAREALVELTLLLRSHMFKELSQKETPPASTSTTGPLEGVAGVME 512

Query: 532 AASPIDITPAREVQTVTDPPAATHQSVQIPATSQPS-KEAAGSVSETVKQNESERREDVP 590
            AS  +   +RE       P +++ ++Q  +T  P  KE  GSV+   K  ESE RE+VP
Sbjct: 513 VASSNNTIQSRE------GPTSSNLNLQQVSTILPQFKEGFGSVA---KAGESEHREEVP 563

Query: 591 TVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVS 633
              +R+ +PLVTRSTLEVVLP+  VPKL+TKS+  L + SE S
Sbjct: 564 VTTSRMAVPLVTRSTLEVVLPEAVVPKLVTKSRNKLAQISEWS 606

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	650
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.833	0.831	0.579	9.6e-174
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.458	0.543	0.335	6.8e-51
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.290	0.304	0.398	2.7e-37
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.233	0.317	0.423	4.1e-37
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.653	0.659	0.290	2e-32
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.629	0.674	0.265	5.2e-24
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.243	0.25	0.303	5.9e-20
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.253	0.285	0.310	1.1e-16
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.253	0.333	0.323	9.6e-14
TAIR|locus:2056951	153	AT2G03110 "AT2G03110" [Arabido	0.226	0.960	0.284	4.1e-11

TAIR|locus:2168367 RCF3 "AT5G53060" [Arabidopsis thaliana (taxid:3702)]

 Score = 1574 (559.1 bits), Expect = 9.6e-174, Sum P(2) = 9.6e-174
 Identities = 327/564 (57%), Positives = 405/564 (71%)

Query:    73 PSLMVTTTYRILCHDMXXXXXXXXXXXXXXXXRQHTGAWINVHELIPGDEERIIEISDTR 132
             P  M TTTYRILCHD                 RQHTGAWINVHEL+PGD ERIIEISD R
Sbjct:    62 PETMATTTYRILCHDAKAGGVIGKSGTIIKSIRQHTGAWINVHELVPGDAERIIEISDNR 121

Query:   133 RRDPEGRMPSFSPAQEALFLIHDRILESDXXXXXXXXXXXXXXXXXXXXXXXXXXXXNRV 192
             RRDP+GRMPSFSPAQEALF +HDRILES+                             RV
Sbjct:   122 RRDPDGRMPSFSPAQEALFSVHDRILESEAQFGYGGPPPEEEEDYGGVRPGG-----GRV 176

Query:   193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDIN 252
              TR+VVSRMHVGCLLGKGGKIIEQMR+ETKT IRILPR+ +LPRCVS+SEEIVQ+VG++N
Sbjct:   177 VTRLVVSRMHVGCLLGKGGKIIEQMRIETKTHIRILPRESNLPRCVSLSEEIVQIVGELN 236

Query:   253 NVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFP--DDDYVPHMNNTARRPSMDGARF 310
              VKNA+AI+SSRLRESQHRDRS+F GR HSP+R F    DDY+P +    RR S D  RF
Sbjct:   237 AVKNALAIVSSRLRESQHRDRSNFQGRSHSPERSFAAAGDDYMPQL----RRQSSD--RF 290

Query:   311 SGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIV 370
                N+R+NN+  R S Y+ EA A P+ ++V   Y E+LVF++LCP DK+ RV+GES+GI+
Sbjct:   291 PRGNFRNNNFSSRQSNYAEEAPAVPVGENV---YSEELVFQILCPADKIVRVVGESQGII 347

Query:   371 ELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDN 430
             +LLQNEIGVD++V+DPV GSDEQIITISSEE PDD  FPAQEALLHIQT+I+DL  DKDN
Sbjct:   348 DLLQNEIGVDVRVSDPVAGSDEQIITISSEEAPDDPFFPAQEALLHIQTQIIDLIPDKDN 407

Query:   431 IITTRLLVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQ 490
             +ITTRLLVPS +  CLEG+ GS+SE+ R TG ++QIL+REE+P C S  D ++QI GEI+
Sbjct:   408 LITTRLLVPSRDSICLEGKAGSVSEISRLTGTSVQILAREEIPRCASINDVVIQITGEIR 467

Query:   491 AARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDP 550
             AAR+ALVE+T  LRS+++++  QKETPP+ST  TG    V  A  +++  +       + 
Sbjct:   468 AAREALVELTLLLRSHMFKELSQKETPPASTSTTGPLEGV--AGVMEVASSNNTIQSREG 525

Query:   551 PAATHQSVQIPATSQPS-KEAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVV 609
             P +++ ++Q  +T  P  KE  GSV+   K  ESE RE+VP   +R+ +PLVTRSTLEVV
Sbjct:   526 PTSSNLNLQQVSTILPQFKEGFGSVA---KAGESEHREEVPVTTSRMAVPLVTRSTLEVV 582

Query:   610 LPDYAVPKLITKSKTLLTRFSEVS 633
             LP+  VPKL+TKS+  L + SE S
Sbjct:   583 LPEAVVPKLVTKSRNKLAQISEWS 606

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2150956 AT5G15270 "AT5G15270" [Arabidopsis thaliana (taxid:3702)]

 Score = 441 (160.3 bits), Expect = 6.8e-51, Sum P(2) = 6.8e-51
 Identities = 108/322 (33%), Positives = 181/322 (56%)

Query:   191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD 250
             +V  +++V    +GC+LG+GG+I++ +R ET  QIRI+ +D ++P C   S+E++Q+ G+
Sbjct:   146 QVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIV-KDRNMPLCALNSDELIQISGE 204

Query:   251 INNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARF 310
             +  VK A+  I+SRL E+  R ++     L S    +P    + H           G R 
Sbjct:   205 VLIVKKALLQIASRLHENPSRSQN-----LLSSSGGYPAGSLMSHAG---------GPRL 250

Query:   311 SGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIV 370
              G      +YG     +S      P +D   P    +   R++ P++ +  VIG+   ++
Sbjct:   251 VGLAPLMGSYGRDAGDWSRPLYQPPRNDP--P--ATEFFIRLVSPVENIASVIGKGGALI 306

Query:   371 ELLQNEIGVDLKV-ADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKD 429
               L+ E    +KV +   +G+D  +ITIS+ E  +D   P  EA++ +Q +  D      
Sbjct:   307 NQLRQETRATIKVDSSRTEGND-CLITISAREVFEDAYSPTIEAVMRLQPKCSDKVERDS 365

Query:   430 NII--TTRLLVPSSEIGCLEGRDGSL-SEMRRSTGANIQILSREEVPACVSGTDELVQIV 486
              ++  TTRLLVPSS IGC+ G+ G++ +EMRR T ANI+IL +E +P   S  DE+VQI 
Sbjct:   366 GLVSFTTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLPKVASDDDEMVQIS 425

Query:   487 GEIQAARDALVEVTTRLRSYLY 508
             GE+  A++AL+++T+RLR+ ++
Sbjct:   426 GELDVAKEALIQITSRLRANVF 447

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2017612 AT1G51580 "AT1G51580" [Arabidopsis thaliana (taxid:3702)]

 Score = 351 (128.6 bits), Expect = 2.7e-37, Sum P(2) = 2.7e-37
 Identities = 79/198 (39%), Positives = 119/198 (60%)

Query:   335 PMSDSVQPF----YGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGS 390
             PM + V PF      E++ FR+LCP DKVG +IG+   +V  LQNE G  +KV+DP   S
Sbjct:   259 PMPEDVGPFNRPVVEEEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDS 318

Query:   391 DEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRD 450
             +E+II IS+ E  +     AQ+ ++ +  RIV++G +    +  RLLV S  IG L G+ 
Sbjct:   319 EERIIVISARENLERRHSLAQDGVMRVHNRIVEIGFEPSAAVVARLLVHSPYIGRLLGKG 378

Query:   451 GSL-SEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLY- 508
             G L SEMRR+TGA+I++ ++++     S  DE+VQ++G ++  +DAL ++  RLR  ++ 
Sbjct:   379 GHLISEMRRATGASIRVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFP 438

Query:   509 -RDFFQKE--TPPSSTGP 523
              R  FQ     PP   GP
Sbjct:   439 GRLPFQGMGGPPPPFMGP 456

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

TAIR|locus:2035807 AT1G14170 "AT1G14170" [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 4.1e-37, Sum P(2) = 4.1e-37
 Identities = 66/156 (42%), Positives = 97/156 (62%)

Query:   353 LCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQE 412
             +CP + VG VIG+  G +  ++ E G  ++V       D+ II ISS+E  +D+  PA  
Sbjct:   274 ICPAENVGGVIGKGGGFINQIRQETGATIRVNTSETDDDDCIIFISSKEFYEDQS-PAVN 332

Query:   413 ALLHIQTRIVD-LGADKDNI-ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR 469
             A + +Q R  + +G D +++ I+TRLLV SS+IGCL G+ G+ +SEMR  T ANI+IL +
Sbjct:   333 AAIRLQQRCSEKVGKDANDLAISTRLLVSSSQIGCLIGKGGAVISEMRSVTRANIRILQK 392

Query:   470 EEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS 505
             E+VP      +E+VQI G   AA  AL +V  RLR+
Sbjct:   393 EDVPKIAREDEEMVQITGSPDAAMKALTQVILRLRA 428

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

TAIR|locus:2161413 AT5G46190 "AT5G46190" [Arabidopsis thaliana (taxid:3702)]

 Score = 377 (137.8 bits), Expect = 2.0e-32, P = 2.0e-32
 Identities = 138/475 (29%), Positives = 212/475 (44%)

Query:    77 VTTTYRILCHDMXXXXXXXXXXXXXXXXRQHTGAWINVHELIPGDEERIIEI--SDTRRR 134
             +   YRILC                   RQ T A I V +  PG  ER+I I  S + ++
Sbjct:    42 LVVVYRILCPSGVMGSVIGKSGKVINLIRQETRARIKVVDPFPGCSERVITIFCSVSEKK 101

Query:   135 DP---EGRMPSFS-P---AQEALFLIHDRILESDXXXXXXXXXXXXXXXXXXXXXXXXXX 187
             D    E     +S P   AQ AL  +HD I+ S                           
Sbjct:   102 DIVDIEYSELDYSVPLCSAQAALLKVHDAIVAS----------------LATAAENTKID 145

Query:   188 XXNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPR--CVSMSEEIV 245
               +    R++V       ++GK G II+ +R  T+  ++++ +D S P   C    + IV
Sbjct:   146 RDDFRECRLLVPSSQCSIVIGKSGSIIKNIRGRTRANVKVVSKDVSDPSHTCAMDFDNIV 205

Query:   246 QVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHS-PDRFFPDDDYVPHMNNTARRPS 304
              + G+  +VK A+  +S+ + +   R++      +   P       D   +       PS
Sbjct:   206 MISGETESVKKALFAVSAIMYKVSPREQIPLDTTVQEVPASIIIPSDLSIYPQ-AGLYPS 264

Query:   305 MDGARFSGSNYRSNNYGPRPSGYSIEAGAAPM---SDSVQP----FYG----EDLVFRML 353
              D     G+N  S+  G  P GY  E  A P+   S S  P    F G    E L  +++
Sbjct:   265 QDSIFQHGANV-SSFIGTLPQGYG-ENAANPVPVFSASALPVVHGFGGSSRSEKLAIKVI 322

Query:   354 CPIDKVGRVIGESEGIVELLQNEIGVDLKVADP-VDGSDEQIITISSEEGPDDELFPAQE 412
             C   K+GRVIG+    ++ ++   G  ++V D   +  D+ +IT+++ E PDD    A E
Sbjct:   323 CSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATESPDDLKSMAVE 382

Query:   413 ALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSL-SEMRRSTGANIQILSREE 471
             A+L +Q +I D   DK   +  +LLV S  IGC+ G+ GS+ SE+R+ T A+I I     
Sbjct:   383 AVLLLQEKINDEDEDK---VKMQLLVSSKVIGCIIGKSGSIISEIRKRTKADIHISKGNN 439

Query:   472 VPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGS 526
              P C    DELV+I GE+   RDAL+++  RLR  + RD   +ET   +  P  S
Sbjct:   440 TPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRD---RETGSRNQPPARS 491

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2831364 AT4G18375 "AT4G18375" [Arabidopsis thaliana (taxid:3702)]

 Score = 302 (111.4 bits), Expect = 5.2e-24, Sum P(2) = 5.2e-24
 Identities = 126/474 (26%), Positives = 218/474 (45%)

Query:    81 YRILCHDMXXXXXXXXXXXXXXXXRQHTGAWINVHELIPGDEERIIEI--SDTRRRDPEG 138
             YRILC                   R +T A I V + + G  +R+I I  S   +++  G
Sbjct:    38 YRILCPIDVVGGVIGKSGKVINAIRHNTKAKIKVFDQLHGCSQRVITIYCSVKEKQEEIG 97

Query:   139 RMPSFS-P---AQEALFLIHDRILESDXXXXXXXXXXXXXXXXXXXXXXXXXXXXNRVAT 194
                S + P   AQ+AL  ++D I+ SD                            N+   
Sbjct:    98 FTKSENEPLCCAQDALLKVYDAIVASDEENNTKTNVDRDD---------------NKEC- 141

Query:   195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPR--CVSMSEEIVQVVGDIN 252
             R++V       L+GK G+ I+++R  T+  ++++ +D S P   C    + +V + G+  
Sbjct:   142 RLLVPFSQSSSLIGKAGENIKRIRRRTRASVKVVSKDVSDPSHVCAMEYDNVVVISGEPE 201

Query:   253 NVKNAVAIISSRL-----RE-----SQHRD--------RSHFHGRLHSPDRFFPDDDYVP 294
             +VK A+  +S+ +     RE     S  +D         S     ++    F+ + D++ 
Sbjct:   202 SVKQALFAVSAIMYKINPRENIPLDSTSQDVPAASVIVPSDLSNSVYPQTGFYSNQDHI- 260

Query:   295 HMNNTARRPSMDGARFSGSNYRSNNYGPRPSG-YSIEAGAAPMSDSVQ-PFYGEDLVFRM 352
              +   A  PS   A  S S+++   Y    +    + A + P++         E+LVF++
Sbjct:   261 -LQQGAGVPSYFNA-LSVSDFQG--YAETAANPVPVFASSLPVTHGFGGSSRSEELVFKV 316

Query:   353 LCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVD--GSDEQIITISSEEGPDDELFPA 410
             LCP+  + RVIG+    ++ ++   G  ++V D     G DE +I +++ E PDD    A
Sbjct:   317 LCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDECVIIVTATESPDDMKSMA 376

Query:   411 QEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR 469
              EA+L +Q  I D   D +N+   +LLV S  IGC+ G+ GS ++E+R+ T ANI I   
Sbjct:   377 VEAVLLLQEYIND--EDAENV-KMQLLVSSKVIGCVIGKSGSVINEIRKRTNANICISKG 433

Query:   470 EEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLY--RDFFQKETPPSST 521
             ++        D+LV++ GE+ + RDAL+++  RLR  +   +D      PP+ T
Sbjct:   434 KK--------DDLVEVSGEVSSVRDALIQIVLRLREDVLGDKDSVATRKPPART 479

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2066020 AT2G22600 "AT2G22600" [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 5.9e-20, Sum P(4) = 5.9e-20
 Identities = 51/168 (30%), Positives = 87/168 (51%)

Query:   348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDEL 407
             +VF+++      G +IG+   I+  LQNE G  + V  P+  S E+++T+S+ E  +   
Sbjct:   277 VVFKIIFTSVVAGGIIGKQGTIIRALQNETGASISVGAPLKVSGERVVTVSARENLESRY 336

Query:   408 FPAQEALLHIQTRIVDLGADKD------N--IITTRLLVPSSEIGCLEGRDGSLSEMRRS 459
               AQ AL  +  R V++  +K       N  I+ T+LLVPS       G +G+  E   +
Sbjct:   337 SHAQNALALVFARSVEIDVEKGLRPGLHNGAIVKTKLLVPSHFANSFNG-NGN-REAIIA 394

Query:   460 TGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYL 507
             TGA++ I    +V   +S  + +++I GE    + AL  V+++LR  L
Sbjct:   395 TGADVHISVGNQVLEWISENEVVIEIKGEYSHVQKALTHVSSKLRENL 442

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2084908 FLK "AT3G04610" [Arabidopsis thaliana (taxid:3702)]

 Score = 241 (89.9 bits), Expect = 1.1e-16, Sum P(2) = 1.1e-16
 Identities = 54/174 (31%), Positives = 97/174 (55%)

Query:   342 PFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEE 401
             P +  + VFRML P  KVG +IG    +++ +  E    +K+ D   G+ E+ + +S +E
Sbjct:   181 PGWPGETVFRMLVPAQKVGSIIGRKGDVIKKIVEETRARIKILDGPPGTTERAVMVSGKE 240

Query:   402 GPDDELFPAQEALLHIQTRIVDLGADKD-------NIITTRLLVPSSEIGCLEGRDG-SL 453
              P+  L P+ + LL +  RIVD G D +       + ++TRLLVP+S+ G L G+ G ++
Sbjct:   241 EPESSLPPSMDGLLRVHMRIVD-GLDGEASQAPPPSKVSTRLLVPASQAGSLIGKQGGTV 299

Query:   454 SEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYL 507
               ++ ++   +++L  E++P      D +V++VGE  +   AL  + + LR +L
Sbjct:   300 KAIQEASACIVRVLGSEDLPVFALQDDRVVEVVGEPTSVHRALELIASHLRKFL 353

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0009911 "positive regulation of flower development" evidence=IMP

TAIR|locus:2120755 PEP "AT4G26000" [Arabidopsis thaliana (taxid:3702)]

 Score = 209 (78.6 bits), Expect = 9.6e-14, P = 9.6e-14
 Identities = 57/176 (32%), Positives = 94/176 (53%)

Query:   342 PFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD-PVDGSDEQIITISSE 400
             P +  D VFRM+ P+ KVG +IG     ++ +  E    +KV D PV+  D +I+ IS +
Sbjct:    68 PGWPGDCVFRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGPVNTPD-RIVLISGK 126

Query:   401 EGPDDELFPAQEALLHIQTRIVDLGADKDNII--------TTRLLVPSSEIGCLEGRDGS 452
             E P+  + PA +A+L +  R+  L  + D+ +        + RLLV S++   L G+ GS
Sbjct:   127 EEPEAYMSPAMDAVLRVFRRVSGLPDNDDDDVQNAGSVFSSVRLLVASTQAINLIGKQGS 186

Query:   453 L-SEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYL 507
             L   +  ++GA+++ILS EE P   +  + +V + GE      AL  +   LR +L
Sbjct:   187 LIKSIVENSGASVRILSEEETPFYAAQDERIVDLQGEALKILKALEAIVGHLRRFL 242

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0048367 "shoot system development" evidence=IMP

GO:0048467 "gynoecium development" evidence=IMP

TAIR|locus:2056951 AT2G03110 "AT2G03110" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 4.1e-11, P = 4.1e-11
 Identities = 47/165 (28%), Positives = 83/165 (50%)

Query:   112 INVHELIPGDEERIIEI---SDTRRRDPEGRMPSFSPAQEALFLIHDRILESDXXXXXXX 168
             + V+E +PG +ER++ I   S+ R R  +       PA +ALF +HD ++  +       
Sbjct:     1 MRVNEALPGCDERVVTIYSNSEERNRIEDDNEDFVCPAFDALFKVHDMVVVEEFDDDDDY 60

Query:   169 XXXXXXXXXXXXXXXXXXXXXNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL 228
                                    V  RM+V    +G L+GKGG II+ +R +T  QIR+ 
Sbjct:    61 NDNDEYSEGQTV-----------VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV- 108

Query:   229 PRDHSLPRC-VSMS-EEIVQVVGDINNVKNAVAIISSRLRESQHR 271
              R+ +LP C +++S +E++Q++GD + V+ A+  ++  L  +  R
Sbjct:   109 -RNDNLPMCALALSHDELLQIIGDPSAVREALYQVAFLLYNNPSR 152

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00150124 hypothetical protein (686 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	650
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-17
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-14
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-09
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	9e-09
pfam00013	59	pfam00013, KH_1, KH domain	9e-09
pfam13014	42	pfam13014, KH_3, KH domain	2e-08
pfam00013	59	pfam00013, KH_1, KH domain	4e-08
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	8e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	5e-06
pfam00013	59	pfam00013, KH_1, KH domain	1e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-05
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-04
pfam13014	42	pfam13014, KH_3, KH domain	1e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.002

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

 Score = 76.7 bits (190), Expect = 1e-17
 Identities = 31/76 (40%), Positives = 40/76 (52%), Gaps = 12/76 (15%)

Query: 80  TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELI-PGDEERIIEISDTRRRDPEG 138
           T R+L    +AG +IGK GS IK IR+ TGA I V + + PG  ER++ IS         
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK------- 53

Query: 139 RMPSFSPAQEALFLIH 154
                S  Q+AL LI 
Sbjct: 54  ----PSAVQKALLLIL 65

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

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

 Score = 67.5 bits (166), Expect = 2e-14
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R++V     G ++GKGG  I+++R ET  +IR+      LP     +E +V + G  + V
Sbjct: 3   RLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSV--LPGS---TERVVTISGKPSAV 57

Query: 255 KNAVAIIS 262
           + A+ +I 
Sbjct: 58  QKALLLIL 65

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

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

 Score = 61.7 bits (151), Expect = 3e-12
 Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
           T RLLVPSS+ G + G+ GS + E+R  TGA I++            T+ +V I G+  A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSA 56

Query: 492 ARDALVEVT 500
            + AL+ + 
Sbjct: 57  VQKALLLIL 65

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

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

 Score = 53.3 bits (129), Expect = 3e-09
 Identities = 23/50 (46%), Positives = 30/50 (60%)

Query: 80  TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEIS 129
           T R+L      G +IGK GS IK IR+ TGA I + +   G EERI+ I+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTIT 50

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

 Score = 51.8 bits (125), Expect = 9e-09
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R++V    VG ++GKGG  I+++R ET  +I+I              E IV + G    V
Sbjct: 3   RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSE------ERIVTITGTPEAV 56

Query: 255 KNAVAII 261
           + A  +I
Sbjct: 57  EKAKELI 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|215657 pfam00013, KH_1, KH domain

 Score = 51.4 bits (124), Expect = 9e-09
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 10/67 (14%)

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R+++    VG ++GKGG  I+++R ET  +IRI              ++ V + G    V
Sbjct: 3   RILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR----------DDTVTISGTPEQV 52

Query: 255 KNAVAII 261
           + A  +I
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|221895 pfam13014, KH_3, KH domain

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 19/41 (46%), Positives = 25/41 (60%)

Query: 89  KAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEIS 129
             G +IGK G  IK IR+ TGA I + +  PG  ERI+ I+
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

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 = 49.5 bits (119), Expect = 4e-08
 Identities = 23/50 (46%), Positives = 27/50 (54%), Gaps = 4/50 (8%)

Query: 80  TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEIS 129
           T RIL    K G +IGK GS IK IR+ TG  I     IP D +  + IS
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIR----IPDDRDDTVTIS 46

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

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

 Score = 46.3 bits (111), Expect = 8e-07
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 7/71 (9%)

Query: 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVD-GSDEQIITISSEEGPDDEL 407
             R+L P  + G +IG+    ++ ++ E G  ++V+  V  GS E+++TIS +  P    
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK--PS--- 55

Query: 408 FPAQEALLHIQ 418
              Q+ALL I 
Sbjct: 56  -AVQKALLLIL 65

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

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

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 22/51 (43%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 79  TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEIS 129
            T  +L    K G +IGK GS IK I + TG  I++    PG EER++EI+
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEIT 51

Length = 68

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 7/65 (10%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
           T R+L+P  ++G + G+ GS + E+R  TG  I+I    +    +SGT E      +++ 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDTVTISGTPE------QVEK 54

Query: 492 ARDAL 496
           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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
           T R+LVPSS +G + G+ GS + E+R  TGA I+I             + +V I G  +A
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEA 55

Query: 492 ARDALVEV 499
              A   +
Sbjct: 56  VEKAKELI 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 = 40.7 bits (96), Expect = 8e-05
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG 249
           + V   +++    VG ++GKGG  I+++  ET  +I I              E +V++ G
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS--------EERVVEITG 52

Query: 250 DINNVKNAVAIISSRL 265
              NV+ A  +I   L
Sbjct: 53  PPENVEKAAELILEIL 68

Length = 68

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 3/67 (4%)

Query: 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELF 408
             R+L P   VGR+IG+    ++ ++ E G  +K+ D   GS+E+I+TI+   G  + + 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTIT---GTPEAVE 57

Query: 409 PAQEALL 415
            A+E +L
Sbjct: 58  KAKELIL 64

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

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

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 6/48 (12%)

Query: 202 HVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG 249
            VG ++GKGG+ I+++R ET  +I+I   +          E IV + G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSG------ERIVTITG 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|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 36.7 bits (86), Expect = 0.002
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 8/54 (14%)

Query: 206 LLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVA 259
           ++GK G  I ++  ET  +IR  P   S         + + + G   NV+ A  
Sbjct: 14  IIGKKGSNIRKIMEETGVKIRF-PDPGS-------KSDTITITGPKENVEKAKE 59

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	650
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.97
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.97
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.97
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.94
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.86
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.54
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.51
PRK13763	180	putative RNA-processing protein; Provisional	99.5
PRK13763	180	putative RNA-processing protein; Provisional	99.48
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.33
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.29
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.24
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.18
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.07
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.05
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.04
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.99
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	98.98
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.98
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.95
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.94
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.9
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.86
PF13014	43	KH_3: KH domain	98.79
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.63
smart00322	69	KH K homology RNA-binding domain.	98.6
PF13014	43	KH_3: KH domain	98.59
smart00322	69	KH K homology RNA-binding domain.	98.53
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.45
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.0
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	97.96
KOG2113	394	consensus Predicted RNA binding protein, contains	97.95
PRK08406	140	transcription elongation factor NusA-like protein;	97.71
KOG2113	394	consensus Predicted RNA binding protein, contains	97.61
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.6
PRK08406	140	transcription elongation factor NusA-like protein;	97.5
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.38
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.36
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.34
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.17
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.09
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.01
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.98
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	96.8
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.5
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.46
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.43
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.42
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.3
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.24
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.23
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.18
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.16
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	95.85
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	95.8
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	95.68
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.63
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.53
TIGR01953	341	NusA transcription termination factor NusA. This m	95.5
TIGR01953	341	NusA transcription termination factor NusA. This m	95.4
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.23
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.21
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.2
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.12
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.98
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.96
PRK00468	75	hypothetical protein; Provisional	94.69
PRK00468	75	hypothetical protein; Provisional	94.58
PRK12327	362	nusA transcription elongation factor NusA; Provisi	94.54
PRK02821	77	hypothetical protein; Provisional	94.33
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.13
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.07
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.04
PRK12329	449	nusA transcription elongation factor NusA; Provisi	93.97
PRK02821	77	hypothetical protein; Provisional	93.96
COG5176	269	MSL5 Splicing factor (branch point binding protein	93.68
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	93.56
PRK00106	535	hypothetical protein; Provisional	93.54
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.52
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.51
PRK09202	470	nusA transcription elongation factor NusA; Validat	93.44
PRK01064	78	hypothetical protein; Provisional	93.34
PRK00106	535	hypothetical protein; Provisional	93.22
PRK01064	78	hypothetical protein; Provisional	93.18
PRK12704	520	phosphodiesterase; Provisional	93.12
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	93.07
PRK12704	520	phosphodiesterase; Provisional	93.04
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	92.96
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	92.36
COG5176	269	MSL5 Splicing factor (branch point binding protein	91.9
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	91.34
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	90.86
PRK12705	508	hypothetical protein; Provisional	89.95
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	87.85
COG1855	604	ATPase (PilT family) [General function prediction	85.06
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	84.74
PRK13764	602	ATPase; Provisional	84.49
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	84.42
PRK12705	508	hypothetical protein; Provisional	83.82
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	83.16
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	82.11
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	81.8
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	80.63
COG1855	604	ATPase (PilT family) [General function prediction	80.53

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=4.9e-44  Score=388.40  Aligned_cols=371  Identities=39%  Similarity=0.598  Sum_probs=285.0

Q ss_pred             CCCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHH
Q 006320           74 SLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLI  153 (650)
Q Consensus        74 ~~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i  153 (650)
                      .++...+||+||+.+.+|.||||+|.+|++||++|.++|+|.+..++|.|||++|+|...+      ...+.+++|+.++
T Consensus        38 ~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~------~~~~~~~~al~ka  111 (485)
T KOG2190|consen   38 GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE------LNLSPATDALFKA  111 (485)
T ss_pred             CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc------ccCCchHHHHHHH
Confidence            3444556999999999999999999999999999999999999999999999999996211      1577889999999


Q ss_pred             HHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCC
Q 006320          154 HDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHS  233 (650)
Q Consensus       154 ~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~  233 (650)
                      ++.|......+.   ....+.+.         -....+++++|+||..++|+||||+|+.||+|+++|||+|+|.+  ++
T Consensus       112 ~~~iv~~~~~d~---~~~~d~~~---------~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~--~~  177 (485)
T KOG2190|consen  112 FDMIVFKLEEDD---EAAEDNGE---------DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSS--DM  177 (485)
T ss_pred             HHHHhhcccccc---cccccCCc---------cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecC--CC
Confidence            999887533111   01111110         01123689999999999999999999999999999999999986  47


Q ss_pred             CCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320          234 LPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGS  313 (650)
Q Consensus       234 lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~  313 (650)
                      +|.   .++|.|+|.|.+++|.+|+..|..+|+++...          +|..+...-.|.|.........+..+..++  
T Consensus       178 lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~----------~~~~~~st~~y~P~~~~~~~~~~s~~~~~~--  242 (485)
T KOG2190|consen  178 LPN---STERAVTISGEPDAVKKALVQISSRLLENPPR----------SPPPLVSTIPYRPSASQGGPVLPSTAQTSP--  242 (485)
T ss_pred             CCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCc----------CCCCCCCcccCCCcccccCccccccccCCc--
Confidence            898   67888999999999999999999999997533          111111122233311100000000000000  


Q ss_pred             CCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCcc
Q 006320          314 NYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQ  393 (650)
Q Consensus       314 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er  393 (650)
                                  .+      .+...   ...+.+..+++.||.++++.|||++|..|+.|+.++++.|.+.++..+   +
T Consensus       243 ------------~~------~~~~~---~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~  298 (485)
T KOG2190|consen  243 ------------DA------HPFGG---IVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---R  298 (485)
T ss_pred             ------------cc------ccccc---cccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---c
Confidence                        00      00000   112367788999999999999999999999999999999999875443   9


Q ss_pred             EEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCC-CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCC
Q 006320          394 IITISSEEGPDDELFPAQEALLHIQTRIVDLGADK-DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREE  471 (650)
Q Consensus       394 ~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~-~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~  471 (650)
                      +|+++..+-+.+..+.|++|+++++.++.+...+. ...++.+|+||++++||||||+|+ |.+||+.|||.|+|..+++
T Consensus       299 ~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~  378 (485)
T KOG2190|consen  299 IVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEE  378 (485)
T ss_pred             eeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccc
Confidence            99999999899999999999999999988865544 667999999999999999999999 9999999999999998776


Q ss_pred             CCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          472 VPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       472 ~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ..   ..++++++|+|.......|..+|..++...
T Consensus       379 ~~---~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~  410 (485)
T KOG2190|consen  379 VS---GVREALVQITGMLREDLLAQYLIRARLSAP  410 (485)
T ss_pred             cC---CcceeEEEecchhHHHHhhhhhcccccccC
Confidence            42   357999999999988888887775544433

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=2e-41  Score=343.72  Aligned_cols=357  Identities=26%  Similarity=0.392  Sum_probs=271.1

Q ss_pred             CccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecC-CCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHH
Q 006320           76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHEL-IPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIH  154 (650)
Q Consensus        76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~  154 (650)
                      -...++|+|+|..++|.||||.|+|||.|...|.|+|+|... ..|..|++|+|.++.    |+       +-+|+++|+
T Consensus       196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tp----Eg-------~s~Ac~~IL  264 (584)
T KOG2193|consen  196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTP----EG-------TSKACKMIL  264 (584)
T ss_pred             ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCc----cc-------hHHHHHHHH
Confidence            456899999999999999999999999999999999999753 558899999999984    33       468888888


Q ss_pred             HHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCC
Q 006320          155 DRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSL  234 (650)
Q Consensus       155 ~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~l  234 (650)
                      +.|........+                      ...+.++++..+.+||+||||.|.+||+|+.+||++|.|++- ..|
T Consensus       265 eimqkEA~~~k~----------------------~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~l-qel  321 (584)
T KOG2193|consen  265 EIMQKEAVDDKV----------------------AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKL-QEL  321 (584)
T ss_pred             HHHHHhhhccch----------------------hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeeh-hhh
Confidence            888654322211                      256689999999999999999999999999999999999864 334


Q ss_pred             CCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCC------CCCCCCCCc--cCCCCCCCCCCCCCCCCCCCC
Q 006320          235 PRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHF------HGRLHSPDR--FFPDDDYVPHMNNTARRPSMD  306 (650)
Q Consensus       235 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~------~~~~~~p~~--~~~~~~~~p~~~~~~~~~~~~  306 (650)
                      ...  ..||+|+|.|+.|+|.+|..+|+.+|+++...|...+      .+.+..|.-  |++...+.|.           
T Consensus       322 s~y--npERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~P-----------  388 (584)
T KOG2193|consen  322 SLY--NPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPP-----------  388 (584)
T ss_pred             ccc--CccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCC-----------
Confidence            332  5699999999999999999999999999887664322      111111100  1100000000           


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC
Q 006320          307 GARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP  386 (650)
Q Consensus       307 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~  386 (650)
                        .|+...               ...+.++..-.  ..++....+|.||...+|+|||++|..||+|...+||+|+|..+
T Consensus       389 --h~~Ps~---------------v~~a~p~~~~h--q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp  449 (584)
T KOG2193|consen  389 --HFPPSP---------------VTFASPYPLFH--QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP  449 (584)
T ss_pred             --CCCCCc---------------cccCCCchhhh--cCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC
Confidence              000000               00001111100  11256678999999999999999999999999999999999876


Q ss_pred             C-CCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC---CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcC
Q 006320          387 V-DGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG---ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG  461 (650)
Q Consensus       387 ~-~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~---~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tg  461 (650)
                      . ++..+|+|+|+|   ++++.++|+.-   |+.+|.+..   +..+..+...+.||++.+|+||||||. ++|+++.|+
T Consensus       450 E~pdvseRMViItG---ppeaqfKAQgr---ifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~  523 (584)
T KOG2193|consen  450 EIPDVSERMVIITG---PPEAQFKAQGR---IFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTS  523 (584)
T ss_pred             CCCCcceeEEEecC---ChHHHHhhhhh---hhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhcccc
Confidence            3 677899999995   56777777765   456666543   234556788899999999999999999 999999999


Q ss_pred             ceEEEecCCCCCCCCCCCCeE-EEEEecHHHHHHHHHHHHHHHHhhhh
Q 006320          462 ANIQILSREEVPACVSGTDEL-VQIVGEIQAARDALVEVTTRLRSYLY  508 (650)
Q Consensus       462 a~I~i~~~~~~p~~~~~~~r~-v~I~G~~~~v~~A~~~I~~~l~~~~~  508 (650)
                      |.+.|+ +|+.|.   ++|.+ |.|+|...+.+.|...|.++|.++..
T Consensus       524 AeV~vP-rdqtpd---End~vivriiGhfyatq~aQrki~~iv~qvkq  567 (584)
T KOG2193|consen  524 AEVVVP-RDQTPD---ENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQ  567 (584)
T ss_pred             ceEEcc-ccCCCC---ccceeeeeeechhhcchHHHHHHHHHHHHHHH
Confidence            999774 777775   45554 99999999999999999999988743

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=100.00  E-value=1.5e-37  Score=331.35  Aligned_cols=335  Identities=20%  Similarity=0.315  Sum_probs=262.0

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI  157 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i  157 (650)
                      .++-+.-||...+|.||||+|+.|+.|..+++|+|+|.....+..+|-+.++|..           +.+++|..++-+.+
T Consensus        53 ~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~p-----------e~v~~aK~li~evv  121 (600)
T KOG1676|consen   53 VQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSP-----------ENVEVAKQLIGEVV  121 (600)
T ss_pred             ccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCc-----------ccHHHHHHhhhhhh
Confidence            3566778899999999999999999999999999998766556799999999974           35778887777666


Q ss_pred             hhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCc
Q 006320          158 LESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC  237 (650)
Q Consensus       158 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~  237 (650)
                      ........+    ..             ......++.+|+||.+.+|+||||+|++|+.|++++||++.+... ....  
T Consensus       122 ~r~~~~~~~----~~-------------~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd-~~~~--  181 (600)
T KOG1676|consen  122 SRGRPPGGF----PD-------------NQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQD-GSIA--  181 (600)
T ss_pred             hccCCCCCc----cc-------------cCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEec-CCcC--
Confidence            543211110    00             011467899999999999999999999999999999999999853 2222  


Q ss_pred             cCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320          238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRS  317 (650)
Q Consensus       238 ~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~  317 (650)
                       ...++.+.|+|++++|+.|+.+|.++|++....   .+                 ...                     
T Consensus       182 -~~~~KplritGdp~~ve~a~~lV~dil~e~~~~---~~-----------------g~~---------------------  219 (600)
T KOG1676|consen  182 -TGADKPLRITGDPDKVEQAKQLVADILREEDDE---VP-----------------GSG---------------------  219 (600)
T ss_pred             -CCCCCceeecCCHHHHHHHHHHHHHHHHhcccC---CC-----------------ccc---------------------
Confidence             236889999999999999999999999974210   00                 000                     


Q ss_pred             CCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCC-CCCCccEEE
Q 006320          318 NNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPV-DGSDEQIIT  396 (650)
Q Consensus       318 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~-~~~~er~i~  396 (650)
                             ..++...             ....+++|.||..+||.||||+|++||+|+.+||++|.|.... +.+.||++.
T Consensus       220 -------~~~g~~~-------------g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~  279 (600)
T KOG1676|consen  220 -------GHAGVRG-------------GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQ  279 (600)
T ss_pred             -------cccCcCc-------------cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceee
Confidence                   0000000             1344899999999999999999999999999999999997654 488999999


Q ss_pred             ecCCCCCCCcchHHHHHHHHHHHhhhccCC---CCCC-ce--EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecC
Q 006320          397 ISSEEGPDDELFPAQEALLHIQTRIVDLGA---DKDN-II--TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR  469 (650)
Q Consensus       397 I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~---~~~~-~~--~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~  469 (650)
                      |.|   +.+.+..|.+.|-+|+........   .... ..  .+.+.||.+.||.||||||+ ||.|..++||++++.+.
T Consensus       280 IiG---~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~  356 (600)
T KOG1676|consen  280 IIG---TVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ  356 (600)
T ss_pred             eec---CHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC
Confidence            996   478888888888888776654310   0011 12  78899999999999999999 99999999999998753


Q ss_pred             CCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhhhcc
Q 006320          470 EEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDF  511 (650)
Q Consensus       470 ~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~  511 (650)
                         +...+..++++.|+|+..+|+.|+.+|..++-+......
T Consensus       357 ---~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n~~  395 (600)
T KOG1676|consen  357 ---PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPNTP  395 (600)
T ss_pred             ---CCCCCccceEEEEecCcccchHHHHHHHHHhcccCCCCC
Confidence               333456799999999999999999999999988755443

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=100.00  E-value=1.5e-36  Score=323.63  Aligned_cols=294  Identities=19%  Similarity=0.280  Sum_probs=231.7

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      ...+.+..||..+|+++|||+|+.|..|+.++||+|+|.....      ....|.|.++|.+++|+.|+.+|.+++....
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s------~~~~r~~~~~G~pe~v~~aK~li~evv~r~~  125 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPS------GIGYRSVDLTGSPENVEVAKQLIGEVVSRGR  125 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCC------CcccccccccCCcccHHHHHHhhhhhhhccC
Confidence            5678899999999999999999999999999999999864321      1468999999999999999999999987652


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceE
Q 006320          270 HRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLV  349 (650)
Q Consensus       270 ~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  349 (650)
                      .            +..|.                                         ...+            ..+++
T Consensus       126 ~------------~~~~~-----------------------------------------~~q~------------~~~tt  140 (600)
T KOG1676|consen  126 P------------PGGFP-----------------------------------------DNQG------------SVETT  140 (600)
T ss_pred             C------------CCCcc-----------------------------------------ccCC------------cccee
Confidence            0            00000                                         0000            15789


Q ss_pred             EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCC--CCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCC-
Q 006320          350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPV--DGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGA-  426 (650)
Q Consensus       350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~--~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~-  426 (650)
                      .+|+||++++|.||||+|++||+|++.+||++.+....  ....++.+.|+|.   ++.++.|.+++.+|+....+..+ 
T Consensus       141 qeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGd---p~~ve~a~~lV~dil~e~~~~~~g  217 (600)
T KOG1676|consen  141 QEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD---PDKVEQAKQLVADILREEDDEVPG  217 (600)
T ss_pred             eeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCC---HHHHHHHHHHHHHHHHhcccCCCc
Confidence            99999999999999999999999999999998876532  2336789999965   67788888888877664222111 


Q ss_pred             -------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHH
Q 006320          427 -------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVE  498 (650)
Q Consensus       427 -------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~  498 (650)
                             ......+.+|.||++.||.||||+|+ ||+|+.+|||+|+|.+++ .|   .+.+|.++|.|++++|+.|.++
T Consensus       218 ~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd-~p---~speR~~~IiG~~d~ie~Aa~l  293 (600)
T KOG1676|consen  218 SGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD-DP---SSPERPAQIIGTVDQIEHAAEL  293 (600)
T ss_pred             cccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC-CC---CCccceeeeecCHHHHHHHHHH
Confidence                   11123488999999999999999999 999999999999998654 44   3679999999999999999999


Q ss_pred             HHHHHHhhhhhcccccCCCCCCCCCCCCcccccCCCCCCCCCCCccCCcCCCCCCCCCCCCCCCCCCCCcccCCCccccc
Q 006320          499 VTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETV  578 (650)
Q Consensus       499 I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~~~~  578 (650)
                      |.++|.+.....             ++                                      .|.            
T Consensus       294 I~eii~~~~~~~-------------~~--------------------------------------~~~------------  310 (600)
T KOG1676|consen  294 INEIIAEAEAGA-------------GG--------------------------------------GMG------------  310 (600)
T ss_pred             HHHHHHHHhccC-------------CC--------------------------------------CcC------------
Confidence            999999883211             00                                      010            


Q ss_pred             cCCcccccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEEEe
Q 006320          579 KQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLF  642 (650)
Q Consensus       579 ~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~~~  642 (650)
                       +|.+              +.   ...++|.||++.||.||||||++|++|.++|||+|.+--+
T Consensus       311 -~G~P--------------~~---~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~  356 (600)
T KOG1676|consen  311 -GGAP--------------GL---VAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ  356 (600)
T ss_pred             -CCCc--------------cc---eeeEEEeccccccccccCCCccchhhhcccCCccccccCC
Confidence             1111              00   1278999999999999999999999999999999987544

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=99.97  E-value=2.4e-31  Score=270.62  Aligned_cols=284  Identities=18%  Similarity=0.336  Sum_probs=231.5

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      ....+|++||..+||.||||.|++|+.|...|-|+|+|..++.     ++..|+.++|-|++|...+|+++|++++....
T Consensus       197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken-----~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA  271 (584)
T KOG2193|consen  197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN-----AGAAEKIITVHSTPEGTSKACKMILEIMQKEA  271 (584)
T ss_pred             cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc-----CCcccCceEEecCccchHHHHHHHHHHHHHhh
Confidence            4467899999999999999999999999999999999987643     24779999999999999999999999998764


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceE
Q 006320          270 HRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLV  349 (650)
Q Consensus       270 ~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  349 (650)
                      ..+..                                                                      .+++.
T Consensus       272 ~~~k~----------------------------------------------------------------------~~e~p  281 (584)
T KOG2193|consen  272 VDDKV----------------------------------------------------------------------AEEIP  281 (584)
T ss_pred             hccch----------------------------------------------------------------------hhhcc
Confidence            22110                                                                      15778


Q ss_pred             EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC---CCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC-
Q 006320          350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP---VDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG-  425 (650)
Q Consensus       350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~---~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~-  425 (650)
                      ++++--+.++|++|||.|.+||+|.++||++|.|.+-   .--+.||+|++.|+   .+++..|...|.+-+..+.+.. 
T Consensus       282 Lk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGs---iEac~~AE~eImkKlre~yEnDl  358 (584)
T KOG2193|consen  282 LKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS---IEACVQAEAEIMKKLRECYENDL  358 (584)
T ss_pred             hhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEeccc---HHHHHHHHHHHHHHHHHHHhhhH
Confidence            8999999999999999999999999999999999754   23467999999974   5667777666654333222110 


Q ss_pred             ---------------------C-------------------------CCCCceEEEEeecCCcceeeecCCCc-hhhhhh
Q 006320          426 ---------------------A-------------------------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRR  458 (650)
Q Consensus       426 ---------------------~-------------------------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~  458 (650)
                                           +                         ...+.-..+|+||...+|.||||.|. ||.|.+
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                                 0                         01134567999999999999999999 999999


Q ss_pred             hcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhhhcccccCCCCCCCCCCCCcccccCCCCCCC
Q 006320          459 STGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDI  538 (650)
Q Consensus       459 ~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  538 (650)
                      .+||.|+|.+.| .|   +..+|+|+|+|.+++..+|.-.|..+|+|.-+                  +      .    
T Consensus       439 fagASiKIappE-~p---dvseRMViItGppeaqfKAQgrifgKikEenf------------------~------~----  486 (584)
T KOG2193|consen  439 FAGASIKIAPPE-IP---DVSERMVIITGPPEAQFKAQGRIFGKIKEENF------------------F------L----  486 (584)
T ss_pred             hccceeeecCCC-CC---CcceeEEEecCChHHHHhhhhhhhhhhhhhcc------------------C------C----
Confidence            999999998765 44   36799999999999999999999999998711                  0      0    


Q ss_pred             CCCCccCCcCCCCCCCCCCCCCCCCCCCCcccCCCccccccCCcccccCCCccccCCCCccccccceEEEEecCCccccc
Q 006320          539 TPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKL  618 (650)
Q Consensus       539 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~~~~~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~v  618 (650)
                                                 |+                       +         .-+...+|-||...+|.|
T Consensus       487 ---------------------------Pk-----------------------e---------evklethirVPs~~aGRv  507 (584)
T KOG2193|consen  487 ---------------------------PK-----------------------E---------EVKLETHIRVPSSAAGRV  507 (584)
T ss_pred             ---------------------------ch-----------------------h---------hheeeeeeeccchhhhhh
Confidence                                       00                       0         013577899999999999


Q ss_pred             ccCCCcchhhHHHhcCCeEEEEEe
Q 006320          619 ITKSKTLLTRFSEVSLLLHLINLF  642 (650)
Q Consensus       619 IGk~G~~I~~Ir~~SGA~i~i~~~  642 (650)
                      |||||.+++.++.+++|.|.|.-+
T Consensus       508 IGKGGktVnELQnlt~AeV~vPrd  531 (584)
T KOG2193|consen  508 IGKGGKTVNELQNLTSAEVVVPRD  531 (584)
T ss_pred             hccccccHHHHhccccceEEcccc
Confidence            999999999999999999998755

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=99.97  E-value=2.9e-29  Score=241.93  Aligned_cols=292  Identities=23%  Similarity=0.368  Sum_probs=200.4

Q ss_pred             CCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHH
Q 006320           75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIH  154 (650)
Q Consensus        75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~  154 (650)
                      ....+.+|||+.++.+|+||||+|++||+|+.+++|.|.|++.  ..+|||++|+...           ..+-+-++.|+
T Consensus        44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~-----------~ti~~ilk~ii  110 (390)
T KOG2192|consen   44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADI-----------ETIGEILKKII  110 (390)
T ss_pred             hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccH-----------HHHHHHHHHHh
Confidence            3446999999999999999999999999999999999999987  6799999999852           23444444455


Q ss_pred             HHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCC
Q 006320          155 DRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSL  234 (650)
Q Consensus       155 ~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~l  234 (650)
                      -.+++..                         .....+.++|||+.+++|.|||++|+.||+|++++.|+.+|..     
T Consensus       111 p~lee~f-------------------------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift-----  160 (390)
T KOG2192|consen  111 PTLEEGF-------------------------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT-----  160 (390)
T ss_pred             hhhhhCC-------------------------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh-----
Confidence            4443321                         1135688999999999999999999999999999999999873     


Q ss_pred             CCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCC-CCCCCCCCCCc----cC---CCC----CCCCCCC-----
Q 006320          235 PRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRS-HFHGRLHSPDR----FF---PDD----DYVPHMN-----  297 (650)
Q Consensus       235 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~-~~~~~~~~p~~----~~---~~~----~~~p~~~-----  297 (650)
                      .+|..+++|+|.|.|.+..|..+++.|++.|.+.+-+... +|.+...-+..    |.   ...    ...|...     
T Consensus       161 ~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp  240 (390)
T KOG2192|consen  161 ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPP  240 (390)
T ss_pred             ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCC
Confidence            5788899999999999999999999999999998876653 33322211110    10   000    0000000     


Q ss_pred             --CCCCCCCCCCCC------CCCCCCCC--------CCCCCC--CCCC----------CccCCCCCCCCCCCCCCCCceE
Q 006320          298 --NTARRPSMDGAR------FSGSNYRS--------NNYGPR--PSGY----------SIEAGAAPMSDSVQPFYGEDLV  349 (650)
Q Consensus       298 --~~~~~~~~~~~~------~~~~~~~~--------~~~~~~--~~g~----------~~~~~~~~~~~~~~~~~~~~~~  349 (650)
                        .+...|...+..      +...++..        ..+.+.  ..+|          +...+..+..+    +-...++
T Consensus       241 ~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGd----lGGPitT  316 (390)
T KOG2192|consen  241 PPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGD----LGGPITT  316 (390)
T ss_pred             CCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCC----CCCceee
Confidence              000011110000      00000000        000000  0111          11111111111    1134578


Q ss_pred             EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHH
Q 006320          350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLH  416 (650)
Q Consensus       350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~  416 (650)
                      ..+.||.++-|.||||+|+.|++|+.++||.|++.++..++++|+++|+|+   .+++..||-.+..
T Consensus       317 aQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT---qdQIqnAQYLlQn  380 (390)
T KOG2192|consen  317 AQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT---QDQIQNAQYLLQN  380 (390)
T ss_pred             eeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc---HHHHhhHHHHHHH
Confidence            899999999999999999999999999999999999999999999999976   4666666655543

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=99.97  E-value=1.3e-29  Score=244.42  Aligned_cols=279  Identities=22%  Similarity=0.228  Sum_probs=186.8

Q ss_pred             CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC
Q 006320          346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG  425 (650)
Q Consensus       346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~  425 (650)
                      ..+.+++++..+.+|+||||+|++||.|+.+++|+|.|++  ...++|+++|+..+      ....+.|.+|..++++. 
T Consensus        46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd--s~~peri~tisad~------~ti~~ilk~iip~lee~-  116 (390)
T KOG2192|consen   46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILTISADI------ETIGEILKKIIPTLEEG-  116 (390)
T ss_pred             cceeEEEEEecccccceeccccccHHHHhhhccceeeccC--CCCCceeEEEeccH------HHHHHHHHHHhhhhhhC-
Confidence            5689999999999999999999999999999999999977  77889999999653      23444455566666553 


Q ss_pred             CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHH
Q 006320          426 ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR  504 (650)
Q Consensus       426 ~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~  504 (650)
                      +.....+++||||+++++|.|||++|+ |||++++..|+++|+.    -+|+.++||+|.|.|.+..|..+++.|+.+|.
T Consensus       117 f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift----~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~  192 (390)
T KOG2192|consen  117 FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT----ECCPHSTDRVVLIGGKPKRVVECIKIILDLIS  192 (390)
T ss_pred             CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh----ccCCCCcceEEEecCCcchHHHHHHHHHHHhh
Confidence            445668999999999999999999999 9999999999999983    36778999999999999999999999999999


Q ss_pred             hhhhhcccccCCCCC--CCCCCCCcccccCCCCCCCCC--CCccCCcCCCC-----CCCCCCCC----------C-CCCC
Q 006320          505 SYLYRDFFQKETPPS--STGPTGSALVVEAASPIDITP--AREVQTVTDPP-----AATHQSVQ----------I-PATS  564 (650)
Q Consensus       505 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~p-----~~~~~~~~----------~-~~~~  564 (650)
                      +..++.....-.|..  .++.+++|.-.-.-.|.++.|  ++.+ .+..+|     |..++...          . ....
T Consensus       193 e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrgg-qgpp~~~~sdlmay~r~GrpG~rydg~vdFs~det  271 (390)
T KOG2192|consen  193 ESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGG-QGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADET  271 (390)
T ss_pred             cCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCC-CCCCCCCccccceeccCCCCCcccccccccccccc
Confidence            998887422111111  223333332222222332222  1110 000111     11111110          0 0112


Q ss_pred             CCCcccCCCcc----ccccCCccc---ccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhHHHhcCCeE
Q 006320          565 QPSKEAAGSVS----ETVKQNESE---RREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLH  637 (650)
Q Consensus       565 ~~~~~~g~~~~----~~~~~g~~~---~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i  637 (650)
                      |++.-.+++.+    ..-+|+...   ++.+.-..-..+.+|+   +|.+|+||.+.-|.||||||++|++||+.|||.|
T Consensus       272 w~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPi---tTaQvtip~dlggsiigkggqri~~ir~esGA~I  348 (390)
T KOG2192|consen  272 WPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPI---TTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASI  348 (390)
T ss_pred             CCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCce---eeeeEecccccCcceecccchhhhhhhhccCceE
Confidence            33311111000    001111110   0000001111223455   8999999999999999999999999999999999


Q ss_pred             EEEE
Q 006320          638 LINL  641 (650)
Q Consensus       638 ~i~~  641 (650)
                      +|.-
T Consensus       349 kide  352 (390)
T KOG2192|consen  349 KIDE  352 (390)
T ss_pred             EecC
Confidence            9974

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.95  E-value=2.8e-27  Score=257.69  Aligned_cols=158  Identities=37%  Similarity=0.585  Sum_probs=136.2

Q ss_pred             ceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC-
Q 006320          347 DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG-  425 (650)
Q Consensus       347 ~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~-  425 (650)
                      ..++||+|+.+.+|.||||+|.+|++|+.++.++|+|.+...++.+|+|+|+|..... ..+.+++||+++++.+.... 
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~~  120 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKLE  120 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhccc
Confidence            3458999999999999999999999999999999999998999999999999953222 66778888888887766421 


Q ss_pred             ----------CC-CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHH
Q 006320          426 ----------AD-KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAAR  493 (650)
Q Consensus       426 ----------~~-~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~  493 (650)
                                .+ +...+++||+||.+++|+||||+|+ ||+|+++|||+|+|.++ .+|.|   ++|.|+|.|++++|.
T Consensus       121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~s---ter~V~IsG~~~av~  196 (485)
T KOG2190|consen  121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPNS---TERAVTISGEPDAVK  196 (485)
T ss_pred             ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCcc---cceeEEEcCchHHHH
Confidence                      01 1224899999999999999999999 99999999999999865 78985   788899999999999


Q ss_pred             HHHHHHHHHHHhhhhh
Q 006320          494 DALVEVTTRLRSYLYR  509 (650)
Q Consensus       494 ~A~~~I~~~l~~~~~~  509 (650)
                      +|+.+|..+|.++.-+
T Consensus       197 ~al~~Is~~L~~~~~~  212 (485)
T KOG2190|consen  197 KALVQISSRLLENPPR  212 (485)
T ss_pred             HHHHHHHHHHHhcCCc
Confidence            9999999999997533

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.94  E-value=1.6e-25  Score=222.50  Aligned_cols=244  Identities=22%  Similarity=0.309  Sum_probs=173.7

Q ss_pred             CCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEe---cCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHH
Q 006320           75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH---ELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALF  151 (650)
Q Consensus        75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~---~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~  151 (650)
                      .+..+.++||||+..+|.||||+|++|.+|+++|||+|+++   |.+|++.||||.|.|+.           +++...+.
T Consensus        35 e~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~-----------eai~av~e  103 (402)
T KOG2191|consen   35 EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTV-----------EALNAVHE  103 (402)
T ss_pred             CCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccH-----------HHHHHHHH
Confidence            44459999999999999999999999999999999999996   46999999999999973           34555566


Q ss_pred             HHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCC
Q 006320          152 LIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRD  231 (650)
Q Consensus       152 ~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  231 (650)
                      .|.++|.|.........+.   +.|         +..++...++|+||+..+|.||||+|++||.|++++||+|+|+|.+
T Consensus       104 fI~dKire~p~~~~k~v~~---~~p---------qt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk  171 (402)
T KOG2191|consen  104 FIADKIREKPQAVAKPVDI---LQP---------QTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK  171 (402)
T ss_pred             HHHHHHHHhHHhhcCCccc---cCC---------CCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC
Confidence            6777776654333211111   111         2234556799999999999999999999999999999999999743


Q ss_pred             CCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320          232 HSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFS  311 (650)
Q Consensus       232 ~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~  311 (650)
                         |.-....||+|++.|++++..+|+.+|+++|.++++...-.     +  .+|.    ++.+                
T Consensus       172 ---pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scl-----n--~sya----~vsG----------------  221 (402)
T KOG2191|consen  172 ---PTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCL-----N--ISYA----NVSG----------------  221 (402)
T ss_pred             ---CCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCccccee-----c--cchh----cccC----------------
Confidence               44445789999999999999999999999999987422110     0  0000    0000                


Q ss_pred             CCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeC
Q 006320          312 GSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD  385 (650)
Q Consensus       312 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~  385 (650)
                          ...|+.+.-.+|....+.          .+......+-++....|..-|.+|.++-.|-..+|+.+.+++
T Consensus       222 ----pvaNsnPtGspya~~~~~----------~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq  281 (402)
T KOG2191|consen  222 ----PVANSNPTGSPYAYQAHV----------LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQ  281 (402)
T ss_pred             ----cccccCCCCCCCCCCCcc----------ccccchhhccccccccccccccccccceeeecccccceeecc
Confidence                011111111111111111          012233446678888888889999999999889998777765

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.86  E-value=6.2e-21  Score=190.00  Aligned_cols=229  Identities=19%  Similarity=0.257  Sum_probs=163.1

Q ss_pred             CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC---CCCCCccEEEecCCCCCCCcchHHHHHHH-HHHHhh
Q 006320          346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP---VDGSDEQIITISSEEGPDDELFPAQEALL-HIQTRI  421 (650)
Q Consensus       346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~---~~~~~er~i~I~G~~g~~~~~~~a~~ai~-~i~~~i  421 (650)
                      ..+.++|+||...+|.||||+|++|.+||+++||+|++++.   -+++.||++.|+|+-   +    +..+++ .|.++|
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~---e----ai~av~efI~dKi  109 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTV---E----ALNAVHEFIADKI  109 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccH---H----HHHHHHHHHHHHH
Confidence            44899999999999999999999999999999999999876   378999999999862   2    223332 244555


Q ss_pred             hccCC--C----------CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec
Q 006320          422 VDLGA--D----------KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE  488 (650)
Q Consensus       422 ~~~~~--~----------~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~  488 (650)
                      .+...  .          .+..-.++|+||.+.+|.||||||. ||.|++++||.|+|.|.+  |..-.-.+|+|++.|+
T Consensus       110 re~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqervvt~sge  187 (402)
T KOG2191|consen  110 REKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERVVTVSGE  187 (402)
T ss_pred             HHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEEEEecCC
Confidence            54311  0          1112348999999999999999999 999999999999999633  3333456899999999


Q ss_pred             HHHHHHHHHHHHHHHHhhhhhcccccCCCCCCCCCCCCcccccCCCCCCCCCCCccCCcCCCCCCCCCCCCCCCCCCCCc
Q 006320          489 IQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSK  568 (650)
Q Consensus       489 ~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~  568 (650)
                      +++..+|+.+|+++|.+...-..   .++  .++..    .       .+ |+                     ..+.+.
T Consensus       188 ~e~~~~A~~~IL~Ki~eDpqs~s---cln--~sya~----v-------sG-pv---------------------aNsnPt  229 (402)
T KOG2191|consen  188 PEQNMKAVSLILQKIQEDPQSGS---CLN--ISYAN----V-------SG-PV---------------------ANSNPT  229 (402)
T ss_pred             HHHHHHHHHHHHHHhhcCCcccc---eec--cchhc----c-------cC-cc---------------------cccCCC
Confidence            99999999999999988732210   111  11110    0       00 00                     011111


Q ss_pred             ccCCCccccccCCcccccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEEEe
Q 006320          569 EAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLF  642 (650)
Q Consensus       569 ~~g~~~~~~~~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~~~  642 (650)
                      ++++.    + ++                ..+..+++...-+|.-..|..-|.+|.++..|..++|+.+.|.-+
T Consensus       230 Gspya----~-~~----------------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~  282 (402)
T KOG2191|consen  230 GSPYA----Y-QA----------------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA  282 (402)
T ss_pred             CCCCC----C-CC----------------ccccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence            11100    0 00                012234567788899999999999999999999999998888654

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.54  E-value=1.6e-14  Score=138.70  Aligned_cols=140  Identities=17%  Similarity=0.219  Sum_probs=102.7

Q ss_pred             EEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHh--hhccCCCCC
Q 006320          352 MLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTR--IVDLGADKD  429 (650)
Q Consensus       352 i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~--i~~~~~~~~  429 (650)
                      +.||.++++.|||++|++|+.|+++|||+|.+.+     ++..|.|....+.++.+.+|++.|..+..-  ..+...-..
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~g   76 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD   76 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcC
Confidence            5789999999999999999999999999999975     335678831113456777777777654331  111000011


Q ss_pred             CceEEE-EeecC---------CcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHH
Q 006320          430 NIITTR-LLVPS---------SEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVE  498 (650)
Q Consensus       430 ~~~~~~-l~Vp~---------~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~  498 (650)
                      ..++.+ +.|+.         ..+|+|||++|+ ++.|++.|||+|.|.            +..|.|.|++++++.|..+
T Consensus        77 d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v~i~G~~~~~~~A~~~  144 (172)
T TIGR03665        77 DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTVGIIGDPEQVQIAREA  144 (172)
T ss_pred             CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEEEEECCHHHHHHHHHH
Confidence            122222 23333         368999999999 999999999999884            2569999999999999999


Q ss_pred             HHHHHHhhhh
Q 006320          499 VTTRLRSYLY  508 (650)
Q Consensus       499 I~~~l~~~~~  508 (650)
                      |.+++.....
T Consensus       145 i~~li~~~~~  154 (172)
T TIGR03665       145 IEMLIEGAPH  154 (172)
T ss_pred             HHHHHcCCCC
Confidence            9999866543

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.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.51  E-value=9.1e-14  Score=133.40  Aligned_cols=143  Identities=17%  Similarity=0.215  Sum_probs=102.4

Q ss_pred             EEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCC
Q 006320           83 ILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDG  162 (650)
Q Consensus        83 ilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~  162 (650)
                      |.||.+.+|.|||++|++|+.|+++|||+|++.+     ++..|.|. ....       ...++++|..+|.........
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~-~~t~-------d~~~i~kA~~~I~~i~~gf~~   68 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIE-EEDE-------DPLAVMKAREVVKAIGRGFSP   68 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEe-cCCC-------CHHHHHHHHHHHHHHHcCCCH
Confidence            4579999999999999999999999999999996     23568883 1101       134677887777765442111


Q ss_pred             CCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEcc---------ceeeeeecCCchHHHHHHhhcCceEEEecCCCC
Q 006320          163 GGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSR---------MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHS  233 (650)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~  233 (650)
                      +..+. ...+                 .....-+.|+.         ..+|+|||++|++++.|++.|||+|.|.     
T Consensus        69 e~A~~-l~gd-----------------~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----  125 (172)
T TIGR03665        69 EKALK-LLDD-----------------DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----  125 (172)
T ss_pred             HHHHH-hcCC-----------------cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----
Confidence            10000 0000                 11111223333         3689999999999999999999999995     


Q ss_pred             CCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          234 LPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       234 lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                              +..|.|.|++++++.|+.+|.+++...+
T Consensus       126 --------~~~v~i~G~~~~~~~A~~~i~~li~~~~  153 (172)
T TIGR03665       126 --------GKTVGIIGDPEQVQIAREAIEMLIEGAP  153 (172)
T ss_pred             --------CCEEEEECCHHHHHHHHHHHHHHHcCCC
Confidence                    2579999999999999999999996653

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=99.50  E-value=6.6e-14  Score=135.25  Aligned_cols=144  Identities=15%  Similarity=0.201  Sum_probs=104.3

Q ss_pred             eEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEec-CCCCCCCcchHHHHHHHHHHH--hhhcc
Q 006320          348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITIS-SEEGPDDELFPAQEALLHIQT--RIVDL  424 (650)
Q Consensus       348 ~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~-G~~g~~~~~~~a~~ai~~i~~--~i~~~  424 (650)
                      ....+.||.++++.|||++|++|+.|+++|||+|.+.+     ++..|.|. +....++.+.+|++.|..+..  ...+.
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A   77 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKA   77 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHH
Confidence            45779999999999999999999999999999999976     23667775 111345667777777765543  11110


Q ss_pred             CCCCCCceEEEE-ee----c-----CCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHH
Q 006320          425 GADKDNIITTRL-LV----P-----SSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAAR  493 (650)
Q Consensus       425 ~~~~~~~~~~~l-~V----p-----~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~  493 (650)
                      .......+..++ .+    +     ...+|+|||++|+ ++.|++.|||+|.|.            ++.|.|.|++++++
T Consensus        78 ~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~------------~~~v~i~G~~~~~~  145 (180)
T PRK13763         78 LRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY------------GKTVAIIGDPEQVE  145 (180)
T ss_pred             HHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc------------CCEEEEEeCHHHHH
Confidence            000011122222 11    1     1368999999999 999999999999884            23499999999999


Q ss_pred             HHHHHHHHHHHhhhh
Q 006320          494 DALVEVTTRLRSYLY  508 (650)
Q Consensus       494 ~A~~~I~~~l~~~~~  508 (650)
                      .|...|..+++....
T Consensus       146 ~A~~~I~~li~g~~~  160 (180)
T PRK13763        146 IAREAIEMLIEGAPH  160 (180)
T ss_pred             HHHHHHHHHHcCCCc
Confidence            999999999876643

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.48  E-value=3.2e-13  Score=130.55  Aligned_cols=146  Identities=18%  Similarity=0.183  Sum_probs=104.9

Q ss_pred             EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhh
Q 006320           79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRIL  158 (650)
Q Consensus        79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~  158 (650)
                      +...+.||.+.++.|||++|++|+.|+++|||+|++.+.     +..|.|+-....       ....+++|..+|.....
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~-------d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGE-------DPLAVLKARDIVKAIGR   70 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCC-------CHHHHHHHHHHHHHHhc
Confidence            567889999999999999999999999999999999972     356777611100       13467788877776654


Q ss_pred             hcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEE-EEc---------cceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320          159 ESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRM-VVS---------RMHVGCLLGKGGKIIEQMRMETKTQIRIL  228 (650)
Q Consensus       159 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~Vp---------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  228 (650)
                      ..+.+..+. ...                  ..+..++ .+.         ...+|+|||++|++++.|++.|||+|.|.
T Consensus        71 gf~~e~A~~-l~g------------------d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~  131 (180)
T PRK13763         71 GFSPEKALR-LLD------------------DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY  131 (180)
T ss_pred             CCCHHHHHH-HhC------------------CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc
Confidence            211110000 000                  1111111 111         13689999999999999999999999995


Q ss_pred             cCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          229 PRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       229 ~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      .             ..|.|.|++++++.|...|..+++..
T Consensus       132 ~-------------~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        132 G-------------KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             C-------------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence            2             34899999999999999999999665

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.33  E-value=1.7e-11  Score=141.77  Aligned_cols=330  Identities=15%  Similarity=0.165  Sum_probs=201.5

Q ss_pred             CCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCC----------------C---
Q 006320           75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRR----------------D---  135 (650)
Q Consensus        75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~----------------~---  135 (650)
                      ....+..++.+....+..+||++|.+++.++.++.+.|.|++.....+  ...+.+...+                .   
T Consensus       197 ~~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~--~~~i~~~~~~~~~~~~~i~~~~~~le~~~~  274 (753)
T KOG2208|consen  197 NERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSP--SNKIDGRLNSSSSINVEIQEALTRLESEFD  274 (753)
T ss_pred             cceeEEEEeeccccchhhhccccccccccccccceeEEEcccccccch--hhhhccccccceehhhhhHHHHHHhcChhh
Confidence            444578889999999999999999999999999999999986422111  1111111100                0   


Q ss_pred             ------------CCCC-CCCccHHHHHHHHHHHHhhhcCCCC---CCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEc
Q 006320          136 ------------PEGR-MPSFSPAQEALFLIHDRILESDGGG---GFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVS  199 (650)
Q Consensus       136 ------------~~~~-~~~~~~a~~A~~~i~~~i~e~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp  199 (650)
                                  ..+. ...+..+....-.+.-.........   .....+.......+.....-..-....+.+.+.+.
T Consensus       275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~  354 (753)
T KOG2208|consen  275 YDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIF  354 (753)
T ss_pred             hhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeec
Confidence                        0000 0012222222222111111100000   00000000000000000000000134467888899


Q ss_pred             cceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCC
Q 006320          200 RMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGR  279 (650)
Q Consensus       200 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~  279 (650)
                      ...+..++||+|.+|++|++++.|.|.+...        .+.+..+.++|...++.+|...+...+.+...         
T Consensus       355 ~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n---------  417 (753)
T KOG2208|consen  355 PEELKFVIGKKGANIEKIREESQVKIDLPKQ--------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN---------  417 (753)
T ss_pred             HHhhhhhcCCCCccHHHHHHhhhhceecccc--------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc---------
Confidence            9999999999999999999999999999642        15678899999999999999999999988631         


Q ss_pred             CCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccc
Q 006320          280 LHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKV  359 (650)
Q Consensus       280 ~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~v  359 (650)
                                                                                        ......+.+|...+
T Consensus       418 ------------------------------------------------------------------~~~~~~~~iP~k~~  431 (753)
T KOG2208|consen  418 ------------------------------------------------------------------SIVKEEVQIPTKSH  431 (753)
T ss_pred             ------------------------------------------------------------------ccccceeecCccch
Confidence                                                                              02234588999999


Q ss_pred             cceecCCchhHHHHHHHhC-CeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEEee
Q 006320          360 GRVIGESEGIVELLQNEIG-VDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLV  438 (650)
Q Consensus       360 g~IIGk~G~~Ik~l~~~tg-a~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l~V  438 (650)
                      ..|||.+|..|..|..+++ +.|.+..  ..+.....++.+.   ...+..++..+..+.....+  ......++...+.
T Consensus       432 ~~iig~~g~~i~~I~~k~~~v~i~f~~--~~~~~~~~~~~~~---~~dv~~~~~~~~~~~~~a~~--~~~~~~~~~d~~~  504 (753)
T KOG2208|consen  432 KRIIGTKGALINYIMGKHGGVHIKFQN--NNNSSDMVTIRGI---SKDVEKSVSLLKALKADAKN--LKFRDVVTKDKLL  504 (753)
T ss_pred             hhhhccccccHHHHHhhcCcEEEecCC--CCcccccceEecc---ccccchhHHHHHhhhhhhhc--chhhhhhhccccc
Confidence            9999999999999999999 6666654  3444455556643   22233322222222111111  0122346667788


Q ss_pred             cCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          439 PSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       439 p~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      |..+.+..+|+.|. +....+.....+    .+      ..+...++|.|..+.|.+|...+..++...
T Consensus       505 ~~~~~~~~~g~~~~i~d~~~~~~i~~~----~~------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~  563 (753)
T KOG2208|consen  505 PVKYIGKEIGKNGTIRDSLGDKSIFPP----NE------DEDHEKITIEGKLELVLEAPAELKALIEAL  563 (753)
T ss_pred             hHHhhcccccCceeeeccCCceeeccc----cc------ccccceeeecccccchhhhHHHHHhcchhh
Confidence            88888888888777 455555444333    32      134667999999999999988887766554

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.29  E-value=1.7e-11  Score=141.81  Aligned_cols=391  Identities=16%  Similarity=0.165  Sum_probs=238.7

Q ss_pred             EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhh
Q 006320           79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRIL  158 (650)
Q Consensus        79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~  158 (650)
                      ....+-+...+...|+||+|.+|.+|++++.|.|.+++.  +..+..+.+++..           ...++|...+...+.
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~-----------~~~~ka~~~v~~~~~  413 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVS-----------ANDEKAVEDVEKIIA  413 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccc-----------cchhHHHHHHHHHHH
Confidence            556666788899999999999999999999999999984  5677778888853           345666666666665


Q ss_pred             hcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC-ceEEEecCCCCCCCc
Q 006320          159 ESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK-TQIRILPRDHSLPRC  237 (650)
Q Consensus       159 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~lp~~  237 (650)
                      +..                           .......+.+|...+.+|||.+|+.|+.|..+++ ..|..... .     
T Consensus       414 ei~---------------------------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-~-----  460 (753)
T KOG2208|consen  414 EIL---------------------------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-N-----  460 (753)
T ss_pred             hhh---------------------------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-C-----
Confidence            431                           1134667899999999999999999999999999 55555321 1     


Q ss_pred             cCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320          238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRS  317 (650)
Q Consensus       238 ~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~  317 (650)
                        .....+++.|....|..++.++..+.........                                            
T Consensus       461 --~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~~~~--------------------------------------------  494 (753)
T KOG2208|consen  461 --NSSDMVTIRGISKDVEKSVSLLKALKADAKNLKF--------------------------------------------  494 (753)
T ss_pred             --cccccceEeccccccchhHHHHHhhhhhhhcchh--------------------------------------------
Confidence              3345678888888888877777766654321000                                            


Q ss_pred             CCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEe
Q 006320          318 NNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITI  397 (650)
Q Consensus       318 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I  397 (650)
                                                 -...+...+.|..+.+..+|+.|..+..+.++..+.+..     ..++..++|
T Consensus       495 ---------------------------~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~-----~~~~~~i~i  542 (753)
T KOG2208|consen  495 ---------------------------RDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNE-----DEDHEKITI  542 (753)
T ss_pred             ---------------------------hhhhhccccchHHhhcccccCceeeeccCCceeeccccc-----ccccceeee
Confidence                                       022344566788888888888887777666666554433     235678888


Q ss_pred             cCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEEeecCCccee-eecCCCch-hhhhhhcCceEEEecCCCCCCC
Q 006320          398 SSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGC-LEGRDGSL-SEMRRSTGANIQILSREEVPAC  475 (650)
Q Consensus       398 ~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l~Vp~~~~g~-IIGkgG~I-k~I~~~Tga~I~i~~~~~~p~~  475 (650)
                      .|.   .+.+..+..+|..+...+.+       ...+.+.+|..++-. +++++... +..+...|+.+.++...     
T Consensus       543 ~gk---~~~v~~a~~~L~~~~~~~~~-------~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~-----  607 (753)
T KOG2208|consen  543 EGK---LELVLEAPAELKALIEALIK-------ATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSP-----  607 (753)
T ss_pred             ccc---ccchhhhHHHHHhcchhhhh-------hhhhhccCcchheeeeeeccccccccceeecCcccccCCCCC-----
Confidence            865   34455555555433222221       234456666666554 55555555 55666666788554321     


Q ss_pred             CCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhhhcc----cccCCCCCCCCCCCCcccccCCCCCCCCCCCccCCcCCCC
Q 006320          476 VSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDF----FQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPP  551 (650)
Q Consensus       476 ~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p  551 (650)
                        .+.+.++|.|....++.|...+.+.+....--..    .....+..+...++      +.+. ...            
T Consensus       608 --~~~~e~~i~g~~~~v~aa~~~~~~i~~~~~~~~~~~~~i~~~~~~~~~~~~g------~~~~-~~t------------  666 (753)
T KOG2208|consen  608 --TSSDEVSIKGAKDEVKAAKGRLEEIVEYLSAYATTNTKIPDKFHRSIVGYRG------HIIE-EIT------------  666 (753)
T ss_pred             --CchhhhccchhHHHHHHhhccchhhhhhcccccceeeecccccceeeecCCC------cccc-cce------------
Confidence              2233589999999999998888877765422111    11112222211111      1110 000            


Q ss_pred             CCCCCCCCCCCCCCCCcccCCCc--cccccCCcccccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhH
Q 006320          552 AATHQSVQIPATSQPSKEAAGSV--SETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRF  629 (650)
Q Consensus       552 ~~~~~~~~~~~~~~~~~~~g~~~--~~~~~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~I  629 (650)
                                 ..|...+-.+..  .+...+ .....+.......+++.......|.++.||.++++.+||.+|+++.++
T Consensus       667 -----------~~~~~~~~~~~~~~~~s~~~-~~~~~~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~  734 (753)
T KOG2208|consen  667 -----------SKFGVGGYFGDAPTEGSVNT-IHVSGEKMQSEIAKIALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQL  734 (753)
T ss_pred             -----------eecCccceeCCCCCccccCc-chhhhhhhhhhhcccccccccceeeEEeccHHHhhhccCCCCccHHHH
Confidence                       001000000000  000000 000111111222222222223479999999999999999999999999


Q ss_pred             HHhcCCeEEEEE
Q 006320          630 SEVSLLLHLINL  641 (650)
Q Consensus       630 r~~SGA~i~i~~  641 (650)
                      =...+..+.+.-
T Consensus       735 ~~~~~~~~~~~~  746 (753)
T KOG2208|consen  735 EKEFNVNIVVPN  746 (753)
T ss_pred             HHHhccceecCC
Confidence            999888776653

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.24  E-value=1.5e-11  Score=98.73  Aligned_cols=63  Identities=41%  Similarity=0.657  Sum_probs=56.5

Q ss_pred             EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHH
Q 006320          433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEV  499 (650)
Q Consensus       433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  499 (650)
                      +++|+||.+.+|+|||++|+ |++|+++|||+|++.+.+. +   ..++|+|+|+|+++++++|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence            47899999999999999999 9999999999999976443 1   35789999999999999999987

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.18  E-value=5.9e-11  Score=95.22  Aligned_cols=64  Identities=30%  Similarity=0.533  Sum_probs=57.2

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHH
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAII  261 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I  261 (650)
                      +.+|+||..++++|||++|++|++|+++|||+|.+.+...     ....+|+|+|+|++++|.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-----PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-----CCCCceEEEEEeCHHHHHHHHHhh
Confidence            3689999999999999999999999999999999985322     236789999999999999999987

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

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]

Probab=99.07  E-value=2.5e-10  Score=121.99  Aligned_cols=231  Identities=20%  Similarity=0.292  Sum_probs=168.2

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...+.++++|+...|.+++|+.|++|+.|+..++++|.+.+.+  .     ..++.-.+.|-+.+|..|+..+..++.+.
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed--~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~  137 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED--V-----GDERVLLISGFPVQVCKAKAAIHQILTEN  137 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc--C-----CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence            4778899999999999999999999999999999999997632  1     33555566668999999999999998776


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCce
Q 006320          269 QHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDL  348 (650)
Q Consensus       269 ~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~  348 (650)
                      .                                                                             .+
T Consensus       138 ~-----------------------------------------------------------------------------pv  140 (608)
T KOG2279|consen  138 T-----------------------------------------------------------------------------PV  140 (608)
T ss_pred             C-----------------------------------------------------------------------------cc
Confidence            3                                                                             12


Q ss_pred             EEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHH-------HHHhh
Q 006320          349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLH-------IQTRI  421 (650)
Q Consensus       349 ~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~-------i~~~i  421 (650)
                      ...+.+|...+++|+|++|++++.++.-++++|.+.......-.+.+.|.+....   ...|+..+..       +.+.+
T Consensus       141 k~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~---~~~a~~~~~~~~~edeelv~~~  217 (608)
T KOG2279|consen  141 SEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKE---VAAAKHLILEKVSEDEELVKRI  217 (608)
T ss_pred             cccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccch---HHHHHhhhhccccchhHHhhhc
Confidence            3345578999999999999999999999999999987644445678888864321   1222222221       11111


Q ss_pred             hccC------------------------------------C--------------------------------CCCCceE
Q 006320          422 VDLG------------------------------------A--------------------------------DKDNIIT  433 (650)
Q Consensus       422 ~~~~------------------------------------~--------------------------------~~~~~~~  433 (650)
                      .+..                                    .                                .++....
T Consensus       218 ~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i  297 (608)
T KOG2279|consen  218 AESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAI  297 (608)
T ss_pred             hhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccccccccccccc
Confidence            1000                                    0                                0112344


Q ss_pred             EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCC--CCeEEEEEecHHHHHHHHHHHHHHHHhhhhhc
Q 006320          434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSG--TDELVQIVGEIQAARDALVEVTTRLRSYLYRD  510 (650)
Q Consensus       434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~--~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~  510 (650)
                      -.|.+|..++|.|||+.|+ |+.+...+++.+.|..   .|-. +.  .-.++++.|+..-+..|+.++..+.-...+.+
T Consensus       298 ~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t---~pyt-~~v~~~qic~~egkqh~~n~vl~ml~~~~p~~~f~e  373 (608)
T KOG2279|consen  298 PEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT---QPYT-SRVLQLQICVNEGKQHYENSVLEMLTVHVPDIVFAE  373 (608)
T ss_pred             ceeecCcccccchhhhhhhhhhhhhhccCccceEEe---cccc-chhhhhhhheecchhHHHHHHHhhhhccCCcccccc
Confidence            5788999999999999999 9999999999998873   2220 11  12458899999999999998886555555554

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]

Probab=99.05  E-value=1.5e-09  Score=116.24  Aligned_cols=144  Identities=23%  Similarity=0.398  Sum_probs=114.9

Q ss_pred             CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC
Q 006320          346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG  425 (650)
Q Consensus       346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~  425 (650)
                      +++..++.|+.+.+..+||+.|++|+.|++.++++|.+.+. .-.+++..++.|   .+..+.+|+.++.+...      
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~g~e~~~~~~~---~p~~v~~a~a~~~~~~~------  135 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DVGDERVLLISG---FPVQVCKAKAAIHQILT------  135 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cCCcccchhhcc---CCCCCChHHHHHHHHHh------
Confidence            67899999999999999999999999999999999999653 233456667765   35567777776654332      


Q ss_pred             CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHH
Q 006320          426 ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR  504 (650)
Q Consensus       426 ~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~  504 (650)
                        .+..+...+.||+..+++|+|++|. +++|+..++|+|.+....   .|  .-++..+|.|....++.|..++.+++.
T Consensus       136 --~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~--g~~~~~~i~~qqk~~~~a~~~~~~~~~  208 (608)
T KOG2279|consen  136 --ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RL--GLSRLIKISGQQKEVAAAKHLILEKVS  208 (608)
T ss_pred             --cCCcccccccchhhhcccccccchhhhcchhccccccccccccc---cc--ccccceecccccchHHHHHhhhhcccc
Confidence              2346788899999999999999999 999999999999875321   22  346778888888888899999988875


Q ss_pred             hh
Q 006320          505 SY  506 (650)
Q Consensus       505 ~~  506 (650)
                      +.
T Consensus       209 ed  210 (608)
T KOG2279|consen  209 ED  210 (608)
T ss_pred             ch
Confidence            43

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.04  E-value=2.8e-10  Score=90.39  Aligned_cols=60  Identities=18%  Similarity=0.335  Sum_probs=53.4

Q ss_pred             EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHH
Q 006320          434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVT  500 (650)
Q Consensus       434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~  500 (650)
                      .+|.||.+++++|||++|+ |++|+++|||+|+|++.+       +.++.|+|+|+.++|..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence            5789999999999999999 999999999999987433       35778999999999999998873

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=98.99  E-value=2.4e-10  Score=90.13  Aligned_cols=59  Identities=34%  Similarity=0.523  Sum_probs=52.6

Q ss_pred             EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHH
Q 006320          433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEV  499 (650)
Q Consensus       433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  499 (650)
                      |++|.||.+++++|||++|+ |++|+++|||+|+|...        +....|+|+|++++|++|+.+|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence            67899999999999999999 99999999999999632        1245799999999999999886

; 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 ....

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=98.98  E-value=6.6e-10  Score=88.24  Aligned_cols=61  Identities=21%  Similarity=0.304  Sum_probs=54.9

Q ss_pred             EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHH
Q 006320          194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIIS  262 (650)
Q Consensus       194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~  262 (650)
                      .+|.||..++++|||++|++|++|+++|||+|.|.+..        ..++.|+|+|+.++|.+|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--------~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--------SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--------CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999997531        45789999999999999998873

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.

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

Probab=98.98  E-value=1.5e-09  Score=85.77  Aligned_cols=57  Identities=25%  Similarity=0.335  Sum_probs=51.3

Q ss_pred             eEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec-HHHHHHHHHHH
Q 006320          432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-IQAARDALVEV  499 (650)
Q Consensus       432 ~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I  499 (650)
                      ....+.||.+.+|+|||++|+ |++|+++|||+|.|..           ++.|.|+|+ .++++.|+.+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence            467889999999999999999 9999999999998842           457999998 99999999887

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.

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

Probab=98.95  E-value=2.9e-09  Score=84.16  Aligned_cols=58  Identities=22%  Similarity=0.318  Sum_probs=52.7

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHH
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAII  261 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I  261 (650)
                      +...+.||..++++|||++|++|++|+++|||+|.|..            ++.|.|+|+ .+++++|+.+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------------CCEEEEEeCCHHHHHHHHHHh
Confidence            46789999999999999999999999999999999952            357999998 99999999887

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=98.94  E-value=9.7e-10  Score=86.67  Aligned_cols=60  Identities=30%  Similarity=0.449  Sum_probs=54.0

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHH
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAII  261 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I  261 (650)
                      |.+|.||..++++|||++|++|++|+++|||+|.|...         ..+..|+|+|+.++|++|+.+|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD---------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST---------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC---------CCcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999642         1345999999999999999886

; 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 ....

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

Probab=98.90  E-value=4.1e-09  Score=84.00  Aligned_cols=61  Identities=36%  Similarity=0.569  Sum_probs=54.1

Q ss_pred             EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHH
Q 006320          434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEV  499 (650)
Q Consensus       434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  499 (650)
                      .+|.||.+++++|||++|+ |++|+++|||+|.|.....     .+.++.|+|.|..++++.|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence            6799999999999999999 9999999999999975332     34688899999999999999876

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=98.86  E-value=8.4e-09  Score=82.21  Aligned_cols=62  Identities=34%  Similarity=0.549  Sum_probs=55.4

Q ss_pred             EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHH
Q 006320          194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAII  261 (650)
Q Consensus       194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I  261 (650)
                      .+|.||..++++|||++|++|++|+++|||+|.|.+...      ...++.|.|.|..+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~------~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS------GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC------CCCceEEEEEcCHHHHHHHHHHh
Confidence            679999999999999999999999999999999975321      25688999999999999999876

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.

>PF13014 KH_3: KH domain

Probab=98.79  E-value=9.9e-09  Score=75.11  Aligned_cols=42  Identities=45%  Similarity=0.716  Sum_probs=38.6

Q ss_pred             ccceeecCCChHHHHHHHHhCCeEEEec-CCCCCCccEEEEec
Q 006320           89 KAGGVIGKSGSIIKSIRQHTGAWINVHE-LIPGDEERIIEISD  130 (650)
Q Consensus        89 ~vg~IIGk~G~~Ik~I~~~tga~I~v~~-~~~~~~ervi~I~G  130 (650)
                      ++|+|||++|++|++|+++|+|+|+|++ ..++..+++|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5799999999999999999999999998 56678999999987

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

Probab=98.63  E-value=1e-07  Score=90.90  Aligned_cols=139  Identities=21%  Similarity=0.343  Sum_probs=100.5

Q ss_pred             CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCC--cchHHHHHHHHHHH----
Q 006320          346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDD--ELFPAQEALLHIQT----  419 (650)
Q Consensus       346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~--~~~~a~~ai~~i~~----  419 (650)
                      ....+.+.||.+..+.+||+.|++.+.|.+.+++++.+..     .+..|+|..++.+.|  ...+|.+.+..|-.    
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~p   80 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPP   80 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCH
Confidence            3456779999999999999999999999999999999954     557788876643333  33444444432211    


Q ss_pred             ----hhhccCCCCCCceEEEE-----eec------CCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEE
Q 006320          420 ----RIVDLGADKDNIITTRL-----LVP------SSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELV  483 (650)
Q Consensus       420 ----~i~~~~~~~~~~~~~~l-----~Vp------~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v  483 (650)
                          ++.+     + .+.+.+     ++-      ....|+|||++|. -+-|++.|||.|-|.            +..|
T Consensus        81 e~A~~LL~-----d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------------g~tV  142 (194)
T COG1094          81 EKALKLLE-----D-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------------GKTV  142 (194)
T ss_pred             HHHHHHhc-----C-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe------------CcEE
Confidence                0111     1 111111     111      2245999999999 888999999999885            4569


Q ss_pred             EEEecHHHHHHHHHHHHHHHHhhh
Q 006320          484 QIVGEIQAARDALVEVTTRLRSYL  507 (650)
Q Consensus       484 ~I~G~~~~v~~A~~~I~~~l~~~~  507 (650)
                      .|.|.+++|+.|.+.|..++....
T Consensus       143 aiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         143 AIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             EEecChhhhHHHHHHHHHHHcCCC
Confidence            999999999999999999887653

>smart00322 KH K homology RNA-binding domain

Probab=98.60  E-value=1.9e-07  Score=74.67  Aligned_cols=66  Identities=24%  Similarity=0.465  Sum_probs=57.8

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHH
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRL  503 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  503 (650)
                      ..+.++.||...+++|||++|+ |++|++.||++|.+....       .....|.|.|+.++++.|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            3678899999999999999999 999999999999885321       14678999999999999999998876

>PF13014 KH_3: KH domain

Probab=98.59  E-value=8.5e-08  Score=70.16  Aligned_cols=42  Identities=29%  Similarity=0.610  Sum_probs=38.1

Q ss_pred             cccceecCCchhHHHHHHHhCCeEEEeC-CCCCCCccEEEecC
Q 006320          358 KVGRVIGESEGIVELLQNEIGVDLKVAD-PVDGSDEQIITISS  399 (650)
Q Consensus       358 ~vg~IIGk~G~~Ik~l~~~tga~I~i~~-~~~~~~er~i~I~G  399 (650)
                      +|++|||++|++|++|+++|||+|.|++ ..++..++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5799999999999999999999999988 45777889999986

>smart00322 KH K homology RNA-binding domain

Probab=98.53  E-value=4.9e-07  Score=72.27  Aligned_cols=66  Identities=30%  Similarity=0.504  Sum_probs=58.9

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL  265 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  265 (650)
                      .+.++.||..+++.|||++|++|++|++.||++|.+....        .....|.|.|..+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5788999999999999999999999999999999996421        24688999999999999999998876

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

Probab=98.45  E-value=1e-06  Score=84.14  Aligned_cols=148  Identities=19%  Similarity=0.241  Sum_probs=102.5

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCC-CCCCCCCCCccHHHHHHHHHHHH
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRR-RDPEGRMPSFSPAQEALFLIHDR  156 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~-~~~~~~~~~~~~a~~A~~~i~~~  156 (650)
                      ...+.+.||...++.+||+.|++.+.|.+.++++|.++.     .+..|.|..+.. .+|       ....+|...|...
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp-------~~~~ka~d~VkAI   74 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDP-------LALLKARDVVKAI   74 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCCh-------HHHHHHHHHHHHH
Confidence            356778999999999999999999999999999999985     567788887632 122       2234444333221


Q ss_pred             hhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEE-E----EEc------cceeeeeecCCchHHHHHHhhcCceE
Q 006320          157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATR-M----VVS------RMHVGCLLGKGGKIIEQMRMETKTQI  225 (650)
Q Consensus       157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-i----~Vp------~~~vg~IIGk~G~~Ik~I~~~tga~I  225 (650)
                      =.-.+++..+.- .                  ...+.+. |    ++-      ....|+|||++|.+-+.|++.|+|.|
T Consensus        75 grGF~pe~A~~L-L------------------~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I  135 (194)
T COG1094          75 GRGFPPEKALKL-L------------------EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYI  135 (194)
T ss_pred             hcCCCHHHHHHH-h------------------cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeE
Confidence            111111000000 0                  0011111 1    111      12369999999999999999999999


Q ss_pred             EEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          226 RILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       226 ~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      .|.             ...|.|-|.+++|+.|+.+|..++....
T Consensus       136 ~V~-------------g~tVaiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         136 SVY-------------GKTVAIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             EEe-------------CcEEEEecChhhhHHHHHHHHHHHcCCC
Confidence            997             3479999999999999999999998764

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

Probab=98.00  E-value=2.5e-05  Score=70.32  Aligned_cols=65  Identities=18%  Similarity=0.203  Sum_probs=46.8

Q ss_pred             cccceeecCCChHHHHHHHHhCCeEEEecCCC-----------------CCCccEEEEecCCCCCCCCCCCCccHHHHHH
Q 006320           88 MKAGGVIGKSGSIIKSIRQHTGAWINVHELIP-----------------GDEERIIEISDTRRRDPEGRMPSFSPAQEAL  150 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~-----------------~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~  150 (650)
                      .++|.|||++|++||+|+++|||+|.|.....                 ..+.-.|.|++..-        +..++++|+
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~--------~~e~~~~A~   86 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETP--------PEEALAKAV   86 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCc--------HHHHHHHHH
Confidence            67999999999999999999999999975310                 01235688888530        124567777


Q ss_pred             HHHHHHhhhc
Q 006320          151 FLIHDRILES  160 (650)
Q Consensus       151 ~~i~~~i~e~  160 (650)
                      .+|...+.+.
T Consensus        87 ~~I~~ll~~~   96 (120)
T cd02395          87 EAIEELLKPA   96 (120)
T ss_pred             HHHHHHhccC
Confidence            7777666543

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.

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

Probab=97.96  E-value=2.1e-05  Score=70.69  Aligned_cols=66  Identities=24%  Similarity=0.360  Sum_probs=50.6

Q ss_pred             CcceeeecCCCc-hhhhhhhcCceEEEecCCCC-----------CCCCCCCC-eEEEEEec---HHHHHHHHHHHHHHHH
Q 006320          441 SEIGCLEGRDGS-LSEMRRSTGANIQILSREEV-----------PACVSGTD-ELVQIVGE---IQAARDALVEVTTRLR  504 (650)
Q Consensus       441 ~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~-----------p~~~~~~~-r~v~I~G~---~~~v~~A~~~I~~~l~  504 (650)
                      +++|.|||.+|+ ||+|+++|||+|.|..+...           |.....++ -.|.|++.   .+++++|+.+|..+|.
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            567999999999 99999999999999754211           11111222 34999996   4999999999999988


Q ss_pred             hh
Q 006320          505 SY  506 (650)
Q Consensus       505 ~~  506 (650)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            54

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.

>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]

Probab=97.95  E-value=3.4e-05  Score=77.81  Aligned_cols=155  Identities=22%  Similarity=0.285  Sum_probs=106.5

Q ss_pred             ccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHH
Q 006320           77 VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDR  156 (650)
Q Consensus        77 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~  156 (650)
                      ..++...-+|..+++.|.|++|.+||.|+.+|...|+-+.   ..+|-+..++|..           +.|..|.    +.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPs---r~eePiF~vTg~~-----------edv~~aR----re   85 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPS---RGEEPIFPVTGRH-----------EDVRRAR----RE   85 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCC---CCCCCcceeccCc-----------hhHHHHh----hc
Confidence            5688888889999999999999999999999999999875   3466788888853           2344443    33


Q ss_pred             hhhcCCCCCCCCCcccccCCCCCCCCCCCCC-CCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCC
Q 006320          157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRG-GGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLP  235 (650)
Q Consensus       157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp  235 (650)
                      |......++.....       +..++|-... .....+...-+|...+++|.|.+|++|++|++.++..|.-.-+     
T Consensus        86 i~saaeH~~l~~~s-------~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-----  153 (394)
T KOG2113|consen   86 IPSAAEHFGLIRAS-------RSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-----  153 (394)
T ss_pred             Cccccceeeeeeec-------ccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-----
Confidence            32222122110000       0111111111 1345677788899999999999999999999999988866422     


Q ss_pred             CccCCCcceEEEEcCHHH-HHHHH-HHHHHHH
Q 006320          236 RCVSMSEEIVQVVGDINN-VKNAV-AIISSRL  265 (650)
Q Consensus       236 ~~~~~~er~V~I~G~~~~-V~~A~-~~I~~~l  265 (650)
                          ..+.+..++|...+ +++|. ..|...+
T Consensus       154 ----~~~~Vf~Vtg~~~nC~kra~s~eie~ta  181 (394)
T KOG2113|consen  154 ----CGEPVFCVTGAPKNCVKRARSCEIEQTA  181 (394)
T ss_pred             ----CCCceEEEecCCcchhhhccccchhhhh
Confidence                34678899998777 66666 4555544

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.71  E-value=0.00011  Score=67.98  Aligned_cols=103  Identities=19%  Similarity=0.212  Sum_probs=71.2

Q ss_pred             EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhh
Q 006320           80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE  159 (650)
Q Consensus        80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e  159 (650)
                      .+-|+++...+|..||++|++|+.|++..|-+|+|-+-..                            ++...|...+..
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~----------------------------d~~~fI~n~l~P   84 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD----------------------------DPEEFIKNIFAP   84 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC----------------------------CHHHHHHHHcCC
Confidence            5677889999999999999999999999998888765210                            122222222221


Q ss_pred             cCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320          160 SDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL  228 (650)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  228 (650)
                      ......       ..           ..........+.|+....+.+|||+|.+|+.++.-++-.+.|.
T Consensus        85 a~V~~v-------~I-----------~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         85 AAVRSV-------TI-----------KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             CEEEEE-------EE-----------EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            110000       00           0001234677889999999999999999999999999888764

>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]

Probab=97.61  E-value=0.00011  Score=74.28  Aligned_cols=141  Identities=22%  Similarity=0.277  Sum_probs=102.4

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      ..++..+.||..+|+.+.|++|.+||.|+.+|.+.|.-..+         ..+.+..++|..+.|+.|++.|...-+...
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---------~eePiF~vTg~~edv~~aRrei~saaeH~~   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---------GEEPIFPVTGRHEDVRRARREIPSAAEHFG   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---------CCCCcceeccCchhHHHHhhcCccccceee
Confidence            67889999999999999999999999999999999977543         235688899999999999988766332221


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceE
Q 006320          270 HRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLV  349 (650)
Q Consensus       270 ~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  349 (650)
                      ...   +      ..+|.                        +          ...++.               ...+.+
T Consensus        95 l~~---~------s~s~S------------------------g----------g~~~~s---------------~s~qt~  116 (394)
T KOG2113|consen   95 LIR---A------SRSFS------------------------G----------GTNGAS---------------ASGQTT  116 (394)
T ss_pred             eee---e------ccccc------------------------C----------CCcccc---------------ccCCCc
Confidence            000   0      00000                        0          000110               014566


Q ss_pred             EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320          350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE  400 (650)
Q Consensus       350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~  400 (650)
                      ..+.+|...++.|.|..|.+|+.+++.+...|.-+-   .+.+-++.++|.
T Consensus       117 sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v---~~~~~Vf~Vtg~  164 (394)
T KOG2113|consen  117 SYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV---RCGEPVFCVTGA  164 (394)
T ss_pred             eeeeccceeeeeccccccCccchheecccceEeeec---cCCCceEEEecC
Confidence            778899999999999999999999999998887643   345677888874

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.60  E-value=9.3e-05  Score=77.68  Aligned_cols=53  Identities=26%  Similarity=0.272  Sum_probs=47.5

Q ss_pred             ccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCC
Q 006320           77 VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR  132 (650)
Q Consensus        77 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~  132 (650)
                      .+++++|-+-+.+||.|||++|++|+.|+..|+++|+|..   ...+-.|+|.|..
T Consensus        45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~---~~~e~kv~ifg~~   97 (629)
T KOG0336|consen   45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---CDLEVKVTIFGIN   97 (629)
T ss_pred             CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec---cCceeEEEEechH
Confidence            4678899999999999999999999999999999999987   4567779999964

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.50  E-value=0.00027  Score=65.48  Aligned_cols=99  Identities=18%  Similarity=0.303  Sum_probs=69.8

Q ss_pred             eEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHh--hhccC
Q 006320          348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTR--IVDLG  425 (650)
Q Consensus       348 ~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~--i~~~~  425 (650)
                      -...+.|+...+|+.||++|++|+.|++..|-+|.+-.           -+     .+    +.+.|..++..  +.+..
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~s-----~d----~~~fI~n~l~Pa~V~~v~   91 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------YS-----DD----PEEFIKNIFAPAAVRSVT   91 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------cC-----CC----HHHHHHHHcCCCEEEEEE
Confidence            46678889999999999999999999999988887743           11     01    11222222111  11100


Q ss_pred             -CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEE
Q 006320          426 -ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQI  466 (650)
Q Consensus       426 -~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i  466 (650)
                       .+.+....+.+.|+....|..|||+|+ |+.++..++-.+.|
T Consensus        92 I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         92 IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence             012334567788999999999999999 99999999999866

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.38  E-value=0.00056  Score=78.52  Aligned_cols=94  Identities=22%  Similarity=0.270  Sum_probs=72.3

Q ss_pred             ccHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320          143 FSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK  222 (650)
Q Consensus       143 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg  222 (650)
                      +..+.++...|++.+.+.-...    .+-..+               -.....+.||...++.|||+||++|+.|+++||
T Consensus       548 L~~A~~g~~~Il~~m~~al~~p----~~~s~~---------------aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg  608 (719)
T TIGR02696       548 LKQARDARLAILDVMAEAIDTP----DEMSPY---------------APRIITVKIPVDKIGEVIGPKGKMINQIQDETG  608 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCc----cccccC---------------CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHC
Confidence            4456667777777776543211    011112               345778899999999999999999999999999


Q ss_pred             ceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320          223 TQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE  267 (650)
Q Consensus       223 a~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~  267 (650)
                      ++|.|..            +..|.|.+. .+++++|+.+|..++..
T Consensus       609 ~~Idi~d------------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       609 AEISIED------------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CEEEEec------------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            9999952            467899885 89999999999999985

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.36  E-value=0.00048  Score=79.08  Aligned_cols=88  Identities=23%  Similarity=0.251  Sum_probs=67.3

Q ss_pred             chHHHHHHHHHHHhhhccC--C---CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320          407 LFPAQEALLHIQTRIVDLG--A---DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD  480 (650)
Q Consensus       407 ~~~a~~ai~~i~~~i~~~~--~---~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~  480 (650)
                      +..|.++..+|++.+.+..  +   ....+....+.||.+.++.|||.||. ||+|.++|||+|.|.           ++
T Consensus       548 L~~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-----------d~  616 (719)
T TIGR02696       548 LKQARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-----------DD  616 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe-----------cC
Confidence            3445555555554433321  1   12335778899999999999999999 999999999999884           25


Q ss_pred             eEEEEEe-cHHHHHHHHHHHHHHHHh
Q 006320          481 ELVQIVG-EIQAARDALVEVTTRLRS  505 (650)
Q Consensus       481 r~v~I~G-~~~~v~~A~~~I~~~l~~  505 (650)
                      ..|.|.+ +.+++++|+.+|..++..
T Consensus       617 G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       617 GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            6799998 589999999999999885

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.

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=97.34  E-value=0.0017  Score=69.85  Aligned_cols=78  Identities=18%  Similarity=0.305  Sum_probs=58.9

Q ss_pred             cEEEEEEEcc------ceeeeeecCCchHHHHHHhhcCceEEEecCCCC---------CCCcc-CCCcceEEEEcC-HHH
Q 006320          191 RVATRMVVSR------MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHS---------LPRCV-SMSEEIVQVVGD-INN  253 (650)
Q Consensus       191 ~~~~~i~Vp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~---------lp~~~-~~~er~V~I~G~-~~~  253 (650)
                      .++.+|.||-      ++||+|||..|.+.|+|+++|||+|.|.-+...         +.... ...+=.|.|+++ .|+
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            5677788875      479999999999999999999999999752111         11111 112336788886 799


Q ss_pred             HHHHHHHHHHHHhhc
Q 006320          254 VKNAVAIISSRLRES  268 (650)
Q Consensus       254 V~~A~~~I~~~l~~~  268 (650)
                      |++|++.|..+|.+.
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999999874

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.17  E-value=0.001  Score=61.44  Aligned_cols=103  Identities=19%  Similarity=0.248  Sum_probs=69.6

Q ss_pred             EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhh
Q 006320           80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE  159 (650)
Q Consensus        80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e  159 (650)
                      .+=|++....+|..||++|++|+.|++..|-+|+|-+-..+                            -...|.+.+..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D----------------------------~~~fI~N~l~P   85 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN----------------------------LEEFVANKLAP   85 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC----------------------------HHHHHHHcCCC
Confidence            55678899999999999999999999988988888652110                            00111111111


Q ss_pred             cCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320          160 SDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL  228 (650)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  228 (650)
                      ..... .   .-.              ..+......+.|+..+.+..|||+|.+++...+-++-++.|.
T Consensus        86 A~V~~-V---~i~--------------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        86 AEVKN-V---TVS--------------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             ceEEE-E---EEE--------------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            00000 0   000              001335678899999999999999999999999999888764

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.09  E-value=0.001  Score=77.53  Aligned_cols=65  Identities=22%  Similarity=0.347  Sum_probs=56.3

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhh
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRE  267 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~  267 (650)
                      .....+.||...++.|||++|++|+.|+++|||+|.|..            +..|.|.+ ..+.+++|+..|..+..+
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            457789999999999999999999999999999999962            45677776 489999999999988654

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).

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=97.01  E-value=0.0036  Score=67.34  Aligned_cols=75  Identities=19%  Similarity=0.361  Sum_probs=57.5

Q ss_pred             ceEEEEeecC------CcceeeecCCCc-hhhhhhhcCceEEEecCCC----------CCCCCCCCCeE-EEEEec-HHH
Q 006320          431 IITTRLLVPS------SEIGCLEGRDGS-LSEMRRSTGANIQILSREE----------VPACVSGTDEL-VQIVGE-IQA  491 (650)
Q Consensus       431 ~~~~~l~Vp~------~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~----------~p~~~~~~~r~-v~I~G~-~~~  491 (650)
                      ..+.+|.||.      ++||.|||-.|. .|+|+++|||+|.|..+..          +.-...+.+.+ |.|+.+ .++
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            5667788875      478999999999 9999999999999986221          11111234455 999996 689


Q ss_pred             HHHHHHHHHHHHHh
Q 006320          492 ARDALVEVTTRLRS  505 (650)
Q Consensus       492 v~~A~~~I~~~l~~  505 (650)
                      |++|+.+|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999888886

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=96.98  E-value=0.0011  Score=77.36  Aligned_cols=66  Identities=23%  Similarity=0.258  Sum_probs=56.0

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEe-cHHHHHHHHHHHHHHHHhh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG-EIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~  506 (650)
                      .+...++.||.+.++.|||+||+ ||+|+++|||+|.|.           ++..|.|.+ ..+.+++|+.+|..+..+.
T Consensus       549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~~  616 (684)
T TIGR03591       549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-----------DDGTVKIAASDGEAAEAAIKMIEGITAEP  616 (684)
T ss_pred             CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe-----------cCeEEEEEECcHHHHHHHHHHHHhhhccc
Confidence            46778899999999999999999 999999999999884           245577777 5789999999998887653

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).

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=96.80  E-value=0.003  Score=58.38  Aligned_cols=101  Identities=14%  Similarity=0.174  Sum_probs=68.1

Q ss_pred             EEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhcc-CCC
Q 006320          349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDL-GAD  427 (650)
Q Consensus       349 ~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~-~~~  427 (650)
                      ..-+.|....+|..||++|++|+.|++..|=+|.+-.-           +     .|...-+..++.=  .++.+. ..+
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s-----~D~~~fI~N~l~P--A~V~~V~i~~   95 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------S-----ENLEEFVANKLAP--AEVKNVTVSE   95 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------C-----CCHHHHHHHcCCC--ceEEEEEEEc
Confidence            56677888899999999999999999888888877431           1     0000000111100  001110 001


Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEe
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQIL  467 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~  467 (650)
                      .++.....+.||.++.+..|||+|+ |+-..+.++-.+.|.
T Consensus        96 ~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        96 FNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            2334567889999999999999999 999999999888663

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.50  E-value=0.0029  Score=74.39  Aligned_cols=95  Identities=16%  Similarity=0.256  Sum_probs=70.1

Q ss_pred             chHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCce-EEEecCCCCCCCCCC
Q 006320          407 LFPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGAN-IQILSREEVPACVSG  478 (650)
Q Consensus       407 ~~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~-I~i~~~~~~p~~~~~  478 (650)
                      +..|.++...|++.+.+..+      ....+....+.||.+.++.|||.||. ||+|.++||+. |.+.           
T Consensus       654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------  722 (891)
T PLN00207        654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------  722 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------
Confidence            34455555555554443211      23346788899999999999999999 99999999999 8652           


Q ss_pred             CCeEEEEEe-cHHHHHHHHHHHHHHHHhhhhhccc
Q 006320          479 TDELVQIVG-EIQAARDALVEVTTRLRSYLYRDFF  512 (650)
Q Consensus       479 ~~r~v~I~G-~~~~v~~A~~~I~~~l~~~~~~~~~  512 (650)
                      ++-.|.|.+ +.+++++|+.+|.+++.+....+.|
T Consensus       723 ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy  757 (891)
T PLN00207        723 DDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIY  757 (891)
T ss_pred             CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEE
Confidence            345688888 5899999999999988754443444

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.46  E-value=0.0039  Score=73.34  Aligned_cols=65  Identities=25%  Similarity=0.349  Sum_probs=57.0

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCce-EEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQ-IRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE  267 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~  267 (650)
                      .....+.||...++.|||.||.+|+.|.++||++ |.+.            .+-.|.|.+. .+++++|+.+|..++.+
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------------ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------------DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC------------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            4578899999999999999999999999999999 8874            2457888884 89999999999998864

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=96.43  E-value=0.0031  Score=64.92  Aligned_cols=71  Identities=24%  Similarity=0.171  Sum_probs=59.1

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI  157 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i  157 (650)
                      ..+..+++++.+++.|||+.|.|-++|++||+++|.++.+  ++....|+|.|.          ..++|..|+.+|...|
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~----------~~~~V~~a~~Ri~~~i  123 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGI----------SRNCVIQALERIAKLI  123 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeeh----------hHHHHHHHHHHHHHHH
Confidence            4677889999999999999999999999999999999986  444455666664          3678899999988888


Q ss_pred             hhc
Q 006320          158 LES  160 (650)
Q Consensus       158 ~e~  160 (650)
                      .+.
T Consensus       124 ds~  126 (345)
T KOG2814|consen  124 DSD  126 (345)
T ss_pred             Hhh
Confidence            653

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.42  E-value=0.0023  Score=62.19  Aligned_cols=103  Identities=22%  Similarity=0.213  Sum_probs=70.0

Q ss_pred             EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhh
Q 006320           80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE  159 (650)
Q Consensus        80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e  159 (650)
                      .+-++.-...+|..||++|++|+.|.++.|=+|+|-+-.++.                     ..-+.+|+       ..
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d~---------------------~~fI~nal-------~P  128 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSEDP---------------------AEFIKNAL-------AP  128 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCCH---------------------HHHHHHhc-------Cc
Confidence            455666778899999999999999999999888875421100                     11122222       11


Q ss_pred             cCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320          160 SDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP  229 (650)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  229 (650)
                      ... ......+                  .+.....+.||..+.+..|||+|.+++...+-||.++.|..
T Consensus       129 a~v-~~V~~~~------------------~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         129 AEV-LSVNIKE------------------DDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             ceE-eEEEEEe------------------CCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            000 0000000                  01127888999999999999999999999999999999963

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=96.30  E-value=0.0048  Score=65.20  Aligned_cols=73  Identities=26%  Similarity=0.360  Sum_probs=60.5

Q ss_pred             CCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHh
Q 006320          187 GGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLR  266 (650)
Q Consensus       187 ~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~  266 (650)
                      +......+.+.+-+++||.+||++|++|++|+..|+++|+|..-         ..+..|+|-|..+--.+|+..|...+.
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---------~~e~kv~ifg~~~m~~kaka~id~~~~  112 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---------DLEVKVTIFGINHMRKKAKASIDRGQD  112 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence            34466678889999999999999999999999999999999742         457789999998777777777776665


Q ss_pred             hc
Q 006320          267 ES  268 (650)
Q Consensus       267 ~~  268 (650)
                      ..
T Consensus       113 k~  114 (629)
T KOG0336|consen  113 KD  114 (629)
T ss_pred             hh
Confidence            54

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

Probab=96.24  E-value=0.0081  Score=67.81  Aligned_cols=95  Identities=19%  Similarity=0.216  Sum_probs=71.5

Q ss_pred             hHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320          408 FPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD  480 (650)
Q Consensus       408 ~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~  480 (650)
                      .+|.++-++++..+.+...      ....+-..++-|+...++-+||+||+ |++|.++|||+|+|.           ++
T Consensus       522 ~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------dd  590 (692)
T COG1185         522 EQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DD  590 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CC
Confidence            3455555555544443211      12335667888999999999999999 999999999999884           24


Q ss_pred             eEEEEEecH-HHHHHHHHHHHHHHHhhhhhcccc
Q 006320          481 ELVQIVGEI-QAARDALVEVTTRLRSYLYRDFFQ  513 (650)
Q Consensus       481 r~v~I~G~~-~~v~~A~~~I~~~l~~~~~~~~~~  513 (650)
                      -+|.|.++. +.+.+|+..|.+++++......|.
T Consensus       591 Gtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~  624 (692)
T COG1185         591 GTVKIAASDGESAKKAKERIEAITREVEVGEVYE  624 (692)
T ss_pred             CcEEEEecchHHHHHHHHHHHHHHhhcccccEEE
Confidence            468999975 899999999999999887777543

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=96.23  E-value=0.0059  Score=61.30  Aligned_cols=42  Identities=24%  Similarity=0.357  Sum_probs=37.5

Q ss_pred             CCCccEEEEEEecCc------ccceeecCCChHHHHHHHHhCCeEEEe
Q 006320           74 SLMVTTTYRILCHDM------KAGGVIGKSGSIIKSIRQHTGAWINVH  115 (650)
Q Consensus        74 ~~~~~~~~rilip~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~  115 (650)
                      .....++.+++||.+      |||.|+|++|.++|+|+++|+|+|-|-
T Consensus        87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            345578899999985      899999999999999999999999885

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.18  E-value=0.0062  Score=59.18  Aligned_cols=100  Identities=23%  Similarity=0.363  Sum_probs=66.7

Q ss_pred             EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC-CCC
Q 006320          350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG-ADK  428 (650)
Q Consensus       350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~-~~~  428 (650)
                      ....+-.+.+|..||++|++|+.|.++.|=+|.|-.-           +     +|...-+..|+.-  .++.... .+.
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s-----~d~~~fI~nal~P--a~v~~V~~~~~  139 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------S-----EDPAEFIKNALAP--AEVLSVNIKED  139 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------C-----CCHHHHHHHhcCc--ceEeEEEEEeC
Confidence            3444556778999999999999999999976766431           1     1111111122210  0000000 011


Q ss_pred             CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEec
Q 006320          429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILS  468 (650)
Q Consensus       429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~  468 (650)
                      ++. ...+.||.++.+..|||+|. ++-+.+.||-+|.|..
T Consensus       140 d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         140 DGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             CCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            223 78889999999999999999 9999999999999863

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

Probab=96.16  E-value=0.011  Score=66.85  Aligned_cols=96  Identities=22%  Similarity=0.234  Sum_probs=72.6

Q ss_pred             ccHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320          143 FSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK  222 (650)
Q Consensus       143 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg  222 (650)
                      +.+|.+|...|...+.+.-....   .+-..|               ......+.|+.....-+||++|++|++|.++||
T Consensus       521 L~QAk~aRlhIL~~M~~ai~~pr---~els~~---------------aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg  582 (692)
T COG1185         521 LEQAKGARLHILIVMNEAISEPR---KELSPY---------------APRIETIKIDPDKIRDVIGPGGKTIKAITEETG  582 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhh---hhhhcc---------------CCceEEEccCHHHHhhccCCcccchhhhhhhhC
Confidence            44567777777777766432211   111122               234677888999999999999999999999999


Q ss_pred             ceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhhc
Q 006320          223 TQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRES  268 (650)
Q Consensus       223 a~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~~  268 (650)
                      ++|+|.            .+..|.|.++ .+.+.+|+..|..+.++.
T Consensus       583 ~~Idie------------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         583 VKIDIE------------DDGTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             cEEEec------------CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence            999996            2457899887 599999999999999774

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=95.85  E-value=0.032  Score=56.12  Aligned_cols=80  Identities=24%  Similarity=0.338  Sum_probs=54.0

Q ss_pred             CCCceEEEEeecCC------cceeeecCCCc-hhhhhhhcCceEEEecCCC------------CCCCCCCCCe---EEEE
Q 006320          428 KDNIITTRLLVPSS------EIGCLEGRDGS-LSEMRRSTGANIQILSREE------------VPACVSGTDE---LVQI  485 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~------~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~------------~p~~~~~~~r---~v~I  485 (650)
                      +...++.+|+||-+      +||+|||..|. +|.|+++|||+|-|..+..            -|.++.-++.   +|+.
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~  167 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIET  167 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEE
Confidence            44567888999865      78999999999 9999999999999976443            2344333333   3667


Q ss_pred             EecHHHHHHHHHHHHHHHHhhh
Q 006320          486 VGEIQAARDALVEVTTRLRSYL  507 (650)
Q Consensus       486 ~G~~~~v~~A~~~I~~~l~~~~  507 (650)
                      ..++.-+..=+.+-++.|+..+
T Consensus       168 ~~p~~ea~~rl~~AleeI~klL  189 (259)
T KOG1588|consen  168 EAPPAEAYARLAYALEEIKKLL  189 (259)
T ss_pred             eCCHHHHHHHHHHHHHHHHHhc
Confidence            7776555443333344444443

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

Probab=95.80  E-value=0.016  Score=45.61  Aligned_cols=37  Identities=24%  Similarity=0.380  Sum_probs=34.4

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEE
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV  114 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v  114 (650)
                      ...+.+.++.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688899999999999999999999999999998876

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.

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

Probab=95.68  E-value=0.012  Score=46.30  Aligned_cols=36  Identities=22%  Similarity=0.049  Sum_probs=33.6

Q ss_pred             ceEEEEecCCcccccccCCCcchhhHHHhcCCeEEE
Q 006320          604 STLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLI  639 (650)
Q Consensus       604 ~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i  639 (650)
                      ....|.||.+..+.+|||+|.||+.+++..|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578899999999999999999999999999988865

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

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=95.63  E-value=0.014  Score=60.20  Aligned_cols=71  Identities=25%  Similarity=0.440  Sum_probs=58.7

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhhcc
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~~~  269 (650)
                      .....+.|++...++|||++|.+-++|+++|+|+|.++.     |.   .....|+|+| ..++|.+|..+|...+.+..
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~-----p~---~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR-----PN---TNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC-----CC---CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            456778999999999999999999999999999999964     22   2344555555 68999999999999998763

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.53  E-value=0.038  Score=59.04  Aligned_cols=98  Identities=17%  Similarity=0.254  Sum_probs=64.3

Q ss_pred             ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320          357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR  435 (650)
Q Consensus       357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~  435 (650)
                      +-+|+.||++|.+|+.|.++. |=+|.|-.-..+.  ..+ |.      +++++|.         +....-+ +..-...
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~--~~f-I~------Nal~Pa~---------V~~V~i~-~~~~~~~  311 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVP--EIF-IA------RALAPAI---------ISSVKIE-EEEKKAI  311 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCH--HHH-HH------HhCCCce---------eeEEEEc-CCCcEEE
Confidence            447999999999999999988 6677664311000  000 00      0011110         0000001 2234778


Q ss_pred             EeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCC
Q 006320          436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVP  473 (650)
Q Consensus       436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p  473 (650)
                      +.||..+.+..|||+|. ++-..+.||.+|.|.+-++..
T Consensus       312 V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~  350 (374)
T PRK12328        312 VTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSKE  350 (374)
T ss_pred             EEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCCc
Confidence            99999999999999999 999999999999999865543

>TIGR01953 NusA transcription termination factor NusA

Probab=95.50  E-value=0.046  Score=58.27  Aligned_cols=38  Identities=21%  Similarity=0.274  Sum_probs=35.7

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP  229 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  229 (650)
                      ..+.+.||..+.+..|||+|.+++.....||.+|.|..
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            47899999999999999999999999999999999974

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=95.40  E-value=0.043  Score=58.54  Aligned_cols=94  Identities=20%  Similarity=0.417  Sum_probs=62.0

Q ss_pred             ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhcc-CCCCCCceEE
Q 006320          357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDL-GADKDNIITT  434 (650)
Q Consensus       357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~-~~~~~~~~~~  434 (650)
                      +-+|+.||++|.+|+.|.++. |=+|.|-.-..+.  ..+..       +++++|.         +... ..+. ..-..
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~--~~fi~-------nal~Pa~---------v~~v~i~~~-~~~~~  303 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP--AEFIA-------NALSPAK---------VISVEVLDE-DKHSA  303 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCH--HHHHH-------HhcCCce---------EEEEEEEcC-CCcEE
Confidence            447999999999999999998 6677664311000  00000       0011110         0000 0011 23578


Q ss_pred             EEeecCCcceeeecCCCc-hhhhhhhcCceEEEecC
Q 006320          435 RLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR  469 (650)
Q Consensus       435 ~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~  469 (650)
                      .+.||.++.+..|||+|. ++-..+.||.+|.|.+.
T Consensus       304 ~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       304 EVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             EEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            899999999999999999 99999999999999753

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

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.23  E-value=0.055  Score=58.11  Aligned_cols=95  Identities=18%  Similarity=0.211  Sum_probs=64.3

Q ss_pred             cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320           88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF  166 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~  166 (650)
                      +-+|..||++|+.|+.|.++. |-+|+|-.-..+                            ....|...+........ 
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d----------------------------~~~fi~nal~Pa~v~~v-  295 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED----------------------------PAEFVANALSPAKVVSV-  295 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC----------------------------HHHHHHHhCCCceEEEE-
Confidence            458999999999999999998 788887542110                            00111111111000000 


Q ss_pred             CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320          167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP  229 (650)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  229 (650)
                         .   .           .. +....+.+.||..+.++.|||+|.+++.-...||.+|.|..
T Consensus       296 ---~---i-----------~~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        296 ---E---V-----------DD-EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             ---E---E-----------Ec-CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence               0   0           00 12246889999999999999999999999999999999975

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.21  E-value=0.045  Score=58.45  Aligned_cols=96  Identities=16%  Similarity=0.099  Sum_probs=65.0

Q ss_pred             cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320           88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF  166 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~  166 (650)
                      +-+|..||++|++|+.|.++- |=+|+|-.-.++                            -...|...+........ 
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D----------------------------~~~fI~Nal~Pa~V~~V-  301 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV----------------------------PEIFIARALAPAIISSV-  301 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC----------------------------HHHHHHHhCCCceeeEE-
Confidence            458999999999999999998 788887542110                            00111111111000000 


Q ss_pred             CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCC
Q 006320          167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRD  231 (650)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  231 (650)
                      .  .                 ......+.+.||..+.++.|||+|.+++.....||.+|.|..-+
T Consensus       302 ~--i-----------------~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        302 K--I-----------------EEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             E--E-----------------cCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            0  0                 01223788999999999999999999999999999999998643

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.20  E-value=0.017  Score=67.70  Aligned_cols=88  Identities=24%  Similarity=0.259  Sum_probs=64.3

Q ss_pred             hHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320          408 FPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD  480 (650)
Q Consensus       408 ~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~  480 (650)
                      ..|.++..+|++.+.+...      ....+....+.||.+.++.+||.||. ||+|.++||+.|.+.           ++
T Consensus       524 ~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~  592 (693)
T PRK11824        524 EQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DD  592 (693)
T ss_pred             HHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CC
Confidence            3455555566655554211      12234556777899999999999999 999999999988652           24


Q ss_pred             eEEEEEe-cHHHHHHHHHHHHHHHHhh
Q 006320          481 ELVQIVG-EIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       481 r~v~I~G-~~~~v~~A~~~I~~~l~~~  506 (650)
                      -.|.|.+ ..+.+++|+.+|..+..+.
T Consensus       593 G~v~i~~~~~~~~~~a~~~I~~~~~~~  619 (693)
T PRK11824        593 GTVKIAATDGEAAEAAKERIEGITAEP  619 (693)
T ss_pred             ceEEEEcccHHHHHHHHHHHHHhcccC
Confidence            5688888 5789999999998888653

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.12  E-value=0.022  Score=66.64  Aligned_cols=95  Identities=20%  Similarity=0.242  Sum_probs=68.6

Q ss_pred             ccHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320          143 FSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK  222 (650)
Q Consensus       143 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg  222 (650)
                      +..+.++...|++.|.+.-....   .+-..+               ......+.|+...++.+||.||.+|+.|.++||
T Consensus       523 l~~a~~g~~~I~~~M~~aI~~~r---~~~~~~---------------ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~  584 (693)
T PRK11824        523 LEQAKEGRLHILGKMNEAISEPR---AELSPY---------------APRIETIKIPPDKIRDVIGPGGKTIREITEETG  584 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCh---hhhccc---------------CchheeecCCHHHHHHHhcCCchhHHHHHHHHC
Confidence            34566777778877766532221   011111               233456677999999999999999999999999


Q ss_pred             ceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320          223 TQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE  267 (650)
Q Consensus       223 a~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~  267 (650)
                      ++|.+.            .+-.|.|.+. .+.+++|+..|..+..+
T Consensus       585 ~~idi~------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        585 AKIDIE------------DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             CccccC------------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            988774            2456888884 89999999999988854

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.98  E-value=0.069  Score=58.03  Aligned_cols=94  Identities=19%  Similarity=0.186  Sum_probs=63.0

Q ss_pred             cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320           88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF  166 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~  166 (650)
                      +-+|..||++|+.|+.|.++. |=+|+|-.-.++-.+                     -+.+|       +.-...... 
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~---------------------fI~Na-------LsPA~V~~V-  327 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPAT---------------------YIANA-------LSPARVDEV-  327 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---------------------HHHHh-------cCCceeeEE-
Confidence            558999999999999999998 788887542111000                     01111       111000000 


Q ss_pred             CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320          167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL  228 (650)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  228 (650)
                         .   .            .......+.+.||..+.++.|||+|.+++.-...||.+|.|.
T Consensus       328 ---~---i------------~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~  371 (449)
T PRK12329        328 ---R---L------------VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK  371 (449)
T ss_pred             ---E---E------------EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence               0   0            001123578999999999999999999999999999999996

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.96  E-value=1  Score=44.79  Aligned_cols=65  Identities=18%  Similarity=0.231  Sum_probs=56.0

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      .+.+.++....-+|...+|..++.|....||+|.+..           .+..+.|+|+...++.+...|.+++...
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----------SENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            4555666888899999999999999888899999973           3568999999999999999999999774

>PRK00468 hypothetical protein; Provisional

Probab=94.69  E-value=0.038  Score=45.37  Aligned_cols=33  Identities=30%  Similarity=0.344  Sum_probs=29.5

Q ss_pred             CCccEEEEEEecCcccceeecCCChHHHHHHHH
Q 006320           75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQH  107 (650)
Q Consensus        75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~  107 (650)
                      .+..+.+++.|....+|.||||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            345689999999999999999999999999975

>PRK00468 hypothetical protein; Provisional

Probab=94.58  E-value=0.064  Score=44.07  Aligned_cols=34  Identities=18%  Similarity=0.362  Sum_probs=28.5

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcC
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG  461 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tg  461 (650)
                      .+..+.++|.|..+.+|+||||+|. |+.||.--.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            3456888999999999999999999 888886543

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=94.54  E-value=0.078  Score=56.94  Aligned_cols=96  Identities=23%  Similarity=0.391  Sum_probs=62.5

Q ss_pred             ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320          357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR  435 (650)
Q Consensus       357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~  435 (650)
                      +-+|+.||++|.+|+.|.++. |=+|.|-.-..+.  ..+ |.      +++++|.     +. .+. . .+ +..-.+.
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~--~~f-i~------nal~Pa~-----v~-~v~-i-~~-~~~~~~~  306 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP--AEF-VA------NALSPAK-----VV-SVE-V-DD-EEEKAAR  306 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCH--HHH-HH------HhCCCce-----EE-EEE-E-Ec-CCCcEEE
Confidence            447999999999999999888 7677764311100  000 00      0001110     00 000 0 01 2235688


Q ss_pred             EeecCCcceeeecCCCc-hhhhhhhcCceEEEecCC
Q 006320          436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSRE  470 (650)
Q Consensus       436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~  470 (650)
                      +.||..+.+.-|||+|. |+-..+.||.+|.|.+.+
T Consensus       307 v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~  342 (362)
T PRK12327        307 VVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES  342 (362)
T ss_pred             EEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence            99999999999999999 999999999999998643

>PRK02821 hypothetical protein; Provisional

Probab=94.33  E-value=0.074  Score=43.88  Aligned_cols=34  Identities=24%  Similarity=0.327  Sum_probs=28.4

Q ss_pred             CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCc
Q 006320          429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGA  462 (650)
Q Consensus       429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga  462 (650)
                      +....+.|.|....+|+||||+|. |+.||.--.+
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            445788999999999999999999 8888865443

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.13  E-value=0.077  Score=53.79  Aligned_cols=67  Identities=16%  Similarity=0.211  Sum_probs=54.9

Q ss_pred             EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec-HHHHHHHHHHHHHHHHhhhhhc
Q 006320          433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-IQAARDALVEVTTRLRSYLYRD  510 (650)
Q Consensus       433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~~~~~  510 (650)
                      -+.+.||...++++||++|. |+.|.+.|++.|.+-           .+-.|.|.+. .+++++|+..|..+-++....+
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~~  214 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSG  214 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhccC
Confidence            35678999999999999999 999999999999772           2446889996 5688999999888877765444

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.07  E-value=0.1  Score=52.95  Aligned_cols=63  Identities=22%  Similarity=0.291  Sum_probs=54.4

Q ss_pred             EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhhc
Q 006320          194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRES  268 (650)
Q Consensus       194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~~  268 (650)
                      ..+.||..+++.|||++|..|+.|.++++++|.+-.            +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            668899999999999999999999999999999842            346889886 678999999988877665

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.04  E-value=0.098  Score=58.19  Aligned_cols=94  Identities=18%  Similarity=0.237  Sum_probs=63.8

Q ss_pred             cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320           88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF  166 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~  166 (650)
                      +-+|+.||++|+.|+.|.++- |=+|+|-.-.+   +.                         ...|...+........ 
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~---d~-------------------------~~fi~nal~pa~v~~v-  295 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSD---DP-------------------------AQFIINALSPAEVSSV-  295 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCC---CH-------------------------HHHHHHhCCCCEEEEE-
Confidence            448999999999999999998 78888754211   00                         0111111111100000 


Q ss_pred             CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320          167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP  229 (650)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  229 (650)
                      .  .+                 .....+.+.||..+.+..|||+|.+++.....||.+|.|..
T Consensus       296 ~--~~-----------------~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        296 V--VD-----------------EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             E--Ee-----------------CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            0  00                 11237889999999999999999999999999999999974

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=93.97  E-value=0.099  Score=56.85  Aligned_cols=94  Identities=26%  Similarity=0.367  Sum_probs=60.5

Q ss_pred             ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320          357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR  435 (650)
Q Consensus       357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~  435 (650)
                      +-+|+.||++|.+|+.|.++. |=+|.|-.-..+   -...|.      +++++|         ++....-..+..-...
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D---p~~fI~------NaLsPA---------~V~~V~i~~~~~k~a~  338 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD---PATYIA------NALSPA---------RVDEVRLVDPEGRHAH  338 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC---HHHHHH------HhcCCc---------eeeEEEEEcCCCcEEE
Confidence            457999999999999999988 667766431100   000000      000110         0000000011234578


Q ss_pred             EeecCCcceeeecCCCc-hhhhhhhcCceEEEec
Q 006320          436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILS  468 (650)
Q Consensus       436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~  468 (650)
                      +.||..+.+.-|||+|. |+-..+.||.+|.|.+
T Consensus       339 V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        339 VLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            99999999999999999 9999999999998853

>PRK02821 hypothetical protein; Provisional

Probab=93.96  E-value=0.06  Score=44.39  Aligned_cols=35  Identities=26%  Similarity=0.359  Sum_probs=30.2

Q ss_pred             CccEEEEEEecCcccceeecCCChHHHHHHHHhCC
Q 006320           76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGA  110 (650)
Q Consensus        76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga  110 (650)
                      +..+.+.+.|...-+|.||||+|.+|+.||.--.+
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            34578999999999999999999999999987543

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

Probab=93.68  E-value=0.091  Score=50.62  Aligned_cols=39  Identities=23%  Similarity=0.256  Sum_probs=33.1

Q ss_pred             cEEEEEEecC------cccceeecCCChHHHHHHHHhCCeEEEec
Q 006320           78 TTTYRILCHD------MKAGGVIGKSGSIIKSIRQHTGAWINVHE  116 (650)
Q Consensus        78 ~~~~rilip~------~~vg~IIGk~G~~Ik~I~~~tga~I~v~~  116 (650)
                      .+.-++.||.      .|||.|||+.|+|.|+|++.|+|+|-|--
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            3455666664      78999999999999999999999999964

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=93.56  E-value=0.13  Score=58.17  Aligned_cols=50  Identities=30%  Similarity=0.412  Sum_probs=42.2

Q ss_pred             CceEEEEEeeccc-ccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320          346 EDLVFRMLCPIDK-VGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE  400 (650)
Q Consensus       346 ~~~~~~i~vp~~~-vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~  400 (650)
                      +.++..|.+|++. -|+|||+.|.+|+.|+..|||.|.|++     +-..|+|||.
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~f  252 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF  252 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----CCCeEEecCC
Confidence            5677788999854 599999999999999999999999976     2356779976

>PRK00106 hypothetical protein; Provisional

Probab=93.54  E-value=0.13  Score=57.93  Aligned_cols=50  Identities=24%  Similarity=0.430  Sum_probs=42.3

Q ss_pred             CceEEEEEeecc-cccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320          346 EDLVFRMLCPID-KVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE  400 (650)
Q Consensus       346 ~~~~~~i~vp~~-~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~  400 (650)
                      +.++..|.+|++ +-|+|||+.|.+|+.|+.-|||.+.|++     +-..|+|+|.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~v~lS~f  273 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-----TPEVVVLSGF  273 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-----CCCeEEEeCC
Confidence            567778999985 5599999999999999999999999966     3356779986

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

Probab=93.52  E-value=0.087  Score=43.17  Aligned_cols=32  Identities=34%  Similarity=0.418  Sum_probs=29.3

Q ss_pred             CccEEEEEEecCcccceeecCCChHHHHHHHH
Q 006320           76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQH  107 (650)
Q Consensus        76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~  107 (650)
                      +..+.+++-+....+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            55788999999999999999999999999975

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

Probab=93.51  E-value=0.15  Score=41.79  Aligned_cols=33  Identities=21%  Similarity=0.452  Sum_probs=28.5

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhc
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRST  460 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~T  460 (650)
                      .+....++|.|....+|.||||+|. |+-||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            3567889999999999999999999 88888643

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=93.44  E-value=0.15  Score=56.67  Aligned_cols=93  Identities=20%  Similarity=0.336  Sum_probs=61.1

Q ss_pred             cccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEE
Q 006320          358 KVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRL  436 (650)
Q Consensus       358 ~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l  436 (650)
                      -+|+.||++|++|+.|.++. |=+|.|-.-.   ++             ...-...||.-  ..+....-+.+ .-.+.+
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s---~d-------------~~~fi~nal~p--a~v~~v~~~~~-~~~~~v  306 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWS---DD-------------PAQFIINALSP--AEVSSVVVDED-EHSADV  306 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcC---CC-------------HHHHHHHhCCC--CEEEEEEEeCC-CCEEEE
Confidence            37999999999999999988 6677664310   00             00000011100  00000000111 247889


Q ss_pred             eecCCcceeeecCCCc-hhhhhhhcCceEEEecC
Q 006320          437 LVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR  469 (650)
Q Consensus       437 ~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~  469 (650)
                      .||..+.+.-|||+|. |+-..+.||.+|.|...
T Consensus       307 ~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        307 VVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            9999999999999999 99999999999999863

>PRK01064 hypothetical protein; Provisional

Probab=93.34  E-value=0.19  Score=41.55  Aligned_cols=34  Identities=24%  Similarity=0.398  Sum_probs=29.0

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcC
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG  461 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tg  461 (650)
                      .+..+.+++.|.....|.+|||+|. |+.||.-..
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~   60 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV   60 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence            3556889999999999999999999 998887544

>PRK00106 hypothetical protein; Provisional

Probab=93.22  E-value=0.34  Score=54.66  Aligned_cols=66  Identities=20%  Similarity=0.256  Sum_probs=50.4

Q ss_pred             cEEEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhh
Q 006320          191 RVATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRE  267 (650)
Q Consensus       191 ~~~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~  267 (650)
                      .+...+.+|+ .+-|.|||+.|.+|+.+...||+++-|.           .+...|+|+| ++---+-|...+..++.+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid-----------dtp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID-----------DTPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc-----------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            3445566676 7889999999999999999999999996           2334678888 566666677766666655

>PRK01064 hypothetical protein; Provisional

Probab=93.18  E-value=0.11  Score=43.01  Aligned_cols=32  Identities=34%  Similarity=0.510  Sum_probs=29.4

Q ss_pred             CccEEEEEEecCcccceeecCCChHHHHHHHH
Q 006320           76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQH  107 (650)
Q Consensus        76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~  107 (650)
                      +..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            45689999999999999999999999999985

>PRK12704 phosphodiesterase; Provisional

Probab=93.12  E-value=0.17  Score=57.19  Aligned_cols=50  Identities=30%  Similarity=0.395  Sum_probs=42.1

Q ss_pred             CceEEEEEeecc-cccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320          346 EDLVFRMLCPID-KVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE  400 (650)
Q Consensus       346 ~~~~~~i~vp~~-~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~  400 (650)
                      +.++..|.+|++ +-|+|||+.|.+|+.|+.-|||.|.|++     +-..|+|||.
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~~  258 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF  258 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-----CCCeEEEecC
Confidence            566777889985 5599999999999999999999999976     2356779976

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=93.07  E-value=0.36  Score=54.63  Aligned_cols=66  Identities=17%  Similarity=0.221  Sum_probs=50.0

Q ss_pred             cEEEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhh
Q 006320          191 RVATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRE  267 (650)
Q Consensus       191 ~~~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~  267 (650)
                      .+...+-+|+ .+-|.|||+.|.+|+.+...||++|-|..           +...|+|++ ++---+-|...+..++.+
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            3445566676 78899999999999999999999999962           234677888 465556677777666655

>PRK12704 phosphodiesterase; Provisional

Probab=93.04  E-value=0.31  Score=55.12  Aligned_cols=66  Identities=17%  Similarity=0.202  Sum_probs=49.6

Q ss_pred             EEEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhhc
Q 006320          192 VATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRES  268 (650)
Q Consensus       192 ~~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~~  268 (650)
                      +...+.+|+ .+-|.|||+.|.+|+.+...||++|-|.           .+...|.|+| .+---+.|...+...+.+.
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid-----------dtp~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID-----------DTPEAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc-----------CCCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            344455665 7889999999999999999999999996           2335788998 4555556777776666553

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=92.96  E-value=0.28  Score=54.17  Aligned_cols=94  Identities=20%  Similarity=0.296  Sum_probs=68.5

Q ss_pred             cHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCc
Q 006320          144 SPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKT  223 (650)
Q Consensus       144 ~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga  223 (650)
                      -+|.+|...|.+.+.+.-....   ..+.+|               ..+...+.|+.+....+||.+|...|+|..|||+
T Consensus       567 ~~a~~ar~~Il~~m~k~i~~Pr---~~~~~y---------------~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGa  628 (760)
T KOG1067|consen  567 QKAREARLQILDIMEKNINSPR---GSDKEY---------------SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGA  628 (760)
T ss_pred             HhhhHHHHHHHHHHHhhcCCcc---cCcccc---------------CceeeEEeecchhhheeecCccceeeeEeeeccc
Confidence            3455566667777765432221   123333               3468889999999999999999999999999995


Q ss_pred             eEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhhc
Q 006320          224 QIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRES  268 (650)
Q Consensus       224 ~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~~  268 (650)
                      .-.+.             +..+.|.. +..+.++|+..|..++.+.
T Consensus       629 i~~vD-------------e~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  629 ISQVD-------------EGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             eeeec-------------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            44442             45677776 4889999999999998775

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=92.36  E-value=0.29  Score=53.98  Aligned_cols=71  Identities=20%  Similarity=0.189  Sum_probs=58.3

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEe-cHHHHHHHHHHHHHHHHh
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG-EIQAARDALVEVTTRLRS  505 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  505 (650)
                      +..++...|-|+.++...+||.+|. .|+|..+||+.-++            ++..++|.- ++.+.++|++.|..++..
T Consensus       593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             ccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            3457888999999999999999999 99999999955543            355677776 578999999999998887


Q ss_pred             hhhhc
Q 006320          506 YLYRD  510 (650)
Q Consensus       506 ~~~~~  510 (650)
                      ....+
T Consensus       661 ~~~~~  665 (760)
T KOG1067|consen  661 DQVQD  665 (760)
T ss_pred             ccccc
Confidence            55555

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

Probab=91.90  E-value=0.23  Score=47.90  Aligned_cols=41  Identities=20%  Similarity=0.389  Sum_probs=34.4

Q ss_pred             CcEEEEEEEcc------ceeeeeecCCchHHHHHHhhcCceEEEecC
Q 006320          190 NRVATRMVVSR------MHVGCLLGKGGKIIEQMRMETKTQIRILPR  230 (650)
Q Consensus       190 ~~~~~~i~Vp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  230 (650)
                      ..++-++.||-      ++||+|||..|++.++|++.|+|+|-|..+
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            45566677763      579999999999999999999999999753

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=91.34  E-value=4.6  Score=40.05  Aligned_cols=130  Identities=15%  Similarity=0.142  Sum_probs=82.9

Q ss_pred             EEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcC
Q 006320           82 RILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESD  161 (650)
Q Consensus        82 rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~  161 (650)
                      .+.++....-.+...+|..++.|....||+|.+..     ++..|.|+|++.           .+..+...|.+.+ .  
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~-----------~~~~i~~~i~~~l-~--   89 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKS-----------TAEYIEASINEIL-S--   89 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHH-----------HHHHHHHHHHHHH-h--
Confidence            34445677778889999999999888899999986     456799999742           1222222222222 1  


Q ss_pred             CCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeee----cCCchHHHHHHhhcCceEEEecCCCCCCCc
Q 006320          162 GGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLL----GKGGKIIEQMRMETKTQIRILPRDHSLPRC  237 (650)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~lp~~  237 (650)
                                                  ...+..+-++.-.-..-.    -.....++.|++.|++.|...+.       
T Consensus        90 ----------------------------~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~-------  134 (210)
T PF14611_consen   90 ----------------------------NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD-------  134 (210)
T ss_pred             ----------------------------hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC-------
Confidence                                        223444444432111111    12366889999999999998642       


Q ss_pred             cCCCcceEEEE-----cCHHHHHHHHHHHHHHHhhcc
Q 006320          238 VSMSEEIVQVV-----GDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       238 ~~~~er~V~I~-----G~~~~V~~A~~~I~~~l~~~~  269 (650)
                          +..+.|.     -....+..|+..+...+...+
T Consensus       135 ----~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~~~~  167 (210)
T PF14611_consen  135 ----GNKLKISWLASPENEKRADRAKRLLLWALDYNP  167 (210)
T ss_pred             ----CCeEEEEEEeeccccchHHHHHHHHHHhccCCc
Confidence                2234444     357888999999998885443

>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]

Probab=90.86  E-value=0.18  Score=48.37  Aligned_cols=62  Identities=24%  Similarity=0.249  Sum_probs=49.8

Q ss_pred             EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      +++=.=-+..+|+|+||+|. =--|++.|.++|-+.            +..|.|-|..++++-|...|+.+|-..
T Consensus       170 tL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  170 TLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             cccchhHHHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence            44434446788999999999 456999999999553            456999999999999999999887544

>PRK12705 hypothetical protein; Provisional

Probab=89.95  E-value=0.45  Score=53.38  Aligned_cols=50  Identities=30%  Similarity=0.409  Sum_probs=40.8

Q ss_pred             CceEEEEEeecccc-cceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320          346 EDLVFRMLCPIDKV-GRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE  400 (650)
Q Consensus       346 ~~~~~~i~vp~~~v-g~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~  400 (650)
                      +.++..+.+|++.. |+|||+.|.+|+.|+..||+.+.|.+     ....|+|++.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~V~ls~f  246 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD-----TPEAVVISSF  246 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC-----Cccchhhccc
Confidence            56677788997655 99999999999999999999999976     2244667765

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=87.85  E-value=0.25  Score=40.24  Aligned_cols=32  Identities=22%  Similarity=0.335  Sum_probs=27.6

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhC
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTG  109 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tg  109 (650)
                      ...+.+.|..+..|.||||.|.++++||.-.+
T Consensus        28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            45777888999999999999999999997654

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

Probab=85.06  E-value=1.7  Score=47.45  Aligned_cols=39  Identities=23%  Similarity=0.399  Sum_probs=36.3

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCC
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRD  231 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  231 (650)
                      ...+.||..+++.+|||+|.+|++|+++.|-+|.|.+.+
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            578899999999999999999999999999999998754

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=84.74  E-value=0.55  Score=38.23  Aligned_cols=34  Identities=18%  Similarity=0.229  Sum_probs=29.2

Q ss_pred             CceEEEEEeecccccceecCCchhHHHHHHHhCC
Q 006320          346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGV  379 (650)
Q Consensus       346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga  379 (650)
                      +...+.+.|..+..|.||||.|.+++.||.-.+.
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            4567888999999999999999999999876543

>PRK13764 ATPase; Provisional

Probab=84.49  E-value=1.8  Score=49.84  Aligned_cols=66  Identities=17%  Similarity=0.269  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHhhhccCC--CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCC
Q 006320          409 PAQEALLHIQTRIVDLGA--DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPA  474 (650)
Q Consensus       409 ~a~~ai~~i~~~i~~~~~--~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~  474 (650)
                      .|.+.|.+...++.....  +........+.||...++.+|||+|. |++|++..|..|+|.+.++.+.
T Consensus       456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~~  524 (602)
T PRK13764        456 LAEKEIEREIKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPG  524 (602)
T ss_pred             HHHHHHHHHHHHhcCCceEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcccccc
Confidence            355556655555542111  11245567889999999999999999 9999999999999998776553

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

Probab=84.42  E-value=1.6  Score=34.17  Aligned_cols=34  Identities=24%  Similarity=0.333  Sum_probs=27.1

Q ss_pred             EEEEEEecCcccceeecCCChHHHHHHHHhCCeE
Q 006320           79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWI  112 (650)
Q Consensus        79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I  112 (650)
                      ....+.+.....|.+||++|++|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4555566665689999999999999999988444

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.

>PRK12705 hypothetical protein; Provisional

Probab=83.82  E-value=2.1  Score=48.16  Aligned_cols=64  Identities=17%  Similarity=0.168  Sum_probs=43.2

Q ss_pred             EEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320          193 ATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE  267 (650)
Q Consensus       193 ~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~  267 (650)
                      ...+-+|+ .+-|.|||+.|.+|+.+...||+.+-|..    .|       +.|.|.+- +.--+.|...+..++.+
T Consensus       199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----tp-------~~V~ls~fdp~rreia~~~l~~Li~d  264 (508)
T PRK12705        199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD----TP-------EAVVISSFNPIRREIARLTLEKLLAD  264 (508)
T ss_pred             eeeeecCChHhhccccCccchhHHHHHHhhCCceEecC----Cc-------cchhhcccCccchHHHHHHHHHHHhc
Confidence            34455554 67899999999999999999999999962    23       23445552 44444455555555444

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

Probab=83.16  E-value=0.85  Score=36.86  Aligned_cols=36  Identities=36%  Similarity=0.515  Sum_probs=28.4

Q ss_pred             EEEEecCcc-----cceeecCCChHHHHHHHHh-CCeEEEec
Q 006320           81 YRILCHDMK-----AGGVIGKSGSIIKSIRQHT-GAWINVHE  116 (650)
Q Consensus        81 ~rilip~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~v~~  116 (650)
                      ..+.+-+..     +|..||++|+.|+.|.++. |-+|+|-+
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            345566666     9999999999999999999 89998854

>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]

Probab=82.11  E-value=0.39  Score=56.94  Aligned_cols=70  Identities=19%  Similarity=0.129  Sum_probs=57.3

Q ss_pred             EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      .-++.+|-....+|||+||+ |+.++..|||-|.+..  .-|+  ...+|.+.+.|.++.++.|...|.-.+.+-
T Consensus      1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielek--mq~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEK--MQPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred             ccccccchhhhhhhhccCcchhhhHhhccceEEehhh--cCCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence            34677888899999999999 9999999999999853  1232  256889999999999999988887666554

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

Probab=81.80  E-value=0.94  Score=36.62  Aligned_cols=36  Identities=25%  Similarity=0.558  Sum_probs=28.5

Q ss_pred             EEEEeecCCc-----ceeeecCCCc-hhhhhhhc-CceEEEec
Q 006320          433 TTRLLVPSSE-----IGCLEGRDGS-LSEMRRST-GANIQILS  468 (650)
Q Consensus       433 ~~~l~Vp~~~-----~g~IIGkgG~-Ik~I~~~T-ga~I~i~~  468 (650)
                      .+.+.|-+..     +|.+||++|+ |+.|.++. |-+|+|.-
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            3456676666     8999999999 99999999 99998863

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

Probab=80.63  E-value=2.3  Score=33.32  Aligned_cols=35  Identities=26%  Similarity=0.432  Sum_probs=28.1

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCceE
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQI  225 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I  225 (650)
                      .....+.+.....+.+||++|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35566677766789999999999999999887543

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.

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

Probab=80.53  E-value=2.4  Score=46.35  Aligned_cols=64  Identities=20%  Similarity=0.208  Sum_probs=45.4

Q ss_pred             hHHHHHHHHHHHhhhccCC--CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCC
Q 006320          408 FPAQEALLHIQTRIVDLGA--DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREE  471 (650)
Q Consensus       408 ~~a~~ai~~i~~~i~~~~~--~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~  471 (650)
                      ..|.+.+.....++.....  +......+.+.||...++.+|||+|. |++|++..|-+|.|.+.+.
T Consensus       460 ~~a~~~i~~~i~r~~p~~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         460 KLAEEEIEREIKRYLPGDVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            3455555555555443111  11123457788999999999999999 9999999999999987553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	650
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		3e-06

>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains Length = 160

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/125 (29%), Positives = 67/125 (53%), Gaps = 11/125 (8%)
Query: 348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDEL 407
           L  R+L    +VG +IG+    V+ ++ E G  + +++      E+IIT++   GP + +
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLA---GPTNAI 59
Query: 408 FPAQEALL-----HIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDG-SLSEMRRSTG 461
           F A   ++      I + + +  A     +T RL+VP+S+ G L G+ G  + E+R STG
Sbjct: 60  FKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTG 119
Query: 462 ANIQI 466
           A +Q+
Sbjct: 120 AQVQV 124

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	650
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-38
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-24
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-36
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-25
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-11
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-06
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-04
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-35
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-22
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-15
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-10
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-32
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-26
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-30
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	7e-20
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-12
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	6e-16
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-09
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	4e-08
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	9e-07
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-15
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-10
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-07
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-06
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-14
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-08
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-07
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	6e-05
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	5e-11
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-05
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-12
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-08
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-07
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	8e-06
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	9e-12
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	5e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	8e-06
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	9e-12
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-07
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-11
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	8e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	5e-06
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-11
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	6e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	4e-11
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	8e-10
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	9e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	6e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	5e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-08
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	8e-05
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
1we8_A	104	Tudor and KH domain containing protein; structural	4e-07
1we8_A	104	Tudor and KH domain containing protein; structural	4e-07
1we8_A	104	Tudor and KH domain containing protein; structural	5e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	1e-06
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	5e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	3e-05
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-05
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	6e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-04

>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 =  139 bits (351), Expect = 2e-38
 Identities = 35/196 (17%), Positives = 73/196 (37%), Gaps = 25/196 (12%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH---ELIPGDEERIIEISDTRRR 134
               ++L     AG +IGK G  I  +++ TGA I +    +  PG  ER+  I  T   
Sbjct: 5   QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI-- 62

Query: 135 DPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVAT 194
                             I ++I E         +   +      +              
Sbjct: 63  ---------EALNAVHGFIAEKIREMP-------QNVAKTEPVSILQPQTTVNPDRANQV 106

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           +++V     G ++GKGG  ++ +  ++   +++  +    P  +++   +V V G+    
Sbjct: 107 KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQK----PDGINLQNRVVTVSGEPEQN 162

Query: 255 KNAVAIISSRLRESQH 270
           + AV +I  +++E   
Sbjct: 163 RKAVELIIQKIQEDPQ 178

>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 = 98.4 bits (245), Expect = 6e-24
 Identities = 33/175 (18%), Positives = 74/175 (42%), Gaps = 18/175 (10%)

Query: 345 GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVA---DPVDGSDEQIITIS-SE 400
           G     ++L P    G +IG+    +  LQ E G  +K++   D   G+ E++  I  + 
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 401 EGPDDELFPAQEALLHIQTRIVDL----------GADKDNIITTRLLVPSSEIGCLEGRD 450
           E  +       E +  +   +               + D     +++VP+S  G + G+ 
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122

Query: 451 GS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR 504
           G+ +  +   +GA +Q+  +   P  ++  + +V + GE +  R A+  +  +++
Sbjct: 123 GATVKAIMEQSGAWVQLSQK---PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQ 174

>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 = 62.2 bits (151), Expect = 2e-11
 Identities = 20/107 (18%), Positives = 41/107 (38%), Gaps = 3/107 (2%)

Query: 188 GGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQV 247
            G++   ++++     G ++GKGG+ I Q++ ET   I++       P     +E +  +
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGT---TERVCLI 58

Query: 248 VGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVP 294
            G I  +      I+ ++RE            +  P      D    
Sbjct: 59  QGTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQ 105

>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 = 57.2 bits (138), Expect = 1e-09
 Identities = 21/110 (19%), Positives = 41/110 (37%), Gaps = 13/110 (11%)

Query: 54  NNNTSINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWIN 113
                               +       +I+  +  AG +IGK G+ +K+I + +GAW+ 
Sbjct: 79  MPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQ 138

Query: 114 V--HELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESD 161
           +         + R++ +S      PE         ++A+ LI  +I E  
Sbjct: 139 LSQKPDGINLQNRVVTVSGE----PEQ-------NRKAVELIIQKIQEDP 177

>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 =  131 bits (331), Expect = 7e-36
 Identities = 45/192 (23%), Positives = 76/192 (39%), Gaps = 34/192 (17%)

Query: 77  VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDP 136
           VT T R+L H  + G +IGK G  +K +R+ +GA IN+ E      ERII ++       
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPT---- 56

Query: 137 EGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRM 196
                  +   +A  +I D++ E                                V  R+
Sbjct: 57  -------NAIFKAFAMIIDKLEEDISSS----------------MTNSTAASRPPVTLRL 93

Query: 197 VVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKN 256
           VV     G L+GKGG  I+++R  T  Q+++           + +E  + + G   ++  
Sbjct: 94  VVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDM-----LPNSTERAITIAGIPQSIIE 148

Query: 257 AVAIISSRLRES 268
            V  I   + E+
Sbjct: 149 CVKQICVVMLET 160

>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 =  101 bits (252), Expect = 5e-25
 Identities = 40/165 (24%), Positives = 79/165 (47%), Gaps = 15/165 (9%)

Query: 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDD 405
             L  R+L    +VG +IG+    V+ ++ E G  + +++      E+IIT++   GP +
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA---GPTN 57

Query: 406 ELFPAQEALLHI-----QTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRS 459
            +F A   ++        + + +  A     +T RL+VP+S+ G L G+ G  + E+R S
Sbjct: 58  AIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRES 117

Query: 460 TGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR 504
           TGA +Q+          + T+  + I G  Q+  + + ++   + 
Sbjct: 118 TGAQVQVAGDM----LPNSTERAITIAGIPQSIIECVKQICVVML 158

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 62.1 bits (151), Expect = 1e-11
 Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 12/104 (11%)

Query: 58  SINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH-E 116
                +  ++      +     T R++    + G +IGK G  IK IR+ TGA + V  +
Sbjct: 68  DKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD 127

Query: 117 LIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILES 160
           ++P   ER I I+   +              E +  I   +LE+
Sbjct: 128 MLPNSTERAITIAGIPQS-----------IIECVKQICVVMLET 160

>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 = 7e-06
 Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 8/95 (8%)

Query: 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIV 486
           K+  +T RLL+   E+G + G+ G  + +MR  +GA I I          +  + ++ + 
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLA 53

Query: 487 GEIQAARDALVEVTTRLRSYLYRDFFQKETPPSST 521
           G   A   A   +  +L   +              
Sbjct: 54  GPTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPP 88

>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 = 42.1 bits (99), Expect = 1e-04
 Identities = 18/96 (18%), Positives = 41/96 (42%), Gaps = 7/96 (7%)

Query: 329 IEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVA-DPV 387
           +E   +    +        +  R++ P  + G +IG+    ++ ++   G  ++VA D +
Sbjct: 70  LEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDML 129

Query: 388 DGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVD 423
             S E+ ITI+   G    +    E +  I   +++
Sbjct: 130 PNSTERAITIA---GIPQSI---IECVKQICVVMLE 159

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score =  130 bits (329), Expect = 2e-35
 Identities = 40/188 (21%), Positives = 69/188 (36%), Gaps = 15/188 (7%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPE 137
           +    +       G VIG++G +IK I+   G  I          ERI +I+        
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPP----- 56

Query: 138 GRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMV 197
                   AQ A  +I D +L S   G   G      G G G G       G       +
Sbjct: 57  ------DRAQHAAEIITD-LLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFI 109

Query: 198 VSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNA 257
           V     G ++GKGG+ I+ +  ++  +I +     + P     + ++  + G    +  A
Sbjct: 110 VPTGKTGLIIGKGGETIKSISQQSGARIEL---QRNPPPNADPNMKLFTIRGTPQQIDYA 166

Query: 258 VAIISSRL 265
             +I  ++
Sbjct: 167 RQLIEEKI 174

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 93.8 bits (233), Expect = 2e-22
 Identities = 32/178 (17%), Positives = 65/178 (36%), Gaps = 26/178 (14%)

Query: 347 DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDE 406
             +  +  P   VG VIG +  +++ +QN+ GV ++       + E+I  I+   GP D 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQIT---GPPDR 58

Query: 407 LFPAQEALLHI--------------------QTRIVDLGADKDNIITTRLLVPSSEIGCL 446
              A E +  +                    + +          +     +VP+ + G +
Sbjct: 59  AQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLI 118

Query: 447 EGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRL 503
            G+ G  +  + + +GA I++      P       +L  I G  Q    A   +  ++
Sbjct: 119 IGKGGETIKSISQQSGARIELQ--RNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 73.7 bits (181), Expect = 2e-15
 Identities = 42/230 (18%), Positives = 80/230 (34%), Gaps = 64/230 (27%)

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
            + + R  VG ++G+ G++I++++ +   +I+  P D + P      E I Q+ G  +  
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP------ERIAQITGPPDRA 59

Query: 255 KNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSN 314
           ++A  II+  LR  Q                              A  P   G    G  
Sbjct: 60  QHAAEIITDLLRSVQ------------------------------AGNPGGPGPGGRGRG 89

Query: 315 YRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQ 374
               N+   P G   E                   F  + P  K G +IG+    ++ + 
Sbjct: 90  RGQGNWNMGPPGGLQE-------------------FNFIVPTGKTGLIIGKGGETIKSIS 130

Query: 375 NEIGVDLKVA---DPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRI 421
            + G  +++     P    + ++ TI    G   ++     A   I+ +I
Sbjct: 131 QQSGARIELQRNPPPNADPNMKLFTIR---GTPQQI---DYARQLIEEKI 174

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 59.5 bits (144), Expect = 2e-10
 Identities = 23/115 (20%), Positives = 35/115 (30%), Gaps = 14/115 (12%)

Query: 46  NNNTNNIMNNNTSINNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIR 105
            +                 R   N           +  +    K G +IGK G  IKSI 
Sbjct: 71  RSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSIS 130

Query: 106 QHTGAWINVHELIP---GDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI 157
           Q +GA I +    P       ++  I  T ++              A  LI ++I
Sbjct: 131 QQSGARIELQRNPPPNADPNMKLFTIRGTPQQ-----------IDYARQLIEEKI 174

>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 =  121 bits (305), Expect = 3e-32
 Identities = 33/195 (16%), Positives = 68/195 (34%), Gaps = 37/195 (18%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHEL-IPGDEERIIEISDTRRRDP 136
               ++       G +IGK G  IK + +   A I +     P  + R++ I+      P
Sbjct: 2   QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP----P 57

Query: 137 EGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRM 196
           E          +A   I+ ++ E +  G                          ++ T +
Sbjct: 58  EA-------QFKAQGRIYGKLKEENFFGP---------------------KEEVKLETHI 89

Query: 197 VVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKN 256
            V     G ++GKGGK + +++  T  ++ +              + IV+++G     + 
Sbjct: 90  RVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQT----PDENDQVIVKIIGHFYASQM 145

Query: 257 AVAIISSRLRESQHR 271
           A   I   L + + +
Sbjct: 146 AQRKIRDILAQVKQQ 160

>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 =  104 bits (261), Expect = 3e-26
 Identities = 36/162 (22%), Positives = 73/162 (45%), Gaps = 8/162 (4%)

Query: 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP-VDGSDEQIITISSEEGPD 404
           E  + ++  P   VG +IG+    ++ L       +K+A P    S  +++ I+   GP 
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIIT---GPP 57

Query: 405 DELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGAN 463
           +  F AQ  +          G  ++  + T + VP+S  G + G+ G  ++E++  T A 
Sbjct: 58  EAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAE 117

Query: 464 IQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS 505
           + +  R++ P        +V+I+G   A++ A  ++   L  
Sbjct: 118 VVV-PRDQTPD--ENDQVIVKIIGHFYASQMAQRKIRDILAQ 156

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

 Score = 58.2 bits (141), Expect = 3e-10
 Identities = 22/98 (22%), Positives = 35/98 (35%), Gaps = 13/98 (13%)

Query: 66  ANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV--HELIPGDEE 123
              N   P   V     I      AG VIGK G  +  ++  T A + V   +    +++
Sbjct: 72  KEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQ 131

Query: 124 RIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESD 161
            I++I         G    F  +Q A   I D + +  
Sbjct: 132 VIVKII--------G---HFYASQMAQRKIRDILAQVK 158

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

 Score =  116 bits (292), Expect = 2e-30
 Identities = 40/193 (20%), Positives = 78/193 (40%), Gaps = 34/193 (17%)

Query: 79  TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHE--LIPGDEERIIEISDTRRRDP 136
           T   I+    KAG VIGK G  IK +++  G  + + +      + ++ + I        
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDP---- 57

Query: 137 EGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRM 196
                     Q+A  ++ D + E D GG                G     G        +
Sbjct: 58  -------YKVQQACEMVMDILRERDQGGF---------------GDRNEYGSRIGGGIDV 95

Query: 197 VVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKN 256
            V R  VG ++G+ G++I++++ +   +I+    D + P      E+I  ++G  +  ++
Sbjct: 96  PVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP------EKIAHIMGPPDRCEH 149

Query: 257 AVAIISSRLRESQ 269
           A  II+  L+  +
Sbjct: 150 AARIINDLLQSLR 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 = 86.0 bits (213), Expect = 7e-20
 Identities = 31/166 (18%), Positives = 62/166 (37%), Gaps = 17/166 (10%)

Query: 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD--PVDGSDEQIITISSEEGPDDE 406
           V  ++ P  K G VIG+    ++ LQ   GV + +      + + ++ + I    G   +
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII---GDPYK 59

Query: 407 LFPAQEALLHI------QTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRS 459
           +  A E ++ I                        + VP   +G + GR G  + +++  
Sbjct: 60  VQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQND 119

Query: 460 TGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS 505
            G  IQ    +      +G +++  I+G       A   +   L+S
Sbjct: 120 AGVRIQFKQDDG-----TGPEKIAHIMGPPDRCEHAARIINDLLQS 160

>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 = 64.8 bits (158), Expect = 2e-12
 Identities = 19/105 (18%), Positives = 34/105 (32%), Gaps = 11/105 (10%)

Query: 59  INNSNNRANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELI 118
           +   +     +  +    +     +       G VIG+SG +IK I+   G  I   +  
Sbjct: 71  LRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD 130

Query: 119 PGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGG 163
               E+I  I     R            + A  +I+D +     G
Sbjct: 131 GTGPEKIAHIMGPPDR-----------CEHAARIINDLLQSLRSG 164

>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 = 72.3 bits (178), Expect = 6e-16
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 11/85 (12%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPE 137
             T ++      AG +IGK G  IK IR  +GA I + E + G E+RII I+ T     +
Sbjct: 6   IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT----QD 61

Query: 138 GRMPSFSPAQEALFLIHDRILESDG 162
                    Q A +L+ + + +  G
Sbjct: 62  Q-------IQNAQYLLQNSVKQYSG 79

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 19/85 (22%), Positives = 44/85 (51%), Gaps = 6/85 (7%)

Query: 187 GGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQ 246
             G  + T++ + +   G ++GKGG+ I+Q+R E+   I+I   D  L       + I+ 
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGS---EDRIIT 55

Query: 247 VVGDINNVKNAVAIISSRLRESQHR 271
           + G  + ++NA  ++ + +++   +
Sbjct: 56  ITGTQDQIQNAQYLLQNSVKQYSGK 80

>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 = 50.0 bits (120), Expect = 4e-08
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEI 489
           IITT++ +P    G + G+ G  + ++R  +GA+I+I    E        D ++ I G  
Sbjct: 6   IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-----GSEDRIITITGTQ 60

Query: 490 QAARDALVEVTTRLRSYLYRDF 511
              ++A   +   ++ Y  + F
Sbjct: 61  DQIQNAQYLLQNSVKQYSGKFF 82

>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 = 46.1 bits (110), Expect = 9e-07
 Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 6/77 (7%)

Query: 345 GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPD 404
           G  +  ++  P D  G +IG+    ++ +++E G  +K+ +P++GS+++IITI+   G  
Sbjct: 4   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT---GTQ 60

Query: 405 DELFPAQEALLHIQTRI 421
           D+    Q A   +Q  +
Sbjct: 61  DQ---IQNAQYLLQNSV 74

>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 = 71.2 bits (175), Expect = 2e-15
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 11/85 (12%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPE 137
             T ++      AG +IGK G  IK IR  +GA I + E + G E+RII I+ T     +
Sbjct: 13  IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT----QD 68

Query: 138 GRMPSFSPAQEALFLIHDRILESDG 162
                    Q A +L+ + + +  G
Sbjct: 69  Q-------IQNAQYLLQNSVKQYSG 86

>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 = 55.4 bits (134), Expect = 6e-10
 Identities = 22/97 (22%), Positives = 47/97 (48%), Gaps = 10/97 (10%)

Query: 175 GGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSL 234
           G     G  G    G  + T++ + +   G ++GKGG+ I+Q+R E+   I+I   D  L
Sbjct: 1   GSHMSYGDLG----GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPL 53

Query: 235 PRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHR 271
                  + I+ + G  + ++NA  ++ + +++   +
Sbjct: 54  E---GSEDRIITITGTQDQIQNAQYLLQNSVKQYSGK 87

>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 = 48.5 bits (116), Expect = 1e-07
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 425 GADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELV 483
           G     IITT++ +P    G + G+ G  + ++R  +GA+I+I    E        D ++
Sbjct: 7   GDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-----GSEDRII 61

Query: 484 QIVGEIQAARDALVEVTTRLRSYLYRDF 511
            I G     ++A   +   ++ Y  + F
Sbjct: 62  TITGTQDQIQNAQYLLQNSVKQYSGKFF 89

>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 = 45.4 bits (108), Expect = 2e-06
 Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 6/77 (7%)

Query: 345 GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPD 404
           G  +  ++  P D  G +IG+    ++ +++E G  +K+ +P++GS+++IITI+   G  
Sbjct: 11  GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT---GTQ 67

Query: 405 DELFPAQEALLHIQTRI 421
           D++   Q A   +Q  +
Sbjct: 68  DQI---QNAQYLLQNSV 81

>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 = 67.7 bits (166), Expect = 2e-14
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 11/88 (12%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPE 137
            TT+ +   +   G +IG+ G+ I  IRQ +GA I +   + G   R + I+ +      
Sbjct: 5   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS----AA 60

Query: 138 GRMPSFSPAQEALFLIHDRILESDGGGG 165
                      A +LI+ R+    G G 
Sbjct: 61  S-------ISLAQYLINARLSSEKGMGC 81

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 188 GGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQV 247
            G++    + +    +GC++G+ G  I ++R  +  QI+I             S   V +
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI------ANPVEGSSGRQVTI 55

Query: 248 VGDINNVKNAVAIISSRLRESQ 269
            G   ++  A  +I++RL   +
Sbjct: 56  TGSAASISLAQYLINARLSSEK 77

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQ 490
            T  L +P++ IGC+ GR G+ ++E+R+ +GA I+I +  E       +   V I G   
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE-----GSSGRQVTITGSAA 60

Query: 491 AARDALVEVTTRLRS 505
           +   A   +  RL S
Sbjct: 61  SISLAQYLINARLSS 75

>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 = 41.1 bits (97), Expect = 6e-05
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 345 GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPD 404
           G      +  P + +G +IG     +  ++   G  +K+A+PV+GS  + +TI+   G  
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT---GSA 59

Query: 405 DELFPAQEALLHIQTRI 421
             +     A   I  R+
Sbjct: 60  ASI---SLAQYLINARL 73

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 13/83 (15%)

Query: 77  VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDP 136
           VT T R+L H  + G +IGK G  +K +R+ +GA IN+ E      ERII ++       
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP----T 56

Query: 137 EGRMPSFSPAQEALFLIHDRILE 159
                      +A  +I D++ E
Sbjct: 57  NA-------IFKAFAMIIDKLEE 72

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
           R+++    VG ++GK G+ +++MR E+  +I I           +  E I+ + G  N +
Sbjct: 8   RLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--------NCPERIITLAGPTNAI 59

Query: 255 KNAVAIISSRLRE 267
             A A+I  +L E
Sbjct: 60  FKAFAMIIDKLEE 72

>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 = 57.7 bits (140), Expect = 5e-11
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIV 486
           K+  +T RLL+   E+G + G+ G  + +MR  +GA I I          +  + ++ + 
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLA 53

Query: 487 GEIQAARDALVEVTTRLR 504
           G   A   A   +  +L 
Sbjct: 54  GPTNAIFKAFAMIIDKLE 71

>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 = 41.1 bits (97), Expect = 4e-05
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDD 405
             L  R+L    +VG +IG+    V+ ++ E G  + +++      E+IIT++   GP +
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA---GPTN 57

Query: 406 ELFPAQEALLHIQTRIVD 423
            +    +A   I  ++ +
Sbjct: 58  AI---FKAFAMIIDKLEE 72

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

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 11/82 (13%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPE 137
           TT++ +   +   G +IG+ G+ I  IRQ +GA I +   + G  +R + I+ +      
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS----AA 59

Query: 138 GRMPSFSPAQEALFLIHDRILE 159
                      A +LI+ R+  
Sbjct: 60  S-------ISLAQYLINVRLSS 74

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

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVV 248
               +  + +    +GC++G+ G  I ++R  +  QI+I    + +      ++  V + 
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKI---ANPVE---GSTDRQVTIT 55

Query: 249 GDINNVKNAVAIISSRLRE 267
           G   ++  A  +I+ RL  
Sbjct: 56  GSAASISLAQYLINVRLSS 74

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIV 486
           K    +  L +P+  IGC+ GR G+ ++E+R+ +GA I+I +  E       TD  V I 
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVE-----GSTDRQVTIT 55

Query: 487 GEIQAARDALVEVTTRLRS 505
           G   +   A   +  RL S
Sbjct: 56  GSAASISLAQYLINVRLSS 74

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

 Score = 43.1 bits (102), Expect = 8e-06
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 345 GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPD 404
            +     +  P D +G +IG     +  ++   G  +K+A+PV+GS ++ +TI+   G  
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTIT---GSA 58

Query: 405 DELFPAQEALLHIQTRI 421
             +     A   I  R+
Sbjct: 59  ASI---SLAQYLINVRL 72

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

 Score = 61.0 bits (148), Expect = 9e-12
 Identities = 25/111 (22%), Positives = 38/111 (34%), Gaps = 13/111 (11%)

Query: 77  VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDP 136
           +     +       G VIG+SG +IK I+   G  I   +      E+I  I       P
Sbjct: 9   IGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP----P 64

Query: 137 EGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRG 187
           +         + A  +I+D +     G    G         GG G G  +G
Sbjct: 65  DR-------CEHAARIINDLLQSLRSGPP--GPPGGPGMPPGGRGRGRGQG 106

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

 Score = 55.9 bits (135), Expect = 5e-10
 Identities = 22/102 (21%), Positives = 47/102 (46%), Gaps = 8/102 (7%)

Query: 184 GFRGGGNRVAT--RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMS 241
           G    G+R+     + V R  VG ++G+ G++I++++ +   +I+    D + P      
Sbjct: 1   GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP------ 54

Query: 242 EEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSP 283
           E+I  ++G  +  ++A  II+  L+  +        G    P
Sbjct: 55  EKIAHIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPP 96

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

 Score = 44.0 bits (104), Expect = 8e-06
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 6/95 (6%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
              + VP   +G + GR G  + +++   G  IQ    +      +G +++  I+G    
Sbjct: 12  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAHIMGPPDR 66

Query: 492 ARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGS 526
              A   +   L+S           P    G  G 
Sbjct: 67  CEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGR 101

>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 = 60.5 bits (147), Expect = 9e-12
 Identities = 18/102 (17%), Positives = 36/102 (35%), Gaps = 13/102 (12%)

Query: 66  ANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV--HELIPGDEE 123
           ++ +             I+    KAG VIGK G  IK +++  G  + +          +
Sbjct: 2   SSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGAD 61

Query: 124 RIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGG 165
           + + I+      P          Q+A  ++ + I +   G  
Sbjct: 62  KPLRITGD----PYK-------VQQAKEMVLELIRDQGSGPS 92

>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 = 54.7 bits (132), Expect = 1e-09
 Identities = 16/91 (17%), Positives = 41/91 (45%), Gaps = 4/91 (4%)

Query: 178 GGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237
           G  G  G   G       +++     G ++GKGG+ I+Q++     ++ ++         
Sbjct: 1   GSSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ---- 56

Query: 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRES 268
            + +++ +++ GD   V+ A  ++   +R+ 
Sbjct: 57  NTGADKPLRITGDPYKVQQAKEMVLELIRDQ 87

>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 = 47.8 bits (114), Expect = 3e-07
 Identities = 14/79 (17%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 425 GADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELV 483
             D        +++P+S+ G + G+ G  + +++   G  + ++         +G D+ +
Sbjct: 8   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPL 64

Query: 484 QIVGE---IQAARDALVEV 499
           +I G+   +Q A++ ++E+
Sbjct: 65  RITGDPYKVQQAKEMVLEL 83

>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 = 60.1 bits (146), Expect = 1e-11
 Identities = 21/100 (21%), Positives = 34/100 (34%), Gaps = 11/100 (11%)

Query: 66  ANSNPKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERI 125
           ++ +          T      D   G +IG+ G  I  I+Q +G  I +     G  ER 
Sbjct: 2   SSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERS 61

Query: 126 IEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGG 165
             ++ T    PE         Q A  L+   + +   G  
Sbjct: 62  CMLTGT----PES-------VQSAKRLLDQIVEKGRSGPS 90

>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 = 52.0 bits (125), Expect = 8e-09
 Identities = 20/92 (21%), Positives = 42/92 (45%), Gaps = 6/92 (6%)

Query: 178 GGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237
           G  G  G +   + +     V    VG ++G+GG+ I +++ E+  +I+I P    LP  
Sbjct: 1   GSSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP-- 58

Query: 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQ 269
               E    + G   +V++A  ++   + + +
Sbjct: 59  ----ERSCMLTGTPESVQSAKRLLDQIVEKGR 86

>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 = 44.3 bits (105), Expect = 5e-06
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG- 487
           +++T    VP   +G + GR G  +S +++ +G  IQI             +    + G 
Sbjct: 13  SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLTGT 67

Query: 488 --EIQAARDALVEVTTRLRS 505
              +Q+A+  L ++  + RS
Sbjct: 68  PESVQSAKRLLDQIVEKGRS 87

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 14/86 (16%)

Query: 77  VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH---ELIPGDEERIIEISDTRR 133
           +     +   +   G ++GK G  +   ++ TGA I +    E +PG   R + I+ +  
Sbjct: 1   MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-- 58

Query: 134 RDPEGRMPSFSPAQEALFLIHDRILE 159
             P          Q A +LI  R+  
Sbjct: 59  --PAA-------TQAAQYLISQRVTY 75

>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 = 55.4 bits (134), Expect = 4e-10
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINN 253
             M V    VG +LGKGGK + + +  T  +I+I  +   LP         V + G    
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSPAA 61

Query: 254 VKNAVAIISSRLRE 267
            + A  +IS R+  
Sbjct: 62  TQAAQYLISQRVTY 75

>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 = 49.2 bits (118), Expect = 6e-08
 Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
              + VP + +G + G+ G  L E +  TGA IQI  + E        +  V I G   A
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--TRNRRVTITGSPAA 61

Query: 492 ARDALVEVTTRLRS 505
            + A   ++ R+  
Sbjct: 62  TQAAQYLISQRVTY 75

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

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 13/84 (15%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV--HELIPGDEERIIEISDTRRRD 135
            T   I+    KAG VIGK G  IK +++  G  + +        + ++ + I       
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD---- 68

Query: 136 PEGRMPSFSPAQEALFLIHDRILE 159
           P          Q+A  ++ D + E
Sbjct: 69  PYK-------VQQACEMVMDILRE 85

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

 Score = 54.7 bits (132), Expect = 8e-10
 Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 4/89 (4%)

Query: 179 GVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCV 238
           G       GG N     +++     G ++GKGG+ I+Q++     ++ +  +D S     
Sbjct: 1   GQFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMIL-IQDGSQN--- 56

Query: 239 SMSEEIVQVVGDINNVKNAVAIISSRLRE 267
           +  ++ ++++GD   V+ A  ++   LRE
Sbjct: 57  TNVDKPLRIIGDPYKVQQACEMVMDILRE 85

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

 Score = 46.2 bits (110), Expect = 9e-07
 Identities = 11/79 (13%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 425 GADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELV 483
                N     +++P+ + G + G+ G  + +++   G  + ++         +  D+ +
Sbjct: 7   ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPL 63

Query: 484 QIVGE---IQAARDALVEV 499
           +I+G+   +Q A + ++++
Sbjct: 64  RIIGDPYKVQQACEMVMDI 82

>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 = 58.1 bits (141), Expect = 6e-11
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 14/86 (16%)

Query: 77  VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH---ELIPGDEERIIEISDTRR 133
           +     I   +   G ++GK G  +   ++ TGA I +    E +PG   R + I+ +  
Sbjct: 1   MKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-- 58

Query: 134 RDPEGRMPSFSPAQEALFLIHDRILE 159
             P          Q A +LI  R+  
Sbjct: 59  --PAA-------TQAAQYLISQRVTY 75

>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 = 56.2 bits (136), Expect = 3e-10
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINN 253
             + V    VG +LGKGGK + + +  T  +I+I  +   LP         V + G    
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT---RNRRVTITGSPAA 61

Query: 254 VKNAVAIISSRLRESQHR 271
            + A  +IS R+   Q  
Sbjct: 62  TQAAQYLISQRVTYEQGV 79

>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 = 48.9 bits (117), Expect = 1e-07
 Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
              + VP + +G + G+ G  L E +  TGA IQI  + E        +  V I G   A
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--TRNRRVTITGSPAA 61

Query: 492 ARDALVEVTTRLRS 505
            + A   ++ R+  
Sbjct: 62  TQAAQYLISQRVTY 75

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

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 24/111 (21%), Positives = 37/111 (33%), Gaps = 14/111 (12%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIP---GDEERIIEISDTRRR 134
                      K G VIG+ G  +K+I Q TGA++ +   +P       ++  I  +   
Sbjct: 6   GGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGS--- 62

Query: 135 DPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGF 185
            P+           A  LI ++I       G         G  G    G F
Sbjct: 63  -PQQ-------IDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPGPF 105

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

 Score = 47.6 bits (113), Expect = 5e-07
 Identities = 12/91 (13%), Positives = 31/91 (34%), Gaps = 3/91 (3%)

Query: 188 GGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQV 247
                     +     G ++G+GG+ ++ +  +T   + I      LP     + ++  +
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI---SRQLPPNGDPNFKLFII 59

Query: 248 VGDINNVKNAVAIISSRLRESQHRDRSHFHG 278
            G    + +A  +I  ++            G
Sbjct: 60  RGSPQQIDHAKQLIEEKIEGPLCPVGPGPGG 90

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

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 12/96 (12%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
                +P+ + G + GR G  +  + + TGA ++I    ++P       +L  I G  Q 
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFIIRGSPQQ 65

Query: 492 ARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSA 527
              A           L  +  +    P   GP G  
Sbjct: 66  IDHAK---------QLIEEKIEGPLCPVGPGPGGPG 92

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 55.9 bits (134), Expect = 5e-09
 Identities = 29/202 (14%), Positives = 58/202 (28%), Gaps = 33/202 (16%)

Query: 70  PKDPSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEIS 129
             +          +     +   +IGK G   K I + T   I +       E   + I+
Sbjct: 25  EDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWIT 79

Query: 130 DTRR-RDPEGRMPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGG 188
            T+   DP           +A  ++            F    E EY     +        
Sbjct: 80  STKETEDPLA-------VWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNE 132

Query: 189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVV 248
            N +           G ++G+ G+  + +   +   + +  +              V ++
Sbjct: 133 KNALPRV-------RGRIIGRKGRTRQIIEEMSGASVSVYGK-------------TVAII 172

Query: 249 GDINNVKNAVAIISSRLRESQH 270
           G+   ++ A   I    R S H
Sbjct: 173 GNPIQIEIAKTAIEKLARGSPH 194

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

 Score = 56.8 bits (136), Expect = 2e-08
 Identities = 66/471 (14%), Positives = 139/471 (29%), Gaps = 141/471 (29%)

Query: 234 LPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDY- 292
           +P+ +   EEI  ++   + V   + +  + L   Q      F   +          +Y 
Sbjct: 41  MPKSILSKEEIDHIIMSKDAVSGTLRLFWT-LLSKQEEMVQKFVEEVL-------RINYK 92

Query: 293 --VPHMNNTARRPSMDGARFSGSNYRSNNYG----------PRPSGYSIEAGAAPMSDSV 340
             +  +    R+PSM    +     R   Y            R   Y ++   A +    
Sbjct: 93  FLMSPIKTEQRQPSMMTRMYI--EQRDRLYNDNQVFAKYNVSRLQPY-LKLRQALLELRP 149

Query: 341 QPF---YGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQI--I 395
                  G      +L      G   G++   +++  +               D +I  +
Sbjct: 150 AKNVLIDG------VL------G--SGKTWVALDVCLSY--------KVQCKMDFKIFWL 187

Query: 396 TISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGSLSE 455
            + +   P+  L   Q+ L  I     +  +  D+    +L + S +           +E
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDP---NWTSRSDHSSNIKLRIHSIQ-----------AE 233

Query: 456 MRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAAR--DAL-----VEVTTR------ 502
           +RR       +L  +    C      L+ ++  +Q A+  +A      + +TTR      
Sbjct: 234 LRR-------LLKSKPYENC------LL-VLLNVQNAKAWNAFNLSCKILLTTRFKQVTD 279

Query: 503 -LRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPA---REVQTVTDP------PA 552
            L +             + T     +L+      +D  P    REV T  +P        
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLL---LKYLDCRPQDLPREVLTT-NPRRLSIIAE 335

Query: 553 ATHQSVQIPATSQPSKEAAGS-VSETVK-----QNESERR----------EDVPTVINRV 596
           +        AT    K      ++  ++        +E R                    
Sbjct: 336 SIRDG---LATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH------ 386

Query: 597 PLPLVTRSTLEVV---LPDYAVPKLITK--SKTLLTR-FSEVSLLLHLINL 641
               +    L ++   +    V  ++ K    +L+ +   E ++ +  I L
Sbjct: 387 ----IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYL 433

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

 Score = 42.9 bits (100), Expect = 3e-04
 Identities = 78/608 (12%), Positives = 161/608 (26%), Gaps = 202/608 (33%)

Query: 3   RSRSKRNYYY-----DHQDYDGDTMGRTKPRYNHYYQPNNNYRHRGNNNNNTNNIMNNNT 57
            S+ +             +Y    M   K       QP+   R         + + N+N 
Sbjct: 72  LSKQEEMVQKFVEEVLRINYKF-LMSPIKTEQR---QPSMMTR---MYIEQRDRLYNDNQ 124

Query: 58  SINNSN-NRANSNPKDPSLMVTTTYR-------ILCHDMKAGGVIGKS---GSIIKSIRQ 106
                N +R       P L +            +L   +   G  GK+     +  S + 
Sbjct: 125 VFAKYNVSR-----LQPYLKLRQALLELRPAKNVLIDGV--LG-SGKTWVALDVCLSYKV 176

Query: 107 HTGA-----WINVHELIPGDEERIIEI----------SDTRRRDPEGRMP-SFSPAQEAL 150
                    W+N+        E ++E+          + T R D    +       Q  L
Sbjct: 177 QCKMDFKIFWLNLKNC--NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234

Query: 151 -FLIHDR-------ILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMH 202
             L+  +       +L  +                              V      +  +
Sbjct: 235 RRLLKSKPYENCLLVLL-N------------------------------VQNAKAWNAFN 263

Query: 203 VGC---LLGKGGKIIEQMRMETKTQIRI------LPRDHS---LPRCVSMS-----EEIV 245
           + C   L  +  ++ + +   T T I +      L  D     L + +         E++
Sbjct: 264 LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVL 323

Query: 246 QVVGDINNVKN--AVAIISSRLRESQHRDRSHF-----HGRLHS----------PD---- 284
                     N   ++II+  +R+                +L +          P     
Sbjct: 324 TT--------NPRRLSIIAESIRD--GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373

Query: 285 RF-----FPDDDYVPHM-------NNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAG 332
            F     FP   ++P +       +       +   +     Y      P+ S  SI   
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL--HKYSLVEKQPKESTISI--- 428

Query: 333 AAPMSDSVQPFYGEDLVFRMLCPIDKVG---RVIGESEGIVELLQNEIGVDLKVADPVDG 389
                          +   +   ++      R I +   I +   ++   DL +   +D 
Sbjct: 429 -------------PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD---DL-IPPYLDQ 471

Query: 390 SDEQIIT---ISSEEGPDDELFPA--------QEALLHIQTRIVDLGADKDNIITTRL-- 436
                I     + E      LF          ++ + H  T     G+  + +   +   
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYK 531

Query: 437 --LVPSSEIGCLEGRDGSLSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARD 494
             +  +      E    ++ +       N+ I S+         TD L++I   + A  +
Sbjct: 532 PYICDNDPK--YERLVNAILDFLPKIEENL-ICSKY--------TD-LLRIA--LMAEDE 577

Query: 495 ALVEVTTR 502
           A+ E   +
Sbjct: 578 AIFEEAHK 585

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 17/96 (17%), Positives = 38/96 (39%), Gaps = 8/96 (8%)

Query: 176 GGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLP 235
           G  G  G        + +  + + + H   ++GK G+ ++ + ++T T+I+I PR     
Sbjct: 1   GSSGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI-PRPDD-- 57

Query: 236 RCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHR 271
                    +++ G    ++ A   +     E   R
Sbjct: 58  -----PSNQIKITGTKEGIEKARHEVLLISAEQDKR 88

>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 = 40.9 bits (96), Expect = 8e-05
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 79  TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR 132
            +  +         VIGK+G  ++ +   T   I +    P D    I+I+ T+
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTK 68

>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 = 39.3 bits (92), Expect = 3e-04
 Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 20/102 (19%)

Query: 423 DLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDE 481
           D+ A      +  + +P      + G++G  L ++   T   IQI   ++          
Sbjct: 8   DIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-------PSN 60

Query: 482 LVQIVGE---IQAARDALVEVTTRLRSYLYRDFFQKETPPSS 520
            ++I G    I+ AR  ++ ++             K + PSS
Sbjct: 61  QIKITGTKEGIEKARHEVLLIS---------AEQDKRSGPSS 93

>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 = 47.9 bits (114), Expect = 4e-07
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 4/97 (4%)

Query: 178 GGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237
           G  G  G       V  ++ V +  VG ++G+GG+ I  +   +  +I            
Sbjct: 1   GSSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---- 56

Query: 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRS 274
             +   ++++ G    V  A  +I  ++ E +   + 
Sbjct: 57  TLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKR 93

>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 = 47.9 bits (114), Expect = 4e-07
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 13/85 (15%)

Query: 79  TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGD--EERIIEISDTRRRDP 136
              ++       G +IG+ G  I+SI + +GA I   +   G     R+I+IS T++   
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE-- 72

Query: 137 EGRMPSFSPAQEALFLIHDRILESD 161
                       A  LI +++ E +
Sbjct: 73  ---------VAAAKHLILEKVSEDE 88

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 41.7 bits (98), Expect = 5e-05
 Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 7/98 (7%)

Query: 427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQI 485
            ++  +  +L VP   +G + GR G  +  + +++GA I     ++          L++I
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIKI 66

Query: 486 VGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGP 523
            G  +    A   +  ++      +  +K    S++GP
Sbjct: 67  SGTQKEVAAAKHLILEKVSE---DEELRKRIAHSASGP 101

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 48.5 bits (115), Expect = 1e-06
 Identities = 35/191 (18%), Positives = 56/191 (29%), Gaps = 32/191 (16%)

Query: 80  TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGR 139
              +     + G VIG  G +   I + TG  I V       E  ++ +       PE  
Sbjct: 5   RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVE------PEAE 53

Query: 140 MPSFSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVS 199
                   +A  ++    L       F   EE++      V      G       R+   
Sbjct: 54  GIPPVNLMKAAEVVKAISLGFPPEKAFRLLEEDQI--LVVVDLKQVVGDSQNHLKRI--- 108

Query: 200 RMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVA 259
               G ++G+GG+    +   T T I +              E  V ++GD      A  
Sbjct: 109 ---KGRIIGEGGRARRTIEEMTDTYINV-------------GEYEVAIIGDYERAMAAKQ 152

Query: 260 IISSRLRESQH 270
            I        H
Sbjct: 153 AIEMLAEGRMH 163

>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 = 45.2 bits (107), Expect = 3e-06
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG 249
                 + V   +   ++G+ G +I Q+R+E    I+   +D       +  ++ + + G
Sbjct: 15  RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG-----NQPQDQITITG 69

Query: 250 DINNVKNAVAIISSRLRESQ 269
              N + A   I   + E +
Sbjct: 70  YEKNTEAARDAILRIVGELE 89

>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 = 44.4 bits (105), Expect = 5e-06
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG 249
             V+  + +       ++G  GK I ++  E K  IR        P+  +     V V G
Sbjct: 15  QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-------PQSGAPDPNCVTVTG 67

Query: 250 DINNVKNAVAIISSRLRE 267
              NV+ A+  I +   E
Sbjct: 68  LPENVEEAIDHILNLEEE 85

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 43.5 bits (102), Expect = 3e-05
 Identities = 25/181 (13%), Positives = 51/181 (28%), Gaps = 50/181 (27%)

Query: 89  KAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQE 148
             G  IG  G+ I+  R+  G    V  +   ++     I                  ++
Sbjct: 14  LMGLAIGTHGANIQQARKVPG----VTAIDLDEDTCTFHIY----------GEDQDAVKK 59

Query: 149 ALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLG 208
           A                                    R         + V R  VG ++G
Sbjct: 60  A------------------------------------RSFLEFAEDVIQVPRNLVGKVIG 83

Query: 209 KGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES 268
           K GK+I+++  ++      +  ++               VG  +++ NA  ++   L   
Sbjct: 84  KNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYL 143

Query: 269 Q 269
           +
Sbjct: 144 K 144

>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 = 41.5 bits (97), Expect = 4e-05
 Identities = 21/93 (22%), Positives = 31/93 (33%), Gaps = 14/93 (15%)

Query: 73  PSLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR 132
            S    TT ++       G V+G  G+ IK I+Q T  +I        D+E +  ++   
Sbjct: 4   GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVT---PGRDKEPVFAVTGM- 59

Query: 133 RRDPEGRMPSFSPAQEALFLIHDRILESDGGGG 165
              PE           A   I   I    G   
Sbjct: 60  ---PEN-------VDRAREEIEAHITLRSGPSS 82

>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 = 40.3 bits (94), Expect = 1e-04
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 183 GGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSE 242
           G     G +   ++ V    VG ++G  G  I++++  T T I    RD          E
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---------KE 51

Query: 243 EIVQVVGDINNVKNAVAIISSRLRE 267
            +  V G   NV  A   I + +  
Sbjct: 52  PVFAVTGMPENVDRAREEIEAHITL 76

>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 = 41.7 bits (98), Expect = 6e-05
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 8/78 (10%)

Query: 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDI 251
           V   + V       ++G+ G  I +M  E +  I +   +        +  +I+ + G  
Sbjct: 17  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE--------LQSDIIAITGLA 68

Query: 252 NNVKNAVAIISSRLRESQ 269
            N+  A A +  R++E Q
Sbjct: 69  ANLDRAKAGLLERVKELQ 86

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 8/73 (10%)

Query: 189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVV 248
                  + +       L+GK G  I +++ + K  +RI P D            ++++ 
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI-PPDSE-------KSNLIRIE 53

Query: 249 GDINNVKNAVAII 261
           GD   V+ A   +
Sbjct: 54  GDPQGVQQAKREL 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	650
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.9
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.9
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.9
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.89
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.88
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.88
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.88
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.88
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.87
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.87
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.86
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.81
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.69
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.67
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.56
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.56
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.4
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.37
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.34
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.34
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.33
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.33
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.31
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.31
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.31
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.3
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.3
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.29
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.28
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.28
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.28
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.28
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.28
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.28
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.26
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.25
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.24
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.24
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.24
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.24
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.23
1we8_A	104	Tudor and KH domain containing protein; structural	99.22
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.22
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.21
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.2
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.19
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.18
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.15
1we8_A	104	Tudor and KH domain containing protein; structural	99.15
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.12
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.09
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.08
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.08
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.08
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.03
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.98
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.96
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.96
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.85
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.83
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.53
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.5
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.3
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.29
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.26
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.23
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.93
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.76
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.63
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.52
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.18
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.16
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	96.97
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.89
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.87
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.86
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.29
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.9
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	93.8
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	93.57
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.53
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.14
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	92.7
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.2
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	91.58
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.65

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.90  E-value=4.9e-24  Score=205.48  Aligned_cols=172  Identities=20%  Similarity=0.320  Sum_probs=132.7

Q ss_pred             CccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecC---CCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHH
Q 006320           76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHEL---IPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFL  152 (650)
Q Consensus        76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~  152 (650)
                      ..+++++|+||.+++|.||||+|++|++|+++|||+|+|++.   .+++.+|+|+|+|+           ..++.+|..+
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~-----------~~~v~~A~~~   71 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT-----------IEALNAVHGF   71 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEEC-----------HHHHHHHHHH
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeC-----------HHHHHHHHHH
Confidence            457999999999999999999999999999999999999753   56789999999996           3468888888


Q ss_pred             HHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCC
Q 006320          153 IHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDH  232 (650)
Q Consensus       153 i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~  232 (650)
                      |.+.+.+........  ......     .+..........+++|+||..++|+||||+|++|++|+++|||+|+|.+.. 
T Consensus        72 I~~~~~~~~~~~~~~--~~~~~~-----~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~-  143 (178)
T 2anr_A           72 IAEKIREMPQNVAKT--EPVSIL-----QPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP-  143 (178)
T ss_dssp             HHHHHTCCCCC------------------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-
T ss_pred             HHHHHhccCCccccC--Cccccc-----CCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCC-
Confidence            888886543211000  000000     000000113457899999999999999999999999999999999997532 


Q ss_pred             CCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          233 SLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       233 ~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                         .+....++.|+|+|+.++|.+|+.+|.++|++++
T Consensus       144 ---~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          144 ---DGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             -------CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             ---CCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence               2334678999999999999999999999999875

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

Probab=99.90  E-value=1.9e-23  Score=198.48  Aligned_cols=156  Identities=21%  Similarity=0.300  Sum_probs=131.6

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecC-CCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHH
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHEL-IPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDR  156 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~  156 (650)
                      +-+++|+||.+++|.||||+|++|++|+++|||+|+|++. .+++.+|+|+|+|+           ..++.+|..+|.+.
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~-----------~e~v~~A~~~I~~~   70 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP-----------PEAQFKAQGRIYGK   70 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEEC-----------HHHHHHHHHHHHHH
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcC-----------HHHHHHHHHHHHHH
Confidence            3589999999999999999999999999999999999875 57889999999996           45788999999988


Q ss_pred             hhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCC
Q 006320          157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPR  236 (650)
Q Consensus       157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~  236 (650)
                      +.+....           ++          ......+++|+||..++|+||||+|++|++|+++|||+|.|..  +..|.
T Consensus        71 ~~e~~~~-----------~~----------~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~--~~~~~  127 (163)
T 3krm_A           71 LKEENFF-----------GP----------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR--DQTPD  127 (163)
T ss_dssp             HHHTTSS-----------CS----------SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCT--TCCCC
T ss_pred             Hhccccc-----------cc----------ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECC--CCCCC
Confidence            8764211           00          1134568899999999999999999999999999999999964  33343


Q ss_pred             ccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          237 CVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       237 ~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                        ...++.|+|+|++++|++|+.+|.+++.+..
T Consensus       128 --~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~  158 (163)
T 3krm_A          128 --ENDQVIVKIIGHFYASQMAQRKIRDILAQVK  158 (163)
T ss_dssp             --TTSEEEEEEEECHHHHHHHHHHHHHHHHHHT
T ss_pred             --CCCceEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence              1345589999999999999999999998853

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

Probab=99.90  E-value=1.7e-23  Score=198.74  Aligned_cols=155  Identities=21%  Similarity=0.369  Sum_probs=125.3

Q ss_pred             ceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC-CCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC
Q 006320          347 DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP-VDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG  425 (650)
Q Consensus       347 ~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~-~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~  425 (650)
                      ..+++|+||.+++|.|||++|++|++|+++|||+|+|++. .+++.+|+|+|+|+   .+++..|...|+.+........
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~---~e~v~~A~~~I~~~~~e~~~~~   78 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP---PEAQFKAQGRIYGKLKEENFFG   78 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEEC---HHHHHHHHHHHHHHHHHTTSSC
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcC---HHHHHHHHHHHHHHHhcccccc
Confidence            3578999999999999999999999999999999999875 46788999999974   4555555555554433221112


Q ss_pred             CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHH
Q 006320          426 ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR  504 (650)
Q Consensus       426 ~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~  504 (650)
                      +..+...+.+|+||.+++|+||||+|+ |++|+++|||+|+|. ++..|.  ..+++.|+|+|++++|++|+.+|.++|+
T Consensus        79 ~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~-~~~~~~--~~~~~~v~I~G~~~~v~~A~~~I~~~i~  155 (163)
T 3krm_A           79 PKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVP-RDQTPD--ENDQVIVKIIGHFYASQMAQRKIRDILA  155 (163)
T ss_dssp             SSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECC-TTCCCC--TTSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             cccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEEC-CCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            234456788999999999999999999 999999999999986 344453  2334489999999999999999999999


Q ss_pred             hhh
Q 006320          505 SYL  507 (650)
Q Consensus       505 ~~~  507 (650)
                      +..
T Consensus       156 ~~~  158 (163)
T 3krm_A          156 QVK  158 (163)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            863

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=99.89  E-value=1.5e-23  Score=198.50  Aligned_cols=158  Identities=30%  Similarity=0.444  Sum_probs=131.8

Q ss_pred             ccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHH
Q 006320           77 VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDR  156 (650)
Q Consensus        77 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~  156 (650)
                      .+++++|+||.+++|.||||+|++|++|+++|||+|+|++.  ++.+|+|+|+|+           ..++.+|..+|.+.
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~-----------~~~v~~A~~~I~~~   69 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGP-----------TNAIFKAFAMIIDK   69 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEE-----------HHHHHHHHHHHHHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeC-----------HHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999999985  678999999996           34688999999888


Q ss_pred             hhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCC
Q 006320          157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPR  236 (650)
Q Consensus       157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~  236 (650)
                      +.+...... .    ...           ......++++|+||..++|+||||+|++|++|+++|||+|+|.+  +.+|.
T Consensus        70 i~e~~~~~~-~----~~~-----------~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~--~~~~~  131 (160)
T 2jzx_A           70 LEEDISSSM-T----NST-----------AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG--DMLPN  131 (160)
T ss_dssp             HHHHHTSCC-C----SSS-----------CCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC--CCSTT
T ss_pred             HHhhccccC-C----CCc-----------cCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC--CCCCC
Confidence            876422110 0    000           01134689999999999999999999999999999999999964  33454


Q ss_pred             ccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          237 CVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       237 ~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                         ..++.|+|+|++++|++|+.+|.+++.++
T Consensus       132 ---~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  160 (160)
T 2jzx_A          132 ---STERAITIAGIPQSIIECVKQICVVMLET  160 (160)
T ss_dssp             ---CCEEEEEEEECHHHHHHHHHHHHHHHHHC
T ss_pred             ---CCceEEEEEcCHHHHHHHHHHHHHHHhcC
Confidence               67899999999999999999999998763

>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=99.88  E-value=2.1e-23  Score=201.11  Aligned_cols=155  Identities=19%  Similarity=0.354  Sum_probs=124.8

Q ss_pred             CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC---CCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhh
Q 006320          346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP---VDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIV  422 (650)
Q Consensus       346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~---~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~  422 (650)
                      .+++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.+|+|+|+|+   .+++.+|.++|..+.....
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~---~~~v~~A~~~I~~~~~~~~   80 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT---IEALNAVHGFIAEKIREMP   80 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEEC---HHHHHHHHHHHHHHHTCCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeC---HHHHHHHHHHHHHHHhccC
Confidence            67899999999999999999999999999999999999764   24678999999975   4566666666655433211


Q ss_pred             ccC--------------CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEe
Q 006320          423 DLG--------------ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG  487 (650)
Q Consensus       423 ~~~--------------~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G  487 (650)
                      ...              ...+...+++|+||.+++|+||||+|+ ||+|+++|||+|+|.+..+   ++.+++++|+|+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~---~~~~~~~~v~I~G  157 (178)
T 2anr_A           81 QNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD---GINLQNRVVTVSG  157 (178)
T ss_dssp             CC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-------CCEEEEEEES
T ss_pred             CccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCC---CCCCCceEEEEEc
Confidence            100              011234789999999999999999999 9999999999999975433   3346789999999


Q ss_pred             cHHHHHHHHHHHHHHHHhh
Q 006320          488 EIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       488 ~~~~v~~A~~~I~~~l~~~  506 (650)
                      ++++|++|+.+|.++|++.
T Consensus       158 ~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          158 EPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             SHHHHHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHHHHHHhC
Confidence            9999999999999999876

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

Probab=99.88  E-value=4.8e-23  Score=216.09  Aligned_cols=227  Identities=15%  Similarity=0.154  Sum_probs=162.0

Q ss_pred             CCcEEEEEEEccceeeeeecCCc--hHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHh
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGG--KIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLR  266 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G--~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~  266 (650)
                      .+.+++++.||..+|++||||+|  ++|++|+++|||+|+|+..+..- .........|+|+|.+++|++|+.+|.+++-
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~-~~~~~ks~~VtItG~~enVE~AR~~I~~l~P  105 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGG-TTPDPFAQQVTITGYFGDVDRARMLMRRNCH  105 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCS-SSCCTTTTEEEEEEEHHHHHHHHHHHHHSCE
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccc-cCCcCCCCeEEEEcCHHHHHHHHHHHHhcCC
Confidence            57899999999999999999999  99999999999999996432000 0112345789999999999999999987321


Q ss_pred             hcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCC
Q 006320          267 ESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGE  346 (650)
Q Consensus       267 ~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~  346 (650)
                                                                                                      
T Consensus       106 --------------------------------------------------------------------------------  105 (376)
T 3n89_A          106 --------------------------------------------------------------------------------  105 (376)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             ceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCC--CCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhcc
Q 006320          347 DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVD--GSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDL  424 (650)
Q Consensus       347 ~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~--~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~  424 (650)
                       +++.+.+|...+..  ..-+..|.+ ++.++++|.|+....  +.....|+|+|.   ...+..|.+|+.++++.+.+.
T Consensus       106 -l~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~---~~nv~~akeA~~~Ll~~l~~~  178 (376)
T 3n89_A          106 -FTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITAR---EKNQHELIEAAKRLNEILFRE  178 (376)
T ss_dssp             -EEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEE---GGGHHHHHHHHHHHHHHHCC-
T ss_pred             -ceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcC---hhhHHHHHHHHHHHHHHHHhh
Confidence             12223333322211  011223433 567899999865321  223678999964   566777888888887777654


Q ss_pred             CCCCCCceEEEEeecCCcceeeecCCC--c-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHH
Q 006320          425 GADKDNIITTRLLVPSSEIGCLEGRDG--S-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTT  501 (650)
Q Consensus       425 ~~~~~~~~~~~l~Vp~~~~g~IIGkgG--~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~  501 (650)
                      .....+.+++.|.|+..+|..|||++|  . |++|+++|||+|+++..++... .......|+|+|..++|.+|..+|++
T Consensus       179 e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d-~~~~~~~ItItGs~e~V~~Ark~I~~  257 (376)
T 3n89_A          179 SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNE-TRGNIYEIKVVGNIDNVLKARRYIMD  257 (376)
T ss_dssp             -CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC----------CCEEEEEEESCHHHHHHHHHHHHH
T ss_pred             hcccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCccc-ccCCceEEEEEeCHHHHHHHHHHHHh
Confidence            333456799999999999999999999  4 6999999999998865432110 01234579999999999999999999


Q ss_pred             HHH
Q 006320          502 RLR  504 (650)
Q Consensus       502 ~l~  504 (650)
                      +|=
T Consensus       258 lLP  260 (376)
T 3n89_A          258 LLP  260 (376)
T ss_dssp             TSE
T ss_pred             hCC
Confidence            884

>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=99.88  E-value=1.6e-22  Score=192.20  Aligned_cols=158  Identities=26%  Similarity=0.397  Sum_probs=128.2

Q ss_pred             EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecC--CCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHH
Q 006320           79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHEL--IPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDR  156 (650)
Q Consensus        79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~--~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~  156 (650)
                      ++++|+||.+++|.||||+|++|++|+++|||+|+|.+.  .++..+|+|+|+|+           ..++.+|+.+|.+.
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~-----------~~~v~~A~~~I~~i   70 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD-----------PYKVQQACEMVMDI   70 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEEC-----------HHHHHHHHHHHHHH
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcC-----------HHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999753  34678999999995           34688999999988


Q ss_pred             hhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCC
Q 006320          157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPR  236 (650)
Q Consensus       157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~  236 (650)
                      +.+.... .+.  ...+|++            ....+++|.||..++|+||||+|++|++|+++|||+|.|.+.+   + 
T Consensus        71 i~e~~~~-~~~--~~~~~~~------------~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~---~-  131 (164)
T 2jvz_A           71 LRERDQG-GFG--DRNEYGS------------RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---G-  131 (164)
T ss_dssp             TTCSSSC-CCS--SCSSCTT------------SCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC---T-
T ss_pred             HHhccCC-CCC--CccccCC------------CCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC---C-
Confidence            8664321 100  0011221            1234688999999999999999999999999999999997532   2 


Q ss_pred             ccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          237 CVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       237 ~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                        ...++.|+|+|++++|++|+.+|.+++.+.
T Consensus       132 --~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A          132 --TGPEKIAHIMGPPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             --TSSEEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             --CCCcEEEEEEcCHHHHHHHHHHHHHHHhhh
Confidence              256899999999999999999999999764

>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=99.88  E-value=1.4e-22  Score=194.45  Aligned_cols=168  Identities=23%  Similarity=0.358  Sum_probs=127.5

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI  157 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i  157 (650)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.+..+++.+|+|+|+|+           ..++.+|+.+|.+.+
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~-----------~~~v~~A~~~I~~~~   70 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-----------PDRAQHAAEIITDLL   70 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEEC-----------HHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeC-----------HHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999987666788999999996           346889999988888


Q ss_pred             hhcCCCCCCCCCcccccCCCC-CCCCC--CC--CCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCC
Q 006320          158 LESDGGGGFYGEEEEEYGGGG-GVGGG--GF--RGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDH  232 (650)
Q Consensus       158 ~e~~~~~~~~~~~~~~~~~~~-~~~~~--~~--~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~  232 (650)
                      .+........      .++.+ +.+.+  ..  ......++++|+||..++|+||||+|++|++|+++|||+|+|...  
T Consensus        71 ~~~~~~~~~~------~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~--  142 (174)
T 1j4w_A           71 RSVQAGNPGG------PGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRN--  142 (174)
T ss_dssp             HHHC-----------------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECC--
T ss_pred             HhcccCCCCC------CCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCC--
Confidence            7653211000      00000 00000  00  001234688999999999999999999999999999999999752  


Q ss_pred             CCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320          233 SLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL  265 (650)
Q Consensus       233 ~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  265 (650)
                       .+.+..+.++.|+|+|++++|.+|+.+|.++|
T Consensus       143 -~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          143 -PPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             -CTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             -CCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence             13344577899999999999999999999864

>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=99.87  E-value=1.8e-22  Score=193.70  Aligned_cols=152  Identities=20%  Similarity=0.313  Sum_probs=123.4

Q ss_pred             ceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCC
Q 006320          347 DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGA  426 (650)
Q Consensus       347 ~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~  426 (650)
                      ..+++|+||.+++|.|||++|++|++|+++|||+|+|.+...++.+|+|+|+|+   .+++.+|.++|..+.........
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~---~~~v~~A~~~I~~~~~~~~~~~~   78 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP---PDRAQHAAEIITDLLRSVQAGNP   78 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEEC---HHHHHHHHHHHHHHHHHHC----
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeC---HHHHHHHHHHHHHHHHhcccCCC
Confidence            357899999999999999999999999999999999987556778899999975   56777777777666554321100


Q ss_pred             --------------------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEE
Q 006320          427 --------------------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQI  485 (650)
Q Consensus       427 --------------------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I  485 (650)
                                          ......+++|.||.+++|+||||+|+ ||+|+++|||+|+|...  .+.+..+++++|+|
T Consensus        79 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~~~~~~~~~v~I  156 (174)
T 1j4w_A           79 GGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRN--PPPNADPNMKLFTI  156 (174)
T ss_dssp             -------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECC--CTTTSCTTEEEEEE
T ss_pred             CCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCC--CCCCCCCCceEEEE
Confidence                                01124688999999999999999999 99999999999999753  23344567899999


Q ss_pred             EecHHHHHHHHHHHHHHH
Q 006320          486 VGEIQAARDALVEVTTRL  503 (650)
Q Consensus       486 ~G~~~~v~~A~~~I~~~l  503 (650)
                      +|++++|++|+.+|.++|
T Consensus       157 ~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          157 RGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             ECCHHHHHHHHHHHHHHC
T ss_pred             ECCHHHHHHHHHHHHHhC
Confidence            999999999999998864

>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=99.87  E-value=1.4e-22  Score=191.79  Aligned_cols=151  Identities=26%  Similarity=0.454  Sum_probs=123.8

Q ss_pred             CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHh-hhcc
Q 006320          346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTR-IVDL  424 (650)
Q Consensus       346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~-i~~~  424 (650)
                      ..++++|+||.+++|.|||++|++|++|+++|||+|+|++  .++.+|.|+|+|+   .+++.+|...|+.+... +...
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~--~~~~~r~v~I~G~---~~~v~~A~~~I~~~i~e~~~~~   77 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP---TNAIFKAFAMIIDKLEEDISSS   77 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEEC--CTTTEEEEEEEEE---HHHHHHHHHHHHHHHHHHHTSC
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcC--CCCCceEEEEEeC---HHHHHHHHHHHHHHHHhhcccc
Confidence            4578999999999999999999999999999999999987  3677899999975   45666666666544322 2111


Q ss_pred             CC----CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHH
Q 006320          425 GA----DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEV  499 (650)
Q Consensus       425 ~~----~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  499 (650)
                      ..    .....++++|+||.+++|+||||+|+ |++|+++|||+|+|.+ +..|.   ++++.|+|+|++++|++|+.+|
T Consensus        78 ~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~-~~~~~---~~~~~v~I~G~~~~v~~A~~~I  153 (160)
T 2jzx_A           78 MTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG-DMLPN---STERAITIAGIPQSIIECVKQI  153 (160)
T ss_dssp             CCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC-CCSTT---CCEEEEEEEECHHHHHHHHHHH
T ss_pred             CCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC-CCCCC---CCceEEEEEcCHHHHHHHHHHH
Confidence            00    12236899999999999999999999 9999999999999964 33443   5789999999999999999999


Q ss_pred             HHHHHh
Q 006320          500 TTRLRS  505 (650)
Q Consensus       500 ~~~l~~  505 (650)
                      .++|.+
T Consensus       154 ~~~i~e  159 (160)
T 2jzx_A          154 CVVMLE  159 (160)
T ss_dssp             HHHHHH
T ss_pred             HHHHhc
Confidence            999876

>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=99.86  E-value=8.3e-22  Score=187.23  Aligned_cols=151  Identities=21%  Similarity=0.315  Sum_probs=120.8

Q ss_pred             eEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCC--CCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC
Q 006320          348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPV--DGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG  425 (650)
Q Consensus       348 ~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~--~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~  425 (650)
                      ++++|+||.+++|.|||++|++|++|+++|||+|.|.+..  ++..+|.|+|+|+   .+++.+|.++|+.+........
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~---~~~v~~A~~~I~~ii~e~~~~~   78 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD---PYKVQQACEMVMDILRERDQGG   78 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEEC---HHHHHHHHHHHHHHTTCSSSCC
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcC---HHHHHHHHHHHHHHHHhccCCC
Confidence            5789999999999999999999999999999999997532  4567899999974   4566666666665543222100


Q ss_pred             CC------CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHH
Q 006320          426 AD------KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVE  498 (650)
Q Consensus       426 ~~------~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~  498 (650)
                      ..      ....++++|.||.+++|+||||+|+ |++|+++|||+|+|.+.+  +   .+.++.|+|+|++++|+.|+.+
T Consensus        79 ~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~--~---~~~~~~v~I~G~~~~v~~A~~~  153 (164)
T 2jvz_A           79 FGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G---TGPEKIAHIMGPPDRCEHAARI  153 (164)
T ss_dssp             CSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC--T---TSSEEEEEEESCHHHHHHHHHH
T ss_pred             CCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC--C---CCCcEEEEEEcCHHHHHHHHHH
Confidence            00      0113568999999999999999999 999999999999997543  1   2457899999999999999999


Q ss_pred             HHHHHHhh
Q 006320          499 VTTRLRSY  506 (650)
Q Consensus       499 I~~~l~~~  506 (650)
                      |.++|++.
T Consensus       154 I~~~i~~~  161 (164)
T 2jvz_A          154 INDLLQSL  161 (164)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhhh
Confidence            99999875

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

Probab=99.81  E-value=3.3e-19  Score=187.03  Aligned_cols=279  Identities=10%  Similarity=0.119  Sum_probs=183.2

Q ss_pred             CccEEEEEEecCcccceeecCCC--hHHHHHHHHhCCeEEEecCC-----CCCCccEEEEecCCCCCCCCCCCCccHHHH
Q 006320           76 MVTTTYRILCHDMKAGGVIGKSG--SIIKSIRQHTGAWINVHELI-----PGDEERIIEISDTRRRDPEGRMPSFSPAQE  148 (650)
Q Consensus        76 ~~~~~~rilip~~~vg~IIGk~G--~~Ik~I~~~tga~I~v~~~~-----~~~~ervi~I~G~~~~~~~~~~~~~~~a~~  148 (650)
                      ...+++.+.||..++..||||+|  ++|++|+++|+|+|+|++..     +......|+|+|.           ..++++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~-----------~enVE~   95 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGY-----------FGDVDR   95 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEE-----------HHHHHH
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcC-----------HHHHHH
Confidence            45799999999999999999999  99999999999999999864     1235578999996           346777


Q ss_pred             HHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320          149 ALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL  228 (650)
Q Consensus       149 A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  228 (650)
                      |..+|.+.+                                 .+++.+.+|...+..  ..-+..|.+ ++..+++|.+.
T Consensus        96 AR~~I~~l~---------------------------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp  139 (376)
T 3n89_A           96 ARMLMRRNC---------------------------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFV  139 (376)
T ss_dssp             HHHHHHHSC---------------------------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEE
T ss_pred             HHHHHHhcC---------------------------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeC
Confidence            777666422                                 234555555433222  111345555 67789999986


Q ss_pred             cCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCC
Q 006320          229 PRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGA  308 (650)
Q Consensus       229 ~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~  308 (650)
                      +..+.    .......|+|+|...+|.+|++++..++.........                                  
T Consensus       140 ~~~~~----~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e~~----------------------------------  181 (376)
T 3n89_A          140 DAPEK----NGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPA----------------------------------  181 (376)
T ss_dssp             EEC---------CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--CC----------------------------------
T ss_pred             Ccccc----cCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhhcc----------------------------------
Confidence            43110    0123567999999977777666666665543210000                                  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCc--hhHHHHHHHhCCeEEEeCC
Q 006320          309 RFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESE--GIVELLQNEIGVDLKVADP  386 (650)
Q Consensus       309 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G--~~Ik~l~~~tga~I~i~~~  386 (650)
                                                         ....++..|.|+.++|..|||++|  ..|++|+++|||+|.|++.
T Consensus       182 -----------------------------------~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~  226 (376)
T 3n89_A          182 -----------------------------------PENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCY  226 (376)
T ss_dssp             -----------------------------------CSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC--
T ss_pred             -----------------------------------cccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCC
Confidence                                               003568899999999999999998  5679999999999999864


Q ss_pred             CCC----CCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcC
Q 006320          387 VDG----SDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG  461 (650)
Q Consensus       387 ~~~----~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tg  461 (650)
                      ...    .....|+|+|+   .+++..|.++|+.+.            ++.+-+.++...+-.-.-.--. |-.+.++.+
T Consensus       227 ~d~~d~~~~~~~ItItGs---~e~V~~Ark~I~~lL------------Pv~l~Fd~~~~d~~~~~~~~~~~~~~~~~~~~  291 (376)
T 3n89_A          227 NNRNETRGNIYEIKVVGN---IDNVLKARRYIMDLL------------PISMCFNIKNTDMAEPSRVSDRNIHMIIDESG  291 (376)
T ss_dssp             -------CCEEEEEEESC---HHHHHHHHHHHHHTS------------EEEEEEEEEGGGBC--------CBEEEECTTS
T ss_pred             CCcccccCCceEEEEEeC---HHHHHHHHHHHHhhC------------CEEEEEecCCcccccccccchhHHHHHHHhcC
Confidence            221    23478999965   677788887777553            5666676665544333334444 666889999


Q ss_pred             ceEEEecCCCCCCCCCCCC---eEEEEEecH
Q 006320          462 ANIQILSREEVPACVSGTD---ELVQIVGEI  489 (650)
Q Consensus       462 a~I~i~~~~~~p~~~~~~~---r~v~I~G~~  489 (650)
                      +.|.|.++...|..-.++|   ..|.|...-
T Consensus       292 v~~~~~~~~~~~~~~~~~~~~~~~~~~~s~e  322 (376)
T 3n89_A          292 IILKMTPSVYEPADLLSGEVPLNCASLRSKE  322 (376)
T ss_dssp             CEEEEEEEEECCSSSSCCCEEEEEEEEEEEG
T ss_pred             eEEEEeecCCCchhhcccccccceEEEEEEe
Confidence            9999987553342111111   237777753

>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=99.69  E-value=1.7e-17  Score=153.43  Aligned_cols=136  Identities=19%  Similarity=0.276  Sum_probs=100.8

Q ss_pred             ceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCC
Q 006320          347 DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGA  426 (650)
Q Consensus       347 ~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~  426 (650)
                      .++.+++||.+.+|++||++|++|+.|++++|++|....   ... ..+++.+.  .++.+..|.. ++       +.  
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~---~~~-~~~i~~~~--~p~~v~~~~~-~l-------~~--   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD---EDT-CTFHIYGE--DQDAVKKARS-FL-------EF--   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEE---TTT-TEEEEEES--SHHHHHHHHH-HH-------CE--
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccC---CCc-hheeeccC--CHHHHHHHHH-hh-------hc--
Confidence            457899999999999999999999999999995443332   122 34555542  2233333322 11       11  


Q ss_pred             CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCc-eEEEecCCCCCCCCCCCCe--EEEEEecHHHHHHHHHHHHHH
Q 006320          427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGA-NIQILSREEVPACVSGTDE--LVQIVGEIQAARDALVEVTTR  502 (650)
Q Consensus       427 ~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga-~I~i~~~~~~p~~~~~~~r--~v~I~G~~~~v~~A~~~I~~~  502 (650)
                           ...++.||.+++|++|||+|+ ||+|++.||+ +|+|.+.++...  ..+++  .|+|+|++++|++|+.+|.++
T Consensus        67 -----~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~--~~~~~~~~vtI~G~~~~v~~Ak~li~~~  139 (144)
T 2qnd_A           67 -----AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPFVFVGTKDSIANATVLLDYH  139 (144)
T ss_dssp             -----EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC--CCCTTEEEEEEEEEHHHHHHHHHHHHHH
T ss_pred             -----ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc--cccCCeeEEEEEeCHHHHHHHHHHHHHH
Confidence                 138899999999999999999 9999999997 999987543211  12333  489999999999999999999


Q ss_pred             HHh
Q 006320          503 LRS  505 (650)
Q Consensus       503 l~~  505 (650)
                      |.+
T Consensus       140 l~~  142 (144)
T 2qnd_A          140 LNY  142 (144)
T ss_dssp             HHT
T ss_pred             HHh
Confidence            875

>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=99.67  E-value=2e-16  Score=146.25  Aligned_cols=137  Identities=21%  Similarity=0.283  Sum_probs=101.3

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI  157 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i  157 (650)
                      .++.+|++|.+.+|.+||++|++|++|++++|  |++.+.. ...+. +.+.+..          .    +++..+...+
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~-~i~~~~~----------p----~~v~~~~~~l   64 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCT-FHIYGED----------Q----DAVKKARSFL   64 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTE-EEEEESS----------H----HHHHHHHHHH
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchh-eeeccCC----------H----HHHHHHHHhh
Confidence            46889999999999999999999999999999  5553321 23344 4444421          1    2233332222


Q ss_pred             hhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCc-eEEEecCCCCCCC
Q 006320          158 LESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKT-QIRILPRDHSLPR  236 (650)
Q Consensus       158 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga-~I~i~~~~~~lp~  236 (650)
                       +                               ....++.||..++|++|||+|.+|+.|++.||| +|+|.+.++... 
T Consensus        65 -~-------------------------------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~-  111 (144)
T 2qnd_A           65 -E-------------------------------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV-  111 (144)
T ss_dssp             -C-------------------------------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC-
T ss_pred             -h-------------------------------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc-
Confidence             1                               114889999999999999999999999999997 999986433211 


Q ss_pred             ccCCCc--ceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          237 CVSMSE--EIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       237 ~~~~~e--r~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                        ...+  +.|+|+|++++|++|+.+|.++|..
T Consensus       112 --~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          112 --PQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             --CCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             --cccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence              1233  3589999999999999999999975

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

Probab=99.56  E-value=4.1e-15  Score=146.23  Aligned_cols=151  Identities=15%  Similarity=0.138  Sum_probs=111.2

Q ss_pred             ccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHH
Q 006320           77 VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDR  156 (650)
Q Consensus        77 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~  156 (650)
                      ......+.||.+++|.|||++|++|+.|+++|||+|+|+.     +++.|+|+++....      ...++++|..+|...
T Consensus        32 aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~------d~~~i~kA~~~I~~i  100 (219)
T 2e3u_A           32 FKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETE------DPLAVWKARDIVLAI  100 (219)
T ss_dssp             -CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCC------SHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCC------CHHHHHHHHHHHHHH
Confidence            3457799999999999999999999999999999999984     25678998864211      135688888888876


Q ss_pred             hhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEc-----------cceeeeeecCCchHHHHHHhhcCceE
Q 006320          157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVS-----------RMHVGCLLGKGGKIIEQMRMETKTQI  225 (650)
Q Consensus       157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp-----------~~~vg~IIGk~G~~Ik~I~~~tga~I  225 (650)
                      +...+.+.+.....                  +......+.++           ...+|+||||+|++|+.|++.|||+|
T Consensus       101 ~rg~~~e~g~~ll~------------------dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I  162 (219)
T 2e3u_A          101 GRGFSPERAFRLLN------------------EGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASV  162 (219)
T ss_dssp             HTTCCHHHHGGGGS------------------TTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEE
T ss_pred             hccCCccccceecc------------------CCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceE
Confidence            63221111000000                  11111122222           12689999999999999999999999


Q ss_pred             EEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          226 RILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       226 ~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      .|.             ++.|.|.|+.++|+.|+.+|.+++...+
T Consensus       163 ~v~-------------~~~v~i~G~~~~i~~A~~~i~~li~g~~  193 (219)
T 2e3u_A          163 SVY-------------GKTVAIIGNPIQIEIAKTAIEKLARGSP  193 (219)
T ss_dssp             EEE-------------TTEEEEEECHHHHHHHHHHHHHHHTTCC
T ss_pred             EEC-------------CeEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence            995             3579999999999999999999997654

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

Probab=99.56  E-value=5.5e-15  Score=145.31  Aligned_cols=143  Identities=14%  Similarity=0.165  Sum_probs=106.9

Q ss_pred             EEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCC--CCCcchHHHHHHHHHHHh--hhc-
Q 006320          349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEG--PDDELFPAQEALLHIQTR--IVD-  423 (650)
Q Consensus       349 ~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g--~~~~~~~a~~ai~~i~~~--i~~-  423 (650)
                      ..++.||.++++.|||++|++|+.|+++|||+|.+..     +++.|+|.++..  ..+.+.+|.+.|..+..-  ... 
T Consensus        35 i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~g  109 (219)
T 2e3u_A           35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERA  109 (219)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             EEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCcccc
Confidence            5689999999999999999999999999999999963     357789987542  245677777777665410  000 


Q ss_pred             -cCCCCCCceEEEEeec-----------CCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHH
Q 006320          424 -LGADKDNIITTRLLVP-----------SSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQ  490 (650)
Q Consensus       424 -~~~~~~~~~~~~l~Vp-----------~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~  490 (650)
                       ...+ +......+.++           +..+|+||||+|+ |+.|++.|||+|.|.            ++.|+|.|+++
T Consensus       110 ~~ll~-dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~------------~~~v~i~G~~~  176 (219)
T 2e3u_A          110 FRLLN-EGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY------------GKTVAIIGNPI  176 (219)
T ss_dssp             GGGGS-TTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE------------TTEEEEEECHH
T ss_pred             ceecc-CCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC------------CeEEEEEeCHH
Confidence             0001 11111122222           2368999999999 999999999999884            35699999999


Q ss_pred             HHHHHHHHHHHHHHhhhhh
Q 006320          491 AARDALVEVTTRLRSYLYR  509 (650)
Q Consensus       491 ~v~~A~~~I~~~l~~~~~~  509 (650)
                      +++.|..+|.++|......
T Consensus       177 ~i~~A~~~i~~li~g~~~~  195 (219)
T 2e3u_A          177 QIEIAKTAIEKLARGSPHG  195 (219)
T ss_dssp             HHHHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHcCCCcH
Confidence            9999999999999765433

>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=99.40  E-value=1.6e-13  Score=111.56  Aligned_cols=69  Identities=26%  Similarity=0.500  Sum_probs=63.1

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      ..++++|+||.+.+|.||||||+ ||+|+++|||+|+|.+.       ...+|+|+|+|+++++++|+.+|.++|++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-------CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999 99999999999999743       13589999999999999999999999986

>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=99.37  E-value=6.3e-13  Score=108.05  Aligned_cols=71  Identities=28%  Similarity=0.499  Sum_probs=64.5

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|.+.        ...+|.|+|+|++++|.+|+.+|.++|+++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--------~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--------NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--------CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--------CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            46799999999999999999999999999999999999742        146899999999999999999999999863

>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=99.34  E-value=9.8e-13  Score=107.90  Aligned_cols=73  Identities=27%  Similarity=0.373  Sum_probs=62.7

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      ..+++|.||.+.+|+|||++|+ |++|+++|||+|+|.+.++.  +..+.++.|+|+|+++++++|+.+|.++|++
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCC--STTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCC--CCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            3678999999999999999999 99999999999999764321  1235689999999999999999999998764

>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=99.34  E-value=1.1e-12  Score=107.66  Aligned_cols=74  Identities=28%  Similarity=0.402  Sum_probs=64.8

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      .++.+|+||..++|+||||+|++|++|+++|||+|+|.+..+..|.   +.++.|+|+|++++|.+|+.+|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~---~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG---TRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTT---CCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCC---CceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            3578999999999999999999999999999999999864333343   6789999999999999999999998764

>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=99.33  E-value=2e-12  Score=107.67  Aligned_cols=72  Identities=25%  Similarity=0.513  Sum_probs=64.4

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ..++.+|.||.+.+|+||||+|+ |++|+++|||+|+|..  ..|   .++++.|+|+|++++|++|+.+|.+++++.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~--~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE--PLE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECC--TTS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcC--CCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999 9999999999999963  222   356899999999999999999999999876

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

Probab=99.33  E-value=7.1e-13  Score=108.71  Aligned_cols=72  Identities=32%  Similarity=0.521  Sum_probs=64.3

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ..++.+|.||.+++|+|||+||+ |++|+++|||+|+|..  .   ++.++++.|+|+|+++++++|+.+|.++|++.
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~--~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN--P---VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECC--C---CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcC--C---CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            46889999999999999999999 9999999999999964  2   23467899999999999999999999998764

>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=99.31  E-value=2.5e-12  Score=107.04  Aligned_cols=74  Identities=27%  Similarity=0.399  Sum_probs=65.4

Q ss_pred             CccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHH
Q 006320           76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHD  155 (650)
Q Consensus        76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~  155 (650)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|+|++..++..+|+|+|+|+           ..++++|+.+|.+
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~-----------~~~v~~A~~~I~~   71 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS-----------AASISLAQYLINA   71 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEEC-----------HHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcC-----------HHHHHHHHHHHHH
Confidence            34689999999999999999999999999999999999998777889999999996           3578899999998


Q ss_pred             Hhhhc
Q 006320          156 RILES  160 (650)
Q Consensus       156 ~i~e~  160 (650)
                      .+.+.
T Consensus        72 ~i~~~   76 (82)
T 1wvn_A           72 RLSSE   76 (82)
T ss_dssp             HTC--
T ss_pred             HHHhh
Confidence            88654

>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=99.31  E-value=3.8e-12  Score=122.04  Aligned_cols=140  Identities=16%  Similarity=0.170  Sum_probs=104.4

Q ss_pred             EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCC--CCCCcchHHHHHHHHHHHhhh--ccC
Q 006320          350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEE--GPDDELFPAQEALLHIQTRIV--DLG  425 (650)
Q Consensus       350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~--g~~~~~~~a~~ai~~i~~~i~--~~~  425 (650)
                      +++.||...++.|||++|++++.|++.+|++|.+..     .++.++|..+.  +.+..+.+|.+.|..+..-..  +..
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~e~A~   80 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAF   80 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHHHG
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHHHhh
Confidence            689999999999999999999999999999999964     46777887432  334567778777765443110  000


Q ss_pred             CCCCCceEEE-Eeec----------CCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHH
Q 006320          426 ADKDNIITTR-LLVP----------SSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAAR  493 (650)
Q Consensus       426 ~~~~~~~~~~-l~Vp----------~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~  493 (650)
                      .-.++.+... +.++          ....|+||||+|. |+.|++.|||+|.|.            ++.|.|.|++++++
T Consensus        81 ~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~------------~~~v~i~G~~~~i~  148 (191)
T 1tua_A           81 RLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG------------EYEVAIIGDYERAM  148 (191)
T ss_dssp             GGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC------------SSEEEEEEEHHHHH
T ss_pred             hcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc------------CCEEEEEeChHHHH
Confidence            0001122222 3233          2468999999999 999999999999884            34799999999999


Q ss_pred             HHHHHHHHHHHhh
Q 006320          494 DALVEVTTRLRSY  506 (650)
Q Consensus       494 ~A~~~I~~~l~~~  506 (650)
                      .|...|..++...
T Consensus       149 ~Ar~~i~~li~g~  161 (191)
T 1tua_A          149 AAKQAIEMLAEGR  161 (191)
T ss_dssp             HHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCC
Confidence            9999999998654

>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=99.31  E-value=2.3e-12  Score=123.57  Aligned_cols=146  Identities=19%  Similarity=0.199  Sum_probs=109.0

Q ss_pred             EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhh
Q 006320           80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE  159 (650)
Q Consensus        80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e  159 (650)
                      .++++||...+|.|||++|++++.|+++++++|+++.     .++.|+|..+.+..      ....+++|..+|......
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~------dp~~i~KA~dlI~ai~rg   73 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGI------PPVNLMKAAEVVKAISLG   73 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTS------CHHHHHHHHHHHHHHHHT
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCC------CHHHHHHHHHHHHHHHcC
Confidence            4689999999999999999999999999999999974     47788887543211      245678888888665543


Q ss_pred             cCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEE-EEEEc----------cceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320          160 SDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVAT-RMVVS----------RMHVGCLLGKGGKIIEQMRMETKTQIRIL  228 (650)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~i~Vp----------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  228 (650)
                      ...+..+                   ...++...+ .+.++          ..+.|+||||+|.+|+.|++.|||+|.|.
T Consensus        74 f~~e~A~-------------------~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~  134 (191)
T 1tua_A           74 FPPEKAF-------------------RLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG  134 (191)
T ss_dssp             CCHHHHG-------------------GGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC
T ss_pred             CCHHHhh-------------------hcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc
Confidence            2211100                   000112223 33343          23589999999999999999999999995


Q ss_pred             cCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          229 PRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       229 ~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                                   +..|.|.|+.++++.|...|..++...
T Consensus       135 -------------~~~v~i~G~~~~i~~Ar~~i~~li~g~  161 (191)
T 1tua_A          135 -------------EYEVAIIGDYERAMAAKQAIEMLAEGR  161 (191)
T ss_dssp             -------------SSEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             -------------CCEEEEEeChHHHHHHHHHHHHHHcCC
Confidence                         247999999999999999999999754

>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=99.30  E-value=4.7e-12  Score=105.35  Aligned_cols=73  Identities=23%  Similarity=0.496  Sum_probs=65.9

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ..++.+|+||..++|.||||+|++|++|+++|||+|+|..   ..|   ...++.|+|+|++++|++|+.+|.+++.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~---~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE---PLE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECC---TTS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcC---CCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            5689999999999999999999999999999999999963   123   267899999999999999999999999875

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

Probab=99.30  E-value=2.6e-12  Score=105.36  Aligned_cols=73  Identities=21%  Similarity=0.444  Sum_probs=65.7

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ..++.+|+||..++|+|||++|++|++|+++|||+|+|..   ..+   .+.++.|+|+|++++|.+|+.+|.+++.+.
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~---~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN---PVE---GSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECC---CCT---TCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcC---CCC---CCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4678999999999999999999999999999999999974   122   377999999999999999999999999763

>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=99.29  E-value=2.3e-12  Score=108.49  Aligned_cols=75  Identities=28%  Similarity=0.390  Sum_probs=66.4

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      ++.+|+||..++|+|||++|++|++|+++|||+|+|....+..|.   +.++.|+|+|++++|.+|+.+|.+++.+..
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g---~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG---TRNRRVTITGSPAATQAAQYLISQRVTYEQ   77 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTT---SCEEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCC---CCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            478999999999999999999999999999999999864333343   678999999999999999999999998753

>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=99.28  E-value=3.7e-12  Score=106.03  Aligned_cols=73  Identities=22%  Similarity=0.427  Sum_probs=64.8

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ..++.+|+||..++|+||||+|++|++|+++|||+|+|...      +....++.|+|+|++++|++|+.+|.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~------~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP------VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC------CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC------CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            56899999999999999999999999999999999999742      22367999999999999999999999999876

>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=99.28  E-value=2.2e-12  Score=108.71  Aligned_cols=77  Identities=26%  Similarity=0.318  Sum_probs=66.2

Q ss_pred             eEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhhhc
Q 006320          432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRD  510 (650)
Q Consensus       432 ~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~  510 (650)
                      .+++|.||.+.+|+|||+||+ |++|+++|||+|+|.+.++.  +..++++.|+|+|++++++.|+.+|.++|.+...+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~--~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~r   80 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVR   80 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCB--STTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccccc
Confidence            578999999999999999999 99999999999999754321  123578999999999999999999999998865543

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

Probab=99.28  E-value=5.7e-12  Score=105.62  Aligned_cols=73  Identities=18%  Similarity=0.394  Sum_probs=63.5

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      ...+.+|.||.+.+|+||||+|+ ||+|+++|||+|+|......   ....+|.|+|+|+++++++|+.+|.+++++
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~---~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---NTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCS---STTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            45788999999999999999999 99999999999999753221   235788999999999999999999998864

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.28  E-value=7.1e-12  Score=106.59  Aligned_cols=74  Identities=20%  Similarity=0.398  Sum_probs=66.7

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++.+|+||..++|+||||+|++|++|+++|||+|+|....   +   ...++.|+|+|++++|++|+.+|.+++.+.
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~---~---g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---G---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC---C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999999997421   2   256899999999999999999999999885

>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=99.28  E-value=2e-12  Score=107.37  Aligned_cols=71  Identities=17%  Similarity=0.289  Sum_probs=62.5

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      .....+++|.||.+.+|+||||+|+ ||+|+++|||+|+|++.+        ++++|+|+|++++|++|+.+|.+++...
T Consensus         6 ~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~--------~~~~v~ItG~~e~v~~A~~~I~~~i~~r   77 (83)
T 2dgr_A            6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD--------KEPVFAVTGMPENVDRAREEIEAHITLR   77 (83)
T ss_dssp             SCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS--------SCCEEEEEECTTTHHHHHHHHHHHHHSC
T ss_pred             CCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC--------CCCeEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            3456889999999999999999999 999999999999996432        3678999999999999999999976654

>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=99.28  E-value=3.8e-12  Score=107.59  Aligned_cols=74  Identities=24%  Similarity=0.519  Sum_probs=66.8

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++.+|.||..+++.||||+|++|++|+++|||+|+|..   ..|   ...++.|+|+|++++|++|+.+|.+++.+.
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~---~~~---~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE---PLE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECS---CCS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecC---CCC---CCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            46789999999999999999999999999999999999963   123   367899999999999999999999999875

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

Probab=99.26  E-value=5.2e-12  Score=110.50  Aligned_cols=73  Identities=21%  Similarity=0.267  Sum_probs=63.4

Q ss_pred             eEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       432 ~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      .+++|+||.+++|+||||+|+ ||+|+++|||+|+|.... .| ....++++|+|+|++++|++|+.+|.++|++.
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~-~~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQL-PP-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCC-CT-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCcc-CC-CCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            378999999999999999999 999999999999997432 22 22356799999999999999999999998876

>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=99.25  E-value=8e-12  Score=106.73  Aligned_cols=76  Identities=16%  Similarity=0.378  Sum_probs=66.9

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++.+|+||..++++||||+|++|++|+++|||+|+|.....  +  ....+|.|+|+|++++|++|+.+|.+++.+.
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~--~--~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP--Q--NTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC--C--SSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCC--C--CCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            57789999999999999999999999999999999999975321  1  1246899999999999999999999999875

>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=99.24  E-value=3.7e-12  Score=105.84  Aligned_cols=70  Identities=26%  Similarity=0.319  Sum_probs=63.3

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      ....+.+|.||.+++|+||||+|++|++|+++|||+|+|...         .+++.|+|+|++++|++|+.+|.+++..
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~---------~~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---------DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS---------SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC---------CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999999999743         2368999999999999999999998765

>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=99.24  E-value=1.5e-11  Score=104.67  Aligned_cols=73  Identities=25%  Similarity=0.236  Sum_probs=65.6

Q ss_pred             ccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHH
Q 006320           77 VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDR  156 (650)
Q Consensus        77 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~  156 (650)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|++..+++.+|+|+|+|+           ..++++|..+|.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~-----------~e~v~~A~~~I~~~   81 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT-----------PESVQSAKRLLDQI   81 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEEC-----------HHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeC-----------HHHHHHHHHHHHHH
Confidence            3589999999999999999999999999999999999998767788999999996           34788999999888


Q ss_pred             hhhc
Q 006320          157 ILES  160 (650)
Q Consensus       157 i~e~  160 (650)
                      +.+.
T Consensus        82 i~~~   85 (92)
T 1x4n_A           82 VEKG   85 (92)
T ss_dssp             HHHT
T ss_pred             HHhc
Confidence            8664

>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=99.24  E-value=1.2e-11  Score=105.70  Aligned_cols=76  Identities=11%  Similarity=0.200  Sum_probs=67.1

Q ss_pred             CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       427 ~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      +.++.++.+|.||.++++.|||+||+ |++|+++|||+|+|+...      ..+++.|+|+|.+++|++|+.+|..++++
T Consensus        12 ~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g------~~~~~~V~I~G~~e~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC------CCCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            45678999999999999999999999 999999999999996432      12467899999999999999999999998


Q ss_pred             hhh
Q 006320          506 YLY  508 (650)
Q Consensus       506 ~~~  508 (650)
                      +..
T Consensus        86 ~~~   88 (95)
T 2ctm_A           86 YLA   88 (95)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            854

>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=99.24  E-value=6.7e-12  Score=106.09  Aligned_cols=72  Identities=35%  Similarity=0.534  Sum_probs=65.8

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI  157 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i  157 (650)
                      .++++|+||.+++|.||||+|++|++|+++|||+|+|++..+++.+|+|+|+|+           .+++++|..+|.+.+
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 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-----------QDQIQNAQYLLQNSV   81 (89)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEE-----------HHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcC-----------HHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998777889999999997           347889999999888


Q ss_pred             hhc
Q 006320          158 LES  160 (650)
Q Consensus       158 ~e~  160 (650)
                      .+.
T Consensus        82 ~e~   84 (89)
T 1j5k_A           82 KQY   84 (89)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            764

>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=99.23  E-value=5.7e-12  Score=107.65  Aligned_cols=75  Identities=17%  Similarity=0.391  Sum_probs=65.3

Q ss_pred             CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ...++.+|+||.+.+|+||||+|+ ||+|+++|||+|+|..... +.  ..+++.|+|+|++++|++|+.+|.++|++.
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~-~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QN--TGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC-CS--SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCC-CC--CCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            356899999999999999999999 9999999999999974322 11  246899999999999999999999999875

>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=99.22  E-value=1.7e-11  Score=106.77  Aligned_cols=76  Identities=20%  Similarity=0.303  Sum_probs=65.4

Q ss_pred             CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhh
Q 006320          429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYL  507 (650)
Q Consensus       429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  507 (650)
                      ..+.+.+|.||.+.+|+||||+|+ ||+|+++|||+|+|....+  .+ ..+++.|+|+|+.+++++|+.+|.+++++..
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~--~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE--GT-LLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC--CS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC--CC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            456889999999999999999999 9999999999999975322  11 2358899999999999999999999997654

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

Probab=99.22  E-value=1.2e-11  Score=108.25  Aligned_cols=73  Identities=14%  Similarity=0.296  Sum_probs=64.2

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      +++|+||.+++++||||+|++|++|+++|||+|+|....  .+ .....++.|+|+|+.++|++|+.+|.+++.+.
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~--~~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQL--PP-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCC--CT-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCcc--CC-CCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            789999999999999999999999999999999997532  12 12356899999999999999999999999875

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

Probab=99.21  E-value=1.4e-11  Score=107.24  Aligned_cols=71  Identities=21%  Similarity=0.388  Sum_probs=62.3

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ..+++|+||.+.+++||||+|+ ||+|+++|||+|+|.+.+  +   ...+|+|+|+|++++|++|+.+|.+++.+.
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~--~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G---TGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC--S---SSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC--C---CCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            3578999999999999999999 999999999999997432  1   246889999999999999999999999886

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

Probab=99.20  E-value=4.3e-11  Score=100.24  Aligned_cols=75  Identities=20%  Similarity=0.410  Sum_probs=65.0

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      ......+|.||..++|+||||+|++|++|+++|||+|.|....  .+  ....+|.|+|+|++++|++|+.+|.+++.+
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~--~~--~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG--SQ--NTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSS--CS--STTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCC--CC--CCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            3567899999999999999999999999999999999997521  11  236789999999999999999999998864

>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=99.19  E-value=2.4e-11  Score=103.74  Aligned_cols=74  Identities=18%  Similarity=0.242  Sum_probs=65.0

Q ss_pred             CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       427 ~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      ..+..++.+|.||.+.+|.|||+||+ ||+|+++|||+|+|++.+       +.++.|+|+|+++++++|+.+|.+++++
T Consensus        12 ~l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~   84 (94)
T 2cte_A           12 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAE   84 (94)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HhCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhc
Confidence            34567999999999999999999999 999999999999886422       2356899999999999999999999988


Q ss_pred             hh
Q 006320          506 YL  507 (650)
Q Consensus       506 ~~  507 (650)
                      ..
T Consensus        85 ~~   86 (94)
T 2cte_A           85 QD   86 (94)
T ss_dssp             HH
T ss_pred             cc
Confidence            74

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

Probab=99.18  E-value=2.5e-11  Score=105.73  Aligned_cols=71  Identities=23%  Similarity=0.428  Sum_probs=63.6

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      .+++|+||.+++++||||+|++|++|+++|+|+|+|.+.+   +   ...+|.|+|+|++++|++|+.+|.+++.+.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~---~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---G---TGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC---S---SSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC---C---CCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            4789999999999999999999999999999999997422   2   256899999999999999999999999875

>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=99.15  E-value=6.2e-11  Score=101.66  Aligned_cols=73  Identities=15%  Similarity=0.226  Sum_probs=63.6

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ...+++|.||.+.|+.|||+||+ |++|+++|||+|+|+...+ |   ...++.|+|+|..+++++|+.+|..++++.
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~-~---~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999 9999999999999975332 2   235788999999999999999999998764

>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=99.15  E-value=4.4e-11  Score=104.11  Aligned_cols=76  Identities=18%  Similarity=0.354  Sum_probs=66.3

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      ..++.+|+||..++|+||||+|++|++|+++|||+|+|.....   .+ ...++.|+|+|+.++|++|+.+|.+++.+.+
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~---~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GT-LLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC---CS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC---CC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            5678999999999999999999999999999999999975321   11 2468999999999999999999999998764

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

Probab=99.12  E-value=4.4e-11  Score=96.55  Aligned_cols=66  Identities=15%  Similarity=0.235  Sum_probs=58.1

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHH
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRL  503 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  503 (650)
                      ..+.+|.||.+.+|.|||+||+ |++|+++|||+|+|++..       +.++.|+|+|+.+++++|+.+|.+++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4678899999999999999999 999999999999996432       24678999999999999999998753

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

Probab=99.09  E-value=6.5e-11  Score=95.50  Aligned_cols=68  Identities=19%  Similarity=0.297  Sum_probs=60.3

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL  265 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  265 (650)
                      ...+..|.||..+++.|||++|++|++|+++|||+|+|....        ..++.|+|+|..++|++|+.+|..++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g--------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC--------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            456899999999999999999999999999999999997421        25689999999999999999998753

>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=99.08  E-value=9.1e-11  Score=100.16  Aligned_cols=74  Identities=23%  Similarity=0.221  Sum_probs=65.4

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      +..++..|.||..+++.|||++|++|++|+++|||+|+|....+       ..++.|+|+|..++|++|+.+|..++.+.
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-------PDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-------SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC-------CCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999999964211       34679999999999999999999999875


Q ss_pred             c
Q 006320          269 Q  269 (650)
Q Consensus       269 ~  269 (650)
                      .
T Consensus        87 ~   87 (95)
T 2ctm_A           87 L   87 (95)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.08  E-value=1.3e-10  Score=99.64  Aligned_cols=74  Identities=19%  Similarity=0.284  Sum_probs=64.8

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++.|.||..+++.|||++|++|++|+++|||+|+|....+  +.   ..++.|+|+|..++|.+|+.+|..++.+.
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~---~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GN---QPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CS---SCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CC---CCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            3468999999999999999999999999999999999975321  21   36789999999999999999999999774

>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=99.08  E-value=8.8e-11  Score=100.21  Aligned_cols=73  Identities=16%  Similarity=0.324  Sum_probs=65.0

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++.+|.||..+++.|||++|++|++|+++|||+|+|.+.+        ..++.|+|+|+.++|.+|+.+|.+++.+.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~--------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC--------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            4568999999999999999999999999999999999996421        23579999999999999999999999876


Q ss_pred             c
Q 006320          269 Q  269 (650)
Q Consensus       269 ~  269 (650)
                      .
T Consensus        86 ~   86 (94)
T 2cte_A           86 D   86 (94)
T ss_dssp             H
T ss_pred             c
Confidence            4

>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=99.03  E-value=2.1e-10  Score=99.60  Aligned_cols=71  Identities=20%  Similarity=0.247  Sum_probs=62.4

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYL  507 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  507 (650)
                      .+.+..|.||.+.+|.|||+||+ |++|+++|||+|+|....       +..+.|+|+|+.+++++|+.+|.+++++..
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            36889999999999999999999 999999999999996432       124589999999999999999999988764

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

Probab=98.98  E-value=3.9e-10  Score=97.43  Aligned_cols=68  Identities=12%  Similarity=0.258  Sum_probs=60.2

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhh-cCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhh
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRS-TGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLY  508 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~-Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  508 (650)
                      .++.+|.||+.+|++|||++|+ |++|+++ ++++|+|+.          .++.|+|+|+++.|++|..+|..++++...
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999 9999996 699998863          245899999999999999999999987643

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

Probab=98.96  E-value=6.2e-10  Score=96.63  Aligned_cols=70  Identities=21%  Similarity=0.282  Sum_probs=62.3

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      .++..|.||..+++.|||++|++|++|+++|||+|+|...+        ...+.|+|+|..++|++|+.+|..++.+.
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g--------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE--------LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT--------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC--------CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            47899999999999999999999999999999999997421        23468999999999999999999998764

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

Probab=98.96  E-value=5.4e-10  Score=95.19  Aligned_cols=73  Identities=18%  Similarity=0.236  Sum_probs=64.5

Q ss_pred             CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhc-CceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHH
Q 006320          427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRST-GANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR  504 (650)
Q Consensus       427 ~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~T-ga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~  504 (650)
                      +.++.++..|.||..+|+.|||+||+ |++|+++| ||+|+|+...       +..+.|+|.|+.++|++|+.+|.+++.
T Consensus        12 e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           12 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-------SGSDTVVIRGPSSDVEKAKKQLLHLAE   84 (95)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-------TTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            45678999999999999999999999 99999999 9999986322       235679999999999999999999998


Q ss_pred             hh
Q 006320          505 SY  506 (650)
Q Consensus       505 ~~  506 (650)
                      +.
T Consensus        85 e~   86 (95)
T 2ctj_A           85 EK   86 (95)
T ss_dssp             HH
T ss_pred             hh
Confidence            76

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

Probab=98.85  E-value=2.4e-09  Score=91.19  Aligned_cols=72  Identities=17%  Similarity=0.237  Sum_probs=64.3

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhc-CceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMET-KTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      ++.++..|.||..+++.|||++|++|++|+++| ||+|+|....        +..+.|+|.|..++|++|+.+|.+++.+
T Consensus        14 ~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g--------~~~~~V~I~G~~~~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           14 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG--------SGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT--------TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC--------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            567789999999999999999999999999999 9999996421        3467899999999999999999999987


Q ss_pred             c
Q 006320          268 S  268 (650)
Q Consensus       268 ~  268 (650)
                      .
T Consensus        86 ~   86 (95)
T 2ctj_A           86 K   86 (95)
T ss_dssp             H
T ss_pred             h
Confidence            5

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

Probab=98.83  E-value=4.2e-09  Score=90.91  Aligned_cols=68  Identities=15%  Similarity=0.251  Sum_probs=61.3

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhh-cCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRME-TKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ  269 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~  269 (650)
                      .++.+|.||..+|++|||++|++|++|+++ ++++|.|+.           .++.|+|+|+++.|.+|+.+|..++.+..
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----------~~~~ItI~G~~~~V~~a~~~I~~~v~el~   94 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----------GEDKITLEGPTEDVSVAQEQIEGMVKDLI   94 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----------SSCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----------CCCEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999997 589999852           35689999999999999999999998754

>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=98.53  E-value=6.3e-08  Score=80.99  Aligned_cols=68  Identities=18%  Similarity=0.215  Sum_probs=58.2

Q ss_pred             CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCce-EEEecCCCCCCCCCCCCeEEEEEe-cHHHHHHHHHHHHHHHHh
Q 006320          429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGAN-IQILSREEVPACVSGTDELVQIVG-EIQAARDALVEVTTRLRS  505 (650)
Q Consensus       429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~-I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  505 (650)
                      ...+...|.||.+.+|.+||+||+ |++|+++|||+ |.|.          +++..|+|.| +.+++++|+.+|..+...
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~----------eddG~V~I~g~~~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD----------EDTGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE----------TTTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE----------cCCCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            457889999999999999999999 99999999998 9884          1357899999 899999999887655444


Q ss_pred             h
Q 006320          506 Y  506 (650)
Q Consensus       506 ~  506 (650)
                      +
T Consensus        82 ~   82 (91)
T 2cpq_A           82 I   82 (91)
T ss_dssp             C
T ss_pred             E
Confidence            4

>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=98.50  E-value=1e-07  Score=79.66  Aligned_cols=66  Identities=20%  Similarity=0.238  Sum_probs=58.1

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCce-EEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHH
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQ-IRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRL  265 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l  265 (650)
                      ...+...|.||...++.+||++|++|++|+++||++ |.|..           ++..|+|.| +.+++++|+.+|..+-
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----------ddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----------DTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----------TTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----------CCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            456789999999999999999999999999999998 99962           257899999 7999999999886643

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.30  E-value=1.9e-06  Score=75.96  Aligned_cols=74  Identities=18%  Similarity=0.042  Sum_probs=57.1

Q ss_pred             ccEEEEEEecCc-------ccceeecCCChHHHHHHHHhCCeEEEecCCC----------CCCccEEEEecCCCCCCCCC
Q 006320           77 VTTTYRILCHDM-------KAGGVIGKSGSIIKSIRQHTGAWINVHELIP----------GDEERIIEISDTRRRDPEGR  139 (650)
Q Consensus        77 ~~~~~rilip~~-------~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~----------~~~ervi~I~G~~~~~~~~~  139 (650)
                      ..+.-+|.||.+       ++|.|||++|.+||+|+++|||+|.|.....          ..++-.|.|++..       
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~-------   82 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPK-------   82 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESS-------
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCC-------
Confidence            468889999876       7999999999999999999999999973211          1144568888753       


Q ss_pred             CCCccHHHHHHHHHHHHhhhc
Q 006320          140 MPSFSPAQEALFLIHDRILES  160 (650)
Q Consensus       140 ~~~~~~a~~A~~~i~~~i~e~  160 (650)
                         ...+++|+.+|.+.+.+.
T Consensus        83 ---~e~i~~A~~~Ie~Ll~~v  100 (119)
T 2yqr_A           83 ---PEGLAAAKKLCENLLQTV  100 (119)
T ss_dssp             ---HHHHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHHhhch
Confidence               456888888888777653

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.29  E-value=2.4e-06  Score=75.36  Aligned_cols=79  Identities=10%  Similarity=0.150  Sum_probs=59.8

Q ss_pred             CcEEEEEEEccc-------eeeeeecCCchHHHHHHhhcCceEEEecCCCC-C---CCccCCCcceEEEEcC-HHHHHHH
Q 006320          190 NRVATRMVVSRM-------HVGCLLGKGGKIIEQMRMETKTQIRILPRDHS-L---PRCVSMSEEIVQVVGD-INNVKNA  257 (650)
Q Consensus       190 ~~~~~~i~Vp~~-------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-l---p~~~~~~er~V~I~G~-~~~V~~A  257 (650)
                      ..++.+|.||-.       +++.|||++|.+||+|+++|||+|.|..++.. +   .......+-.|.|++. .+++++|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            467888988865       68999999999999999999999999743211 0   0000123447888765 9999999


Q ss_pred             HHHHHHHHhhc
Q 006320          258 VAIISSRLRES  268 (650)
Q Consensus       258 ~~~I~~~l~~~  268 (650)
                      +.+|..++.+.
T Consensus        90 ~~~Ie~Ll~~v  100 (119)
T 2yqr_A           90 KKLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHhhch
Confidence            99999999763

>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=98.26  E-value=2.1e-06  Score=77.27  Aligned_cols=80  Identities=23%  Similarity=0.311  Sum_probs=62.7

Q ss_pred             CCcEEEEEEEccc------eeeeeecCCchHHHHHHhhcCceEEEecCCCCC----------CCccCCCcceEEEEcC-H
Q 006320          189 GNRVATRMVVSRM------HVGCLLGKGGKIIEQMRMETKTQIRILPRDHSL----------PRCVSMSEEIVQVVGD-I  251 (650)
Q Consensus       189 ~~~~~~~i~Vp~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~l----------p~~~~~~er~V~I~G~-~  251 (650)
                      ...++.+|.||..      ++|.|||++|.+||+|+++|||+|.|..++...          +......+-.|.|++. .
T Consensus         4 ~~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~   83 (131)
T 1k1g_A            4 ATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTM   83 (131)
T ss_dssp             -CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSH
T ss_pred             CceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCH
Confidence            3578999999988      788999999999999999999999997532110          0001123568889995 8


Q ss_pred             HHHHHHHHHHHHHHhhc
Q 006320          252 NNVKNAVAIISSRLRES  268 (650)
Q Consensus       252 ~~V~~A~~~I~~~l~~~  268 (650)
                      +++.+|+.+|..+|.+.
T Consensus        84 e~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           84 ENVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHhcc
Confidence            99999999999999763

>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=98.23  E-value=2.3e-06  Score=76.96  Aligned_cols=77  Identities=16%  Similarity=0.297  Sum_probs=60.8

Q ss_pred             CceEEEEeecCC------cceeeecCCCc-hhhhhhhcCceEEEecCCCCC-----------CCCCCCCeEEEEEe-cHH
Q 006320          430 NIITTRLLVPSS------EIGCLEGRDGS-LSEMRRSTGANIQILSREEVP-----------ACVSGTDELVQIVG-EIQ  490 (650)
Q Consensus       430 ~~~~~~l~Vp~~------~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p-----------~~~~~~~r~v~I~G-~~~  490 (650)
                      ..++.+|.||.+      ++|.|||.+|. ||+|+++|||+|.|..+....           ......+-.|.|++ +.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            357889999988      78999999999 999999999999997643211           00112244599999 589


Q ss_pred             HHHHHHHHHHHHHHhh
Q 006320          491 AARDALVEVTTRLRSY  506 (650)
Q Consensus       491 ~v~~A~~~I~~~l~~~  506 (650)
                      ++++|+.+|..+|...
T Consensus        85 ~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999999764

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.93  E-value=3.3e-06  Score=76.38  Aligned_cols=73  Identities=25%  Similarity=0.366  Sum_probs=55.0

Q ss_pred             eEEEEeecCCc------ceeeecCCCc-hhhhhhhcCceEEEecCCCC------------CCCCCCCCe-EEEEEec-H-
Q 006320          432 ITTRLLVPSSE------IGCLEGRDGS-LSEMRRSTGANIQILSREEV------------PACVSGTDE-LVQIVGE-I-  489 (650)
Q Consensus       432 ~~~~l~Vp~~~------~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~------------p~~~~~~~r-~v~I~G~-~-  489 (650)
                      ++.+|.||.+.      +|.|||.+|. +|+|+++|||+|.|..+...            |.++..++. -|.|++. + 
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            56788888665      8999999999 99999999999999865421            111122333 4889994 3 


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 006320          490 ----QAARDALVEVTTRLR  504 (650)
Q Consensus       490 ----~~v~~A~~~I~~~l~  504 (650)
                          ..+++|+++|..+|.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                378999999988886

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.76  E-value=1.8e-05  Score=71.57  Aligned_cols=76  Identities=21%  Similarity=0.244  Sum_probs=56.0

Q ss_pred             EEEEEEEccce------eeeeecCCchHHHHHHhhcCceEEEecCCCCC-----------CCccC-CCcceEEEEcC-H-
Q 006320          192 VATRMVVSRMH------VGCLLGKGGKIIEQMRMETKTQIRILPRDHSL-----------PRCVS-MSEEIVQVVGD-I-  251 (650)
Q Consensus       192 ~~~~i~Vp~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~l-----------p~~~~-~~er~V~I~G~-~-  251 (650)
                      ++.+|.||-..      +|.|||.+|.++|+|+++|||+|.|..+....           |.... ..+-.|.|++. . 
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            56788888654      89999999999999999999999998543211           11001 12237888885 3 


Q ss_pred             ----HHHHHHHHHHHHHHhh
Q 006320          252 ----NNVKNAVAIISSRLRE  267 (650)
Q Consensus       252 ----~~V~~A~~~I~~~l~~  267 (650)
                          ..+.+|+.+|..+|..
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             hhHHHHHHHHHHHHHHHCCC
Confidence                3799999999998864

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.63  E-value=4.5e-05  Score=85.95  Aligned_cols=92  Identities=18%  Similarity=0.163  Sum_probs=68.6

Q ss_pred             cHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCc
Q 006320          144 SPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKT  223 (650)
Q Consensus       144 ~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga  223 (650)
                      ..+.++...|++.+.+.-....   .+-.+|               -.....+.||...++.|||+||++|+.|+++|||
T Consensus       537 ~~A~~g~~~I~~~m~~al~~~~---~~~~~~---------------ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~  598 (630)
T 3u1k_A          537 QQASVAKKEILQIMNKTISKPR---ASRKEN---------------GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGV  598 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSCC---SSCCTT---------------CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---hhhccc---------------CCeEEEEEeChhHhheeECCCChhHHHHHHHHCC
Confidence            4566666777777766543221   111122               2457889999999999999999999999999999


Q ss_pred             eEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHH
Q 006320          224 QIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRL  265 (650)
Q Consensus       224 ~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l  265 (650)
                      +|.|.            ++..|.|.+. .+++++|+.+|..++
T Consensus       599 ~I~I~------------d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          599 TISQV------------DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEC------------SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             EEEEc------------CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            99995            2468999997 789999999987765

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.52  E-value=4.5e-05  Score=85.93  Aligned_cols=85  Identities=19%  Similarity=0.177  Sum_probs=63.0

Q ss_pred             hHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320          408 FPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD  480 (650)
Q Consensus       408 ~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~  480 (650)
                      ..|.++..+|++.+.+...      ....+....|.||.+.++.|||+||+ ||+|+++|||+|.|.           ++
T Consensus       537 ~~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~-----------d~  605 (630)
T 3u1k_A          537 QQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV-----------DE  605 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC-----------SS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc-----------CC
Confidence            3455555555554443211      12346778899999999999999999 999999999999884           24


Q ss_pred             eEEEEEec-HHHHHHHHHHHHHHH
Q 006320          481 ELVQIVGE-IQAARDALVEVTTRL  503 (650)
Q Consensus       481 r~v~I~G~-~~~v~~A~~~I~~~l  503 (650)
                      -.|.|.|. .+++++|+++|.+++
T Consensus       606 G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          606 ETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             SEEEEEESSHHHHHHHHHHTTC--
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHHh
Confidence            57999996 688999999887654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.18  E-value=0.00026  Score=64.38  Aligned_cols=104  Identities=22%  Similarity=0.281  Sum_probs=73.2

Q ss_pred             EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhh
Q 006320           79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRIL  158 (650)
Q Consensus        79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~  158 (650)
                      -.+.|+++...+|..||++|+.|+.|+++.|-+|+|-+-..   +                         ....|.+.+.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~---d-------------------------~~~fI~naLs   87 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS---D-------------------------LERIVKNLFP   87 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS---S-------------------------HHHHHHHHST
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC---C-------------------------HHHHHHHhcC
Confidence            36778999999999999999999999999999999865211   1                         0111112221


Q ss_pred             hcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320          159 ESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL  228 (650)
Q Consensus       159 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  228 (650)
                      .......   ..+.              . +....+.+.||..+.++.|||+|.+++-...-||.+|.|.
T Consensus        88 PA~V~~V---~i~~--------------~-~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           88 GVKIESI---NVRE--------------R-NGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             TSCEEEE---EEEE--------------E-TTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             CceEEEE---EEee--------------c-CCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            1100000   0000              0 1345788999999999999999999999999999988875

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.16  E-value=0.00071  Score=59.93  Aligned_cols=70  Identities=17%  Similarity=0.151  Sum_probs=58.9

Q ss_pred             EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhh
Q 006320          433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLY  508 (650)
Q Consensus       433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  508 (650)
                      .+.+.|...+++.|+|++|+ |++|+..|+|.|+|..-+      .++.-.|+|.|.+..-..|+.+|.++..-+-.
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~------s~g~tEVtIfG~~~~Q~rak~MI~sLA~~hr~  127 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG------PERRAEIWIFGPPPFRRDVDRMLTDLAHYCRM  127 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC------TTSCEEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC------CCCcEEEEEECCHHHHHHHHHHHHHHHHHHHH
Confidence            46678999999999999999 999999999999996432      13345599999999999999999998876543

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=96.97  E-value=0.0013  Score=58.23  Aligned_cols=69  Identities=13%  Similarity=0.151  Sum_probs=60.3

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...+.|...+++.|+|++|+.|+.|+..|++.|+|...+.       +..-.|+|.|++..-.+|+.+|..+..-.
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-------~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-------ERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-------TSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-------CCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            4778999999999999999999999999999999975321       45678999999999999999999887654

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.89  E-value=0.00035  Score=79.64  Aligned_cols=95  Identities=17%  Similarity=0.198  Sum_probs=22.5

Q ss_pred             hHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320          408 FPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD  480 (650)
Q Consensus       408 ~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~  480 (650)
                      ..|.++..+|+..+.+...      ....+....+.||.+.++.|||+||. ||+|.++|||+|.|.           ++
T Consensus       540 ~~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~-----------dd  608 (726)
T 4aid_A          540 AQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN-----------DD  608 (726)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSCCSSCCSSCCC-------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE-----------CC
Confidence            3455555555555443221      12235667889999999999999999 999999999999773           24


Q ss_pred             eEEEEEec-HHHHHHHHHHHHHHHHhhhhhcccc
Q 006320          481 ELVQIVGE-IQAARDALVEVTTRLRSYLYRDFFQ  513 (650)
Q Consensus       481 r~v~I~G~-~~~v~~A~~~I~~~l~~~~~~~~~~  513 (650)
                      ..|.|.+. .+++++|+..|..++.+...-+.|.
T Consensus       609 G~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~  642 (726)
T 4aid_A          609 GVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYD  642 (726)
T ss_dssp             -----CCSCHHHHHHHHHC---------------
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEE
Confidence            45788875 8899999999999988776655443

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.87  E-value=0.00049  Score=78.44  Aligned_cols=96  Identities=18%  Similarity=0.271  Sum_probs=26.1

Q ss_pred             ccHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320          143 FSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK  222 (650)
Q Consensus       143 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg  222 (650)
                      +..+.++...|++.+.+.-....   .+-..|.               .....+.||...++.|||+||++|+.|.++||
T Consensus       539 L~~A~~g~~~I~~~m~~al~~~r---~~~~~~a---------------p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg  600 (726)
T 4aid_A          539 LAQAKEGRAHILGEMNKAMDAPR---ADVGDFA---------------PKIETINIPTDKIREVIGSGGKVIREIVATTG  600 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCC---SSCCSSC---------------CC------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhh---hhhcccC---------------CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHC
Confidence            34556666667777665432211   1112222               23677899999999999999999999999999


Q ss_pred             ceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhhc
Q 006320          223 TQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRES  268 (650)
Q Consensus       223 a~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~~  268 (650)
                      ++|.|..            +..|.|.+. .+++++|+..|..++.+.
T Consensus       601 ~~idi~d------------dG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          601 AKVDIND------------DGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             -------------------------CCSCHHHHHHHHHC--------
T ss_pred             CceeEEC------------CceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            9999852            356778775 899999999999988653

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=96.86  E-value=0.00049  Score=62.56  Aligned_cols=100  Identities=16%  Similarity=0.330  Sum_probs=70.9

Q ss_pred             eEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHH--hhhccC
Q 006320          348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQT--RIVDLG  425 (650)
Q Consensus       348 ~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~--~i~~~~  425 (650)
                      -...+.|+...+|+.||++|++|+.|+++.|-+|.+-.-..                +.    .+.+...+.  ++....
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~----------------d~----~~fI~naLsPA~V~~V~   95 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS----------------DL----ERIVKNLFPGVKIESIN   95 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS----------------SH----HHHHHHHSTTSCEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC----------------CH----HHHHHHhcCCceEEEEE
Confidence            46778899999999999999999999999999998754111                10    011111000  011000


Q ss_pred             C-CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEe
Q 006320          426 A-DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQIL  467 (650)
Q Consensus       426 ~-~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~  467 (650)
                      - ..+....+.+.||.++.+..|||+|. ++-..+.||.+|.|.
T Consensus        96 i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           96 VRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             EEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             EeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            0 01345678899999999999999999 999999999998774

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.29  E-value=0.024  Score=55.98  Aligned_cols=96  Identities=17%  Similarity=0.200  Sum_probs=65.1

Q ss_pred             cccceeecCCChHHHHH-HHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320           88 MKAGGVIGKSGSIIKSI-RQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF  166 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I-~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~  166 (650)
                      +-+|+-||++|++|+.| ++-.|-+|+|-.-.+   +                         ....|...+..+......
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~---d-------------------------p~~fi~nalsPA~V~~V~  177 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD---D-------------------------PARFVANALSPAKVVSVS  177 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS---S-------------------------HHHHHHHHTTTSCCSEEE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecC---C-------------------------HHHHHHhccCCcceEEEE
Confidence            55899999999999999 666788888864211   1                         111122222221110000


Q ss_pred             CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecC
Q 006320          167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPR  230 (650)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  230 (650)
                      .  .+                 .....+.+.||..+.++-|||+|.+++.-...||.+|.|...
T Consensus       178 i--~~-----------------~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          178 V--ID-----------------QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             E--EE-----------------TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             E--Ec-----------------CCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            0  00                 112378899999999999999999999999999999999753

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=94.90  E-value=0.038  Score=57.61  Aligned_cols=96  Identities=17%  Similarity=0.200  Sum_probs=66.7

Q ss_pred             cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320           88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF  166 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~  166 (650)
                      +-+|..||++|++|+.|.++. |-+|+|-+-.   +                         +....|...+..+......
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s---~-------------------------dp~~fi~nalsPA~V~~V~  300 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD---D-------------------------DPARFVANALSPAKVVSVS  300 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC---S-------------------------SHHHHHHHHTTTSCCSEEE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC---C-------------------------CHHHHHHHhcCCcceeEEE
Confidence            568999999999999999998 8888886521   1                         1111222222221110000


Q ss_pred             CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecC
Q 006320          167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPR  230 (650)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  230 (650)
                      .  .+                 +....+.+.||..+.++.|||+|.+++.....||.+|.|...
T Consensus       301 ~--~~-----------------~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          301 V--ID-----------------QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             E--EE-----------------TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             E--Ec-----------------CCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            0  00                 123478999999999999999999999999999999999753

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=93.80  E-value=0.039  Score=57.50  Aligned_cols=97  Identities=23%  Similarity=0.303  Sum_probs=64.2

Q ss_pred             ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320          357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR  435 (650)
Q Consensus       357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~  435 (650)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.                .+...-+..|+.  =.++....--.+..-.+.
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s----------------~dp~~fi~nals--PA~V~~V~~~~~~~~~a~  310 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD----------------DDPARFVANALS--PAKVVSVSVIDQTARAAR  310 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC----------------SSHHHHHHHHTT--TSCCSEEEEEETTTTEEE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC----------------CCHHHHHHHhcC--CcceeEEEEEcCCCcEEE
Confidence            457999999999999999998 7777764311                111000111110  000000000011245788


Q ss_pred             EeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCC
Q 006320          436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREE  471 (650)
Q Consensus       436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~  471 (650)
                      +.||..+.+..|||+|. ++-..+.||.+|.|.+..+
T Consensus       311 V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  347 (366)
T 1k0r_A          311 VVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  347 (366)
T ss_dssp             EEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESSC
T ss_pred             EEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHHH
Confidence            99999999999999999 9999999999999986543

>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=93.57  E-value=0.051  Score=53.66  Aligned_cols=95  Identities=20%  Similarity=0.281  Sum_probs=62.5

Q ss_pred             ccccceecCCchhHHHH-HHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHH--hhhccCCCCCCceE
Q 006320          357 DKVGRVIGESEGIVELL-QNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQT--RIVDLGADKDNIIT  433 (650)
Q Consensus       357 ~~vg~IIGk~G~~Ik~l-~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~--~i~~~~~~~~~~~~  433 (650)
                      +-+|+.||++|++|+.| ++-.|-+|.|-.-.                ++.    .+.|...+.  ++....-..+..-.
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s----------------~dp----~~fi~nalsPA~V~~V~i~~~~~~~  185 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD----------------DDP----ARFVANALSPAKVVSVSVIDQTARA  185 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC----------------SSH----HHHHHHHTTTSCCSEEEEEETTTTE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEec----------------CCH----HHHHHhccCCcceEEEEEEcCCCcE
Confidence            44799999999999999 56667777764311                010    011111100  00000000112357


Q ss_pred             EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCC
Q 006320          434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREE  471 (650)
Q Consensus       434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~  471 (650)
                      +.+.||..+.+.-|||+|. |+-..+.||.+|.|.+..+
T Consensus       186 a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          186 ARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             EEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             EEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            8899999999999999999 9999999999999986543

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=93.53  E-value=0.019  Score=65.66  Aligned_cols=94  Identities=19%  Similarity=0.202  Sum_probs=8.3

Q ss_pred             hHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320          408 FPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD  480 (650)
Q Consensus       408 ~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~  480 (650)
                      ..|.++..+|++.+.+...      ....+....+.||.+.++.+||+||. |++|.++||+.|.|-           .+
T Consensus       530 ~~A~~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~-----------~d  598 (723)
T 3cdi_A          530 NQAKGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE-----------DD  598 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHCC-------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEec-----------CC
Confidence            3445555555554443211      11234567788999999999999999 999999999999773           24


Q ss_pred             eEEEEEec-HHHHHHHHHHHHHHHHhhhhhccc
Q 006320          481 ELVQIVGE-IQAARDALVEVTTRLRSYLYRDFF  512 (650)
Q Consensus       481 r~v~I~G~-~~~v~~A~~~I~~~l~~~~~~~~~  512 (650)
                      ..|.|.+. .+.+++|++.|..++.+...-+.|
T Consensus       599 g~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~  631 (723)
T 3cdi_A          599 GTVKIAATDGEKAKHAIRRIEEITAEIEVGRVY  631 (723)
T ss_dssp             ---------------------------------
T ss_pred             ccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEE
Confidence            45777664 577788888887776655444443

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=93.14  E-value=0.027  Score=64.41  Aligned_cols=64  Identities=23%  Similarity=0.329  Sum_probs=0.0

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE  267 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~  267 (650)
                      ....+.||...++.+||++|.+|+.|.++||+.|.|..            +..|.|.+. .+.+++|+..|..++.+
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------------dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------------DGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------------CccEEEecCCHHHHHHHHHHHHHHhhh
Confidence            45678899999999999999999999999999998852            345677664 67788888887776644

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=92.70  E-value=0.18  Score=52.34  Aligned_cols=95  Identities=23%  Similarity=0.250  Sum_probs=65.2

Q ss_pred             cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320           88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF  166 (650)
Q Consensus        88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~  166 (650)
                      +-+|+.||.+|+.|+.|.++- |-+|+|-.-.+                            +....|...+.........
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~----------------------------d~~~fi~nal~Pa~v~~v~  296 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSD----------------------------DPKQLIANALAPATVIEVE  296 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCS----------------------------SHHHHHHHHTCSSCCSEEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCC----------------------------CHHHHHHHhcCccEEEEEE
Confidence            458999999999999999998 78888754210                            1111222222111100000


Q ss_pred             CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320          167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP  229 (650)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  229 (650)
                      .  .+                 +....+.+.||..+.++-|||+|.+++.-...||.+|.|..
T Consensus       297 ~--~d-----------------~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          297 I--LD-----------------KENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             E--EE-----------------TTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             E--Ec-----------------CCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            0  00                 12347899999999999999999999999999999999974

>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=92.20  E-value=0.019  Score=65.96  Aligned_cols=62  Identities=23%  Similarity=0.266  Sum_probs=21.9

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec-HHHHHHHHHHHHHHH
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-IQAARDALVEVTTRL  503 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l  503 (650)
                      +....+.||.+.++-+||++|. ||+|.++||+.|.|-           .+..|.|... .++.++|+..|..+.
T Consensus       597 p~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~-----------~dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          597 PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE-----------DDGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CBCCCC------------------CTTCCCCCSCC-------------------CCCBSSHHHHCC---------
T ss_pred             ceeEEEEEChHHeehcccccceeeehhhHhhCCEEEec-----------CCceEEEecCCHHHHHHHHHHHHHhc
Confidence            4456788999999999999999 999999999999774           1445777764 567777776666654

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=91.58  E-value=0.11  Score=53.99  Aligned_cols=95  Identities=25%  Similarity=0.355  Sum_probs=61.9

Q ss_pred             ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320          357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR  435 (650)
Q Consensus       357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~  435 (650)
                      +-+|+.||.+|.+|+.+.++. |-+|.+-.-           +     ++...-...||.  =.++....-..+..-.+.
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~-----------s-----~d~~~fi~nal~--Pa~v~~v~~~d~~~~~~~  306 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKW-----------S-----DDPKQLIANALA--PATVIEVEILDKENKAAR  306 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC-----------C-----SSHHHHHHHHTC--SSCCSEEEEEETTTTEEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEec-----------C-----CCHHHHHHHhcC--ccEEEEEEEEcCCCCEEE
Confidence            457999999999999999987 666665321           1     010000011110  000000000012345788


Q ss_pred             EeecCCcceeeecCCCc-hhhhhhhcCceEEEecC
Q 006320          436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR  469 (650)
Q Consensus       436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~  469 (650)
                      +.||..+.+.-|||+|. |+--.+.||.+|.|.+.
T Consensus       307 v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          307 VLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            99999999999999999 99999999999999754

>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=90.65  E-value=0.032  Score=64.12  Aligned_cols=61  Identities=16%  Similarity=0.214  Sum_probs=20.7

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHH
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRL  265 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l  265 (650)
                      ...+.||...++.+||++|++|+.|++++|+.|.|..            +..|.|... .+..++|+..|..+.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC--------------------CCCBSSHHHHCC---------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecC------------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3457899999999999999999999999999999852            345667664 677777877776654

---

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	650
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	4e-13
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-12
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-09
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-04
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-12
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	6e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-07
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-06
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-12
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	6e-08
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-07
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-10
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,	9e-05
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-11
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	6e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-04
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-10
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	7e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-07
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	0.002
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	7e-07
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-05
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	5e-05
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-10
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-08
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-05
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-04
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-09
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-06
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-04
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	4e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-05
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	0.002
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	9e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	3e-04
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	6e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	8e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	0.001
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	0.002

>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 = 62.5 bits (152), Expect = 4e-13
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 13/83 (15%)

Query: 77  VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDP 136
           VT T R+L H  + G +IGK G  +K +R+ +GA IN+ E      ERII ++       
Sbjct: 2   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP----T 55

Query: 137 EGRMPSFSPAQEALFLIHDRILE 159
                      +A  +I D++ E
Sbjct: 56  NA-------IFKAFAMIIDKLEE 71

>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 = 60.2 bits (146), Expect = 3e-12
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDI 251
           +  R+++    VG ++GK G+ +++MR E+  +I I   +          E I+ + G  
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN--------CPERIITLAGPT 55

Query: 252 NNVKNAVAIISSRLRE 267
           N +  A A+I  +L E
Sbjct: 56  NAIFKAFAMIIDKLEE 71

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (127), Expect = 1e-09
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG 487
           +  +T RLL+   E+G + G+ G  + +MR  +GA I I          +  + ++ + G
Sbjct: 1   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAG 53

Query: 488 EIQAARDALVEVTTRLR 504
              A   A   +  +L 
Sbjct: 54  PTNAIFKAFAMIIDKLE 70

>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 = 38.6 bits (90), Expect = 1e-04
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 8/76 (10%)

Query: 348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDEL 407
           L  R+L    +VG +IG+    V+ ++ E G  + +++      E+IIT++   GP +  
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLA---GPTNA- 57

Query: 408 FPAQEALLHIQTRIVD 423
               +A   I  ++ +
Sbjct: 58  --IFKAFAMIIDKLEE 71

>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 = 60.2 bits (146), Expect = 2e-12
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 11/79 (13%)

Query: 79  TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEG 138
           TT+ +   +   G +IG+ G+ I  IRQ +GA I +   + G   R + I+ +       
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS----AAS 57

Query: 139 RMPSFSPAQEALFLIHDRI 157
                     A +LI+ R+
Sbjct: 58  -------ISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (128), Expect = 6e-10
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD 250
           +    + +    +GC++G+ G  I ++R  +  QI+I                 V + G 
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSS------GRQVTITGS 54

Query: 251 INNVKNAVAIISSRL 265
             ++  A  +I++RL
Sbjct: 55  AASISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQ 490
            T  L +P++ IGC+ GR G+ ++E+R+ +GA I+I +  E       +   V I G   
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE-----GSSGRQVTITGSAA 56

Query: 491 AARDALVEVTTRL 503
           +   A   +  RL
Sbjct: 57  SISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 351 RMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPA 410
            +  P + +G +IG     +  ++   G  +K+A+PV+GS  + +TI+   G        
Sbjct: 5   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT---GSAAS---I 58

Query: 411 QEALLHIQTRI 421
             A   I  R+
Sbjct: 59  SLAQYLINARL 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 = 60.0 bits (145), Expect = 7e-12
 Identities = 18/102 (17%), Positives = 38/102 (37%), Gaps = 4/102 (3%)

Query: 178 GGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237
           G  G  G       V  ++ V +  VG ++G+GG+ I  +   +  +I            
Sbjct: 1   GSSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE----SEG 56

Query: 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGR 279
             +   ++++ G    V  A  +I  ++ E +   +   H  
Sbjct: 57  TLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKRIAHSA 98

>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 = 6e-08
 Identities = 18/93 (19%), Positives = 39/93 (41%), Gaps = 7/93 (7%)

Query: 432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQ 490
           +  +L VP   +G + GR G  +  + +++GA I     ++          L++I G  +
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIKISGTQK 71

Query: 491 AARDALVEVTTRLRSYLYRDFFQKETPPSSTGP 523
               A   +  ++      +  +K    S++GP
Sbjct: 72  EVAAAKHLILEKVSE---DEELRKRIAHSASGP 101

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.9 bits (111), Expect = 3e-07
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 13/84 (15%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPG--DEERIIEISDTRRRD 135
               ++       G +IG+ G  I+SI + +GA I   +   G     R+I+IS T    
Sbjct: 14  PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT---- 69

Query: 136 PEGRMPSFSPAQEALFLIHDRILE 159
            +           A  LI +++ E
Sbjct: 70  QKE-------VAAAKHLILEKVSE 86

>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 = 57.5 bits (139), Expect = 3e-11
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINN 253
             M V    VG +LGKGGK + + +  T  +I+I  +   LP         V + G    
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT---RNRRVTITGSPAA 61

Query: 254 VKNAVAIISSRL 265
            + A  +IS R+
Sbjct: 62  TQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (133), Expect = 1e-10
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 14/84 (16%)

Query: 77  VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV---HELIPGDEERIIEISDTRR 133
           +     +   +   G ++GK G  +   ++ TGA I +    E +PG   R + I+ +  
Sbjct: 1   MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-- 58

Query: 134 RDPEGRMPSFSPAQEALFLIHDRI 157
             P          Q A +LI  R+
Sbjct: 59  --PAA-------TQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
              + VP + +G + G+ G  L E +  TGA IQI  + E        +  V I G   A
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--TRNRRVTITGSPAA 61

Query: 492 ARDALVEVTTRL 503
            + A   ++ R+
Sbjct: 62  TQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (91), Expect = 9e-05
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 9/76 (11%)

Query: 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVA---DPVDGSDEQIITISSEEGPDD 405
           +  M  P + VG ++G+    +   Q   G  ++++   + + G+  + +TI+   G   
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT---GSPA 60

Query: 406 ELFPAQEALLHIQTRI 421
                Q A   I  R+
Sbjct: 61  A---TQAAQYLISQRV 73

>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 = 56.8 bits (137), Expect = 4e-11
 Identities = 17/79 (21%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVV 248
           G  + T++ + +   G ++GKGG+ I+Q+R E+   I+I              + I+ + 
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE------GSEDRIITIT 54

Query: 249 GDINNVKNAVAIISSRLRE 267
           G  + ++NA  ++ + +++
Sbjct: 55  GTQDQIQNAQYLLQNSVKQ 73

>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 = 54.5 bits (131), Expect = 4e-10
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 11/81 (13%)

Query: 79  TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEG 138
            T ++      AG +IGK G  IK IR  +GA I + E + G E+RII I+ T     + 
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT----QDQ 59

Query: 139 RMPSFSPAQEALFLIHDRILE 159
                   Q A +L+ + + +
Sbjct: 60  -------IQNAQYLLQNSVKQ 73

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (114), Expect = 6e-08
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE 488
            IITT++ +P    G + G+ G  + ++R  +GA+I+I    E        D ++ I G 
Sbjct: 2   PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-----GSEDRIITITGT 56

Query: 489 IQAARDALVEVTTRLRSY 506
               ++A   +   ++ Y
Sbjct: 57  QDQIQNAQYLLQNSVKQY 74

>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 = 38.7 bits (90), Expect = 1e-04
 Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 6/77 (7%)

Query: 345 GEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPD 404
           G  +  ++  P D  G +IG+    ++ +++E G  +K+ +P++GS+++IITI+   G  
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT---GTQ 57

Query: 405 DELFPAQEALLHIQTRI 421
           D+    Q A   +Q  +
Sbjct: 58  DQ---IQNAQYLLQNSV 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 = 56.1 bits (135), Expect = 1e-10
 Identities = 13/80 (16%), Positives = 38/80 (47%), Gaps = 4/80 (5%)

Query: 188 GGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQV 247
           G       +++     G ++GKGG+ I+Q++     ++ ++          + +++ +++
Sbjct: 4   GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG----PQNTGADKPLRI 59

Query: 248 VGDINNVKNAVAIISSRLRE 267
            GD   V+ A  ++   +R+
Sbjct: 60  TGDPYKVQQAKEMVLELIRD 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.0 bits (114), Expect = 7e-08
 Identities = 14/79 (17%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQI 485
           D        +++P+S+ G + G+ G  + +++   G  + ++         +G D+ ++I
Sbjct: 3   DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRI 59

Query: 486 VGEIQAARDALVEVTTRLR 504
            G+    + A   V   +R
Sbjct: 60  TGDPYKVQQAKEMVLELIR 78

>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 = 46.9 bits (111), Expect = 2e-07
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 13/84 (15%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV--HELIPGDEERIIEISDTRRRD 135
                I+    KAG VIGK G  IK +++  G  + +          ++ + I+     D
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG----D 62

Query: 136 PEGRMPSFSPAQEALFLIHDRILE 159
           P          Q+A  ++ + I +
Sbjct: 63  PYK-------VQQAKEMVLELIRD 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD--PVDGSDEQIITISSEEGPDDE 406
           V  ++ P  K G VIG+    ++ LQ   GV + +    P +   ++ + I+   G   +
Sbjct: 9   VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT---GDPYK 65

Query: 407 LFPAQEALLHI 417
           +  A+E +L +
Sbjct: 66  VQQAKEMVLEL 76

>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 = 55.6 bits (134), Expect = 1e-10
 Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 11/82 (13%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPE 137
             T      D   G +IG+ G  I  I+Q +G  I +     G  ER   ++ T    PE
Sbjct: 7   VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT----PE 62

Query: 138 GRMPSFSPAQEALFLIHDRILE 159
                    Q A  L+   + +
Sbjct: 63  S-------VQSAKRLLDQIVEK 77

>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 = 54.4 bits (131), Expect = 3e-10
 Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDI 251
           +     V    VG ++G+GG+ I +++ E+  +I+I P    LP      E    + G  
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP------ERSCMLTGTP 61

Query: 252 NNVKNAVAIISSRLRESQ 269
            +V++A  ++   + + +
Sbjct: 62  ESVQSAKRLLDQIVEKGR 79

>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 = 45.2 bits (107), Expect = 7e-07
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIV 486
           + +++T    VP   +G + GR G  +S +++ +G  IQI             +    + 
Sbjct: 4   QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLT 58

Query: 487 GEIQAARDALVEVTTRLR 504
           G  ++ + A   +   + 
Sbjct: 59  GTPESVQSAKRLLDQIVE 76

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.6 bits (95), Expect = 3e-05
 Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 3/67 (4%)

Query: 351 RMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPA 410
               P   VG +IG     +  +Q E G  +++A    G  E+   ++   G  + +  A
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLT---GTPESVQSA 67

Query: 411 QEALLHI 417
           +  L  I
Sbjct: 68  KRLLDQI 74

>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 = 54.9 bits (132), Expect = 2e-10
 Identities = 12/71 (16%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
             +V     G ++GKGG+ I+ +  ++  +I +     + P     + ++  + G    +
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIEL---QRNPPPNADPNMKLFTIRGTPQQI 60

Query: 255 KNAVAIISSRL 265
             A  +I  ++
Sbjct: 61  DYARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 14/81 (17%)

Query: 80  TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV---HELIPGDEERIIEISDTRRRDP 136
            +  +    K G +IGK G  IKSI Q +GA I +            ++  I  T ++  
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ-- 59

Query: 137 EGRMPSFSPAQEALFLIHDRI 157
                       A  LI ++I
Sbjct: 60  ---------IDYARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (100), Expect = 4e-06
 Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 435 RLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAAR 493
             +VP+ + G + G+ G  +  + + +GA I++              +L  I G  Q   
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPP--NADPNMKLFTIRGTPQQID 61

Query: 494 DALVEVTTRL 503
            A   +  ++
Sbjct: 62  YARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 9/75 (12%)

Query: 350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVA---DPVDGSDEQIITISSEEGPDDE 406
           F  + P  K G +IG+    ++ +  + G  +++     P    + ++ TI    G   +
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIR---GTPQQ 59

Query: 407 LFPAQEALLHIQTRI 421
                 A   I+ +I
Sbjct: 60  ---IDYARQLIEEKI 71

>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 = 54.1 bits (130), Expect = 4e-10
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 11/82 (13%)

Query: 78  TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPE 137
           +    +       G VIG++G +IK I+   G  I          ERI +I+      P+
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP----PD 57

Query: 138 GRMPSFSPAQEALFLIHDRILE 159
                   AQ A  +I D +  
Sbjct: 58  R-------AQHAAEIITDLLRS 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 = 50.3 bits (120), Expect = 1e-08
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNV 254
            + + R  VG ++G+ G++I++++ +   +I+  P D + P      E I Q+ G  +  
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP------ERIAQITGPPDRA 59

Query: 255 KNAVAIISSRLRESQ 269
           ++A  II+  LR  Q
Sbjct: 60  QHAAEIITDLLRSVQ 74

>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 = 39.9 bits (93), Expect = 5e-05
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 6/74 (8%)

Query: 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA 491
              + +P   +G + GR+G  + +++   G  IQ    +      +  + + QI G    
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDR 58

Query: 492 ARDALVEVTTRLRS 505
           A+ A   +T  LRS
Sbjct: 59  AQHAAEIITDLLRS 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 = 37.2 bits (86), Expect = 4e-04
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELF 408
           +  +  P   VG VIG +  +++ +QN+ GV ++       + E+I  I+   GP D   
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQIT---GPPDRAQ 60

Query: 409 PAQEALLHI 417
            A E +  +
Sbjct: 61  HAAEIITDL 69

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (122), Expect = 7e-09
 Identities = 13/82 (15%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG 249
            + +  + + + H   ++GK G+ ++ + ++T T+I+I   D             +++ G
Sbjct: 8   TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD--------PSNQIKITG 59

Query: 250 DINNVKNAVAIISSRLRESQHR 271
               ++ A   +     E   R
Sbjct: 60  TKEGIEKARHEVLLISAEQDKR 81

>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 = 43.9 bits (104), Expect = 2e-06
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 79  TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR 132
            +  +         VIGK+G  ++ +   T   I +    P D    I+I+ T+
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTK 61

>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 = 38.9 bits (91), Expect = 1e-04
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 8/75 (10%)

Query: 426 ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQ 484
           A      +  + +P      + G++G  L ++   T   IQI   ++           ++
Sbjct: 4   ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-------PSNQIK 56

Query: 485 IVGEIQAARDALVEV 499
           I G  +    A  EV
Sbjct: 57  ITGTKEGIEKARHEV 71

>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 = 49.8 bits (119), Expect = 1e-08
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG 249
             V+  + +       ++G  GK I ++  E K  IR        P+  +     V V G
Sbjct: 8   QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-------PQSGAPDPNCVTVTG 60

Query: 250 DINNVKNAVAIISSRLRE 267
              NV+ A+  I +   E
Sbjct: 61  LPENVEEAIDHILNLEEE 78

>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 = 49.0 bits (117), Expect = 4e-08
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 10/84 (11%)

Query: 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDI 251
           V   + V       ++G+ G  I +M  E +  I +   +           +I+ + G  
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--------QSDIIAITGLA 61

Query: 252 NNVKNAVAIISSRLR--ESQHRDR 273
            N+  A A +  R++  +++  DR
Sbjct: 62  ANLDRAKAGLLERVKELQAEQEDR 85

>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 = 41.3 bits (97), Expect = 2e-05
 Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 74  SLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR 132
             +V  T  +         VIG+ GS I+ +       I+V    P  +  II I+   
Sbjct: 5   EALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITGLA 61

>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 = 35.6 bits (82), Expect = 0.002
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 8/76 (10%)

Query: 432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQ 490
           +T  + VP      + G+ GS + +M      NI + + E          +++ I G   
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-------QSDIIAITGLAA 62

Query: 491 AARDALVEVTTRLRSY 506
               A   +  R++  
Sbjct: 63  NLDRAKAGLLERVKEL 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 = 47.9 bits (114), Expect = 9e-08
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINN 253
             + V   +   ++G+ G +I Q+R+E    I+   +D       +  ++ + + G   N
Sbjct: 12  LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG-----NQPQDQITITGYEKN 66

Query: 254 VKNAVAIISSRLRESQ 269
            + A   I   + E +
Sbjct: 67  TEAARDAILRIVGELE 82

>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 = 37.5 bits (87), Expect = 3e-04
 Identities = 9/54 (16%), Positives = 17/54 (31%), Gaps = 1/54 (1%)

Query: 80  TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELI-PGDEERIIEISDTR 132
              +         +IG+ G++I  IR      I   +       +  I I+   
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYE 64

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.5 bits (87), Expect = 4e-04
 Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-- 488
               + V       + GR G+ ++++R     NIQ   +++     +   + + I G   
Sbjct: 10  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQITITGYEK 65

Query: 489 -IQAARDALVEVTTRLRS 505
             +AARDA++ +   L  
Sbjct: 66  NTEAARDAILRIVGELEQ 83

>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 = 45.6 bits (108), Expect = 4e-07
 Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 9/83 (10%)

Query: 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRME-TKTQIRILPRDHSLPRCVSMSEEIVQVV 248
           N     + +       L+G  G++I  +  E     I                 + V + 
Sbjct: 8   NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS--------GSDTVVIR 59

Query: 249 GDINNVKNAVAIISSRLRESQHR 271
           G  ++V+ A   +     E Q +
Sbjct: 60  GPSSDVEKAKKQLLHLAEEKQTK 82

>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 = 44.0 bits (104), Expect = 1e-06
 Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 8/70 (11%)

Query: 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDI 251
               + +       L+GK G  I +++ + K  +RI P D            ++++ GD 
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI-PPDSE-------KSNLIRIEGDP 56

Query: 252 NNVKNAVAII 261
             V+ A   +
Sbjct: 57  QGVQQAKREL 66

>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 = 36.6 bits (85), Expect = 6e-04
 Identities = 11/57 (19%), Positives = 19/57 (33%), Gaps = 4/57 (7%)

Query: 76  MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR 132
           M      I         +IGKSG+ I  I+      + +      ++  +I I    
Sbjct: 4   MDYVEINI--DHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGDP 56

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 6/48 (12%)

Query: 82  RILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEIS 129
            +     K G VIG    +I  I++ TGA I +      +++  I I 
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI------EDDGTIYIG 47

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 35.8 bits (83), Expect = 8e-04
 Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 6/55 (10%)

Query: 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGP 403
           +  +  P+DK+G VIG    ++  +Q + G ++ +       D+  I I + +GP
Sbjct: 4   IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI------EDDGTIYIGAADGP 52

>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 = 36.3 bits (84), Expect = 0.001
 Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 4/58 (6%)

Query: 83  ILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRM 140
           +     + G VIG  G +   I + TG  I     +  +   +I   +     P   M
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVIT----VDTENSMVIVEPEAEGIPPVNLM 60

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 6/47 (12%)

Query: 83  ILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEIS 129
           +  +  +   VIGK GS+IK ++      I V       +  +I ++
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVV------GQNGLIWVN 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	650
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.45
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.43
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.42
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.42
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.42
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.41
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.4
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.39
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.38
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.37
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.36
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.36
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.35
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.34
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.33
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.33
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.32
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.27
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.21
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.2
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.2
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.19
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.19
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.16
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.09
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.97
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.95
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.94
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.93
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.93
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.52
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.51
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.5
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.46
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.41
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.39
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.37
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.15
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.12
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.01
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.9
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.78
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.37
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.1
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	93.77
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	93.66
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	92.13
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	91.58
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	85.71
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	84.75

>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=99.45  E-value=1.9e-14  Score=114.49  Aligned_cols=69  Identities=26%  Similarity=0.500  Sum_probs=62.5

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      ..++++|+||.+++|+||||+|+ |++|+++|||+|+|.+.       ...+|+|+|+|++++|.+|+.+|.++|+|
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            36899999999999999999999 99999999999999642       13579999999999999999999999975

>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=99.43  E-value=1.2e-13  Score=111.21  Aligned_cols=71  Identities=25%  Similarity=0.501  Sum_probs=64.0

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      .+|.+|.||.+++|+|||++|+ |++|+++|||+|+|....  +   .+++++|+|+|++++|++|+.+|.++|+++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~--~---~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL--E---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT--S---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC--C---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4788999999999999999999 999999999999996422  2   356889999999999999999999999986

>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=99.42  E-value=4.8e-14  Score=115.17  Aligned_cols=75  Identities=17%  Similarity=0.383  Sum_probs=66.5

Q ss_pred             CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ...++.+|+||.+++|+|||++|+ |++|+++|||+|+|.+.+..+   .+.+|+|+|+|++++|.+|+.+|.++|++.
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999 999999999999997644333   357899999999999999999999999763

>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=99.42  E-value=8.1e-14  Score=110.77  Aligned_cols=70  Identities=29%  Similarity=0.501  Sum_probs=63.8

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|.+.     .   ..+|+|+|+|++++|.+|+.+|.++|+|
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-----~---~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----N---CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----C---CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-----C---CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            35799999999999999999999999999999999999742     1   4589999999999999999999999875

>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=99.42  E-value=8.6e-14  Score=111.59  Aligned_cols=70  Identities=29%  Similarity=0.406  Sum_probs=61.5

Q ss_pred             eEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHH
Q 006320          432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRL  503 (650)
Q Consensus       432 ~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  503 (650)
                      .+++|.||.+++|+||||+|+ |++|+++|||+|+|.+.++..  ..+++|+|+|+|++++|++|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            357899999999999999999 999999999999997654432  2357899999999999999999999875

>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=99.41  E-value=7.7e-14  Score=110.91  Aligned_cols=69  Identities=20%  Similarity=0.378  Sum_probs=60.1

Q ss_pred             EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHH
Q 006320          433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRL  503 (650)
Q Consensus       433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  503 (650)
                      +.+|+||.+++|+||||+|+ |++|+++|||+|+|.+..+ + +..+++|+|+|+|++++|++|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~-~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-P-NADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-T-TSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-C-CCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            46899999999999999999 9999999999999975432 2 23457889999999999999999999874

>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=99.40  E-value=1.6e-13  Score=110.05  Aligned_cols=71  Identities=30%  Similarity=0.420  Sum_probs=63.2

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL  265 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  265 (650)
                      ..++|+||..++|+||||+|++|++|+++|||+|+|.+.++..+.   ..+|.|+|+|++++|++|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~---~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG---TRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTT---CCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCC---CCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            367999999999999999999999999999999999865443343   67999999999999999999999875

>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=99.39  E-value=1.7e-13  Score=108.82  Aligned_cols=70  Identities=16%  Similarity=0.345  Sum_probs=61.2

Q ss_pred             EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320          193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL  265 (650)
Q Consensus       193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  265 (650)
                      +.+|+||..++|+||||+|++|++|+++|||+|+|.+.....   ....+|.|+|+|++++|++|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPN---ADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTT---SCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCC---CCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            468999999999999999999999999999999997543222   2367899999999999999999999864

>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=99.38  E-value=1.5e-13  Score=110.15  Aligned_cols=71  Identities=24%  Similarity=0.400  Sum_probs=63.6

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ..+++|.||.+++|+||||+|+ |++|+++|||+|+|...+.     ...+++|+|+|++++|+.|+.+|.++|++.
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT-----SCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC-----CCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999 9999999999999975432     246889999999999999999999999875

>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=99.37  E-value=4.7e-13  Score=107.55  Aligned_cols=73  Identities=23%  Similarity=0.490  Sum_probs=65.2

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ..++.+|.||..++|+|||++|++|++|+++|||+|+|.+.   .+   ...++.|+|+|++++|.+|+.+|.+++++.
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~---~~---~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC---CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999999999999642   12   267899999999999999999999999874

>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=99.37  E-value=3.2e-13  Score=106.89  Aligned_cols=68  Identities=24%  Similarity=0.438  Sum_probs=61.3

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL  265 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  265 (650)
                      ++.+|.||..++|+||||+|++|++|+++|||+|.|.+..   +   ...+|.|+|+|++++|++|+.+|.++|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~---~---~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV---E---GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC---T---TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC---C---CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5889999999999999999999999999999999996421   2   367899999999999999999999876

>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=99.36  E-value=3.7e-13  Score=106.50  Aligned_cols=69  Identities=29%  Similarity=0.457  Sum_probs=63.5

Q ss_pred             cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320           78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI  157 (650)
Q Consensus        78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i  157 (650)
                      +++.+|+||.+++|.||||+|++|++|+++|||+|+|++..+++.+|+|+|+|+           .+++++|..+|.++|
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~-----------~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS-----------AASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEEC-----------HHHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeC-----------HHHHHHHHHHHHHHc
Confidence            378999999999999999999999999999999999998888889999999997           457899999988876

>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=99.36  E-value=2.7e-13  Score=110.65  Aligned_cols=76  Identities=16%  Similarity=0.378  Sum_probs=67.2

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      +..++.+|+||..++++||||+|++|++|+++|||+|.|.+. ...+   ...+|.|+|+|++++|.+|+.+|.++|++.
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~-~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQD-GPQN---TGADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCS-CCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccC-CCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999999999753 2222   367899999999999999999999999763

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=6.3e-13  Score=108.37  Aligned_cols=75  Identities=11%  Similarity=0.208  Sum_probs=66.2

Q ss_pred             CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       427 ~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      +.++.++..+.||..+|++|||++|+ |++|+++|||+|+|++.++      .+++.|+|+|++++|++|+.+|.+++++
T Consensus         5 e~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~------~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           5 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             HhhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC------CCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            45667889999999999999999999 9999999999999865432      2356899999999999999999999999


Q ss_pred             hh
Q 006320          506 YL  507 (650)
Q Consensus       506 ~~  507 (650)
                      ++
T Consensus        79 ~~   80 (81)
T d2ctma1          79 YL   80 (81)
T ss_dssp             HH
T ss_pred             Hh
Confidence            85

>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=99.35  E-value=6.6e-13  Score=113.66  Aligned_cols=78  Identities=19%  Similarity=0.275  Sum_probs=67.6

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ...+++.+|+||..++|+||||+|+ ||+|+++|||+|+|...++.   ....+|+|+|+|++++|++|+.+|.++|++.
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            4557899999999999999999999 99999999999999754432   2346889999999999999999999999875


Q ss_pred             hh
Q 006320          507 LY  508 (650)
Q Consensus       507 ~~  508 (650)
                      ..
T Consensus        88 ~~   89 (104)
T d1we8a_          88 EE   89 (104)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=99.34  E-value=5e-13  Score=107.06  Aligned_cols=72  Identities=25%  Similarity=0.499  Sum_probs=64.2

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++|.||..++|+||||+|++|++|+++|||+|+|...+   +   ...++.|+|+|++++|.+|+.+|.++|++.
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~---~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD---G---TTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT---T---SCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC---C---CCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            35799999999999999999999999999999999997532   2   256899999999999999999999999763

>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=99.33  E-value=1.4e-12  Score=111.58  Aligned_cols=78  Identities=18%  Similarity=0.341  Sum_probs=67.8

Q ss_pred             CCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          188 GGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       188 ~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      ....++.+|+||..++++||||+|.+|++|+++|||+|.|.+...    .....+|+|+|+|++++|.+|+.+|.++|.+
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE----GTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC----CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCC----CCCCCccEEEEEeCHHHHHHHHHHHHHHHhC
Confidence            356788999999999999999999999999999999999975322    1225689999999999999999999999977


Q ss_pred             cc
Q 006320          268 SQ  269 (650)
Q Consensus       268 ~~  269 (650)
                      ..
T Consensus        87 ~~   88 (104)
T d1we8a_          87 DE   88 (104)
T ss_dssp             HH
T ss_pred             cH
Confidence            53

>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=99.33  E-value=1.1e-12  Score=106.34  Aligned_cols=74  Identities=20%  Similarity=0.398  Sum_probs=66.6

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++.+|.||..++|+|||++|++|++|+++|||+|.|.+..   +   .+.++.|+|+|++++|.+|+.+|.++|.+.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~---~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---G---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC---C---CCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4678999999999999999999999999999999999997531   2   267899999999999999999999999874

>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=99.32  E-value=1e-12  Score=107.04  Aligned_cols=73  Identities=18%  Similarity=0.263  Sum_probs=64.9

Q ss_pred             CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       427 ~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      ...+.++.+|.||..++|+|||++|+ |++|+++|||+|+|++.+       +.++.|+|+|+.++|++|+.+|.+++.+
T Consensus         5 ~~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-------~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           5 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HhcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC-------CCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999 999999999999886432       3567899999999999999999999987


Q ss_pred             h
Q 006320          506 Y  506 (650)
Q Consensus       506 ~  506 (650)
                      .
T Consensus        78 ~   78 (81)
T d2ctea1          78 Q   78 (81)
T ss_dssp             H
T ss_pred             H
Confidence            5

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.32  E-value=9.1e-13  Score=106.94  Aligned_cols=74  Identities=19%  Similarity=0.340  Sum_probs=65.4

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      ....++.+|.||.+++|+|||++|+ |++|+++|||+|+|.+.+  +   .+++++|+|+|++++|+.|+.+|.++|.+.
T Consensus         4 ~~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~--~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           4 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--G---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             cCCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC--C---CCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            3457899999999999999999999 999999999999997432  1   356889999999999999999999999864

>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=99.27  E-value=3.2e-12  Score=104.91  Aligned_cols=72  Identities=15%  Similarity=0.228  Sum_probs=64.0

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      .++++|.||..++++|||++|+ |++|+++|||+|+|++.+. +   ..++++|+|+|+.++|+.|+.+|.+++++.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-~---~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-C---CCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            5788999999999999999999 9999999999999975432 2   356789999999999999999999999875

>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=99.24  E-value=2.8e-12  Score=104.75  Aligned_cols=73  Identities=16%  Similarity=0.205  Sum_probs=64.0

Q ss_pred             CCCceEEEEeecCCcceeeecCCCc-hhhhhhh-cCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320          428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRS-TGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS  505 (650)
Q Consensus       428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~-Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  505 (650)
                      ..+.++.+|.||..+||+|||++|+ |++|+++ ++++|+++..+       +.++.|+|+|++++|++|+.+|.+++++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~-------~~~~~v~I~G~~~~v~~A~~~I~~~v~e   78 (82)
T d2ctja1           6 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-------SGSDTVVIRGPSSDVEKAKKQLLHLAEE   78 (82)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-------TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC-------CCCceEEEeCCHHHHHHHHHHHHHHHhh
Confidence            4567899999999999999999999 9999977 69999886432       4578899999999999999999999998


Q ss_pred             hh
Q 006320          506 YL  507 (650)
Q Consensus       506 ~~  507 (650)
                      ..
T Consensus        79 ~~   80 (82)
T d2ctja1          79 KQ   80 (82)
T ss_dssp             HS
T ss_pred             hh
Confidence            63

>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=99.21  E-value=5.4e-12  Score=102.70  Aligned_cols=73  Identities=23%  Similarity=0.231  Sum_probs=64.3

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      +..++..+.||..++++|||++|++|++|+++|||+|+|.+.++       ..++.|+|+|++++|++|+.+|.+++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-------~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-------PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-------SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-------CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            35667899999999999999999999999999999999965322       33578999999999999999999999875

>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=99.20  E-value=7.1e-12  Score=99.25  Aligned_cols=65  Identities=15%  Similarity=0.245  Sum_probs=58.1

Q ss_pred             ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHH
Q 006320          431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTR  502 (650)
Q Consensus       431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~  502 (650)
                      ..+++|.||.++|++|||++|+ |++|+++|||+|+|++.+       ++++.|+|+|++++|++|+.+|.++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC-------CCCCEEEEECCHHHHHHHHHHHHHH
Confidence            4678899999999999999999 999999999999986422       4567899999999999999999875

>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=99.20  E-value=8.3e-12  Score=102.36  Aligned_cols=73  Identities=19%  Similarity=0.282  Sum_probs=64.6

Q ss_pred             cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ..+++|.||..++++|||++|++|++|+++|||+|+|++...     ....++.|+|+|+.++|.+|+.+|.+++.+.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-----~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-----GNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-----CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-----CCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            457899999999999999999999999999999999975321     2366889999999999999999999999874

>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=99.19  E-value=7.2e-12  Score=104.32  Aligned_cols=71  Identities=20%  Similarity=0.247  Sum_probs=63.4

Q ss_pred             CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhh
Q 006320          430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYL  507 (650)
Q Consensus       430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  507 (650)
                      ..++..|.||.++|++|||++|+ |++|+++|||+|.|++.+       +.++.|+|+|+.++|++|+.+|.+++.+..
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-------~~~~~v~I~G~~~~V~~A~~~I~~~v~e~~   79 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKELQ   79 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC-------CCcceEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            36899999999999999999999 999999999999886432       346789999999999999999999998653

>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=99.19  E-value=6.5e-12  Score=102.21  Aligned_cols=72  Identities=17%  Similarity=0.324  Sum_probs=65.1

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ...++.+|.||..++++|||++|++|++|+++|||+|.|++.+        +.++.|+|+|+.++|++|+.+|++++.+.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~--------~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--------DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC--------CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            4567999999999999999999999999999999999996432        45789999999999999999999999875

>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=99.16  E-value=1e-11  Score=102.97  Aligned_cols=71  Identities=11%  Similarity=0.269  Sum_probs=62.6

Q ss_pred             CCCCceEEEEeecCCcceeeecCCCc-hhhhhhh-cCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHH
Q 006320          427 DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRS-TGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR  504 (650)
Q Consensus       427 ~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~-Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~  504 (650)
                      ..++.++..|.||+.+|++|||++|+ |++|+++ +|++|+++.          .+..|+|+|++++|++|+.+|.++++
T Consensus        16 ~~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~----------~~~~v~i~G~~~~ve~Ak~~I~~iv~   85 (90)
T d2ctfa1          16 KANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVK   85 (90)
T ss_dssp             CCCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HcCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC----------CCceEEEeCCHHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999 9999999 589998852          24579999999999999999999998


Q ss_pred             hhh
Q 006320          505 SYL  507 (650)
Q Consensus       505 ~~~  507 (650)
                      +..
T Consensus        86 el~   88 (90)
T d2ctfa1          86 DLI   88 (90)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            864

>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=99.14  E-value=1.6e-11  Score=100.07  Aligned_cols=73  Identities=18%  Similarity=0.243  Sum_probs=64.1

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhh-cCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRME-TKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      ++.++.+|.||..+|++|||++|++|++|+++ ++|+|++...+        ..++.|+|+|++++|++|+.+|.+++.+
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~--------~~~~~v~I~G~~~~v~~A~~~I~~~v~e   78 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG--------SGSDTVVIRGPSSDVEKAKKQLLHLAEE   78 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT--------TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC--------CCCceEEEeCCHHHHHHHHHHHHHHHhh
Confidence            45678999999999999999999999999987 58999986421        4578999999999999999999999987


Q ss_pred             cc
Q 006320          268 SQ  269 (650)
Q Consensus       268 ~~  269 (650)
                      ..
T Consensus        79 ~~   80 (82)
T d2ctja1          79 KQ   80 (82)
T ss_dssp             HS
T ss_pred             hh
Confidence            53

>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=99.14  E-value=1.9e-11  Score=96.79  Aligned_cols=68  Identities=19%  Similarity=0.297  Sum_probs=60.6

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL  265 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  265 (650)
                      ...+++|.||..++++|||++|++|++|+++|||+|+|.+.+        +.++.|+|+|++++|++|+.+|++++
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~--------~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC--------CCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            456889999999999999999999999999999999996421        45789999999999999999998863

>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=99.09  E-value=3.9e-11  Score=99.80  Aligned_cols=71  Identities=21%  Similarity=0.268  Sum_probs=64.1

Q ss_pred             CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      -.++..|.||..+|+.|||++|++|++|+++|||+|.|++.+        +.++.|+|+|+.++|++|+.+|.+++.+.
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~--------~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE--------LQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT--------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC--------CCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999996532        45678999999999999999999999764

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=3.6e-10  Score=93.41  Aligned_cols=69  Identities=14%  Similarity=0.260  Sum_probs=62.0

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhc-CceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMET-KTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE  267 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~  267 (650)
                      ...++..|.||..+|++|||++|++|++|++++ +++|.+..           .+..|+|+|++++|++|+.+|.+++.+
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~-----------~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-----------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            356899999999999999999999999999995 89999952           246799999999999999999999987


Q ss_pred             c
Q 006320          268 S  268 (650)
Q Consensus       268 ~  268 (650)
                      .
T Consensus        87 l   87 (90)
T d2ctfa1          87 L   87 (90)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.95  E-value=2.6e-10  Score=92.67  Aligned_cols=63  Identities=11%  Similarity=0.141  Sum_probs=56.3

Q ss_pred             EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhh
Q 006320          434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYL  507 (650)
Q Consensus       434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  507 (650)
                      ..+.||.+.+|.|||++|+ |++|+++|||+|+|.           .+..|+|+|++++++.|+.+|..++++..
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~-----------~~g~v~I~G~~e~v~~A~~~I~~i~~ea~   66 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVG-----------QNGLIWVNGDRRKVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEEC-----------TTSEEEEESCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEEC-----------CCCEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            4578999999999999999 999999999999984           24579999999999999999988887753

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.94  E-value=4e-10  Score=91.58  Aligned_cols=63  Identities=24%  Similarity=0.286  Sum_probs=57.5

Q ss_pred             EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      ..+.||.++++.|||++|++|++|+++|||+|.|..            +..|+|+|++++|.+|+.+|..++++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            458899999999999999999999999999999952            357999999999999999999998875

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=3.9e-10  Score=90.33  Aligned_cols=65  Identities=20%  Similarity=0.228  Sum_probs=57.3

Q ss_pred             CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHH
Q 006320          189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISS  263 (650)
Q Consensus       189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~  263 (650)
                      ...++.+|.||.+++|+|||++|++|++|+++|||+|.+..          ..+..|+|.| ++++|++|+.+|..
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~----------~~~g~v~I~g~~~eav~~A~~~Ie~   70 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD----------EDTGTFRIYGESADAVKKARGFLEF   70 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE----------TTTTEEEEEESSHHHHHHHHHHHSC
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec----------CCCceEEEEECCHHHHHHHHHHHHH
Confidence            35678999999999999999999999999999999998863          2357899999 69999999999953

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=3.1e-10  Score=90.99  Aligned_cols=63  Identities=19%  Similarity=0.260  Sum_probs=55.4

Q ss_pred             CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEe-cHHHHHHHHHHHH
Q 006320          429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG-EIQAARDALVEVT  500 (650)
Q Consensus       429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~  500 (650)
                      .+.++.+|.||.+.+|.|||+||+ |++|+++|||+|.+..         ++++.|+|.| ++++|++|+.+|.
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~---------~~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD---------EDTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHS
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec---------CCCceEEEEECCHHHHHHHHHHHH
Confidence            346788999999999999999999 9999999999998752         2357899999 6999999999984

>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=98.52  E-value=1.5e-09  Score=84.66  Aligned_cols=61  Identities=7%  Similarity=0.058  Sum_probs=46.1

Q ss_pred             EEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec-HHHHHHHHHHHHHHHHhh
Q 006320          435 RLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-IQAARDALVEVTTRLRSY  506 (650)
Q Consensus       435 ~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  506 (650)
                      -+.||.+.+|.|||++|+ ||+|+++|||+|+|.           .+..|+|+|. .++++.|..+|..+.++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~-----------~~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA-----------NNGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEEC-----------TTSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEc-----------CCCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            477999999999999999 999999999999883           1346999996 679999999997766654

>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=98.51  E-value=4e-08  Score=79.30  Aligned_cols=63  Identities=19%  Similarity=0.209  Sum_probs=51.6

Q ss_pred             EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEE-----ecHHHHHHHHHHHHHHHHhh
Q 006320          434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIV-----GEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~l~~~  506 (650)
                      +.+.||.+.+|.|||+||+ ||+|+++|||+|+|.++          +..|.+.     |.+.++++|...|.++.|.+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d----------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC----------CCeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            4688999999999999999 99999999999999532          2345554     46889999999998877655

>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=98.50  E-value=2.5e-09  Score=83.43  Aligned_cols=62  Identities=13%  Similarity=0.094  Sum_probs=47.7

Q ss_pred             EEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhhc
Q 006320          195 RMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRES  268 (650)
Q Consensus       195 ~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~~  268 (650)
                      .+.||...++.||||+|++|++|+++|||+|.|..            +..|+|+|. .+++++|+.+|..+.++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~------------~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------------NGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT------------TSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC------------CCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            47899999999999999999999999999999942            346999996 789999999998766553

>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=98.46  E-value=9.4e-08  Score=77.05  Aligned_cols=64  Identities=17%  Similarity=0.173  Sum_probs=52.9

Q ss_pred             EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEE-----EcCHHHHHHHHHHHHHHHhhc
Q 006320          194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQV-----VGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I-----~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      +.+.||...+|.|||++|++|++|+++|||+|+|...           +..|.+     .|.+.++.+|...|.++.+..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d-----------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC-----------CCeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            3589999999999999999999999999999999632           234444     456889999999999887654

>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=98.41  E-value=1.8e-07  Score=75.63  Aligned_cols=63  Identities=14%  Similarity=0.119  Sum_probs=55.8

Q ss_pred             EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhhc
Q 006320          194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRES  268 (650)
Q Consensus       194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~~  268 (650)
                      ..+.||.+.++.|||++|++|+.|+++|||+|.|..            +-.|.|.|. .+.+..|+.+|..+.++.
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d------------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET------------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC------------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999962            246999995 899999999999987764

>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=98.39  E-value=1.5e-08  Score=74.31  Aligned_cols=48  Identities=27%  Similarity=0.362  Sum_probs=16.0

Q ss_pred             EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCC
Q 006320           79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR  132 (650)
Q Consensus        79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~  132 (650)
                      ...+|.||.+++|.|||++|++||.|+++|||+|+|.+      +..|.|++..
T Consensus         3 ~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~~   50 (54)
T d1e3ha4           3 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAAD   50 (54)
T ss_dssp             BCC---------------------CHHHHSCCCC--------------CCCCBS
T ss_pred             eEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEecC
Confidence            34578899999999999999999999999999999985      4678888864

>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=98.37  E-value=1.6e-07  Score=75.81  Aligned_cols=61  Identities=11%  Similarity=0.114  Sum_probs=53.3

Q ss_pred             EEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec-HHHHHHHHHHHHHHHHhh
Q 006320          435 RLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-IQAARDALVEVTTRLRSY  506 (650)
Q Consensus       435 ~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  506 (650)
                      .+.||.+.++.|||+||+ |+.|+++|||+|.|.           ++-.|.|.|. .+.+..|+.+|..+.++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~-----------d~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA-----------RNGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEE-----------TTTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEEC-----------CCcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            477999999999999999 999999999999984           1346999995 889999999998887765

>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=98.15  E-value=6.2e-07  Score=74.84  Aligned_cols=52  Identities=19%  Similarity=0.226  Sum_probs=46.3

Q ss_pred             ceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320          443 IGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY  506 (650)
Q Consensus       443 ~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  506 (650)
                      .|+|||+||. |+.|++.|||.|.|.            +..|.|.|++++++.|+.+|..++.+.
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~------------d~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVG------------EYEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEEC------------SSEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEe------------CCeEEEEECchhHHHHHHHHHHHHcCC
Confidence            6899999999 999999999999883            235788899999999999999999764

>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=98.12  E-value=6.9e-07  Score=74.56  Aligned_cols=54  Identities=24%  Similarity=0.304  Sum_probs=47.9

Q ss_pred             eeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320          202 HVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES  268 (650)
Q Consensus       202 ~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~  268 (650)
                      +.|.|||++|++|+.|++.|||+|.|.             +..|.|.|++++++.|+.+|..++.+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~-------------d~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG-------------EYEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC-------------SSEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe-------------CCeEEEEECchhHHHHHHHHHHHHcCC
Confidence            368999999999999999999999995             235778899999999999999999764

>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=98.01  E-value=3e-07  Score=67.23  Aligned_cols=44  Identities=11%  Similarity=0.089  Sum_probs=12.5

Q ss_pred             eEEEEecCCcccccccCCCcchhhHHHhcCCeEEEEEeeeEEEe
Q 006320          605 TLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKVY  648 (650)
Q Consensus       605 t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~~~~~~~~~  648 (650)
                      ..+|.||.+++|.|||+||++|+.|++.|||.|.|.-+--|.+|
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~ddg~v~I~   47 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIG   47 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------CCC
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeCCeEEEEE
Confidence            45689999999999999999999999999999999877666554

>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=97.90  E-value=1.4e-05  Score=68.59  Aligned_cols=76  Identities=18%  Similarity=0.401  Sum_probs=59.4

Q ss_pred             ceEEEEeecCCc------ceeeecCCCc-hhhhhhhcCceEEEecCCCC----------CCCCCCCCeE-EEEEec-HHH
Q 006320          431 IITTRLLVPSSE------IGCLEGRDGS-LSEMRRSTGANIQILSREEV----------PACVSGTDEL-VQIVGE-IQA  491 (650)
Q Consensus       431 ~~~~~l~Vp~~~------~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~----------p~~~~~~~r~-v~I~G~-~~~  491 (650)
                      .++.+|+||-+.      +|.|||.+|+ +|.|+++|||+|.|..+...          +.....++.+ |.|+++ .+.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            367789999875      8999999999 99999999999999865431          1112234445 889996 679


Q ss_pred             HHHHHHHHHHHHHhh
Q 006320          492 ARDALVEVTTRLRSY  506 (650)
Q Consensus       492 v~~A~~~I~~~l~~~  506 (650)
                      +..|+.+|..+|...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999998653

>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=3.1e-05  Score=66.44  Aligned_cols=78  Identities=23%  Similarity=0.339  Sum_probs=59.3

Q ss_pred             cEEEEEEEccce------eeeeecCCchHHHHHHhhcCceEEEecCCCC---------CCCccCCC-cceEEEEcC-HHH
Q 006320          191 RVATRMVVSRMH------VGCLLGKGGKIIEQMRMETKTQIRILPRDHS---------LPRCVSMS-EEIVQVVGD-INN  253 (650)
Q Consensus       191 ~~~~~i~Vp~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~---------lp~~~~~~-er~V~I~G~-~~~  253 (650)
                      .++.+|+||-..      +|.|||.+|+++|+|+++|||+|.|.-+...         -+.....+ .=.|.|+++ .+.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            467888998764      8999999999999999999999999754221         01111112 236778886 789


Q ss_pred             HHHHHHHHHHHHhhc
Q 006320          254 VKNAVAIISSRLRES  268 (650)
Q Consensus       254 V~~A~~~I~~~l~~~  268 (650)
                      +.+|+.+|..+|...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999764

>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=97.37  E-value=4.7e-05  Score=66.05  Aligned_cols=73  Identities=25%  Similarity=0.345  Sum_probs=53.6

Q ss_pred             eEEEEeecCC------cceeeecCCCc-hhhhhhhcCceEEEecCCCC------------CCCCCCCCeE-EEEEecH--
Q 006320          432 ITTRLLVPSS------EIGCLEGRDGS-LSEMRRSTGANIQILSREEV------------PACVSGTDEL-VQIVGEI--  489 (650)
Q Consensus       432 ~~~~l~Vp~~------~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~------------p~~~~~~~r~-v~I~G~~--  489 (650)
                      ++.+|+||.+      ++|.|||.+|. +|.|+++|||+|.|..+...            |.....++.+ |.|++.-  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            4567888854      67999999999 99999999999999876532            1111233455 8888852  


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 006320          490 ----QAARDALVEVTTRLR  504 (650)
Q Consensus       490 ----~~v~~A~~~I~~~l~  504 (650)
                          ..+.+|+.+|..+|.
T Consensus        82 ~~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHcC
Confidence                357788888877773

>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=97.10  E-value=0.00019  Score=62.15  Aligned_cols=76  Identities=21%  Similarity=0.225  Sum_probs=54.7

Q ss_pred             EEEEEEEcc------ceeeeeecCCchHHHHHHhhcCceEEEecCCCCC-----------CCccC-CCcceEEEEcCH--
Q 006320          192 VATRMVVSR------MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSL-----------PRCVS-MSEEIVQVVGDI--  251 (650)
Q Consensus       192 ~~~~i~Vp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~l-----------p~~~~-~~er~V~I~G~~--  251 (650)
                      ++.+|.||-      +++|.|||.+|.++|+|+++|||+|.|.-+...-           +.... ..+=-|.|++..  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            466778874      3689999999999999999999999998653210           00011 234467788752  


Q ss_pred             ----HHHHHHHHHHHHHHhh
Q 006320          252 ----NNVKNAVAIISSRLRE  267 (650)
Q Consensus       252 ----~~V~~A~~~I~~~l~~  267 (650)
                          ..+.+|+.+|..+|..
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p  101 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVP  101 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHHHHcCC
Confidence                3588899999988854

>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=93.77  E-value=0.014  Score=43.73  Aligned_cols=38  Identities=18%  Similarity=0.139  Sum_probs=34.9

Q ss_pred             cceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEE
Q 006320          603 RSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLIN  640 (650)
Q Consensus       603 ~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~  640 (650)
                      .....|+||++.....|||+|.|++-..+.+|.+|-|-
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~   62 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR   62 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEE
Confidence            35788999999999999999999999999999998774

>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=93.66  E-value=0.017  Score=43.33  Aligned_cols=37  Identities=14%  Similarity=0.039  Sum_probs=34.4

Q ss_pred             ceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEE
Q 006320          604 STLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLIN  640 (650)
Q Consensus       604 ~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~  640 (650)
                      .+..|+||++..+..|||+|.|++-..+.+|.+|-|-
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~   63 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK   63 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeE
Confidence            4688999999999999999999999999999998774

>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=92.13  E-value=0.038  Score=41.22  Aligned_cols=38  Identities=26%  Similarity=0.257  Sum_probs=35.4

Q ss_pred             EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320          192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP  229 (650)
Q Consensus       192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  229 (650)
                      ..+.+.||..+.+..|||+|.+++-..+.||.+|.|..
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            36889999999999999999999999999999999975

>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=91.58  E-value=0.043  Score=41.08  Aligned_cols=39  Identities=26%  Similarity=0.364  Sum_probs=35.2

Q ss_pred             eEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCC
Q 006320          432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSRE  470 (650)
Q Consensus       432 ~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~  470 (650)
                      -.+.+.||..+.+..|||+|. |+-..+.||.+|+|.+-+
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~~   66 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIM   66 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEECC
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEcc
Confidence            467899999999999999999 999999999999997543

>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=85.71  E-value=0.077  Score=43.97  Aligned_cols=46  Identities=11%  Similarity=-0.039  Sum_probs=37.1

Q ss_pred             cceEEEEecC-CcccccccCCCcchhhHHHhcCCe------EEEEEeeeEEEe
Q 006320          603 RSTLEVVLPD-YAVPKLITKSKTLLTRFSEVSLLL------HLINLFNFVKVY  648 (650)
Q Consensus       603 ~~t~~v~IP~-~~~g~vIGk~G~~I~~Ir~~SGA~------i~i~~~~~~~~~  648 (650)
                      .+..++.|+. +.-+-|||++|+.|++|+..+-..      ..++++-||||.
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~ar~~le~~~~~kV~L~L~VKV~  100 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVK  100 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHTTSCEEEEEEEEET
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHHHHHHHHHHhCCCeEEEEEEEEC
Confidence            3678899999 888999999999999998765432      367888889884

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=84.75  E-value=0.079  Score=44.21  Aligned_cols=45  Identities=11%  Similarity=-0.023  Sum_probs=36.5

Q ss_pred             cceEEEEecC-CcccccccCCCcchhhHHHhcCCe------EEEEEeeeEEE
Q 006320          603 RSTLEVVLPD-YAVPKLITKSKTLLTRFSEVSLLL------HLINLFNFVKV  647 (650)
Q Consensus       603 ~~t~~v~IP~-~~~g~vIGk~G~~I~~Ir~~SGA~------i~i~~~~~~~~  647 (650)
                      .+..++.|+. +.-+-|||++|+.|++|...+-..      ..++++-||||
T Consensus        49 ~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~aR~~le~~~~~kV~L~L~VKV  100 (118)
T d1wf3a2          49 YIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYLDLEVKV  100 (118)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHTSEEEEEEEEEE
T ss_pred             EEEEEEEeCccchhhhhhccCchhHHHHHHHHHHHHHHHhCCCeEEEEEEEE
Confidence            4678899999 788899999999999887665443      35788888988