Citrus Sinensis ID: 009173

---

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-
Protein Sequence
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS
Secondary Structure (PSIPRED)
cccccccHHHHHHcccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccEEEEcccHHHHHHHHHHcccEEEccccccccccEEEEEcccccccccHHHHHHHHHHHHHHHcccccccccccccccccEEEEEEEEcccEEEEEcccccHHHHHHHHHccEEEEccccccccccccccEEEEcccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccEEcccccHHHHHHHHHccEEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHcHHHHHHHHcccccEEEccccccccccccccccccccccccccccccccccccccHHHHccccccccccccEccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccEHHHHHHHcccEEEEccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEEcccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccHccccccccccccccccccccHcccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mtgsrfneanlqeTIHKPLEVAFQESICRPVETILHetirrpvdtiphetihrpldtisHETIRRSleavphdtiarpveavPQEILWRSLesgpqeilrrplevfapesshrssealsIETQHRLFGAVSQEILPDLHVDILSQrnsvlttapsssisyvsavrplslesdRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGafisvgatmpecdERLITVtasegpesryspaQKAVVLVFSRLIegtsekgldfssnkgllVNARLVVASNQvgcllgkggtiiSEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVtgrlrdnhfsgtlntartrstssvltetspysrlkdpasfgvhssvavshdfsqppltqgmdhlglshsldcpsspklwtaqtvtgvhlrgssdvgrgwsqglshhkgglelgsgsksaivtNTTVEiivpenvigsvygengsnLLRLRQISGakvivheprlgstdrivvisgtpDETQAAQSLLQAFILTGPS
Flexible Loop (DISEMBL)
mtgsrfneanlqetihkplevafQESICRPVETILhetirrpvdtiphetihrpldtishETIRRSLEavphdtiarpveavpQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVlttapsssisyvSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTasegpesryspaQKAVVLVFSRLIEGTsekgldfssnKGLLVNARLVVASNQVgcllgkggtiisemrkVTGTSIRIISDQLLKCISENDRvvqisgefskvKDAVYNVtgrlrdnhfsgtlntartrstssvltetspysrlkdPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKgglelgsgskSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAkvivheprlgstDRIVVISGTPDETQAAQSLLQAFILTGPS
Low Complexity Region (SEG)
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQglshhkgglelgsgsksAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS
Disordered region (IsUnstruct)
**************IHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSL*******************************QHRLFGAVSQEILPDLHVDILSQRNSVLTT*****ISYVSAVRPL******VATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT************QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS******************************************************************KLWTAQTVTGVHLRGSSDVGRGWS****************KSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG**********LLQAFIL****
Disordered Region (DISOPRED)
*************TI***************************************************************************************************************************************************************************SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL*******************NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS***********************************VAVSHDFSQPPLT*****************************************SQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV******STDRIVVISGTPDETQAAQSLLQAFILT***
Disordered Region (DISEMBL)
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVF************SIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNT***************YSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS
Disordered Region (DISPRO)
****RFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAV*QEILWRSL*SGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDI*S***************************************QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK********GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTR*TSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRG******************************TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS
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	541	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.539	0.481	0.284	6e-28
Q61990	362	Poly(rC)-binding protein	yes	no	0.595	0.889	0.275	2e-21
O19048	356	Poly(rC)-binding protein	no	no	0.576	0.876	0.268	2e-21
P60335	356	Poly(rC)-binding protein	no	no	0.576	0.876	0.268	2e-21
Q15365	356	Poly(rC)-binding protein	no	no	0.576	0.876	0.268	2e-21
Q5E9A3	356	Poly(rC)-binding protein	no	no	0.576	0.876	0.268	2e-21
P57721	371	Poly(rC)-binding protein	no	no	0.563	0.822	0.254	4e-20
P57722	371	Poly(rC)-binding protein	no	no	0.571	0.832	0.251	7e-20
Q15366	365	Poly(rC)-binding protein	yes	no	0.589	0.873	0.275	3e-19
P38151	413	PAB1-binding protein 2 OS	yes	no	0.606	0.794	0.227	1e-10

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

 Score =  125 bits (315), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 104/365 (28%), Positives = 181/365 (49%), Gaps = 73/365 (20%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC--DERLITVTAS 238
           ++ +E+ F++LC    +  VIGKGG+ I+ ++  +G+ I V  +  +C  DE +I VTA+
Sbjct: 307 SRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDECVIIVTAT 366

Query: 239 EGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGT 298
           E P+   S A +AV+L+   + +  +E            V  +L+V+S  +GC++GK G+
Sbjct: 367 ESPDDMKSMAVEAVLLLQEYINDEDAEN-----------VKMQLLVSSKVIGCVIGKSGS 415

Query: 299 IISEMRKVTGTSIRIISDQLLKCIS--ENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSG 356
           +I+E+RK T  +I         CIS  + D +V++SGE S V+DA+  +  RLR++   G
Sbjct: 416 VINEIRKRTNANI---------CISKGKKDDLVEVSGEVSSVRDALIQIVLRLREDVL-G 465

Query: 357 TLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLD 416
             ++  TR          P +R  D  SF   SS A    ++ P     M          
Sbjct: 466 DKDSVATR---------KPPAR-TDNCSFLSGSSNA---GYTLPSFMSSM---------- 502

Query: 417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSG---SKSAIVTNTTVEI 473
                      + +G H  GS   G               LGS    S   + +++ +EI
Sbjct: 503 ----------ASTSGFHGYGSFPAGDNV------------LGSTGPYSYGRLPSSSALEI 540

Query: 474 IVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQ 533
           ++P + +  V G+ G NL  +R+ISGA + +   +    D I ++SGT ++ + A++L+Q
Sbjct: 541 LIPAHAMSKVMGKGGGNLENIRRISGAMIEISASKTSHGDHIALLSGTLEQMRCAENLVQ 600

Query: 534 AFILT 538
           AF+++
Sbjct: 601 AFVMS 605

Arabidopsis thaliana (taxid: 3702)

>sp|Q61990|PCBP2_MOUSE Poly(rC)-binding protein 2 OS=Mus musculus GN=Pcbp2 PE=1 SV=1

 Score =  104 bits (260), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 99/360 (27%), Positives = 164/360 (45%), Gaps = 38/360 (10%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+    GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
            TG  +++  D L    +  +R + I+G    + + V  +   + ++   G     R + 
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYRPKP 182

Query: 366 TSSVLTETSP---YSRLKDPASFG-VHSSVAVSHDFSQPPL----TQGM-----DHLGLS 412
           +SS +        YS   D ASF     S+ ++ D   PPL     QG        L   
Sbjct: 183 SSSPVIFAGGQDRYSTGSDSASFPHTTPSMCLNPDLEGPPLEAYTIQGQYAIPQPDLTKL 242

Query: 413 HSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVE 472
           H L    S    T        +  SS   +G+  GL               A    T+ E
Sbjct: 243 HQLAMQQSHFPMTHGNTGFSGIESSSPEVKGYWAGLD--------------ASAQTTSHE 288

Query: 473 IIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL 532
           + +P ++IG + G  G+ +  +RQ+SGA++ +  P  GSTDR V I+G+      AQ L+
Sbjct: 289 LTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 348

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.

Mus musculus (taxid: 10090)

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

 Score =  104 bits (259), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 99/369 (26%), Positives = 167/369 (45%), Gaps = 57/369 (15%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
            TG  +++  D L    +  +R + I+G    V + V  +   + +     TL+ +    
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLE-----TLSQSPQGR 177

Query: 366 TSSVLTETSPYS----------RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSL 415
             ++  +  P S          R  D A +  H++    HD   PPL             
Sbjct: 178 VMTIPYQPMPASSPVICAGGQDRCSDAAGY-PHAT----HDLEGPPL------------- 219

Query: 416 DCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIV--------- 466
               +  +    T++ + L   + V R  S     H G    G  S S  V         
Sbjct: 220 ---DAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWASLDA 276

Query: 467 -TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDET 525
            T TT E+ +P N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+    
Sbjct: 277 STQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 336

Query: 526 QAAQSLLQA 534
             AQ L+ A
Sbjct: 337 SLAQYLINA 345

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 =  104 bits (259), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 99/369 (26%), Positives = 167/369 (45%), Gaps = 57/369 (15%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
            TG  +++  D L    +  +R + I+G    V + V  +   + +     TL+ +    
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLE-----TLSQSPQGR 177

Query: 366 TSSVLTETSPYS----------RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSL 415
             ++  +  P S          R  D A +  H++    HD   PPL             
Sbjct: 178 VMTIPYQPMPASSPVICAGGQDRCSDAAGY-PHAT----HDLEGPPL------------- 219

Query: 416 DCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIV--------- 466
               +  +    T++ + L   + V R  S     H G    G  S S  V         
Sbjct: 220 ---DAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWASLDA 276

Query: 467 -TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDET 525
            T TT E+ +P N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+    
Sbjct: 277 STQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 336

Query: 526 QAAQSLLQA 534
             AQ L+ A
Sbjct: 337 SLAQYLINA 345

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 =  104 bits (259), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 99/369 (26%), Positives = 167/369 (45%), Gaps = 57/369 (15%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
            TG  +++  D L    +  +R + I+G    V + V  +   + +     TL+ +    
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLE-----TLSQSPQGR 177

Query: 366 TSSVLTETSPYS----------RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSL 415
             ++  +  P S          R  D A +  H++    HD   PPL             
Sbjct: 178 VMTIPYQPMPASSPVICAGGQDRCSDAAGY-PHAT----HDLEGPPL------------- 219

Query: 416 DCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIV--------- 466
               +  +    T++ + L   + V R  S     H G    G  S S  V         
Sbjct: 220 ---DAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWASLDA 276

Query: 467 -TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDET 525
            T TT E+ +P N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+    
Sbjct: 277 STQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 336

Query: 526 QAAQSLLQA 534
             AQ L+ A
Sbjct: 337 SLAQYLINA 345

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 =  104 bits (259), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 99/369 (26%), Positives = 167/369 (45%), Gaps = 57/369 (15%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
            TG  +++  D L    +  +R + I+G    V + V  +   + +     TL+ +    
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLE-----TLSQSPQGR 177

Query: 366 TSSVLTETSPYS----------RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSL 415
             ++  +  P S          R  D A +  H++    HD   PPL             
Sbjct: 178 VMTIPYQPMPASSPVICAGGQDRCSDAAGY-PHAT----HDLEGPPL------------- 219

Query: 416 DCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIV--------- 466
               +  +    T++ + L   + V R  S     H G    G  S S  V         
Sbjct: 220 ---DAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWASLDA 276

Query: 467 -TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDET 525
            T TT E+ +P N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+    
Sbjct: 277 STQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 336

Query: 526 QAAQSLLQA 534
             AQ L+ A
Sbjct: 337 SLAQYLINA 345

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

Bos taurus (taxid: 9913)

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

 Score =  100 bits (248), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 91/358 (25%), Positives = 158/358 (44%), Gaps = 53/358 (14%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER++T+T   GP    
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTIT---GPTD-- 98

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLL----VNARLVVASNQVGCLLGKGGTIIS 301
                A+   F+ +     E  ++  SN        V  RLVV ++Q G L+GKGG+ I 
Sbjct: 99  -----AIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIK 153

Query: 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTA 361
           E+R+ TG  +++  D L    +  +R V ISG    +   V  +   + ++   G     
Sbjct: 154 EIRESTGAQVQVAGDMLP---NSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPY 210

Query: 362 RTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSP 421
           R +  S+ +             ++ +    A+ H           D L   H L    +P
Sbjct: 211 RPKPASTPVI-------FAGGQAYTIQGQYAIPHP----------DQLTKLHQLAMQQTP 253

Query: 422 KLWTAQTVTG-----VHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVP 476
                QT        + L  S +     +Q L     GL+       A    +T E+ +P
Sbjct: 254 FPPLGQTNPAFPGEKLPLHSSEE-----AQNLMGQSSGLD-------ASPPASTHELTIP 301

Query: 477 ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQA 534
            ++IG + G  G+ +  +RQ+SGA++ +     GS++R + I+GTP     AQ L+ A
Sbjct: 302 NDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGTPANISLAQYLINA 359

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

Homo sapiens (taxid: 9606)

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

 Score = 99.4 bits (246), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 89/354 (25%), Positives = 156/354 (44%), Gaps = 45/354 (12%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER++T+T   GP    
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTIT---GPTDAI 100

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +  E       +  +     V  RLVV ++Q G L+GKGG+ I E+R+
Sbjct: 101 F---KAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRE 157

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
            TG  +++  D L    +  +R V ISG    +   V  +   + ++   G     R + 
Sbjct: 158 STGAQVQVAGDMLP---NSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYRPKP 214

Query: 366 TSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWT 425
            S+ +             ++ +    A+ H           D L   H L    +P    
Sbjct: 215 ASTPVI-------FAGGQAYTIQGQYAIPHP----------DQLTKLHQLAMQQTPFPPL 257

Query: 426 AQTVTG-----VHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVI 480
            QT        + L  S +     +Q L     GL+       A    +T E+ +P ++I
Sbjct: 258 GQTNPAFPGEKLPLHSSEE-----AQNLMGQSSGLD-------ASPPASTHELTIPNDLI 305

Query: 481 GSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQA 534
           G + G  G+ +  +RQ+SGA++ +     GS++R + I+GTP     AQ L+ A
Sbjct: 306 GCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGTPANISLAQYLINA 359

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

Mus musculus (taxid: 10090)

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

 Score = 97.4 bits (241), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 101/366 (27%), Positives = 165/366 (45%), Gaps = 47/366 (12%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+    GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT----GRLRDNHFSGTLNTA 361
            TG  +++  D L    +  +R + I+G    + + V  +       L  +   G     
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLETLSQSPPKGVTIPY 182

Query: 362 RTRSTSSVLTETSP---YSRLKDPASFG-VHSSVAVSHDFSQPPL----TQG-----MDH 408
           R + +SS +        YS   D ASF     S+ ++ D   PPL     QG        
Sbjct: 183 RPKPSSSPVIFAGGQDRYSTGSDSASFPHTTPSMCLNPDLEGPPLEAYTIQGQYAIPQPD 242

Query: 409 LGLSHSLDCPSS--PKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIV 466
           L   H L    S  P        +G+    S +V   W         GL+       A  
Sbjct: 243 LTKLHQLAMQQSHFPMTHGNTGFSGIE-SSSPEVKGYW---------GLD-------ASA 285

Query: 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQ 526
             T+ E+ +P ++IG + G  G+ +  +RQ+SGA++ +  P  GSTDR V I+G+     
Sbjct: 286 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASIS 345

Query: 527 AAQSLL 532
            AQ L+
Sbjct: 346 LAQYLI 351

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|P38151|PBP2_YEAST PAB1-binding protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PBP2 PE=1 SV=1

 Score = 68.6 bits (166), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 90/396 (22%), Positives = 166/396 (41%), Gaps = 68/396 (17%)

Query: 167 LSLESDRVATLDARTQQQ-----------EVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215
           L  E  RVA  DA +              +V  R+LC       ++G  G  I  ++SE 
Sbjct: 37  LEAEIKRVALKDADSHSDNDHDSPDNVPSDVHLRMLCLVKHASLIVGHKGATISRIKSET 96

Query: 216 GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE--GTSEKGLDFSSN 273
            A I++   +    ER++ V  +           KA  ++   L+E  G  + G D   +
Sbjct: 97  SARINISNNIRGVPERIVYVRGT------CDDVAKAYGMIVRALLEEHGNEDNGEDIEIS 150

Query: 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
             LL+   L      +GC++GK G+ + E+  ++   +    +QLL     NDR++ I+G
Sbjct: 151 INLLIPHHL------MGCIIGKRGSRLREIEDLSAAKLFASPNQLLLS---NDRILTING 201

Query: 334 EFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAV 393
               V DA++  T      + S TL   +  S    +  +  Y     P  F   +SV +
Sbjct: 202 ----VPDAIHIATF-----YISQTLLNFQMESPQKNVKRSIYYQ----PTQF---NSVLI 245

Query: 394 SHDFSQP------------PLTQGMDH-----LGLSHSLDCPSSPKLWTAQTVTGVHLRG 436
            H  SQP            P  + + +     L +S +L   ++P+  TA        + 
Sbjct: 246 DH--SQPNTIFHQRNHQYHPSDKLLSYKPNKNLPISSTLLSMATPQYTTASVANATAFQP 303

Query: 437 SSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQ 496
           +  +       ++   G +   +     ++     EI + E  +G+V G++G ++  +++
Sbjct: 304 NFVI-----PNVTVLDGPVISPAPGNHLLMNFVQQEIFIDEKFVGNVIGKDGKHINSVKE 358

Query: 497 ISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL 532
            +G  +I+ +P  GS++R + I GT   +QAA  L+
Sbjct: 359 STGCSIIIQDPVEGSSERRLTIRGTFMASQAAIMLI 394

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

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	541
225464083	648	PREDICTED: KH domain-containing protein	0.739	0.617	0.677	1e-152
296088778	585	unnamed protein product [Vitis vinifera]	0.739	0.683	0.677	1e-151
147789223	569	hypothetical protein VITISV_022038 [Viti	0.739	0.702	0.677	1e-150
449438568	658	PREDICTED: KH domain-containing protein	0.754	0.620	0.616	1e-132
356546743	663	PREDICTED: poly(rC)-binding protein 3-li	0.695	0.567	0.636	1e-128
449516663	643	PREDICTED: KH domain-containing protein	0.720	0.606	0.597	1e-126
356557593	710	PREDICTED: KH domain-containing protein	0.695	0.529	0.581	1e-126
255563372	698	Poly(rC)-binding protein, putative [Rici	0.719	0.557	0.541	1e-122
356519471	591	PREDICTED: KH domain-containing protein	0.696	0.637	0.580	1e-119
356528011	433	PREDICTED: KH domain-containing protein	0.696	0.870	0.572	1e-119

>gi|225464083|ref|XP_002269250.1| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  543 bits (1400), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 284/419 (67%), Positives = 333/419 (79%), Gaps = 19/419 (4%)

Query: 125 RLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQ 184
           R    V Q+ LPD  VD+  QR SVL   PS++ISY S  RPLS+ ++R++TLD +T QQ
Sbjct: 238 RPLEVVPQQSLPDPRVDLFQQRGSVLPPIPSNTISYASGSRPLSINTERISTLDPKTSQQ 297

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           EV F+ILCSND+VG VIGKGGTI++ALQ+EAGA ISVGA + ECDERLIT+TASE PESR
Sbjct: 298 EVIFKILCSNDRVGGVIGKGGTIVKALQNEAGASISVGAPVAECDERLITITASENPESR 357

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
           YSPAQ  V+LVF+R IE   EKGLD S +KG  V+ARLVV SNQVGCL+GKGGTIISEMR
Sbjct: 358 YSPAQNGVILVFNRSIEAGIEKGLD-SGSKGSPVSARLVVPSNQVGCLMGKGGTIISEMR 416

Query: 305 KVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF-SGTLNTAR 362
           K +G  IRII SDQ+ KC SEND+VVQISGEF  V+D +Y++TGRLRDN F S TLN A 
Sbjct: 417 KASGAGIRIIGSDQVPKCASENDQVVQISGEFVNVQDGLYHITGRLRDNLFPSKTLNGAG 476

Query: 363 TRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQ-PPLTQGMDHLGLSHSLDCPSSP 421
            RS SS + E SPY R++DPASFG+HSSV VS  FS+   LTQ MDHLGLSHSLD P+SP
Sbjct: 477 IRS-SSAMNEISPYGRVRDPASFGLHSSVGVSPSFSRHTTLTQSMDHLGLSHSLDHPTSP 535

Query: 422 KLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIG 481
           +LW +QTVTGV+ R              + KGG+ELGSGSKSAI+TNTTVEI++PENVIG
Sbjct: 536 RLWPSQTVTGVNPR--------------NIKGGIELGSGSKSAIITNTTVEIVIPENVIG 581

Query: 482 SVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGP 540
           SVYGENG+NL RLR+ISGAKV +HEPR G++DRIV+ISGTPDETQAAQSLLQAFI TGP
Sbjct: 582 SVYGENGNNLARLRKISGAKVTLHEPRPGTSDRIVIISGTPDETQAAQSLLQAFIHTGP 640

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088778|emb|CBI38228.3| unnamed protein product [Vitis vinifera]

 Score =  540 bits (1391), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 284/419 (67%), Positives = 333/419 (79%), Gaps = 19/419 (4%)

Query: 125 RLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQ 184
           R    V Q+ LPD  VD+  QR SVL   PS++ISY S  RPLS+ ++R++TLD +T QQ
Sbjct: 175 RPLEVVPQQSLPDPRVDLFQQRGSVLPPIPSNTISYASGSRPLSINTERISTLDPKTSQQ 234

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           EV F+ILCSND+VG VIGKGGTI++ALQ+EAGA ISVGA + ECDERLIT+TASE PESR
Sbjct: 235 EVIFKILCSNDRVGGVIGKGGTIVKALQNEAGASISVGAPVAECDERLITITASENPESR 294

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
           YSPAQ  V+LVF+R IE   EKGLD S +KG  V+ARLVV SNQVGCL+GKGGTIISEMR
Sbjct: 295 YSPAQNGVILVFNRSIEAGIEKGLD-SGSKGSPVSARLVVPSNQVGCLMGKGGTIISEMR 353

Query: 305 KVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF-SGTLNTAR 362
           K +G  IRII SDQ+ KC SEND+VVQISGEF  V+D +Y++TGRLRDN F S TLN A 
Sbjct: 354 KASGAGIRIIGSDQVPKCASENDQVVQISGEFVNVQDGLYHITGRLRDNLFPSKTLNGAG 413

Query: 363 TRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQ-PPLTQGMDHLGLSHSLDCPSSP 421
            RS SS + E SPY R++DPASFG+HSSV VS  FS+   LTQ MDHLGLSHSLD P+SP
Sbjct: 414 IRS-SSAMNEISPYGRVRDPASFGLHSSVGVSPSFSRHTTLTQSMDHLGLSHSLDHPTSP 472

Query: 422 KLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIG 481
           +LW +QTVTGV+ R              + KGG+ELGSGSKSAI+TNTTVEI++PENVIG
Sbjct: 473 RLWPSQTVTGVNPR--------------NIKGGIELGSGSKSAIITNTTVEIVIPENVIG 518

Query: 482 SVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGP 540
           SVYGENG+NL RLR+ISGAKV +HEPR G++DRIV+ISGTPDETQAAQSLLQAFI TGP
Sbjct: 519 SVYGENGNNLARLRKISGAKVTLHEPRPGTSDRIVIISGTPDETQAAQSLLQAFIHTGP 577

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147789223|emb|CAN69138.1| hypothetical protein VITISV_022038 [Vitis vinifera]

 Score =  539 bits (1389), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 284/419 (67%), Positives = 333/419 (79%), Gaps = 19/419 (4%)

Query: 125 RLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQ 184
           R    V Q+ LPD  VD+  QR SVL   PS++ISY S  RPLS+ ++R++TLD +T QQ
Sbjct: 159 RPLEVVPQQSLPDPRVDLFQQRGSVLPPIPSNTISYASGSRPLSINTERISTLDPKTSQQ 218

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           EV F+ILCSND+VG VIGKGGTI++ALQ+EAGA ISVGA + ECDERLIT+TASE PESR
Sbjct: 219 EVIFKILCSNDRVGGVIGKGGTIVKALQNEAGASISVGAPVAECDERLITITASENPESR 278

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
           YSPAQ  V+LVF+R IE   EKGLD S +KG  V+ARLVV SNQVGCL+GKGGTIISEMR
Sbjct: 279 YSPAQNGVILVFNRSIEAGIEKGLD-SGSKGSPVSARLVVPSNQVGCLMGKGGTIISEMR 337

Query: 305 KVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF-SGTLNTAR 362
           K +G  IRII SDQ+ KC SEND+VVQISGEF  V+D +Y++TGRLRDN F S TLN A 
Sbjct: 338 KASGAGIRIIGSDQVPKCASENDQVVQISGEFVNVQDGLYHITGRLRDNLFPSKTLNGAG 397

Query: 363 TRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQ-PPLTQGMDHLGLSHSLDCPSSP 421
            RS SS + E SPY R++DPASFG+HSSV VS  FS+   LTQ MDHLGLSHSLD P+SP
Sbjct: 398 IRS-SSAMNEISPYGRVRDPASFGLHSSVGVSPSFSRHTTLTQSMDHLGLSHSLDHPTSP 456

Query: 422 KLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIG 481
           +LW +QTVTGV+ R              + KGG+ELGSGSKSAI+TNTTVEI++PENVIG
Sbjct: 457 RLWPSQTVTGVNPR--------------NIKGGIELGSGSKSAIITNTTVEIVIPENVIG 502

Query: 482 SVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGP 540
           SVYGENG+NL RLR+ISGAKV +HEPR G++DRIV+ISGTPDETQAAQSLLQAFI TGP
Sbjct: 503 SVYGENGNNLARLRKISGAKVTLHEPRPGTSDRIVIISGTPDETQAAQSLLQAFIHTGP 561

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438568|ref|XP_004137060.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  478 bits (1230), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 257/417 (61%), Positives = 316/417 (75%), Gaps = 9/417 (2%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           AV  E LPDLH+D + QRNSVL   PSSS  + S +  LS+++D +  +D    QQ+V F
Sbjct: 247 AVIHETLPDLHMDHILQRNSVLPILPSSSNIFASGIHSLSIDADMLPPVDTNVAQQDVVF 306

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           +ILC+ND++G VIGKGGTI+RALQ+E+GA +SVG ++  CDERLI++TASE  ESRYSPA
Sbjct: 307 KILCANDRIGGVIGKGGTIVRALQNESGATVSVGPSVTGCDERLISITASENIESRYSPA 366

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
           QKAVVLVFSR ++   EK  + SS+KG  V ARLVV SNQVGC+LGKGG IISE+RKVTG
Sbjct: 367 QKAVVLVFSRSVDVAIEKWQE-SSSKGSPVVARLVVPSNQVGCVLGKGGVIISEIRKVTG 425

Query: 309 TSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS-- 365
           T+IRII SDQ+  C +E+D +VQISGEFS V+DA+YNVTGRLRDN FS  L+ + TR+  
Sbjct: 426 TNIRIISSDQVPNCAAESDEIVQISGEFSNVQDALYNVTGRLRDNLFSSVLSNSGTRNGG 485

Query: 366 TSSVLTETSPYSRLKDPASFGVHSSVAVSH-DFSQPPLTQGMDHLGLSHSLDCPSSPKLW 424
            +SV  ETSPY R++D A     + V  SH  F Q    Q  D LGLSHSLD PSSP LW
Sbjct: 486 GTSVYPETSPYGRVRDTAPLVRSTPVGTSHGSFMQHSTAQSSDDLGLSHSLDSPSSPGLW 545

Query: 425 TAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVY 484
             Q+++G+  R  SD GR    GL  H+ G++LGSG+K+AIVTNTTVEI+VP++VI  VY
Sbjct: 546 PPQSLSGISSRAISDAGR----GLPSHRSGVQLGSGNKTAIVTNTTVEIVVPDDVISLVY 601

Query: 485 GENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS 541
           GENG+NL RLRQISGAKVIVHEP   ++DR++VISGTPDETQAAQSLL AFILTG S
Sbjct: 602 GENGTNLTRLRQISGAKVIVHEPDPITSDRLIVISGTPDETQAAQSLLHAFILTGSS 658

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546743|ref|XP_003541782.1| PREDICTED: poly(rC)-binding protein 3-like [Glycine max]

 Score =  464 bits (1193), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 243/382 (63%), Positives = 290/382 (75%), Gaps = 6/382 (1%)

Query: 160 YVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219
           Y + V  LS E +RV++L+ +  QQEVSFRILCSND+VG VIGKGG I+RALQSE GA I
Sbjct: 285 YATRVHSLSAEVNRVSSLEPKALQQEVSFRILCSNDRVGGVIGKGGNIVRALQSETGATI 344

Query: 220 SVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVN 279
           S+G  + EC++RLIT+ ASE PESRYSPAQKA VLVFSR IE   EK LD   NKG  V 
Sbjct: 345 SIGPLVAECEDRLITIAASENPESRYSPAQKAAVLVFSRSIEVGFEKELDSGLNKGSTVT 404

Query: 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFSKV 338
            RLVV S+QVGCL+GKGG I+SE+RK TG +IRII +DQ+ KC S+ND+VVQISGEFS V
Sbjct: 405 VRLVVPSSQVGCLIGKGGVIVSEIRKATGANIRIIGTDQVPKCASDNDQVVQISGEFSSV 464

Query: 339 KDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFS 398
           +DA+YN TGRLRDN F  T N+A TRS SS+  +TSPY   +D    G       SH  S
Sbjct: 465 QDALYNATGRLRDNLFVSTQNSAGTRSLSSLRVDTSPYGIQQDFVPHGSQLPATTSHCLS 524

Query: 399 QPPLTQGMDHLGLSHSLDCPSSPKLWTAQ-TVTGVHLRGSSDVGRGWSQGLSHHKGGLEL 457
           +    QG+DHLGLS +LD PSSP LWT    + G++ R  +D    +S GL+  KGGLEL
Sbjct: 525 RHTFAQGIDHLGLSRNLDHPSSPGLWTRNLDLAGINSRSIND----FSLGLTSRKGGLEL 580

Query: 458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVV 517
            SGSKSAIVTNTTVEI+VP++ I  VYGENG NL+RLRQISGAKV++HEPR G++DRI+V
Sbjct: 581 VSGSKSAIVTNTTVEIVVPDDTIDCVYGENGRNLVRLRQISGAKVVIHEPRPGTSDRIIV 640

Query: 518 ISGTPDETQAAQSLLQAFILTG 539
           ISGTPDETQAAQSLLQAFIL+G
Sbjct: 641 ISGTPDETQAAQSLLQAFILSG 662

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449516663|ref|XP_004165366.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  457 bits (1175), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 248/415 (59%), Positives = 302/415 (72%), Gaps = 25/415 (6%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           AV  E LPDLH+D + QRNSVL   PSSS  + S +  LS+++D +  +D    QQ+V F
Sbjct: 252 AVIHETLPDLHMDHILQRNSVLPILPSSSNIFASGIHSLSIDADMLPPVDTNVAQQDVVF 311

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           +ILC+ND++G VIGKGGTI+RALQ+E+GA +SVG ++  CDERLI++TASE  ESRYSPA
Sbjct: 312 KILCANDRIGGVIGKGGTIVRALQNESGATVSVGPSVTGCDERLISITASENIESRYSPA 371

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
           QKAVVLVFSR ++   EK  + SS+KG  V ARLVV SNQVGC+LGKGG IISE+RKVTG
Sbjct: 372 QKAVVLVFSRSVDVAIEKWQE-SSSKGSPVVARLVVPSNQVGCVLGKGGVIISEIRKVTG 430

Query: 309 TSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTS 367
           T+IRII SDQ+  C +E+D +VQISGEFS V+DA+YNVTGRLRDN F             
Sbjct: 431 TNIRIISSDQVPNCAAESDEIVQISGEFSNVQDALYNVTGRLRDNLF------------- 477

Query: 368 SVLTETSPYSRLKDPASFGVHSSVAVSH-DFSQPPLTQGMDHLGLSHSLDCPSSPKLWTA 426
                  PY R++D A     + V  SH  F Q    Q  D LGLSHSLD PSSP LW  
Sbjct: 478 -----LVPYGRVRDTAPLVRSTPVGTSHGSFMQHSTAQSSDDLGLSHSLDSPSSPGLWPP 532

Query: 427 QTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGE 486
           Q+++G+  R  SD GR    GL  H+ G++LGSG+K+AIVTNTTVEI+VP++VI  VYGE
Sbjct: 533 QSLSGISSRAISDAGR----GLPSHRSGVQLGSGNKTAIVTNTTVEIVVPDDVISLVYGE 588

Query: 487 NGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS 541
           NG+NL RLRQISGAKVIVHEP   + DR++VISGTPDETQAAQSLL AFILTG S
Sbjct: 589 NGTNLTRLRQISGAKVIVHEPDPITNDRLIVISGTPDETQAAQSLLHAFILTGSS 643

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557593|ref|XP_003547100.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  457 bits (1175), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 245/421 (58%), Positives = 292/421 (69%), Gaps = 45/421 (10%)

Query: 160 YVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219
           Y + +  L  E +RV++L+ +  +QEV+FRILCSND+VG VIGKGG I+RALQSE GA I
Sbjct: 293 YATRIHSLPTEVNRVSSLEPKALKQEVTFRILCSNDRVGGVIGKGGNIVRALQSETGATI 352

Query: 220 SVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVN 279
           S+G  + EC++RLIT+ ASE PESRYSPAQKA VLVFSR IE   EKGLD   NKG +V 
Sbjct: 353 SIGPAVAECEDRLITIAASENPESRYSPAQKAAVLVFSRSIEVGFEKGLDSGLNKGSIVT 412

Query: 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFSKV 338
            RLVV S+QVGCL+GKGG I+SEMRK TG +IRII +DQ+ KC S+ND+VVQISGEFS V
Sbjct: 413 VRLVVPSSQVGCLIGKGGVIVSEMRKATGANIRIIGTDQVPKCASDNDQVVQISGEFSSV 472

Query: 339 KDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFS 398
           +DA+YN  GRLRDN F  T N+A TRS SS+  +TSPY R +D    G     A SH  S
Sbjct: 473 QDALYNAMGRLRDNLFVSTQNSAGTRSLSSLRVDTSPYGRQQDVVPLGSQLPPATSHSLS 532

Query: 399 QPPLTQGMDHLGLSHSLDCPSSPKLWTAQ------------------------------- 427
           +    QG+DHLGLS +LD PSSP LWT                                 
Sbjct: 533 RHTFAQGIDHLGLSRNLDHPSSPGLWTRNLDRPSSPGLWTRNLDRPSSPGLWTRNLDHRP 592

Query: 428 ---------TVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPEN 478
                    TV G++ RG +D    +S GL+  KGGLEL SGSKSAIVTNT VEI+VP++
Sbjct: 593 SSPGLWAPPTVAGINSRGIND----FSLGLTSRKGGLELVSGSKSAIVTNTIVEIVVPDD 648

Query: 479 VIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT 538
            I  VYGENGSNL RLRQISGA V+VHEPR G++DRI+VISGTPDETQAAQSLLQAFIL+
Sbjct: 649 TIDCVYGENGSNLARLRQISGANVVVHEPRPGTSDRIIVISGTPDETQAAQSLLQAFILS 708

Query: 539 G 539
           G
Sbjct: 709 G 709

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563372|ref|XP_002522689.1| Poly(rC)-binding protein, putative [Ricinus communis] gi|223538165|gb|EEF39776.1| Poly(rC)-binding protein, putative [Ricinus communis]

 Score =  445 bits (1145), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 261/482 (54%), Positives = 306/482 (63%), Gaps = 93/482 (19%)

Query: 125 RLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQ 184
           + F AV QE LP++ V+I  QRN ++ T  ++++S         LE+DRV +LD +  QQ
Sbjct: 244 KYFEAVPQEPLPEMRVEIAPQRNIMVPTMQNNAVSCAPVPHNFLLETDRVPSLDMKLFQQ 303

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           EV F+ILC ND VG VIGKGGTII+ALQ+E GA I++GAT+ E DERLITV ASE PESR
Sbjct: 304 EVVFKILCPNDMVGGVIGKGGTIIKALQNETGASITIGATIAESDERLITVIASENPESR 363

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
           YS AQKAVVLVFS                       RLVV SNQVGCLLGKGG IIS+MR
Sbjct: 364 YSAAQKAVVLVFS-----------------------RLVVPSNQVGCLLGKGGIIISDMR 400

Query: 305 KVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTART 363
           K TGTSI+I++ DQL KC+ EN++VVQISG+F  VKDAVY+VTGRLRDN FS  L+T  T
Sbjct: 401 KTTGTSIKILAGDQLPKCVPENEQVVQISGDFMNVKDAVYHVTGRLRDNLFSSALSTPVT 460

Query: 364 RSTSSVLTETSPYSRLKDPA---------------------------------------- 383
           RST +V+TE SPY RLK+P                                         
Sbjct: 461 RST-TVITEASPYGRLKEPLRDAFKEPLNTFREPLGDAFRDPLRAAMRGPLRDARRDPLR 519

Query: 384 -SFGVHSSVAVSHDFSQPPLTQGMDHL----GLSHS-------------------LDCPS 419
            SFG      +     +PP      +L    G+SHS                   LD P 
Sbjct: 520 DSFGDTLRDQLRDTLKEPPRGPAPYNLHPPIGVSHSLNRHNTLTQSMDHLGLSHSLDGPI 579

Query: 420 SPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENV 479
           SP+LW +QT+ G++ R   D  RG++      KGGLELGSGSKSAIVTNTTVEI VPENV
Sbjct: 580 SPRLWASQTMAGINPRVVPDASRGFTS----FKGGLELGSGSKSAIVTNTTVEIRVPENV 635

Query: 480 IGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG 539
           IGSVYGEN SNL RLRQISGAKVIVHEPRLGS+DRI+VISGTPDETQAAQSLLQAFILTG
Sbjct: 636 IGSVYGENDSNLTRLRQISGAKVIVHEPRLGSSDRIIVISGTPDETQAAQSLLQAFILTG 695

Query: 540 PS 541
            S
Sbjct: 696 QS 697

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356519471|ref|XP_003528396.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  436 bits (1120), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 241/415 (58%), Positives = 296/415 (71%), Gaps = 38/415 (9%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           +V  E L +LH+D   QR+S L+T  + S    S    LS E +RV+ LD +  QQEV+F
Sbjct: 213 SVPLESLTNLHIDRRLQRSSTLSTLSNRSNGNASGAPKLSAEVNRVSALDPKALQQEVTF 272

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE-GPESRYSP 247
           RI+CSND+VGAVIGKGG+I+RALQ+E+GA IS G ++ EC++RL+T+TASE  PESRYSP
Sbjct: 273 RIICSNDRVGAVIGKGGSIVRALQNESGAIISFGPSLVECEDRLVTITASEQNPESRYSP 332

Query: 248 AQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307
           AQKAVVLVFS+ +E   EKGLD  S K   V A+LVV SNQVGCLLGKGG I+SEMRK T
Sbjct: 333 AQKAVVLVFSKSVEAGVEKGLDMGSKKESYVTAQLVVPSNQVGCLLGKGGAIVSEMRKAT 392

Query: 308 GTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRST 366
           G +IR+I +D++ KC+S+ND++VQISGEFS V+ A+YN TGRLRDN F  T N+   RS 
Sbjct: 393 GANIRVIGNDKVPKCVSDNDQLVQISGEFSNVQAAIYNATGRLRDNLFVSTQNSGGARSL 452

Query: 367 SSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTA 426
           SSVL+   P              +VAVS   ++             HSL     P L   
Sbjct: 453 SSVLSGGKP--------------TVAVSLSLNR-------------HSL-----PGLQAP 480

Query: 427 QTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGE 486
           QTV G++ R    V  G S+GL+  KGGLEL SGSK+AIVTNTTV+I VP++VIGSVYGE
Sbjct: 481 QTVAGINSR----VTNGVSRGLTSQKGGLELVSGSKTAIVTNTTVQIAVPDDVIGSVYGE 536

Query: 487 NGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS 541
           NGSNL RLRQISGAKVIVHEPR G++DR ++ISGTPDET+AAQSLLQAFIL G S
Sbjct: 537 NGSNLARLRQISGAKVIVHEPRPGTSDRTIIISGTPDETRAAQSLLQAFILAGSS 591

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528011|ref|XP_003532599.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  435 bits (1118), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 237/414 (57%), Positives = 293/414 (70%), Gaps = 37/414 (8%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           +V  E L +LH+D   QR+S L+T  + S    S    LS E +RV+ LD +  QQEV+F
Sbjct: 56  SVPLESLTNLHIDHHLQRSSTLSTLSNRSNGNASGAHKLSAEVNRVSALDPKAYQQEVTF 115

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           RI+CSND+VGAVIGKGG+I+RALQ+E+GA ISVG ++ EC++RL+T+TASE PES YSPA
Sbjct: 116 RIICSNDRVGAVIGKGGSIVRALQNESGAIISVGPSLVECEDRLVTITASENPESTYSPA 175

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
           QKAVVLVFS+ +E   EKGL+  S K   V ARLVV SNQVGCLLGKGG I+SEMRK TG
Sbjct: 176 QKAVVLVFSKSVEAGVEKGLELGSKKEPYVTARLVVPSNQVGCLLGKGGAIVSEMRKATG 235

Query: 309 TSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTS 367
            +IR+I +DQ+  C+S+ND++VQISG FS V+ A++N TGRLRD+ F  T N+   RS S
Sbjct: 236 ANIRVIGNDQVPMCVSDNDQLVQISGVFSNVQAAIHNATGRLRDHLFVSTQNSGGARSLS 295

Query: 368 SVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQ 427
           SVL    P                                 L +SHSL+  S P L   Q
Sbjct: 296 SVLAGGQPT--------------------------------LAISHSLNRHSLPGLQAPQ 323

Query: 428 TVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGEN 487
           TV G++ RG++    G S+GL   KGGLEL SGSK+AIVTNTTV+I+VP++VIGSVYGEN
Sbjct: 324 TVAGINSRGTN----GVSRGLISRKGGLELISGSKTAIVTNTTVQIVVPDDVIGSVYGEN 379

Query: 488 GSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGPS 541
           GSNL RLRQISGAKVIVHEPR G++DR ++ISGTPDET+AAQSLLQAFIL G S
Sbjct: 380 GSNLARLRQISGAKVIVHEPRPGTSDRTIIISGTPDETRAAQSLLQAFILAGSS 433

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	541
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.626	0.545	0.382	5.5e-54
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.353	0.302	0.405	2.3e-37
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.458	0.380	0.289	1.9e-31
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.310	0.306	0.365	2.6e-26
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.391	0.329	0.347	1.3e-23
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.301	0.268	0.329	1.5e-25
MGI|MGI:108202	362	Pcbp2 "poly(rC) binding protei	0.609	0.911	0.269	3.2e-24
UNIPROTKB|Q5E9A3	356	PCBP1 "Poly(rC)-binding protei	0.597	0.907	0.268	4e-23
UNIPROTKB|Q15365	356	PCBP1 "Poly(rC)-binding protei	0.597	0.907	0.268	4e-23
MGI|MGI:1345635	356	Pcbp1 "poly(rC) binding protei	0.597	0.907	0.268	4e-23

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

 Score = 558 (201.5 bits), Expect = 5.5e-54, P = 5.5e-54
 Identities = 141/369 (38%), Positives = 203/369 (55%)

Query:   183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPE 242
             ++EV+FR+LC  DKVG++IGKGG ++RALQ+E+GA I V     + +ER+I ++A E  E
Sbjct:   273 EEEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLE 332

Query:   243 SRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISE 302
              R+S AQ  V+ V +R++E      + F  +  ++  ARL+V S  +G LLGKGG +ISE
Sbjct:   333 RRHSLAQDGVMRVHNRIVE------IGFEPSAAVV--ARLLVHSPYIGRLLGKGGHLISE 384

Query:   303 MRKVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTA 361
             MR+ TG SIR+ + DQ  K  S++D +VQ+ G    V+DA++ +  RLR+  F G L   
Sbjct:   385 MRRATGASIRVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRLPFQ 444

Query:   362 RTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQP--PLTQGMDH-LGLSH----S 414
                          PY   + P  FG     A    +  P  P  +   H  G        
Sbjct:   445 GMGGPPPPFM--GPYP--EPPPPFGPRQYPASPDRYHSPVGPFHERHCHGPGFDRPPGPG 500

Query:   415 LDCPSSPKLWTAQTVTGVHLRGS--SDVGRGWSQXXXXXXXXXXXXXXXXXAIVTNTTVE 472
              D P SP  WT Q     H  G    DV  G++                   ++T+  VE
Sbjct:   501 FDRPPSPMSWTPQPGIDGHPGGMVPPDVNHGFA--------LRNEPIGSENPVMTSANVE 552

Query:   473 IIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL 532
             I++P+  +G VYGEN SNL  ++Q+SGA V+VH+P+ G+T+ +VV+SGT D+   AQSLL
Sbjct:   553 IVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLL 612

Query:   533 QAFILTGPS 541
              AFIL G S
Sbjct:   613 HAFILCGQS 621

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 326 (119.8 bits), Expect = 2.3e-37, Sum P(3) = 2.3e-37
 Identities = 81/200 (40%), Positives = 123/200 (61%)

Query:   155 SSSISYVSAVRPLSLESDRVATLDA-RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQS 213
             SSS+S  + +    + S+R    D   + +++V F+I+ ++   G +IGK GTIIRALQ+
Sbjct:   249 SSSLSNATEI----VASNRHLPYDGGNSTERKVVFKIIFTSVVAGGIIGKQGTIIRALQN 304

Query:   214 EAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273
             E GA ISVGA +    ER++TV+A E  ESRYS AQ A+ LVF+R +E   EKGL    +
Sbjct:   305 ETGASISVGAPLKVSGERVVTVSARENLESRYSHAQNALALVFARSVEIDVEKGLRPGLH 364

Query:   274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI-ISDQLLKCISENDRVVQIS 332
              G +V  +L+V S+      G G     E    TG  + I + +Q+L+ ISEN+ V++I 
Sbjct:   365 NGAIVKTKLLVPSHFANSFNGNGNR---EAIIATGADVHISVGNQVLEWISENEVVIEIK 421

Query:   333 GEFSKVKDAVYNVTGRLRDN 352
             GE+S V+ A+ +V+ +LR+N
Sbjct:   422 GEYSHVQKALTHVSSKLREN 441

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

 Score = 270 (100.1 bits), Expect = 1.9e-31, Sum P(2) = 1.9e-31
 Identities = 77/266 (28%), Positives = 135/266 (50%)

Query:   109 ESSHRSSEALS--IETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRP 166
             ES HR          +  R F A   + +P L      Q +         + ++ S    
Sbjct:   251 ESQHRDRSNFQGRSHSPERSFAAAGDDYMPQLR----RQSSDRFPRGNFRNNNFSSRQSN 306

Query:   167 LSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMP 226
              + E+  V  +      +E+ F+ILC  DK+  V+G+   II  LQ+E G  + V   + 
Sbjct:   307 YAEEAPAVP-VGENVYSEELVFQILCPADKIVRVVGESQGIIDLLQNEIGVDVRVSDPVA 365

Query:   227 ECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVAS 286
               DE++IT+++ E P+  + PAQ+A++ + +++I        D   +K  L+  RL+V S
Sbjct:   366 GSDEQIITISSEEAPDDPFFPAQEALLHIQTQII--------DLIPDKDNLITTRLLVPS 417

Query:   287 NQVGCLLGKGGTIISEMRKVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNV 345
                 CL GK G++ SE+ ++TGTS++I++ +++ +C S ND V+QI+GE    ++A+  +
Sbjct:   418 RDSICLEGKAGSV-SEISRLTGTSVQILAREEIPRCASINDVVIQITGEIRAAREALVEL 476

Query:   346 TGRLRDNHFSGTLNTARTRSTSSVLT 371
             T  LR + F   L+   T   S+  T
Sbjct:   477 TLLLRSHMFK-ELSQKETPPASTSTT 501

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 = 292 (107.8 bits), Expect = 2.6e-26, Sum P(2) = 2.6e-26
 Identities = 65/178 (36%), Positives = 104/178 (58%)

Query:   183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITV------T 236
             + +  FR LC   K+G+VIG+GG I++ L+++  + I +G  +P CDER+IT+      T
Sbjct:    47 RDDTVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSDET 106

Query:   237 ASEGP-ESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGK 295
              + G  E   SPAQ A+  +  R++   +    + S      V A+L+V S+Q+GC+LG+
Sbjct:   107 NAFGDGEKVLSPAQDALFRIHDRVVADDARS--EDSPEGEKQVTAKLLVPSDQIGCILGR 164

Query:   296 GGTIISEMRKVTGTSIRIISDQLLK-CISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352
             GG I+  +R  TG  IRI+ D+ +  C   +D ++QISGE   VK A+  +  RL +N
Sbjct:   165 GGQIVQNIRSETGAQIRIVKDRNMPLCALNSDELIQISGEVLIVKKALLQIASRLHEN 222

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

 Score = 299 (110.3 bits), Expect = 1.3e-23, P = 1.3e-23
 Identities = 80/230 (34%), Positives = 129/230 (56%)

Query:   181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDER-LITVTASE 239
             ++ ++++ +++CS+ K+G VIGKGG  I+ ++  +G+ I V  +    D+  +ITVTA+E
Sbjct:   312 SRSEKLAIKVICSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATE 371

Query:   240 GPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTI 299
              P+   S A +AV+L+         EK  D   +K   V  +L+V+S  +GC++GK G+I
Sbjct:   372 SPDDLKSMAVEAVLLL--------QEKINDEDEDK---VKMQLLVSSKVIGCIIGKSGSI 420

Query:   300 ISEMRKVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF---- 354
             ISE+RK T   I I   +   KC   ND +V+ISGE S V+DA+  +  RLRD+      
Sbjct:   421 ISEIRKRTKADIHISKGNNTPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRE 480

Query:   355 SGTLNTARTRS-TSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLT 403
             +G+ N    RS  ++  + +S  + L  P SF        S DF++ P T
Sbjct:   481 TGSRNQPPARSENNNFFSSSSSNTGLALPQSFMSSVPQVASVDFNRRPET 530

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 = 232 (86.7 bits), Expect = 1.5e-25, Sum P(2) = 1.5e-25
 Identities = 62/188 (32%), Positives = 108/188 (57%)

Query:   181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC--DERLITVTAS 238
             ++ +E+ F++LC    +  VIGKGG+ I+ ++  +G+ I V  +  +C  DE +I VTA+
Sbjct:   307 SRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDECVIIVTAT 366

Query:   239 EGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGT 298
             E P+   S A +AV+L+   + +  +E            V  +L+V+S  +GC++GK G+
Sbjct:   367 ESPDDMKSMAVEAVLLLQEYINDEDAEN-----------VKMQLLVSSKVIGCVIGKSGS 415

Query:   299 IISEMRKVTGTSIRIISDQLLKCISEN--DRVVQISGEFSKVKDAVYNVTGRLRDNHFSG 356
             +I+E+RK T  +I         CIS+   D +V++SGE S V+DA+  +  RLR++   G
Sbjct:   416 VINEIRKRTNANI---------CISKGKKDDLVEVSGEVSSVRDALIQIVLRLREDVL-G 465

Query:   357 TLNTARTR 364
               ++  TR
Sbjct:   466 DKDSVATR 473

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

MGI|MGI:108202 Pcbp2 "poly(rC) binding protein 2" [Mus musculus (taxid:10090)]

 Score = 283 (104.7 bits), Expect = 3.2e-24, P = 3.2e-24
 Identities = 95/352 (26%), Positives = 166/352 (47%)

Query:   186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
             ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+    GP +  
Sbjct:    14 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA---GPTNAI 68

Query:   246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
                 KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct:    69 F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 125

Query:   306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
              TG  +++  D L    +  +R + I+G    + + V  +   + ++   G     R + 
Sbjct:   126 STGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYRPKP 182

Query:   366 TSSVLTETSP---YSRLKDPASFGVHS--SVAVSHDFSQPPLTQGMDHLGLSHSLDCPSS 420
             +SS +        YS   D ASF  H+  S+ ++ D   PPL +     G  +++  P  
Sbjct:   183 SSSPVIFAGGQDRYSTGSDSASFP-HTTPSMCLNPDLEGPPL-EAYTIQG-QYAIPQPDL 239

Query:   421 PKLWTAQTVTGVHLRGSSDVGRGWSQXXXXXXXXXXXXXXXXXAIVTNTTVEIIVPENVI 480
              KL     +   H   +     G+S                  +  T T+ E+ +P ++I
Sbjct:   240 TKLHQL-AMQQSHFPMTHG-NTGFSGIESSSPEVKGYWAGLDASAQT-TSHELTIPNDLI 296

Query:   481 GSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL 532
             G + G  G+ +  +RQ+SGA++ +  P  GSTDR V I+G+      AQ L+
Sbjct:   297 GCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 348

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0019899 "enzyme binding" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=ISO

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0045087 "innate immune response" evidence=IEA

GO:0050687 "negative regulation of defense response to virus" evidence=ISO

GO:0051607 "defense response to virus" evidence=IEA

UNIPROTKB|Q5E9A3 PCBP1 "Poly(rC)-binding protein 1" [Bos taurus (taxid:9913)]

 Score = 273 (101.2 bits), Expect = 4.0e-23, P = 4.0e-23
 Identities = 96/358 (26%), Positives = 164/358 (45%)

Query:   186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
             ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+T   GP +  
Sbjct:    14 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NCPERIITLT---GPTNAI 68

Query:   246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
                 KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct:    69 F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query:   306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS---GTLNTA- 361
              TG  +++  D L    +  +R + I+G    V + V  +   + +       G + T  
Sbjct:   126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIP 182

Query:   362 -RTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLT----QGMDHLGLSHSLD 416
              +    SS +       R  D A +  H++    HD   PPL     QG   +     LD
Sbjct:   183 YQPMPASSPVICAGGQDRCSDAAGYP-HAT----HDLEGPPLDAYSIQGQHTIS---PLD 234

Query:   417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQXXXXXXXXXXXXXXXXXAIVTNTTVEIIVP 476
                  ++   Q+   + + G    G G++                  +  T TT E+ +P
Sbjct:   235 LAKLNQVARQQSHFAM-MHG----GTGFAGIDSSSPEVKGYWASLDAS--TQTTHELTIP 287

Query:   477 ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQA 534
              N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+      AQ L+ A
Sbjct:   288 NNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|Q15365 PCBP1 "Poly(rC)-binding protein 1" [Homo sapiens (taxid:9606)]

 Score = 273 (101.2 bits), Expect = 4.0e-23, P = 4.0e-23
 Identities = 96/358 (26%), Positives = 164/358 (45%)

Query:   186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
             ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+T   GP +  
Sbjct:    14 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NCPERIITLT---GPTNAI 68

Query:   246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
                 KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct:    69 F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query:   306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS---GTLNTA- 361
              TG  +++  D L    +  +R + I+G    V + V  +   + +       G + T  
Sbjct:   126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIP 182

Query:   362 -RTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLT----QGMDHLGLSHSLD 416
              +    SS +       R  D A +  H++    HD   PPL     QG   +     LD
Sbjct:   183 YQPMPASSPVICAGGQDRCSDAAGYP-HAT----HDLEGPPLDAYSIQGQHTIS---PLD 234

Query:   417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQXXXXXXXXXXXXXXXXXAIVTNTTVEIIVP 476
                  ++   Q+   + + G    G G++                  +  T TT E+ +P
Sbjct:   235 LAKLNQVARQQSHFAM-MHG----GTGFAGIDSSSPEVKGYWASLDAS--TQTTHELTIP 287

Query:   477 ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQA 534
              N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+      AQ L+ A
Sbjct:   288 NNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=NAS

GO:0005737 "cytoplasm" evidence=NAS

GO:0016071 "mRNA metabolic process" evidence=NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1345635 Pcbp1 "poly(rC) binding protein 1" [Mus musculus (taxid:10090)]

 Score = 273 (101.2 bits), Expect = 4.0e-23, P = 4.0e-23
 Identities = 96/358 (26%), Positives = 164/358 (45%)

Query:   186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
             ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+T   GP +  
Sbjct:    14 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NCPERIITLT---GPTNAI 68

Query:   246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
                 KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct:    69 F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query:   306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS---GTLNTA- 361
              TG  +++  D L    +  +R + I+G    V + V  +   + +       G + T  
Sbjct:   126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIP 182

Query:   362 -RTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLT----QGMDHLGLSHSLD 416
              +    SS +       R  D A +  H++    HD   PPL     QG   +     LD
Sbjct:   183 YQPMPASSPVICAGGQDRCSDAAGYP-HAT----HDLEGPPLDAYSIQGQHTIS---PLD 234

Query:   417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQXXXXXXXXXXXXXXXXXAIVTNTTVEIIVP 476
                  ++   Q+   + + G    G G++                  +  T TT E+ +P
Sbjct:   235 LAKLNQVARQQSHFAM-MHG----GTGFAGIDSSSPEVKGYWASLDAS--TQTTHELTIP 287

Query:   477 ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQA 534
              N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+      AQ L+ A
Sbjct:   288 NNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

GO:0003677 "DNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=ISO

GO:0003723 "RNA binding" evidence=ISO;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=TAS

GO:0008494 "translation activator activity" evidence=TAS

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0045727 "positive regulation of translation" evidence=TAS

---

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: GSVIVG00001893001 SubName- Full=Chromosome undetermined scaffold_123, whole genome shotgun sequence; (817 aa) (Vitis vinifera)

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	541
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-16
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-14
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-13
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-11
pfam00013	59	pfam00013, KH_1, KH domain	1e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-09
pfam00013	59	pfam00013, KH_1, KH domain	3e-09
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-07
pfam13014	42	pfam13014, KH_3, KH domain	2e-07
pfam00013	59	pfam00013, KH_1, KH domain	6e-07
pfam13014	42	pfam13014, KH_3, KH domain	8e-07
pfam13014	42	pfam13014, KH_3, KH domain	3e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-06
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	4e-05
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	6e-05
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.001
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.001

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

 Score = 72.9 bits (180), Expect = 3e-16
 Identities = 27/63 (42%), Positives = 39/63 (61%), Gaps = 3/63 (4%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           RL+V S+Q G ++GKGG+ I E+R+ TG  IR+    L       +RVV ISG+ S V+ 
Sbjct: 3   RLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGS---TERVVTISGKPSAVQK 59

Query: 341 AVY 343
           A+ 
Sbjct: 60  ALL 62

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 = 66.7 bits (164), Expect = 4e-14
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 7/71 (9%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM-PECDERLITVTASEGPESRY 245
           + R+L  + + G++IGKGG+ I+ ++ E GA I V  ++ P   ER++T++         
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK------P 54

Query: 246 SPAQKAVVLVF 256
           S  QKA++L+ 
Sbjct: 55  SAVQKALLLIL 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 = 64.9 bits (159), Expect = 2e-13
 Identities = 22/64 (34%), Positives = 42/64 (65%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T  ++VP +++G + G+ GS +  +R+ +GAK+ + +   GS +RIV I+GTP+  + A+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 530 SLLQ 533
            L+ 
Sbjct: 61  ELIL 64

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

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

 Score = 57.3 bits (139), Expect = 8e-11
 Identities = 19/70 (27%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQ 526
              T+E+++P + +G + G+ GS + ++ + +G K+ +  P  GS +R+V I+G P+  +
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI--PGPGSEERVVEITGPPENVE 58

Query: 527 AAQSLLQAFI 536
            A  L+   +
Sbjct: 59  KAAELILEIL 68

Length = 68

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

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 21/63 (33%), Positives = 39/63 (61%), Gaps = 4/63 (6%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T  I++P + +G + G+ GSN+  +R+ +G K+ + + R    D  V ISGTP++ + A+
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR----DDTVTISGTPEQVEKAK 56

Query: 530 SLL 532
            L+
Sbjct: 57  ELI 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 = 56.0 bits (136), Expect = 3e-10
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           R++V S+ VG ++GKGG+ I E+R+ TG  I+I            +R+V I+G    V+ 
Sbjct: 3   RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----GSEERIVTITGTPEAVEK 58

Query: 341 AVY 343
           A  
Sbjct: 59  AKE 61

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 = 53.7 bits (130), Expect = 1e-09
 Identities = 18/53 (33%), Positives = 33/53 (62%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + R+L  +  VG +IGKGG+ I+ ++ E GA I +  +    +ER++T+T + 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTP 53

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 = 52.6 bits (127), Expect = 3e-09
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 8/62 (12%)

Query: 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVK 339
            R+++  ++VG ++GKGG+ I E+R+ TG  IRI  D+        D  V ISG   +V+
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR--------DDTVTISGTPEQVE 53

Query: 340 DA 341
            A
Sbjct: 54  KA 55

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 = 52.5 bits (127), Expect = 4e-09
 Identities = 25/60 (41%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL-GSTDRIVVISGTPDETQAA 528
           T+ ++VP +  GS+ G+ GS +  +R+ +GAK+ V +  L GST+R+V ISG P   Q A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

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 = 47.7 bits (114), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V   +++ +++VG ++GKGG+ I ++ + TG  I I            +RVV+I+G    
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG------SEERVVEITGPPEN 56

Query: 338 VKDAVYNVTGRL 349
           V+ A   +   L
Sbjct: 57  VEKAAELILEIL 68

Length = 68

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 18/41 (43%), Positives = 26/41 (63%)

Query: 196 KVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT 236
            VGA+IGKGG  I+ ++ E GA I +    P   ER++T+T
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 = 46.4 bits (111), Expect = 6e-07
 Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 4/53 (7%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + RIL   DKVG +IGKGG+ I+ ++ E G  I +    P+  +  +T++ + 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRI----PDDRDDTVTISGTP 49

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 = 45.2 bits (108), Expect = 8e-07
 Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 288 QVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
            VG ++GKGG  I E+R+ TG  I+I            +R+V I+G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPK----PEPGSGERIVTITG 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|221895 pfam13014, KH_3, KH domain

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 15/41 (36%), Positives = 28/41 (68%)

Query: 480 IGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG 520
           +G++ G+ G  +  +R+ +GAK+ + +P  GS +RIV I+G
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

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

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

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
            V+  +L   DKVG +IGKGG+ I+ ++ E G  I +    P  +ER++ +T   
Sbjct: 2   PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPP 54

Length = 68

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

 Score = 41.3 bits (98), Expect = 4e-05
 Identities = 15/64 (23%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T E+ +P+ +   + G+ GSN+ ++ + +G K+    P  GS    + I+G  +  + A+
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF--PDPGSKSDTITITGPKENVEKAK 58

Query: 530 SLLQ 533
             + 
Sbjct: 59  EEIL 62

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

>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 40.6 bits (96), Expect = 6e-05
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 11/61 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVL 254
           DK+  VIG GG  I+ +  E G  I +       D+  + + AS+        A+KA  +
Sbjct: 11  DKIRDVIGPGGKTIKKIIEETGVKIDIE------DDGTVYIAASDKEA-----AEKAKKM 59

Query: 255 V 255
           +
Sbjct: 60  I 60

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. Length = 61

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 41.6 bits (99), Expect = 0.001
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 11/58 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAV 252
           DK+  VIG GG  IR +  E GA I +       D+  + + A++G       A+ A 
Sbjct: 563 DKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATDGEA-----AEAAK 609

Length = 693

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 41.3 bits (98), Expect = 0.001
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 17/72 (23%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVL 254
           DK+  VIG GG +IR +  E GA I +       D+  + + AS+G E+    A+ A+  
Sbjct: 560 DKIRDVIGPGGKVIREITEETGAKIDIE------DDGTVKIAASDG-EA----AEAAI-- 606

Query: 255 VFSRLIEG-TSE 265
              ++IEG T+E
Sbjct: 607 ---KMIEGITAE 615

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) [Transcription, Degradation of RNA]. Length = 684

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	541
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.97
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.97
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.95
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.92
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.87
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.7
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.65
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.63
PRK13763	180	putative RNA-processing protein; Provisional	99.57
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.57
PRK13763	180	putative RNA-processing protein; Provisional	99.5
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.43
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.36
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.29
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.25
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.24
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.24
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.18
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.03
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.03
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.02
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.9
PF13014	43	KH_3: KH domain	98.88
smart00322	69	KH K homology RNA-binding domain.	98.87
PF13014	43	KH_3: KH domain	98.86
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.65
smart00322	69	KH K homology RNA-binding domain.	98.63
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.62
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.55
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.54
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.16
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.12
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.05
KOG2113	394	consensus Predicted RNA binding protein, contains	98.02
KOG2113	394	consensus Predicted RNA binding protein, contains	97.85
PRK08406	140	transcription elongation factor NusA-like protein;	97.84
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.49
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.46
PRK08406	140	transcription elongation factor NusA-like protein;	97.45
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.36
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.25
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.07
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.99
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	96.89
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.86
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.7
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.7
PRK00106	535	hypothetical protein; Provisional	96.65
PRK12704	520	phosphodiesterase; Provisional	96.49
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.47
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.43
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.41
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.37
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.36
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.35
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.04
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.01
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	95.92
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	95.87
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.7
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.56
PRK00468	75	hypothetical protein; Provisional	95.37
TIGR01953	341	NusA transcription termination factor NusA. This m	95.3
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.22
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.19
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.18
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.08
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	95.08
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	95.07
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.0
PRK02821	77	hypothetical protein; Provisional	94.99
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.82
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.74
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.72
PRK12705	508	hypothetical protein; Provisional	94.72
COG0195	190	NusA Transcription elongation factor [Transcriptio	94.68
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.65
PRK12704	520	phosphodiesterase; Provisional	94.64
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	94.44
PRK00106	535	hypothetical protein; Provisional	94.37
PRK00468	75	hypothetical protein; Provisional	94.29
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.26
PRK01064	78	hypothetical protein; Provisional	94.03
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.91
COG5176	269	MSL5 Splicing factor (branch point binding protein	93.82
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	93.82
PRK02821	77	hypothetical protein; Provisional	92.97
PRK01064	78	hypothetical protein; Provisional	92.3
PRK09202	470	nusA transcription elongation factor NusA; Validat	91.77
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	91.24
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	90.8
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	90.04
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	88.84
PRK12705	508	hypothetical protein; Provisional	88.71
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	88.0
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	86.07
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	85.91
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	85.32
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	84.87
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	84.27
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	83.15
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	83.09
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	82.69

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

Probab=100.00  E-value=8.7e-36  Score=288.08  Aligned_cols=324  Identities=26%  Similarity=0.402  Sum_probs=213.8

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (541)
Q Consensus       182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e  261 (541)
                      ....+.++||+.++.+|+||||+|++||+|+.+++|.|+|++  .+.++|+++|+...+          .+..|+.+++.
T Consensus        44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd--s~~peri~tisad~~----------ti~~ilk~iip  111 (390)
T KOG2192|consen   44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILTISADIE----------TIGEILKKIIP  111 (390)
T ss_pred             hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccC--CCCCceeEEEeccHH----------HHHHHHHHHhh
Confidence            455699999999999999999999999999999999999986  567999999998644          45555555443


Q ss_pred             cccccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHH
Q 009173          262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA  341 (541)
Q Consensus       262 ~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A  341 (541)
                      .. +.++    .....+.++|+|..+++|.|||++|++||++++++.|+.+|..+-   |..++||+|.|.|.+..|..+
T Consensus       112 ~l-ee~f----~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c---~p~stdrv~l~~g~~k~v~~~  183 (390)
T KOG2192|consen  112 TL-EEGF----QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTEC---CPHSTDRVVLIGGKPKRVVEC  183 (390)
T ss_pred             hh-hhCC----CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhcc---CCCCcceEEEecCCcchHHHH
Confidence            21 1111    234568899999999999999999999999999999999998664   445999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcccccccC-CC----Cc---cccCCCCCCCCCCCcccccccccc---CCCCCCCC----CccCC
Q 009173          342 VYNVTGRLRDNHFSGTLNTARTRS-TS----SV---LTETSPYSRLKDPASFGVHSSVAV---SHDFSQPP----LTQGM  406 (541)
Q Consensus       342 ~~lI~~~l~e~~~~~~~~~~~~~~-~~----~~---~~~~~p~~~~~~p~~~~~~~~~g~---~~~~~r~~----~~~~~  406 (541)
                      ++.|++.|.|.+.++...++.... ++    ..   +-...|..+...|-+-+..++.+.   -...+|..    -..+|
T Consensus       184 i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~  263 (390)
T KOG2192|consen  184 IKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGM  263 (390)
T ss_pred             HHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccc
Confidence            999999999988776544433221 11    00   001111111100000000000000   00000100    00022


Q ss_pred             CccCCCCCCCCCC---CCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccce
Q 009173          407 DHLGLSHSLDCPS---SPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSV  483 (541)
Q Consensus       407 ~~~~~~~~~~~p~---~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~I  483 (541)
                      ..+.....|..+.   ++..|.    .+|.|.+....       ..+.-+....+.....   ..+|.+|+||.++-|.|
T Consensus       264 vdFs~detw~saidtw~~Sewq----maYePQgGs~y-------dysyAG~~GsYGdlGG---PitTaQvtip~dlggsi  329 (390)
T KOG2192|consen  264 VDFSADETWPSAIDTWSPSEWQ----MAYEPQGGSGY-------DYSYAGGYGSYGDLGG---PITTAQVTIPKDLGGSI  329 (390)
T ss_pred             ccccccccCCCcCCCcCccccc----cccCCCCCCCC-------CccccccccccCCCCC---ceeeeeEecccccCcce
Confidence            2222222222111   112221    11111111000       0000000000000001   24789999999999999


Q ss_pred             eeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          484 YGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       484 IGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      |||||.+|++|++++||.|+|++|..++.+|+|+|+||.+|++.||+|+|+.+..+
T Consensus       330 igkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  330 IGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             ecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999999753

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

Probab=100.00  E-value=7.3e-36  Score=316.98  Aligned_cols=283  Identities=22%  Similarity=0.314  Sum_probs=219.4

Q ss_pred             CCcccccCCCCcccccccccCCCccccccc--c-hhhcccCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEec
Q 009173          146 RNSVLTTAPSSSISYVSAVRPLSLESDRVA--T-LDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG  222 (541)
Q Consensus       146 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~  222 (541)
                      ..+|.+.+.|...++..+++.+.....+--  . .........++..|+||++.+|+||||+|++||+||+++||++.+-
T Consensus        96 ~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~i  175 (600)
T KOG1676|consen   96 IGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILV  175 (600)
T ss_pred             cccccccccCCcccHHHHHHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEE
Confidence            356777788877777777777765433321  0 1122335668999999999999999999999999999999999977


Q ss_pred             CCC--CCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc---cCCCCCCCCCceeEEEEEeccccccccccccc
Q 009173          223 ATM--PECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE---KGLDFSSNKGLLVNARLVVASNQVGCLLGKGG  297 (541)
Q Consensus       223 ~~~--~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~---~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG  297 (541)
                      ...  .....+.+.|+|.++.      +..|..++.+.|.|..-+   .+.+++.......+.++.||.+.||.||||+|
T Consensus       176 qd~~~~~~~~KplritGdp~~------ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgG  249 (600)
T KOG1676|consen  176 QDGSIATGADKPLRITGDPDK------VEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGG  249 (600)
T ss_pred             ecCCcCCCCCCceeecCCHHH------HHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCc
Confidence            542  2237789999998774      667777777655542211   11223333455568999999999999999999


Q ss_pred             chhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCC
Q 009173          298 TIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYS  377 (541)
Q Consensus       298 ~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~  377 (541)
                      ++||+|+.+||++|+|..|..|.   +.||.+.|.|+.+.|+.|.++|.++|.+.....                     
T Consensus       250 E~IKklq~etG~KIQfkpDd~p~---speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~---------------------  305 (600)
T KOG1676|consen  250 EMIKKLQNETGAKIQFKPDDDPS---SPERPAQIIGTVDQIEHAAELINEIIAEAEAGA---------------------  305 (600)
T ss_pred             hHHHHHhhccCceeEeecCCCCC---CccceeeeecCHHHHHHHHHHHHHHHHHHhccC---------------------
Confidence            99999999999999999887774   889999999999999999999999997532000                     


Q ss_pred             CCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCccc
Q 009173          378 RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLEL  457 (541)
Q Consensus       378 ~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~  457 (541)
                                                 +                                    ++|..|.+   +    
T Consensus       306 ---------------------------~------------------------------------~~~~~G~P---~----  315 (600)
T KOG1676|consen  306 ---------------------------G------------------------------------GGMGGGAP---G----  315 (600)
T ss_pred             ---------------------------C------------------------------------CCcCCCCc---c----
Confidence                                       0                                    00112222   0    


Q ss_pred             CCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC--CCCCCCccEEEEEeCHHHHHHHHHHHHHH
Q 009173          458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE--PRLGSTDRIVVISGTPDETQAAQSLLQAF  535 (541)
Q Consensus       458 ~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~--p~~~s~~RiItIsGtpeqV~~Aq~LI~~~  535 (541)
                               ....+++.||.++||+||||||+|||.|.++|||++.+..  |..+..++.|+|+|++.||+.|++||+.+
T Consensus       316 ---------~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~k  386 (600)
T KOG1676|consen  316 ---------LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDK  386 (600)
T ss_pred             ---------ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHH
Confidence                     0127899999999999999999999999999999999984  44566899999999999999999999999


Q ss_pred             Hh
Q 009173          536 IL  537 (541)
Q Consensus       536 I~  537 (541)
                      +-
T Consensus       387 vg  388 (600)
T KOG1676|consen  387 VG  388 (600)
T ss_pred             hc
Confidence            84

>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=2.3e-32  Score=294.04  Aligned_cols=331  Identities=27%  Similarity=0.426  Sum_probs=213.8

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhc
Q 009173          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG  262 (541)
Q Consensus       183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~  262 (541)
                      ....++||||+.+.+|.||||+|.+||+|+.+|+++|+|.+..++|.||+++|+|.... ...+++++|+.++++.++..
T Consensus        40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-~~~~~~~~al~ka~~~iv~~  118 (485)
T KOG2190|consen   40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-LNLSPATDALFKAFDMIVFK  118 (485)
T ss_pred             CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-ccCCchHHHHHHHHHHHhhc
Confidence            34456999999999999999999999999999999999999999999999999995322 26677899999999887763


Q ss_pred             cc---ccCCCCC-CCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHH
Q 009173          263 TS---EKGLDFS-SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKV  338 (541)
Q Consensus       263 ~~---~~g~~~~-~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V  338 (541)
                      ..   ....+.+ ......++++|+||.+++|+||||+|+.||+|+++|||+|+|.++.+|.   .++|.|+|.|.+++|
T Consensus       119 ~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av  195 (485)
T KOG2190|consen  119 LEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAV  195 (485)
T ss_pred             ccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHH
Confidence            11   1111222 1122368999999999999999999999999999999999999889998   578899999999999


Q ss_pred             HHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCCC------------------------CC---CC-Cccccccc
Q 009173          339 KDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSR------------------------LK---DP-ASFGVHSS  390 (541)
Q Consensus       339 ~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~------------------------~~---~p-~~~~~~~~  390 (541)
                      .+|+..|..+|+++.-..   .       ..+....||.+                        ..   +. ..+..+..
T Consensus       196 ~~al~~Is~~L~~~~~~~---~-------~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~  265 (485)
T KOG2190|consen  196 KKALVQISSRLLENPPRS---P-------PPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSD  265 (485)
T ss_pred             HHHHHHHHHHHHhcCCcC---C-------CCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchh
Confidence            999999999999864110   0       00111122211                        00   00 00000000


Q ss_pred             c--cc---CCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCccc
Q 009173          391 V--AV---SHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAI  465 (541)
Q Consensus       391 ~--g~---~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~  465 (541)
                      .  ++   .....+.- -+..+. ....+...+  ......+....  +...-...-...........    ......+ 
T Consensus       266 ~~~~v~g~~~~~i~~l-~~~~~~-~i~v~~~~~--~~~i~~s~~e~--~~~~~s~a~~a~~~~~~~~~----~~~~~~~-  334 (485)
T KOG2190|consen  266 KVGSVIGKGGLVIRAL-RNETGA-SISVGDSRT--DRIVTISAREN--PEDRYSMAQEALLLVQPRIS----ENAGDDL-  334 (485)
T ss_pred             hceeeecCCCccchhh-hhhcCC-ceEeccccC--cceeeeccccC--cccccccchhhhhhcccccc----ccccccc-
Confidence            0  00   00000000 000000 000000000  00000000000  00000000000000000000    0000111 


Q ss_pred             ccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCC--CCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          466 VTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL--GSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       466 ~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~--~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ....+.++.||.+++|+||||+|++|.+||+.|||.|.|.+...  ...++.++|+|+..+...|++++.+++..
T Consensus       335 ~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~  409 (485)
T KOG2190|consen  335 TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSA  409 (485)
T ss_pred             cceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccccc
Confidence            23478999999999999999999999999999999999997665  77999999999999999999999887754

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

Probab=99.97  E-value=3.3e-31  Score=281.66  Aligned_cols=247  Identities=24%  Similarity=0.408  Sum_probs=193.8

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (541)
Q Consensus       184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~  263 (541)
                      ..++.+..||.++||.||||+|+.|..|+.++||+|++........+|.|.++|.++.      +..|. .++..+++..
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~------v~~aK-~li~evv~r~  124 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPEN------VEVAK-QLIGEVVSRG  124 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCccc------HHHHH-Hhhhhhhhcc
Confidence            4567789999999999999999999999999999999887667789999999999875      34443 3444455444


Q ss_pred             ccc-CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHH
Q 009173          264 SEK-GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV  342 (541)
Q Consensus       264 ~~~-g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~  342 (541)
                      ... ++.. ......++.+++||++.+|+||||+|++||.|++.+||++.+..|..-  +...++.+.|+|++++|+.|.
T Consensus       125 ~~~~~~~~-~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~--~~~~~KplritGdp~~ve~a~  201 (600)
T KOG1676|consen  125 RPPGGFPD-NQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSI--ATGADKPLRITGDPDKVEQAK  201 (600)
T ss_pred             CCCCCccc-cCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCc--CCCCCCceeecCCHHHHHHHH
Confidence            311 1111 112456789999999999999999999999999999999999865421  124678999999999999999


Q ss_pred             HHHHHHhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCc
Q 009173          343 YNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPK  422 (541)
Q Consensus       343 ~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~  422 (541)
                      .||.++|+|.. .+++                                        +..   ++                
T Consensus       202 ~lV~dil~e~~-~~~~----------------------------------------g~~---~~----------------  221 (600)
T KOG1676|consen  202 QLVADILREED-DEVP----------------------------------------GSG---GH----------------  221 (600)
T ss_pred             HHHHHHHHhcc-cCCC----------------------------------------ccc---cc----------------
Confidence            99999998521 1000                                        000   00                


Q ss_pred             cccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEE
Q 009173          423 LWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKV  502 (541)
Q Consensus       423 ~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I  502 (541)
                               ++.+          .|                   ...+.+|.||..+||.||||+|++||.|+.+|||+|
T Consensus       222 ---------~g~~----------~g-------------------~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KI  263 (600)
T KOG1676|consen  222 ---------AGVR----------GG-------------------GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKI  263 (600)
T ss_pred             ---------cCcC----------cc-------------------ccceeEEeccccceeeEEecCchHHHHHhhccCcee
Confidence                     0000          00                   124789999999999999999999999999999999


Q ss_pred             EEeC-CCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          503 IVHE-PRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       503 ~I~~-p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      +|-. ..+.+.+|.+.|.|++++|++|.+||.++|++
T Consensus       264 QfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~  300 (600)
T KOG1676|consen  264 QFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE  300 (600)
T ss_pred             EeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence            9974 33477899999999999999999999999976

>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=1.1e-31  Score=273.00  Aligned_cols=287  Identities=23%  Similarity=0.361  Sum_probs=203.3

Q ss_pred             cccCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC-CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHH
Q 009173          180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSR  258 (541)
Q Consensus       180 ~~~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~-~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~  258 (541)
                      +...-+..+|+|||..+||+||||.|++||.|-..|.|+|+|... ..+..|++++|.|+++.      +-+|+.+|++-
T Consensus       193 ~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg------~s~Ac~~ILei  266 (584)
T KOG2193|consen  193 KQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG------TSKACKMILEI  266 (584)
T ss_pred             cccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc------hHHHHHHHHHH
Confidence            344567899999999999999999999999999999999999865 56889999999999776      55566555543


Q ss_pred             HhhcccccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCc-ccccCCCCCceEEEEcCHHH
Q 009173          259 LIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQ-LLKCISENDRVVQISGEFSK  337 (541)
Q Consensus       259 i~e~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~-~P~~~~s~ervVtItGt~e~  337 (541)
                      +..+....      .....+.++++-.+.+||++|||.|.+||+|+++||++|.|.+-. +-  .-+.||.+++.|+.++
T Consensus       267 mqkEA~~~------k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels--~ynpERTItVkGsiEa  338 (584)
T KOG2193|consen  267 MQKEAVDD------KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELS--LYNPERTITVKGSIEA  338 (584)
T ss_pred             HHHhhhcc------chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhc--ccCccceEEecccHHH
Confidence            32211110      122456789999999999999999999999999999999998321 21  1256999999999999


Q ss_pred             HHHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccc-cccccCCCCCCCCCccCCCccCCCCCCC
Q 009173          338 VKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVH-SSVAVSHDFSQPPLTQGMDHLGLSHSLD  416 (541)
Q Consensus       338 V~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~-~~~g~~~~~~r~~~~~~~~~~~~~~~~~  416 (541)
                      |.+|..+|+.+|+++...+.....-.-          |..+...+..++.. ++.++++                   ..
T Consensus       339 c~~AE~eImkKlre~yEnDl~a~s~q~----------~l~P~l~~~~l~~f~ssS~~~~-------------------Ph  389 (584)
T KOG2193|consen  339 CVQAEAEIMKKLRECYENDLAAMSLQC----------HLPPGLNLPALGLFPSSSAVSP-------------------PH  389 (584)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHhhccC----------CCCcccCccccCCCCcccccCC-------------------CC
Confidence            999999999999987544422111100          00000000000000 0000000                   00


Q ss_pred             CCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHh
Q 009173          417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQ  496 (541)
Q Consensus       417 ~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq  496 (541)
                      +|++|...++       +.             +       +..    .-++...+.+.||...+|+|||++|.+||+|.+
T Consensus       390 ~~Ps~v~~a~-------p~-------------~-------~~h----q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~R  438 (584)
T KOG2193|consen  390 FPPSPVTFAS-------PY-------------P-------LFH----QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSR  438 (584)
T ss_pred             CCCCccccCC-------Cc-------------h-------hhh----cCcchhheeeeccHHHHHHHHhhcchhHHHHHH
Confidence            0111111000       00             0       000    001346789999999999999999999999999


Q ss_pred             HhCCEEEEeCC-CCCCCccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173          497 ISGAKVIVHEP-RLGSTDRIVVISGTPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       497 ~SGA~I~I~~p-~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~~  540 (541)
                      .+||+|+|..| -++.++|+|+|+|.|++..+||..|..+|.+..
T Consensus       439 fagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  439 FAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             hccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence            99999999854 467899999999999999999999999998754

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

Probab=99.95  E-value=1.9e-26  Score=229.35  Aligned_cols=267  Identities=25%  Similarity=0.370  Sum_probs=193.1

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC---CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (541)
Q Consensus       185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~---~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e  261 (541)
                      .+.+|+|||+..+|.||||||++|.+||++|||+|++++.   .|+..||+|.|+|+-+.      +......|.++|.|
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea------i~av~efI~dKire  111 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA------LNAVHEFIADKIRE  111 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH------HHHHHHHHHHHHHH
Confidence            3999999999999999999999999999999999999975   78999999999998652      33334445666665


Q ss_pred             ccccc-C-CCC--CCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHH
Q 009173          262 GTSEK-G-LDF--SSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK  337 (541)
Q Consensus       262 ~~~~~-g-~~~--~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~  337 (541)
                      ..... + .+-  ....+..-.++++||++.+|.||||+|.+||.|++++||.|+|+. +.|...+-.||+|++.|++++
T Consensus       112 ~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP-qkpt~~sLqervvt~sge~e~  190 (402)
T KOG2191|consen  112 KPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP-QKPTGISLQERVVTVSGEPEQ  190 (402)
T ss_pred             hHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc-cCCCCccceeEEEEecCCHHH
Confidence            43221 1 110  111222245899999999999999999999999999999999983 334445678999999999999


Q ss_pred             HHHHHHHHHHHhhccccCC-CcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCC
Q 009173          338 VKDAVYNVTGRLRDNHFSG-TLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLD  416 (541)
Q Consensus       338 V~~A~~lI~~~l~e~~~~~-~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~  416 (541)
                      ..+|+.+|.++|.+++... +++              .+|.....|                                  
T Consensus       191 ~~~A~~~IL~Ki~eDpqs~scln--------------~sya~vsGp----------------------------------  222 (402)
T KOG2191|consen  191 NMKAVSLILQKIQEDPQSGSCLN--------------ISYANVSGP----------------------------------  222 (402)
T ss_pred             HHHHHHHHHHHhhcCCcccceec--------------cchhcccCc----------------------------------
Confidence            9999999999998876332 222              111100000                                  


Q ss_pred             CCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHh
Q 009173          417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQ  496 (541)
Q Consensus       417 ~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq  496 (541)
                                  ..+++|.+-+-.                   .....+....+..+.++....|..-|.+|.++-.|..
T Consensus       223 ------------vaNsnPtGspya-------------------~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~  271 (402)
T KOG2191|consen  223 ------------VANSNPTGSPYA-------------------YQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSG  271 (402)
T ss_pred             ------------ccccCCCCCCCC-------------------CCCccccccchhhccccccccccccccccccceeeec
Confidence                        000111100000                   0000111234567788999999999999999999999


Q ss_pred             HhCCEEEEeCC---CCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          497 ISGAKVIVHEP---RLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       497 ~SGA~I~I~~p---~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+|+.+.|.+.   ..+...+ .-+.|.+-.+..|-.+|..++.+
T Consensus       272 ~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~  315 (402)
T KOG2191|consen  272 FTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVAS  315 (402)
T ss_pred             ccccceeeccccccccccccc-ccccchhhhhhhhhhHHHHhhcc
Confidence            99999988743   2344555 77889999999999998887654

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

Probab=99.92  E-value=4.4e-25  Score=225.10  Aligned_cols=240  Identities=26%  Similarity=0.396  Sum_probs=189.9

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC---CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHH
Q 009173          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (541)
Q Consensus       183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~---~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i  259 (541)
                      ..++.+|++-.+..||++|||.|.+||+|+.+||++|.|++-   .....||.|++.|+-+.      +..|-.+|+.++
T Consensus       277 ~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEa------c~~AE~eImkKl  350 (584)
T KOG2193|consen  277 AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEA------CVQAEAEIMKKL  350 (584)
T ss_pred             hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHH------HHHHHHHHHHHH
Confidence            467899999999999999999999999999999999999863   33467999999996553      677777777766


Q ss_pred             hhc---cc---------ccCC--------CCC---------C-------------CCCceeEEEEEeccccccccccccc
Q 009173          260 IEG---TS---------EKGL--------DFS---------S-------------NKGLLVNARLVVASNQVGCLLGKGG  297 (541)
Q Consensus       260 ~e~---~~---------~~g~--------~~~---------~-------------~~~~~vt~~l~VP~~~vG~IIGKgG  297 (541)
                      .+.   +.         ..++        .+.         +             .......++|.||...||.||||+|
T Consensus       351 re~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG  430 (584)
T KOG2193|consen  351 RECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKG  430 (584)
T ss_pred             HHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcc
Confidence            542   11         0000        000         0             0113446899999999999999999


Q ss_pred             chhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCC
Q 009173          298 TIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYS  377 (541)
Q Consensus       298 ~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~  377 (541)
                      ..||.|.+.+||.|+|..-..|+   ..+|.|+|+|.+++.-+|+-.|..+|.|..|..                     
T Consensus       431 ~hIKql~RfagASiKIappE~pd---vseRMViItGppeaqfKAQgrifgKikEenf~~---------------------  486 (584)
T KOG2193|consen  431 QHIKQLSRFAGASIKIAPPEIPD---VSERMVIITGPPEAQFKAQGRIFGKIKEENFFL---------------------  486 (584)
T ss_pred             hhHHHHHHhccceeeecCCCCCC---cceeEEEecCChHHHHhhhhhhhhhhhhhccCC---------------------
Confidence            99999999999999998544665   789999999999999999999999997643210                     


Q ss_pred             CCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCccc
Q 009173          378 RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLEL  457 (541)
Q Consensus       378 ~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~  457 (541)
                                                                 |.                              ..   
T Consensus       487 -------------------------------------------Pk------------------------------ee---  490 (584)
T KOG2193|consen  487 -------------------------------------------PK------------------------------EE---  490 (584)
T ss_pred             -------------------------------------------ch------------------------------hh---
Confidence                                                       00                              00   


Q ss_pred             CCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC-CCCCC-ccEEEEEeCHHHHHHHHHHHHHH
Q 009173          458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP-RLGST-DRIVVISGTPDETQAAQSLLQAF  535 (541)
Q Consensus       458 ~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p-~~~s~-~RiItIsGtpeqV~~Aq~LI~~~  535 (541)
                               .....+|.||...+|+||||||.|+++|+..|+|.|.|+++ .+|.+ .-+|.|.|.--+++.||.-|.+.
T Consensus       491 ---------vklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~i  561 (584)
T KOG2193|consen  491 ---------VKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHI  561 (584)
T ss_pred             ---------heeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHH
Confidence                     12467999999999999999999999999999999999843 34443 45677999999999999998887


Q ss_pred             Hh
Q 009173          536 IL  537 (541)
Q Consensus       536 I~  537 (541)
                      +.
T Consensus       562 v~  563 (584)
T KOG2193|consen  562 VN  563 (584)
T ss_pred             HH
Confidence            75

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

Probab=99.87  E-value=1.6e-21  Score=194.46  Aligned_cols=164  Identities=24%  Similarity=0.447  Sum_probs=135.0

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEc--cCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcccc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF  354 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~--~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~  354 (541)
                      .+.++++||+..+|.||||||++|.++|++|||+|+++  +|++|.   ++||++.|+|+.+++....+.|.++|+|.+.
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG---TTeRvcli~Gt~eai~av~efI~dKire~p~  114 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG---TTERVCLIQGTVEALNAVHEFIADKIREKPQ  114 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC---ccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence            47899999999999999999999999999999999999  678997   8999999999999999999999999997541


Q ss_pred             CCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccC
Q 009173          355 SGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHL  434 (541)
Q Consensus       355 ~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~  434 (541)
                      ...                -       ++..                              .   .|+     . +   .
T Consensus       115 ~~~----------------k-------~v~~------------------------------~---~pq-----t-~---~  129 (402)
T KOG2191|consen  115 AVA----------------K-------PVDI------------------------------L---QPQ-----T-P---D  129 (402)
T ss_pred             hhc----------------C-------Cccc------------------------------c---CCC-----C-c---c
Confidence            100                0       0000                              0   000     0 0   0


Q ss_pred             CCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCC---CC
Q 009173          435 RGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL---GS  511 (541)
Q Consensus       435 ~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~---~s  511 (541)
                      |                                ....++.||...+|.||||+|.+||.|++++||.|+|...++   .-
T Consensus       130 r--------------------------------~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sL  177 (402)
T KOG2191|consen  130 R--------------------------------IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISL  177 (402)
T ss_pred             c--------------------------------cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccc
Confidence            0                                023789999999999999999999999999999999984332   22


Q ss_pred             CccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173          512 TDRIVVISGTPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       512 ~~RiItIsGtpeqV~~Aq~LI~~~I~~~~  540 (541)
                      .+|.||++|++++..+|.+||.++|.++.
T Consensus       178 qervvt~sge~e~~~~A~~~IL~Ki~eDp  206 (402)
T KOG2191|consen  178 QERVVTVSGEPEQNMKAVSLILQKIQEDP  206 (402)
T ss_pred             eeEEEEecCCHHHHHHHHHHHHHHhhcCC
Confidence            68999999999999999999999998753

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

Probab=99.70  E-value=1.9e-16  Score=171.24  Aligned_cols=158  Identities=30%  Similarity=0.479  Sum_probs=129.8

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc---------CHHHHHHHHHHHHH
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG---------EFSKVKDAVYNVTG  347 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG---------t~e~V~~A~~lI~~  347 (541)
                      ..+++|+++...+|.||||+|.+||+|+..+.++|+|. +..|+   ..+|+|+|+|         ..+++.+|..+|..
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~-~~~~~---c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~  117 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVN-ESLPG---CPERIITITGNRVELNLSPATDALFKAFDMIVF  117 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceee-cCCCC---CCcceEEEecccccccCCchHHHHHHHHHHHhh
Confidence            34589999999999999999999999999999999997 23555   4699999999         99999999999988


Q ss_pred             HhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccc
Q 009173          348 RLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQ  427 (541)
Q Consensus       348 ~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~  427 (541)
                      .+.++....                                                                       
T Consensus       118 ~~~~d~~~~-----------------------------------------------------------------------  126 (485)
T KOG2190|consen  118 KLEEDDEAA-----------------------------------------------------------------------  126 (485)
T ss_pred             ccccccccc-----------------------------------------------------------------------
Confidence            775221000                                                                       


Q ss_pred             ccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC
Q 009173          428 TVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP  507 (541)
Q Consensus       428 ~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p  507 (541)
                                .++.            +  ...+      ...++++.||.+.+|+||||+|+.||+||+.|||+|.|...
T Consensus       127 ----------~d~~------------~--~~~~------~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~  176 (485)
T KOG2190|consen  127 ----------EDNG------------E--DASG------PEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD  176 (485)
T ss_pred             ----------ccCC------------c--cccC------CceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC
Confidence                      0000            0  0000      02689999999999999999999999999999999999854


Q ss_pred             -CCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          508 -RLGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       508 -~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                       .+.+++|.|+|+|.+++|.+|...|..+|...
T Consensus       177 ~lP~ster~V~IsG~~~av~~al~~Is~~L~~~  209 (485)
T KOG2190|consen  177 MLPNSTERAVTISGEPDAVKKALVQISSRLLEN  209 (485)
T ss_pred             CCCcccceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence             68889999999999999999999999999863

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

Probab=99.65  E-value=9.7e-16  Score=149.32  Aligned_cols=217  Identities=19%  Similarity=0.364  Sum_probs=151.1

Q ss_pred             hhhhccCceeeeccccccCCCCCccCCCCCcccccCCCCcccccccccCCCcccccccchhh-cccCCceEEEEEecccc
Q 009173          118 LSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDA-RTQQQEVSFRILCSNDK  196 (541)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~rilvP~~~  196 (541)
                      +-+--||+.+.++|-+--.-..+ .-..+-+++++++-....++.    +.  ..-.+.++. .+-...+.+||||..+.
T Consensus        61 avigkgg~nik~lr~d~na~v~v-pds~~peri~tisad~~ti~~----il--k~iip~lee~f~~~~pce~rllihqs~  133 (390)
T KOG2192|consen   61 AVIGKGGKNIKALRTDYNASVSV-PDSSGPERILTISADIETIGE----IL--KKIIPTLEEGFQLPSPCELRLLIHQSL  133 (390)
T ss_pred             ceeccccccHHHHhhhccceeec-cCCCCCceeEEEeccHHHHHH----HH--HHHhhhhhhCCCCCCchhhhhhhhhhh
Confidence            56778899999888663110000 012234566666533211110    00  011122221 22344578999999999


Q ss_pred             ccceeccCchHHHHHHHHhCCeEEecC-CCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc----------
Q 009173          197 VGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE----------  265 (541)
Q Consensus       197 vG~IIGKgG~~Ik~Iq~eTGa~I~I~~-~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~----------  265 (541)
                      +|.|||++|+.||.|+++..|+++|-- .-|.+.+|+|.|.|.++.      ++..+..|++.+.|..+.          
T Consensus       134 ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~------v~~~i~~il~~i~e~pikgsa~py~p~f  207 (390)
T KOG2192|consen  134 AGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKR------VVECIKIILDLISESPIKGSAQPYDPNF  207 (390)
T ss_pred             ccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcch------HHHHHHHHHHHhhcCCcCCcCCcCCccc
Confidence            999999999999999999999999763 478899999999998775      666666666655441100          


Q ss_pred             ---------------------------------------------cC---------CCC---------------------
Q 009173          266 ---------------------------------------------KG---------LDF---------------------  270 (541)
Q Consensus       266 ---------------------------------------------~g---------~~~---------------------  270 (541)
                                                                   .+         .+|                     
T Consensus       208 yd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~Sewqma  287 (390)
T KOG2192|consen  208 YDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMA  287 (390)
T ss_pred             cCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccc
Confidence                                                         00         000                     


Q ss_pred             --------------------CCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEE
Q 009173          271 --------------------SSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQ  330 (541)
Q Consensus       271 --------------------~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVt  330 (541)
                                          +.-.+...|.++.||.+.-|.||||||+.|++|+.++||.|+|.. .+   .++.||+++
T Consensus       288 YePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide-pl---eGsedrIit  363 (390)
T KOG2192|consen  288 YEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE-PL---EGSEDRIIT  363 (390)
T ss_pred             cCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC-cC---CCCCceEEE
Confidence                                000124467899999999999999999999999999999999951 12   347899999


Q ss_pred             EEcCHHHHHHHHHHHHHHhhc
Q 009173          331 ISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       331 ItGt~e~V~~A~~lI~~~l~e  351 (541)
                      |+|+.++++.|++++...++.
T Consensus       364 ItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  364 ITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             EeccHHHHhhHHHHHHHHHHh
Confidence            999999999999999998874

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.63  E-value=1.2e-15  Score=144.81  Aligned_cols=136  Identities=24%  Similarity=0.355  Sum_probs=104.3

Q ss_pred             EEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEE---EcCHHHHHHHHHHHHHHhhccccCCCc
Q 009173          282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI---SGEFSKVKDAVYNVTGRLRDNHFSGTL  358 (541)
Q Consensus       282 l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtI---tGt~e~V~~A~~lI~~~l~e~~~~~~~  358 (541)
                      +.||.+.+|.|||+||++|+.|+++|||+|.|..+         +..|.|   +++++++.+|..+|..+.+.....+.+
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~   72 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE---------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKAL   72 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC---------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHH
Confidence            57899999999999999999999999999999522         357888   899999999999999977521100000


Q ss_pred             ccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCC
Q 009173          359 NTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSS  438 (541)
Q Consensus       359 ~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~  438 (541)
                      .-                        +                   +       ..         +              
T Consensus        73 ~l------------------------~-------------------g-------d~---------y--------------   79 (172)
T TIGR03665        73 KL------------------------L-------------------D-------DD---------Y--------------   79 (172)
T ss_pred             Hh------------------------c-------------------C-------Cc---------c--------------
Confidence            00                        0                   0       00         0              


Q ss_pred             CCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEec---------cCcccceeeCCcchHHHHHhHhCCEEEEeCCCC
Q 009173          439 DVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVP---------ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL  509 (541)
Q Consensus       439 d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP---------~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~  509 (541)
                                                    .-.-+.|+         ...+|+|||++|++++.|+..|||+|.|++   
T Consensus        80 ------------------------------~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~---  126 (172)
T TIGR03665        80 ------------------------------MLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG---  126 (172)
T ss_pred             ------------------------------eEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC---
Confidence                                          00001111         237899999999999999999999999963   


Q ss_pred             CCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          510 GSTDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       510 ~s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                          ..|.|.|++++++.|+.+|+.+|
T Consensus       127 ----~~v~i~G~~~~~~~A~~~i~~li  149 (172)
T TIGR03665       127 ----KTVGIIGDPEQVQIAREAIEMLI  149 (172)
T ss_pred             ----CEEEEECCHHHHHHHHHHHHHHH
Confidence                67999999999999999999988

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=99.57  E-value=2.3e-14  Score=137.07  Aligned_cols=149  Identities=22%  Similarity=0.323  Sum_probs=106.9

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE----cCHHHHHHHHHHHHHHhhccc
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS----GEFSKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt----Gt~e~V~~A~~lI~~~l~e~~  353 (541)
                      ....+.||.+.+|.|||++|++|+.|+++|||+|.+..+         +..|.|.    ++++++.+|+.+|..+++...
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~   73 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS   73 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC
Confidence            356899999999999999999999999999999999522         3678885    899999999999999886211


Q ss_pred             cCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccccccccc
Q 009173          354 FSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVH  433 (541)
Q Consensus       354 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~  433 (541)
                      ..+.+..                        +                   +       ..         +...      
T Consensus        74 ~e~A~~l------------------------~-------------------g-------d~---------y~~~------   88 (180)
T PRK13763         74 PEKALRL------------------------L-------------------D-------DD---------YVLE------   88 (180)
T ss_pred             HHHHHHH------------------------h-------------------C-------CC---------ceEE------
Confidence            0000000                        0                   0       00         0000      


Q ss_pred             CCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCc
Q 009173          434 LRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTD  513 (541)
Q Consensus       434 ~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~  513 (541)
                      --...++.                  ..          . ......+|+|||++|++++.|+..|||+|.|.+       
T Consensus        89 Vi~i~~~~------------------~~----------~-~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------  132 (180)
T PRK13763         89 VIDLSDYG------------------DS----------P-NALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------  132 (180)
T ss_pred             EEEhhhcc------------------CC----------h-hHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------
Confidence            00000000                  00          0 011237899999999999999999999999963       


Q ss_pred             cEEEEEeCHHHHHHHHHHHHHHH
Q 009173          514 RIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       514 RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      +.|.|.|++++++.|+..|+..+
T Consensus       133 ~~v~i~G~~~~~~~A~~~I~~li  155 (180)
T PRK13763        133 KTVAIIGDPEQVEIAREAIEMLI  155 (180)
T ss_pred             CEEEEEeCHHHHHHHHHHHHHHH
Confidence            45999999999999999999988

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.57  E-value=9.7e-15  Score=138.70  Aligned_cols=138  Identities=20%  Similarity=0.269  Sum_probs=98.8

Q ss_pred             EEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEe---cCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173          190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT---ASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (541)
Q Consensus       190 ilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~It---G~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~  266 (541)
                      |.||.+.+|.|||+||++||.|+++|||+|++.+     ++..|.|.   +.+.      .+++|...|.........+.
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~------~i~kA~~~I~~i~~gf~~e~   70 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL------AVMKAREVVKAIGRGFSPEK   70 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH------HHHHHHHHHHHHHcCCCHHH
Confidence            5689999999999999999999999999999984     33568883   3222      36666665544221101100


Q ss_pred             CCCCCCCCCceeEEE-EEecc---------cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHH
Q 009173          267 GLDFSSNKGLLVNAR-LVVAS---------NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS  336 (541)
Q Consensus       267 g~~~~~~~~~~vt~~-l~VP~---------~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e  336 (541)
                      -+  .. .+..++.+ +.|+.         ..+|+|||++|++++.|++.|||+|.|.           +..|.|.|+++
T Consensus        71 A~--~l-~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G~~~  136 (172)
T TIGR03665        71 AL--KL-LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIGDPE  136 (172)
T ss_pred             HH--Hh-cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEECCHH
Confidence            00  00 01112222 23333         3689999999999999999999999994           36799999999


Q ss_pred             HHHHHHHHHHHHhhcc
Q 009173          337 KVKDAVYNVTGRLRDN  352 (541)
Q Consensus       337 ~V~~A~~lI~~~l~e~  352 (541)
                      +++.|..+|.+++.+.
T Consensus       137 ~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       137 QVQIAREAIEMLIEGA  152 (172)
T ss_pred             HHHHHHHHHHHHHcCC
Confidence            9999999999999643

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=9.5e-14  Score=132.82  Aligned_cols=141  Identities=18%  Similarity=0.225  Sum_probs=100.0

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEe----cCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT----ASEGPESRYSPAQKAVVLVFSRLIE  261 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~It----G~~~~~~~~s~a~~Ai~~i~~~i~e  261 (541)
                      +...+.||.+.+|.|||++|++||.|+++|||+|++.+     ++..|.|.    ++++      .+++|...|.+....
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~------~i~kA~~~I~ai~~g   71 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPL------AVLKARDIVKAIGRG   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHH------HHHHHHHHHHHHhcC
Confidence            46778999999999999999999999999999999984     34677886    3222      256666555442221


Q ss_pred             cccccCCCCCCCCCceeEEEE-Eec---------ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEE
Q 009173          262 GTSEKGLDFSSNKGLLVNARL-VVA---------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI  331 (541)
Q Consensus       262 ~~~~~g~~~~~~~~~~vt~~l-~VP---------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtI  331 (541)
                      ...+..+.  . .+..+..++ .|.         ...+|+|||++|++++.|++.|||+|.|.           ++.|.|
T Consensus        72 f~~e~A~~--l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~-----------~~~v~i  137 (180)
T PRK13763         72 FSPEKALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY-----------GKTVAI  137 (180)
T ss_pred             CCHHHHHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc-----------CCEEEE
Confidence            01110000  0 011112221 111         13689999999999999999999999994           235899


Q ss_pred             EcCHHHHHHHHHHHHHHhhc
Q 009173          332 SGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       332 tGt~e~V~~A~~lI~~~l~e  351 (541)
                      .|++++++.|...|..+++.
T Consensus       138 ~G~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763        138 IGDPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             EeCHHHHHHHHHHHHHHHcC
Confidence            99999999999999999964

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.43  E-value=2.9e-13  Score=108.07  Aligned_cols=63  Identities=40%  Similarity=0.675  Sum_probs=58.6

Q ss_pred             EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCC-CCCccEEEEEeCHHHHHHHHHHHH
Q 009173          471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL-GSTDRIVVISGTPDETQAAQSLLQ  533 (541)
Q Consensus       471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~-~s~~RiItIsGtpeqV~~Aq~LI~  533 (541)
                      .+|.||.+++|+|||++|++|++|++.|||+|.|.+... +..+|.|+|+|++++++.|..||+
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            589999999999999999999999999999999996554 678999999999999999999984

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=99.36  E-value=4e-12  Score=135.08  Aligned_cols=292  Identities=19%  Similarity=0.258  Sum_probs=181.3

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (541)
Q Consensus       182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e  261 (541)
                      .+.++.+++.|+...|-.+|||+|++|+.|+..++++|.+..... .+++.-++.|.+.+   ++++..+   ++.++.+
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~-g~e~~~~~~~~p~~---v~~a~a~---~~~~~~~  136 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV-GDERVLLISGFPVQ---VCKAKAA---IHQILTE  136 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC-CcccchhhccCCCC---CChHHHH---HHHHHhc
Confidence            456789999999999999999999999999999999999986432 35677777775443   3344433   3444432


Q ss_pred             cccccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHH
Q 009173          262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA  341 (541)
Q Consensus       262 ~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A  341 (541)
                                   +..+...+.+|...+++|+|++|.++++|+..++|+|.+..+..    ..-.+...|.|....+..|
T Consensus       137 -------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr----~g~~~~~~i~~qqk~~~~a  199 (608)
T KOG2279|consen  137 -------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR----LGLSRLIKISGQQKEVAAA  199 (608)
T ss_pred             -------------CCcccccccchhhhcccccccchhhhcchhcccccccccccccc----cccccceecccccchHHHH
Confidence                         34566788999999999999999999999999999999863321    1346788888999999999


Q ss_pred             HHHHHHHhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCC
Q 009173          342 VYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSP  421 (541)
Q Consensus       342 ~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p  421 (541)
                      ..++.+++.++.-.-. .++...--  -.+...|.+...    -++..              ++....+.-..+...   
T Consensus       200 ~~~~~~~~~edeelv~-~~~e~~q~--rvprk~p~n~~~----~~m~~--------------~~~s~~~h~~~~t~~---  255 (608)
T KOG2279|consen  200 KHLILEKVSEDEELVK-RIAESAQT--RVPRKQPINVRR----EDMTE--------------PGGAGEPHLWKNTSS---  255 (608)
T ss_pred             HhhhhccccchhHHhh-hchhhccc--CCCCCCCccccc----hhhcc--------------cccCCccccCccchh---
Confidence            9999999976542110 00100000  000011111100    00000              000000000000000   


Q ss_pred             ccccccccccccCCCCCCCC------CCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHH
Q 009173          422 KLWTAQTVTGVHLRGSSDVG------RGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLR  495 (541)
Q Consensus       422 ~~~~~~~~~g~~~~g~~d~~------~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Ir  495 (541)
                        .+.++.++.+ +..++..      +.|...    .      .|....-......+|.+|...+|.+||+.|.+++.+.
T Consensus       256 --s~spg~~~~~-~eg~dm~v~vsk~~s~~~~----~------d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~ys  322 (608)
T KOG2279|consen  256 --SMSPGAPLVT-KEGGDMAVVVSKEGSWEKP----S------DDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYS  322 (608)
T ss_pred             --ccCCCCCCcc-cCCCcceeEEecccccCCc----c------ccccccccccccceeecCcccccchhhhhhhhhhhhh
Confidence              0001111111 0001100      011111    0      1111122234678999999999999999999999999


Q ss_pred             hHhCCEEEEeC-CCCCC--CccEEEEEeCHHHHHHHHHHHHH
Q 009173          496 QISGAKVIVHE-PRLGS--TDRIVVISGTPDETQAAQSLLQA  534 (541)
Q Consensus       496 q~SGA~I~I~~-p~~~s--~~RiItIsGtpeqV~~Aq~LI~~  534 (541)
                      ..|++.+.|-- +..+.  .-.++.+.|+..-++.+-.||..
T Consensus       323 sasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~  364 (608)
T KOG2279|consen  323 SASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTV  364 (608)
T ss_pred             hccCccceEEeccccchhhhhhhheecchhHHHHHHHhhhhc
Confidence            99999988863 22221  22678899999999999999873

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.29  E-value=4.6e-12  Score=101.12  Aligned_cols=65  Identities=42%  Similarity=0.647  Sum_probs=58.0

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHH
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT  346 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~  346 (541)
                      +++|+||.+++|+||||+|.+|++|+++|||+|.+..+..+   ..++|+|+|+|+++++++|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP---GSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCC---CCCceEEEEEeCHHHHHHHHHhhC
Confidence            36899999999999999999999999999999999854332   367899999999999999999873

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.25  E-value=1e-11  Score=97.95  Aligned_cols=61  Identities=21%  Similarity=0.449  Sum_probs=55.9

Q ss_pred             EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHH
Q 009173          471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQ  533 (541)
Q Consensus       471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~  533 (541)
                      .++.||.+++|+|||++|++|++|++.|||+|.|++..  ..++.|+|+|+++++..|+.+|+
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            57899999999999999999999999999999997543  57899999999999999999874

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.24  E-value=7.2e-12  Score=98.13  Aligned_cols=60  Identities=30%  Similarity=0.629  Sum_probs=55.3

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHH
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL  532 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI  532 (541)
                      |.+|.||.+++|+|||++|++|++|++.|||+|.|++.  + ....|+|+|+++++++|+.+|
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--D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999765  3 556999999999999999987

; 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=99.24  E-value=2.3e-11  Score=95.92  Aligned_cols=63  Identities=33%  Similarity=0.693  Sum_probs=58.4

Q ss_pred             EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHH
Q 009173          471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQ  533 (541)
Q Consensus       471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~  533 (541)
                      .+|.||.+++|+|||++|++|++|++.|||+|.|.+...+..++.|+|+|+.++++.|+.+|+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence            578999999999999999999999999999999987666678899999999999999999874

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.

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

Probab=99.18  E-value=5.7e-11  Score=93.72  Aligned_cols=58  Identities=19%  Similarity=0.437  Sum_probs=53.4

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHH
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQ  533 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~  533 (541)
                      +..+.||.+++|+|||+||++|++|++.|||+|.|++      ++.|.|+|+ +++++.|+.+|+
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence            5688999999999999999999999999999999975      368999999 999999999874

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.03  E-value=2e-10  Score=89.96  Aligned_cols=60  Identities=35%  Similarity=0.528  Sum_probs=53.8

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHH
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV  345 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI  345 (541)
                      |.+|.||.+++|+|||++|++|++|+++|||+|.|+.+       ..+..|+|+|++++|++|+.+|
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            57899999999999999999999999999999999743       1245899999999999999886

; 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=99.03  E-value=3.6e-10  Score=89.03  Aligned_cols=60  Identities=20%  Similarity=0.333  Sum_probs=54.3

Q ss_pred             EEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHH
Q 009173          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV  345 (541)
Q Consensus       280 ~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI  345 (541)
                      .++.||..++|+|||++|++|++|+++|||+|.++...      +.++.|+|+|+.++|..|+.+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------CCCCEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999997432      4578999999999999999886

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=99.02  E-value=5.3e-10  Score=88.20  Aligned_cols=58  Identities=21%  Similarity=0.313  Sum_probs=52.5

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-HHHHHHHHHHH
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNV  345 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-~e~V~~A~~lI  345 (541)
                      .+..+.||.+++|+||||+|++|++|+++|||+|.|..          ++.|.|+|+ .++++.|+.+|
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            35688999999999999999999999999999999942          467999998 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.

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

Probab=98.90  E-value=2.7e-09  Score=84.02  Aligned_cols=53  Identities=34%  Similarity=0.616  Sum_probs=48.3

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCC
Q 009173          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (541)
Q Consensus       188 ~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~  240 (541)
                      .+|.||..++|.|||++|++|++|+++|||+|.|.+...+..++.|.|.|..+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~   54 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPE   54 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHH
Confidence            57999999999999999999999999999999999765567899999999854

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=98.88  E-value=3e-09  Score=77.81  Aligned_cols=42  Identities=40%  Similarity=0.743  Sum_probs=38.9

Q ss_pred             cccceeccCchHHHHHHHHhCCeEEecC-CCCCCCcceEEEec
Q 009173          196 KVGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTA  237 (541)
Q Consensus       196 ~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~-~~~~~~eRvV~ItG  237 (541)
                      ++|+||||+|++|++|+++|||+|+|++ ..++..+|.|+|+|
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            4899999999999999999999999998 46788999999997

>smart00322 KH K homology RNA-binding domain

Probab=98.87  E-value=1.3e-08  Score=80.09  Aligned_cols=66  Identities=26%  Similarity=0.606  Sum_probs=59.5

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      .+.+|.||.+++|++||++|++|++|++.+|++|.+.....  ....|+|.|++++++.|+.+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            56899999999999999999999999999999999964332  5789999999999999999998876

>PF13014 KH_3: KH domain

Probab=98.86  E-value=3.9e-09  Score=77.19  Aligned_cols=42  Identities=33%  Similarity=0.683  Sum_probs=38.7

Q ss_pred             cccceeeCCcchHHHHHhHhCCEEEEeC-CCCCCCccEEEEEe
Q 009173          479 VIGSVYGENGSNLLRLRQISGAKVIVHE-PRLGSTDRIVVISG  520 (541)
Q Consensus       479 ~vG~IIGkgGs~Ik~Irq~SGA~I~I~~-p~~~s~~RiItIsG  520 (541)
                      ++|+|||++|++|++|+++|||+|+|++ ..++..++.|+|+|
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            5899999999999999999999999986 55677899999998

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

Probab=98.65  E-value=1.6e-08  Score=107.99  Aligned_cols=146  Identities=25%  Similarity=0.388  Sum_probs=122.7

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcccc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF  354 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~  354 (541)
                      ...+.++++|+...+-+++||+|.+|+.|+..++++|.+-.++.+     .+++-.+.|-+.++..|...++.++.++. 
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~~-  138 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-----DERVLLISGFPVQVCKAKAAIHQILTENT-  138 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-----cccchhhccCCCCCChHHHHHHHHHhcCC-
Confidence            356788999999999999999999999999999999999866554     36677777899999999999999885210 


Q ss_pred             CCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccC
Q 009173          355 SGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHL  434 (541)
Q Consensus       355 ~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~  434 (541)
                                                                                                      
T Consensus       139 --------------------------------------------------------------------------------  138 (608)
T KOG2279|consen  139 --------------------------------------------------------------------------------  138 (608)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCcc
Q 009173          435 RGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDR  514 (541)
Q Consensus       435 ~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~R  514 (541)
                                                       .+..+..+|...+++|+|++|.++..|+.-|+|+|.+......-..+
T Consensus       139 ---------------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~  185 (608)
T KOG2279|consen  139 ---------------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSR  185 (608)
T ss_pred             ---------------------------------cccccccchhhhcccccccchhhhcchhccccccccccccccccccc
Confidence                                             02235577889999999999999999999999999998664444678


Q ss_pred             EEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          515 IVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       515 iItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      .+.|.|....+..|+.++.+.++..
T Consensus       186 ~~~i~~qqk~~~~a~~~~~~~~~ed  210 (608)
T KOG2279|consen  186 LIKISGQQKEVAAAKHLILEKVSED  210 (608)
T ss_pred             ceecccccchHHHHHhhhhccccch
Confidence            8999999999999999999988653

>smart00322 KH K homology RNA-binding domain

Probab=98.63  E-value=1.1e-07  Score=74.61  Aligned_cols=66  Identities=32%  Similarity=0.553  Sum_probs=58.6

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l  349 (541)
                      .+.++.||...+|.+||++|.+|++|++.||++|.+..+.      .....+.|.|+.+++..|..+|.+.+
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            5778999999999999999999999999999999996321      14678999999999999999998876

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

Probab=98.62  E-value=2.3e-07  Score=88.48  Aligned_cols=142  Identities=21%  Similarity=0.284  Sum_probs=100.7

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE  265 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~  265 (541)
                      ..+.+.||...+|.+||+.|++.+.|.+.+++++.+.     ..+..|.|..+....++ ...++|...+.+  +..   
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp-~~~~ka~d~VkA--Igr---   76 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP-LALLKARDVVKA--IGR---   76 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh-HHHHHHHHHHHH--Hhc---
Confidence            4567899999999999999999999999999999997     56778999876321111 124455433322  211   


Q ss_pred             cCCCCCCC---CCceeEEEE------Eec-----ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEE
Q 009173          266 KGLDFSSN---KGLLVNARL------VVA-----SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI  331 (541)
Q Consensus       266 ~g~~~~~~---~~~~vt~~l------~VP-----~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtI  331 (541)
                       |+++...   ....+.+.+      .-+     ....|+|||++|.|.+-|++.|||.|.|.           +..|.|
T Consensus        77 -GF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-----------g~tVai  144 (194)
T COG1094          77 -GFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-----------GKTVAI  144 (194)
T ss_pred             -CCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-----------CcEEEE
Confidence             2221100   000111111      111     22459999999999999999999999995           357999


Q ss_pred             EcCHHHHHHHHHHHHHHhh
Q 009173          332 SGEFSKVKDAVYNVTGRLR  350 (541)
Q Consensus       332 tGt~e~V~~A~~lI~~~l~  350 (541)
                      .|.+++|+.|...|..++.
T Consensus       145 iG~~~~v~iAr~AVemli~  163 (194)
T COG1094         145 IGGFEQVEIAREAVEMLIN  163 (194)
T ss_pred             ecChhhhHHHHHHHHHHHc
Confidence            9999999999999999996

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.55  E-value=4.4e-07  Score=104.02  Aligned_cols=233  Identities=18%  Similarity=0.243  Sum_probs=159.8

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCC-CCCHHHHHHHHHHHH---
Q 009173          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES-RYSPAQKAVVLVFSR---  258 (541)
Q Consensus       183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~-~~s~a~~Ai~~i~~~---  258 (541)
                      ..-+..++.+-...++.+||+||.+++.++.++.+.|.|+...-  ......|.|..+... .....+.++.++-..   
T Consensus       198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~  275 (753)
T KOG2208|consen  198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSINVEIQEALTRLESEFDY  275 (753)
T ss_pred             ceeEEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceehhhhhHHHHHHhcChhhh
Confidence            34478899999999999999999999999999999999986411  111111112100000 000011221111110   


Q ss_pred             ----------------------Hhh---------cc-ccc-------CCCCC-------------CCCCceeEEEEEecc
Q 009173          259 ----------------------LIE---------GT-SEK-------GLDFS-------------SNKGLLVNARLVVAS  286 (541)
Q Consensus       259 ----------------------i~e---------~~-~~~-------g~~~~-------------~~~~~~vt~~l~VP~  286 (541)
                                            +..         .. ..+       +.+.+             .-....+.+.+.|-.
T Consensus       276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~  355 (753)
T KOG2208|consen  276 DEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP  355 (753)
T ss_pred             hhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence                                  000         00 000       00000             001244778899999


Q ss_pred             cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCCcccccccCC
Q 009173          287 NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRST  366 (541)
Q Consensus       287 ~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~~~~~~~~~~  366 (541)
                      ..+..++||+|.+|.+|++.+.+.+.+...      ++++..+.++|...++.+|...+...+.+-..            
T Consensus       356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------------  417 (753)
T KOG2208|consen  356 EELKFVIGKKGANIEKIREESQVKIDLPKQ------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN------------  417 (753)
T ss_pred             HhhhhhcCCCCccHHHHHHhhhhceecccc------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc------------
Confidence            999999999999999999999999999631      35678899999999999999999988854210            


Q ss_pred             CCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcC
Q 009173          367 SSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQ  446 (541)
Q Consensus       367 ~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~  446 (541)
                                                                            +                         
T Consensus       418 ------------------------------------------------------~-------------------------  418 (753)
T KOG2208|consen  418 ------------------------------------------------------S-------------------------  418 (753)
T ss_pred             ------------------------------------------------------c-------------------------
Confidence                                                                  0                         


Q ss_pred             CCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHH
Q 009173          447 GLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQ  526 (541)
Q Consensus       447 g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~  526 (541)
                                           ....++.+|+..+.++||.+|..|+.|...+|+ +.|..+........+++.|.-..+.
T Consensus       419 ---------------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~  476 (753)
T KOG2208|consen  419 ---------------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVE  476 (753)
T ss_pred             ---------------------cccceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCCCcccccceEeccccccc
Confidence                                 023478999999999999999999999999997 7776666666777888888877777


Q ss_pred             HHHHHHHHHH
Q 009173          527 AAQSLLQAFI  536 (541)
Q Consensus       527 ~Aq~LI~~~I  536 (541)
                      .++.++..+.
T Consensus       477 ~~~~~~~~~~  486 (753)
T KOG2208|consen  477 KSVSLLKALK  486 (753)
T ss_pred             hhHHHHHhhh
Confidence            7666555443

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

Probab=98.54  E-value=4.4e-07  Score=86.58  Aligned_cols=146  Identities=18%  Similarity=0.257  Sum_probs=103.9

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-----CHHHHHHHHHHHHHHhhccc
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-----EFSKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-----t~e~V~~A~~lI~~~l~e~~  353 (541)
                      ...+.||...+|.+||+.|.+-+.|.+.+++++.+.         +.+..|+|.-     +|..+.+|...|..+-+-..
T Consensus         9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD---------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~   79 (194)
T COG1094           9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID---------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFP   79 (194)
T ss_pred             eeeeecCchhheeeecccccchHHHHhhcCeEEEEE---------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCC
Confidence            456899999999999999999999999999999995         3345666654     57889999888887664211


Q ss_pred             cCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccccccccc
Q 009173          354 FSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVH  433 (541)
Q Consensus       354 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~  433 (541)
                      ....+.                                                                          
T Consensus        80 pe~A~~--------------------------------------------------------------------------   85 (194)
T COG1094          80 PEKALK--------------------------------------------------------------------------   85 (194)
T ss_pred             HHHHHH--------------------------------------------------------------------------
Confidence            000000                                                                          


Q ss_pred             CCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEe-c----cCcccceeeCCcchHHHHHhHhCCEEEEeCCC
Q 009173          434 LRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIV-P----ENVIGSVYGENGSNLLRLRQISGAKVIVHEPR  508 (541)
Q Consensus       434 ~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~I-P----~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~  508 (541)
                                             +... ...+..-...++.- +    ....|+|||++|.+.+.|...|||.|.|..  
T Consensus        86 -----------------------LL~d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g--  139 (194)
T COG1094          86 -----------------------LLED-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG--  139 (194)
T ss_pred             -----------------------HhcC-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC--
Confidence                                   0000 00000000000011 1    235699999999999999999999999964  


Q ss_pred             CCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          509 LGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       509 ~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                           ..|-|.|.+++++.|+..|..+|..
T Consensus       140 -----~tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         140 -----KTVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             -----cEEEEecChhhhHHHHHHHHHHHcC
Confidence                 5799999999999999999998864

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

Probab=98.16  E-value=4.8e-06  Score=74.58  Aligned_cols=61  Identities=20%  Similarity=0.333  Sum_probs=50.3

Q ss_pred             CcccceeeCCcchHHHHHhHhCCEEEEeCCCCC-----------------CCccEEEEEeC---HHHHHHHHHHHHHHHh
Q 009173          478 NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLG-----------------STDRIVVISGT---PDETQAAQSLLQAFIL  537 (541)
Q Consensus       478 ~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~-----------------s~~RiItIsGt---peqV~~Aq~LI~~~I~  537 (541)
                      +++|.|||++|++||+|+++|||+|.|......                 ...-.|.|++.   .+.+++|..+|+.++.
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            789999999999999999999999999753110                 12257889995   5899999999999886


Q ss_pred             c
Q 009173          538 T  538 (541)
Q Consensus       538 ~  538 (541)
                      .
T Consensus        95 ~   95 (120)
T cd02395          95 P   95 (120)
T ss_pred             c
Confidence            4

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

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.12  E-value=5.4e-06  Score=95.23  Aligned_cols=142  Identities=15%  Similarity=0.271  Sum_probs=107.1

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (541)
Q Consensus       184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~  263 (541)
                      ..+...+-+-...+..|+||+|.+|.+|+++++|.|.+..  .+..+..+.++|.....   ..+.+.+..++..+..  
T Consensus       345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~---~ka~~~v~~~~~ei~n--  417 (753)
T KOG2208|consen  345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSAND---EKAVEDVEKIIAEILN--  417 (753)
T ss_pred             cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccch---hHHHHHHHHHHHhhhc--
Confidence            3467778888999999999999999999999999999986  45677889999975542   2233334333333221  


Q ss_pred             cccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccC-eeEEEccCcccccCCCCCceEEEEcCHHHHHHHH
Q 009173          264 SEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG-TSIRIISDQLLKCISENDRVVQISGEFSKVKDAV  342 (541)
Q Consensus       264 ~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TG-A~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~  342 (541)
                                  +.+...+.+|...+..+||.+|..|++|..++| .+|+...+.      +....+++.|....+..+.
T Consensus       418 ------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------~~~~~~~~~~~~~dv~~~~  479 (753)
T KOG2208|consen  418 ------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------NSSDMVTIRGISKDVEKSV  479 (753)
T ss_pred             ------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC------cccccceEeccccccchhH
Confidence                        134557899999999999999999999999999 666665332      2345588899988888877


Q ss_pred             HHHHHHhh
Q 009173          343 YNVTGRLR  350 (541)
Q Consensus       343 ~lI~~~l~  350 (541)
                      .+...+..
T Consensus       480 ~~~~~~~~  487 (753)
T KOG2208|consen  480 SLLKALKA  487 (753)
T ss_pred             HHHHhhhh
Confidence            77766654

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

Probab=98.05  E-value=7e-06  Score=73.54  Aligned_cols=66  Identities=29%  Similarity=0.363  Sum_probs=50.9

Q ss_pred             ccccccccccccchhhhhhcccCeeEEEccCc-c-----------cccCCCCC-ceEEEEcCH---HHHHHHHHHHHHHh
Q 009173          286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQ-L-----------LKCISEND-RVVQISGEF---SKVKDAVYNVTGRL  349 (541)
Q Consensus       286 ~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~-~-----------P~~~~s~e-rvVtItGt~---e~V~~A~~lI~~~l  349 (541)
                      -+++|.|||++|.+||+|+++|||+|.|..+. .           |..+..++ -.|.|++..   +++.+|+.+|..++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            35789999999999999999999999998431 0           11111122 349999965   99999999999999


Q ss_pred             hc
Q 009173          350 RD  351 (541)
Q Consensus       350 ~e  351 (541)
                      .+
T Consensus        94 ~~   95 (120)
T cd02395          94 KP   95 (120)
T ss_pred             cc
Confidence            74

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=98.02  E-value=8.3e-06  Score=82.21  Aligned_cols=150  Identities=21%  Similarity=0.343  Sum_probs=107.7

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcccc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF  354 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~  354 (541)
                      ...++..+.||..+++.+.|++|.+||.|+.+|...|+-+..       ..+.++.++|..+.|..|++.|...-.....
T Consensus        23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr-------~eePiF~vTg~~edv~~aRrei~saaeH~~l   95 (394)
T KOG2113|consen   23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR-------GEEPIFPVTGRHEDVRRARREIPSAAEHFGL   95 (394)
T ss_pred             CCccceeeecCcccceeecccCccccchhhhhhcceeccCCC-------CCCCcceeccCchhHHHHhhcCccccceeee
Confidence            367888999999999999999999999999999999988721       2345799999999999998776543311000


Q ss_pred             CCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccC
Q 009173          355 SGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHL  434 (541)
Q Consensus       355 ~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~  434 (541)
                                                                 .|..                   +             
T Consensus        96 -------------------------------------------~~~s-------------------~-------------  100 (394)
T KOG2113|consen   96 -------------------------------------------IRAS-------------------R-------------  100 (394)
T ss_pred             -------------------------------------------eeec-------------------c-------------
Confidence                                                       0000                   0             


Q ss_pred             CCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCcc
Q 009173          435 RGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDR  514 (541)
Q Consensus       435 ~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~R  514 (541)
                          .++    .|.+...            ...+++.++.+|...+|.|.|..|.+|+.|++.+...|.-.-   ...+-
T Consensus       101 ----s~S----gg~~~~s------------~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v---~~~~~  157 (394)
T KOG2113|consen  101 ----SFS----GGTNGAS------------ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV---RCGEP  157 (394)
T ss_pred             ----ccc----CCCcccc------------ccCCCceeeeccceeeeeccccccCccchheecccceEeeec---cCCCc
Confidence                000    0000000            012467789999999999999999999999999988877642   23567


Q ss_pred             EEEEEeCHHH-HHHHH
Q 009173          515 IVVISGTPDE-TQAAQ  529 (541)
Q Consensus       515 iItIsGtpeq-V~~Aq  529 (541)
                      ++-++|-+.. +++|.
T Consensus       158 Vf~Vtg~~~nC~kra~  173 (394)
T KOG2113|consen  158 VFCVTGAPKNCVKRAR  173 (394)
T ss_pred             eEEEecCCcchhhhcc
Confidence            8999998887 56665

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

Probab=97.85  E-value=1e-05  Score=81.62  Aligned_cols=146  Identities=20%  Similarity=0.274  Sum_probs=104.2

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (541)
Q Consensus       184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~  263 (541)
                      +.++..+-+|...++.|.|++|.+||.|+.+|...|+-+.   -..|-++.++|..+.      +..|...+...  .+.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPs---r~eePiF~vTg~~ed------v~~aRrei~sa--aeH   92 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPS---RGEEPIFPVTGRHED------VRRARREIPSA--AEH   92 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCC---CCCCCcceeccCchh------HHHHhhcCccc--cce
Confidence            5688889999999999999999999999999999998762   234567888998664      44444443320  011


Q ss_pred             c---------ccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC
Q 009173          264 S---------EKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE  334 (541)
Q Consensus       264 ~---------~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt  334 (541)
                      +         ..+. .+.......+...-+|-..+|.|.|..|.+|+.|++.+...|.-+..       ..+.++.++|.
T Consensus        93 ~~l~~~s~s~Sgg~-~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-------~~~~Vf~Vtg~  164 (394)
T KOG2113|consen   93 FGLIRASRSFSGGT-NGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-------CGEPVFCVTGA  164 (394)
T ss_pred             eeeeeecccccCCC-ccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-------CCCceEEEecC
Confidence            1         0111 11112334456778899999999999999999999999999887621       24678999999


Q ss_pred             HHH-HHHHH-HHHHHH
Q 009173          335 FSK-VKDAV-YNVTGR  348 (541)
Q Consensus       335 ~e~-V~~A~-~lI~~~  348 (541)
                      +.+ +++|. ..|+..
T Consensus       165 ~~nC~kra~s~eie~t  180 (394)
T KOG2113|consen  165 PKNCVKRARSCEIEQT  180 (394)
T ss_pred             Ccchhhhccccchhhh
Confidence            988 55565 444443

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.84  E-value=2.1e-05  Score=72.38  Aligned_cols=102  Identities=20%  Similarity=0.325  Sum_probs=69.5

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~  266 (541)
                      .+.++|+...+|+.||++|++|+.|++..|-+|.|-.           -+  ++       ..+-+..++..   .... 
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~s--~d-------~~~fI~n~l~P---a~V~-   88 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------YS--DD-------PEEFIKNIFAP---AAVR-   88 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------cC--CC-------HHHHHHHHcCC---CEEE-
Confidence            6678899999999999999999999999998888742           11  11       12222222111   0000 


Q ss_pred             CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEE
Q 009173          267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI  313 (541)
Q Consensus       267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I  313 (541)
                      .... ...+....+.+.|+....|..|||+|++++.++..+|-.+.|
T Consensus        89 ~v~I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         89 SVTI-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EEEE-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            0000 001223456788999999999999999999999999887766

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.49  E-value=0.00028  Score=80.11  Aligned_cols=66  Identities=18%  Similarity=0.275  Sum_probs=58.0

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      ......+.||.+++|.|||+||++||+|+++||++|.|.          .+..|.|.+ +.+++++|+.+|..+...
T Consensus       576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~----------d~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE----------DDGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe----------cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            345678999999999999999999999999999999994          356788888 678999999999998863

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=97.46  E-value=0.00027  Score=80.21  Aligned_cols=62  Identities=23%  Similarity=0.455  Sum_probs=56.5

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL  537 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~  537 (541)
                      ...+.||.+++|.|||.||.+||.|.++|||+|.|.+      +..|.|.+ +.+++++|+.+|+..+.
T Consensus       579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            5688999999999999999999999999999999976      37788888 58899999999998876

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.45  E-value=0.00025  Score=65.33  Aligned_cols=37  Identities=19%  Similarity=0.299  Sum_probs=33.5

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      ....+.|+.+..|..|||+|.||+.+++.+|-++.|.
T Consensus        99 ~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         99 KVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             EEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            3567889999999999999999999999999998874

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

Probab=97.36  E-value=0.00076  Score=72.16  Aligned_cols=75  Identities=23%  Similarity=0.352  Sum_probs=57.8

Q ss_pred             eeEEEEEec------ccccccccccccchhhhhhcccCeeEEEcc-----Cc------ccccCCCCCce-EEEEc-CHHH
Q 009173          277 LVNARLVVA------SNQVGCLLGKGGTIISEMRKVTGTSIRIIS-----DQ------LLKCISENDRV-VQISG-EFSK  337 (541)
Q Consensus       277 ~vt~~l~VP------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~-----d~------~P~~~~s~erv-VtItG-t~e~  337 (541)
                      .++-++.||      -++||+|||..|.|.|+|+++|||+|.|-+     |.      +.......|.+ +.|++ +.++
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            566788888      468999999999999999999999999973     11      11111244555 88887 5678


Q ss_pred             HHHHHHHHHHHhhc
Q 009173          338 VKDAVYNVTGRLRD  351 (541)
Q Consensus       338 V~~A~~lI~~~l~e  351 (541)
                      |++|+.+|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999976

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.25  E-value=0.00037  Score=64.15  Aligned_cols=102  Identities=21%  Similarity=0.271  Sum_probs=68.1

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~  266 (541)
                      .+-++|....+|+.||++|++|+.|++..|=+|.|-.           -+.  ++       ..-+...+   .......
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe-----------ys~--D~-------~~fI~N~l---~PA~V~~   90 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE-----------YSE--NL-------EEFVANKL---APAEVKN   90 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE-----------cCC--CH-------HHHHHHcC---CCceEEE
Confidence            6668889999999999999999999988888887642           111  11       11111111   0000000


Q ss_pred             CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEE
Q 009173          267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI  313 (541)
Q Consensus       267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I  313 (541)
                       ... ...+......+.||.+..+..|||+|.+++...+.+|-++.|
T Consensus        91 -V~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952        91 -VTV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI  135 (141)
T ss_pred             -EEE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence             000 001223457788999999999999999999999999887766

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=97.07  E-value=0.001  Score=76.25  Aligned_cols=65  Identities=22%  Similarity=0.382  Sum_probs=55.4

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      .....+.||.+++|.|||+||++||+|+++|||+|.|.          .+..|.|.+ ..+.+.+|..+|..+..+
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE----------DDGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            45678999999999999999999999999999999994          245677776 677899999999888753

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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=96.99  E-value=0.0011  Score=75.89  Aligned_cols=63  Identities=21%  Similarity=0.341  Sum_probs=54.6

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL  537 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~  537 (541)
                      ....+.||.+++|.|||+||.+||.|.++|||+|.|.+      +..|.|.+ ..+.+++|+..|.....
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence            35788999999999999999999999999999999975      25677766 57889999999988764

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=96.89  E-value=0.0017  Score=59.82  Aligned_cols=37  Identities=16%  Similarity=0.239  Sum_probs=33.4

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      ....+.||.+..+..|||+|.|++..++.+|-++.|.
T Consensus       100 ~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952       100 KVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             EEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            3568899999999999999999999999999998774

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

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

Probab=96.86  E-value=0.0019  Score=68.09  Aligned_cols=66  Identities=15%  Similarity=0.221  Sum_probs=55.3

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      ....+.|-.++||.|||+||++|++|+..|.++|+|....   .+-.|+|-|...--.+|+..|..++.
T Consensus        47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~~  112 (629)
T KOG0336|consen   47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQD  112 (629)
T ss_pred             CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhhh
Confidence            3457788899999999999999999999999999997533   35789999998877888887776653

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.70  E-value=0.0039  Score=69.21  Aligned_cols=68  Identities=25%  Similarity=0.517  Sum_probs=59.3

Q ss_pred             ceEEEEEecc-CcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173          468 NTTVEIIVPE-NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       468 ~~t~~V~IP~-~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~  540 (541)
                      .++..|.+|+ ++-|+|||+.|.||+.+...||++|.|++.+     ..|+||| +|---+.|+..|...|..|+
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~dgr  272 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQDGR  272 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHHcCC
Confidence            4677889999 5669999999999999999999999997642     5688999 78888999999999998875

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.70  E-value=0.0044  Score=59.87  Aligned_cols=102  Identities=27%  Similarity=0.314  Sum_probs=67.9

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~  266 (541)
                      .+-+.+-.+.+|..||++|++|+.|+++.|=+|.|-.             -++++       ..-+..++....-.... 
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe-------------~s~d~-------~~fI~nal~Pa~v~~V~-  135 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE-------------WSEDP-------AEFIKNALAPAEVLSVN-  135 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE-------------eCCCH-------HHHHHHhcCcceEeEEE-
Confidence            3445556677999999999999999999996666532             22232       11111122100000000 


Q ss_pred             CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173          267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (541)
Q Consensus       267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~  314 (541)
                         .. ..+.. ...+.||.++.+..|||+|.+++-..+.||-++.|.
T Consensus       136 ---~~-~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~  178 (190)
T COG0195         136 ---IK-EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE  178 (190)
T ss_pred             ---EE-eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence               00 00112 678889999999999999999999999999999996

>PRK00106 hypothetical protein; Provisional

Probab=96.65  E-value=0.005  Score=68.29  Aligned_cols=68  Identities=29%  Similarity=0.581  Sum_probs=59.6

Q ss_pred             ceEEEEEecc-CcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173          468 NTTVEIIVPE-NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       468 ~~t~~V~IP~-~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~  540 (541)
                      .++..|.+|+ ++-|+|||+.|.||+.+...||+++.|++.+     ..|+||| +|---+.|+..|...|..|+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~dgr  293 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKDGR  293 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence            4667889999 5669999999999999999999999997643     5688999 89999999999999998875

>PRK12704 phosphodiesterase; Provisional

Probab=96.49  E-value=0.0069  Score=67.38  Aligned_cols=68  Identities=24%  Similarity=0.506  Sum_probs=57.1

Q ss_pred             ceEEEEEecc-CcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173          468 NTTVEIIVPE-NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       468 ~~t~~V~IP~-~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~  540 (541)
                      .++..|.+|+ ++-|+|||+.|.||+.+...||++|.|++.     ...|+||| +|---+.|+..|...+..|.
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~~~~~rre~a~~~l~~l~~dg~  278 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPIRREIARLALEKLVQDGR  278 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEecCChhhHHHHHHHHHHHHhcCC
Confidence            4667889998 566999999999999999999999999764     26788999 67777888888888877653

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

Probab=96.47  E-value=0.0029  Score=66.75  Aligned_cols=68  Identities=26%  Similarity=0.295  Sum_probs=55.7

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l  349 (541)
                      .......+.|-+++||.|||+||++|+.||..|+++|+|.+.       ..+-.|+|-|...--.+|...|...+
T Consensus        44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~-------~~e~kv~ifg~~~m~~kaka~id~~~  111 (629)
T KOG0336|consen   44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC-------DLEVKVTIFGINHMRKKAKASIDRGQ  111 (629)
T ss_pred             CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc-------CceeEEEEechHHHHHHHHhhHhhhh
Confidence            345667888999999999999999999999999999999743       34678999999887667766665444

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

Probab=96.43  E-value=0.0032  Score=62.96  Aligned_cols=41  Identities=22%  Similarity=0.438  Sum_probs=36.6

Q ss_pred             CCceEEEEEeccc------cccceeccCchHHHHHHHHhCCeEEecC
Q 009173          183 QQEVSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVGA  223 (541)
Q Consensus       183 ~~~~~~rilvP~~------~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~  223 (541)
                      .-.++.|++||.+      +||.|+|.+|.++|+|+++|||+|.|-.
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG  135 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG  135 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence            3457889999988      6999999999999999999999999863

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

Probab=96.41  E-value=0.0051  Score=48.45  Aligned_cols=36  Identities=31%  Similarity=0.541  Sum_probs=33.9

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEEe
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV  221 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I  221 (541)
                      ..+.+.|+.+.+|..|||+|.+|+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            688899999999999999999999999999988876

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.37  E-value=0.0048  Score=71.80  Aligned_cols=66  Identities=18%  Similarity=0.292  Sum_probs=56.9

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCee-EEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS-IRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~-I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      ......+.||.+++|.|||.||.+||+|.++||++ |.+.          .+-.|.|.+ +.+++++|+.+|.++..+
T Consensus       683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            34567899999999999999999999999999999 8773          246788888 788999999999998764

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

Probab=96.36  E-value=0.005  Score=48.49  Aligned_cols=36  Identities=22%  Similarity=0.528  Sum_probs=33.7

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEE
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV  504 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I  504 (541)
                      ....+.||.+..|.+|||+|.+|+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            468999999999999999999999999999988876

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.

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

Probab=96.35  E-value=0.0077  Score=64.70  Aligned_cols=61  Identities=23%  Similarity=0.421  Sum_probs=48.5

Q ss_pred             CcccceeeCCcchHHHHHhHhCCEEEEeC------CC---------CCCCc-cEEEEEe-CHHHHHHHHHHHHHHHhc
Q 009173          478 NVIGSVYGENGSNLLRLRQISGAKVIVHE------PR---------LGSTD-RIVVISG-TPDETQAAQSLLQAFILT  538 (541)
Q Consensus       478 ~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~------p~---------~~s~~-RiItIsG-tpeqV~~Aq~LI~~~I~~  538 (541)
                      +++|+|||..|.|.|+|.++|||+|.|--      -+         +...+ =-+.|++ |.|.|++|..+|+.+|.+
T Consensus       153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence            69999999999999999999999999962      01         11122 2467777 577899999999999975

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.04  E-value=0.0059  Score=71.07  Aligned_cols=63  Identities=11%  Similarity=0.266  Sum_probs=55.6

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCE-EEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAK-VIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL  537 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~-I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~  537 (541)
                      ....+.||.+++|.|||.||.+|+.|.++||+. |.|.+      +-.|.|.+ +.+.+++|+.+|.+...
T Consensus       685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            467889999999999999999999999999999 99865      36688887 58899999999998865

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

Probab=96.01  E-value=0.0093  Score=61.38  Aligned_cols=68  Identities=16%  Similarity=0.260  Sum_probs=56.6

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~  538 (541)
                      ....+.++..+.|.|||+.|.+.+.|+++|+++|.++.  +.++...|+|+| ..++|.+|...|.-+|-+
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~--p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids  125 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR--PNTNKEEIKIIGISRNCVIQALERIAKLIDS  125 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC--CCCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence            34577899999999999999999999999999999954  454555566655 688999999999888865

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

Probab=95.92  E-value=0.011  Score=66.34  Aligned_cols=64  Identities=19%  Similarity=0.328  Sum_probs=56.3

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCH-HHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTP-DETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtp-eqV~~Aq~LI~~~I~~  538 (541)
                      ...++.|+.++++-|||+||.+|++|.++|||+|.|.+      +..|.|.++. +.+++|+..|.++...
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence            56788999999999999999999999999999999963      3568898875 7899999999998753

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

Probab=95.87  E-value=0.019  Score=64.47  Aligned_cols=66  Identities=21%  Similarity=0.330  Sum_probs=57.5

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCH-HHHHHHHHHHHHHhhccc
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEF-SKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~-e~V~~A~~lI~~~l~e~~  353 (541)
                      -...+.|+.+.++-+||+||++|++|.++|||+|.|.          .+..|.|.++. +.+.+|+..|..+.++-.
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e  618 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------DDGTVKIAASDGESAKKAKERIEAITREVE  618 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence            3567889999999999999999999999999999994          35678899876 788899999999997644

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.70  E-value=0.021  Score=57.22  Aligned_cols=60  Identities=18%  Similarity=0.314  Sum_probs=52.2

Q ss_pred             EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Q 009173          471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFI  536 (541)
Q Consensus       471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I  536 (541)
                      +.+.||.++++.+||++|.+|+.|.+.++++|.|..      +..|-|+|+ .+.+++|+.+|+..=
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~e  207 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKIE  207 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999999999964      367888886 668999999998653

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.56  E-value=0.015  Score=67.07  Aligned_cols=64  Identities=22%  Similarity=0.369  Sum_probs=54.0

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      ....+.||.+.++.+||.||.+||+|.++||++|.+.          .+..|.|.+ ..+++.+|..+|..+..+
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            4457778999999999999999999999999988772          246788888 678899999999888754

>PRK00468 hypothetical protein; Provisional

Probab=95.37  E-value=0.018  Score=47.33  Aligned_cols=34  Identities=29%  Similarity=0.534  Sum_probs=30.2

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHh
Q 009173          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA  215 (541)
Q Consensus       182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eT  215 (541)
                      ....+.+++.|..+.+|.||||+|.+|+.|+.--
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            4456899999999999999999999999998754

>TIGR01953 NusA transcription termination factor NusA

Probab=95.30  E-value=0.042  Score=57.99  Aligned_cols=94  Identities=27%  Similarity=0.386  Sum_probs=62.0

Q ss_pred             cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173          196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK  274 (541)
Q Consensus       196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~  274 (541)
                      -+|+.||++|++|+.|.++. |=+|.|-.             =++++       ..   .+..-+.......- .. .+.
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~-------~~---fi~nal~Pa~v~~v-~i-~~~  298 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIE-------------YSDDP-------AE---FIANALSPAKVISV-EV-LDE  298 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEE-------------cCCCH-------HH---HHHHhcCCceEEEE-EE-EcC
Confidence            48999999999999999998 66776632             11121       00   11110100000000 00 001


Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS  315 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~  315 (541)
                       ....+.+.||.++.+..|||+|.+++-..+.||.+|.|..
T Consensus       299 -~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       299 -DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             -CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence             1236789999999999999999999999999999999963

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.22  E-value=0.031  Score=59.18  Aligned_cols=92  Identities=24%  Similarity=0.254  Sum_probs=61.6

Q ss_pred             cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173          196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK  274 (541)
Q Consensus       196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~  274 (541)
                      -+|+.||++|++|+.|.++. |=+|.|-.             =++++       ..   .+..-+.......- ..  . 
T Consensus       252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~-------------~s~D~-------~~---fI~Nal~Pa~V~~V-~i--~-  304 (374)
T PRK12328        252 PIGATVGVKGVRINAVSKELNGENIDCIE-------------YSNVP-------EI---FIARALAPAIISSV-KI--E-  304 (374)
T ss_pred             hHHhhcCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH-------HH---HHHHhCCCceeeEE-EE--c-
Confidence            48999999999999999998 66666532             11221       11   11111110000000 00  0 


Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~  314 (541)
                      ...-...+.||..+.+..|||+|.+++-..+.||.+|.|.
T Consensus       305 ~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~  344 (374)
T PRK12328        305 EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN  344 (374)
T ss_pred             CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence            1123678899999999999999999999999999999998

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

Probab=95.19  E-value=0.03  Score=54.07  Aligned_cols=37  Identities=35%  Similarity=0.592  Sum_probs=31.8

Q ss_pred             eEEEEEec------cCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          469 TTVEIIVP------ENVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       469 ~t~~V~IP------~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      .+-.+.||      .++||.+||..|+++|+++..|+|+|-|-
T Consensus       148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR  190 (269)
T COG5176         148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR  190 (269)
T ss_pred             ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence            44556665      37999999999999999999999999995

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

Probab=95.18  E-value=0.02  Score=58.94  Aligned_cols=69  Identities=20%  Similarity=0.277  Sum_probs=56.1

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE-cCHHHHHHHHHHHHHHhhcc
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-GEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt-Gt~e~V~~A~~lI~~~l~e~  352 (541)
                      ....+.|++...|.|||++|.|.++|+++|+++|.+++-   .   ++...++|+ +..++|.+|...|...|.+.
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p---~---~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP---N---TNKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC---C---CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            456788999999999999999999999999999999732   1   233444444 57889999999999988654

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.08  E-value=0.039  Score=55.27  Aligned_cols=64  Identities=20%  Similarity=0.292  Sum_probs=53.7

Q ss_pred             EEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHH-HHHHHHHHHHHHhhccc
Q 009173          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS-KVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       280 ~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e-~V~~A~~lI~~~l~e~~  353 (541)
                      +.+.||.++++.+||++|.+|+.|.+.++++|.+-          .+-.|.|.|... ++.+|..+|..+-++..
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------QNGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            56889999999999999999999999999999882          245788888655 88888888888776554

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

Probab=95.08  E-value=0.029  Score=56.24  Aligned_cols=38  Identities=32%  Similarity=0.691  Sum_probs=33.8

Q ss_pred             ceEEEEEecc------CcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          468 NTTVEIIVPE------NVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       468 ~~t~~V~IP~------~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      ..+.+|.||-      ++||+|+|..|.++|+|+++|||+|-|-
T Consensus        91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            3567788874      5999999999999999999999999995

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

Probab=95.07  E-value=0.0079  Score=69.92  Aligned_cols=70  Identities=21%  Similarity=0.179  Sum_probs=60.1

Q ss_pred             cceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC-CCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE-PRLGSTDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       467 ~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~-p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      ......+.+|.+...+|||+||+||+.+|..+||.|+|.+ -.....+|.+++.|.|+.+..|-.+|...|
T Consensus      1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred             cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence            3455678899999999999999999999999999999986 233467999999999999999998886554

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.00  E-value=0.051  Score=57.73  Aligned_cols=94  Identities=28%  Similarity=0.295  Sum_probs=62.3

Q ss_pred             cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173          196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK  274 (541)
Q Consensus       196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~  274 (541)
                      -+|+.||++|++|+.|.++. |=+|.|-.             =++++       ..-   +..-+.......- .- . .
T Consensus       246 pvGa~iG~~G~rI~~i~~el~gekIdiv~-------------~s~d~-------~~f---i~nal~Pa~v~~v-~i-~-~  299 (362)
T PRK12327        246 AKGACVGPKGQRVQNIVSELKGEKIDIID-------------WSEDP-------AEF---VANALSPAKVVSV-EV-D-D  299 (362)
T ss_pred             chheeECCCChhHHHHHHHhCCCeEEEEE-------------cCCCH-------HHH---HHHhCCCceEEEE-EE-E-c
Confidence            48999999999999999998 76777632             11121       111   1111110000000 00 0 0


Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS  315 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~  315 (541)
                      .....+.+.||.++.+..|||+|.+++--...||.+|.|..
T Consensus       300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            11236789999999999999999999999999999999973

>PRK02821 hypothetical protein; Provisional

Probab=94.99  E-value=0.024  Score=46.79  Aligned_cols=36  Identities=28%  Similarity=0.523  Sum_probs=30.9

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCC
Q 009173          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA  217 (541)
Q Consensus       182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa  217 (541)
                      ....+.+.|.|..+.+|.||||+|.+|+.|+.--.+
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            344578999999999999999999999999987543

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.82  E-value=0.052  Score=59.61  Aligned_cols=93  Identities=27%  Similarity=0.384  Sum_probs=62.0

Q ss_pred             cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173          196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK  274 (541)
Q Consensus       196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~  274 (541)
                      -+|+.||++|++|+.|.++. |=+|.|-.             =++++          ...+..-+.......-.   .+.
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~pa~v~~v~---~~~  299 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIIL-------------WSDDP----------AQFIINALSPAEVSSVV---VDE  299 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCCEEEEEE---EeC
Confidence            38999999999999999998 66776632             11121          01111111110000000   000


Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS  315 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~  315 (541)
                       ..-.+.+.||..+.+..|||+|.+++-..+.||.+|.|..
T Consensus       300 -~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        300 -DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             -CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence             1136789999999999999999999999999999999973

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.74  E-value=0.83  Score=44.63  Aligned_cols=63  Identities=16%  Similarity=0.259  Sum_probs=53.4

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhh
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR  350 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~  350 (541)
                      .+.+.++....-.++..+|..+++|-...||+|.+..+         +..+.|+|+...+..+...|.+.+.
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~---------~~~i~I~g~k~~~~~i~~~i~~~l~   89 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS---------ENRIRITGTKSTAEYIEASINEILS   89 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC---------CcEEEEEccHHHHHHHHHHHHHHHh
Confidence            34555568888999999999999998888999999633         5689999999999999999888885

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.72  E-value=0.048  Score=58.80  Aligned_cols=93  Identities=27%  Similarity=0.329  Sum_probs=61.0

Q ss_pred             cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173          196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK  274 (541)
Q Consensus       196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~  274 (541)
                      -+|+.||++|++|+.|.++. |=+|.|-.             =++++       ..   .|..-+........ .. .+ 
T Consensus       278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~-------------ys~Dp-------~~---fI~NaLsPA~V~~V-~i-~~-  331 (449)
T PRK12329        278 PVGACIGARGSRIQAVVNELRGEKIDVIR-------------WSPDP-------AT---YIANALSPARVDEV-RL-VD-  331 (449)
T ss_pred             hhhccCCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH-------HH---HHHHhcCCceeeEE-EE-Ec-
Confidence            48999999999999999998 66666532             11221       11   11111100000000 00 00 


Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~  314 (541)
                      .....+.+.||.++.+..|||+|.+++--...||.+|.|.
T Consensus       332 ~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~  371 (449)
T PRK12329        332 PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK  371 (449)
T ss_pred             CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence            1123568999999999999999999999999999999885

>PRK12705 hypothetical protein; Provisional

Probab=94.72  E-value=0.039  Score=61.03  Aligned_cols=68  Identities=22%  Similarity=0.458  Sum_probs=54.9

Q ss_pred             ceEEEEEeccC-cccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173          468 NTTVEIIVPEN-VIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       468 ~~t~~V~IP~~-~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~  540 (541)
                      .++..|.+|++ +-|+|||+.|.||+.+...||+.|.|++-+     ..|+|++ .|.--+.|+..+...|..|+
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~fdp~rreia~~~l~~Li~dgr  266 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSFNPIRREIARLTLEKLLADGR  266 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhcccCccchHHHHHHHHHHHhcCC
Confidence            35678889985 559999999999999999999999997643     4477777 47777788888888877664

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=94.68  E-value=0.049  Score=52.72  Aligned_cols=37  Identities=19%  Similarity=0.398  Sum_probs=34.4

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE  506 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~  506 (541)
                      ...+.||.+..+.+|||+|.|++.+.+.||-++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            5688899999999999999999999999999999963

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.65  E-value=0.089  Score=58.57  Aligned_cols=64  Identities=20%  Similarity=0.322  Sum_probs=49.3

Q ss_pred             EEEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       279 t~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      +..+.+|+ ++-|+||||.|.+|+-++..||+++.|  |+.|       ..|+|+| +|---+-|...+..++.|
T Consensus       205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~ii--ddtp-------~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--DDTP-------EAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEE--cCCC-------CeEEecCCchHHHHHHHHHHHHHHHc
Confidence            34567887 567999999999999999999999999  5444       4677888 565556676666666654

>PRK12704 phosphodiesterase; Provisional

Probab=94.64  E-value=0.083  Score=58.89  Aligned_cols=64  Identities=20%  Similarity=0.314  Sum_probs=48.3

Q ss_pred             EEEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       279 t~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      +..+.+|+ ++-|+||||.|.+|+-++..||++|.|  |+.|       ..|.|+| ++---+.|...+...+.|
T Consensus       211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~ii--ddtp-------~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--DDTP-------EAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEE--cCCC-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence            33566787 677999999999999999999999999  5444       4788998 555544566666665544

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=94.44  E-value=0.03  Score=64.50  Aligned_cols=62  Identities=23%  Similarity=0.399  Sum_probs=53.0

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL  537 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~  537 (541)
                      ...+.||.++++.+||.||.+|+.|.++||++|.|.+      +..|.|.+ ..+.+++|+.+|+....
T Consensus       555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~  617 (693)
T PRK11824        555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITA  617 (693)
T ss_pred             heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhcc
Confidence            3567779999999999999999999999999888844      36688888 58889999999998764

>PRK00106 hypothetical protein; Provisional

Probab=94.37  E-value=0.12  Score=57.54  Aligned_cols=64  Identities=23%  Similarity=0.371  Sum_probs=49.7

Q ss_pred             EEEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       279 t~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      +..+.+|+ ++-|+||||.|.+|+-+...||+++.|  |+.|       ..|.|+| +|---+-|...+..++.|
T Consensus       226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdlii--ddtp-------~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVII--DDTP-------EVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEE--cCCC-------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            34567887 677999999999999999999999999  5444       4688888 666666676666666654

>PRK00468 hypothetical protein; Provisional

Probab=94.29  E-value=0.037  Score=45.53  Aligned_cols=32  Identities=34%  Similarity=0.468  Sum_probs=28.6

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV  306 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~  306 (541)
                      +..+.+++.+..+.+|+||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            45578899999999999999999999999974

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

Probab=94.26  E-value=0.051  Score=44.69  Aligned_cols=33  Identities=27%  Similarity=0.535  Sum_probs=29.8

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHh
Q 009173          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA  215 (541)
Q Consensus       183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eT  215 (541)
                      ...+.++|.+..+.+|.||||+|.+|+.|+.--
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            567899999999999999999999999999753

>PRK01064 hypothetical protein; Provisional

Probab=94.03  E-value=0.056  Score=44.82  Aligned_cols=34  Identities=21%  Similarity=0.513  Sum_probs=30.4

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHh
Q 009173          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA  215 (541)
Q Consensus       182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eT  215 (541)
                      ....+.+++.|..+..|.+|||+|.+|+.|+.-.
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            3567899999999999999999999999999853

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

Probab=93.91  E-value=0.049  Score=44.81  Aligned_cols=32  Identities=31%  Similarity=0.493  Sum_probs=29.0

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV  306 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~  306 (541)
                      +....+++.+..+.+|.||||+|.+|+.||--
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            55778999999999999999999999999964

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

Probab=93.82  E-value=0.16  Score=49.14  Aligned_cols=40  Identities=23%  Similarity=0.437  Sum_probs=34.4

Q ss_pred             CceeEEEEEec------ccccccccccccchhhhhhcccCeeEEEc
Q 009173          275 GLLVNARLVVA------SNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (541)
Q Consensus       275 ~~~vt~~l~VP------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~  314 (541)
                      ...++-++.||      .++||.|||..|.|.|+|++.|+|+|.|-
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR  190 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR  190 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence            34556677777      57899999999999999999999999997

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=93.82  E-value=1  Score=44.02  Aligned_cols=126  Identities=16%  Similarity=0.178  Sum_probs=84.7

Q ss_pred             EEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCC
Q 009173          190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLD  269 (541)
Q Consensus       190 ilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~  269 (541)
                      +.++....-.+...+|..++.|-...||+|.+.     .++..+.|+|++.       ..+.+...+.++...       
T Consensus        30 v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~-----~~~~~i~I~g~k~-------~~~~i~~~i~~~l~~-------   90 (210)
T PF14611_consen   30 VWLQPDEFFLLLTGNGRILENLAARNGAKIEVS-----RSENRIRITGTKS-------TAEYIEASINEILSN-------   90 (210)
T ss_pred             EEecchheeeeecCCchHHHHHHHhcCceEEEe-----cCCcEEEEEccHH-------HHHHHHHHHHHHHhh-------
Confidence            333577788899999999999988889999997     4667899999765       444554444444432       


Q ss_pred             CCCCCCceeEEEEEeccccccccc----ccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE-----cCHHHHHH
Q 009173          270 FSSNKGLLVNARLVVASNQVGCLL----GKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-----GEFSKVKD  340 (541)
Q Consensus       270 ~~~~~~~~vt~~l~VP~~~vG~II----GKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt-----Gt~e~V~~  340 (541)
                             ..+..+.++.-.--.-.    -.....++.|++.|++.|+...+         +..+.|+     -....+..
T Consensus        91 -------i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~---------~~~~~i~~~~~~~~~~~~~~  154 (210)
T PF14611_consen   91 -------IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD---------GNKLKISWLASPENEKRADR  154 (210)
T ss_pred             -------cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC---------CCeEEEEEEeeccccchHHH
Confidence                   22344444422111111    11356789999999999998633         2344454     46678888


Q ss_pred             HHHHHHHHhh
Q 009173          341 AVYNVTGRLR  350 (541)
Q Consensus       341 A~~lI~~~l~  350 (541)
                      |.+++.-.+.
T Consensus       155 a~RlL~~a~~  164 (210)
T PF14611_consen  155 AKRLLLWALD  164 (210)
T ss_pred             HHHHHHHhcc
Confidence            9999888874

>PRK02821 hypothetical protein; Provisional

Probab=92.97  E-value=0.083  Score=43.68  Aligned_cols=32  Identities=31%  Similarity=0.486  Sum_probs=28.8

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCC
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGA  500 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA  500 (541)
                      ...++.+...-+|+||||+|.+|+.||..-.|
T Consensus        31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             EEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            57899999999999999999999999987654

>PRK01064 hypothetical protein; Provisional

Probab=92.30  E-value=0.12  Score=42.78  Aligned_cols=32  Identities=28%  Similarity=0.466  Sum_probs=28.8

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV  306 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~  306 (541)
                      ...+.+++.|..+..|++|||+|.+|+.||.-
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            45678899999999999999999999999975

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=91.77  E-value=0.29  Score=53.90  Aligned_cols=37  Identities=22%  Similarity=0.511  Sum_probs=34.9

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE  506 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~  506 (541)
                      ...+.||.+..+..|||+|.|++..++.||.+|.|..
T Consensus       303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             EEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            6789999999999999999999999999999999963

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=91.24  E-value=0.12  Score=41.96  Aligned_cols=35  Identities=26%  Similarity=0.376  Sum_probs=29.2

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCC
Q 009173          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA  217 (541)
Q Consensus       183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa  217 (541)
                      .....+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            34557788889999999999999999999976543

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

Probab=90.80  E-value=0.2  Score=48.29  Aligned_cols=54  Identities=30%  Similarity=0.424  Sum_probs=48.9

Q ss_pred             ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhh
Q 009173          286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR  350 (541)
Q Consensus       286 ~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~  350 (541)
                      +..+|+|+||+|.|---|++.|.++|.+.           +..+-|-|..++++.|...|+.+|-
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~kIHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSKIHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec-----------CceEEEeecchhhHHHHHhhHhhhc
Confidence            55789999999999999999999999984           4578999999999999999999985

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

Probab=90.04  E-value=0.45  Score=36.94  Aligned_cols=35  Identities=34%  Similarity=0.495  Sum_probs=28.6

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCeE
Q 009173          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI  219 (541)
Q Consensus       185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I  219 (541)
                      .....+.+.....|.+|||+|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35666777776789999999999999999988443

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.

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

Probab=88.84  E-value=0.33  Score=39.27  Aligned_cols=35  Identities=37%  Similarity=0.547  Sum_probs=27.7

Q ss_pred             EEEEecccc-----ccceeccCchHHHHHHHHh-CCeEEec
Q 009173          188 FRILCSNDK-----VGAVIGKGGTIIRALQSEA-GAFISVG  222 (541)
Q Consensus       188 ~rilvP~~~-----vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~  222 (541)
                      .++.|-+..     +|..||++|+.|+.|.++. |-+|+|-
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            456666666     9999999999999999999 8888764

>PRK12705 hypothetical protein; Provisional

Probab=88.71  E-value=0.72  Score=51.22  Aligned_cols=62  Identities=23%  Similarity=0.282  Sum_probs=42.4

Q ss_pred             EEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhh
Q 009173          280 ARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLR  350 (541)
Q Consensus       280 ~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~  350 (541)
                      ..+.+|+ ++-|+||||.|.+|+.++..||+.+.|  |+.|.       .|.|.+ ++.--+.|...+..++.
T Consensus       200 s~v~lp~demkGriIGreGrNir~~E~~tGvdlii--ddtp~-------~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLII--DDTPE-------AVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             eeeecCChHhhccccCccchhHHHHHHhhCCceEe--cCCcc-------chhhcccCccchHHHHHHHHHHHh
Confidence            3456776 567999999999999999999999999  44443       455555 33333344444444443

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

Probab=88.00  E-value=0.53  Score=55.65  Aligned_cols=71  Identities=15%  Similarity=0.124  Sum_probs=58.5

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ..++.+|-....+|||+||.+|+.++..|||-|.+.+- -|+  ...||.+.+.|.++.++.|...|.-.+.|-
T Consensus      1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm-q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM-QPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred             ccccccchhhhhhhhccCcchhhhHhhccceEEehhhc-CCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence            34677888889999999999999999999999999631 111  146899999999999999988887777553

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

Probab=86.07  E-value=1.3  Score=34.38  Aligned_cols=34  Identities=24%  Similarity=0.389  Sum_probs=27.0

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEE
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKV  502 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I  502 (541)
                      ....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            3455666655689999999999999999998544

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=85.91  E-value=0.37  Score=39.05  Aligned_cols=33  Identities=15%  Similarity=0.300  Sum_probs=27.9

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCe
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGT  309 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA  309 (541)
                      ...+.+.+..+..|.||||.|.+++.||--.++
T Consensus        28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            346788889999999999999999999976543

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=85.32  E-value=0.46  Score=38.87  Aligned_cols=35  Identities=26%  Similarity=0.370  Sum_probs=29.5

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEE
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS  220 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~  220 (541)
                      ....+.+.....|.|||++|++|+.|....+-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            35668889999999999999999999988765553

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

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=84.87  E-value=0.88  Score=37.32  Aligned_cols=34  Identities=32%  Similarity=0.494  Sum_probs=26.9

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCeEE
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS  220 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~  220 (541)
                      .+.+-+..+..|.+|||.|+++..||--+..-++
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            3445666788999999999999999988765444

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

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

Probab=84.27  E-value=0.86  Score=36.85  Aligned_cols=36  Identities=22%  Similarity=0.387  Sum_probs=28.7

Q ss_pred             EEEEEeccCc-----ccceeeCCcchHHHHHhHh-CCEEEEe
Q 009173          470 TVEIIVPENV-----IGSVYGENGSNLLRLRQIS-GAKVIVH  505 (541)
Q Consensus       470 t~~V~IP~~~-----vG~IIGkgGs~Ik~Irq~S-GA~I~I~  505 (541)
                      ...|.|-...     +|..||++|++|+.|.++. |-+|.|-
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            3456666666     8999999999999999999 9999885

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

Probab=83.15  E-value=0.82  Score=44.19  Aligned_cols=56  Identities=16%  Similarity=0.396  Sum_probs=50.1

Q ss_pred             cCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          477 ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       477 ~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      +..+|+|+||+|.+--.|...|..+|.+.+       ..|-|-|+-+++..|+..|...|+..
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccC
Confidence            457899999999999999999999999954       56999999999999999999998753

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=83.09  E-value=0.49  Score=38.70  Aligned_cols=34  Identities=24%  Similarity=0.441  Sum_probs=28.6

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEE
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKV  502 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I  502 (541)
                      ....+.+-...-|.|||++|++|++|++..+-.+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            4567888899999999999999999988775444

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

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

Probab=82.69  E-value=4.8  Score=44.72  Aligned_cols=66  Identities=21%  Similarity=0.313  Sum_probs=54.8

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      ...+...+.|+.++...+||.+|...|+|..+||+.-.+  |         +..++|.. +..+.++|++.|..++.+
T Consensus       594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v--D---------e~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV--D---------EGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             cCceeeEEeecchhhheeecCccceeeeEeeeccceeee--c---------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            456677899999999999999999999999999965555  2         45677776 677888999999998865

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	541
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		9e-11
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		4e-09
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		6e-09
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		5e-08
1wvn_A	82	Crsytal Structure Of Domain 3 Of Human Alpha Polyc		2e-07
1ec6_A	87	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		8e-07
1dt4_A	73	Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Bind		2e-06
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		4e-06
1dtj_A	76	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		5e-06
1x4n_A	92	Solution Structure Of Kh Domain In Fuse Binding Pro		8e-05
3krm_A	163	Imp1 Kh34 Length = 163		1e-04
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		9e-04

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 46/148 (31%), Positives = 81/148 (54%), Gaps = 11/148 (7%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+    GP +  
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLA---GPTNAI 59
Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct: 60  F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 116
Query: 306 VTGTSIRIISDQLLKCISENDRVVQISG 333
            TG  +++  D L    +  +R + I+G
Sbjct: 117 STGAQVQVAGDMLP---NSTERAITIAG 141

>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A Single_stranded 10mer Dna Oligonucleotide Length = 89

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 43/64 (67%)
Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T ++ +P+++ GS+ G+ G  + ++R  SGA + + EP  GS DRI+ I+GT D+ Q AQ
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 530 SLLQ 533
            LLQ
Sbjct: 75  YLLQ 78

>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp K In Complex With Ssdna Length = 82

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 27/64 (42%), Positives = 43/64 (67%)
Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T ++ +P+++ GS+ G+ G  + ++R  SGA + + EP  GS DRI+ I+GT D+ Q AQ
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 67
Query: 530 SLLQ 533
            LLQ
Sbjct: 68  YLLQ 71

>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 42/64 (65%)
Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T ++ +P+++  S+ G+ G  + ++R  SGA + + EP  GS DRI+ I+GT D+ Q AQ
Sbjct: 15  TTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 530 SLLQ 533
            LLQ
Sbjct: 75  YLLQ 78

>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding Protein Length = 82

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 42/68 (61%)
Query: 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQ 526
           + TT E+ +P N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+     
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASIS 63
Query: 527 AAQSLLQA 534
            AQ L+ A
Sbjct: 64  LAQYLINA 71

>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Bound To 20-Mer Rna Hairpin Length = 87

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 44/65 (67%), Gaps = 3/65 (4%)
Query: 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH---EPRLGSTDRIVVISGTPDETQA 527
           VEI VPEN++G++ G+ G  L+  ++++GA++ +    E   G+ +R V I+G+P  TQA
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 528 AQSLL 532
           AQ L+
Sbjct: 65  AQYLI 69

>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding Domain Length = 73

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/65 (40%), Positives = 43/65 (66%), Gaps = 3/65 (4%)
Query: 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH---EPRLGSTDRIVVISGTPDETQA 527
           VEI VPEN++G++ G+ G  L+  ++++G ++ +    E   G+ +R V I+GTP  TQA
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQA 64
Query: 528 AQSLL 532
           AQ L+
Sbjct: 65  AQYLI 69

>pdb|2P2R|A Chain A, Crystal Structure Of The Third Kh Domain Of Human Poly(C)- Binding Protein-2 In Complex With C-Rich Strand Of Human Telomeric Dna Length = 76

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 39/64 (60%)
Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
           T+ E+ +P ++IG + G  G+ +  +RQ SGA++ +  P  GSTDR V I+G+      A
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLA 64
Query: 529 QSLL 532
           Q L+
Sbjct: 65  QYLI 68

>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Length = 76

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 25/65 (38%), Positives = 44/65 (67%), Gaps = 3/65 (4%)
Query: 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH---EPRLGSTDRIVVISGTPDETQA 527
           VE+ VPEN++G++ G+ G  L+  ++++GA++ +    E   G+ +R V I+G+P  TQA
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 528 AQSLL 532
           AQ L+
Sbjct: 65  AQYLI 69

>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1 Length = 92

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T E  VP+ ++G + G  G  + R++Q SG K+ +     G  +R  +++GTP+  Q+A+
Sbjct: 16  TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAK 75
Query: 530 SLLQAFILTGPS 541
            LL   +  G S
Sbjct: 76  RLLDQIVEKGRS 87

>pdb|3KRM|A Chain A, Imp1 Kh34 Length = 163

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 40/141 (28%), Positives = 70/141 (49%), Gaps = 16/141 (11%)
Query: 197 VGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTASEGPESRYSPAQKAVVLV 255
           VGA+IGK G  I+ L   A A I +     P+   R++ +T    PE+++    KA   +
Sbjct: 14  VGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP--PEAQF----KAQGRI 67
Query: 256 FSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315
           + +L E        F   + + +   + V ++  G ++GKGG  ++E++ +T   + +  
Sbjct: 68  YGKLKEENF-----FGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122
Query: 316 DQLLKCISENDRV-VQISGEF 335
           DQ      END+V V+I G F
Sbjct: 123 DQ---TPDENDQVIVKIIGHF 140

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 39/73 (53%)
Query: 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQ 526
           T+ T E  VP+ ++G + G  G  + +++Q SG KV +     G  +R V ++G P+  Q
Sbjct: 14  TSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQ 73
Query: 527 AAQSLLQAFILTG 539
            A+ +L   +  G
Sbjct: 74  KAKMMLDDIVSRG 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	541
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-40
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	6e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	8e-08
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-37
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-10
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-10
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-09
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-36
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-11
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	6e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-07
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-35
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-12
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-11
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-09
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	9e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-31
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-12
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	6e-08
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	6e-22
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-10
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-21
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	4e-12
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	5e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-21
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	5e-11
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-09
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	8e-21
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-12
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-10
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-20
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-19
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	6e-19
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	7e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-16
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-14
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-07
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-14
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-10
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-10
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	3e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	5e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	3e-10
1we8_A	104	Tudor and KH domain containing protein; structural	7e-12
1we8_A	104	Tudor and KH domain containing protein; structural	3e-08
1we8_A	104	Tudor and KH domain containing protein; structural	2e-06
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-11
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	5e-08
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-10
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	9e-04
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	2e-10
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	8e-10
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	3e-09
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	3e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	9e-08
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	5e-04
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	6e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	1e-06
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-05
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	1e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	5e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	5e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	6e-04
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	9e-04

>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 =  142 bits (360), Expect = 2e-40
 Identities = 44/170 (25%), Positives = 84/170 (49%), Gaps = 11/170 (6%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241
           +   ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+      
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPT-- 56

Query: 242 ESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIIS 301
               +   KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I 
Sbjct: 57  ----NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIK 112

Query: 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
           E+R+ TG  +++  D      +  +R + I+G    + + V  +   + +
Sbjct: 113 EIRESTGAQVQVAGDM---LPNSTERAITIAGIPQSIIECVKQICVVMLE 159

>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 = 58.6 bits (142), Expect = 2e-10
 Identities = 15/73 (20%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
            T+ +++    +GS+ G+ G ++ ++R+ SGA++ + E      +RI+ ++G  +    A
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKA 62

Query: 529 QSLLQAFILTGPS 541
            +++   +    S
Sbjct: 63  FAMIIDKLEEDIS 75

>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 = 57.5 bits (139), Expect = 5e-10
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH-EPRLGSTDRIV 516
            + S +A     T+ ++VP +  GS+ G+ G  +  +R+ +GA+V V  +    ST+R +
Sbjct: 78  MTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAI 137

Query: 517 VISGTPDETQAAQSLLQAFIL 537
            I+G P         +   +L
Sbjct: 138 TIAGIPQSIIECVKQICVVML 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 = 57.1 bits (138), Expect = 6e-10
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 7/85 (8%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV-GATMPECDERLITVT 236
                +  V+ R++    + G++IGKGG  I+ ++   GA + V G  +P   ER IT+ 
Sbjct: 81  STAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIA 140

Query: 237 ASEGPESRYSPAQKAVVLVFSRLIE 261
               P+S      + V  +   ++E
Sbjct: 141 GI--PQS----IIECVKQICVVMLE 159

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

 Score = 50.9 bits (122), Expect = 8e-08
 Identities = 21/100 (21%), Positives = 44/100 (44%), Gaps = 6/100 (6%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +  RL++   +VG ++GK G  + +MR+ +G  I I         +  +R++ ++G  + 
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG------NCPERIITLAGPTNA 58

Query: 338 VKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYS 377
           +  A   +  +L ++  S   N+         L    P S
Sbjct: 59  IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPAS 98

>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 =  134 bits (340), Expect = 2e-37
 Identities = 36/175 (20%), Positives = 76/175 (43%), Gaps = 8/175 (4%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEG 240
            +   ++L  +   G++IGKGG  I  LQ E GA I +       P   ER+  +  +  
Sbjct: 4   SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE 63

Query: 241 PESRYSPAQKAVVLVFSRLI---EGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGG 297
             +         +    + +   E  S      + N       +++V ++  G ++GKGG
Sbjct: 64  ALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG 123

Query: 298 TIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352
             +  + + +G  +++        I+  +RVV +SGE  + + AV  +  +++++
Sbjct: 124 ATVKAIMEQSGAWVQLSQKP--DGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

>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 = 58.7 bits (142), Expect = 2e-10
 Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 2/98 (2%)

Query: 445 SQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV 504
            Q ++  +    L   +         V+IIVP +  G + G+ G+ +  + + SGA V +
Sbjct: 80  PQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL 139

Query: 505 --HEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGP 540
                 +   +R+V +SG P++ + A  L+   I   P
Sbjct: 140 SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP 177

>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 = 58.3 bits (141), Expect = 4e-10
 Identities = 16/73 (21%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH---EPRLGSTDRIVVISGTPDE 524
              +++++P    GS+ G+ G  +++L++ +GA + +    +   G+T+R+ +I GT + 
Sbjct: 5   QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64

Query: 525 TQAAQSLLQAFIL 537
             A    +   I 
Sbjct: 65  LNAVHGFIAEKIR 77

>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 = 55.6 bits (134), Expect = 3e-09
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITV 235
                 +    +I+  N   G +IGKGG  ++A+  ++GA++ +           R++TV
Sbjct: 96  TTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTV 155

Query: 236 TASEGPESRYSPAQKAVVLVFSRLIE 261
           +    PE      +KAV L+  ++ E
Sbjct: 156 SGE--PEQ----NRKAVELIIQKIQE 175

>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 = 52.5 bits (126), Expect = 3e-08
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           ++++ S   G ++GKGG  I +++K TG +I++   +     +  +RV  I G    +  
Sbjct: 9   KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTT-ERVCLIQGTIEALNA 67

Query: 341 AVYNVTGRLRDNH 353
               +  ++R+  
Sbjct: 68  VHGFIAEKIREMP 80

>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 =  132 bits (333), Expect = 2e-36
 Identities = 36/169 (21%), Positives = 70/169 (41%), Gaps = 14/169 (8%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG-ATMPECDERLITVTASEGPE 242
           ++   ++      VGA+IGK G  I+ L   A A I +     P+   R++ +T      
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPP--- 57

Query: 243 SRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISE 302
                  KA   ++ +L E        F   + + +   + V ++  G ++GKGG  ++E
Sbjct: 58  ---EAQFKAQGRIYGKLKEEN-----FFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNE 109

Query: 303 MRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
           ++ +T   + +  DQ       +  +V+I G F   + A   +   L  
Sbjct: 110 LQNLTAAEVVVPRDQTPD--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 = 61.3 bits (149), Expect = 2e-11
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL-GSTDRIVVISGTPDETQA 527
             V++ +P   +G++ G+ G ++ +L + + A + +  P    S  R+V+I+G P+    
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFK 62

Query: 528 AQSLLQAFILTGP 540
           AQ  +   +    
Sbjct: 63  AQGRIYGKLKEEN 75

>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 = 53.2 bits (128), Expect = 2e-08
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV--HEPRLGSTDRIVVISGTPDETQA 527
              I VP +  G V G+ G  +  L+ ++ A+V+V   +    +   IV I G    +Q 
Sbjct: 86  ETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQM 145

Query: 528 AQSLLQAFI 536
           AQ  ++  +
Sbjct: 146 AQRKIRDIL 154

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

 Score = 51.3 bits (123), Expect = 6e-08
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           ++ + +  VG ++GK G  I ++ +    SI+I   +         R+V I+G       
Sbjct: 6   QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDS---KVRMVIITGPPEAQFK 62

Query: 341 AVYNVTGRLRDNHFSG 356
           A   + G+L++ +F G
Sbjct: 63  AQGRIYGKLKEENFFG 78

>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 = 49.0 bits (117), Expect = 4e-07
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC--DERLITVTAS 238
            ++ ++   I       G VIGKGG  +  LQ+   A + V         D+ ++ +   
Sbjct: 80  KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGH 139

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
               +    +Q A   +   L +
Sbjct: 140 --FYA----SQMAQRKIRDILAQ 156

>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 =  129 bits (326), Expect = 2e-35
 Identities = 31/174 (17%), Positives = 60/174 (34%), Gaps = 10/174 (5%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
                +      VG VIG+ G +I+ +Q++AG  I          ER+  +T        
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 245 YSPAQKAVVLVFSRLIEGT---------SEKGLDFSSNKGLLVNARLVVASNQVGCLLGK 295
            +     ++        G            +G       G L     +V + + G ++GK
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 296 GGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL 349
           GG  I  + + +G  I  +          N ++  I G   ++  A   +  ++
Sbjct: 122 GGETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 63.7 bits (155), Expect = 4e-12
 Identities = 15/68 (22%), Positives = 33/68 (48%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
             +++ +P   +G V G NG  + +++  +G ++        + +RI  I+G PD  Q A
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHA 62

Query: 529 QSLLQAFI 536
             ++   +
Sbjct: 63  AEIITDLL 70

>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 = 60.7 bits (147), Expect = 5e-11
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE---PRLGSTDR 514
           G+ +            IVP    G + G+ G  +  + Q SGA++ +     P      +
Sbjct: 93  GNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMK 152

Query: 515 IVVISGTPDETQAAQSLLQAFI 536
           +  I GTP +   A+ L++  I
Sbjct: 153 LFTIRGTPQQIDYARQLIEEKI 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 = 55.6 bits (134), Expect = 2e-09
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + +    VG ++G+ G +I +++   G  I+   D      +  +R+ QI+G   + + 
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG----TTPERIAQITGPPDRAQH 61

Query: 341 AVYNVTGRLRDN 352
           A   +T  LR  
Sbjct: 62  AAEIITDLLRSV 73

>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 = 54.1 bits (130), Expect = 9e-09
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC---DERLITVTAS 238
                 F  +    K G +IGKGG  I+++  ++GA I +    P     + +L T+  +
Sbjct: 100 PGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT 159

Query: 239 EGPESRYSPAQKAVVLVFSRL 259
             P+        A  L+  ++
Sbjct: 160 --PQQ----IDYARQLIEEKI 174

>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 =  117 bits (295), Expect = 4e-31
 Identities = 33/167 (19%), Positives = 67/167 (40%), Gaps = 11/167 (6%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITVTASEGPESR 244
              I+    K G VIGKGG  I+ LQ  AG  + +    +     ++ + +    G   +
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII---GDPYK 59

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
              A + V+ +     +G      ++ S  G      + V  + VG ++G+ G +I +++
Sbjct: 60  VQQACEMVMDILRERDQGGFGDRNEYGSRIG--GGIDVPVPRHSVGVVIGRSGEMIKKIQ 117

Query: 305 KVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
              G  I+   D      +  +++  I G   + + A   +   L+ 
Sbjct: 118 NDAGVRIQFKQDDG----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 = 65.2 bits (159), Expect = 1e-12
 Identities = 14/81 (17%), Positives = 36/81 (44%)

Query: 456 ELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRI 515
             G  ++        +++ VP + +G V G +G  + +++  +G ++   +      ++I
Sbjct: 78  GFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKI 137

Query: 516 VVISGTPDETQAAQSLLQAFI 536
             I G PD  + A  ++   +
Sbjct: 138 AHIMGPPDRCEHAARIINDLL 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 = 59.4 bits (144), Expect = 1e-10
 Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE--PRLGSTDRIVVISGTPDETQ 526
           T  EI++P    G V G+ G  + +L++ +G K+I+ +   +  + D+ + I G P + Q
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQ 61

Query: 527 AAQSLLQAFILTGPS 541
            A  ++   +     
Sbjct: 62  QACEMVMDILRERDQ 76

>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 = 56.3 bits (136), Expect = 1e-09
 Identities = 12/59 (20%), Positives = 24/59 (40%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT 236
           +    +      +      VG VIG+ G +I+ +Q++AG  I          E++  + 
Sbjct: 83  NEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 141

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

 Score = 51.7 bits (124), Expect = 6e-08
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            +++ + + G ++GKGG  I ++++  G  + +I D      +  D+ ++I G+  KV+ 
Sbjct: 5   EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN--TNVDKPLRIIGDPYKVQQ 62

Query: 341 AVYNVTGRLRDNH 353
           A   V   LR+  
Sbjct: 63  ACEMVMDILRERD 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 = 88.9 bits (221), Expect = 6e-22
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 465 IVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDE 524
           + + TT E+ +P N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+   
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 61

Query: 525 TQAAQSLLQAFI 536
              AQ L+ A +
Sbjct: 62  ISLAQYLINARL 73

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
            + +  +   N+ +G +IG+ G  I  ++  +GA I +   +     R +T+T S    S
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS--AAS 61

Query: 244 RYSPAQKAVVLVFSRLIE 261
                  A  L+ +RL  
Sbjct: 62  ----ISLAQYLINARLSS 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 = 56.1 bits (136), Expect = 2e-10
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 4/79 (5%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
               L + +N +GC++G+ G  I+E+R+++G  I+I +         + R V I+G  + 
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV----EGSSGRQVTITGSAAS 61

Query: 338 VKDAVYNVTGRLRDNHFSG 356
           +  A Y +  RL      G
Sbjct: 62  ISLAQYLINARLSSEKGMG 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 = 87.7 bits (218), Expect = 2e-21
 Identities = 27/68 (39%), Positives = 44/68 (64%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
            T ++ +P+++ GS+ G+ G  + ++R  SGA + + EP  GS DRI+ I+GT D+ Q A
Sbjct: 7   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 66

Query: 529 QSLLQAFI 536
           Q LLQ  +
Sbjct: 67  QYLLQNSV 74

>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 = 61.1 bits (149), Expect = 4e-12
 Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
                ++ ++    D  G++IGKGG  I+ ++ E+GA I +   +   ++R+IT+T +  
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-- 59

Query: 241 PESRYSPAQKAVVLVFSRLIE 261
            +      Q A  L+ + + +
Sbjct: 60  QDQ----IQNAQYLLQNSVKQ 76

>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 = 55.0 bits (133), Expect = 5e-10
 Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334
           G ++  ++ +  +  G ++GKGG  I ++R  +G SI+I            DR++ I+G 
Sbjct: 4   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE----GSEDRIITITGT 59

Query: 335 FSKVKDAVYNVTGRLRDN 352
             ++++A Y +   ++  
Sbjct: 60  QDQIQNAQYLLQNSVKQY 77

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

 Score = 85.8 bits (213), Expect = 6e-21
 Identities = 24/68 (35%), Positives = 41/68 (60%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
           T+ E+ +P ++IG + G  G+ +  +RQ+SGA++ +  P  GSTDR V I+G+      A
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLA 64

Query: 529 QSLLQAFI 536
           Q L+   +
Sbjct: 65  QYLINVRL 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 = 57.7 bits (140), Expect = 5e-11
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 6/80 (7%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241
           + Q  S  +   ND +G +IG+ G  I  ++  +GA I +   +    +R +T+T S   
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS--A 58

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            S       A  L+  RL  
Sbjct: 59  AS----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 = 53.5 bits (129), Expect = 1e-09
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
           K    +  L + ++ +GC++G+ G  I+E+R+++G  I+I +          DR V I+G
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV----EGSTDRQVTITG 56

Query: 334 EFSKVKDAVYNVTGRLRD 351
             + +  A Y +  RL  
Sbjct: 57  SAASISLAQYLINVRLSS 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 = 85.8 bits (213), Expect = 8e-21
 Identities = 27/68 (39%), Positives = 44/68 (64%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
            T ++ +P+++ GS+ G+ G  + ++R  SGA + + EP  GS DRI+ I+GT D+ Q A
Sbjct: 14  ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 73

Query: 529 QSLLQAFI 536
           Q LLQ  +
Sbjct: 74  QYLLQNSV 81

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 60.8 bits (148), Expect = 6e-12
 Identities = 19/81 (23%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
             ++ ++    D  G++IGKGG  I+ ++ E+GA I +   +   ++R+IT+T +   + 
Sbjct: 12  PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT--QDQ 69

Query: 244 RYSPAQKAVVLVFSRLIEGTS 264
                Q A  L+ + + + + 
Sbjct: 70  ----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 = 55.0 bits (133), Expect = 6e-10
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 270 FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVV 329
           +    G ++  ++ +  +  G ++GKGG  I ++R  +G SI+I            DR++
Sbjct: 6   YGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE----GSEDRII 61

Query: 330 QISGEFSKVKDAVYNVTGRLRDN 352
            I+G   ++++A Y +   ++  
Sbjct: 62  TITGTQDQIQNAQYLLQNSVKQY 84

>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 = 85.2 bits (211), Expect = 2e-20
 Identities = 25/84 (29%), Positives = 43/84 (51%)

Query: 458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVV 517
           GS       +  T E  VP+ ++G + G  G  + R++Q SG K+ +     G  +R  +
Sbjct: 4   GSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCM 63

Query: 518 ISGTPDETQAAQSLLQAFILTGPS 541
           ++GTP+  Q+A+ LL   +  G S
Sbjct: 64  LTGTPESVQSAKRLLDQIVEKGRS 87

>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 = 53.2 bits (128), Expect = 3e-09
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + Q+  ++      +  VG +IG+GG  I  +Q E+G  I +        ER   +T + 
Sbjct: 9   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT- 67

Query: 240 GPESRYSPAQKAVVLVFSRLIEGTS 264
            PES     Q A  L+   + +G S
Sbjct: 68  -PES----VQSAKRLLDQIVEKGRS 87

>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 = 48.6 bits (116), Expect = 1e-07
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 4/66 (6%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +     V    VG ++G+GG  IS +++ +G  I+I  D         +R   ++G    
Sbjct: 15  MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS----GGLPERSCMLTGTPES 70

Query: 338 VKDAVY 343
           V+ A  
Sbjct: 71  VQSAKR 76

>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 = 80.8 bits (200), Expect = 4e-19
 Identities = 25/72 (34%), Positives = 45/72 (62%), Gaps = 3/72 (4%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH---EPRLGSTDRIVVISGTPDE 524
              VE+ VPEN++G++ G+ G  L+  ++++GA++ +    E   G+ +R V I+G+P  
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 525 TQAAQSLLQAFI 536
           TQAAQ L+   +
Sbjct: 62  TQAAQYLISQRV 73

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 9/80 (11%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGP 241
           +    +    + VGA++GKGG  +   Q   GA I +   G  +P    R +T+T S  P
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS--P 59

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            +     Q A  L+  R+  
Sbjct: 60  AA----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 = 55.0 bits (133), Expect = 4e-10
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  N VG +LGKGG  + E +++TG  I+ IS +        +R V I+G  +  + 
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 341 AVYNVTGRLRD 351
           A Y ++ R+  
Sbjct: 65  AQYLISQRVTY 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 = 80.8 bits (200), Expect = 6e-19
 Identities = 26/72 (36%), Positives = 45/72 (62%), Gaps = 3/72 (4%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH---EPRLGSTDRIVVISGTPDE 524
              VEI VPEN++G++ G+ G  L+  ++++GA++ +    E   G+ +R V I+G+P  
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 525 TQAAQSLLQAFI 536
           TQAAQ L+   +
Sbjct: 62  TQAAQYLISQRV 73

>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 = 54.7 bits (132), Expect = 7e-10
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 9/80 (11%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGP 241
           +    I    + VGA++GKGG  +   Q   GA I +   G  +P    R +T+T S  P
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS--P 59

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            +     Q A  L+  R+  
Sbjct: 60  AA----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 = 54.3 bits (131), Expect = 1e-09
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  N VG +LGKGG  + E +++TG  I+ IS +        +R V I+G  +  + 
Sbjct: 6   EIAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 341 AVYNVTGRLRDNH 353
           A Y ++ R+    
Sbjct: 65  AQYLISQRVTYEQ 77

>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 = 74.0 bits (182), Expect = 2e-16
 Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV--HEPRLGSTDRI 515
           GS        N   EI++P +  G V G+ G  + +L++ +G K+++    P+    D+ 
Sbjct: 4   GSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKP 63

Query: 516 VVISGTPDETQAAQSLLQAFILTGPS 541
           + I+G P + Q A+ ++   I    S
Sbjct: 64  LRITGDPYKVQQAKEMVLELIRDQGS 89

>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 = 55.5 bits (134), Expect = 5e-10
 Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            +++ +++ G ++GKGG  I ++++  G  + +I D      +  D+ ++I+G+  KV+ 
Sbjct: 18  EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG--PQNTGADKPLRITGDPYKVQQ 75

Query: 341 AVYNVTGRLRD 351
           A   V   +RD
Sbjct: 76  AKEMVLELIRD 86

>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 = 52.8 bits (127), Expect = 5e-09
 Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG--ATMPECDERLITVTASE 239
                   I+    K G VIGKGG  I+ LQ  AG  + +          ++ + +T   
Sbjct: 11  GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD- 69

Query: 240 GPESRYSPAQKAVVLVFSRLIE 261
            P       Q+A  +V   + +
Sbjct: 70  -PYK----VQQAKEMVLELIRD 86

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

 Score = 69.0 bits (169), Expect = 1e-14
 Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 6/89 (6%)

Query: 453 GGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGST 512
           G +  GS           +++ VP + +G V G +G  + +++  +G ++   +      
Sbjct: 1   GAMATGSR------IGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP 54

Query: 513 DRIVVISGTPDETQAAQSLLQAFILTGPS 541
           ++I  I G PD  + A  ++   + +  S
Sbjct: 55  EKIAHIMGPPDRCEHAARIINDLLQSLRS 83

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

 Score = 54.8 bits (132), Expect = 1e-09
 Identities = 12/52 (23%), Positives = 22/52 (42%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
              +      VG VIG+ G +I+ +Q++AG  I          E++  +   
Sbjct: 12  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP 63

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

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  + VG ++G+ G +I +++   G  I+   D      +  +++  I G   + + 
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRCEH 69

Query: 341 AVY 343
           A  
Sbjct: 70  AAR 72

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

 Score = 67.8 bits (166), Expect = 2e-14
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV--HEPRLGSTDRIVVISGTPDET 525
            T  EI++P    G V G+ G  + +L++ +G K+I+     +  + D+ + I G P + 
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV 72

Query: 526 QAAQSLLQAFI 536
           Q A  ++   +
Sbjct: 73  QQACEMVMDIL 83

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

 Score = 57.0 bits (138), Expect = 1e-10
 Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 8/86 (9%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITV 235
           +A   Q      I+    K G VIGKGG  I+ LQ  AG  + +    +     ++ + +
Sbjct: 6   NANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRI 65

Query: 236 TASEGPESRYSPAQKAVVLVFSRLIE 261
                P       Q+A  +V   L E
Sbjct: 66  IGD--PYK----VQQACEMVMDILRE 85

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

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            +++ + + G ++GKGG  I ++++  G  + +I D      +  D+ ++I G+  KV+ 
Sbjct: 17  EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN--TNVDKPLRIIGDPYKVQQ 74

Query: 341 AVYNVTGRLRD 351
           A   V   LR+
Sbjct: 75  ACEMVMDILRE 85

>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 = 63.8 bits (156), Expect = 3e-13
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241
           +   ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+      
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP--T 56

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            +      KA  ++  +L 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 = 63.4 bits (155), Expect = 5e-13
 Identities = 17/75 (22%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +  RL++   +VG ++GK G  + +MR+ +G  I  IS+      +  +R++ ++G  + 
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARIN-ISEG-----NCPERIITLAGPTNA 58

Query: 338 VKDAVYNVTGRLRDN 352
           +  A   +  +L ++
Sbjct: 59  IFKAFAMIIDKLEED 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 = 55.4 bits (134), Expect = 3e-10
 Identities = 14/67 (20%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T+ +++    +GS+ G+ G ++ ++R+ SGA++ + E      +RI+ ++G  +    A 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAF 63

Query: 530 SLLQAFI 536
           +++   +
Sbjct: 64  AMIIDKL 70

>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 = 61.0 bits (148), Expect = 7e-12
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 458 GSGSKSAIVTNT--TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGS--TD 513
            SGS   +  NT    ++ VP+  +G + G  G  +  + + SGAK+   +   G+    
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS 61

Query: 514 RIVVISGTPDETQAAQSLLQAFI 536
           R++ ISGT  E  AA+ L+   +
Sbjct: 62  RLIKISGTQKEVAAAKHLILEKV 84

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG--ATMPECDERLITVTAS 238
           T+   V  ++      VG +IG+GG  IR++   +GA I+    +       RLI ++ +
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
              +        A  L+  ++ E
Sbjct: 70  --QKE----VAAAKHLILEKVSE 86

>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 = 45.6 bits (108), Expect = 2e-06
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           +L V    VG ++G+GG  I  + K +G  I    +   +      R+++ISG   +V  
Sbjct: 18  QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES--EGTLLLSRLIKISGTQKEVAA 75

Query: 341 AVY 343
           A +
Sbjct: 76  AKH 78

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

 Score = 59.9 bits (145), Expect = 2e-11
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV---HEPRLGSTDRIVVISGTPDET 525
             +   +P +  G V G  G N+  + Q +GA V +     P      ++ +I G+P + 
Sbjct: 7   GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQI 66

Query: 526 QAAQSLLQAFI 536
             A+ L++  I
Sbjct: 67  DHAKQLIEEKI 77

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

 Score = 51.0 bits (122), Expect = 3e-08
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
              + +++ G ++G+GG  +  + + TG  +  IS QL      N ++  I G   ++  
Sbjct: 10  TFSIPTHKCGLVIGRGGENVKAINQQTGAFVE-ISRQLPPNGDPNFKLFIIRGSPQQIDH 68

Query: 341 AVYNVTGRLRDN 352
           A   +  ++   
Sbjct: 69  AKQLIEEKIEGP 80

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

 Score = 50.3 bits (120), Expect = 5e-08
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECD---ERLITVTAS 238
                         K G VIG+GG  ++A+  + GAF+ +   +P       +L  +  S
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGS 62

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
             P+        A  L+  ++  
Sbjct: 63  --PQQ----IDHAKQLIEEKIEG 79

>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 = 58.5 bits (141), Expect = 2e-10
 Identities = 29/155 (18%), Positives = 50/155 (32%), Gaps = 31/155 (20%)

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           + +   D +G  IG  G  I+  +         G T  + DE   T              
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVP------GVTAIDLDEDTCTFH------------ 48

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
                      I G  +  +  + +        + V  N VG ++GK G +I E+   +G
Sbjct: 49  -----------IYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSG 97

Query: 309 -TSIRIISDQLLKCISENDRV-VQISGEFSKVKDA 341
              +RI ++       E   V     G    + +A
Sbjct: 98  VVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANA 132

>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 = 38.8 bits (90), Expect = 9e-04
 Identities = 19/76 (25%), Positives = 27/76 (35%), Gaps = 6/76 (7%)

Query: 464 AIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTD------RIVV 517
           + +      I VP N++G V G+NG  +  +   SG   +  E                V
Sbjct: 62  SFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFV 121

Query: 518 ISGTPDETQAAQSLLQ 533
             GT D    A  LL 
Sbjct: 122 FVGTKDSIANATVLLD 137

>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 = 56.1 bits (135), Expect = 2e-10
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 460 GSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVIS 519
           GS  +    TT+++ VP  V+G V G  G+ + R++Q +   ++         + +  ++
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---DKEPVFAVT 57

Query: 520 GTPDETQAAQSLLQAFILTGPS 541
           G P+    A+  ++A I     
Sbjct: 58  GMPENVDRAREEIEAHITLRSG 79

>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 = 58.2 bits (140), Expect = 8e-10
 Identities = 24/181 (13%), Positives = 67/181 (37%), Gaps = 26/181 (14%)

Query: 170 ESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECD 229
           + + V   D   +  +    +    D++  +IGK G   + ++      I++     + +
Sbjct: 18  DGEIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITI-----DSE 72

Query: 230 ERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK---------GLDFSSNKGLLVNA 280
              + +T+++  E   +   KA  +V +     + E+          L+  +   +++  
Sbjct: 73  TGEVWITSTKETEDPLA-VWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGN 131

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
                    G ++G+ G     + +++G S+ +             + V I G   +++ 
Sbjct: 132 EKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV-----------YGKTVAIIGNPIQIEI 180

Query: 341 A 341
           A
Sbjct: 181 A 181

>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 = 53.2 bits (128), Expect = 3e-09
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 459 SGSKSAIV----TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDR 514
           SGS   IV    T  +  + +P+     V G+NG  L  L   +  K+ +  PR      
Sbjct: 3   SGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSN 60

Query: 515 IVVISGTPDETQAAQSLLQAFI 536
            + I+GT +  + A+  +    
Sbjct: 61  QIKITGTKEGIEKARHEVLLIS 82

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
              Q + S  +    +    VIGK G  ++ L+ +    I +    P+     I +T ++
Sbjct: 11  ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTK 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 = 42.0 bits (99), Expect = 3e-05
 Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
            +A + +       ++GK G  + ++   T T I+I          +    ++I+G    
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEG 70

Query: 338 VKDAVY 343
           ++ A +
Sbjct: 71  IEKARH 76

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

 Score = 48.1 bits (115), Expect = 9e-08
 Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
             VEI +       + G++G+N+ R++      V +  P       ++ I G P   Q A
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQA 62

Query: 529 QSLLQAFI 536
           +  L    
Sbjct: 63  KRELLELA 70

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 6/65 (9%)

Query: 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336
           +    + +       L+GK G  I+ ++     S+RI  D       E   +++I G+  
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS------EKSNLIRIEGDPQ 57

Query: 337 KVKDA 341
            V+ A
Sbjct: 58  GVQQA 62

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 459 SGSKSAIVTN----TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDR 514
           SGS  +I  +      VE+ +P  +  S+ G  G  +  + +  G  V +H P  GS   
Sbjct: 3   SGSSGSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSD 61

Query: 515 IVVISGTPDETQAAQSLLQAFI 536
            VVI G   + + A+  L    
Sbjct: 62  TVVIRGPSSDVEKAKKQLLHLA 83

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

 Score = 47.1 bits (112), Expect = 6e-07
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T+E+ VP ++   V G+ GS + ++       + V  P       I+ I+G       A+
Sbjct: 18  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANLDRAK 75

Query: 530 SLLQAFI 536
           + L   +
Sbjct: 76  AGLLERV 82

>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 = 48.1 bits (114), Expect = 1e-06
 Identities = 29/160 (18%), Positives = 56/160 (35%), Gaps = 19/160 (11%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYS 246
              +    +++GAVIG  G +   +    G  I+V                      + +
Sbjct: 5   RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAA 64

Query: 247 PAQKAVVLVFS-----RLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIIS 301
              KA+ L F      RL+E   ++ L     K ++ +          G ++G+GG    
Sbjct: 65  EVVKAISLGFPPEKAFRLLEE--DQILVVVDLKQVVGD-SQNHLKRIKGRIIGEGGRARR 121

Query: 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
            + ++T T I +            +  V I G++ +   A
Sbjct: 122 TIEEMTDTYINV-----------GEYEVAIIGDYERAMAA 150

>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 = 45.6 bits (108), Expect = 2e-06
 Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP-RLGSTDRIVVISGTPDETQ 526
           +  + + V       + G  G+ + ++R      +   +          + I+G    T+
Sbjct: 16  SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 75

Query: 527 AAQSLLQAFI-----LTGPS 541
           AA+  +   +     ++GPS
Sbjct: 76  AARDAILRIVGELEQMSGPS 95

>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 = 42.1 bits (99), Expect = 3e-05
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 7/84 (8%)

Query: 458 GSGSKSAIVTN----TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTD 513
            SGS   IV       + ++ +   V   + G  G  + ++       +    P+ G+ D
Sbjct: 2   SSGSSGRIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF--PQSGAPD 59

Query: 514 -RIVVISGTPDETQAAQSLLQAFI 536
              V ++G P+  + A   +    
Sbjct: 60  PNCVTVTGLPENVEEAIDHILNLE 83

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 41.9 bits (97), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 14/40 (35%)

Query: 84  QEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQ 123
           Q +  + L++         L+++A +    S+ AL+I+  
Sbjct: 20  QAL--KKLQAS--------LKLYADD----SAPALAIKAT 45

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 42.1 bits (100), Expect = 5e-04
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 11/58 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAV 252
           DK+  VIGKGG++IRAL  E G  I +       D+  + + A++G +     A+ A+
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIE------DDGTVKIAATDGEK-----AKHAI 615

>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 Length = 757

 Score = 41.8 bits (99), Expect = 5e-04
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 11/58 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAV 252
           DK+G VIG    +I  +Q + GA I++       D+  I + A++GP      A+ A 
Sbjct: 607 DKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADGPA-----AEAAR 653

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 41.4 bits (98), Expect = 6e-04
 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 6/46 (13%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
            K    +G GG  ++ LQ+E G  IS        DE   +V A   
Sbjct: 576 SKRAKFVGPGGYNLKKLQAETGVTISQV------DEETFSVFAPTP 615

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 40.9 bits (97), Expect = 9e-04
 Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
           DK+  VIG GG +IR + +  GA + +       D+ ++ V+AS+G
Sbjct: 579 DKIREVIGSGGKVIREIVATTGAKVDIN------DDGVVKVSASDG 618

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	541
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.93
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.92
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.91
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.91
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.91
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.91
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.91
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.9
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.9
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.84
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.75
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.73
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.62
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.61
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.59
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.58
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.58
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.53
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.52
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.52
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.51
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.49
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.48
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.47
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.47
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.45
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.45
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.45
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.44
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.43
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.41
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.4
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.4
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.39
1we8_A	104	Tudor and KH domain containing protein; structural	99.37
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.35
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.35
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.34
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.33
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.33
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.33
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.31
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.29
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.28
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.27
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.24
1we8_A	104	Tudor and KH domain containing protein; structural	99.24
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.23
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.2
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.2
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.18
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.15
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.15
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.11
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.05
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.03
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.91
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.85
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.82
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.67
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.52
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.43
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.29
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.18
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.08
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.96
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.67
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.67
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.57
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.38
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.21
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.88
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.55
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.52
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.38
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	94.98
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	93.68
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.12
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	92.9
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	92.47
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	91.91
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	91.89
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.62

>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=99.93  E-value=8.3e-26  Score=210.80  Aligned_cols=154  Identities=23%  Similarity=0.401  Sum_probs=130.0

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC-CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccc
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS  264 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~-~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~  264 (541)
                      -+++|+||.+.+|.||||+|++||+|+++|||+|+|.+. .+++.+|+|+|+|+++.      +.+|..+|+..+.+...
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~------v~~A~~~I~~~~~e~~~   76 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA------QFKAQGRIYGKLKEENF   76 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHH------HHHHHHHHHHHHHHTTS
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHH------HHHHHHHHHHHHhcccc
Confidence            488999999999999999999999999999999999976 57889999999997653      77787777776655421


Q ss_pred             ccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHH
Q 009173          265 EKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYN  344 (541)
Q Consensus       265 ~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~l  344 (541)
                           +.+......+.+|.||.+++|+||||+|++|++|++.|||+|.|..+..|.  ...++.|+|+|++++|++|+.+
T Consensus        77 -----~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~--~~~~~~v~I~G~~~~v~~A~~~  149 (163)
T 3krm_A           77 -----FGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPD--ENDQVIVKIIGHFYASQMAQRK  149 (163)
T ss_dssp             -----SCSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCC--TTSEEEEEEEECHHHHHHHHHH
T ss_pred             -----cccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCC--CCCceEEEEEeCHHHHHHHHHH
Confidence                 112234567889999999999999999999999999999999998766665  2334489999999999999999


Q ss_pred             HHHHhhcc
Q 009173          345 VTGRLRDN  352 (541)
Q Consensus       345 I~~~l~e~  352 (541)
                      |.+++++.
T Consensus       150 I~~~i~~~  157 (163)
T 3krm_A          150 IRDILAQV  157 (163)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999753

>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=99.93  E-value=5.6e-26  Score=211.33  Aligned_cols=156  Identities=29%  Similarity=0.520  Sum_probs=129.4

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (541)
Q Consensus       184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~  263 (541)
                      ..++++|+||.+.+|.||||+|++||+|+++|||+|+|++.  ++.+|.|+|+|+.+.      +.+|..++...+.+..
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~------v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNA------IFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHH------HHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHH------HHHHHHHHHHHHHhhc
Confidence            35899999999999999999999999999999999999873  578999999997542      6777777776555432


Q ss_pred             cccCCCC-CCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHH
Q 009173          264 SEKGLDF-SSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV  342 (541)
Q Consensus       264 ~~~g~~~-~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~  342 (541)
                      . ..... .......++.++.||.+++|+||||+|++|++|+++|||+|+|.++..|.   ++++.|+|+|++++|++|+
T Consensus        75 ~-~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~---~~~~~v~I~G~~~~v~~A~  150 (160)
T 2jzx_A           75 S-SSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN---STERAITIAGIPQSIIECV  150 (160)
T ss_dssp             T-SCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTT---CCEEEEEEEECHHHHHHHH
T ss_pred             c-ccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCC---CCceEEEEEcCHHHHHHHH
Confidence            1 11110 01123457899999999999999999999999999999999998766665   6789999999999999999


Q ss_pred             HHHHHHhhc
Q 009173          343 YNVTGRLRD  351 (541)
Q Consensus       343 ~lI~~~l~e  351 (541)
                      .+|.+++.|
T Consensus       151 ~~I~~~i~e  159 (160)
T 2jzx_A          151 KQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            999999865

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.92  E-value=1.9e-25  Score=211.42  Aligned_cols=161  Identities=22%  Similarity=0.401  Sum_probs=127.8

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC---CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHh
Q 009173          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (541)
Q Consensus       184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~---~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~  260 (541)
                      .+++++|+||.+.+|.||||+|++||+|+++|||+|+|.+.   .+++.+|+|+|+|+.++      +.+|..+|.+.+.
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~------v~~A~~~I~~~~~   77 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA------LNAVHGFIAEKIR   77 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHH------HHHHHHHHHHHHT
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHH------HHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999999864   46789999999997553      6777777666554


Q ss_pred             hcccccC-------CCC--CCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEE
Q 009173          261 EGTSEKG-------LDF--SSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI  331 (541)
Q Consensus       261 e~~~~~g-------~~~--~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtI  331 (541)
                      +......       ..+  ........+.+|.||.+++|+||||+|++|++|+++|||+|+|..+.  .+..++++.|+|
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~--~~~~~~~~~v~I  155 (178)
T 2anr_A           78 EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP--DGINLQNRVVTV  155 (178)
T ss_dssp             CCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC------CCEEEEEE
T ss_pred             ccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCC--CCCCCCceEEEE
Confidence            3221000       000  01123457889999999999999999999999999999999998442  223367899999


Q ss_pred             EcCHHHHHHHHHHHHHHhhcc
Q 009173          332 SGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       332 tGt~e~V~~A~~lI~~~l~e~  352 (541)
                      +|++++|++|+.+|.++++++
T Consensus       156 ~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          156 SGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             ESSHHHHHHHHHHHHHHHHSC
T ss_pred             EcCHHHHHHHHHHHHHHHHhC
Confidence            999999999999999999865

>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=99.91  E-value=2.2e-24  Score=201.17  Aligned_cols=152  Identities=24%  Similarity=0.386  Sum_probs=127.7

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCC
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGT  357 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~  357 (541)
                      .+++|+||.+++|.||||+|++|++|+++|||+|+|..+..|+   +.+|.|+|+|+++++.+|+.+|.+++.+..+.  
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~---~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~--   77 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPD---SKVRMVIITGPPEAQFKAQGRIYGKLKEENFF--   77 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTT---CSEEEEEEEECHHHHHHHHHHHHHHHHHTTSS--
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCC---CCceEEEEEcCHHHHHHHHHHHHHHHhccccc--
Confidence            4789999999999999999999999999999999998654554   78999999999999999999999998753100  


Q ss_pred             cccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCC
Q 009173          358 LNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGS  437 (541)
Q Consensus       358 ~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~  437 (541)
                                                                                    .|             .  
T Consensus        78 --------------------------------------------------------------~~-------------~--   80 (163)
T 3krm_A           78 --------------------------------------------------------------GP-------------K--   80 (163)
T ss_dssp             --------------------------------------------------------------CS-------------S--
T ss_pred             --------------------------------------------------------------cc-------------c--
Confidence                                                                          00             0  


Q ss_pred             CCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC-CCCCC-ccE
Q 009173          438 SDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP-RLGST-DRI  515 (541)
Q Consensus       438 ~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p-~~~s~-~Ri  515 (541)
                                     ..            ...+.+|.||.+++|+|||++|++|++|++.|||+|.|.+. .+++. ++.
T Consensus        81 ---------------~~------------~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~  133 (163)
T 3krm_A           81 ---------------EE------------VKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVI  133 (163)
T ss_dssp             ---------------CC------------CCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEE
T ss_pred             ---------------cC------------CceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceE
Confidence                           00            01467999999999999999999999999999999999853 23343 458


Q ss_pred             EEEEeCHHHHHHHHHHHHHHHhc
Q 009173          516 VVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       516 ItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      |+|+|++++|++|+.+|+++|..
T Consensus       134 v~I~G~~~~v~~A~~~I~~~i~~  156 (163)
T 3krm_A          134 VKIIGHFYASQMAQRKIRDILAQ  156 (163)
T ss_dssp             EEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999875

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

Probab=99.91  E-value=2.6e-24  Score=200.51  Aligned_cols=159  Identities=20%  Similarity=0.398  Sum_probs=128.3

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCC
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGT  357 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~  357 (541)
                      ++.+|+||.+++|+||||+|++|++|+++|||+|++..+. + +....++.|+|+|++++|.+|+.+|.+++.+....  
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~-~-~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~--   77 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-S-QNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQG--   77 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCT-T-SSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSC--
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCC-C-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCC--
Confidence            5789999999999999999999999999999999997542 1 12367899999999999999999999998643100  


Q ss_pred             cccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCC
Q 009173          358 LNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGS  437 (541)
Q Consensus       358 ~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~  437 (541)
                                       +|.                                           +.       ..|+++  
T Consensus        78 -----------------~~~-------------------------------------------~~-------~~~~~~--   88 (164)
T 2jvz_A           78 -----------------GFG-------------------------------------------DR-------NEYGSR--   88 (164)
T ss_dssp             -----------------CCS-------------------------------------------SC-------SSCTTS--
T ss_pred             -----------------CCC-------------------------------------------Cc-------cccCCC--
Confidence                             000                                           00       000000  


Q ss_pred             CCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEE
Q 009173          438 SDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVV  517 (541)
Q Consensus       438 ~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiIt  517 (541)
                                     .              ..+.+|.||.+++|+|||++|++|++|++.|||+|.|.+..+...++.|+
T Consensus        89 ---------------~--------------~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~  139 (164)
T 2jvz_A           89 ---------------I--------------GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAH  139 (164)
T ss_dssp             ---------------C--------------SSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEE
T ss_pred             ---------------C--------------CceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEE
Confidence                           0              02357899999999999999999999999999999998766666789999


Q ss_pred             EEeCHHHHHHHHHHHHHHHhc
Q 009173          518 ISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       518 IsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      |+|++++++.|+.+|+++|..
T Consensus       140 I~G~~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A          140 IMGPPDRCEHAARIINDLLQS  160 (164)
T ss_dssp             EESCHHHHHHHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHhh
Confidence            999999999999999998864

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

Probab=99.91  E-value=1.3e-24  Score=204.98  Aligned_cols=170  Identities=22%  Similarity=0.354  Sum_probs=126.0

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCC
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSG  356 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~  356 (541)
                      ..+.+|+||.+++|+||||+|++|++|+++|||+|+|..+ .+   ...+|.|+|+|++++|.+|+.+|.+++.+.... 
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~---~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~-   76 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD-DG---TTPERIAQITGPPDRAQHAAEIITDLLRSVQAG-   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC-TT---SCSEEEEEEEECHHHHHHHHHHHHHHHHHHC---
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecC-CC---CCCccEEEEEeCHHHHHHHHHHHHHHHHhcccC-
Confidence            3578999999999999999999999999999999999742 12   256899999999999999999999999753200 


Q ss_pred             CcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCC
Q 009173          357 TLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRG  436 (541)
Q Consensus       357 ~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g  436 (541)
                      .                  +         +.+.+.+      +     ++                           ++ 
T Consensus        77 ~------------------~---------~~~~p~~------~-----~~---------------------------~~-   90 (174)
T 1j4w_A           77 N------------------P---------GGPGPGG------R-----GR---------------------------GR-   90 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             C------------------C---------CCCCCCC------C-----CC---------------------------CC-
Confidence            0                  0         0000000      0     00                           00 


Q ss_pred             CCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC---CCCCCc
Q 009173          437 SSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP---RLGSTD  513 (541)
Q Consensus       437 ~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p---~~~s~~  513 (541)
                         ....|..+.+                ....+.+|.||.+++|+||||+|++|++|++.|||+|+|.+.   ..++.+
T Consensus        91 ---~~~~~~~~~~----------------~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~  151 (174)
T 1j4w_A           91 ---GQGNWNMGPP----------------GGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNM  151 (174)
T ss_dssp             --------------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTE
T ss_pred             ---CCCccccCCC----------------CCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCc
Confidence               0001211111                012578999999999999999999999999999999999853   234678


Q ss_pred             cEEEEEeCHHHHHHHHHHHHHHH
Q 009173          514 RIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       514 RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      +.|+|+|+++++++|+.||+++|
T Consensus       152 ~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          152 KLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEEEEECCHHHHHHHHHHHHHHC
T ss_pred             eEEEEECCHHHHHHHHHHHHHhC
Confidence            99999999999999999999875

>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=99.91  E-value=1.6e-24  Score=204.94  Aligned_cols=170  Identities=24%  Similarity=0.408  Sum_probs=131.6

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc--CcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS--DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~--d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~  353 (541)
                      ..++.+|+||.+++|.||||+|++|++|+++|||+|+|..  +..|+   +.+|.|+|+|+.++|.+|+.+|.+++.+..
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 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPG---TTERVCLIQGTIEALNAVHGFIAEKIREMP   80 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTT---SSEEEEEEEECHHHHHHHHHHHHHHHTCCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCC---CCCceEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            4678999999999999999999999999999999999984  33454   678999999999999999999999997532


Q ss_pred             cCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccccccccc
Q 009173          354 FSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVH  433 (541)
Q Consensus       354 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~  433 (541)
                      ....      .               .+++.+                                      ..        
T Consensus        81 ~~~~------~---------------~~~~~~--------------------------------------~~--------   93 (178)
T 2anr_A           81 QNVA------K---------------TEPVSI--------------------------------------LQ--------   93 (178)
T ss_dssp             CC------------------------------------------------------------------------------
T ss_pred             Cccc------c---------------CCcccc--------------------------------------cC--------
Confidence            1000      0               000000                                      00        


Q ss_pred             CCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCC--CCC
Q 009173          434 LRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPR--LGS  511 (541)
Q Consensus       434 ~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~--~~s  511 (541)
                      +...        ..     .            ....+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..  +++
T Consensus        94 ~~~~--------~~-----~------------~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~  148 (178)
T 2anr_A           94 PQTT--------VN-----P------------DRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINL  148 (178)
T ss_dssp             -------------------C------------GGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----C
T ss_pred             CccC--------CC-----C------------CCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCC
Confidence            0000        00     0            0125789999999999999999999999999999999998542  345


Q ss_pred             CccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173          512 TDRIVVISGTPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       512 ~~RiItIsGtpeqV~~Aq~LI~~~I~~~~  540 (541)
                      .++.|+|+|+++++++|+.+|.++|....
T Consensus       149 ~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          149 QNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             CEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             CceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            78999999999999999999999998753

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

Probab=99.91  E-value=1.8e-24  Score=204.10  Aligned_cols=158  Identities=22%  Similarity=0.347  Sum_probs=123.9

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccc
Q 009173          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS  264 (541)
Q Consensus       185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~  264 (541)
                      ..+++|+||.+.+|.||||+|++||+|+++|||+|+|.+..+++.+|+|+|+|+.+.      +.+|+.+|.+.+.+...
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~~~~~~~   75 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR------AQHAAEIITDLLRSVQA   75 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHH------HHHHHHHHHHHHHHHC-
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHH------HHHHHHHHHHHHHhccc
Confidence            468899999999999999999999999999999999987667788999999998553      66776666554433211


Q ss_pred             cc-C--------C-----CCC-CCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceE
Q 009173          265 EK-G--------L-----DFS-SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVV  329 (541)
Q Consensus       265 ~~-g--------~-----~~~-~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervV  329 (541)
                      .. +        .     ++. .......+.+|.||.+++|+||||+|++|++|+++|||+|+|..+.. .+..++++.|
T Consensus        76 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~~~~~v  154 (174)
T 1j4w_A           76 GNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-PNADPNMKLF  154 (174)
T ss_dssp             ----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-TTSCTTEEEE
T ss_pred             CCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCC-CCCCCCceEE
Confidence            00 0        0     000 00123468899999999999999999999999999999999985433 2345678999


Q ss_pred             EEEcCHHHHHHHHHHHHHHh
Q 009173          330 QISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       330 tItGt~e~V~~A~~lI~~~l  349 (541)
                      +|+|++++|++|+++|.++|
T Consensus       155 ~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          155 TIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEECCHHHHHHHHHHHHHHC
T ss_pred             EEECCHHHHHHHHHHHHHhC
Confidence            99999999999999999875

>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=99.90  E-value=3.6e-24  Score=199.10  Aligned_cols=156  Identities=24%  Similarity=0.439  Sum_probs=129.6

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccC
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS  355 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~  355 (541)
                      ..++.+|+||.+++|.||||+|++|++|+++|||+|+|..+      +..+|.|+|+|+.++|.+|+.+|.+++.+....
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~------~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~   76 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG------NCPERIITLAGPTNAIFKAFAMIIDKLEEDISS   76 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC------TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHTS
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC------CCCceEEEEEeCHHHHHHHHHHHHHHHHhhccc
Confidence            46789999999999999999999999999999999999743      245799999999999999999999998753210


Q ss_pred             CCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCC
Q 009173          356 GTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLR  435 (541)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~  435 (541)
                      .                                                 +           +.+.            ..
T Consensus        77 ~-------------------------------------------------~-----------~~~~------------~~   84 (160)
T 2jzx_A           77 S-------------------------------------------------M-----------TNST------------AA   84 (160)
T ss_dssp             C-------------------------------------------------C-----------CSSS------------CC
T ss_pred             c-------------------------------------------------C-----------CCCc------------cC
Confidence            0                                                 0           0000            00


Q ss_pred             CCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC-CCCCCCcc
Q 009173          436 GSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE-PRLGSTDR  514 (541)
Q Consensus       436 g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~-p~~~s~~R  514 (541)
                                .                   ....+.++.||.+++|+|||++|++|++|++.|||+|+|.+ +.+++.++
T Consensus        85 ----------~-------------------~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~  135 (160)
T 2jzx_A           85 ----------S-------------------RPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTER  135 (160)
T ss_dssp             ----------C-------------------CCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEE
T ss_pred             ----------C-------------------CCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCce
Confidence                      0                   00157899999999999999999999999999999999984 45677899


Q ss_pred             EEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          515 IVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       515 iItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .|+|+|+++++++|+.+|.+++..
T Consensus       136 ~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          136 AITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             EEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEcCHHHHHHHHHHHHHHHhc
Confidence            999999999999999999998864

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

Probab=99.90  E-value=8.2e-24  Score=197.11  Aligned_cols=155  Identities=21%  Similarity=0.332  Sum_probs=123.4

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC--CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~--~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~  263 (541)
                      ++++|+||.+.+|.||||+|++||+|+++|||+|+|.+.  .++..+|+|+|+|+.+.      +.+|..+|...+.+..
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~ii~e~~   75 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK------VQQACEMVMDILRERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHH------HHHHHHHHHHHTTCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHH------HHHHHHHHHHHHHhcc
Confidence            588999999999999999999999999999999999754  34678999999997543      6677777766544322


Q ss_pred             cccCCCCCCC--CCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHH
Q 009173          264 SEKGLDFSSN--KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA  341 (541)
Q Consensus       264 ~~~g~~~~~~--~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A  341 (541)
                       ..++.....  .....+.+|.||.+++|+||||+|++|++|+++|||+|.|..+. +   .+.++.|+|+|++++|+.|
T Consensus        76 -~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~-~---~~~~~~v~I~G~~~~v~~A  150 (164)
T 2jvz_A           76 -QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-G---TGPEKIAHIMGPPDRCEHA  150 (164)
T ss_dssp             -SCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC-T---TSSEEEEEEESCHHHHHHH
T ss_pred             -CCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC-C---CCCcEEEEEEcCHHHHHHH
Confidence             111111100  11134678999999999999999999999999999999997432 2   2457999999999999999


Q ss_pred             HHHHHHHhhc
Q 009173          342 VYNVTGRLRD  351 (541)
Q Consensus       342 ~~lI~~~l~e  351 (541)
                      +.+|.+++++
T Consensus       151 ~~~I~~~i~~  160 (164)
T 2jvz_A          151 ARIINDLLQS  160 (164)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9999999875

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

Probab=99.84  E-value=1.3e-20  Score=195.94  Aligned_cols=220  Identities=9%  Similarity=0.091  Sum_probs=156.1

Q ss_pred             CCceEEEEEeccccccceeccCc--hHHHHHHHHhCCeEEecCCC-----CCCCcceEEEecCCCCCCCCCHHHHHHHHH
Q 009173          183 QQEVSFRILCSNDKVGAVIGKGG--TIIRALQSEAGAFISVGATM-----PECDERLITVTASEGPESRYSPAQKAVVLV  255 (541)
Q Consensus       183 ~~~~~~rilvP~~~vG~IIGKgG--~~Ik~Iq~eTGa~I~I~~~~-----~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i  255 (541)
                      ...+++.+-||...++.||||||  ++|++|+++|||+|+|++..     +......|+|+|..++      +.+|..++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~en------VE~AR~~I  100 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGD------VDRARMLM  100 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHH------HHHHHHHH
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHH------HHHHHHHH
Confidence            45699999999999999999999  99999999999999998754     1234578999998764      66666655


Q ss_pred             HHHHhhcccccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCH
Q 009173          256 FSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEF  335 (541)
Q Consensus       256 ~~~i~e~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~  335 (541)
                      .+ +                ..+++.+.+|...++.  ...+..|.. ++..+++|.++..  |...+.....|+|+|..
T Consensus       101 ~~-l----------------~Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~--~~~~~~~sd~V~IrG~~  158 (376)
T 3n89_A          101 RR-N----------------CHFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDA--PEKNGIVTTYLRITARE  158 (376)
T ss_dssp             HH-S----------------CEEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEE--C-----CEEEEEEEEEG
T ss_pred             Hh-c----------------CCceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCc--ccccCCCCCEEEEEcCh
Confidence            43 1                1345666676644332  222345555 6789999998632  11111124579999999


Q ss_pred             HHHHHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCC
Q 009173          336 SKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSL  415 (541)
Q Consensus       336 e~V~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~  415 (541)
                      .++.+|.+.+..+++...-..                                         .+                
T Consensus       159 ~nv~~akeA~~~Ll~~l~~~e-----------------------------------------~~----------------  181 (376)
T 3n89_A          159 KNQHELIEAAKRLNEILFRES-----------------------------------------PA----------------  181 (376)
T ss_dssp             GGHHHHHHHHHHHHHHHCC-------------------------------------------CC----------------
T ss_pred             hhHHHHHHHHHHHHHHHHhhh-----------------------------------------cc----------------
Confidence            888777766666664210000                                         00                


Q ss_pred             CCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCc--chHHH
Q 009173          416 DCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENG--SNLLR  493 (541)
Q Consensus       416 ~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgG--s~Ik~  493 (541)
                        +                                               ....+.+|.|+..++..|||++|  ..|+.
T Consensus       182 --~-----------------------------------------------~~~~s~~v~V~~~~H~~IIGk~G~n~~Ikk  212 (376)
T 3n89_A          182 --P-----------------------------------------------ENNFTLHFTLSTYYVDQVLGSSSTAQLMPV  212 (376)
T ss_dssp             --C-----------------------------------------------SSCEEEEEEEEGGGHHHHTCCTTSCCHHHH
T ss_pred             --c-----------------------------------------------ccceEEEEEeCHHHHHHhhcCCCcchHHHH
Confidence              0                                               00257899999999999999999  45699


Q ss_pred             HHhHhCCEEEEeCCCC--C--CCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          494 LRQISGAKVIVHEPRL--G--STDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       494 Irq~SGA~I~I~~p~~--~--s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      |+++|||+|.+++...  +  .....|+|+|++++|..|+..|++++
T Consensus       213 Ir~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          213 IERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             HHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             HHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            9999999999964321  1  23578999999999999999999865

>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=99.75  E-value=4.7e-18  Score=155.56  Aligned_cols=134  Identities=24%  Similarity=0.316  Sum_probs=105.3

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCC
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSG  356 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~  356 (541)
                      .++.++.||.+.+|.+||++|++|+.|++++|.+|....+       +.+..+...+++++|.+|..+    |. .    
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~-------~~~~~i~~~~~p~~v~~~~~~----l~-~----   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE-------DTCTFHIYGEDQDAVKKARSF----LE-F----   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHH----HC-E----
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC-------CchheeeccCCHHHHHHHHHh----hh-c----
Confidence            4678999999999999999999999999999944433222       234555555679999888542    21 0    


Q ss_pred             CcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCC
Q 009173          357 TLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRG  436 (541)
Q Consensus       357 ~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g  436 (541)
                                                                                                      
T Consensus        67 --------------------------------------------------------------------------------   66 (144)
T 2qnd_A           67 --------------------------------------------------------------------------------   66 (144)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCC-EEEEeCCCCC---CC
Q 009173          437 SSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGA-KVIVHEPRLG---ST  512 (541)
Q Consensus       437 ~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA-~I~I~~p~~~---s~  512 (541)
                                                      ...+|.||.+.+|++|||+|.||+.|++.||| +|+|......   .+
T Consensus        67 --------------------------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~  114 (144)
T 2qnd_A           67 --------------------------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQE  114 (144)
T ss_dssp             --------------------------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCC
T ss_pred             --------------------------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCcccc
Confidence                                            12588999999999999999999999999997 9999842211   12


Q ss_pred             cc--EEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          513 DR--IVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       513 ~R--iItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ++  .|+|+|++++|+.|+.||++.|.+
T Consensus       115 ~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          115 EGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             TTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             CCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            33  589999999999999999999864

>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=99.73  E-value=5.3e-18  Score=155.26  Aligned_cols=137  Identities=19%  Similarity=0.250  Sum_probs=98.9

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccc
Q 009173          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS  264 (541)
Q Consensus       185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~  264 (541)
                      .++.+|+||.+.+|++||++|++|++|++++|  |++... ...+++.+...++++       ....+..+    .+.  
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~-~~~~~~~i~~~~~p~-------~v~~~~~~----l~~--   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDL-DEDTCTFHIYGEDQD-------AVKKARSF----LEF--   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEE-ETTTTEEEEEESSHH-------HHHHHHHH----HCE--
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEecc-CCCchheeeccCCHH-------HHHHHHHh----hhc--
Confidence            46889999999999999999999999999999  444321 122344443333322       22222111    110  


Q ss_pred             ccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCe-eEEEccCcccccCCCCCc--eEEEEcCHHHHHHH
Q 009173          265 EKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGT-SIRIISDQLLKCISENDR--VVQISGEFSKVKDA  341 (541)
Q Consensus       265 ~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA-~I~I~~d~~P~~~~s~er--vVtItGt~e~V~~A  341 (541)
                                   ...++.||.+++|++|||+|.+|+.|++.||| +|+|..+.-+.. ..+++  .|+|+|++++|+.|
T Consensus        67 -------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~-~~~~~~~~vtI~G~~~~v~~A  132 (144)
T 2qnd_A           67 -------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV-PQEEGMVPFVFVGTKDSIANA  132 (144)
T ss_dssp             -------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC-CCCTTEEEEEEEEEHHHHHHH
T ss_pred             -------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc-cccCCeeEEEEEeCHHHHHHH
Confidence                         13789999999999999999999999999997 999984321111 12343  48999999999999


Q ss_pred             HHHHHHHhhc
Q 009173          342 VYNVTGRLRD  351 (541)
Q Consensus       342 ~~lI~~~l~e  351 (541)
                      +.+|.++|.+
T Consensus       133 k~li~~~l~~  142 (144)
T 2qnd_A          133 TVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHh
Confidence            9999999963

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

Probab=99.62  E-value=8.2e-16  Score=149.76  Aligned_cols=147  Identities=15%  Similarity=0.200  Sum_probs=106.2

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE  265 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~  265 (541)
                      -..++.||.+.+|.|||++|++|+.|+++|||+|++..     +++.|+|.++.... ....+++|...|.+.......+
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~-d~~~i~kA~~~I~~i~rg~~~e  107 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETE-DPLAVWKARDIVLAIGRGFSPE  107 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCC-SHHHHHHHHHHHHHHHTTCCHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCC-CHHHHHHHHHHHHHHhccCCcc
Confidence            36689999999999999999999999999999999973     46789999864211 1124677776665533111111


Q ss_pred             cCCCCCCCCCceeEEEEEec-----------ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC
Q 009173          266 KGLDFSSNKGLLVNARLVVA-----------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE  334 (541)
Q Consensus       266 ~g~~~~~~~~~~vt~~l~VP-----------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt  334 (541)
                      .+... . .+....-.+.|+           ...+|+||||+|++|+.|++.|||+|.|.           ++.|.|.|+
T Consensus       108 ~g~~l-l-~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~-----------~~~v~i~G~  174 (219)
T 2e3u_A          108 RAFRL-L-NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY-----------GKTVAIIGN  174 (219)
T ss_dssp             HHGGG-G-STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE-----------TTEEEEEEC
T ss_pred             cccee-c-cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC-----------CeEEEEEeC
Confidence            00000 0 011111123333           23689999999999999999999999994           357999999


Q ss_pred             HHHHHHHHHHHHHHhhc
Q 009173          335 FSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       335 ~e~V~~A~~lI~~~l~e  351 (541)
                      +++++.|+.+|.+++..
T Consensus       175 ~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          175 PIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHcC
Confidence            99999999999999964

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

Probab=99.61  E-value=1.3e-15  Score=148.33  Aligned_cols=143  Identities=23%  Similarity=0.213  Sum_probs=109.4

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-----HHHHHHHHHHHHHHhhc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-----FSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-----~e~V~~A~~lI~~~l~e  351 (541)
                      .....+.||.+.+|.|||++|++|+.|+++|||+|+|..         .++.|+|.|+     ++++++|..+|..+.+.
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~---------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg  103 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS---------ETGEVWITSTKETEDPLAVWKARDIVLAIGRG  103 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT---------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTT
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc---------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhcc
Confidence            346699999999999999999999999999999999952         3567888886     69999999999998852


Q ss_pred             cccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccccccc
Q 009173          352 NHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTG  431 (541)
Q Consensus       352 ~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g  431 (541)
                      .....                                                +..               +.       
T Consensus       104 ~~~e~------------------------------------------------g~~---------------ll-------  113 (219)
T 2e3u_A          104 FSPER------------------------------------------------AFR---------------LL-------  113 (219)
T ss_dssp             CCHHH------------------------------------------------HGG---------------GG-------
T ss_pred             CCccc------------------------------------------------cce---------------ec-------
Confidence            11000                                                000               00       


Q ss_pred             ccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEE-----------eccCcccceeeCCcchHHHHHhHhCC
Q 009173          432 VHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEII-----------VPENVIGSVYGENGSNLLRLRQISGA  500 (541)
Q Consensus       432 ~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~-----------IP~~~vG~IIGkgGs~Ik~Irq~SGA  500 (541)
                         .  .+.                            ....+.           .+...+|+||||+|++|+.|++.|||
T Consensus       114 ---~--dd~----------------------------~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~  160 (219)
T 2e3u_A          114 ---N--EGE----------------------------YLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGA  160 (219)
T ss_dssp             ---S--TTC----------------------------EEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             ---c--CCc----------------------------cceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCc
Confidence               0  000                            000111           12346899999999999999999999


Q ss_pred             EEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          501 KVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       501 ~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      +|.|++       +.|+|.|++++++.|+.+|.++|..
T Consensus       161 ~I~v~~-------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          161 SVSVYG-------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             EEEEET-------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             eEEECC-------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            999964       6799999999999999999999943

>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=99.59  E-value=1.2e-15  Score=126.14  Aligned_cols=73  Identities=36%  Similarity=0.599  Sum_probs=66.9

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~~  540 (541)
                      ..+.+|.||.+++|+|||+||++|++|++.|||+|+|.++.+++.+|.|+|+|+++++++|+.+|++++.+.+
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSEK   77 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC---
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhhh
Confidence            4789999999999999999999999999999999999987778889999999999999999999999987643

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

Probab=99.58  E-value=2e-15  Score=123.07  Aligned_cols=72  Identities=33%  Similarity=0.599  Sum_probs=67.9

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      ..+.+|.||.+++|+|||+||++|++|++.|||+|+|.++.+++.+|.|+|+|+++++++|+.||++++.+.
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            368899999999999999999999999999999999998888889999999999999999999999998753

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.58  E-value=4.3e-15  Score=122.91  Aligned_cols=71  Identities=38%  Similarity=0.633  Sum_probs=67.1

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||.+++|+||||+|++|++|++.|||+|+|+++.+++.+|.|+|+|+++++++|+.+|++++..
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999999877788899999999999999999999999865

>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=99.53  E-value=1.6e-14  Score=122.06  Aligned_cols=73  Identities=30%  Similarity=0.537  Sum_probs=68.2

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~~  540 (541)
                      ..+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..+++.+|.|+|+|+++++++|+.||+++|...+
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            4789999999999999999999999999999999999977677789999999999999999999999998754

>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=99.52  E-value=1.5e-14  Score=117.74  Aligned_cols=70  Identities=34%  Similarity=0.636  Sum_probs=64.0

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC---CCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP---RLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p---~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+|.||.+++|+|||+||++|++|++.|||+|+|++.   .+++.++.|+|+|+++++++|+.+|++++..
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            678999999999999999999999999999999999853   3577889999999999999999999998754

>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=99.52  E-value=9.9e-15  Score=122.64  Aligned_cols=71  Identities=38%  Similarity=0.633  Sum_probs=67.2

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||.+++|+||||+|++|++|++.|||+|+|+++.+++.+|.|+|+|+++++++|+.+|++++..
T Consensus        13 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            47889999999999999999999999999999999999877788899999999999999999999999865

>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=99.51  E-value=1.7e-14  Score=116.67  Aligned_cols=69  Identities=20%  Similarity=0.452  Sum_probs=64.5

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||.+++|+|||+||++|++|++.|||+|+|++.  ++.+|.|+|+|+++++++|+.+|.++|.+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            3688999999999999999999999999999999999864  56789999999999999999999999875

>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=99.49  E-value=6.5e-14  Score=133.32  Aligned_cols=140  Identities=18%  Similarity=0.215  Sum_probs=110.1

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE-----cCHHHHHHHHHHHHHHhhccc
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-----GEFSKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt-----Gt~e~V~~A~~lI~~~l~e~~  353 (541)
                      ..++.||...+|.|||++|++++.|++.+|++|++.         ..++.|+|.     |++.++.+|..+|....+...
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id---------~~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~   75 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD---------TENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFP   75 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE---------TTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE---------cCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Confidence            368999999999999999999999999999999995         346788888     999999999999998886321


Q ss_pred             cCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccccccccc
Q 009173          354 FSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVH  433 (541)
Q Consensus       354 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~  433 (541)
                      +.+.+.                                                                          
T Consensus        76 ~e~A~~--------------------------------------------------------------------------   81 (191)
T 1tua_A           76 PEKAFR--------------------------------------------------------------------------   81 (191)
T ss_dssp             HHHHGG--------------------------------------------------------------------------
T ss_pred             HHHhhh--------------------------------------------------------------------------
Confidence            110000                                                                          


Q ss_pred             CCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEe----------ccCcccceeeCCcchHHHHHhHhCCEEE
Q 009173          434 LRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIV----------PENVIGSVYGENGSNLLRLRQISGAKVI  503 (541)
Q Consensus       434 ~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~I----------P~~~vG~IIGkgGs~Ik~Irq~SGA~I~  503 (541)
                                             +...      ......+.+          +....|+|||++|.||+.|+..|||+|.
T Consensus        82 -----------------------Ll~D------d~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~  132 (191)
T 1tua_A           82 -----------------------LLEE------DQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYIN  132 (191)
T ss_dssp             -----------------------GGST------TEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEE
T ss_pred             -----------------------cccC------cceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEE
Confidence                                   0000      000011112          2447899999999999999999999999


Q ss_pred             EeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          504 VHEPRLGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       504 I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      |++       +.|.|.|++++++.|+..|..+|.
T Consensus       133 v~~-------~~v~i~G~~~~i~~Ar~~i~~li~  159 (191)
T 1tua_A          133 VGE-------YEVAIIGDYERAMAAKQAIEMLAE  159 (191)
T ss_dssp             ECS-------SEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             EcC-------CEEEEEeChHHHHHHHHHHHHHHc
Confidence            964       489999999999999999999996

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

Probab=99.48  E-value=1.2e-13  Score=114.94  Aligned_cols=69  Identities=26%  Similarity=0.433  Sum_probs=63.1

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPR--LGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~--~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|.|.+..  +.+.+|.|+|+|+++++++|+.+|++++.
T Consensus        14 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             EEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             EEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999998643  35678999999999999999999999875

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.47  E-value=6e-14  Score=133.55  Aligned_cols=145  Identities=18%  Similarity=0.236  Sum_probs=104.5

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~  266 (541)
                      .++++||...+|.|||++|++++.|++++||+|.+.     ..++.|+|..+....+ ...+++|...|.+-......+.
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id-----~~~~~V~i~t~~~t~d-p~~i~KA~dlI~ai~rgf~~e~   78 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-----TENSMVIVEPEAEGIP-PVNLMKAAEVVKAISLGFPPEK   78 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE-----TTTTEEEEEESSTTSC-HHHHHHHHHHHHHHHHTCCHHH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE-----cCCCeEEEEeCCCCCC-HHHHHHHHHHHHHHHcCCCHHH
Confidence            468999999999999999999999999999999997     3578889984422111 1247777766643221110000


Q ss_pred             CCCCCCCCCceeEEEEEec----------ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHH
Q 009173          267 GLDFSSNKGLLVNARLVVA----------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS  336 (541)
Q Consensus       267 g~~~~~~~~~~vt~~l~VP----------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e  336 (541)
                      ..  ..-.+..+.-.+.++          ....|+||||+|.+|+.|+..|||+|.|.           ++.|.|.|+++
T Consensus        79 A~--~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~-----------~~~v~i~G~~~  145 (191)
T 1tua_A           79 AF--RLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG-----------EYEVAIIGDYE  145 (191)
T ss_dssp             HG--GGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SSEEEEEEEHH
T ss_pred             hh--hcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc-----------CCEEEEEeChH
Confidence            00  000111222233344          23689999999999999999999999994           34899999999


Q ss_pred             HHHHHHHHHHHHhh
Q 009173          337 KVKDAVYNVTGRLR  350 (541)
Q Consensus       337 ~V~~A~~lI~~~l~  350 (541)
                      +++.|...|.+++.
T Consensus       146 ~i~~Ar~~i~~li~  159 (191)
T 1tua_A          146 RAMAAKQAIEMLAE  159 (191)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHc
Confidence            99999999999995

>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=99.47  E-value=3.8e-14  Score=118.48  Aligned_cols=70  Identities=36%  Similarity=0.643  Sum_probs=64.8

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC---CCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP---RLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p---~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+|.||.+++|+|||+||++|++|++.|||+|+|.+.   .+++.++.|+|+|++++++.|+.+|+++|..
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999853   3577889999999999999999999999865

>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=99.45  E-value=9.2e-14  Score=117.90  Aligned_cols=73  Identities=25%  Similarity=0.451  Sum_probs=65.8

Q ss_pred             cceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCC--CCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL--GSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       467 ~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~--~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|.+...  ...+|.|+|+|+++++++|+.+|++++...
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            3578999999999999999999999999999999999986432  347899999999999999999999999763

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

Probab=99.45  E-value=8.7e-14  Score=120.62  Aligned_cols=70  Identities=19%  Similarity=0.453  Sum_probs=64.7

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+.+.+|.|+|+|+++++++|+.+|++++.+
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~   80 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS   80 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4679999999999999999999999999999999998766667789999999999999999999999875

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

Probab=99.45  E-value=9.4e-14  Score=120.65  Aligned_cols=71  Identities=23%  Similarity=0.357  Sum_probs=64.1

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPR---LGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~---~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..   .++.++.|+|+|+++++++|+.+|+++|...
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            3679999999999999999999999999999999998642   3457899999999999999999999998753

>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=99.44  E-value=9.7e-14  Score=112.24  Aligned_cols=70  Identities=23%  Similarity=0.491  Sum_probs=64.2

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      ..++.+|+||.+++|+||||||++|++|+++|||+|+|..+      +..+|.|+|+|+++++.+|+.+|.++|++
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            45789999999999999999999999999999999999754      24689999999999999999999999975

>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=99.43  E-value=8.4e-14  Score=115.40  Aligned_cols=68  Identities=24%  Similarity=0.475  Sum_probs=61.6

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||.+++|+||||+|++||+|+++|||+|+|....   +++.|+|+|+++++++|+++|.+.+..
T Consensus         9 ~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~---~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            9 QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS---SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             ceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC---CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999999996422   368999999999999999999998754

>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=99.41  E-value=2.4e-13  Score=110.53  Aligned_cols=71  Identities=31%  Similarity=0.485  Sum_probs=63.3

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccC--cccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD--QLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d--~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|+|.++  ..|   ++.++.|+|+|+++++++|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST---TCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCC---CCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999853  234   36789999999999999999999998853

>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=99.40  E-value=3.2e-13  Score=111.55  Aligned_cols=74  Identities=28%  Similarity=0.578  Sum_probs=65.1

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      +..++.+|.||.+++|+||||+|++|++|+++|||+|+|..+ .   .++.++.|+|+|+++++++|+.+|.+++.+.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~-~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-V---EGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-C---TTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC-C---CCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            356789999999999999999999999999999999999742 2   2467899999999999999999999999754

>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=99.40  E-value=5.3e-13  Score=110.32  Aligned_cols=74  Identities=26%  Similarity=0.581  Sum_probs=65.7

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|..+ .|   +++++.|+|+|++++|++|+.+|.+++.+.
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-TS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC-CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            346889999999999999999999999999999999999732 23   367899999999999999999999999753

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

Probab=99.39  E-value=2.6e-13  Score=110.45  Aligned_cols=72  Identities=28%  Similarity=0.563  Sum_probs=64.8

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      ..++.+|.||.+++|+||||+|++|++|++.|||+|+|... .   .++.++.|+|+|+++++++|+.+|.+++.+
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-V---EGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC-C---TTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC-C---CCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            45788999999999999999999999999999999999742 2   346789999999999999999999999864

>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=99.37  E-value=6.3e-13  Score=114.83  Aligned_cols=70  Identities=27%  Similarity=0.451  Sum_probs=63.4

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCC--CCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLG--STDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~--s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..++  +.++.|+|+|+++++++|+.+|++++..
T Consensus        15 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             EEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            678999999999999999999999999999999999864433  3689999999999999999999999854

>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=99.35  E-value=5.4e-13  Score=111.48  Aligned_cols=72  Identities=31%  Similarity=0.476  Sum_probs=64.7

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccC--cccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD--QLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d--~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|.|..+  ..|+   +.++.|+|+|++++++.|+.+|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g---~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG---TRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTT---SCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCC---CCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            578999999999999999999999999999999999843  2343   67899999999999999999999999764

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

Probab=99.35  E-value=1e-12  Score=114.11  Aligned_cols=73  Identities=15%  Similarity=0.299  Sum_probs=64.6

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|..+..|. .+.+++.|+|+|+.++|++|+.+|.+++.+.
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPN-GDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTT-CCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCC-CCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            679999999999999999999999999999999998554332 2356799999999999999999999999753

>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=99.34  E-value=6.3e-13  Score=110.15  Aligned_cols=69  Identities=20%  Similarity=0.283  Sum_probs=62.5

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhh
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR  350 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~  350 (541)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|+|++.       ..+++|+|+|+++++++|+++|.+++.
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~-------~~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR-------DKEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS-------SSCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC-------CCCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            456788999999999999999999999999999999999742       236899999999999999999999875

>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=99.33  E-value=1.7e-12  Score=109.62  Aligned_cols=74  Identities=22%  Similarity=0.353  Sum_probs=66.0

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|..+. +   +..++.|+|+|++++|++|+.+|.+++.+.
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            4568899999999999999999999999999999999997442 2   356899999999999999999999999753

>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=99.33  E-value=1e-12  Score=110.27  Aligned_cols=75  Identities=25%  Similarity=0.569  Sum_probs=66.5

Q ss_pred             CCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ....++.+|.||.+++|+||||+|++|++|+++|||+|+|..+ .|   .++++.|+|+|+++++++|+.+|.+++.+.
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~-~~---~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC-CS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC-CC---CCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3567889999999999999999999999999999999999732 23   367899999999999999999999999753

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

Probab=99.33  E-value=2.7e-12  Score=106.71  Aligned_cols=74  Identities=24%  Similarity=0.396  Sum_probs=64.7

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|.|..+..+  ..+.+|.|+|+|+++++++|+.+|.++++|
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            34678999999999999999999999999999999999865432  236789999999999999999999998853

>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=99.31  E-value=1.8e-12  Score=109.85  Aligned_cols=76  Identities=24%  Similarity=0.405  Sum_probs=66.8

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|.|.++..+.  ...+|.|+|+|++++|++|+.+|.+++.+.
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 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN--TGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS--SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            4567899999999999999999999999999999999998553321  246899999999999999999999999753

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

Probab=99.29  E-value=2.4e-12  Score=103.45  Aligned_cols=67  Identities=21%  Similarity=0.323  Sum_probs=60.5

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      .++.+|.||.+++|.|||+||++|++|+++|||+|.|+++  +..++.|+|+|+++++++|+.+|.+.+
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 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC--CCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            3678999999999999999999999999999999999753  346789999999999999999998753

>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=99.28  E-value=3.4e-12  Score=108.21  Aligned_cols=70  Identities=20%  Similarity=0.332  Sum_probs=62.6

Q ss_pred             cceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       467 ~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+.+|.||.+++|.|||+||.+|++|+++|||+|+|+++  +..++.|+|+|+++++++|+.+|++.+..
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~--~~~~~~V~I~G~~e~v~~A~~~I~~i~~~   84 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKEGIEKARHEVLLISAE   84 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC--CCCCCeEEEEECHHHHHHHHHHHHHHhhc
Confidence            35789999999999999999999999999999999999653  23458999999999999999999998854

>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=99.27  E-value=7e-12  Score=106.91  Aligned_cols=70  Identities=13%  Similarity=0.218  Sum_probs=62.9

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCC-CCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPR-LGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~-~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      ..+..|.||.+++|.|||+||++|++|++.|||+|+|++.. +...++.|+|+|+++++++|+.+|...+.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~   86 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVG   86 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999997543 23367999999999999999999999875

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

Probab=99.24  E-value=5.9e-12  Score=109.08  Aligned_cols=71  Identities=18%  Similarity=0.358  Sum_probs=62.9

Q ss_pred             eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      .+.+|.||.+++|+||||+|++||+|+++|||+|+|..+. +   .+.+|.|+|+|+++++++|+.+|.+++.+.
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            3679999999999999999999999999999999997442 1   256899999999999999999999999754

>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=99.24  E-value=8.2e-12  Score=107.81  Aligned_cols=76  Identities=24%  Similarity=0.331  Sum_probs=65.7

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ....+.+|.||.+++|+||||+|++|++|+++|||+|+|..+..+  ..+.++.|+|+|+.+++++|+.+|.+++.+.
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~--~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG--TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC--SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC--CCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            456788999999999999999999999999999999999743211  1235899999999999999999999999764

>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=99.23  E-value=1.2e-11  Score=105.15  Aligned_cols=70  Identities=10%  Similarity=0.184  Sum_probs=62.6

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||.+++|.|||+||++|++|+++|||+|+|++. .+..++.|+|+|+++++++|+.+|.+.+..
T Consensus        16 ~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           16 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS-GAPDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCT-TCSCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCC-CCCCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999753 223568999999999999999999998754

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

Probab=99.20  E-value=1.4e-11  Score=98.93  Aligned_cols=67  Identities=21%  Similarity=0.315  Sum_probs=59.9

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l  349 (541)
                      ..+..|.||.+++|.|||+||++|++|+++|||+|.|+.+.      ..++.|+|+|+.+++++|+.+|.+++
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            45789999999999999999999999999999999997442      35689999999999999999998764

>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=99.20  E-value=1.7e-11  Score=104.47  Aligned_cols=72  Identities=13%  Similarity=0.179  Sum_probs=63.9

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      .++..|.||..++|.||||+|++|++|+++|||+|.|+.+.-|.   ..++.|+|+|+.+++.+|+.+|..++.+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~---~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN---QPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCS---SCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCC---CCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999999999999998543332   4678999999999999999999999864

>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=99.18  E-value=2.3e-11  Score=105.02  Aligned_cols=68  Identities=22%  Similarity=0.311  Sum_probs=61.3

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+|.||.+++|.|||+||++|++|+++|||+|+|.++  +...+.|+|+|+++++++|+.+|.+.+..
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~--g~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC--CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            678999999999999999999999999999999999754  33457999999999999999999998753

>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=99.15  E-value=4e-11  Score=101.80  Aligned_cols=75  Identities=13%  Similarity=0.195  Sum_probs=65.6

Q ss_pred             CCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccc
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~  353 (541)
                      ....++..|.||.+++|.|||++|++|++|+++|||+|+|+.+.     ..+++.|+|+|.+++|++|+.+|..++.+..
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-----~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~   87 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-----APDPNCVTVTGLPENVEEAIDHILNLEEEYL   87 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-----CSCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-----CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999999999997431     1346799999999999999999999987643

>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=99.15  E-value=2.7e-11  Score=102.64  Aligned_cols=72  Identities=17%  Similarity=0.248  Sum_probs=63.8

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ...++.+|.||.+++|.||||||++|++|+++|||+|.|+...      ..++.|+|+|+++++.+|+.+|..++.+.
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            4568899999999999999999999999999999999997321      23578999999999999999999999764

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

Probab=99.11  E-value=1.2e-10  Score=121.28  Aligned_cols=76  Identities=16%  Similarity=0.125  Sum_probs=62.9

Q ss_pred             CCceeEEEEEeccccccccccccc--chhhhhhcccCeeEEEccCcccc-cCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGG--TIISEMRKVTGTSIRIISDQLLK-CISENDRVVQISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG--~tIkeIr~~TGA~I~I~~d~~P~-~~~s~ervVtItGt~e~V~~A~~lI~~~l  349 (541)
                      ..+.+|.++.||..+++.||||+|  ++|++|+++|||+|+++....+. ........|+|+|.+++|++|+..|.+.+
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~  104 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC  104 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSC
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcC
Confidence            467899999999999999999999  99999999999999998332000 01134568999999999999999888743

>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=99.05  E-value=1.3e-10  Score=100.17  Aligned_cols=70  Identities=16%  Similarity=0.231  Sum_probs=62.0

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ..+..|.||.+++|.|||+||++|++|+++|||+|.|+.+.      ...+.|+|+|+.+++++|+.+|..++.+.
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            47889999999999999999999999999999999997431      23468999999999999999999998653

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

Probab=99.04  E-value=2e-10  Score=97.41  Aligned_cols=70  Identities=21%  Similarity=0.320  Sum_probs=63.1

Q ss_pred             cceEEEEEeccCcccceeeCCcchHHHHHhHh-CCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQIS-GAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       467 ~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~S-GA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ...+..|.||.++++.|||+||.+|++|+++| ||+|.|++  .++..+.|+|+|+.+++++|+.+|++.+..
T Consensus        15 ~~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           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCC--CCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            35788999999999999999999999999999 99999964  455678999999999999999999998864

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

Probab=99.03  E-value=3.7e-10  Score=97.10  Aligned_cols=65  Identities=17%  Similarity=0.348  Sum_probs=59.2

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhH-hCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQI-SGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~-SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+|.||..++++|||++|++|++|++. ++++|.+++     .++.|+|+|++++|++|+..|++++..
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHH
Confidence            68899999999999999999999999997 589999865     357999999999999999999998854

>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=98.91  E-value=9.8e-10  Score=93.18  Aligned_cols=73  Identities=16%  Similarity=0.257  Sum_probs=64.6

Q ss_pred             CCceeEEEEEecccccccccccccchhhhhhccc-CeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVT-GTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~T-GA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ..+.++..|.||..+++.|||++|++|++|+++| ||+|.|+.+      ++..+.|+|+|+..+|++|+.+|..++.+.
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~------g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC------CCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            3567789999999999999999999999999999 999999743      234568999999999999999999999754

>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=98.85  E-value=1.8e-09  Score=90.49  Aligned_cols=63  Identities=25%  Similarity=0.459  Sum_probs=57.1

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCE-EEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHH
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAK-VIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAF  535 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~-I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~  535 (541)
                      ....+|.||.+++|.|||+||.+|++|++.|||+ |.|.+     ++..|+|.| +.+++++|+.+|...
T Consensus        14 ~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~~ea~~~A~~~I~~i   78 (91)
T 2cpq_A           14 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             ceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECCHHHHHHHHHHHHhh
Confidence            4788999999999999999999999999999998 99974     248899999 899999999998653

>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=98.82  E-value=4.8e-09  Score=90.09  Aligned_cols=67  Identities=15%  Similarity=0.255  Sum_probs=60.1

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcc-cCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKV-TGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~-TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      .++.+|.||..+++.|||++|++|++|+++ ++++|.|++         .++.|+|+|+++.|.+|+.+|..++.+.
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~---------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC---------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            378899999999999999999999999996 599999863         2568999999999999999999998754

>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=98.67  E-value=2e-08  Score=84.07  Aligned_cols=67  Identities=24%  Similarity=0.287  Sum_probs=58.5

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCee-EEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhh
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS-IRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLR  350 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~-I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~  350 (541)
                      ...+...|.||.+++|.+||++|++|++|+++|||+ |.|..         .+..|+|.| +.+++++|+.+|..+-.
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e---------ddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc---------CCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            455788999999999999999999999999999998 99942         258899999 89999999988876554

>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=98.52  E-value=1.6e-07  Score=84.12  Aligned_cols=73  Identities=14%  Similarity=0.323  Sum_probs=60.0

Q ss_pred             ccceEEEEEeccC------cccceeeCCcchHHHHHhHhCCEEEEeCCC----------------CCCCccEEEEEe-CH
Q 009173          466 VTNTTVEIIVPEN------VIGSVYGENGSNLLRLRQISGAKVIVHEPR----------------LGSTDRIVVISG-TP  522 (541)
Q Consensus       466 ~~~~t~~V~IP~~------~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~----------------~~s~~RiItIsG-tp  522 (541)
                      +...+..|.||.+      ++|.|||++|.+||+|+++|||+|.|....                ....+-.|.|++ ++
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            3457889999987      889999999999999999999999997410                011356788999 58


Q ss_pred             HHHHHHHHHHHHHHhc
Q 009173          523 DETQAAQSLLQAFILT  538 (541)
Q Consensus       523 eqV~~Aq~LI~~~I~~  538 (541)
                      +.+++|+.+|+.++..
T Consensus        84 e~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           84 ENVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            8999999999999864

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.43  E-value=6.3e-07  Score=78.85  Aligned_cols=70  Identities=24%  Similarity=0.253  Sum_probs=54.9

Q ss_pred             eEEEEEeccC-------cccceeeCCcchHHHHHhHhCCEEEEeCCCC----------CCCccEEEEEe-CHHHHHHHHH
Q 009173          469 TTVEIIVPEN-------VIGSVYGENGSNLLRLRQISGAKVIVHEPRL----------GSTDRIVVISG-TPDETQAAQS  530 (541)
Q Consensus       469 ~t~~V~IP~~-------~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~----------~s~~RiItIsG-tpeqV~~Aq~  530 (541)
                      .+..|.||-+       ++|.|||++|.+||+|+++|||+|.|.....          ...+-.|.|++ +++++++|+.
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            4567777754       7899999999999999999999999962110          11334677775 5999999999


Q ss_pred             HHHHHHhc
Q 009173          531 LLQAFILT  538 (541)
Q Consensus       531 LI~~~I~~  538 (541)
                      ||++++..
T Consensus        92 ~Ie~Ll~~   99 (119)
T 2yqr_A           92 LCENLLQT   99 (119)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhhc
Confidence            99998863

>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=98.29  E-value=1.1e-06  Score=78.61  Aligned_cols=76  Identities=18%  Similarity=0.285  Sum_probs=59.9

Q ss_pred             ceeEEEEEeccc------ccccccccccchhhhhhcccCeeEEEccC-ccc-----------ccCCCCCceEEEEc-CHH
Q 009173          276 LLVNARLVVASN------QVGCLLGKGGTIISEMRKVTGTSIRIISD-QLL-----------KCISENDRVVQISG-EFS  336 (541)
Q Consensus       276 ~~vt~~l~VP~~------~vG~IIGKgG~tIkeIr~~TGA~I~I~~d-~~P-----------~~~~s~ervVtItG-t~e  336 (541)
                      ..++.++.||..      ++|.|||++|.+||+|+++|||+|.|... ...           ......+-.|.|++ +.+
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            457889999987      89999999999999999999999999731 100           00112244588999 688


Q ss_pred             HHHHHHHHHHHHhhc
Q 009173          337 KVKDAVYNVTGRLRD  351 (541)
Q Consensus       337 ~V~~A~~lI~~~l~e  351 (541)
                      ++++|+.+|..++.+
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999964

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.18  E-value=4e-06  Score=73.69  Aligned_cols=76  Identities=14%  Similarity=0.076  Sum_probs=57.0

Q ss_pred             ceeEEEEEeccc-------ccccccccccchhhhhhcccCeeEEEccCc------ccccCCCCCceEEEEc-CHHHHHHH
Q 009173          276 LLVNARLVVASN-------QVGCLLGKGGTIISEMRKVTGTSIRIISDQ------LLKCISENDRVVQISG-EFSKVKDA  341 (541)
Q Consensus       276 ~~vt~~l~VP~~-------~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~------~P~~~~s~ervVtItG-t~e~V~~A  341 (541)
                      ..++.++.||-.       ++|.|||++|.+||+|+++|||+|.|....      ........+-.|.|++ +.+++++|
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            356778888865       789999999999999999999999996221      0000011233577775 68999999


Q ss_pred             HHHHHHHhhc
Q 009173          342 VYNVTGRLRD  351 (541)
Q Consensus       342 ~~lI~~~l~e  351 (541)
                      +.+|.+++.+
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999999864

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.08  E-value=2.2e-06  Score=77.34  Aligned_cols=73  Identities=27%  Similarity=0.291  Sum_probs=54.8

Q ss_pred             eEEEEEecccc------cccccccccchhhhhhcccCeeEEEccCc-------------ccccCCCCCc-eEEEEcCHH-
Q 009173          278 VNARLVVASNQ------VGCLLGKGGTIISEMRKVTGTSIRIISDQ-------------LLKCISENDR-VVQISGEFS-  336 (541)
Q Consensus       278 vt~~l~VP~~~------vG~IIGKgG~tIkeIr~~TGA~I~I~~d~-------------~P~~~~s~er-vVtItGt~e-  336 (541)
                      ++.++.||-..      +|.|||++|.++|+|+++|||+|.|-+..             .|+.+..++. -|.|++... 
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            45678888554      89999999999999999999999998421             1211122333 488998533 


Q ss_pred             -----HHHHHHHHHHHHhh
Q 009173          337 -----KVKDAVYNVTGRLR  350 (541)
Q Consensus       337 -----~V~~A~~lI~~~l~  350 (541)
                           .+++|+.+|..+|.
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                 78999999999885

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.96  E-value=5.2e-06  Score=74.87  Aligned_cols=39  Identities=23%  Similarity=0.434  Sum_probs=35.5

Q ss_pred             eEEEEEecccc------ccceeccCchHHHHHHHHhCCeEEecCC
Q 009173          186 VSFRILCSNDK------VGAVIGKGGTIIRALQSEAGAFISVGAT  224 (541)
Q Consensus       186 ~~~rilvP~~~------vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~  224 (541)
                      ++-||.||.+.      +|.|||.+|.++|+|+++|||+|.|...
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGk   46 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGK   46 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEEST
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecC
Confidence            57789999776      9999999999999999999999999864

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.67  E-value=8.6e-05  Score=65.95  Aligned_cols=67  Identities=13%  Similarity=0.222  Sum_probs=59.4

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      -..+.+.++.++.|+|++|+.|+.|++.|.|.|+|..-.+ ++.-.|+|-|++..-..|+.+|+....
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            3577889999999999999999999999999999986533 367889999999999999999998763

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.67  E-value=4.3e-05  Score=84.83  Aligned_cols=64  Identities=17%  Similarity=0.202  Sum_probs=53.9

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-HHHHHHHHHHHHHHh
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRL  349 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-~e~V~~A~~lI~~~l  349 (541)
                      ......+.||.+++|.|||+||++||+|+++|||+|.|.          .+..|.|.|. .+++++|+.+|..++
T Consensus       565 ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~----------d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          565 GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV----------DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC----------SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc----------CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            345678999999999999999999999999999999994          3568999986 578899998887654

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.57  E-value=2.9e-05  Score=86.26  Aligned_cols=62  Identities=16%  Similarity=0.298  Sum_probs=54.1

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFI  536 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I  536 (541)
                      ....+.||.+++|.|||+||.+||.|.++|||+|.|.+      +..|.|.|+ ++.+++|+.+|.+.+
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            36789999999999999999999999999999999964      368999986 788999999998764

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.38  E-value=6.9e-05  Score=67.92  Aligned_cols=104  Identities=22%  Similarity=0.328  Sum_probs=72.0

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc
Q 009173          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE  265 (541)
Q Consensus       186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~  265 (541)
                      -.+.++|+...+|+.||++|++|+.|+++.|-+|.|-.             =+.++       .   ..+..-+......
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~-------------~s~d~-------~---~fI~naLsPA~V~   92 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE-------------YSSDL-------E---RIVKNLFPGVKIE   92 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE-------------CCSSH-------H---HHHHHHSTTSCEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE-------------cCCCH-------H---HHHHHhcCCceEE
Confidence            36779999999999999999999999999999998742             11121       1   1111111110000


Q ss_pred             cCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173          266 KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (541)
Q Consensus       266 ~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~  314 (541)
                      . .... ..+......+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus        93 ~-V~i~-~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           93 S-INVR-ERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             E-EEEE-EETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             E-EEEe-ecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            0 0000 002345678899999999999999999999999999988773

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.21  E-value=0.0005  Score=61.04  Aligned_cols=68  Identities=21%  Similarity=0.145  Sum_probs=58.4

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      ...+.|.+..++.|+|++|+.|++|+..|++.|++..-     ..++.-.|+|.|++..-.+|+.+|......
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~-----~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVW-----GPERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC-----CTTSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc-----CCCCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            45788999999999999999999999999999999632     113456699999999999999999988753

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.88  E-value=0.00052  Score=77.13  Aligned_cols=66  Identities=23%  Similarity=0.389  Sum_probs=11.7

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-HHHHHHHHHHHHHHhhcc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-~e~V~~A~~lI~~~l~e~  352 (541)
                      .....+.||.+++|.|||+||++||+|+++||++|.|.          .+..|.|.+. .+++++|+.+|..++.+.
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~----------ddG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN----------DDGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             CC-----------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE----------CCceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            34568899999999999999999999999999999984          2456777775 788899999998888643

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.55  E-value=0.00046  Score=77.55  Aligned_cols=62  Identities=24%  Similarity=0.373  Sum_probs=11.2

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHHh
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFIL  537 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I~  537 (541)
                      ...+.||.+++|.|||+||.+|+.|.++|||+|.|.+      +..|.|.++ .+.+++|+..|..++.
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d------dG~v~I~~~~~~~~~~A~~~i~~i~~  633 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDGAKIKAAIDWIKSITD  633 (726)
T ss_dssp             -------------------------------------------------CCSCHHHHHHHHHC------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC------CceEEEEeCCHHHHHHHHHHHHHHhh
Confidence            4578999999999999999999999999999999964      255777665 8899999999988764

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=96.52  E-value=0.00064  Score=61.54  Aligned_cols=36  Identities=25%  Similarity=0.607  Sum_probs=33.7

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~  314 (541)
                      .+.++|+...+|..||++|+.|+.|+++.|-+|.|.
T Consensus        37 r~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV   72 (144)
T 2cxc_A           37 RLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVV   72 (144)
T ss_dssp             EEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEE
T ss_pred             EEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEE
Confidence            578999999999999999999999999999999885

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.38  E-value=0.02  Score=59.14  Aligned_cols=96  Identities=27%  Similarity=0.293  Sum_probs=64.8

Q ss_pred             ccccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCC
Q 009173          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (541)
Q Consensus       195 ~~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~  273 (541)
                      +-+|+.||++|++|+.|.++. |=+|.|-.             =++++          ...+..-+........ . .. 
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~-------------~s~dp----------~~fi~nalsPA~V~~V-~-~~-  302 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIID-------------YDDDP----------ARFVANALSPAKVVSV-S-VI-  302 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEE-------------CCSSH----------HHHHHHHTTTSCCSEE-E-EE-
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCcceeEE-E-EE-
Confidence            469999999999999999998 77777642             22222          1111111111100000 0 00 


Q ss_pred             CCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccC
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD  316 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d  316 (541)
                      ......+.+.||..+.+..|||+|.+++-..+.||.+|.|..+
T Consensus       303 ~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          303 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            0113367899999999999999999999999999999999743

>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=94.98  E-value=0.024  Score=55.58  Aligned_cols=95  Identities=24%  Similarity=0.272  Sum_probs=61.8

Q ss_pred             ccccceeccCchHHHHH-HHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCC
Q 009173          195 DKVGAVIGKGGTIIRAL-QSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (541)
Q Consensus       195 ~~vG~IIGKgG~~Ik~I-q~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~  273 (541)
                      +-+|+-||++|++|+.| ++-.|=+|.|-.             =++++          ...+..-+......... . .+
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~-------------~s~dp----------~~fi~nalsPA~V~~V~-i-~~  180 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIID-------------YDDDP----------ARFVANALSPAKVVSVS-V-ID  180 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEE-------------CCSSH----------HHHHHHHTTTSCCSEEE-E-EE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEE-------------ecCCH----------HHHHHhccCCcceEEEE-E-Ec
Confidence            34999999999999999 555677777642             22222          11111111111000000 0 00


Q ss_pred             CCceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS  315 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~  315 (541)
                      . ....+.+.||..+.+.-|||+|.+++--.+.||.+|.|..
T Consensus       181 ~-~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  221 (251)
T 2asb_A          181 Q-TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  221 (251)
T ss_dssp             T-TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             C-CCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceE
Confidence            1 1136789999999999999999999999999999999973

>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=93.68  E-value=0.061  Score=52.78  Aligned_cols=37  Identities=16%  Similarity=0.390  Sum_probs=35.0

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      ....+.||.+..+.-|||+|.|++.-.+.||.+|.|.
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~  220 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR  220 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecce
Confidence            3679999999999999999999999999999999997

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=93.12  E-value=0.019  Score=65.05  Aligned_cols=61  Identities=18%  Similarity=0.315  Sum_probs=20.1

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-HHHHHHHHHHHHHHh
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRL  349 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-~e~V~~A~~lI~~~l  349 (541)
                      ...+.||.+++|.+||++|++|++|++++|+.|.|.          .+..|.|.+. ....++|...|..+.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~----------~dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE----------DDGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC------------------CCCBSSHHHHCC---------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEec----------CCceEEEecCCHHHHHHHHHHHHHhc
Confidence            446789999999999999999999999999999884          2456777764 556666766665544

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=92.90  E-value=0.034  Score=62.65  Aligned_cols=65  Identities=25%  Similarity=0.417  Sum_probs=0.0

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e  351 (541)
                      .....+.||.++++.+||+||.+|++|.+++|+.|.|.          .+..|.|.+ +...+++|..+|..++.+
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~----------~dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE----------DDGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEec----------CCccEEEecCCHHHHHHHHHHHHHHhhh
Confidence            34567889999999999999999999999999999883          245667766 456777787777766543

>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=92.47  E-value=0.12  Score=53.53  Aligned_cols=37  Identities=16%  Similarity=0.390  Sum_probs=35.1

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      ....+.||.+..+..|||+|.|++-..+.||.+|.|.
T Consensus       307 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~  343 (366)
T 1k0r_A          307 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR  343 (366)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEE
T ss_pred             cEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeee
Confidence            4679999999999999999999999999999999996

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=91.91  E-value=0.029  Score=63.16  Aligned_cols=61  Identities=21%  Similarity=0.329  Sum_probs=0.0

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFI  536 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I  536 (541)
                      ...+.||.++++.|||+||.+|+.|.+.+|+.|.|.+      +..|.|++. .+..++|+..|..++
T Consensus       561 ~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~~~~~~a~~~i~~i~  622 (723)
T 3cdi_A          561 IHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEKAKHAIRRIEEIT  622 (723)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             EEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCHHHHHHHHHHHHHHh
Confidence            4578899999999999999999999999999998864      356777665 667788888877664

>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=91.89  E-value=0.17  Score=52.08  Aligned_cols=95  Identities=32%  Similarity=0.371  Sum_probs=62.8

Q ss_pred             ccccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCC
Q 009173          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (541)
Q Consensus       195 ~~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~  273 (541)
                      +-+|+.||.+|++|+.+.++. |=+|.|-             .=++++          ...+..-+.......-   ...
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii-------------~~s~d~----------~~fi~nal~Pa~v~~v---~~~  298 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVL-------------KWSDDP----------KQLIANALAPATVIEV---EIL  298 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEE-------------ECCSSH----------HHHHHHHTCSSCCSEE---EEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEE-------------ecCCCH----------HHHHHHhcCccEEEEE---EEE
Confidence            358999999999999999998 6666653             222222          1111111111000000   000


Q ss_pred             CCceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS  315 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~  315 (541)
                      .+....+.+.||..+.+.-|||+|.+++--.+.||.+|.|..
T Consensus       299 d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          299 DKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             ETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            011236789999999999999999999999999999999863

>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=90.62  E-value=0.013  Score=66.28  Aligned_cols=59  Identities=19%  Similarity=0.410  Sum_probs=20.1

Q ss_pred             EEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Q 009173          472 EIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFI  536 (541)
Q Consensus       472 ~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I  536 (541)
                      .+.||.+++|.|||++|.+|+.|.+.+||.|.|.+      +..|.|++. .+..++|+..|....
T Consensus       601 ~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          601 TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CC------------------CTTCCCCCSCC--------------CCCBSSHHHHCC---------
T ss_pred             EEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999964      356788765 667777877776654

---

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	541
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-16
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	6e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-15
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-15
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	9e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	7e-15
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-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-14
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-08
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-13
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-10
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-13
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-08
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-13
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-12
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	4e-11
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-12
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-06
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	6e-12
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	1e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-11
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-06
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-05
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-11
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	4e-10
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	0.001
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-09
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	2e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	5e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	3e-04
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.002
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	4e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	5e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	0.001
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	5e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.002
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.004

>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 = 72.2 bits (177), Expect = 1e-16
 Identities = 26/68 (38%), Positives = 42/68 (61%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
           TT E+ +P N+IG + G  G+N+  +RQ+SGA++ +  P  GS+ R V I+G+      A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 529 QSLLQAFI 536
           Q L+ A +
Sbjct: 62  QYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (132), Expect = 2e-10
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           + +  +   N+ +G +IG+ G  I  ++  +GA I +   +     R +T+T S    S 
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS--AAS- 57

Query: 245 YSPAQKAVVLVFSRL 259
                 A  L+ +RL
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 = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
               L + +N +GC++G+ G  I+E+R+++G  I+I +         + R V I+G  + 
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP----VEGSSGRQVTITGSAAS 57

Query: 338 VKDAVYNVTGRL 349
           +  A Y +  RL
Sbjct: 58  ISLAQYLINARL 69

>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 = 69.1 bits (169), Expect = 2e-15
 Identities = 21/68 (30%), Positives = 38/68 (55%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
            T E  VP+ ++G + G  G  + R++Q SG K+ +     G  +R  +++GTP+  Q+A
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSA 67

Query: 529 QSLLQAFI 536
           + LL   +
Sbjct: 68  KRLLDQIV 75

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.8 bits (137), Expect = 5e-11
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + Q+  ++      +  VG +IG+GG  I  +Q E+G  I +        ER   +T + 
Sbjct: 2   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT- 60

Query: 240 GPESRYSPAQKAVVLVFSRLIEG 262
            PES     Q A  L+   + +G
Sbjct: 61  -PES----VQSAKRLLDQIVEKG 78

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (127), Expect = 1e-09
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +     V    VG ++G+GG  IS +++ +G  I+I  D         +R   ++G    
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD----SGGLPERSCMLTGTPES 63

Query: 338 VKDAVYNVTGRLRDN 352
           V+ A   +   +   
Sbjct: 64  VQSAKRLLDQIVEKG 78

>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 = 68.7 bits (168), Expect = 2e-15
 Identities = 27/68 (39%), Positives = 44/68 (64%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
            T ++ +P+++ GS+ G+ G  + ++R  SGA + + EP  GS DRI+ I+GT D+ Q A
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 63

Query: 529 QSLLQAFI 536
           Q LLQ  +
Sbjct: 64  QYLLQNSV 71

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.8 bits (124), Expect = 2e-09
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334
           G ++  ++ +  +  G ++GKGG  I ++R  +G SI+I            DR++ I+G 
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP----LEGSEDRIITITGT 56

Query: 335 FSKVKDAVYNVTGRLR 350
             ++++A Y +   ++
Sbjct: 57  QDQIQNAQYLLQNSVK 72

>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 = 50.3 bits (120), Expect = 9e-09
 Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ ++    D  G++IGKGG  I+ ++ E+GA I +   +   ++R+IT+T +   +   
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT--QDQ-- 59

Query: 246 SPAQKAVVLVFSRLIE 261
              Q A  L+ + + +
Sbjct: 60  --IQNAQYLLQNSVKQ 73

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.6 bits (165), Expect = 7e-15
 Identities = 15/69 (21%), Positives = 34/69 (49%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQA 527
           +  +++ +P   +G V G NG  + +++  +G ++        + +RI  I+G PD  Q 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 528 AQSLLQAFI 536
           A  ++   +
Sbjct: 62  AAEIITDLL 70

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 1e-08
 Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + +    VG ++G+ G +I +++   G  I+   D      +  +R+ QI+G   + + 
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD----DGTTPERIAQITGPPDRAQH 61

Query: 341 AVYNVTGRLRD 351
           A   +T  LR 
Sbjct: 62  AAEIITDLLRS 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 = 47.9 bits (114), Expect = 5e-08
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
              +      VG VIG+ G +I+ +Q++AG  I          ER+  +T  
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP 55

>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 = 65.6 bits (160), Expect = 3e-14
 Identities = 25/70 (35%), Positives = 45/70 (64%), Gaps = 3/70 (4%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV---HEPRLGSTDRIVVISGTPDETQ 526
            VE+ VPEN++G++ G+ G  L+  ++++GA++ +    E   G+ +R V I+G+P  TQ
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 527 AAQSLLQAFI 536
           AAQ L+   +
Sbjct: 64  AAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.5 bits (139), Expect = 2e-11
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  N VG +LGKGG  + E +++TG  I+I            +R V I+G  +  + 
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG-EFLPGTRNRRVTITGSPAATQA 64

Query: 341 AVYNVTGRL 349
           A Y ++ R+
Sbjct: 65  AQYLISQRV 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 = 49.1 bits (117), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGPESR 244
             +    + VGA++GKGG  +   Q   GA I +   G  +P    R +T+T S  P + 
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS--PAA- 61

Query: 245 YSPAQKAVVLVFSRL 259
               Q A  L+  R+
Sbjct: 62  ---TQAAQYLISQRV 73

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.8 bits (155), Expect = 3e-13
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 459 SGSKSAIVTNTTV--EIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLG--STDR 514
           SGS   +  NT V  ++ VP+  +G + G  G  +  + + SGAK+   +   G     R
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR 62

Query: 515 IVVISGTPDETQAAQSLLQAFI 536
           ++ ISGT  E  AA+ L+   +
Sbjct: 63  LIKISGTQKEVAAAKHLILEKV 84

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.0 bits (132), Expect = 4e-10
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V  +L V    VG ++G+GG  I  + K +G  I    +   +      R+++ISG   +
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES--EGTLLLSRLIKISGTQKE 72

Query: 338 VKDAVYNVTGRLRDN 352
           V  A + +  ++ ++
Sbjct: 73  VAAAKHLILEKVSED 87

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITVTAS 238
           T+   V  ++      VG +IG+GG  IR++   +GA I+    +       RLI ++ +
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
              +        A  L+  ++ E
Sbjct: 70  --QKE----VAAAKHLILEKVSE 86

>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 = 62.6 bits (152), Expect = 4e-13
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV---HEPRLGSTDRIVVISGTPDETQ 526
               IVP    G + G+ G  +  + Q SGA++ +     P      ++  I GTP +  
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 527 AAQSLLQAFI 536
            A+ L++  I
Sbjct: 62  YARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.3 bits (133), Expect = 1e-10
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
             +V + + G ++GKGG  I  + + +G  I +  +        N ++  I G   ++  
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP-PPNADPNMKLFTIRGTPQQIDY 62

Query: 341 AVY 343
           A  
Sbjct: 63  ARQ 65

>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 = 48.4 bits (115), Expect = 3e-08
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGPESR 244
           F  +    K G +IGKGG  I+++  ++GA I +        + + +L T+  +  P+  
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT--PQQ- 59

Query: 245 YSPAQKAVVLVFSRL 259
                 A  L+  ++
Sbjct: 60  ---IDYARQLIEEKI 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 = 61.7 bits (150), Expect = 6e-13
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +  RL++   +VG ++GK G  + +MR+ +G  I I            +R++ ++G  + 
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN------CPERIITLAGPTNA 57

Query: 338 VKDAVYNVTGRLRD 351
           +  A   +  +L +
Sbjct: 58  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 = 2e-12
 Identities = 14/69 (20%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQA 527
             T+ +++    +GS+ G+ G ++ ++R+ SGA++ + E      +RI+ ++G  +    
Sbjct: 3   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFK 60

Query: 528 AQSLLQAFI 536
           A +++   +
Sbjct: 61  AFAMIIDKL 69

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (137), Expect = 4e-11
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+       +  
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGP--TNA-- 57

Query: 246 SPAQKAVVLVFSRLIE 261
               KA  ++  +L E
Sbjct: 58  --IFKAFAMIIDKLEE 71

>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 = 60.1 bits (146), Expect = 3e-12
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQ 526
           T  +  + +P+     V G+NG  L  L   +  K+ +  PR       + I+GT +  +
Sbjct: 8   TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKEGIE 65

Query: 527 AAQSLLQAFI 536
            A+  +    
Sbjct: 66  KARHEVLLIS 75

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
            +A + +       ++GK G  + ++   T T I+I          +    ++I+G    
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEG 63

Query: 338 VKDAVY 343
           ++ A +
Sbjct: 64  IEKARH 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 = 43.5 bits (103), Expect = 2e-06
 Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           Q + S  +    +    VIGK G  ++ L+ +    I +    P+     I +T ++
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTK 61

>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 = 59.6 bits (144), Expect = 6e-12
 Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV--HEPRLGSTDRIVVISGTPDET 525
           N   EI++P +  G V G+ G  + +L++ +G K+++    P+    D+ + I+G P + 
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKV 66

Query: 526 QAAQSLLQAFI 536
           Q A+ ++   I
Sbjct: 67  QQAKEMVLELI 77

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.7 bits (134), Expect = 1e-10
 Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
               +++ +++ G ++GKGG  I ++++  G  + +I D      +  D+ ++I+G+  K
Sbjct: 8   AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG--PQNTGADKPLRITGDPYK 65

Query: 338 VKDAVYNVTGRLRD 351
           V+ A   V   +RD
Sbjct: 66  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 = 46.9 bits (111), Expect = 1e-07
 Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
                 I+    K G VIGKGG  I+ LQ  AG  + +    P+       +  +  P  
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK 65

Query: 244 RYSPAQKAVVLVFSRLIE 261
                Q+A  +V   + +
Sbjct: 66  ----VQQAKEMVLELIRD 79

>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 = 57.2 bits (138), Expect = 4e-11
 Identities = 9/73 (12%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 465 IVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKV-IVHEPRLGSTDRIVVISGTPD 523
            + +  + + V       + G  G+ + ++R      +    +         + I+G   
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 65

Query: 524 ETQAAQSLLQAFI 536
            T+AA+  +   +
Sbjct: 66  NTEAARDAILRIV 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 = 44.5 bits (105), Expect = 1e-06
 Identities = 9/71 (12%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V       ++G+ G +I+++R     +I+          ++    + I+G     + 
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDK---DDGNQPQDQITITGYEKNTEA 69

Query: 341 AVYNVTGRLRD 351
           A   +   + +
Sbjct: 70  ARDAILRIVGE 80

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 1/59 (1%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG-ATMPECDERLITVTASE 239
             +     +         +IG+ G +I  ++ E    I           +  IT+T  E
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYE 64

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 7e-11
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQ 529
           T+E+ VP ++   V G+ GS + ++       + V  P       I+ I+G       A+
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANLDRAK 68

Query: 530 SLLQAFI 536
           + L   +
Sbjct: 69  AGLLERV 75

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V   + V  +    ++G+ G+ I +M      +I + +            ++ I+G  + 
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP------ELQSDIIAITGLAAN 63

Query: 338 VKDAVYNVTGRLRD 351
           +  A   +  R+++
Sbjct: 64  LDRAKAGLLERVKE 77

>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 = 39.8 bits (93), Expect = 5e-05
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           V+  +    D    VIG+ G+ IR +  E    I V    P  + +   +  +    +  
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV----PAPELQSDIIAITGLAAN-- 63

Query: 246 SPAQKAVVLVFSRLIEGTSEK 266
               +A   +  R+ E  +E+
Sbjct: 64  --LDRAKAGLLERVKELQAEQ 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 = 53.6 bits (129), Expect = 4e-10
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
             VEI +       + G++G+N+ R++      V +  P       ++ I G P   Q A
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQA 62

Query: 529 QSLLQA 534
           +  L  
Sbjct: 63  KRELLE 68

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336
           +    + +       L+GK G  I+ ++     S+RI  D       E   +++I G+  
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS------EKSNLIRIEGDPQ 57

Query: 337 KVKDAV 342
            V+ A 
Sbjct: 58  GVQQAK 63

>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 = 35.5 bits (82), Expect = 0.001
 Identities = 8/53 (15%), Positives = 16/53 (30%), Gaps = 2/53 (3%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
               I   +     +IGK G  I  ++ +    + +          LI +   
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGD 55

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.0 bits (127), Expect = 1e-09
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 465 IVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDE 524
           +      E +V E+++G   G +GSN+ + R++ G   I  +   G      +   + D 
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTG---TFRIYGESADA 60

Query: 525 TQAAQSLLQA 534
            + A+  L+ 
Sbjct: 61  VKKARGFLEF 70

>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 = 49.9 bits (119), Expect = 2e-08
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 465 IVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDE 524
           +     VE+ +P  +  S+ G  G  +  + +  G  V +H P  GS    VVI G   +
Sbjct: 6   LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSD 64

Query: 525 TQAAQSLLQAFI 536
            + A+  L    
Sbjct: 65  VEKAKKQLLHLA 76

>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 = 47.3 bits (113), Expect = 5e-08
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 6/58 (10%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
               +    DK+G VIG    +I  +Q + GA I++       D+  I + A++GP +
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADGPAA 54

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 36.6 bits (85), Expect = 3e-04
 Identities = 10/53 (18%), Positives = 25/53 (47%), Gaps = 10/53 (18%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
            + +  +++G ++G    +I+++++ TG  I I          E+D  + I  
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI----------EDDGTIYIGA 48

>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 = 47.1 bits (112), Expect = 1e-07
 Identities = 7/68 (10%), Positives = 22/68 (32%), Gaps = 1/68 (1%)

Query: 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAA 528
            + ++ +   V   + G  G  + ++       +   +         V ++G P+  + A
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD-PNCVTVTGLPENVEEA 68

Query: 529 QSLLQAFI 536
              +    
Sbjct: 69  IDHILNLE 76

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (92), Expect = 6e-05
 Identities = 10/65 (15%), Positives = 24/65 (36%), Gaps = 5/65 (7%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V+  + +       ++G  G  I ++       IR          + +   V ++G    
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-----APDPNCVTVTGLPEN 64

Query: 338 VKDAV 342
           V++A+
Sbjct: 65  VEEAI 69

>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 = 35.2 bits (81), Expect = 0.002
 Identities = 11/59 (18%), Positives = 18/59 (30%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
            +Q VS  +   +     +IG  G  IR +  E    I    +       +      E 
Sbjct: 6   LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN 64

>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 = 45.5 bits (108), Expect = 4e-07
 Identities = 8/62 (12%), Positives = 26/62 (41%), Gaps = 6/62 (9%)

Query: 473 IIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL 532
           + +    +  V G+ GS +  L+     +++V +      + ++ ++G   +   A+  +
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIAEEAI 58

Query: 533 QA 534
             
Sbjct: 59  YL 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 = 38.6 bits (90), Expect = 1e-04
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 6/50 (12%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           +  +  +V  VIGK G++I+ L+SE    I VG         LI V    
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVG------QNGLIWVNGDR 48

>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 = 38.6 bits (90), Expect = 1e-04
 Identities = 12/74 (16%), Positives = 30/74 (40%), Gaps = 10/74 (13%)

Query: 284 VASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVY 343
           +   +V  ++GK G++I  ++      I +            + ++ ++G+  KV  A  
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVV----------GQNGLIWVNGDRRKVSIAEE 56

Query: 344 NVTGRLRDNHFSGT 357
            +    ++ H  G 
Sbjct: 57  AIYLIEQEAHTEGL 70

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 9/32 (28%), Positives = 16/32 (50%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221
           +    +++GAVIG  G +   +    G  I+V
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITV 38

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.1 bits (86), Expect = 5e-04
 Identities = 9/43 (20%), Positives = 22/43 (51%)

Query: 284 VASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISEND 326
           V   ++G ++G  G + +E+ + TGT I + ++  +  +    
Sbjct: 9   VKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEA 51

>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 = 35.9 bits (83), Expect = 0.001
 Identities = 10/64 (15%), Positives = 21/64 (32%)

Query: 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQS 530
           + + V    +G+V G  G     + + +G  + V                 P     A  
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAE 64

Query: 531 LLQA 534
           +++A
Sbjct: 65  VVKA 68

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG 222
           +  S  KV  VIG+  ++++ L+ +    I V 
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA 37

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 11/62 (17%), Positives = 19/62 (30%), Gaps = 5/62 (8%)

Query: 473 IIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL 532
           I +    +  V G+N S    L   SG  + V         RI     +    +     +
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-----NGRIWATCPSRFSEEILIEAI 59

Query: 533 QA 534
           + 
Sbjct: 60  RK 61

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
           I     KV  VIGK  ++   L S++G  I V       +   I  T  
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA------NNGRIWATCP 47

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	541
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.65
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.6
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.58
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.57
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.56
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.51
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.51
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.49
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.48
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.46
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.44
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.44
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.42
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.42
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.4
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.36
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.36
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.36
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.28
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.27
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.25
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.23
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.2
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.19
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.18
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.12
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.08
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.07
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.06
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.99
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.88
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.74
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.71
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.7
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.64
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.52
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.45
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.44
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.36
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.28
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.84
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.74
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.49
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.34
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.02
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	93.99
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	93.69
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	93.54
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	85.5
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	81.8

>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=99.65  E-value=6.7e-17  Score=127.95  Aligned_cols=69  Identities=38%  Similarity=0.630  Sum_probs=66.0

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      +|.+|.||.+++|+|||++|++|++|++.|||+|.|+++.+++.+|.|+|+|++++|+.|+.||+++|.
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   70 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLS   70 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHcC
Confidence            688999999999999999999999999999999999988888899999999999999999999999873

>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=99.62  E-value=4.8e-16  Score=124.44  Aligned_cols=70  Identities=39%  Similarity=0.655  Sum_probs=66.9

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .|.+|.||.+++|+|||++|++|++|++.|||+|+|.++.+++.+|.|+|+|++++|+.|+.+|+++|..
T Consensus         4 ~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           4 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            6889999999999999999999999999999999999888888999999999999999999999999863

>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=99.60  E-value=2.9e-16  Score=125.47  Aligned_cols=71  Identities=21%  Similarity=0.456  Sum_probs=67.3

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      .+++|.||.+++|+|||++|++|++|++.|||+|+|+...+++.+|.|+|+|+++++++|+.+|.++|.+-
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999999998888888999999999999999999999999763

>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=99.58  E-value=9.3e-16  Score=121.57  Aligned_cols=67  Identities=27%  Similarity=0.517  Sum_probs=61.1

Q ss_pred             EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC---CCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE---PRLGSTDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~---p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      +.+|.||.+++|+||||+|++|++|++.|||+|+|..   +.+++.+|.|+|+|++++|++|+.||+++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4689999999999999999999999999999999973   344667899999999999999999999875

>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=99.57  E-value=1.9e-15  Score=122.14  Aligned_cols=73  Identities=30%  Similarity=0.537  Sum_probs=69.1

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTGP  540 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~~  540 (541)
                      ..+.+|.||.+++|+|||++|.+|++|++.|||+|.|.++.+++.++.|+|+|++++|++|+.+|.++|..++
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~r   79 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   79 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHccC
Confidence            4789999999999999999999999999999999999988888899999999999999999999999998764

>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=99.56  E-value=1.9e-15  Score=120.75  Aligned_cols=68  Identities=35%  Similarity=0.654  Sum_probs=62.5

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC---CCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE---PRLGSTDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~---p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      .+.++.||.+++|+|||++|++|++|++.|||+|+|.+   +.+++.+|.|+|+|++++|+.|+.||+++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            46899999999999999999999999999999999974   335667999999999999999999999986

>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=99.51  E-value=6.9e-15  Score=119.43  Aligned_cols=71  Identities=27%  Similarity=0.521  Sum_probs=65.0

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC--CCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE--PRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~--p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      +.+.+|.||..++|+|||++|++|++|++.|||+|.|.+  +.+...+|.|+|+|++++|++|+.+|+++|..
T Consensus         7 ~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           7 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             cEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999999999999974  34566789999999999999999999998853

>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=99.51  E-value=8.6e-15  Score=115.90  Aligned_cols=67  Identities=21%  Similarity=0.463  Sum_probs=62.6

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      .+.+|.||.+.+|+|||++|++|++|++.|||+|+|.++  +..+|+|+|+|+++++.+|+.+|.++|.
T Consensus         4 vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~   70 (71)
T d2axya1           4 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLE   70 (71)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC--CCCcceEEEEECHHHHHHHHHHHHHHhc
Confidence            689999999999999999999999999999999999753  5568999999999999999999999986

>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=99.49  E-value=1.2e-14  Score=115.10  Aligned_cols=70  Identities=19%  Similarity=0.380  Sum_probs=62.2

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l  349 (541)
                      +.+|.||++++|+||||+|++|++|++.|||+|+|..+..+. ..+++|.|+|+|++++|++|+.+|.++|
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            468999999999999999999999999999999998554433 3467899999999999999999999875

>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=99.48  E-value=1.4e-14  Score=114.62  Aligned_cols=70  Identities=23%  Similarity=0.490  Sum_probs=63.7

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      .+++++|+||++++|+||||+|++|++|++.|||+|+++.+.      ..+|+|+|+|++++|.+|+.+|.++|+|
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 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN------CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC------CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC------CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            357899999999999999999999999999999999997432      4579999999999999999999999864

>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=99.47  E-value=4e-14  Score=113.02  Aligned_cols=73  Identities=25%  Similarity=0.560  Sum_probs=64.9

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ..+|.++.||.+++|+||||+|++|++|+++|||+|+|..+ .   ..+++++|+|+|++++|.+|+.+|.++++++
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-L---EGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-T---SCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC-C---CCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            35788999999999999999999999999999999999632 1   2367899999999999999999999999763

>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=99.46  E-value=3.2e-14  Score=113.42  Aligned_cols=70  Identities=30%  Similarity=0.491  Sum_probs=61.6

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l  349 (541)
                      +++|.||++++|+||||+|++|++|+++|||+|+|..+.-+ ..++++|.|+|+|++++|++|+.+|.++|
T Consensus         4 ~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF-LPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCC-STTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            57999999999999999999999999999999999843211 12367899999999999999999999886

>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=99.44  E-value=4.5e-14  Score=114.56  Aligned_cols=75  Identities=24%  Similarity=0.404  Sum_probs=66.7

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCc-ccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQ-LLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~-~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ...++.+|.||..++|+||||+|++|++|+++|||+|+|.++. .+   .+.+|.|+|+|++++|.+|+.+|.++|+|.
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            4568899999999999999999999999999999999998442 33   367899999999999999999999999753

>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=99.44  E-value=8.7e-14  Score=118.17  Aligned_cols=71  Identities=25%  Similarity=0.396  Sum_probs=63.8

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPR--LGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~--~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||.+++|+|||++|.+|++|++.|||+|+|.++.  ....+|+|+|+|++++|+.|+.+|+++|..
T Consensus        14 ~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhC
Confidence            36789999999999999999999999999999999997543  344689999999999999999999999953

>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=99.42  E-value=6.6e-14  Score=110.41  Aligned_cols=69  Identities=25%  Similarity=0.431  Sum_probs=61.9

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHH
Q 009173          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (541)
Q Consensus       185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i  259 (541)
                      +++.+|+||++.+|+||||+|++|++|+++|||+|+|++..+++.+|+|+|+|+++.      +.+|..+|.+++
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 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS------ISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHH------HHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHH------HHHHHHHHHHHc
Confidence            368899999999999999999999999999999999998888899999999998764      778887777654

>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=99.42  E-value=7.1e-14  Score=111.33  Aligned_cols=71  Identities=23%  Similarity=0.383  Sum_probs=63.3

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      ..+++|.||.+++|+||||+|.+|++|+++|||+|+|..+. +   .+.++.|+|+|++++|++|+.+|.++|++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-G---TTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT-T---SCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC-C---CCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            35789999999999999999999999999999999997432 1   25678999999999999999999999974

>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=99.40  E-value=1.4e-13  Score=111.62  Aligned_cols=70  Identities=20%  Similarity=0.306  Sum_probs=64.0

Q ss_pred             cceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       467 ~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      +..+.+|.||..++|+|||++|++|++|++.|||+|.++  ..++.++.|+|+|++++|++|+.+|++++..
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p--~~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIP--RPDDPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCC--CTTSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEEC--CCCCCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999995  4456789999999999999999999998864

>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=99.39  E-value=2.7e-13  Score=110.61  Aligned_cols=70  Identities=13%  Similarity=0.213  Sum_probs=64.0

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC-CCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE-PRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~-p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      .+.+|.||..++|+|||++|++|++|++.|||+|++++ +..+..++.|+|+|++++|++|+.+|+++|..
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999999974 45567789999999999999999999998864

>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=99.36  E-value=3.8e-13  Score=114.09  Aligned_cols=77  Identities=23%  Similarity=0.332  Sum_probs=67.3

Q ss_pred             CCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       274 ~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ....++.+|.||..++|+||||+|.+|++|+++|||+|.|.++..+  ....+|+|+|+|++++|.+|+.+|.++|.+.
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            4567889999999999999999999999999999999999743222  2356799999999999999999999999764

>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=99.36  E-value=2.4e-13  Score=107.37  Aligned_cols=66  Identities=21%  Similarity=0.322  Sum_probs=60.3

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I  536 (541)
                      ...+|.||..++|+|||++|++|++|++.|||+|.|++  +++.++.|+|+|++++|++|+.+|++.+
T Consensus         5 ~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~--~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCC--CCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCC--CCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999999954  4566789999999999999999999853

>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=99.36  E-value=3.6e-13  Score=108.54  Aligned_cols=74  Identities=22%  Similarity=0.353  Sum_probs=65.9

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ...++.+|.||..++|+|||++|.+|++|+++|||+|.|.+.. +   +++++.|+|+|++++|++|+.+|.++|.++
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            4578899999999999999999999999999999999997421 2   367899999999999999999999999753

>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=99.34  E-value=3.3e-13  Score=109.57  Aligned_cols=70  Identities=21%  Similarity=0.312  Sum_probs=62.1

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHh-CCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQIS-GAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~S-GA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      ..+.+|.||..++|+|||++|++|++|++.+ |++|.++  ..++.++.|+|+|++++|++|+.+|++.+...
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFP--VEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECC--CTTTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEe--CCCCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            4688999999999999999999999999875 8888774  45667899999999999999999999998754

>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=99.34  E-value=6.6e-13  Score=107.54  Aligned_cols=69  Identities=10%  Similarity=0.204  Sum_probs=61.3

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFIL  537 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~  537 (541)
                      ..+.+|.||..++|+|||++|++|++|++.|||+|.|++.. +.+.+.|+|+|++++|++|+.+|++.+.
T Consensus         9 ~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-~~~~~~v~I~G~~~~V~~A~~~I~~i~~   77 (81)
T d2ctma1           9 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEE   77 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc-CCCCCEEEEeCCHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999996542 2345789999999999999999998875

>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=99.28  E-value=2e-12  Score=105.33  Aligned_cols=72  Identities=13%  Similarity=0.180  Sum_probs=64.2

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      .+++++.||..++|+|||++|++|++|+++|||+|+|+....+   ..+++.|+|+|+.++|.+|+.+|.+++.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~---~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG---NQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTC---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCC---CCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999844333   36788999999999999999999999875

>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=99.27  E-value=2e-12  Score=106.87  Aligned_cols=69  Identities=20%  Similarity=0.252  Sum_probs=62.9

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||..++|+|||++|++|++|++.|||+|.++  ..++.++.|+|+|++++|++|+.+|++++..
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p--~~~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVP--APELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECC--CTTTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEEC--CCCCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            37899999999999999999999999999999999995  3466778999999999999999999998853

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=1.4e-12  Score=104.83  Aligned_cols=64  Identities=25%  Similarity=0.433  Sum_probs=57.3

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHH
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAF  535 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~  535 (541)
                      ..+.+|.||.+++|+|||+||++|++|++.|||+|.+.+.    .++.|+|.| +++++++|+.||+..
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999999999998653    347899999 799999999999743

>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=99.24  E-value=3.4e-12  Score=103.26  Aligned_cols=73  Identities=14%  Similarity=0.208  Sum_probs=64.2

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      .+.++.++.||..++|.|||++|.+|++|+++|||+|+|+.+.-     .+++.|+|+|++++|++|+.+|.++++|+
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            45678899999999999999999999999999999999974321     23578999999999999999999999865

>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=99.23  E-value=3.6e-12  Score=103.08  Aligned_cols=72  Identities=17%  Similarity=0.246  Sum_probs=64.4

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      ...++.++.||..++|+|||++|.+|++|+++|||+|.++..      ++.++.|+|+|+.++|.+|+.+|.+++.+.
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 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC------CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999999743      245688999999999999999999998763

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.20  E-value=7.9e-12  Score=101.69  Aligned_cols=62  Identities=13%  Similarity=0.244  Sum_probs=56.9

Q ss_pred             EEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173          472 EIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG  539 (541)
Q Consensus       472 ~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~  539 (541)
                      .+.||.+++|+|||++|++|++|++.|||+|.|.+      ++.|+|+|++++++.|+.+|+..+...
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999954      368999999999999999999887654

>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=99.19  E-value=7.7e-12  Score=98.56  Aligned_cols=67  Identities=22%  Similarity=0.325  Sum_probs=60.1

Q ss_pred             eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (541)
Q Consensus       277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l  349 (541)
                      ..++++.||..++|.|||++|++|++|+++|||+|+|+++      +++++.|+|+|++++|++|+.+|.++.
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~------~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD------SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC------CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC------CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999743      245788999999999999999998864

>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=99.18  E-value=7.6e-12  Score=101.33  Aligned_cols=72  Identities=17%  Similarity=0.267  Sum_probs=63.3

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcc-cCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV-TGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~-TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~  352 (541)
                      .+.++.+|.||..++|+||||+|++|++|+++ ++++|.++..      +++++.|+|+|++++|++|+.+|.+++.|.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC------CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            45678999999999999999999999999987 5999988632      246789999999999999999999999764

>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=99.12  E-value=2e-11  Score=100.77  Aligned_cols=70  Identities=16%  Similarity=0.246  Sum_probs=63.2

Q ss_pred             ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      ..++..+.||..++|.|||++|.+|++|+++|||+|.|+..      +++++.|+|+|+.++|++|+.+|.+++.+
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP------ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT------TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC------CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999743      24567899999999999999999999875

>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=99.08  E-value=1e-10  Score=96.33  Aligned_cols=66  Identities=17%  Similarity=0.327  Sum_probs=59.4

Q ss_pred             ceEEEEEeccCcccceeeCCcchHHHHHhH-hCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          468 NTTVEIIVPENVIGSVYGENGSNLLRLRQI-SGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       468 ~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~-SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..+.+|.||..++++|||++|++|++|++. +|++|.+++     ....|+|+|++++|++|+.+|++.+..
T Consensus        20 ~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~-----~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          20 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-----CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999 489999954     247899999999999999999998753

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=5.2e-11  Score=95.43  Aligned_cols=66  Identities=23%  Similarity=0.289  Sum_probs=57.5

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHH
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGR  348 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~  348 (541)
                      ...++.++.||.+++|+|||+||++|++|++.|||+|.+..+        .++.|+|.| ++++|++|+.+|..+
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~--------~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC--------CCceEEEEECCHHHHHHHHHHHHHh
Confidence            346788999999999999999999999999999999988532        357899999 699999999998543

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.06  E-value=7.4e-11  Score=95.83  Aligned_cols=63  Identities=17%  Similarity=0.253  Sum_probs=57.4

Q ss_pred             EEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccc
Q 009173          281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       281 ~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~  353 (541)
                      -+.||.+++|.||||+|++|++|+++|||+|.|..          +..|+|+|++++++.|+.+|..++++..
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~----------~g~v~I~G~~e~v~~A~~~I~~i~~ea~   66 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ----------NGLIWVNGDRRKVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT----------TSEEEEESCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC----------CCEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            57899999999999999999999999999999942          4689999999999999999999987654

>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=98.99  E-value=2.7e-10  Score=93.66  Aligned_cols=68  Identities=15%  Similarity=0.258  Sum_probs=61.1

Q ss_pred             CceeEEEEEecccccccccccccchhhhhhcc-cCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV-TGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~-TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      .+.++..+.||..+++.|||++|++|++|+++ +|++|.++.         .+..|+|+|++++|++|+.+|.+++.+
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            45689999999999999999999999999998 589999963         256899999999999999999999875

>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=98.88  E-value=1.7e-10  Score=93.57  Aligned_cols=61  Identities=18%  Similarity=0.313  Sum_probs=51.6

Q ss_pred             EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEE-----EeCHHHHHHHHHHHHHHH
Q 009173          471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVI-----SGTPDETQAAQSLLQAFI  536 (541)
Q Consensus       471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItI-----sGtpeqV~~Aq~LI~~~I  536 (541)
                      .+|.||.+++|.|||+||++|++|+++|||+|+|+...     ..+.+     .|.+.++++|+.+|.+.-
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~-----g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN-----SMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT-----TEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC-----CeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999996432     34444     457899999999998753

>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=98.74  E-value=2.1e-10  Score=89.69  Aligned_cols=60  Identities=15%  Similarity=0.079  Sum_probs=46.6

Q ss_pred             EEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHHh
Q 009173          472 EIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFIL  537 (541)
Q Consensus       472 ~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I~  537 (541)
                      -+.||.+++|.|||++|++|++|++.|||+|.|.+      +..|+|+|. ++.++.|+.+|+....
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~------~g~v~I~g~~~~~v~~A~~~I~~i~~   64 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCPSRFSEEILIEAIRKIEN   64 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT------TSEEEC-----CTTCCTHHHHTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC------CCEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999954      357999995 7889999999976544

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.71  E-value=5.9e-10  Score=87.02  Aligned_cols=62  Identities=10%  Similarity=0.101  Sum_probs=47.7

Q ss_pred             EEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-HHHHHHHHHHHHHHhhcc
Q 009173          281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDN  352 (541)
Q Consensus       281 ~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-~e~V~~A~~lI~~~l~e~  352 (541)
                      -+.||.+++|.||||+|++|++|+++|||+|.|..          +..|+|+|. .+++..|..+|..+.++.
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            46799999999999999999999999999999942          457999995 679999999998776543

>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=98.70  E-value=1.4e-08  Score=82.27  Aligned_cols=61  Identities=15%  Similarity=0.103  Sum_probs=54.9

Q ss_pred             EEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHHhc
Q 009173          472 EIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFILT  538 (541)
Q Consensus       472 ~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I~~  538 (541)
                      .+.||.+++|.|||+||++|+.|+..|||+|.|.+.      ..|.|.|. .+.+..|+.+|+.....
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~~~~~~A~~~I~~I~~e   65 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999999999642      57999995 89999999999987654

>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=98.64  E-value=1.5e-08  Score=81.78  Aligned_cols=62  Identities=19%  Similarity=0.263  Sum_probs=51.9

Q ss_pred             EEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE-----cCHHHHHHHHHHHHHHhh
Q 009173          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-----GEFSKVKDAVYNVTGRLR  350 (541)
Q Consensus       280 ~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt-----Gt~e~V~~A~~lI~~~l~  350 (541)
                      +.+.||.+.+|.||||+|++|++|+++|||+|+|..+         +..|.+.     |.+.++++|..+|.++.+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d---------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE---------NSMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT---------TTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC---------CCeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            3589999999999999999999999999999999633         2344443     578899999999988765

>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=98.52  E-value=6.3e-08  Score=78.40  Aligned_cols=63  Identities=10%  Similarity=0.090  Sum_probs=55.2

Q ss_pred             EEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-HHHHHHHHHHHHHHhhccc
Q 009173          281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNH  353 (541)
Q Consensus       281 ~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-~e~V~~A~~lI~~~l~e~~  353 (541)
                      -+.||.+++|.|||+||++|+.|+++|||+|.|..          +..|.|.|. .+.+..|..+|..+.++..
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d----------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~   67 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR----------NGRIHLECPNEDLEAIAVMAIKIIDEEAY   67 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET----------TTEEEEECSCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC----------CcEEEEEeCCHHHHHHHHHHHHHHHHhch
Confidence            46799999999999999999999999999999942          357999995 7888999999999887644

>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=98.45  E-value=8.9e-09  Score=76.03  Aligned_cols=47  Identities=30%  Similarity=0.497  Sum_probs=15.4

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCC
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE  239 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~  239 (541)
                      ..+|.||.+.+|.|||+||++||.|+++|||+|++.      ++..|+|+|..
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~------ddg~v~I~a~~   50 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAAD   50 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe------CCeEEEEEecC
Confidence            456889999999999999999999999999999996      46789998853

>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=98.44  E-value=7.1e-08  Score=80.66  Aligned_cols=53  Identities=21%  Similarity=0.310  Sum_probs=47.9

Q ss_pred             cccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173          479 VIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT  538 (541)
Q Consensus       479 ~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~  538 (541)
                      ..|+|||+||.+|+.|++.|||+|.|++       ..|.|.|++++++.|+.+|..+|..
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d-------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC-------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            4799999999999999999999999954       3588899999999999999999854

>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=98.36  E-value=1.3e-08  Score=75.21  Aligned_cols=45  Identities=20%  Similarity=0.484  Sum_probs=14.0

Q ss_pred             EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC
Q 009173          471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT  521 (541)
Q Consensus       471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt  521 (541)
                      ..+.||.+++|.|||+||.+||.|+++|||+|.|.+      +..|+|.|+
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~   49 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAA   49 (54)
T ss_dssp             C---------------------CHHHHSCCCC--------------CCCCB
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEec
Confidence            478899999999999999999999999999999964      467888775

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.28  E-value=2e-07  Score=77.85  Aligned_cols=53  Identities=21%  Similarity=0.322  Sum_probs=47.5

Q ss_pred             ccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173          288 QVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (541)
Q Consensus       288 ~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e  351 (541)
                      +.|+|||++|++|+.|++.|||+|.|.           +..|.|.|+++++..|..+|..++.+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~-----------d~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG-----------EYEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe-----------CCeEEEEECchhHHHHHHHHHHHHcC
Confidence            479999999999999999999999993           23577889999999999999999964

>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=97.84  E-value=1.6e-05  Score=68.12  Aligned_cols=75  Identities=20%  Similarity=0.339  Sum_probs=56.9

Q ss_pred             eeEEEEEeccc------ccccccccccchhhhhhcccCeeEEEcc-Cc----------ccccCCCCCce-EEEEcC-HHH
Q 009173          277 LVNARLVVASN------QVGCLLGKGGTIISEMRKVTGTSIRIIS-DQ----------LLKCISENDRV-VQISGE-FSK  337 (541)
Q Consensus       277 ~vt~~l~VP~~------~vG~IIGKgG~tIkeIr~~TGA~I~I~~-d~----------~P~~~~s~erv-VtItGt-~e~  337 (541)
                      .++.++.||-.      ++|.|||.+|.++|+|+++|||+|.|-+ ..          .+.....++.. |.|+++ .+.
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            35678889865      4899999999999999999999999972 11          11111233444 888885 668


Q ss_pred             HHHHHHHHHHHhhc
Q 009173          338 VKDAVYNVTGRLRD  351 (541)
Q Consensus       338 V~~A~~lI~~~l~e  351 (541)
                      +..|+.+|..+|.+
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999964

>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=97.74  E-value=3.3e-05  Score=66.02  Aligned_cols=69  Identities=13%  Similarity=0.393  Sum_probs=53.9

Q ss_pred             eEEEEEeccC------cccceeeCCcchHHHHHhHhCCEEEEeC--C--------CC-----CCCc-cEEEEEeC-HHHH
Q 009173          469 TTVEIIVPEN------VIGSVYGENGSNLLRLRQISGAKVIVHE--P--------RL-----GSTD-RIVVISGT-PDET  525 (541)
Q Consensus       469 ~t~~V~IP~~------~vG~IIGkgGs~Ik~Irq~SGA~I~I~~--p--------~~-----~s~~-RiItIsGt-peqV  525 (541)
                      .+.+|.||-+      ++|.|||.+|+++|+|+++|||+|.|--  .        ..     ..++ =-|.|++. ++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            5678888865      5899999999999999999999999951  0        00     0122 34677875 7789


Q ss_pred             HHHHHHHHHHHh
Q 009173          526 QAAQSLLQAFIL  537 (541)
Q Consensus       526 ~~Aq~LI~~~I~  537 (541)
                      ++|..+|+.+|.
T Consensus        83 ~~A~~~i~~ll~   94 (122)
T d1k1ga_          83 KKAVEQIRNILK   94 (122)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH
Confidence            999999999984

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.49  E-value=3.8e-05  Score=66.49  Aligned_cols=73  Identities=29%  Similarity=0.287  Sum_probs=53.9

Q ss_pred             eEEEEEecc------cccccccccccchhhhhhcccCeeEEEccCc-------------ccccCCCCCce-EEEEcCH--
Q 009173          278 VNARLVVAS------NQVGCLLGKGGTIISEMRKVTGTSIRIISDQ-------------LLKCISENDRV-VQISGEF--  335 (541)
Q Consensus       278 vt~~l~VP~------~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~-------------~P~~~~s~erv-VtItGt~--  335 (541)
                      ++.++.||-      +++|+|||.+|.++|+|+++|||+|.|-+..             .|.....+|.. |.|++..  
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            355778883      4789999999999999999999999998311             11111234444 8888863  


Q ss_pred             ----HHHHHHHHHHHHHhh
Q 009173          336 ----SKVKDAVYNVTGRLR  350 (541)
Q Consensus       336 ----e~V~~A~~lI~~~l~  350 (541)
                          ..+.+|+.+|..+|.
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                358889999998884

>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=97.34  E-value=7.7e-05  Score=64.53  Aligned_cols=38  Identities=24%  Similarity=0.405  Sum_probs=34.1

Q ss_pred             eEEEEEeccc------cccceeccCchHHHHHHHHhCCeEEecC
Q 009173          186 VSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVGA  223 (541)
Q Consensus       186 ~~~rilvP~~------~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~  223 (541)
                      ++-||+||.+      .+|.|||.+|.++|+|+++|||+|.|-.
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrG   45 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRG   45 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEES
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEe
Confidence            5678889865      5899999999999999999999999975

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.02  E-value=0.013  Score=44.13  Aligned_cols=37  Identities=19%  Similarity=0.393  Sum_probs=34.8

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      ....+.||.+..+..|||+|.|++-..+.||.+|.|.
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            4678999999999999999999999999999999995

>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=93.99  E-value=0.013  Score=44.14  Aligned_cols=37  Identities=16%  Similarity=0.390  Sum_probs=35.0

Q ss_pred             eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173          469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH  505 (541)
Q Consensus       469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~  505 (541)
                      ....+.||++..+..|||+|.|++-..+.||.+|.|.
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~   62 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR   62 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEE
Confidence            4678999999999999999999999999999999996

>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=93.69  E-value=0.016  Score=43.57  Aligned_cols=38  Identities=34%  Similarity=0.406  Sum_probs=35.5

Q ss_pred             EEEEEecccccccccccccchhhhhhcccCeeEEEccC
Q 009173          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD  316 (541)
Q Consensus       279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d  316 (541)
                      .+.+.||.++.+..|||+|.+++-..+.||.+|.|..+
T Consensus        27 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          27 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             EEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            67889999999999999999999999999999999755

>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=93.54  E-value=0.024  Score=42.72  Aligned_cols=37  Identities=27%  Similarity=0.385  Sum_probs=34.5

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCeEEecC
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~  223 (541)
                      .+.+.||.+..+..|||+|.+||-..+-||.+|.|..
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            6778999999999999999999999999999999863

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=85.50  E-value=0.5  Score=36.67  Aligned_cols=58  Identities=16%  Similarity=-0.008  Sum_probs=47.6

Q ss_pred             EEEeccCcccceeeCCcc-hHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHH
Q 009173          472 EIIVPENVIGSVYGENGS-NLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAF  535 (541)
Q Consensus       472 ~V~IP~~~vG~IIGkgGs-~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~  535 (541)
                      -+.||..++.+++|++++ -|+.|.+.+++.|.|..      +..|-|.| +++.+-++...|...
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~------NGrIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL------NGKIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET------TTEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec------CcEEEEECCCHHHHHHHHHHHHHH
Confidence            568899999999999998 78999999999999964      36688888 577777766666543

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.80  E-value=0.26  Score=39.01  Aligned_cols=31  Identities=23%  Similarity=0.326  Sum_probs=26.8

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCC
Q 009173          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGA  217 (541)
Q Consensus       187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa  217 (541)
                      .+++.|-...-|.||||+|+.|++|+++-.-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k   66 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQK   66 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHH
Confidence            4668889999999999999999999887643