Citrus Sinensis ID: 002338

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-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930----

MVKVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTTASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEGMDDFEDSGHHKENSDIESEKDDTDEKPVAESLSVPNSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDRALGLGSASISSTKHGIETTQFDLSEEDKHVERTATVRDKPYISKAERRKLKKGQGSSVVDPKVEREKERGKDASSQPESIVRKTKIEGGKISRGQKGKLKKMKEKYGDQDEEERNIRMALLAVSTLTCTIGVT

cccccccHHHHHHHHHHHHHHccccEEEEEcccccEEEEEEEcccccccccccccEEEEEEcccEEEEccccccccccccHHHHHHHHHcccccEEEEEEccccEEEEEEEcccccEEEEEEEEEEcccEEEEcccccEEEEEccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccHHHHHHHHcccccHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHcccccccEEEccccccccccHHHHccccccEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEEcccEEEEEEcccHHHHHHHHHHcccccEEEEEccccccEEEEEcccccccccHHHHHHHHHHHHHHHccccccccccEEEEEccccccccccccccccEEEEEEcccccccccccEEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHccccccccccHHHHHHHHcccccccccccHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccccccccccc

cccHHccHHHHHHHHHHHHHHHcccHHEEEcccccEEEEEEEcccccccccccccEEEEEEccEEEEEccccccccccccHHHHHHHHHHHcccEHEEHHccccEEEEEEEcccccEEEEEEEEEccccEEEEccccEEEEEEEccccccccEEEEEEEEccHHHccccccccHHHHHHHHHHHccccccccHHHHHcccccccccHHHHHHHHHHccHHHHHHHHHHcccccccccHHHHHHHHcHccccHHHHHHHHHHccccccccHHHccHcHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEccccccccccccccccccEEHccccccHHHHcccccEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHccccccccEEEEEEcccccccccccccccccEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHccccHHEHHEEEEEEcccEEEEEcccHHHHHHHHHHHcccccEEEEEccccccEEEEEcccccccccHHHHHHHHHHHHHHHHHHHcccEEEEEEEcccccccccccccEccccEEEEEccccccccccEEEEEEEEEEcccccccccccHEEEccccccccccccccHHHHHHHHHHHccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHcccccEEEccc

MVKVRMNTADVAAEVKCLRRLIGmrcsnvydlspkTYIFKLMnssgvtesgeSEKVLLLMESGVRLHTTAyardkkntpsgfTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQgnilltdseFTVLTLLRShrdddkgvaimsrhrypTEICRVFERTTASKLHAALtsskepdanepdkvnedgnnvsnaskenlggqkggksfdlsknsnknsndgarakqptlKTVLGEalgygpalsehiildtglvpnmklsevnkleDNAIQVLVLAVAKFEDWLQdvisgdivpegYILMqnkhlgkdhpptesgsstqiydEFCPLLLNqfrsrefvkfeTFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEErkagnpvaglIDKLYLERNCMSLLlsnnldemddeektlpveKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLhgasstviknhrpeqpvppltlnqagcftvchsqawdskmvtsawwvyphqvsktaptgeyltvgsfmirgkknflpphplimgFGLLfrldesslgshlnerrvrgeeegmddfedsghhkensdiesekddtdekpvaeslsvpnsahpapshtnasnvdshefpaedktisngidskIFDIarnvaapvtpqLEDLIDRALglgsasisstkhgiettqfdlseedkhvertatvrdkpyiskaerrklkkgqgssvvdpkverekergkdassqpesIVRKTkieggkisrgqkgKLKKMKEKYGDQDEEERNIRMALLAVSTLTCTIGVT

mvkvrmntadvaaEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTtayardkkntpsgftlklrkhirtrrledvrqLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRshrdddkgvaimsrhrypteICRVFERTTASKLHAaltsskepdanepdkvnedgnnvsnaskenlggqkggksfdlSKNSnknsndgarakqptLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKeerkagnpvaglidklYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYElkkkqeskqektITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNerrvrgeeegmddfedsghhkensdiesekddtdEKPVAESLSVPNSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDRALGLGsasisstkhgiettqfdlseedkhvertatvrdkpyiskaerrklkkgqgssvvdpkverekergkdassqpesivrktkieggkisrgqkgklkkmkekygdqdeeeRNIRMALlavstltctigvt

MVKVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTTASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLsknsnknsnDGARAKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELkkkqeskqekTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEGMDDFEDSGHHKENSDIESEKDDTDEKPVAESLSVPNSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDRALGLGSASISSTKHGIETTQFDLSEEDKHVERTATVRDKPYISKAERRKLKKGQGSSVVDPKVEREKERGKDASSQPESIVRKTKIEGGKISRGQkgklkkmkekYGDQDEEERNIRMALLAVSTLTCTIGVT

********ADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNS**********KVLLLMESGVRLHTTAYARD***TPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTT*******************************************************************KTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQN****************QIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSK*************************************EVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNL***********VEKVEVDLALSAHANARRWYE***************************RLQILQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIK********PPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLD************************************************************************************IDSKIFDIARNVAAPVTPQLEDLIDRALGLG**************************************************************************************************************IRMALLAVSTLTCTIG**

**KVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTTAYARDK*NTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHR*****VAIMSRHRYPTEICRVFERTTASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKN******DGARAKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIE******************LNKIHMDQENR**TLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELKKKQES*********************************************NWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVS*T*****YLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLG***************************************************************************************************************************************************************************************************************KEKYGDQDEEERNIRMALL************

MVKVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTTASKL*****************VNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHL************TQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIE************DAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYEL************************KTRLQILQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEE******************************************************EFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDRALGLGSASISSTKHGIETTQFDLSEEDKHVERTATVRDKPYISKAE********************************SIVRKTKIEGGKIS********************ERNIRMALLAVSTLTCTIGVT

*****MNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVT*SGESEKVLLLMESGVRLHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTTASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKH***********SSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNN*****DEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGE**********************************************************************************************************************************************************************************************GKLKKMKEKYGDQDEEERNIRMALLAVSTLTC*****

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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		934	2.2.26 [Sep-21-2011]
Q8CCP0		1064	Nuclear export mediator f	yes	no	0.690	0.606	0.416	1e-154
Q9VBX1		992	Nuclear export mediator f	yes	no	0.860	0.810	0.372	1e-137
O60524		1076	Nuclear export mediator f	yes	no	0.5	0.434	0.457	1e-120
Q9USN8		1021	Uncharacterized protein C	yes	no	0.705	0.645	0.338	1e-101
Q12532		1038	Translation-associated el	yes	no	0.677	0.609	0.276	2e-56
Q59020		671	Uncharacterized protein M	yes	no	0.368	0.512	0.290	5e-33
O34693		572	Uncharacterized protein Y	yes	no	0.123	0.201	0.281	0.0008

>sp\|Q8CCP0\|NEMF_MOUSE Nuclear export mediator factor Nemf OS=Mus musculus GN=Nemf PE=1 SV=2	Back alignment and function desciption

 Score =  547 bits (1410), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 310/745 (41%), Positives = 431/745 (57%), Gaps = 100/745 (13%)

Query: 2   VKVRMNTADVAAEVKCLR-RLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLM 60
           +K R +T D+ A +  L   L+GMR +NVYD+  KTY+ +L             K  LL+
Sbjct: 1   MKSRFSTVDLRAVLAELNASLLGMRVNNVYDVDNKTYLIRLQKPDF--------KATLLL 52

Query: 61  ESGVRLHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYV 120
           ESG+R+HTT +   K   PS F +K RKH+++RRL   +QLG DRI+ FQFG    A+++
Sbjct: 53  ESGIRIHTTEFEWPKNMMPSSFAMKCRKHLKSRRLVSAKQLGVDRIVDFQFGSDEAAYHL 112

Query: 121 ILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTTASKLHAA 180
           I+ELY +GNI+LTD E+ +L +LR   D+   V    R RYP +  R             
Sbjct: 113 IIELYDRGNIVLTDYEYLILNILRFRTDEADDVKFAVRERYPIDHAR------------- 159

Query: 181 LTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTL 240
                   A EP    E    V  A+                             K   L
Sbjct: 160 --------AAEPLLTLERLTEVIAAA----------------------------PKGEVL 183

Query: 241 KTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVIS 300
           K VL   L YGPAL EH ++++G   N K+ E  KLE   I+ +++ V + ED+L+   +
Sbjct: 184 KRVLNPLLPYGPALIEHCLIESGFSGNAKVDE--KLESKDIEKILVCVQRAEDYLRK--T 239

Query: 301 GDIVPEGYILMQNK---HLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAA 357
            +   +GYI+ + +    L  D P          Y+EF P L +Q     +++FE+FD A
Sbjct: 240 SNFNGKGYIIQKREAKPSLDADKP----AEDILTYEEFHPFLFSQHLQCPYIEFESFDKA 295

Query: 358 LDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNL 417
           +DEFYSKIE Q+ + +   +E  A  KL+ +  D ENR+  L+Q  +      ELIE NL
Sbjct: 296 VDEFYSKIEGQKIDLKALQQEKQALKKLDNVRKDHENRLEALQQAQEIDKLKGELIEMNL 355

Query: 418 EDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNN-- 475
           + VD AI  VR ALAN++ W ++  +VKE +  G+PVA  I +L L+ N +++LL N   
Sbjct: 356 QIVDRAIQVVRSALANQIDWTEIGVIVKEAQAQGDPVACAIKELKLQTNHVTMLLRNPYL 415

Query: 476 LDEMDDEEKTLPVEK----------------------------VEVDLALSAHANARRWY 507
           L E +D +    +E                             V+VDL+LSA+ANA+++Y
Sbjct: 416 LSEEEDGDGDASIENSDAEAPKGKKKKQKNKQLQKPQKNKPLLVDVDLSLSAYANAKKYY 475

Query: 508 ELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFNWFISSE 567
           + K+    K ++T+ A  KAFK+AEKKT+  + + +TV +I   RKV+WFEKF WFISSE
Sbjct: 476 DHKRYAAKKTQRTVEAAEKAFKSAEKKTKQTLKEVQTVTSIQKARKVYWFEKFLWFISSE 535

Query: 568 NYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCF 627
           NYL+I GRD QQNE+IVKRY++ GD+YVHADLHGA+S VIKN   E P+PP TL +AG  
Sbjct: 536 NYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNPTGE-PIPPRTLTEAGTM 594

Query: 628 TVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLL 687
            +C+S AWD++++TSAWWVY HQVSKTAPTGEYLT GSFMIRGKKNFLPP  L+MGF  L
Sbjct: 595 ALCYSAAWDARVITSAWWVYHHQVSKTAPTGEYLTTGSFMIRGKKNFLPPSYLMMGFSFL 654

Query: 688 FRLDESSLGSHLNERRVRGEEEGMD 712
           F++DES +  H  ER+VR ++E M+
Sbjct: 655 FKVDESCVWRHRGERKVRVQDEDME 679

Plays a role in nuclear export.
Mus musculus (taxid: 10090)

>sp\|Q9VBX1\|NEMF_DROME Nuclear export mediator factor NEMF homolog OS=Drosophila melanogaster GN=Clbn PE=1 SV=2	Back alignment and function description

>sp\|O60524\|NEMF_HUMAN Nuclear export mediator factor NEMF OS=Homo sapiens GN=NEMF PE=1 SV=4	Back alignment and function description

>sp\|Q9USN8\|YJY1_SCHPO Uncharacterized protein C132.01c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC132.01c PE=1 SV=2	Back alignment and function description

>sp\|Q12532\|TAE2_YEAST Translation-associated element 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TAE2 PE=1 SV=1	Back alignment and function description

>sp\|Q59020\|Y1625_METJA Uncharacterized protein MJ1625 OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ1625 PE=4 SV=1	Back alignment and function description

>sp\|O34693\|YLOA_BACSU Uncharacterized protein YloA OS=Bacillus subtilis (strain 168) GN=yloA PE=2 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		934
225432064		1110	PREDICTED: nuclear export mediator facto	0.959	0.807	0.768	0.0
255556494		1092	conserved hypothetical protein [Ricinus	0.933	0.798	0.744	0.0
449441522		1119	PREDICTED: nuclear export mediator facto	0.972	0.811	0.738	0.0
449485009		1090	PREDICTED: nuclear export mediator facto	0.972	0.833	0.738	0.0
357448763		1146	Serologically defined colon cancer antig	0.971	0.791	0.718	0.0
356529076		1131	PREDICTED: nuclear export mediator facto	0.963	0.795	0.718	0.0
297795761		1080	EMB1441 [Arabidopsis lyrata subsp. lyrat	0.946	0.818	0.711	0.0
356558107		1119	PREDICTED: nuclear export mediator facto	0.968	0.808	0.733	0.0
15240582		1080	zinc knuckle (CCHC-type) family protein	0.946	0.818	0.706	0.0
296083204		993	unnamed protein product [Vitis vinifera]	0.794	0.747	0.783	0.0

>gi\|225432064\|ref\|XP_002273922.1\| PREDICTED: nuclear export mediator factor Nemf-like [Vitis vinifera]	Back alignment and taxonomy information

 Score = 1422 bits (3681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 713/928 (76%), Positives = 788/928 (84%), Gaps = 32/928 (3%)

Query: 1   MVKVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLM 60
           MVKVRMNTADVAAE+KCLRRLIGMRC+NVYDLSPKTY+FKLMNSSGVTESGESEKVLLLM
Sbjct: 1   MVKVRMNTADVAAEIKCLRRLIGMRCANVYDLSPKTYMFKLMNSSGVTESGESEKVLLLM 60

Query: 61  ESGVRLHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYV 120
           ESGVRLHTTAY RDK  TPSGFTLKLRKHIRTRRLEDVRQLGYDR++LFQFGLG NAHYV
Sbjct: 61  ESGVRLHTTAYVRDKSMTPSGFTLKLRKHIRTRRLEDVRQLGYDRVVLFQFGLGANAHYV 120

Query: 121 ILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTTASKLHAA 180
           ILELYAQGNILLTDSEF V+TLLRSHRDDDKGVAIMSRHRYP EICRVFERT  +KL AA
Sbjct: 121 ILELYAQGNILLTDSEFMVMTLLRSHRDDDKGVAIMSRHRYPVEICRVFERTATTKLQAA 180

Query: 181 LTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTL 240
           LTS KE ++NE  + +E GN VS+A +E  G  KG KS + SKN+N    DGARAKQ TL
Sbjct: 181 LTSPKESESNEAVEASEGGNKVSDAPREKQGNNKGVKSSEPSKNTN----DGARAKQATL 236

Query: 241 KTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVIS 300
           KTVLGEALGYGPALSEHIILD GL+PN K+++ +K + + IQ L  +V KFE+WL+DVIS
Sbjct: 237 KTVLGEALGYGPALSEHIILDAGLIPNTKVTKDSKFDIDTIQRLAQSVTKFENWLEDVIS 296

Query: 301 GDIVPEGYILMQNKHLGKDHPPTESGSSTQ-IYDEFCPLLLNQFRSREFVKFETFDAALD 359
           GD VPEGYILMQNK  GKD PP++    +Q IYDEFCP+LLNQF+SREFVKFETFDAALD
Sbjct: 297 GDQVPEGYILMQNKIFGKDCPPSQPDRGSQVIYDEFCPILLNQFKSREFVKFETFDAALD 356

Query: 360 EFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLED 419
           EFYSKIESQR+EQQ KAKE +A  KL KI +DQENRVHTLK+EVD  +KMAELIEYNLED
Sbjct: 357 EFYSKIESQRSEQQQKAKEGSAMQKLTKIRVDQENRVHTLKKEVDHCIKMAELIEYNLED 416

Query: 420 VDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEM 479
           VDAAILAVRVALAN M+WEDLARMVKEE+K+GNPVAGLIDKLYLERNCM+LLLSNNLDEM
Sbjct: 417 VDAAILAVRVALANGMNWEDLARMVKEEKKSGNPVAGLIDKLYLERNCMTLLLSNNLDEM 476

Query: 480 DDEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQI 539
           DD+EKTLPV+KVEVDLALSAHANARRWYE KK+QE+KQEKT+ AH KAFKAAEKKTRLQ+
Sbjct: 477 DDDEKTLPVDKVEVDLALSAHANARRWYEQKKRQENKQEKTVIAHEKAFKAAEKKTRLQL 536

Query: 540 LQEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADL 599
            QEKTVA ISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGD+Y+HADL
Sbjct: 537 SQEKTVATISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDLYIHADL 596

Query: 600 HGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGE 659
           HGASSTVIKNH+PE PVPPLTLNQAGCFTVCHSQAWDSK+VTSAWWVYPHQVSKTAPTGE
Sbjct: 597 HGASSTVIKNHKPEHPVPPLTLNQAGCFTVCHSQAWDSKIVTSAWWVYPHQVSKTAPTGE 656

Query: 660 YLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEGMDDFEDSGH 719
           YLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEG  DFE++  
Sbjct: 657 YLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEGAQDFEENES 716

Query: 720 HKENSDIESEKDDTDEKPVAESLSVPNSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSK 779
            K NSD ESEK++TDEK  AES                      + P E++ + NG DS+
Sbjct: 717 LKGNSDSESEKEETDEKRTAES----------------------KIPLEERNMLNGNDSE 754

Query: 780 -IFDIARNVAAPVTPQLEDLIDRALGLGSASISSTKHGIETTQFDLSEEDKHVERTATVR 838
            I DI+    + V PQLEDLIDRAL LGS + S  K+ +ET+Q DL EE  H +R ATVR
Sbjct: 755 HIADISGGHVSSVNPQLEDLIDRALELGSNTASGKKYALETSQVDL-EEHNHEDRKATVR 813

Query: 839 DKPYISKAERRKLKKGQGSSVVDP---KVEREKERGKDASSQPESIVRKTKIEGGKISRG 895
           +KPYISKAERRKLKKGQ +S  D      + E E    ++SQP+  V+ ++  GGKISRG
Sbjct: 814 EKPYISKAERRKLKKGQKTSTSDAGGDHGQEEIEENNVSTSQPDKDVKNSQPAGGKISRG 873

Query: 896 QKGKLKKMKEKYGDQDEEERNIRMALLA 923
           QKGKLKKMKEKY DQDEEER+IRMALLA
Sbjct: 874 QKGKLKKMKEKYADQDEEERSIRMALLA 901

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255556494\|ref\|XP_002519281.1\| conserved hypothetical protein [Ricinus communis] gi\|223541596\|gb\|EEF43145.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|449441522\|ref\|XP_004138531.1\| PREDICTED: nuclear export mediator factor Nemf-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449485009\|ref\|XP_004157045.1\| PREDICTED: nuclear export mediator factor NEMF homolog [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357448763\|ref\|XP_003594657.1\| Serologically defined colon cancer antigen-like protein [Medicago truncatula] gi\|355483705\|gb\|AES64908.1\| Serologically defined colon cancer antigen-like protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356529076\|ref\|XP_003533123.1\| PREDICTED: nuclear export mediator factor Nemf-like [Glycine max]	Back alignment and taxonomy information

>gi\|297795761\|ref\|XP_002865765.1\| EMB1441 [Arabidopsis lyrata subsp. lyrata] gi\|297311600\|gb\|EFH42024.1\| EMB1441 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|356558107\|ref\|XP_003547349.1\| PREDICTED: nuclear export mediator factor NEMF homolog [Glycine max]	Back alignment and taxonomy information

>gi\|15240582\|ref\|NP_199804.1\| zinc knuckle (CCHC-type) family protein [Arabidopsis thaliana] gi\|8777424\|dbj\|BAA97014.1\| unnamed protein product [Arabidopsis thaliana] gi\|332008489\|gb\|AED95872.1\| zinc knuckle (CCHC-type) family protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|296083204\|emb\|CBI22840.3\| unnamed protein product [Vitis vinifera]	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		934
TAIR\|locus:2158844		1080	emb1441 "embryo defective 1441	0.738	0.638	0.662	0.0
MGI\|MGI:1918305		1064	Nemf "nuclear export mediator	0.465	0.408	0.395	7.8e-154
UNIPROTKB\|F1N8T0		1071	NEMF "Uncharacterized protein"	0.474	0.413	0.402	5.4e-153
UNIPROTKB\|F1MKA1		1079	NEMF "Uncharacterized protein"	0.464	0.402	0.413	8.8e-153
UNIPROTKB\|F1SHY2		1078	NEMF "Uncharacterized protein"	0.463	0.401	0.406	1.1e-152
UNIPROTKB\|O60524		1076	NEMF "Nuclear export mediator	0.467	0.406	0.393	2.3e-152
DICTYBASE\|DDB_G0289583		1268	DDB_G0289583 "DUF814 family pr	0.451	0.332	0.389	7.7e-144
ZFIN\|ZDB-GENE-060929-284		883	zgc:153813 "zgc:153813" [Danio	0.702	0.742	0.379	1.6e-143
UNIPROTKB\|G3V5V3		999	NEMF "Nuclear export mediator	0.467	0.437	0.393	1e-139
FB\|FBgn0259152		992	Clbn "Caliban" [Drosophila mel	0.618	0.582	0.392	3.7e-133

TAIR\|locus:2158844 emb1441 "embryo defective 1441" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2312 (818.9 bits), Expect = 0., Sum P(2) = 0.
 Identities = 480/725 (66%), Positives = 549/725 (75%)

Query:   207 KENLGGQKGGKSFDLXXXXXXXXXDGARAKQPTLKTVLGEALGYGPALSEHIILDTGLVP 266
             KE  GG+KGGKS            D   AKQ TLK +LG+ALGYGP LSEHIILD GLVP
Sbjct:   197 KEQNGGKKGGKS-----------NDSTGAKQYTLKNILGDALGYGPQLSEHIILDAGLVP 245

Query:   267 NMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHPPTESG 326
               KLSE  KL+DN IQ+LV AV  FEDWL+D+I+G  VPEGYILMQ + L  D   +ESG
Sbjct:   246 TTKLSEDKKLDDNEIQLLVQAVIVFEDWLEDIINGQKVPEGYILMQKQILAND-TTSESG 304

Query:   327 SSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLN 386
                ++YDEFC +LLNQF+SR + KFETFDAALDEFYSKIESQR+EQQ KAKED+A  KLN
Sbjct:   305 GVKKMYDEFCSILLNQFKSRVYEKFETFDAALDEFYSKIESQRSEQQQKAKEDSASLKLN 364

Query:   387 KIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKE 446
             KI  DQENRV  LK+EV+  V MAELIEYNLEDVDAAILAVRVALA  M W+DLARMVKE
Sbjct:   365 KIRQDQENRVQILKKEVNHCVNMAELIEYNLEDVDAAILAVRVALAKGMGWDDLARMVKE 424

Query:   447 ERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRW 506
             E+K GNPVAG+ID+LYLE+NCM+LLL NNLDEMDD+EKT+PVEKVEVDL+LSAH NARRW
Sbjct:   425 EKKLGNPVAGVIDRLYLEKNCMTLLLCNNLDEMDDDEKTVPVEKVEVDLSLSAHGNARRW 484

Query:   507 YELXXXXXXXXXXTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFNWFISS 566
             YE+          T++AH KAF+AAEKKTR Q+ QEK VA ISHMRKVHWFEKFNWFISS
Sbjct:   485 YEMKKKQETKQEKTVSAHEKAFRAAEKKTRHQLSQEKVVATISHMRKVHWFEKFNWFISS 544

Query:   567 ENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGC 626
             ENYLVISGRDAQQNEMIVKRYMSKGD+YVHA+LHGASSTVIKNH+PEQ VPPLTLNQAGC
Sbjct:   545 ENYLVISGRDAQQNEMIVKRYMSKGDLYVHAELHGASSTVIKNHKPEQNVPPLTLNQAGC 604

Query:   627 FTVCHSQAWDSKMVTSAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGL 686
             FTVCHSQAWDSK+VTSAWWVYPHQV+KTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGL
Sbjct:   605 FTVCHSQAWDSKIVTSAWWVYPHQVTKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGL 664

Query:   687 LFRLDESSLGSHLNERRVRGEEEGMDDFEDSGHHK-ENSDIESEKDDTDEKPVAESLSVP 745
             LFRLDESSLG+HLNERRVRGEEEGM+D     H   E+SD ESE +  +E  V+ S  V 
Sbjct:   665 LFRLDESSLGAHLNERRVRGEEEGMNDVVMETHAPDEHSDTESENEAVNEV-VSASGEVD 723

Query:   746 NSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDRALGL 805
                       + S++D           S+GI  +      NVA+  T QLEDL+DR LGL
Sbjct:   724 LQESSTALSQDTSSLDMS---------SSGITEE------NVAS-ATSQLEDLLDRTLGL 767

Query:   806 GSASISSTKHGIETTQFDLSEEDKHVERTATVRDKPYISKAERRKLKKGQ-GSSVVDPKV 864
             G+A+++  K  IET++ D+ E+ K  E+ A VRDKPY+SKAERRKLK GQ G++  D   
Sbjct:   768 GAATVAGKKDTIETSKDDMEEKMKQEEKNAVVRDKPYMSKAERRKLKMGQSGNTAADGNT 827

Query:   865 EREKE--RGKDASS--QPESIVRKTKIEGGKISRGQXXXXXXXXXXYGDQDEEERNIRMA 920
              +EK+  + KD SS  Q    +   K  G K+SRGQ          Y DQDE+ER IRMA
Sbjct:   828 GQEKQQRKEKDVSSLSQATKSIPDNKPAGEKVSRGQRGKLKKMKEKYADQDEDERKIRMA 887

Query:   921 LLAVS 925
             LLA S
Sbjct:   888 LLASS 892

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

MGI\|MGI:1918305 Nemf "nuclear export mediator factor" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|F1N8T0 NEMF "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MKA1 NEMF "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SHY2 NEMF "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|O60524 NEMF "Nuclear export mediator factor NEMF" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0289583 DDB_G0289583 "DUF814 family protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-060929-284 zgc:153813 "zgc:153813" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|G3V5V3 NEMF "Nuclear export mediator factor NEMF" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

FB\|FBgn0259152 Clbn "Caliban" [Drosophila melanogaster (taxid:7227)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9VBX1	NEMF_DROME	No assigned EC number	0.3720	0.8608	0.8104	yes	no

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:
	GSVIVG00033191001	SubName- Full=Chromosome chr5 scaffold_64, whole genome shotgun sequence; (1090 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00023426001	SubName- Full=Chromosome undetermined scaffold_30, whole genome shotgun sequence; (426 aa)	•	0.408

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		934
COG1293		564	COG1293, COG1293, Predicted RNA-binding protein ho	1e-70
pfam05670		90	pfam05670, DUF814, Domain of unknown function (DUF	2e-28
pfam05833		447	pfam05833, FbpA, Fibronectin-binding protein A N-t	6e-13
pfam05833		447	pfam05833, FbpA, Fibronectin-binding protein A N-t	2e-05

>gnl\|CDD\|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]	Back alignment and domain information

 Score =  244 bits (624), Expect = 1e-70
 Identities = 158/690 (22%), Positives = 263/690 (38%), Gaps = 143/690 (20%)

Query: 3   KVRMNTADVAAEVKCLR-RLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLME 61
           K++ ++ D+AA V+ L+ +L G R   +Y       I  L             + LLL E
Sbjct: 2   KMKFDSLDLAAIVEELKEQLEGGRIDKIYQPGEDELILLLRFGGK-------GRKLLLSE 54

Query: 62  SGVR--LHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHY 119
             VR  +H T   ++    PS F + LRKH++  R+E + QLG+DRI+  +F        
Sbjct: 55  HPVRSRIHLTKKPKENPALPSSFAMLLRKHLKGARIEKIEQLGFDRILELKFKKDEIGDK 114

Query: 120 VILELY-----AQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRYPTEICRVFERTTA 174
           +I+EL+       GN++L D E  ++  LR     D+   I     Y             
Sbjct: 115 IIVELFLEIMGKHGNLILVDEERKIIEALRHVTFSDR--TIKPGEIY------------- 159

Query: 175 SKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGAR 234
                       P A   +   +   +       +                         
Sbjct: 160 ----------ILPPAQLKNPYEQSEEDFKELQLNSGA----------------------- 186

Query: 235 AKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDW 294
                +  +L   LG G  L+E ++   GL   +   ++                 FE+ 
Sbjct: 187 ----DIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDL-----------------FEEE 225

Query: 295 LQDVISGDIVPEGYILMQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFE-T 353
           ++ V          +     +  + +                   L+    + +   E  
Sbjct: 226 IKKVREALEELLNPLKPNYYYKDEKY-------------------LDVVPLKAYADLEKL 266

Query: 354 FDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELI 413
           F+ ALDE + + + ++   + + K +    KL      QE+ +  L++  +   +  EL+
Sbjct: 267 FNEALDEKFERDKIKQLASELEKKLEKELKKLENKLEKQEDELEELEKAAEELRQKGELL 326

Query: 414 EYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLS 473
             NL+ ++  + +VR+A      +       +E +   +                S   S
Sbjct: 327 YANLQLIEEGLKSVRLA-----DFYG----NEEIKIELDK---------------SKTPS 362

Query: 474 NNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEK 533
            N      + K L   KV +D  LS    A  +YE  K    K E       KA +   +
Sbjct: 363 ENAQRYFKKYKKLKGAKVNLDRQLSELKEAIAYYESAKTALEKAEG-----KKAIEEIRE 417

Query: 534 KTRLQIL--QEKTVANISHMRKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKG 591
           +   + L   +K        +K  WFEKF WF+SS+ +LVI GR+A+QNE +VK+Y  K 
Sbjct: 418 ELIEEGLLKSKKKKR-----KKKEWFEKFRWFVSSDGFLVIGGRNAKQNEELVKKYAEKD 472

Query: 592 DVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVT-SAWWVYPHQ 650
           D++ HAD    S  VIK    E      T+ +A      +S+AW S +V     WV P Q
Sbjct: 473 DLWFHADDIPGSHVVIKTEGKE--PSEETILEAAQLAASYSKAWKSGLVPVDYTWVKPVQ 530

Query: 651 VSKTAPTGEYLTVGSFMIRGKKNFLPPHPL 680
           V K A +GE L  G   IRGK++++    L
Sbjct: 531 VPKGAKSGEVLYKGQKTIRGKRDYITIVKL 560

Length = 564

>gnl\|CDD\|218683 pfam05670, DUF814, Domain of unknown function (DUF814)	Back alignment and domain information

>gnl\|CDD\|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA)	Back alignment and domain information

>gnl\|CDD\|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA)	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		934
KOG2030		911	consensus Predicted RNA-binding protein [General f	100.0
COG1293		564	Predicted RNA-binding protein homologous to eukary	100.0
PF05833		455	FbpA: Fibronectin-binding protein A N-terminus (Fb	100.0
PF05670		90	DUF814: Domain of unknown function (DUF814); Inter	99.95
COG1293		564	Predicted RNA-binding protein homologous to eukary	97.56
KOG3272		207	consensus Predicted coiled-coil protein [General f	97.51
PRK01103		274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	95.99
PRK10445		263	endonuclease VIII; Provisional	95.4
KOG2030		911	consensus Predicted RNA-binding protein [General f	94.55
PRK14811		269	formamidopyrimidine-DNA glycosylase; Provisional	94.5
PRK13945		282	formamidopyrimidine-DNA glycosylase; Provisional	94.01
TIGR00577		272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	93.83
COG0266		273	Nei Formamidopyrimidine-DNA glycosylase [DNA repli	92.8
PF06831		92	H2TH: Formamidopyrimidine-DNA glycosylase H2TH dom	90.91
PRK14810		272	formamidopyrimidine-DNA glycosylase; Provisional	90.43
PF00416		107	Ribosomal_S13: Ribosomal protein S13/S18; InterPro	86.22
COG0099		121	RpsM Ribosomal protein S13 [Translation, ribosomal	85.86
CHL00137		122	rps13 ribosomal protein S13; Validated	85.09
PRK05179		122	rpsM 30S ribosomal protein S13; Validated	84.64
TIGR03631		113	bact_S13 30S ribosomal protein S13. This model des	81.7

>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]	Back alignment and domain information

Probab=100.00  E-value=4.5e-166  Score=1414.57  Aligned_cols=780  Identities=49%  Similarity=0.736  Sum_probs=662.2

Q ss_pred             ccCCCCHHHHHHHHHHHhhhcCCceeEEEecCCCEEEEEEeeCCCCccCCCCceEEEEEeccceEEeecccCCCCCCCcH
Q 002338            2 VKVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTTAYARDKKNTPSG   81 (934)
Q Consensus         2 mK~rms~lDv~a~v~EL~~L~G~RI~nIY~~~~~t~llk~~~~~g~~~~~~~~k~~LliesG~RiHlT~~~~~k~~~Ps~   81 (934)
                      |||||++|||.+.|+||+.|.|+||+|||++++++|+|+|.++         .  .|+++||+|||+|.+.++++.+||+
T Consensus         1 mk~r~~tldi~~~v~elk~L~g~r~~niYdi~~ktyl~K~~~~---------d--~ll~e~GvRih~T~~~~ek~~tpSG   69 (911)
T KOG2030|consen    1 MKQRFNTLDIAATVAELKPLVGMRVNNIYDISNKTYLIKFSNK---------D--ILLVESGVRIHLTQFDQEKSTTPSG   69 (911)
T ss_pred             CcchhHHHHHHHHHHHHHHhhhhhhhceeeccccEEEEEecCC---------c--eEEeeccceeeeeeccccCCCCcch
Confidence            8999999999999999999999999999999999999999987         1  7999999999999999999999999


Q ss_pred             HHHHHHHHccCCceeEEEeeCCCeEEEEEEeeCCceEEEEEEEecCceEEEEcCCCcEEeeecccccCCCccccccCCcc
Q 002338           82 FTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRY  161 (934)
Q Consensus        82 F~m~LRKhL~g~RL~~V~Qlg~DRIV~~~f~~G~~~~~LIvEL~grgNIILtD~~~~IL~~lR~~~~~~~~~~i~~g~~Y  161 (934)
                      |||+|||||+..||++|+|+|+||||+|+||.|+.+++||||||++|||||||.+++||.+||.|+++......+++++|
T Consensus        70 F~~kLRKhik~kRledv~Q~g~DRivvlqfG~g~~~~~lvLE~~d~GNviLtdqe~~i~~llrv~~dd~~~~~~~~rer~  149 (911)
T KOG2030|consen   70 FSMKLRKHIKEKRLEDVRQVGFDRIVVLQFGTGDDEGYLVLEFFDRGNVLLTDQELRILQLLRVRTDDSESSRSASRERF  149 (911)
T ss_pred             HHHHHHHHHhHhhhchhhhcCcceEEEEEecCCCccceEEEEecCCCceEEecccceeeeEEeeeeccccchhhhhhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999988777889999999


Q ss_pred             cCccccccccCChhhhHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCCCccCCchhHH
Q 002338          162 PTEICRVFERTTASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTLK  241 (934)
Q Consensus       162 p~~~~~~~~p~~~~kl~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~e~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~lk  241 (934)
                      |+..+..+..-+..++....                +.                   .+|.         .....+.++.
T Consensus       150 ~~s~~e~~~~k~~~~le~s~----------------dl-------------------k~~~---------~~~q~g~~~~  185 (911)
T KOG2030|consen  150 DFSAKERNEMKSVKKLEKSG----------------DL-------------------KALE---------PKDQNGITLE  185 (911)
T ss_pred             chhhhhhhhccccchhhhcc----------------hH-------------------HHhh---------ccCccccchh
Confidence            98775544322222221100                00                   0000         1112346788


Q ss_pred             HHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecccCCCCCCC
Q 002338          242 TVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHP  321 (934)
Q Consensus       242 ~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~~~~l~~l~~~~~~p~gyi~~~~~~~~~~~~  321 (934)
                      .+|...+++||...+|++..+++.+..+.+....+.+.++..|.++++.+++|+.++.++...|.|||.+.....+.+  
T Consensus       186 ~il~~~~~~g~sk~k~~v~~~~~~~~sKsse~~~~~~~~i~~l~e~v~~~eE~~~elit~~~~~~Gyi~~~k~~~~~s--  263 (911)
T KOG2030|consen  186 SILHIETKEGPSKIKHIVLDMKKGQLSKSSENIKLFDSEIKKLQEAVKDQEEEDRELITGKLGSKGYILEEKEKKPIS--  263 (911)
T ss_pred             hhhhhhccCCCccchhhhhhhcccccccccccccccchhhHHHHHHHHHHHHHHHHHHhCCCcccchhHHhhcccCCC--
Confidence            999999999999999999999998877755555677888999999999999999999999988999997665322211  


Q ss_pred             CCCCCCCCccceeeeeecccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002338          322 PTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQ  401 (934)
Q Consensus       322 ~~~~~~~~~~~~~f~P~~l~q~~~~~~~~f~sf~~AlDeffs~~e~qk~~~~~~~~e~~~~kkLek~~~~qe~ri~~L~~  401 (934)
                           .....|.+||| .+.+|...++..|++|++|+|+|||.+++|+..++....+..+.+||++++++|+++++.|++
T Consensus       264 -----~~~~~y~~f~p-~~~~fKs~~~k~fetf~ea~Def~S~IEsqk~~lr~~~~E~qa~kKld~vr~Dq~~rvq~Lqq  337 (911)
T KOG2030|consen  264 -----TKEFIYDEFHP-LGVQFKSEPVKKFETFNEAVDEFFSTIESQKSELRVKNQELQAEKKLDKVRKDQKERVQELQQ  337 (911)
T ss_pred             -----ccceeeccccc-cccccccchhhhccchhhHHHHHHHHHhhhhHHHHHHhhHhHHHhhhhcchhhHHHHHHHHHH
Confidence                 22468999999 778999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccccCCeEEEeccCCCCCccc
Q 002338          402 EVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDD  481 (934)
Q Consensus       402 e~e~~~~~aeLI~~Nl~~V~~~i~~v~~a~a~g~~W~~i~~~i~~~~~~g~pvA~~I~~l~l~~n~itl~L~d~~d~~d~  481 (934)
                      .++.++++|+||+.|..+|+.+|.+|++++++||+|.+|++|++.++++|||||..|.+++++.|++++.|.|+++|+||
T Consensus       338 ~qe~~~~kAelIe~N~eLVe~~il~I~s~la~~m~W~dieKLik~eqKkGn~vAk~i~~l~l~~n~~t~~L~d~~dd~~d  417 (911)
T KOG2030|consen  338 VQELNRRKAELIEPNPELVEAAILAIQSALAQQMDWKDIEKLIKSEQKKGNPVAKSIDKLKLEKNEATLRLKDPEDDNDD  417 (911)
T ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHHHHccCCcHhHHHHHHHHHhcCchHhhhhhHHHHhhhhheeecCCcccccch
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998777


Q ss_pred             cccCCCceEEEeCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhHHHhhhcccccCce
Q 002338          482 EEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFN  561 (934)
Q Consensus       482 ~~~~~~~v~I~LDl~lSa~~NA~~yy~k~KK~~~K~ekt~~a~~~alk~aE~k~~~~L~~~~~~~~l~~iRk~~wfEKF~  561 (934)
                      +..+.+.+.|+||++|||++||++||.++|+++.|+++|..++++||++++.|++++|++.+++..|.++|+++||||||
T Consensus       418 e~k~~e~~~VeiDLslsA~aNArr~y~~kk~aa~K~kKT~~a~eKAlK~~e~Ki~q~lk~~~~~~~i~k~Rk~~wFEKf~  497 (911)
T KOG2030|consen  418 EKKSSEVIVVEIDLSLSAFANARRYYEMKKEAAEKIKKTVDASEKALKSAERKIEQQLKQVKTVSRIKKIRKVYWFEKFH  497 (911)
T ss_pred             hhccccceeeeeeccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhcccceeehhee
Confidence            77788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCeEEEecCChhhHHHHHHHhcCCCCEEEEecCCCCcEEEEecCCCCCCCCHHHHHHHHHHHHHhccccCCCCcc
Q 002338          562 WFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVT  641 (934)
Q Consensus       562 wFiSSdGylVivGRDa~QNE~LvkKya~~~Diw~HAdi~GAShVIIKn~~~g~~ip~~tL~eAA~lAa~ySkAW~sk~V~  641 (934)
                      |||||+|||||+||||||||+||+|||+|+|||||||+||||||||||+ ++.+|||.||.|||+||+|||+||++++|+
T Consensus       498 wFiSSEg~LVi~GrdaqQnEllvkky~~~~DiY~had~~gaSsviIkN~-~~~eipp~TL~eAg~ma~~~S~aWdakvvs  576 (911)
T KOG2030|consen  498 WFISSEGYLVIGGRDAQQNELLVKKYLEPGDIYVHADLHGASSVIIKNP-PKTEIPPKTLEEAGSMALCYSKAWDAKVVS  576 (911)
T ss_pred             EEEecCcEEEEcCCChhhhhHHHHhhCCCCCeEEecccCCCceEEEeCC-CCCCCChhhHHHHHHHHhHHhhhhcccccc
Confidence            9999999999999999999999999999999999999999999999995 789999999999999999999999999999


Q ss_pred             eEEEEecccccccCCCCceeccCcEEEeeeccccCCCCceeEEEEEEEecccccccccccccccCccCCCCcccccCCCC
Q 002338          642 SAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEGMDDFEDSGHHK  721 (934)
Q Consensus       642 sa~wV~~~QVSKtapsGeyL~~GsFmIrGkKnflpp~~L~mg~gilf~~de~~~~~h~~~r~~~~~~~~~~~~~~~~~~~  721 (934)
                      +|||||++|||||||||||||+||||||||||||||++|+|||||||+||++++++|.++|+++.+++.+.+.+ .  + 
T Consensus       577 saWwv~~dqVSKtaptgeyL~~GSFmIrgkkN~lpp~~LvmG~GlLfrldes~~E~~~~~r~~~~eee~~~~~e-~--e-  652 (911)
T KOG2030|consen  577 SAWWVYPDQVSKTAPTGEYLPTGSFMIRGKKNFLPPHQLVMGLGLLFRLDESSIERHLGERKVEEEEEKEEDEE-P--E-  652 (911)
T ss_pred             cceEEecccccccCCCCccccccceEEecccCCCCchhheecceeEEEeccchhhhhhhhHHHHHHHhhhcccc-h--h-
Confidence            99999999999999999999999999999999999999999999999999999999999999988887664310 0  0 


Q ss_pred             CCCccccccCcCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCchhhhhcccCCCCCCcchhhcccc
Q 002338          722 ENSDIESEKDDTDEKPVAESLSVPNSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDR  801 (934)
Q Consensus       722 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  801 (934)
                          ..++.         ++         ..     +++.               ++            +.++ ..+++.
T Consensus       653 ----~~ee~---------~s---------~~-----~e~~---------------~~------------~~s~-~e~~~~  677 (911)
T KOG2030|consen  653 ----LMEEV---------ES---------KT-----SEIP---------------EE------------VISN-DEFPVN  677 (911)
T ss_pred             ----hhhhc---------cc---------cc-----ccCC---------------cc------------cccc-cccccc
Confidence                00000         00         00     0000               00            0000 001111


Q ss_pred             cccccccccCCCccCccccccccccccccccccccccCCcccchHHHHHhhcCCCCCCCCchhhhhhhccCCCCCCCccc
Q 002338          802 ALGLGSASISSTKHGIETTQFDLSEEDKHVERTATVRDKPYISKAERRKLKKGQGSSVVDPKVEREKERGKDASSQPESI  881 (934)
Q Consensus       802 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~kk~~~~~~~~~~~~~~~~~~~~~~~~~~~~  881 (934)
                      .+  ......|                    .......++++.+.++|..+|+++.+...+....++..-.....++-..
T Consensus       678 ev--~~~~~~G--------------------k~~~~~~~~~~~~~~~~~~~k~~s~~~~~~n~~~~k~~~~e~~~~~is~  735 (911)
T KOG2030|consen  678 EV--KGREKTG--------------------KNVQEESKTFIGKGPKREKKKVQSASKEEDNVGRAKQRIGESSVQPISD  735 (911)
T ss_pred             cc--cccccCC--------------------cchhhhhhhhhhcCccchhhhccccccchhhhhHHHHhhhhcccccccc
Confidence            00  0001111                    1223457889999999999999888765553332222211111111111


Q ss_pred             ccccccCCCCCCCcccchhhhhhhhhcCCChHHHHHHHHHHhccCCccccC
Q 002338          882 VRKTKIEGGKISRGQKGKLKKMKEKYGDQDEEERNIRMALLAVSTLTCTIG  932 (934)
Q Consensus       882 ~~~~~~~~~~~~rg~~~k~kk~~~ky~dqdee~r~~~m~~l~~~~~~~~~~  932 (934)
                      -+.+   .-+.+|||||||||||  |+||||+||+|+|++|+++|+ -+-+
T Consensus       736 ep~~---~~~~~rg~kgklkkmk--y~dQd~~er~~r~~~l~~~~k-ek~~  780 (911)
T KOG2030|consen  736 EPSN---KNQVKRGQKGKLKKMK--YADQDEDERELRMELLKSSGK-EKQQ  780 (911)
T ss_pred             CCcc---hHHHHHhhhhhhhhhh--hcccCchHHHHHHHhcccccc-cccc
Confidence            0111   1356899999999999  999999999999999999998 4433

>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]	Back alignment and domain information

>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO	Back alignment and domain information

>PF05670 DUF814: Domain of unknown function (DUF814); InterPro: IPR008532 This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity	Back alignment and domain information

>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]	Back alignment and domain information

>KOG3272 consensus Predicted coiled-coil protein [General function prediction only]	Back alignment and domain information

>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated	Back alignment and domain information

>PRK10445 endonuclease VIII; Provisional	Back alignment and domain information

>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]	Back alignment and domain information

>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional	Back alignment and domain information

>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional	Back alignment and domain information

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)	Back alignment and domain information

>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]	Back alignment and domain information

>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents	Back alignment and domain information

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional	Back alignment and domain information

>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms	Back alignment and domain information

>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>CHL00137 rps13 ribosomal protein S13; Validated	Back alignment and domain information

>PRK05179 rpsM 30S ribosomal protein S13; Validated	Back alignment and domain information

>TIGR03631 bact_S13 30S ribosomal protein S13	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		934
3doa_A		288	Fibrinogen binding protein; structural genomics, M	8e-33
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05

>3doa_A Fibrinogen binding protein; structural genomics, MCSG., protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp} Length = 288	Back alignment and structure

 Score =  127 bits (321), Expect = 8e-33
 Identities = 58/376 (15%), Positives = 116/376 (30%), Gaps = 99/376 (26%)

Query: 6   MNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVR 65
            +       V+ L+ L   R   +      T +  +            + +L +  +  R
Sbjct: 3   YDGLFTKKMVESLQFLTTGRVHKINQPDNDTILMVV-----RQNRQNHQLLLSIHPNFSR 57

Query: 66  LHTTAYARDKKNTPSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQF----GLGMNAHY-V 120
           L  T    D    P  F    RKH+    +E ++Q+G DR I         +G   +  V
Sbjct: 58  LQLTTKKYDNPFNPPMFARVFRKHLEGGIIESIKQIGNDRRIEIDIKSKDEIGDTIYRTV 117

Query: 121 ILELYA-QGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHR--YPTEICRVFERTTASKL 177
           ILE+     N++L D    ++   +    +       + +R   P               
Sbjct: 118 ILEIMGKHSNLILVDENRKIIEGFKHLTPN------TNHYRTVMPGFNYEAPPT------ 165

Query: 178 HAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQ 237
                              +   N  + +   +       + +++               
Sbjct: 166 -------------------QHKINPYDITGAEVLKYIDFNAGNIA--------------- 191

Query: 238 PTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQD 297
              K +L +  G+ P ++  I+     + +  L E                  F++ + +
Sbjct: 192 ---KQLLNQFEGFSPLITNEIVSRRQFMTSSTLPEA-----------------FDEVMAE 231

Query: 298 VISGDIVPEGYILMQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAA 357
                  P   I  +N   GK              ++F  + LNQF   + V +++ +  
Sbjct: 232 TKL----PPTPIFHKNHETGK--------------EDFYFIKLNQFND-DTVTYDSLNDL 272

Query: 358 LDEFYS-KIESQRAEQ 372
           LD FY  + E +R +Q
Sbjct: 273 LDRFYDARGERERVKQ 288

PyMOL of 3doa

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		934
3doa_A		288	Fibrinogen binding protein; structural genomics, M	100.0
3twl_A		310	Formamidopyrimidine-DNA glycosylase 1; helix two t	95.7
2xzf_A		271	Formamidopyrimidine-DNA glycosylase; hydrolase-DNA	95.05
1ee8_A		266	MUTM (FPG) protein; beta sandwich, zinc finger, he	93.96
1k82_A		268	Formamidopyrimidine-DNA glycosylase; protein-DNA c	93.77
3u6p_A		273	Formamidopyrimidine-DNA glycosylase; DNA glycosyla	93.36
3r8n_M		114	30S ribosomal protein S13; protein biosynthesis, R	89.72
3j20_O		148	30S ribosomal protein S13P; archaea, archaeal, KIN	86.52
3iz6_M		152	40S ribosomal protein S18 (S13P); eukaryotic ribos	86.27
2xzm_M		155	RPS18E; ribosome, translation; 3.93A {Tetrahymena	85.51
2vqe_M		126	30S ribosomal protein S13, 30S ribosomal protein S	84.94
3u5c_S		146	40S ribosomal protein S18-A, 40S ribosomal protein	82.89

>3doa_A Fibrinogen binding protein; structural genomics, MCSG., protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp}	Back alignment and structure

Probab=100.00  E-value=6.4e-45  Score=397.36  Aligned_cols=264  Identities=19%  Similarity=0.268  Sum_probs=195.8

Q ss_pred             CCHHHHHHHHHHHhhhcCCceeEEEecCCCEEEEEEeeCCCCccCCCCceEEEEEe--cc-ceEEeecccCCCCCCCcHH
Q 002338            6 MNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLME--SG-VRLHTTAYARDKKNTPSGF   82 (934)
Q Consensus         6 ms~lDv~a~v~EL~~L~G~RI~nIY~~~~~t~llk~~~~~g~~~~~~~~k~~Llie--sG-~RiHlT~~~~~k~~~Ps~F   82 (934)
                      ||++||+|++.||..|+|+||.||||+++++++|+|++++        ++..|+|+  ++ +|||+|++.+++|..||+|
T Consensus         3 ~d~~~l~a~~~EL~~l~g~ri~kIyq~~~~~l~l~l~~~~--------~~~~L~ls~~p~~~ri~lt~~~~~~p~~p~~F   74 (288)
T 3doa_A            3 YDGLFTKKMVESLQFLTTGRVHKINQPDNDTILMVVRQNR--------QNHQLLLSIHPNFSRLQLTTKKYDNPFNPPMF   74 (288)
T ss_dssp             SCHHHHHHHHHHHGGGTTCEEEEEEEEETTEEEEEEEETT--------EEEEEEEECCTTTCEEEEECC-------CCHH
T ss_pred             ccHHHHHHHHHHHHhhhCceEEEEEcCCCcEEEEEEEcCC--------CceEEEEEECCCceEEEEcCCCCCCCCCCcHH
Confidence            9999999999999669999999999999999999999874        35555555  44 9999999999999999999


Q ss_pred             HHHHHHHccCCceeEEEeeCCCeEEEEEEeeC----Cc-eEEEEEEEecC-ceEEEEcCCCcEEeeecccccC-CCcccc
Q 002338           83 TLKLRKHIRTRRLEDVRQLGYDRIILFQFGLG----MN-AHYVILELYAQ-GNILLTDSEFTVLTLLRSHRDD-DKGVAI  155 (934)
Q Consensus        83 ~m~LRKhL~g~RL~~V~Qlg~DRIV~~~f~~G----~~-~~~LIvEL~gr-gNIILtD~~~~IL~~lR~~~~~-~~~~~i  155 (934)
                      ||.|||||+|+||++|+|+|+||||.|+|+.+    +. .++||+||||+ |||||||++++||+++|+++.+ .+.|.|
T Consensus        75 ~m~LRk~L~g~ri~~i~Q~~~DRIv~~~f~~~~e~g~~~~~~Li~El~gr~SNiIL~d~~~~Il~~lr~v~~~~~~~R~i  154 (288)
T 3doa_A           75 ARVFRKHLEGGIIESIKQIGNDRRIEIDIKSKDEIGDTIYRTVILEIMGKHSNLILVDENRKIIEGFKHLTPNTNHYRTV  154 (288)
T ss_dssp             HHHHHHHHTTCEEEEEEESTTSSEEEEEEEEECTTSCEEEEEEEEECCGGGCEEEEEETTCBEEEESSCBCC-----CCB
T ss_pred             HHHHHHHhCCCEEEEEEECCCceEEEEEEeeccccCCccceEEEEEEcCCCceEEEEcCCCcEeeeeeccCcccccccee
Confidence            99999999999999999999999999999964    33 79999999999 6999999999999999999874 457899


Q ss_pred             ccCCcccCcccc-ccccCC--hhhhHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCCC
Q 002338          156 MSRHRYPTEICR-VFERTT--ASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDG  232 (934)
Q Consensus       156 ~~g~~Yp~~~~~-~~~p~~--~~kl~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~e~~~~~~~~~~~d~~~~~~~~~~~~  232 (934)
                      .+|.+|.+|+.. ..+|.+  .+.+.+.+.                                                  
T Consensus       155 ~pG~~Y~~Pp~~~k~~p~~~~~e~~~~~l~--------------------------------------------------  184 (288)
T 3doa_A          155 MPGFNYEAPPTQHKINPYDITGAEVLKYID--------------------------------------------------  184 (288)
T ss_dssp             STTSBCCCCCCCCCBCGGGCCHHHHGGGCC--------------------------------------------------
T ss_pred             cCCCcccCCccccCCCcccCCHHHHHHHHh--------------------------------------------------
Confidence            999999766642 233332  233322210                                                  


Q ss_pred             ccCCchhHHHHHhhhcCCCHHHHHHH-HHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEEe
Q 002338          233 ARAKQPTLKTVLGEALGYGPALSEHI-ILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILM  311 (934)
Q Consensus       233 ~~~~~~~lk~~L~~~~g~gp~laeei-~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~~~~l~~l~~~~~~p~gyi~~  311 (934)
                       ..+....+.+...+.||||.+|+|+ |+|+|.+.               ..++.+   +.+++..+.. ...|+.|  .
T Consensus       185 -~~~~~l~~~l~~~~~G~s~~la~El~~~ra~~~~---------------~~l~~~---~~~~~~~~~~-~~~p~i~--~  242 (288)
T 3doa_A          185 -FNAGNIAKQLLNQFEGFSPLITNEIVSRRQFMTS---------------STLPEA---FDEVMAETKL-PPTPIFH--K  242 (288)
T ss_dssp             -GGGCCHHHHHHHHBTTCCHHHHHHHHTTSSSCST---------------THHHHH---HHHHHHHHTS-CCCCEEC---
T ss_pred             -hCcchHHHHHHHHcCCCCHHHHHHHHHHHcCCcH---------------HHHHHH---HHHHHHHhhc-CCCcEEE--e
Confidence             0112234555556679999999999 99998531               234444   5666777764 3335432  1


Q ss_pred             cccCCCCCCCCCCCCCCCccceeeeeecccccccccccccccHHHHHHHHHHHH
Q 002338          312 QNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKI  365 (934)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~~~~f~P~~l~q~~~~~~~~f~sf~~AlDeffs~~  365 (934)
                      +.  .             ....+|+||+|.+|.+ +...|+||++|||+||...
T Consensus       243 ~~--~-------------~~~~~f~~~~l~~~~~-~~~~f~s~s~~Ld~yy~~k  280 (288)
T 3doa_A          243 NH--E-------------TGKEDFYFIKLNQFND-DTVTYDSLNDLLDRFYDAR  280 (288)
T ss_dssp             CT--T-------------TCCCCEESSCCTTCCS-CCEECSSHHHHHHHHTCC-
T ss_pred             CC--C-------------CCceEEEEEechhccC-CceeCCCHHHHHHHHHHHh
Confidence            11  0             0234899999999876 6678999999999999875

PyMOL of 3doa

>3twl_A Formamidopyrimidine-DNA glycosylase 1; helix two turns helix, zinc-LESS finger, hydrolase, DNA DAMA repair, DNA-binding, glycosidase, lyase; 1.70A {Arabidopsis thaliana} PDB: 3twm_A* 3twk_A	Back alignment and structure

>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET: VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A* 1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A 1pjj_A*	Back alignment and structure

>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken STR genomics/proteomics initiative, RSGI, structural genomics; 1.90A {Thermus thermophilus} SCOP: a.156.1.2 b.113.1.1 g.39.1.8	Back alignment and structure

>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8	Back alignment and structure

>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair, sequence context; HET: DNA 08Q; 1.60A {Geobacillus stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A* 3u6m_A* 3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A* 2f5q_A* 2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A 3sau_A* 3sar_A* 3sav_A* ...	Back alignment and structure

>3j20_O 30S ribosomal protein S13P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}	Back alignment and structure

>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}	Back alignment and structure

>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_M	Back alignment and structure

>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ...	Back alignment and structure

>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L 3u5g_S 1s1h_M 3jyv_M* 2zkq_m	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		934
d2hkja1		78	Topoisomerase VI-B subunit middle domain {Archaeon	95.23
d1r2za1		94	DNA repair protein MutM (Fpg) {Bacillus stearother	93.57
d1ee8a1		89	DNA repair protein MutM (Fpg) {Thermus thermophilu	92.89
d1tdza1		88	DNA repair protein MutM (Fpg) {Lactococcus lactis	92.88
d1k82a1		88	DNA repair protein MutM (Fpg) {Escherichia coli [T	91.79
d1k3xa1		89	Endonuclease VIII {Escherichia coli [TaxId: 562]}	91.09
d2uubm1		125	Ribosomal protein S13 {Thermus thermophilus [TaxId	87.68
d2gy9m1		114	Ribosomal protein S13 {Escherichia coli [TaxId: 56	87.31

>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]}	Back information, alignment and structure

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Topoisomerase VI-B subunit middle domain
domain: Topoisomerase VI-B subunit middle domain
species: Archaeon Sulfolobus shibatae [TaxId: 2286]

Probab=95.23  E-value=0.013  Score=48.94  Aligned_cols=49  Identities=31%  Similarity=0.435  Sum_probs=39.8

Q ss_pred             HHHHHh-hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338          240 LKTVLG-EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF  291 (934)
Q Consensus       240 lk~~L~-~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~  291 (934)
                      +..++. .+.|+|+.+|+|+|.+||++|..+++   .|+++++.+|+++++.+
T Consensus        26 ~~l~lq~~f~GvGn~~a~Eil~~agi~P~~~~~---~L~~~e~~~L~~air~~   75 (78)
T d2hkja1          26 IKEFLVNEFQSIGDTTADKILELAGLKPNKKVK---NLTEEEITRLVETFKKY   75 (78)
T ss_dssp             HHHHHHHHSSSCCHHHHHHHHHHHTCCTTSBGG---GCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhcccCHHHHHHHHHHhCCCcccccc---cCCHHHHHHHHHHHhhh
Confidence            334444 46699999999999999999998875   68999999999886543

PyMOL of d2hkja1

>d1r2za1 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1tdza1 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]}	Back information, alignment and structure

>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]}	Back information, alignment and structure