Citrus Sinensis ID: 004460

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750--

MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEESAVESKGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS

ccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHHccccccccccccccccccccEEEEEcccHHHHHHHHHHcccccccccccEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHcccccHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHcccccHHHHcccccccccHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc

ccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEEcccccccccccEEEccccHHHHHHHHHHHccccccccEEEEEEcHHHHHHHHHHHHHHHccccccccccccccccHcccHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHcccccccccccccHHccccccccccccccccccccccccccccHccccccccccccccccccccccccccccHcHHHHcccccHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHccHHHHHHcccccccccHHccccccHHcccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccHcccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccHHcccccccccHHHHHcHHcccccHHHHHHHHHHHHHHccccHHHHHcccccHHHHcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc

mvrpafpprppgpvgvlpsvarppvpgipgvrpimppvvrpvplptvtpaekpqtkvyvgkiaptadsDFVLSVLKVCGTvkswkraqypsngtpkgfgfcefESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKEtqdagagkedesvqsvekneptkspenlkdnetgnkeshdptnfgvvteeDRKADQEALEKLTCMVEerlktnplpppppqttadgsgisnselpakardgdsdvDMIRNDiaedklddettsdtkasdhdrpetsspdrsrvhdrrgrdkerDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEilydeeededdsRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLsdnavngslaeesaveskgdpssqngngdestnvpiaasdmrqsgnvparklgfglvgsgkrtavpsvfhveddddadkdkkmrplvpidysteelqaaqphvsganppnLAAAAEFAKRISnvnskeeksdAERERSRrlhdrssqrekdrsdednnrtrdeHKEKILdrdrdrehgldkvktpdnkklldAKQLIDMIPKTKEELFSYEINWAvydkhelhermrpwISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS

mvrpafpprppgpvgvlpSVARPPVPGIPGVRPIMPPVVRPVPLPtvtpaekpqtkvYVGKiaptadsdfVLSVLKVCGTVKswkraqypsngtpkgFGFCEFESAEGVLRALRLLNKFnidgqelmlkVDQATREYLERyvdkktentkklketqdagagkedesvqsvekneptkspenlkdnetgnkeshdptnfgvvteEDRKADQEALEKLTCMVEErlktnplpppppqttadgsgisnselpakardgdsdVDMIRNDiaedklddettsdtkasdhdrpetsspdrsrvhdrrgrdkerdlkrekereidryereaerervrkereqrrkieeaereyerclkdweyrererekerqyekekekererkrkkeilydeeededdsrkrwrrsvleekrrkrirekeedladevreeEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSLAEesaveskgdpssqngngdESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPsvfhveddddadkdkkMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRisnvnskeeksdaerersrrlhdrssqrekdrsdednnrtrdehkekildrdrdrehgldkvktpdnkklldakqlIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKkvetglalrsks

MvrpafpprppgpvgvlpsvaRppvpgipgvrpimppvvrpvplptvtpAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDkktentkklketQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNplpppppQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHdrrgrdkerdlkrekereidryereaerervrkereqrrkieeaereYERCLKDWeyrererekerqyekekekererkrkkeILYdeeededdSRKRWRRSVLeekrrkrirekeedladevreeeeiavakrraeeeqlqqqqrdalklLSDNAVNGSLAEESAVESKGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEddddadkdkkMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS

*************************************VV***************TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYV************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************GFGLV***************************************************************************************************************************************AKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGL******

********************************************************VYVGKIAPTADSDFVLSVLKVCGTVKSWKRA*****GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLE*******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************PKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKV***L******

MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKL*****************************LKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKL********************************************EIDRY************************EYERCLKDWEYR*********************RKKEILY************WRRSVLEEKRRKRIRE************EEIAVAK*************DALKLLSDNAVNG**********************ESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISN*****************************************KEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS

**RPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPP*V************KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTE*****************ESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGV****DRKADQEALEKLTCMVEERLK*************************************************************************************************************QRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRD****L***********************************************************************************************************************************************************************ILDRDRDREHGL***KTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVET********

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MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTKSPENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDSRKRWRRSVLEEKRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNAVNGSLAEESAVESKGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS

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	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		752	2.2.26 [Sep-21-2011]
P49756		843	RNA-binding protein 25 OS	yes	no	0.107	0.096	0.451	4e-24
B2RY56		838	RNA-binding protein 25 OS	yes	no	0.107	0.096	0.451	5e-24
Q8IDX6		3130	Reticulocyte-binding prot	no	no	0.240	0.057	0.236	1e-06

>sp\|P49756\|RBM25_HUMAN RNA-binding protein 25 OS=Homo sapiens GN=RBM25 PE=1 SV=3	Back alignment and function desciption

 Score =  114 bits (284), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 47/104 (45%), Positives = 72/104 (69%)

Query: 644 KQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSST 703
           K LI+ IP  K ELF+Y ++W++ D   +  R+RPWI+KKI E++GEEE TLVD++ S  
Sbjct: 739 KSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKV 798

Query: 704 QDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLA 747
             H     +L+ +  +LD+EAE+F++KMWR+LI+E +  + GL 
Sbjct: 799 MAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGLV 842

RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5'-splice site (5'-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5'-ss usage through the 5'-CGGGCA-3' RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5' ss in a 5'-CGGGCA-3'-dependent manner. Binds to the exonic splicing enhancer 5'-CGGGCA-3' RNA sequence located within exon 2 of the BCL2L1 pre-mRNA.
Homo sapiens (taxid: 9606)

>sp\|B2RY56\|RBM25_MOUSE RNA-binding protein 25 OS=Mus musculus GN=Rbm25 PE=1 SV=2	Back alignment and function description

>sp\|Q8IDX6\|RBP2A_PLAF7 Reticulocyte-binding protein 2 homolog a OS=Plasmodium falciparum (isolate 3D7) GN=PF13_0198 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		752
255568764		948	conserved hypothetical protein [Ricinus	0.985	0.781	0.739	0.0
225424679		958	PREDICTED: uncharacterized protein LOC10	0.985	0.773	0.677	0.0
296086551		828	unnamed protein product [Vitis vinifera]	0.988	0.897	0.680	0.0
357485911		771	RNA-binding protein [Medicago truncatula	0.989	0.964	0.646	0.0
224111298		894	predicted protein [Populus trichocarpa]	0.982	0.826	0.686	0.0
356501735		765	PREDICTED: uncharacterized protein LOC10	0.980	0.963	0.661	0.0
356497763		927	PREDICTED: uncharacterized protein LOC10	0.984	0.798	0.669	0.0
449434915		770	PREDICTED: uncharacterized protein LOC10	0.989	0.966	0.668	0.0
449513686		968	PREDICTED: uncharacterized LOC101214372	0.989	0.768	0.668	0.0
307135981		770	RNA binding motif protein [Cucumis melo	0.972	0.949	0.669	0.0

>gi\|255568764\|ref\|XP_002525353.1\| conserved hypothetical protein [Ricinus communis] gi\|223535316\|gb\|EEF36991.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

 Score =  912 bits (2356), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 572/774 (73%), Positives = 647/774 (83%), Gaps = 33/774 (4%)

Query: 1   MVRPAFPPRPPGPVGVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVG 60
           MVRP FPPRP G +G+LP+ +R  VPGIPGVRP+  P+VRP  +P+VTPAEKP T VYVG
Sbjct: 186 MVRPMFPPRPLGALGILPAASRLLVPGIPGVRPV--PIVRPG-VPSVTPAEKPLTTVYVG 242

Query: 61  KIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFN 120
           KIAPT D+DF+LS+L+ CG VKSWKR Q P++GTP+GFGFCEFESAEGVLRALRLL+KFN
Sbjct: 243 KIAPTVDNDFMLSLLRFCGPVKSWKRPQDPNDGTPRGFGFCEFESAEGVLRALRLLSKFN 302

Query: 121 IDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNEPTK--S 178
           IDGQEL+L V+QATREYLERYV+KKTEN K LKE Q  GA KED    + EK+EP K   
Sbjct: 303 IDGQELVLNVNQATREYLERYVEKKTENLKNLKENQAPGAAKED---GTAEKSEPPKIIG 359

Query: 179 PENLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTA 238
            ++ KD +  NKE++DP NFG+VT+ED++ D+EALEKLT M+EERLKTNPLPPPPPQT A
Sbjct: 360 EDSNKDGDKVNKENNDPANFGIVTDEDKEGDKEALEKLTSMIEERLKTNPLPPPPPQTPA 419

Query: 239 DGSGISNSELPAKARDGDSDVDMIRNDIAEDKLDDETTSD-TKASDHDRPETSSPDRSR- 296
            GSG +NSE PAK+RDGDSD D  R   AEDK DDET SD   A++ DRP T SPDRS  
Sbjct: 420 HGSG-TNSEFPAKSRDGDSDADTTRQ--AEDKNDDETISDHIPATEQDRPGTCSPDRSSR 476

Query: 297 --VHDRRGRDKERDLKREKEREIDRYEREAERERVRKEREQRRKIEEAEREYERCLKDWE 354
                 R RD+ERDLKREKEREI+RYEREAERER+RKEREQRRKIEEAEREYE  LKDWE
Sbjct: 477 KYDRRSRERDRERDLKREKEREIERYEREAERERIRKEREQRRKIEEAEREYEERLKDWE 536

Query: 355 YREREREKERQYEKEKEKERERKRKKEILYDEEEDEDDSRKRWRRSVLEEKRRKRIREKE 414
           YRERE+EK+RQY+KEK+KER+RKR+KEILYDEE D+DDSRK+WRRS L++KRRK+ REKE
Sbjct: 537 YREREKEKQRQYDKEKDKERDRKRRKEILYDEEGDDDDSRKKWRRSALDDKRRKKQREKE 596

Query: 415 EDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGS----LAEESAVESK-- 468
           +D+AD ++EEEE+A AKRRAEEE++QQQQ DA KL  D  +NG+    L EE  VESK  
Sbjct: 597 DDMADRLKEEEEMAEAKRRAEEERIQQQQTDAFKLSFDQVMNGTEMKVLVEEVYVESKDK 656

Query: 469 ----------GDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSV 518
                     GD   QNG  DEST   +  SD+RQSGN PARKLGFGLVGSGKR AVPSV
Sbjct: 657 VVEQDNEGDLGDGVLQNGTVDESTVTSMTESDIRQSGNAPARKLGFGLVGSGKRAAVPSV 716

Query: 519 FHVEDDDDADKDKKMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKE 578
           FH EDDDDADKDKKMRPLVPIDYSTEELQA QP VSGA PP +AAAAEFAKRISNV  KE
Sbjct: 717 FHEEDDDDADKDKKMRPLVPIDYSTEELQAVQPTVSGAQPP-IAAAAEFAKRISNVTPKE 775

Query: 579 EKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNK 638
           EK D ERERSRR HDRSSQR++DR+DED  R RDE K+KIL+RDR+REHGLDKVKTPD +
Sbjct: 776 EKPDMERERSRRSHDRSSQRDRDRNDEDAIRMRDE-KDKILERDRNREHGLDKVKTPDKQ 834

Query: 639 KLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDY 698
           KLLDAKQLIDMIPKTK+ELFSYEINWAVYD+HELHERMRPWISKKITEFLGEEETTLVDY
Sbjct: 835 KLLDAKQLIDMIPKTKDELFSYEINWAVYDRHELHERMRPWISKKITEFLGEEETTLVDY 894

Query: 699 IVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS 752
           IVSST+DHVKASQMLE+LQ+ILDDEAEMFVLKMWRMLIFEIKKVETGLALRS+S
Sbjct: 895 IVSSTRDHVKASQMLEMLQSILDDEAEMFVLKMWRMLIFEIKKVETGLALRSRS 948

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225424679\|ref\|XP_002264457.1\| PREDICTED: uncharacterized protein LOC100263874 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|296086551\|emb\|CBI32140.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|357485911\|ref\|XP_003613243.1\| RNA-binding protein [Medicago truncatula] gi\|355514578\|gb\|AES96201.1\| RNA-binding protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|224111298\|ref\|XP_002315807.1\| predicted protein [Populus trichocarpa] gi\|222864847\|gb\|EEF01978.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356501735\|ref\|XP_003519679.1\| PREDICTED: uncharacterized protein LOC100803051 [Glycine max]	Back alignment and taxonomy information

>gi\|356497763\|ref\|XP_003517728.1\| PREDICTED: uncharacterized protein LOC100809428 [Glycine max]	Back alignment and taxonomy information

>gi\|449434915\|ref\|XP_004135241.1\| PREDICTED: uncharacterized protein LOC101214372 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449513686\|ref\|XP_004164394.1\| PREDICTED: uncharacterized LOC101214372 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|307135981\|gb\|ADN33840.1\| RNA binding motif protein [Cucumis melo subsp. melo]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		752
TAIR\|locus:2195568		899	AT1G60200 [Arabidopsis thalian	0.378	0.317	0.591	8.1e-136
MGI\|MGI:1914289		838	Rbm25 "RNA binding motif prote	0.187	0.168	0.395	3.3e-39
UNIPROTKB\|E1BSR5		782	RBM25 "Uncharacterized protein	0.187	0.180	0.402	7.6e-39
UNIPROTKB\|E1BHM5		843	RBM25 "Uncharacterized protein	0.187	0.167	0.395	9e-39
UNIPROTKB\|P49756		843	RBM25 "RNA-binding protein 25"	0.187	0.167	0.395	9e-39
ZFIN\|ZDB-GENE-030131-5547		833	rbm25 "RNA binding motif prote	0.296	0.267	0.297	6.2e-36
WB\|WBGene00012245		707	W04D2.6 [Caenorhabditis elegan	0.174	0.185	0.364	1.4e-35
FB\|FBgn0028474		998	CG4119 [Drosophila melanogaste	0.223	0.168	0.352	8.7e-32
RGD\|1308755		354	Rbm25 "RNA binding motif prote	0.187	0.398	0.395	1.2e-29
DICTYBASE\|DDB_G0269926		724	DDB_G0269926 "splicing factor	0.220	0.229	0.335	1e-26

TAIR\|locus:2195568 AT1G60200 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 836 (299.3 bits), Expect = 8.1e-136, Sum P(3) = 8.1e-136
 Identities = 174/294 (59%), Positives = 213/294 (72%)

Query:   462 ESAVESKGDPSSQNGNGDESTNVPIAASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHV 521
             ESA E       +NG+G+ES  +    ++     + P++KLGFGLVGSGKRT+VPSVF+ 
Sbjct:   612 ESANEHHAADFEENGSGNESMAID---NNSGSEAHAPSKKLGFGLVGSGKRTSVPSVFYE 668

Query:   522 EXXXXXXXXXXMRPLVPIDYSTEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKS 581
             E          M+PLVPIDYSTEE +A     SG  PP+LA AAEFAKRIS+ N KEE  
Sbjct:   669 EDEDEARKAKKMKPLVPIDYSTEEQEAVAHGGSGNTPPHLALAAEFAKRISSTNPKEETI 728

Query:   582 DAERERSRRLHDRSSQREKDRS---DEDNNRTRDEHKEKILDRDRDREHGLDKVKTPDNK 638
             + E++RSRR HD++S R+++R    D D +R RD            +E G  K K  D K
Sbjct:   729 ETEKQRSRRSHDKASHRDRERERERDRDRDRVRDRGDGHSGPTKDAKESG--KAKIIDTK 786

Query:   639 KLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDY 698
               LDAKQLID IPKTKE+LFSYEINWA+YDKH++HERMRPWISKKI EFLGEEE TLVD+
Sbjct:   787 -FLDAKQLIDTIPKTKEDLFSYEINWAMYDKHQVHERMRPWISKKIMEFLGEEEATLVDF 845

Query:   699 IVSSTQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLALRSKS 752
             IVS+TQ HV+ASQMLELLQ+ILD+EAEMFVLKMWRMLIFEIK+VE G+ ++SK+
Sbjct:   846 IVSNTQQHVQASQMLELLQSILDEEAEMFVLKMWRMLIFEIKRVEAGVPVKSKA 899

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0006397 "mRNA processing" evidence=IEA

MGI\|MGI:1914289 Rbm25 "RNA binding motif protein 25" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BSR5 RBM25 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BHM5 RBM25 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|P49756 RBM25 "RNA-binding protein 25" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-5547 rbm25 "RNA binding motif protein 25" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

WB\|WBGene00012245 W04D2.6 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

FB\|FBgn0028474 CG4119 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

RGD\|1308755 Rbm25 "RNA binding motif protein 25" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0269926 DDB_G0269926 "splicing factor PWI domain-containing protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

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:
	estExt_fgenesh4_pg.C_LG_X0863	hypothetical protein (894 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		752
cd12446		84	cd12446, RRM_RBM25, RNA recognition motif in eukar	8e-35
smart00311		74	smart00311, PWI, PWI, domain in splicing factors	2e-22
pfam01480		74	pfam01480, PWI, PWI domain	2e-14
smart00360		73	smart00360, RRM, RNA recognition motif	6e-12
cd00590		72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-09
cd12398		75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-09
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-09
cd12371		77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-08
cd12671		75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-08
cd12290		80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-07
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-07
PRK12704		520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-06
pfam00076		70	pfam00076, RRM_1, RNA recognition motif	1e-06
TIGR01622		457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-06
pfam14259		69	pfam14259, RRM_6, RNA recognition motif (a	8e-06
TIGR01645		612	TIGR01645, half-pint, poly-U binding splicing fact	1e-05
cd12243		71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-05
pfam13868		349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-05
cd12344		81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-05
PRK12678		672	PRK12678, PRK12678, transcription termination fact	1e-05
cd12365		73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-05
TIGR03319		514	TIGR03319, RNase_Y, ribonuclease Y	2e-05
cd12448		73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
PRK12705		508	PRK12705, PRK12705, hypothetical protein; Provisio	3e-05
pfam02463		1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-05
cd12352		72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	3e-05
PRK10811		1068	PRK10811, rne, ribonuclease E; Reviewed	4e-05
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
cd12450		77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-05
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-05
pfam13868		349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	7e-05
COG5271		4600	COG5271, MDN1, AAA ATPase containing von Willebran	8e-05
pfam09756		189	pfam09756, DDRGK, DDRGK domain	1e-04
pfam02463		1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
PRK10811		1068	PRK10811, rne, ribonuclease E; Reviewed	2e-04
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
pfam13904		261	pfam13904, DUF4207, Domain of unknown function (DU	2e-04
COG3064		387	COG3064, TolA, Membrane protein involved in colici	2e-04
pfam02463		1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
TIGR02169		1164	TIGR02169, SMC_prok_A, chromosome segregation prot	3e-04
TIGR02168		1179	TIGR02168, SMC_prok_B, chromosome segregation prot	3e-04
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
cd12306		73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-04
cd12399		78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-04
cd12384		76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-04
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
COG2268		548	COG2268, COG2268, Uncharacterized protein conserve	5e-04
PTZ00266		1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	5e-04
pfam13868		349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-04
cd12649		81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	6e-04
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-04
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-04
pfam05557		722	pfam05557, MAD, Mitotic checkpoint protein	7e-04
cd12355		80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-04
pfam13868		349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	8e-04
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-04
TIGR02169		1164	TIGR02169, SMC_prok_A, chromosome segregation prot	8e-04
cd12370		76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	8e-04
TIGR02794		346	TIGR02794, tolA_full, TolA protein	8e-04
PRK12585		197	PRK12585, PRK12585, putative monovalent cation/H+	9e-04
pfam13868		349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.001
pfam02463		1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
pfam02463		1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
PRK07735		430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	0.001
COG0724		306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.001
cd12318		82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.001
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
TIGR02169		1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
pfam08648		158	pfam08648, DUF1777, Protein of unknown function (D	0.002
PRK00247		429	PRK00247, PRK00247, putative inner membrane protei	0.002
TIGR00927		1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.002
cd12336		75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.002
cd12382		80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.002
pfam03154		979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
cd12271		72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.003
COG4942		420	COG4942, COG4942, Membrane-bound metallopeptidase	0.003
cd12240		78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.003
cd12390		92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	0.003
cd12273		71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.003
COG2433		652	COG2433, COG2433, Uncharacterized conserved protei	0.003
cd12447		76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.003
TIGR01622		457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.004
TIGR02168		1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004

>gnl\|CDD\|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins	Back alignment and domain information

 Score =  126 bits (319), Expect = 8e-35
 Identities = 44/84 (52%), Positives = 55/84 (65%)

Query: 55  TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 114
           T V+VG I      DF+  +L+ CG V SWKR + PS G  K FGFCEFE  EG LRALR
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 115 LLNKFNIDGQELMLKVDQATREYL 138
           LLN   + G++L++KVD  TR+ L
Sbjct: 61  LLNGLELGGKKLLVKVDAKTRKLL 84

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl\|CDD\|214609 smart00311, PWI, PWI, domain in splicing factors	Back alignment and domain information

>gnl\|CDD\|216523 pfam01480, PWI, PWI domain	Back alignment and domain information

>gnl\|CDD\|214636 smart00360, RRM, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily	Back alignment and domain information

>gnl\|CDD\|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|237177 PRK12704, PRK12704, phosphodiesterase; Provisional	Back alignment and domain information

>gnl\|CDD\|215696 pfam00076, RRM_1, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family	Back alignment and domain information

>gnl\|CDD\|222631 pfam14259, RRM_6, RNA recognition motif (a	Back alignment and domain information

>gnl\|CDD\|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family	Back alignment and domain information

>gnl\|CDD\|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family	Back alignment and domain information

>gnl\|CDD\|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin	Back alignment and domain information

>gnl\|CDD\|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|188306 TIGR03319, RNase_Y, ribonuclease Y	Back alignment and domain information

>gnl\|CDD\|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|237178 PRK12705, PRK12705, hypothetical protein; Provisional	Back alignment and domain information

>gnl\|CDD\|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	Back alignment and domain information

>gnl\|CDD\|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR	Back alignment and domain information

>gnl\|CDD\|236766 PRK10811, rne, ribonuclease E; Reviewed	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin	Back alignment and domain information

>gnl\|CDD\|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|220383 pfam09756, DDRGK, DDRGK domain	Back alignment and domain information

>gnl\|CDD\|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	Back alignment and domain information

>gnl\|CDD\|236766 PRK10811, rne, ribonuclease E; Reviewed	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)	Back alignment and domain information

>gnl\|CDD\|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>gnl\|CDD\|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	Back alignment and domain information

>gnl\|CDD\|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type	Back alignment and domain information

>gnl\|CDD\|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins	Back alignment and domain information

>gnl\|CDD\|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins	Back alignment and domain information

>gnl\|CDD\|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>gnl\|CDD\|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional	Back alignment and domain information

>gnl\|CDD\|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin	Back alignment and domain information

>gnl\|CDD\|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|218636 pfam05557, MAD, Mitotic checkpoint protein	Back alignment and domain information

>gnl\|CDD\|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins	Back alignment and domain information

>gnl\|CDD\|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type	Back alignment and domain information

>gnl\|CDD\|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins	Back alignment and domain information

>gnl\|CDD\|234017 TIGR02794, tolA_full, TolA protein	Back alignment and domain information

>gnl\|CDD\|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter subunit G; Reviewed	Back alignment and domain information

>gnl\|CDD\|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin	Back alignment and domain information

>gnl\|CDD\|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	Back alignment and domain information

>gnl\|CDD\|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated	Back alignment and domain information

>gnl\|CDD\|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type	Back alignment and domain information

>gnl\|CDD\|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)	Back alignment and domain information

>gnl\|CDD\|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated	Back alignment and domain information

>gnl\|CDD\|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	Back alignment and domain information

>gnl\|CDD\|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins	Back alignment and domain information

>gnl\|CDD\|217393 pfam03154, Atrophin-1, Atrophin-1 family	Back alignment and domain information

>gnl\|CDD\|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp	Back alignment and domain information

>gnl\|CDD\|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>gnl\|CDD\|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family	Back alignment and domain information

>gnl\|CDD\|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		752
KOG2253		668	consensus U1 snRNP complex, subunit SNU71 and rela	100.0
PF01480		77	PWI: PWI domain; InterPro: IPR002483 The PWI domai	99.75
smart00311		74	PWI PWI, domain in splicing factors.	99.72
KOG2146		354	consensus Splicing coactivator SRm160/300, subunit	99.69
KOG4661		940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.49
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	99.48
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.47
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	99.45
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.4
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	99.37
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.36
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.32
KOG0122		270	consensus Translation initiation factor 3, subunit	99.31
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.21
PLN03213		759	repressor of silencing 3; Provisional	99.21
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.2
KOG0149		247	consensus Predicted RNA-binding protein SEB4 (RRM	99.2
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.19
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	99.19
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.19
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	99.18
PLN03120		260	nucleic acid binding protein; Provisional	99.18
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	99.13
smart00362		72	RRM_2 RNA recognition motif.	99.12
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.12
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.12
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	99.12
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.11
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	99.11
KOG0107		195	consensus Alternative splicing factor SRp20/9G8 (R	99.09
KOG4207		256	consensus Predicted splicing factor, SR protein su	99.09
COG0724		306	RNA-binding proteins (RRM domain) [General functio	99.07
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.07
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.06
PLN03121		243	nucleic acid binding protein; Provisional	99.06
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.06
smart00360		71	RRM RNA recognition motif.	99.05
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.04
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.03
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.01
KOG0130		170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.0
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	99.0
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.99
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	98.98
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	98.97
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	98.94
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	98.92
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.92
KOG0111		298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.92
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.91
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	98.9
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.88
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.77
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	98.77
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	98.77
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.76
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.75
smart00361		70	RRM_1 RNA recognition motif.	98.71
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.7
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	98.69
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.68
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.66
KOG4208		214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.62
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.58
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.54
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	98.53
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.52
KOG1457		284	consensus RNA binding protein (contains RRM repeat	98.51
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.47
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.43
KOG1548		382	consensus Transcription elongation factor TAT-SF1	98.41
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.38
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	98.33
KOG0153		377	consensus Predicted RNA-binding protein (RRM super	98.31
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	98.29
KOG0226		290	consensus RNA-binding proteins [General function p	98.28
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.26
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	98.25
KOG0151		877	consensus Predicted splicing regulator, contains R	98.22
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	98.21
KOG0533		243	consensus RRM motif-containing protein [RNA proces	98.15
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	98.15
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.14
KOG4209		231	consensus Splicing factor RNPS1, SR protein superf	98.09
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	98.05
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	97.92
KOG4454		267	consensus RNA binding protein (RRM superfamily) [G	97.92
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	97.82
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.79
KOG4660		549	consensus Protein Mei2, essential for commitment t	97.65
KOG1995		351	consensus Conserved Zn-finger protein [General fun	97.61
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	97.57
KOG2253		668	consensus U1 snRNP complex, subunit SNU71 and rela	97.43
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	97.31
KOG4676		479	consensus Splicing factor, arginine/serine-rich [R	97.28
KOG4849		498	consensus mRNA cleavage factor I subunit/CPSF subu	97.16
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.14
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	97.05
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	97.02
KOG1924		1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	97.01
KOG1457		284	consensus RNA binding protein (contains RRM repeat	96.88
KOG3152		278	consensus TBP-binding protein, activator of basal	96.85
KOG1029		1118	consensus Endocytic adaptor protein intersectin [S	96.83
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	96.74
KOG4210		285	consensus Nuclear localization sequence binding pr	96.72
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.71
KOG1924		1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	96.67
KOG2314		698	consensus Translation initiation factor 3, subunit	96.42
KOG2416		718	consensus Acinus (induces apoptotic chromatin cond	96.41
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	96.3
KOG4676		479	consensus Splicing factor, arginine/serine-rich [R	96.25
KOG1855		484	consensus Predicted RNA-binding protein [General f	96.22
COG5175		480	MOT2 Transcriptional repressor [Transcription]	95.95
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	95.91
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	95.62
KOG1548		382	consensus Transcription elongation factor TAT-SF1	95.4
PF08952		146	DUF1866: Domain of unknown function (DUF1866) ; In	95.37
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	95.27
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	95.0
PF05172		100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.88
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	94.55
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	94.19
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	93.96
PF14605		53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	93.51
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	93.34
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	93.08
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	92.84
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	92.75
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	92.68
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	92.56
PTZ00266		1021	NIMA-related protein kinase; Provisional	91.91
KOG0115		275	consensus RNA-binding protein p54nrb (RRM superfam	91.58
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	91.07
KOG1029		1118	consensus Endocytic adaptor protein intersectin [S	91.06
PTZ00266		1021	NIMA-related protein kinase; Provisional	91.0
KOG1996		378	consensus mRNA splicing factor [RNA processing and	90.97
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	90.57
KOG4285		350	consensus Mitotic phosphoprotein [Cell cycle contr	90.51
COG5178		2365	PRP8 U5 snRNP spliceosome subunit [RNA processing	89.89
KOG2068		327	consensus MOT2 transcription factor [Transcription	89.19
PF15023		166	DUF4523: Protein of unknown function (DUF4523)	86.75
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	86.32
PF10309		62	DUF2414: Protein of unknown function (DUF2414); In	84.66
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	84.15
KOG4574		1007	consensus RNA-binding protein (contains RRM and Pu	83.12
PF03467		176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	82.13
KOG2202		260	consensus U2 snRNP splicing factor, small subunit,	80.32

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=1.3e-67  Score=587.12  Aligned_cols=633  Identities=32%  Similarity=0.476  Sum_probs=374.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEccCCCCCCHHHHHHHHhhcCCeeEEEEeecCCCCC
Q 004460           15 GVLPSVARPPVPGIPGVRPIMPPVVRPVPLPTVTPAEKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGT   94 (752)
Q Consensus        15 g~~P~~~~Pp~p~~pg~~P~~~~~~rp~~~p~~~~~~~~~~tVfVgNLp~~vte~~L~~lFs~~G~I~~~ki~~d~~tGk   94 (752)
                      |+...+++|.+|++|++.+.+| . .++..|.. ..-++..+||||||...+....+..++..||.|.+|+++.      
T Consensus         4 ~~~q~a~~P~~~~~~~~~~~~p-~-~~p~qp~~-~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~------   74 (668)
T KOG2253|consen    4 GNTQAAGMPMMPQVPMVGNGVP-Y-VVPIQPVF-QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK------   74 (668)
T ss_pred             ccccCCCCCCCCCCccccCCcc-c-ccCCcccc-cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh------
Confidence            3444455555666666555554 1 11112222 2234578999999999999999999999999999998754      


Q ss_pred             CccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEeecchHHHHHHHHHHhhhhhhhhhhccccCCCCccccccccccCC
Q 004460           95 PKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQATREYLERYVDKKTENTKKLKETQDAGAGKEDESVQSVEKNE  174 (752)
Q Consensus        95 ~kGfgFVeF~~~esA~~Al~~Lng~~I~Gr~L~V~~a~s~kk~le~~k~kkke~~~~~k~~~~~~~~~~~~~~~~~~~~~  174 (752)
                         ||||.|..+....+|++.|+...++|..|.++++..+   +        ++.+..+..+            ...+..
T Consensus        75 ---fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d~q~---~--------~n~~k~~~~~------------~~~~~~  128 (668)
T KOG2253|consen   75 ---FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVDEQT---I--------ENADKEKSIA------------NKESHK  128 (668)
T ss_pred             ---hcccchhhHHHHHHHHHHhcccCCCcchhhccchhhh---h--------cCccccccch------------hhhhcc
Confidence               9999999999999999999999999999999876211   1        0000000000            111112


Q ss_pred             CCCCCc---------ccccCCCCCCCCCCCccccccchhhhhhhHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCCCCCCC
Q 004460          175 PTKSPE---------NLKDNETGNKESHDPTNFGVVTEEDRKADQEALEKLTCMVEERLKTNPLPPPPPQTTADGSGISN  245 (752)
Q Consensus       175 ~~~~~~---------~~~~gd~~~~~~~~v~~~~~~~~ed~~~d~~~~Eki~~~~eer~~~~~~~~~~~~~~~~~~~~~~  245 (752)
                      |.|+.+         ....++...+.++.+++-..++.....+|.-.++.+.+.+++......++.++..+...     .
T Consensus       129 f~p~~srr~e~i~~k~~~l~~~~~~~~~~is~s~~s~~~~~e~d~h~~e~~~~~~~s~~~~~~~~~~~~~~~e~-----~  203 (668)
T KOG2253|consen  129 FVPSSSRRQESIQNKPLSLDEQIHKKSLQISSSAASRRQIAEADDHCLELEKTETESNSALSKEAESKKSPFED-----T  203 (668)
T ss_pred             cCCchhHHHHHhhccccchhHHHHHHHHhccchhhhhhhhHHHHHHHHHHHHhhcccccccCcccccccCchhh-----h
Confidence            222111         11111111222223333222323333334433444444443332211111111100000     0


Q ss_pred             CCCCcCcCCCCCcchhccchhcccccccccccccccCCCCCCCCCCCCccccccccccchhHHHHHHhhHHHHHHHHHHH
Q 004460          246 SELPAKARDGDSDVDMIRNDIAEDKLDDETTSDTKASDHDRPETSSPDRSRVHDRRGRDKERDLKREKEREIDRYEREAE  325 (752)
Q Consensus       246 ~e~p~~~rd~~~~~d~~k~~~~~~~~~~~~~~~~~~~e~er~~~~~~~r~r~r~r~~r~r~re~~r~~ere~~r~~r~re  325 (752)
                      .  +  .+.+.+..+             .+ ......+     ..+..+++.   +++.+...+.|...+.+++.+....
T Consensus       204 ~--~--s~~~~s~td-------------s~-~~~d~~~-----~~s~~~n~~---rd~sr~~~r~R~~~r~Re~~e~~ed  257 (668)
T KOG2253|consen  204 K--D--SKRSFSSTD-------------SG-SESDSAE-----VNSSSLNYC---RDRSRFDRRSRNDRRIRERLEKNED  257 (668)
T ss_pred             c--h--hhhhhcccC-------------cc-ccchhhh-----hcccccccc---hhhccchhhhHHHHHHHHHhhhccc
Confidence            0  0  000000000             00 0000000     000111111   1111111111111111111111112


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHhhcccchhhhhhhhhhh
Q 004460          326 RERVRKEREQRRKIEEAEREYERCLKDWEYREREREKERQYEKEKEKERE------RKRKKEILYDEEEDEDDSRKRWRR  399 (752)
Q Consensus       326 rer~r~~r~~~~k~re~E~~y~er~r~we~RER~r~~~re~ekerere~e------r~r~ke~l~d~dderd~~rk~~r~  399 (752)
                      .+..++.|...++..++|+||+.|++.|+.||+.+++.+++++.+|+++.      ++++++|++||||++|+ .+||++
T Consensus       258 ~~~~re~r~~~~~~~~~E~Ayq~rl~~we~Rer~~~Ke~eke~~ke~~r~~~~~ke~kr~k~~~ed~DD~rdd-~~y~r~  336 (668)
T KOG2253|consen  258 SDEYREDRAATIKSVDPEKAYQTRLVFWEIREQTKEKEREKERLKEKSRQYKREKEAKRLKEFLEDYDDERDD-PKYYRG  336 (668)
T ss_pred             hHHHHHhhhhhhhccChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhcchhhhh-HHHHHH
Confidence            24566778889999999999999999999999998555554444444433      36899999999999997 799999


Q ss_pred             hHHHHHHHHHhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhhhhhccCCCc-------cccccc------c
Q 004460          400 SVLEEKRRKRIREKEEDLADEVREEEEIAVAKRRAEEEQLQQQQRDALKLLSDNAVNGSL-------AEESAV------E  466 (752)
Q Consensus       400 ~~~~~R~r~r~rE~e~D~~DR~rE~eE~~e~~~r~~ee~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~------~  466 (752)
                      ++|.+|++++.+|+|+|.+||.+|++|++|+|++..++..+.....+...+.........       .+....      +
T Consensus       337 s~l~~r~r~~~re~Ead~~dR~qeqee~~E~Kr~~~~~~~~~~~~e~~r~~~~~~~~~~~~~~~a~~ke~e~~~~~~~~q  416 (668)
T KOG2253|consen  337 SALQERLRDREREAEADRRDRHQEQEELEEIKRRHSEEEAEDPSAEEERNMEEEEALDEEEDDEAVRKEPEERDLEESHQ  416 (668)
T ss_pred             HHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHhhhcccccchHHHHHHhhhhhhcchhhHHHHhhCcccccCccccc
Confidence            999999999999999999999999999999999987765432221111111111100000       000000      0


Q ss_pred             cCCCCCCCCCCCCCCCCccc----cccccccCCCcccccccccccCCCCccccCccCCCCCCcchhhcccCCCcccccCC
Q 004460          467 SKGDPSSQNGNGDESTNVPI----AASDMRQSGNVPARKLGFGLVGSGKRTAVPSVFHVEDDDDADKDKKMRPLVPIDYS  542 (752)
Q Consensus       467 ~~~~~~~~~~~~d~~~~~~~----~~~~~~~~~~~~~~k~~~~~~~~~kr~~v~~vf~~~ddee~~~~~~kr~LvPi~y~  542 (752)
                      .-+....+....++.-..+.    -+...-.-..+|...+++|+++++.+..++.+|-.-+...+++...+..++||.|+
T Consensus       417 ~~~e~a~~~~~~~eee~~s~r~~~~~d~~~~i~~~ps~~~~s~~~~~n~~~~~~~~~~~~~e~~~~es~n~~~n~p~~~~  496 (668)
T KOG2253|consen  417 RLGESANQEHSNDEEEIKSQRDDYKPDENDHISHAPSASLASGLVDANDRDSSPRGFKERHEREDDESLNKKINRPILAS  496 (668)
T ss_pred             hHHhhhhhccccchhhcccchhhhhhhhhhhhhcCchhhhhhhccCCCCCCcccccccccccCcchhhhccccccccccc
Confidence            00000000011111000000    00011133566777888899888899999999887666555677778899999998


Q ss_pred             hHHHhhccCCCCCCCCCchHHHHHHHHHhcccCchhhhchHHHHhhhhcccccchhhccccccccchhhhhhhhhhhccc
Q 004460          543 TEELQAAQPHVSGANPPNLAAAAEFAKRISNVNSKEEKSDAERERSRRLHDRSSQREKDRSDEDNNRTRDEHKEKILDRD  622 (752)
Q Consensus       543 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~  622 (752)
                      .....+..     ++.+.+..++.   -+..|++                     ...+ .++|.+-+... ++++++.+
T Consensus       497 ~~~q~~~g-----~sa~~~~i~~k---k~~~~~v---------------------~~~~-~d~Dk~v~~~k-k~vp~dyd  545 (668)
T KOG2253|consen  497 IQNQDEIG-----PSASPIPIAKK---KLPETGV---------------------FRED-DDEDKNVHEKK-KLVPLDYD  545 (668)
T ss_pred             cccccccc-----CCCCccccccc---cCCCccc---------------------cccc-CCcccccchhh-hcccccCC
Confidence            75433322     22111111111   0111110                     0111 12222333333 77777776


Q ss_pred             cccccccccccCcchhhhhhHHhhhhcCCCCchhhhcccccccccchhhhhhhhhhhHHHHHHHhhCCchhHHHHHHHHh
Q 004460          623 RDREHGLDKVKTPDNKKLLDAKQLIDMIPKTKEELFSYEINWAVYDKHELHERMRPWISKKITEFLGEEETTLVDYIVSS  702 (752)
Q Consensus       623 ~~~~~~~~~~~~~~~~~~~~~~~l~~~ip~~k~~lf~~~v~w~~vd~~~~~~~~~pwi~kki~e~lG~ee~~lvd~i~~~  702 (752)
                      ++..- ...+.+.+ .|..++++||.+||++|++||+|+|+|+.||.-+|+.+|+|||+|||+||||++|++||||||++
T Consensus       546 ~n~~~-~~~~~~nd-eK~~~~ksLI~tIP~~keeLf~~pidw~~ld~~lm~~rirpwV~KKIiEflGeeE~tLVdFI~s~  623 (668)
T KOG2253|consen  546 RNQAR-AHSGESND-EKRKRIKSLIETIPTEKEELFAYPIDWDELDSILMNERIRPWVNKKIIEFLGEEEDTLVDFICSN  623 (668)
T ss_pred             hhhcc-cccCCcch-hHHHHHHhhcccCCcchHHHhhCcccHHHHhhHHHHHHHHHHHHHHHHHHhCCcchhHHHHHHHH
Confidence            64211 11122222 24568999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhhccc
Q 004460          703 TQDHVKASQMLELLQTILDDEAEMFVLKMWRMLIFEIKKVETGLA  747 (752)
Q Consensus       703 l~~~~~p~~l~~~l~~~ld~~a~~fv~~lWr~life~~~~~~gl~  747 (752)
                      |+.|.+||+||.+|.++||++|++||+|||||||||+.+++.||+
T Consensus       624 i~~h~~~q~iL~dl~~ilDEdAE~FV~KmWRlLiyel~ar~~g~~  668 (668)
T KOG2253|consen  624 IRQHSSPQQILDDLAMILDEDAEVFVVKMWRLLIYELGARKLGLT  668 (668)
T ss_pred             HHhcCCHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhhhhhccCC
Confidence            999999999999999999999999999999999999999999985

>PF01480 PWI: PWI domain; InterPro: IPR002483 The PWI domain, named after a highly conserved PWI tri-peptide located within its N-terminal region, is a ~80 amino acid module, which is found either at the N terminus or at the C terminus of eukaryotic proteins involved in pre-mRNA processing []	Back alignment and domain information

>smart00311 PWI PWI, domain in splicing factors	Back alignment and domain information

>KOG2146 consensus Splicing coactivator SRm160/300, subunit SRm160 (contains PWI domain) [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]	Back alignment and domain information

>PLN03134 glycine-rich RNA-binding protein 4; Provisional	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PF00076 RRM_1: RNA recognition motif	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>PLN03213 repressor of silencing 3; Provisional	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>PF14259 RRM_6: RNA recognition motif (a	Back alignment and domain information

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>PLN03120 nucleic acid binding protein; Provisional	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]	Back alignment and domain information

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]	Back alignment and domain information

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>PLN03121 nucleic acid binding protein; Provisional	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	Back alignment and domain information

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]	Back alignment and domain information

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability	Back alignment and domain information

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	Back alignment and domain information

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>smart00361 RRM_1 RNA recognition motif	Back alignment and domain information

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]	Back alignment and domain information

>PF13893 RRM_5: RNA recognition motif	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]	Back alignment and domain information

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	Back alignment and domain information

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	Back alignment and domain information

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]	Back alignment and domain information

>KOG0226 consensus RNA-binding proteins [General function prediction only]	Back alignment and domain information

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]	Back alignment and domain information

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]	Back alignment and domain information

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]	Back alignment and domain information

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]	Back alignment and domain information

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]	Back alignment and domain information

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]	Back alignment and domain information

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2	Back alignment and domain information

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]	Back alignment and domain information

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]	Back alignment and domain information

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]	Back alignment and domain information

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]	Back alignment and domain information

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]	Back alignment and domain information

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]	Back alignment and domain information

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes	Back alignment and domain information

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]	Back alignment and domain information

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	Back alignment and domain information

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	Back alignment and domain information

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]	Back alignment and domain information

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]	Back alignment and domain information

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]	Back alignment and domain information

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation	Back alignment and domain information

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]	Back alignment and domain information

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]	Back alignment and domain information

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]	Back alignment and domain information

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]	Back alignment and domain information

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]	Back alignment and domain information

>COG5175 MOT2 Transcriptional repressor [Transcription]	Back alignment and domain information

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	Back alignment and domain information

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function	Back alignment and domain information

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]	Back alignment and domain information

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []	Back alignment and domain information

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]	Back alignment and domain information

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	Back alignment and domain information

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif	Back alignment and domain information

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>PTZ00266 NIMA-related protein kinase; Provisional	Back alignment and domain information

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

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

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PTZ00266 NIMA-related protein kinase; Provisional	Back alignment and domain information

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]	Back alignment and domain information

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]	Back alignment and domain information

>KOG2068 consensus MOT2 transcription factor [Transcription]	Back alignment and domain information

>PF15023 DUF4523: Protein of unknown function (DUF4523)	Back alignment and domain information

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]	Back alignment and domain information

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function	Back alignment and domain information

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)	Back alignment and domain information

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]	Back alignment and domain information

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons	Back alignment and domain information

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]	Back alignment and domain information

Homologous Structure Templates