Citrus Sinensis ID: 012477

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460--
Protein Sequence
MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVFLC
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHccccEEEcccccccccEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEEccccccccccccHHHHHHHHHHcccEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccHHHHHHHcccEEEEccccccccccEEEEcccHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEEEcccEEEEEccccccHHHHHHHHccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEccccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEccccccccccEEEEEcccccHHHHHHHHHHHHHHHHccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHccccccccccccccEcc
Coil and Loop (DISEMBL)
magqrnsygkrshsqtdyadhgpnkrrytgddrdqfiigpedtvyrylcpirkigsiigrggEIVKQLRIdtkskirigetvpgseeRVVTVYsasdetnafedgdkfvspaQDALFKVHDRVIAeelrgdedsdgghqvtakllvpsdqigcvigkggqiVQNIRSETGAQIRIlkdehlpscalrsdeLVQISGEASVVKKALCQIAsrlhdnpsrSQHLLASAIsnshsssgslvgptaatpivgiaplmgpyggykgdtagdwsrslysaprddlsskefslrlvcpvaniggvigkggAIINQIRQEsgaaikvdssstegddclitvsskefFEDTLSATIEAVVRLQprcsekierdsglisfttrllvptsrigcligkggsIITEMRRLTKANIrilpkenlpkiaseddemvQISGDLDLAKDALIQVMTRLRANLfdregavstfvpvflc
Flexible Loop (DISEMBL)
magqrnsygkrshsqtdyadhgpnkrrytgddrdqfiigpedtvyryLCPIRKigsiigrggeivkqlridtkskirigetvpgseervvTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEElrgdedsdggHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAaikvdssstegdDCLITVSSKEFFEDTLSATIEAVVrlqprcsekierdsglisfttrllvptsrigcligkggsiiTEMRRLTKAnirilpkenlpkiaseddEMVQISGDLDLAKDALIQVMTRLRANLfdregavstfvpvflc
Low Complexity Region (SEG)
MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPirkigsiigrggeiVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAsaisnshsssgsLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPvaniggvigkggaiinQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVFLC
Disordered region (IsUnstruct)
*********************************DQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVP***ERVVTVYS*******************DALFKVHDRV******************AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIA*******************************TAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYS********KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAI*********DDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP*I******MVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVFL*
Disordered Region (DISOPRED)
*******************************************VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFK**********************TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAS*ISNSHSSS*SLV************************************************RLVCPVANIGGVIGKGG***********************************FEDTLSATIE***********************TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENL*KIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFD*****STFVPVFLC
Disordered Region (DISEMBL)
*******************DHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELR********HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAI***********GPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESG***********GDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVFLC
Disordered Region (DISPRO)
***************************************PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEE*********GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS*****LA**ISNSHSSSGSLVGPTAATPIVGIAPLM***************************SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVFLC
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVFLC
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	462	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.930	0.709	0.329	1e-53
O00425	579	Insulin-like growth facto	yes	no	0.774	0.618	0.226	2e-16
Q5RB68	556	Insulin-like growth facto	no	no	0.683	0.568	0.242	3e-15
Q5SF07	592	Insulin-like growth facto	yes	no	0.753	0.587	0.243	6e-15
Q9CPN8	579	Insulin-like growth facto	no	no	0.768	0.613	0.227	3e-14
Q9PW80	582	Insulin-like growth facto	no	no	0.761	0.604	0.235	5e-14
P57721	371	Poly(rC)-binding protein	no	no	0.573	0.714	0.270	8e-14
P57722	371	Poly(rC)-binding protein	no	no	0.573	0.714	0.270	1e-13
Q9UNW9	492	RNA-binding protein Nova-	no	no	0.448	0.420	0.255	2e-13
Q9Y6M1	599	Insulin-like growth facto	no	no	0.753	0.580	0.235	3e-13

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

 Score =  211 bits (537), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 161/489 (32%), Positives = 261/489 (53%), Gaps = 59/489 (12%)

Query: 10  KRSHSQTDYADHGPNKRRYTGDD---RDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVK 66
           KR   Q + ++   N++R    D   RD+ +      VYR LCPI  +G +IG+ G+++ 
Sbjct: 6   KRKQIQRNNSESNRNQKRRISHDKINRDELV------VYRILCPIDVVGGVIGKSGKVIN 59

Query: 67  QLRIDTKSKIRIGETVPGSEERVVTVYSA----SDETNAFEDGDKFVSPAQDALFKVHDR 122
            +R +TK+KI++ + + G  +RV+T+Y +     +E    +  ++ +  AQDAL KV+D 
Sbjct: 60  AIRHNTKAKIKVFDQLHGCSQRVITIYCSVKEKQEEIGFTKSENEPLCCAQDALLKVYDA 119

Query: 123 VIA--EELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL-KDE 179
           ++A  EE     + D       +LLVP  Q   +IGK G+ ++ IR  T A ++++ KD 
Sbjct: 120 IVASDEENNTKTNVDRDDNKECRLLVPFSQSSSLIGKAGENIKRIRRRTRASVKVVSKDV 179

Query: 180 HLPS--CALRSDELVQISGEASVVKKALCQIASRLHD-NP-------SRSQHLLASAI-- 227
             PS  CA+  D +V ISGE   VK+AL  +++ ++  NP       S SQ + A+++  
Sbjct: 180 SDPSHVCAMEYDNVVVISGEPESVKQALFAVSAIMYKINPRENIPLDSTSQDVPAASVIV 239

Query: 228 ----SNS-------HSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPR 276
               SNS       +S+   ++   A  P    A  +  + GY    A        S P 
Sbjct: 240 PSDLSNSVYPQTGFYSNQDHILQQGAGVPSYFNALSVSDFQGYAETAANPVPVFASSLPV 299

Query: 277 D-----DLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTE-GDD-C 329
                    S+E   +++CP+ NI  VIGKGG+ I +IR+ SG+ I+V+ S T+ GDD C
Sbjct: 300 THGFGGSSRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDEC 359

Query: 330 LITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGG 389
           +I V++ E  +D  S  +EAV+ LQ    E I  D    +   +LLV +  IGC+IGK G
Sbjct: 360 VIIVTATESPDDMKSMAVEAVLLLQ----EYIN-DEDAENVKMQLLVSSKVIGCVIGKSG 414

Query: 390 SIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDR 449
           S+I E+R+ T ANI I           + D++V++SG++   +DALIQ++ RLR ++   
Sbjct: 415 SVINEIRKRTNANICIS--------KGKKDDLVEVSGEVSSVRDALIQIVLRLREDVLGD 466

Query: 450 EGAVSTFVP 458
           + +V+T  P
Sbjct: 467 KDSVATRKP 475

Arabidopsis thaliana (taxid: 3702)

>sp|O00425|IF2B3_HUMAN Insulin-like growth factor 2 mRNA-binding protein 3 OS=Homo sapiens GN=IGF2BP3 PE=1 SV=2

 Score = 87.8 bits (216), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 95/419 (22%), Positives = 197/419 (47%), Gaps = 61/419 (14%)

Query: 40  PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDE 98
           P D   R L P + +G+IIG+ G  ++ +   T+SKI +  +   G+ E+ +T+ S  + 
Sbjct: 193 PCDLPLRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEG 252

Query: 99  TNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKG 158
           T+A          A  ++ ++  +  A++++  E+      +  K+L  ++ +G +IGK 
Sbjct: 253 TSA----------ACKSILEIMHKE-AQDIKFTEE------IPLKILAHNNFVGRLIGKE 295

Query: 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL---HDN 215
           G+ ++ I  +T  +I I   + L       +  + + G      KA  +I  ++   ++N
Sbjct: 296 GRNLKKIEQDTDTKITISPLQEL--TLYNPERTITVKGNVETCAKAEEEIMKKIRESYEN 353

Query: 216 PSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAP 275
              S +L A  I   + ++  L  PT+  P                 T+G  S      P
Sbjct: 354 DIASMNLQAHLIPGLNLNALGLFPPTSGMP---------------PPTSGPPSAMTPPYP 398

Query: 276 RDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSS 335
           + + S  E ++ L  P  ++G +IGK G  I Q+ + +GA+IK+  +  E  D  + +  
Sbjct: 399 QFEQSETE-TVHLFIPALSVGAIIGKQGQHIKQLSRFAGASIKI--APAEAPDAKVRMV- 454

Query: 336 KEFFEDTLSATIEAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGCLIGKGGS 390
                  ++   EA  + Q R   KI+ ++ +     +     + VP+   G +IGKGG 
Sbjct: 455 ------IITGPPEAQFKAQGRIYGKIKEENFVSPKEEVKLEAHIRVPSFAAGRVIGKGGK 508

Query: 391 IITEMRRLTKANIRILPKENLPKIASEDDE-MVQISGDL---DLAKDALIQVMTRLRAN 445
            + E++ L+ A + ++P++  P    E+D+ +V+I+G      +A+  + +++T+++ +
Sbjct: 509 TVNELQNLSSAEV-VVPRDQTP---DENDQVVVKITGHFYACQVAQRKIQEILTQVKQH 563

RNA-binding protein that act as a regulator of mRNA translation and stability. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binds to sequences in the 3'-UTR of CD44 mRNA.

Homo sapiens (taxid: 9606)

>sp|Q5RB68|IF2B2_PONAB Insulin-like growth factor 2 mRNA-binding protein 2 OS=Pongo abelii GN=IGF2BP2 PE=2 SV=1

 Score = 83.6 bits (205), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 94/388 (24%), Positives = 174/388 (44%), Gaps = 72/388 (18%)

Query: 42  DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDETN 100
           D   R L P + +G+IIG+ G  +K +   T+S++ I  +   G+ E+ VT+++  + T+
Sbjct: 193 DFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTS 252

Query: 101 AFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDG-GHQVTAKLLVPSDQIGCVIGKGG 159
                        +A      R+I E ++ + D      ++  K+L  +  +G +IGK G
Sbjct: 253 -------------EAC-----RMILEIMQKEADETKLAEEIPLKILAHNGLVGRLIGKEG 294

Query: 160 QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRS 219
           + ++ I  ETG +I I   + L       +  + + G       A  +I  +L +  +  
Sbjct: 295 RNLKKIEHETGTKITISSLQDL--SIYNPERTITVKGTVEACASAEIEIMKKLRE--AFE 350

Query: 220 QHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDL 279
             +LA    N+HS   S + P             GP+  +            +S P  ++
Sbjct: 351 NDMLAV---NTHSGYFSSLYPHHQ---------FGPFPHH------------HSYPEQEI 386

Query: 280 SSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFF 339
                 + L  P   +G +IGK GA I Q+ + +GA+IK+  +  EG D    VS +   
Sbjct: 387 ------VNLFIPTQAVGAIIGKKGAHIKQLARFAGASIKI--APAEGPD----VSERMVI 434

Query: 340 EDTLSATIEAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGCLIGKGGSIITE 394
              ++   EA  + Q R   K++ ++       +     + VP+S  G +IGKGG  + E
Sbjct: 435 ---ITGPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNE 491

Query: 395 MRRLTKANIRILPKENLPKIASEDDEMV 422
           ++ LT A + I+P++  P    E++E++
Sbjct: 492 LQNLTSAEV-IVPRDQTP---DENEEVI 515

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.

Pongo abelii (taxid: 9601)

>sp|Q5SF07|IF2B2_MOUSE Insulin-like growth factor 2 mRNA-binding protein 2 OS=Mus musculus GN=Igf2bp2 PE=1 SV=1

 Score = 82.4 bits (202), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 97/399 (24%), Positives = 181/399 (45%), Gaps = 51/399 (12%)

Query: 42  DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDETN 100
           D   R L P + +G+IIG+ G  +K +   T+S++ I  +   G+ E+ VT+++  + T+
Sbjct: 186 DFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTS 245

Query: 101 AFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDG-GHQVTAKLLVPSDQIGCVIGKGG 159
                        +A      R+I E ++ + D      +V  K+L  +  +G +IGK G
Sbjct: 246 -------------EAC-----RMILEIMQKEADETKLAEEVPLKILAHNGFVGRLIGKEG 287

Query: 160 QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD---NP 216
           + ++ I  ETG +I I   + L       +  + + G       A  +I  +L +   N 
Sbjct: 288 RNLKKIEHETGTKITISSLQDL--SIYNPERTITVRGTIEACANAEIEIMKKLREAFEND 345

Query: 217 SRSQHLLASAISNSH-------SSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSR 269
             + +  A+ I   +       S+  S++ P A    V  +P   P+  + G  +  +  
Sbjct: 346 MLAVNQQANLIPGLNLSALGIFSTGLSVLPPPAGPRGVPPSPPYHPFATHSGYFSSLYPH 405

Query: 270 SLYSAPRDDLSSKEF-SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD 328
             +       S  E  ++ L  P   +G +IGK GA I Q+ + +GA+IK+  +  EG D
Sbjct: 406 HHFGPFPHHHSYPEQETVSLFIPTQAVGAIIGKKGAHIKQLARFAGASIKI--APAEGPD 463

Query: 329 CLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGC 383
               VS +      ++   EA  + Q R   K++ ++       +     + VP+S  G 
Sbjct: 464 ----VSERMVI---ITGPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGR 516

Query: 384 LIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMV 422
           +IGKGG  + E++ LT A + I+P++  P    E++E++
Sbjct: 517 VIGKGGKTVNELQNLTSAEV-IVPRDQTP---DENEEVI 551

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.

Mus musculus (taxid: 10090)

>sp|Q9CPN8|IF2B3_MOUSE Insulin-like growth factor 2 mRNA-binding protein 3 OS=Mus musculus GN=Igf2bp3 PE=1 SV=1

 Score = 80.1 bits (196), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 96/422 (22%), Positives = 197/422 (46%), Gaps = 67/422 (15%)

Query: 40  PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDE 98
           P D   R L P + +G+IIG+ G  ++ +   T+SKI +  +   G+ E+ +T+ S  + 
Sbjct: 193 PCDLPLRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENTGAAEKSITILSTPEG 252

Query: 99  TNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKG 158
           T+A          A  ++ ++  +  A++++  E+      +  K+L  ++ +G +IGK 
Sbjct: 253 TSA----------ACKSILEIMHKE-AQDIKFTEE------IPLKILAHNNFVGRLIGKE 295

Query: 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL---HDN 215
           G+ ++ I  +T  +I I   + L       +  + + G      KA  +I  ++   ++N
Sbjct: 296 GRNLKKIEQDTDTKITISPLQEL--TLYNPERTITVKGSVETCAKAEEEIMKKIRESYEN 353

Query: 216 PSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAP---LMGPYGGYKGDTAGDWSRSLY 272
              S +L A  I   + ++  L  PT+  P     P   L  PY                
Sbjct: 354 DIASMNLQAHLIPGLNLNALGLFPPTSGMPPPTSGPPSTLTPPY---------------- 397

Query: 273 SAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
             P+ + S  E ++ L  P  ++G +IGK G  I Q+ + +GA+IK+  +  E  D  + 
Sbjct: 398 --PQFEQSETE-TVHLFIPALSVGAIIGKQGQHIKQLSRFAGASIKI--APAEAPDAKVR 452

Query: 333 VSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGCLIGK 387
           +         ++   EA  + Q R   KI+ ++ +     +     + VP+   G +IGK
Sbjct: 453 MV-------IITGPPEAQFKAQGRIYGKIKEENFVSPKEEVKLEAHIRVPSFAAGRVIGK 505

Query: 388 GGSIITEMRRLTKANIRILPKENLPKIASEDDE-MVQISGDL---DLAKDALIQVMTRLR 443
           GG  + E++ L+ A + ++P++  P    E+D+ +V+I+G      +A+  + +++T+++
Sbjct: 506 GGKTVNELQSLSSAEV-VVPRDQTP---DENDQVVVKITGHFYACQVAQRKIQEILTQVK 561

Query: 444 AN 445
            +
Sbjct: 562 QH 563

RNA-binding protein that act as a regulator of mRNA translation and stability. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binds to sequences in the 3'-UTR of CD44 mRNA.

Mus musculus (taxid: 10090)

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

 Score = 79.3 bits (194), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 99/421 (23%), Positives = 189/421 (44%), Gaps = 69/421 (16%)

Query: 42  DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDETN 100
           D   R L P + +G+IIG+ G  ++ +   T SKI I  +   G+ E+ +TV+S  +  +
Sbjct: 194 DVPLRLLVPTQFVGAIIGKEGATIRNITKQTHSKIDIHRKENAGAAEKPITVHSTPEGCS 253

Query: 101 AFEDGDKFVSPAQDALFKVHDRVIAEELRGDE-DSDGGHQVTAKLLVPSDQIGCVIGKGG 159
           +                    R I E ++ +  D+    ++  K+L  ++ +G +IGK G
Sbjct: 254 S------------------ACRNIMEIMQKEAIDTKITEEIPLKILAHNNFVGRLIGKEG 295

Query: 160 QIVQNIRSETGAQIRI--LKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL---HD 214
           + ++ I  +T  +I I  L+D  L       +  + + G      KA  +I  ++   ++
Sbjct: 296 RNLKKIEQDTDTKITISPLQDLTL----YNPERTITVKGTLDACAKAEEEIMKKVRESYE 351

Query: 215 NPSRSQHLLASAISNSHSSSGSLVGPTAAT----PIVGIAPLMGPYGGYKGDTAGDWSRS 270
           N   + HL ++ I   + ++  L  P AA+    P V   P  G   GY+   A   S +
Sbjct: 352 NDVAAMHLQSNLIPGLNLNALGLF-PGAASGGISPSVVSGPPPGAQAGYQSFGAQMESET 410

Query: 271 LYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCL 330
           ++               L  P   +G +IGK G  I Q+ + +GA+IK+  +  +G D  
Sbjct: 411 VH---------------LFIPALAVGAIIGKQGQHIKQLSRFAGASIKI--APADGIDAK 453

Query: 331 ITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGCLI 385
             +         +S   EA  + Q R   K++ ++       +     + VP+   G +I
Sbjct: 454 QRMV-------IISGPPEAQFKAQGRIFGKLKEENFFGPKEEVKLEAHIKVPSFAAGRVI 506

Query: 386 GKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL---DLAKDALIQVMTRL 442
           GKGG  + E++ LT A + ++P++  P     D  +V+I+G      LA+  + ++++++
Sbjct: 507 GKGGKTVNELQNLTSAEV-VVPRDQTPD--ENDQVVVKITGHFYASQLAQRKIQEIISQV 563

Query: 443 R 443
           R
Sbjct: 564 R 564

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

Danio rerio (taxid: 7955)

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

 Score = 78.6 bits (192), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 144/307 (46%), Gaps = 42/307 (13%)

Query: 46  RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDG 105
           R L   +++GSIIG+ GE VK++R ++ ++I I E      ER+VT+   +D        
Sbjct: 49  RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITGPTDAI------ 100

Query: 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI 165
             F + A  A +K  + +I      +  +     VT +L+VP+ Q G +IGKGG  ++ I
Sbjct: 101 --FKAFAMIA-YKFEEDIINS--MSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEI 155

Query: 166 RSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSR------- 218
           R  TGAQ+++  D  LP+   R+   V ISG    + + + QI   + ++P +       
Sbjct: 156 RESTGAQVQVAGD-MLPNSTERA---VTISGTPDAIIQCVKQICVVMLESPPKGATIPYR 211

Query: 219 -----SQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPY-------GGYKGDT--- 263
                +  + A   + +     ++  P   T +  +A    P+         + G+    
Sbjct: 212 PKPASTPVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNPAFPGEKLPL 271

Query: 264 -AGDWSRSLYSAPRD-DLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDS 321
            + + +++L       D S    +  L  P   IG +IG+ G  IN+IRQ SGA IK+ +
Sbjct: 272 HSSEEAQNLMGQSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKI-A 330

Query: 322 SSTEGDD 328
           ++TEG  
Sbjct: 331 NATEGSS 337

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

Homo sapiens (taxid: 9606)

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

 Score = 78.2 bits (191), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 144/307 (46%), Gaps = 42/307 (13%)

Query: 46  RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDG 105
           R L   +++GSIIG+ GE VK++R ++ ++I I E      ER+VT+   +D        
Sbjct: 49  RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITGPTDAI------ 100

Query: 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI 165
             F + A  A +K  + +I      +  +     VT +L+VP+ Q G +IGKGG  ++ I
Sbjct: 101 --FKAFAMIA-YKFEEDIINS--MSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEI 155

Query: 166 RSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSR------- 218
           R  TGAQ+++  D  LP+   R+   V ISG    + + + QI   + ++P +       
Sbjct: 156 RESTGAQVQVAGD-MLPNSTERA---VTISGTPDAIIQCVKQICVVMLESPPKGATIPYR 211

Query: 219 -----SQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPY-------GGYKGDT--- 263
                +  + A   + +     ++  P   T +  +A    P+         + G+    
Sbjct: 212 PKPASTPVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNPAFPGEKLPL 271

Query: 264 -AGDWSRSLYSAPRD-DLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDS 321
            + + +++L       D S    +  L  P   IG +IG+ G  IN+IRQ SGA IK+ +
Sbjct: 272 HSSEEAQNLMGQSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKI-A 330

Query: 322 SSTEGDD 328
           ++TEG  
Sbjct: 331 NATEGSS 337

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

Mus musculus (taxid: 10090)

>sp|Q9UNW9|NOVA2_HUMAN RNA-binding protein Nova-2 OS=Homo sapiens GN=NOVA2 PE=1 SV=1

 Score = 77.8 bits (190), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 109/231 (47%), Gaps = 24/231 (10%)

Query: 25  KRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET--- 81
           KR  TG++ + F+        + L P    GSIIG+GG+ + QL+ +T + I++ ++   
Sbjct: 23  KRSNTGEEGEYFL--------KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF 74

Query: 82  VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV-IAEELRGDEDSDGGHQV 140
            PG+ ERV  V   ++  NA      F++     + +   +  +   L+     +     
Sbjct: 75  YPGTTERVCLVQGTAEALNAVHS---FIAEKVREIPQAMTKPEVVNILQPQTTMNPDRAK 131

Query: 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV 200
            AKL+VP+   G +IGKGG  V+ +  ++GA +++ +    P      + +V +SGE   
Sbjct: 132 QAKLIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQK---PEGINLQERVVTVSGEPEQ 188

Query: 201 VKKALCQIASRLHDNPSRSQHL------LASAISNSHSSSGSLVGPTAATP 245
           V KA+  I  ++ ++P  S  L      +A  ++NS+ +      P    P
Sbjct: 189 VHKAVSAIVQKVQEDPQSSSCLNISYANVAGPVANSNPTGSPYASPADVLP 239

May regulate RNA splicing or metabolism in a specific subset of developing neurons (By similarity). Binds single strand RNA.

Homo sapiens (taxid: 9606)

>sp|Q9Y6M1|IF2B2_HUMAN Insulin-like growth factor 2 mRNA-binding protein 2 OS=Homo sapiens GN=IGF2BP2 PE=1 SV=2

 Score = 76.6 bits (187), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 94/399 (23%), Positives = 180/399 (45%), Gaps = 51/399 (12%)

Query: 42  DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDETN 100
           D   R L P + +G+IIG+ G  +K +   T+S++ I  +   G+ E+ VT+++  + T+
Sbjct: 193 DFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTS 252

Query: 101 AFEDGDKFVSPAQDALFKVHDRVIAEELRGDED-SDGGHQVTAKLLVPSDQIGCVIGKGG 159
                        +A      R+I E ++ + D +    ++  K+L  +  +G +IGK G
Sbjct: 253 -------------EAC-----RMILEIMQKEADETKLAEEIPLKILAHNGLVGRLIGKEG 294

Query: 160 QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD---NP 216
           + ++ I  ETG +I I   + L       +  + + G       A  +I  +L +   N 
Sbjct: 295 RNLKKIEHETGTKITISSLQDL--SIYNPERTITVKGTVEACASAEIEIMKKLREAFEND 352

Query: 217 SRSQHLLASAISNSH-------SSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSR 269
             + +  A+ I   +       S+  S++ P A       A    P+  + G  +  +  
Sbjct: 353 MLAVNQQANLIPGLNLSALGIFSTGLSVLSPPAGPRGAPPAAPYHPFTTHSGYFSSLYPH 412

Query: 270 SLYSA-PRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD 328
             +   P      ++  + L  P   +G +IGK GA I Q+ + +GA+IK+  +  EG D
Sbjct: 413 HQFGPFPHHHSYPEQEIVNLFIPTQAVGAIIGKKGAHIKQLARFAGASIKI--APAEGPD 470

Query: 329 CLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGC 383
               VS +      ++   EA  + Q R   K++ ++       +     + VP+S  G 
Sbjct: 471 ----VSERMVI---ITGPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGR 523

Query: 384 LIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMV 422
           +IGKGG  + E++ LT A + I+P++  P    E++E++
Sbjct: 524 VIGKGGKTVNELQNLTSAEV-IVPRDQTP---DENEEVI 558

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	462
224141011	531	predicted protein [Populus trichocarpa]	0.989	0.860	0.797	0.0
225452863	548	PREDICTED: KH domain-containing protein	0.991	0.835	0.817	0.0
356572762	548	PREDICTED: KH domain-containing protein	0.991	0.835	0.806	0.0
356550877	561	PREDICTED: KH domain-containing protein	0.991	0.816	0.791	0.0
449527609	546	PREDICTED: KH domain-containing protein	0.967	0.818	0.760	0.0
449447377	545	PREDICTED: KH domain-containing protein	0.967	0.820	0.760	0.0
357496471	553	Poly(rC)-binding protein [Medicago trunc	0.991	0.828	0.761	0.0
357496469	569	Poly(rC)-binding protein [Medicago trunc	0.991	0.804	0.761	0.0
356531744	540	PREDICTED: KH domain-containing protein	0.982	0.840	0.737	0.0
356568682	543	PREDICTED: KH domain-containing protein	0.982	0.836	0.737	0.0

>gi|224141011|ref|XP_002323868.1| predicted protein [Populus trichocarpa] gi|222866870|gb|EEF04001.1| predicted protein [Populus trichocarpa]

 Score =  745 bits (1924), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/460 (79%), Positives = 413/460 (89%), Gaps = 3/460 (0%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGR 60
           MAGQRNSYGKR+HSQ+DY D G NKRR +GDDR++F+I  +DTVYRYLCP RKIGSIIGR
Sbjct: 1   MAGQRNSYGKRAHSQSDY-DIGGNKRRNSGDDRERFVIDSQDTVYRYLCPARKIGSIIGR 59

Query: 61  GGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120
           GGEI+KQLRIDTKSKIR+GETVPG EERVVT+YS SDETN +ED   ++SPAQDALF+VH
Sbjct: 60  GGEIIKQLRIDTKSKIRVGETVPGCEERVVTIYSPSDETNEYEDSGNYISPAQDALFRVH 119

Query: 121 DRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180
           D+VIAE+L+ ++DS+G  QVTAKLLVPSDQIGC+IGKGGQIVQNIRSETGA IRILKDEH
Sbjct: 120 DKVIAEDLQVEDDSEGSPQVTAKLLVPSDQIGCIIGKGGQIVQNIRSETGAVIRILKDEH 179

Query: 181 LPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGP 240
           LP CAL SDELVQISGEA+V+KKAL QIASRLHDNPSRSQHLL SA+ N +SS GSLVGP
Sbjct: 180 LPPCALSSDELVQISGEAAVLKKALYQIASRLHDNPSRSQHLLVSAVPNVYSSVGSLVGP 239

Query: 241 TAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIG 300
           +AA PIVGIAPLMGPYGG+KGDT GDWSRSLYSAPRD+L+SKEFSLR+VCP ANIG VIG
Sbjct: 240 SAAAPIVGIAPLMGPYGGFKGDT-GDWSRSLYSAPRDELASKEFSLRVVCPTANIGAVIG 298

Query: 301 KGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEK 360
           KGG IINQIRQESGA IKVDSS  EGDDCLIT+S+KE + D  S TIEA VRLQPRCSEK
Sbjct: 299 KGGTIINQIRQESGATIKVDSSVAEGDDCLITISAKEIY-DHYSPTIEAAVRLQPRCSEK 357

Query: 361 IERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDE 420
           +ERDSGLISFTTRLLVP+SRIGCL+GKGG+II EMR+LTKA IRI  KENLPK+AS+DDE
Sbjct: 358 MERDSGLISFTTRLLVPSSRIGCLLGKGGAIIDEMRKLTKAIIRIPRKENLPKVASDDDE 417

Query: 421 MVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           MVQI+GDLD+AKDALIQ+  RLRAN+FDREGA+S  +PV 
Sbjct: 418 MVQIAGDLDVAKDALIQISRRLRANVFDREGAMSAILPVL 457

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452863|ref|XP_002283766.1| PREDICTED: KH domain-containing protein At4g18375 [Vitis vinifera] gi|296082939|emb|CBI22240.3| unnamed protein product [Vitis vinifera]

 Score =  742 bits (1916), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/461 (81%), Positives = 419/461 (90%), Gaps = 3/461 (0%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGR 60
           MAGQRNSYGKR+HSQ+DY D+G NKRR  GDDRD F I PEDTVYRYLCP RKIGSIIGR
Sbjct: 1   MAGQRNSYGKRAHSQSDYGDNGGNKRRNPGDDRDPFTIEPEDTVYRYLCPGRKIGSIIGR 60

Query: 61  GGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120
           GGEIVKQLR+DTKSKIRIGETVPG EERVVT+YS+SDETNAF+D D FVSPAQDALF+VH
Sbjct: 61  GGEIVKQLRVDTKSKIRIGETVPGCEERVVTIYSSSDETNAFDDSDTFVSPAQDALFRVH 120

Query: 121 DRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180
           DRV++EE+ G EDS+   QVT +LLVPSDQIGCVIGKGGQI+Q+IRSE+GAQ+RILKD+H
Sbjct: 121 DRVVSEEVHG-EDSEEASQVTVRLLVPSDQIGCVIGKGGQIIQSIRSESGAQVRILKDDH 179

Query: 181 LPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGP 240
           LPSCAL SDELVQISGE S+V+KAL QIASRLHDNPSRSQHLLASA+   +SS GSL+GP
Sbjct: 180 LPSCALSSDELVQISGEPSLVRKALYQIASRLHDNPSRSQHLLASAVPTGYSSGGSLMGP 239

Query: 241 TAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIG 300
           T+  PI+G+APL+G YGGY+GD+ GDWSRSLYSAPRD+ SSKEFSLRLVCP+ NIGGVIG
Sbjct: 240 TSGAPIMGLAPLVGTYGGYRGDS-GDWSRSLYSAPRDEASSKEFSLRLVCPIGNIGGVIG 298

Query: 301 KGGAIINQIRQESGAAIKVDSSST-EGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE 359
           KGG IINQIRQESGAAIKVDS+S  E DDCLI +S+KEFFEDT S TIEA VRLQPRCSE
Sbjct: 299 KGGVIINQIRQESGAAIKVDSTSAAEADDCLIAISAKEFFEDTFSPTIEAAVRLQPRCSE 358

Query: 360 KIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDD 419
           K+ERDSG++SFTTRLLVPTSRIGCLIGKGG+IITEMR+LTKANIRIL KENLPK+ASEDD
Sbjct: 359 KVERDSGIVSFTTRLLVPTSRIGCLIGKGGAIITEMRKLTKANIRILSKENLPKVASEDD 418

Query: 420 EMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           EMVQI+GDLD+AKDALIQV TRLRANLFDREGAVS FVPV 
Sbjct: 419 EMVQIAGDLDVAKDALIQVTTRLRANLFDREGAVSAFVPVL 459

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572762|ref|XP_003554535.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  742 bits (1916), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/461 (80%), Positives = 414/461 (89%), Gaps = 3/461 (0%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGR 60
           M GQR+ YGKR HSQ+D+ D+GPNKRR  GDDR+QF+I  EDTVYRY+CP RKIGS+IGR
Sbjct: 1   MGGQRSGYGKRPHSQSDH-DNGPNKRRNHGDDREQFVIDLEDTVYRYVCPGRKIGSVIGR 59

Query: 61  GGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120
           GGEIVKQLR++TK+KIRIGETVPG EERVVT+YS SDETNA E G  +VSPAQDALFKVH
Sbjct: 60  GGEIVKQLRVETKAKIRIGETVPGCEERVVTIYSPSDETNAVEGGGNYVSPAQDALFKVH 119

Query: 121 DRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180
           DRV+AE+  GD+D DGG QVTAKLLVPSDQIGCVIGKGG IVQNIRSETGAQIRILKD+H
Sbjct: 120 DRVVAEDFHGDQDDDGGQQVTAKLLVPSDQIGCVIGKGGSIVQNIRSETGAQIRILKDDH 179

Query: 181 LPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGP 240
           LP CAL SDELVQI+G+ASVVKKALCQIASRLHDNPSRSQHLL SA+   + + GSL+GP
Sbjct: 180 LPLCALSSDELVQITGDASVVKKALCQIASRLHDNPSRSQHLLTSAVPGVYPAGGSLIGP 239

Query: 241 TAATPIVGIAPLMGPYGGYKGDTAGDW-SRSLYSAPRDDLSSKEFSLRLVCPVANIGGVI 299
            A  PIVGIAPL+G YGGYKGDT GDW  RS+YSAPRD+ S+KEFS+RLVCP  NIGGVI
Sbjct: 240 GAGAPIVGIAPLVGAYGGYKGDT-GDWPPRSMYSAPRDEASTKEFSVRLVCPTGNIGGVI 298

Query: 300 GKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE 359
           GKGG IINQIRQESGA IKVDSS+TEGD+CLI +S+KEFFE+T S TIEA VRLQPRCSE
Sbjct: 299 GKGGMIINQIRQESGATIKVDSSTTEGDECLIAISTKEFFEETFSPTIEAAVRLQPRCSE 358

Query: 360 KIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDD 419
           K+ERDSG+ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI+ KENLPKIASEDD
Sbjct: 359 KVERDSGIISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRIISKENLPKIASEDD 418

Query: 420 EMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           EMVQISGDLD+AKDAL+ V+TRLRANLFDREGA+S+F+PV 
Sbjct: 419 EMVQISGDLDIAKDALVHVLTRLRANLFDREGALSSFLPVL 459

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550877|ref|XP_003543809.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  730 bits (1884), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/461 (79%), Positives = 410/461 (88%), Gaps = 3/461 (0%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGR 60
           M GQR+ YGKR HSQ+D+ D+GPNKRR  GDDR+QF+I  EDTVYRY+CP RKIGS+IGR
Sbjct: 1   MGGQRSGYGKRPHSQSDH-DNGPNKRRNHGDDREQFVIDSEDTVYRYVCPGRKIGSVIGR 59

Query: 61  GGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120
           GGEIVKQLR++TK+KIRIGETVPG EERVVT+Y  SDETNA E G  +VSPAQDALFKVH
Sbjct: 60  GGEIVKQLRVETKAKIRIGETVPGCEERVVTIYGPSDETNAVEGGGNYVSPAQDALFKVH 119

Query: 121 DRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180
           DRV+AE+  GD+D DGG QVTAKLLVPSDQIGCVIGKGG IVQNIR ETGAQIRILKD+H
Sbjct: 120 DRVVAEDFHGDQDDDGGQQVTAKLLVPSDQIGCVIGKGGSIVQNIRGETGAQIRILKDDH 179

Query: 181 LPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGP 240
           LP CAL SDELVQI+G+A+VVKKAL QIASRLHDNPSRSQHLL SA+S  + + GSL+GP
Sbjct: 180 LPMCALSSDELVQITGDAAVVKKALYQIASRLHDNPSRSQHLLTSAVSGVYPAGGSLIGP 239

Query: 241 TAATPIVGIAPLMGPYGGYKGDTAGDW-SRSLYSAPRDDLSSKEFSLRLVCPVANIGGVI 299
            A  PIVGIAPL+G YGGYKGDT GDW  RS+YSAPRD+ SSKEFS+RLVCP  NIGGVI
Sbjct: 240 GAGAPIVGIAPLVGSYGGYKGDT-GDWPPRSMYSAPRDEASSKEFSVRLVCPTGNIGGVI 298

Query: 300 GKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE 359
           GKGG IINQIRQ+SGA IKVDSS+ EGD+CLI +S+KEFFE+T S TIEA VRLQPRCSE
Sbjct: 299 GKGGMIINQIRQDSGATIKVDSSTIEGDECLIAISTKEFFEETFSPTIEAAVRLQPRCSE 358

Query: 360 KIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDD 419
           K+ERDSG+ISFTTRLLVPT+RIGCLIGKGGSIIT+MRRLTKANIRI+ KENLPKIA+EDD
Sbjct: 359 KVERDSGIISFTTRLLVPTTRIGCLIGKGGSIITDMRRLTKANIRIISKENLPKIANEDD 418

Query: 420 EMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           EMVQISGDLD+AKDAL+ V+TRLRANLFDREGA+S F+PV 
Sbjct: 419 EMVQISGDLDVAKDALVHVLTRLRANLFDREGALSAFLPVL 459

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449527609|ref|XP_004170802.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  728 bits (1880), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/460 (76%), Positives = 405/460 (88%), Gaps = 13/460 (2%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGR 60
           MAGQRNSYGKR+HSQ+DY+++G NKRR  G+DRDQF+I  EDTVYRYLCP++KIGS+IGR
Sbjct: 1   MAGQRNSYGKRNHSQSDYSENGGNKRRSHGEDRDQFVIDSEDTVYRYLCPVKKIGSVIGR 60

Query: 61  GGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120
           GGEIVKQLRIDTKSKIRIGETVPGS+ERV+T+YSAS+ETN+ E+   +VSPAQ+ALFK+H
Sbjct: 61  GGEIVKQLRIDTKSKIRIGETVPGSDERVITIYSASNETNSLEESSDYVSPAQEALFKIH 120

Query: 121 DRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180
           DRV+A++   ++   GGHQVTA+LLVPSDQIGC+IGKGGQIVQNIR+ETGAQ+RILKD+H
Sbjct: 121 DRVVADDYMDEDSEGGGHQVTARLLVPSDQIGCIIGKGGQIVQNIRTETGAQVRILKDDH 180

Query: 181 LPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGP 240
           LP CAL SDELVQISGE  +VKKAL QIASRLHDNPSRSQHLLASAI   +SS GSL+ P
Sbjct: 181 LPRCALSSDELVQISGEPLIVKKALYQIASRLHDNPSRSQHLLASAIPGVYSSGGSLMAP 240

Query: 241 TAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIG 300
           T   PI+G+APL+ PYGGYK             APR+DLSSKEFSLRL+CP  NIGGVIG
Sbjct: 241 THGAPIMGLAPLVSPYGGYK-------------APREDLSSKEFSLRLICPTENIGGVIG 287

Query: 301 KGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEK 360
           KGGAIINQIRQE+ AAIKVDSS+TEGDDCLI +SSKEFFED+ S T+EA +RLQPRCSEK
Sbjct: 288 KGGAIINQIRQETKAAIKVDSSATEGDDCLINISSKEFFEDSYSPTLEAALRLQPRCSEK 347

Query: 361 IERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDE 420
           +ERDSG+ISFTTRLLVPTSRIGCLIGKGG+IITE+RRLTKANIRIL KENLPK+A EDDE
Sbjct: 348 VERDSGIISFTTRLLVPTSRIGCLIGKGGAIITELRRLTKANIRILSKENLPKVALEDDE 407

Query: 421 MVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           MVQISGDLD+AK+AL+ ++TRLRANLFDREGA+S  +PV 
Sbjct: 408 MVQISGDLDVAKEALVHIVTRLRANLFDREGALSAVLPVL 447

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447377|ref|XP_004141445.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  728 bits (1880), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/460 (76%), Positives = 405/460 (88%), Gaps = 13/460 (2%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGR 60
           MAGQRNSYGKR+HSQ+DY+++G NKRR  G+DRDQF+I  EDTVYRYLCP++KIGS+IGR
Sbjct: 1   MAGQRNSYGKRNHSQSDYSENGGNKRRSHGEDRDQFVIDSEDTVYRYLCPVKKIGSVIGR 60

Query: 61  GGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120
           GGEIVKQLRIDTKSKIRIGETVPGS+ERV+T+YSAS+ETN+ E+   +VSPAQ+ALFK+H
Sbjct: 61  GGEIVKQLRIDTKSKIRIGETVPGSDERVITIYSASNETNSLEESSDYVSPAQEALFKIH 120

Query: 121 DRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180
           DRV+A++   ++   GGHQVTA+LLVPSDQIGC+IGKGGQIVQNIR+ETGAQ+RILKD+H
Sbjct: 121 DRVVADDYMDEDSEGGGHQVTARLLVPSDQIGCIIGKGGQIVQNIRTETGAQVRILKDDH 180

Query: 181 LPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGP 240
           LP CAL SDELVQISGE  +VKKAL QIASRLHDNPSRSQHLLASAI   +SS GSL+ P
Sbjct: 181 LPRCALSSDELVQISGEPLIVKKALYQIASRLHDNPSRSQHLLASAIPGVYSSGGSLMAP 240

Query: 241 TAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIG 300
           T   PI+G+APL+ PYGGYK             APR+DLSSKEFSLRL+CP  NIGGVIG
Sbjct: 241 THGAPIMGLAPLVSPYGGYK-------------APREDLSSKEFSLRLICPTENIGGVIG 287

Query: 301 KGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEK 360
           KGGAIINQIRQE+ AAIKVDSS+TEGDDCLI +SSKEFFED+ S T+EA +RLQPRCSEK
Sbjct: 288 KGGAIINQIRQETKAAIKVDSSATEGDDCLINISSKEFFEDSYSPTLEAALRLQPRCSEK 347

Query: 361 IERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDE 420
           +ERDSG+ISFTTRLLVPTSRIGCLIGKGG+IITE+RRLTKANIRIL KENLPK+A EDDE
Sbjct: 348 VERDSGIISFTTRLLVPTSRIGCLIGKGGAIITELRRLTKANIRILSKENLPKVALEDDE 407

Query: 421 MVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           MVQISGDLD+AK+AL+ ++TRLRANLFDREGA+S  +PV 
Sbjct: 408 MVQISGDLDVAKEALVHIVTRLRANLFDREGALSAVLPVL 447

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357496471|ref|XP_003618524.1| Poly(rC)-binding protein [Medicago truncatula] gi|355493539|gb|AES74742.1| Poly(rC)-binding protein [Medicago truncatula]

 Score =  679 bits (1753), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/466 (76%), Positives = 408/466 (87%), Gaps = 8/466 (1%)

Query: 1   MAGQR--NSYGKRSHSQTDYADHGPNKRRYTGDDRD--QFIIGPEDTVYRYLCPIRKIGS 56
           M GQR  ++YGKR  SQ+DY   G  +R     DRD  QF+I  EDTV+RYLCP RKIGS
Sbjct: 1   MGGQRERSNYGKRPRSQSDYDGGGNKRRNGGDHDRDREQFVINKEDTVFRYLCPGRKIGS 60

Query: 57  IIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDAL 116
           IIGRGGEIVKQLR++TK+KIRIGETVPG +ERVVTVYS+SDETN  +DGDK VSPA+DAL
Sbjct: 61  IIGRGGEIVKQLRVETKAKIRIGETVPGCDERVVTVYSSSDETNTVDDGDKLVSPAEDAL 120

Query: 117 FKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176
           FK+HDRV+AE+L  D++ +GG QV AKLLVPSDQIGCV+GKGGQIVQN+RSETGAQIRIL
Sbjct: 121 FKIHDRVVAEDLHSDQEEEGGPQVNAKLLVPSDQIGCVLGKGGQIVQNLRSETGAQIRIL 180

Query: 177 KDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGS 236
           KD+H+P+CALRSDELVQISG+A+VVKKAL QIASRLH NPSR+QHLL SA+ + + S GS
Sbjct: 181 KDDHVPACALRSDELVQISGDAAVVKKALHQIASRLHHNPSRTQHLLGSAVPSVYPSGGS 240

Query: 237 LVGPTAATPIVGIAPLMGPYGGYKGDTAGDW-SRSLYSAPRDDL-SSKEFSLRLVCPVAN 294
           L+GPTA  PIVG+APL+GPYGGYK DT GDW  RS+YSAPRD++ SSKEFS+RLVCP  N
Sbjct: 241 LMGPTAGPPIVGMAPLVGPYGGYKSDT-GDWPPRSMYSAPRDEISSSKEFSVRLVCPTGN 299

Query: 295 IGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQ 354
           +GGVIGKGG IINQIRQ+SGA IKVDSS+ +GDDCLIT+S+KEFFE+T S T+EA V LQ
Sbjct: 300 LGGVIGKGGGIINQIRQDSGATIKVDSSA-KGDDCLITISTKEFFEETFSPTVEAAVLLQ 358

Query: 355 PRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKI 414
           PRCSEK ERDSG+ISFTTRLLV +SRIGCLIGKGGSIITEMRRLTK+NIRIL KENLPKI
Sbjct: 359 PRCSEKSERDSGIISFTTRLLVSSSRIGCLIGKGGSIITEMRRLTKSNIRILSKENLPKI 418

Query: 415 ASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           AS+DDEMVQISGDLD+AKDAL+QV+TRLRANLFDREGAV  F+PV 
Sbjct: 419 ASDDDEMVQISGDLDVAKDALVQVLTRLRANLFDREGAVPGFLPVL 464

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357496469|ref|XP_003618523.1| Poly(rC)-binding protein [Medicago truncatula] gi|355493538|gb|AES74741.1| Poly(rC)-binding protein [Medicago truncatula]

 Score =  679 bits (1751), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/466 (76%), Positives = 408/466 (87%), Gaps = 8/466 (1%)

Query: 1   MAGQR--NSYGKRSHSQTDYADHGPNKRRYTGDDRD--QFIIGPEDTVYRYLCPIRKIGS 56
           M GQR  ++YGKR  SQ+DY   G  +R     DRD  QF+I  EDTV+RYLCP RKIGS
Sbjct: 1   MGGQRERSNYGKRPRSQSDYDGGGNKRRNGGDHDRDREQFVINKEDTVFRYLCPGRKIGS 60

Query: 57  IIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDAL 116
           IIGRGGEIVKQLR++TK+KIRIGETVPG +ERVVTVYS+SDETN  +DGDK VSPA+DAL
Sbjct: 61  IIGRGGEIVKQLRVETKAKIRIGETVPGCDERVVTVYSSSDETNTVDDGDKLVSPAEDAL 120

Query: 117 FKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176
           FK+HDRV+AE+L  D++ +GG QV AKLLVPSDQIGCV+GKGGQIVQN+RSETGAQIRIL
Sbjct: 121 FKIHDRVVAEDLHSDQEEEGGPQVNAKLLVPSDQIGCVLGKGGQIVQNLRSETGAQIRIL 180

Query: 177 KDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGS 236
           KD+H+P+CALRSDELVQISG+A+VVKKAL QIASRLH NPSR+QHLL SA+ + + S GS
Sbjct: 181 KDDHVPACALRSDELVQISGDAAVVKKALHQIASRLHHNPSRTQHLLGSAVPSVYPSGGS 240

Query: 237 LVGPTAATPIVGIAPLMGPYGGYKGDTAGDW-SRSLYSAPRDDL-SSKEFSLRLVCPVAN 294
           L+GPTA  PIVG+APL+GPYGGYK DT GDW  RS+YSAPRD++ SSKEFS+RLVCP  N
Sbjct: 241 LMGPTAGPPIVGMAPLVGPYGGYKSDT-GDWPPRSMYSAPRDEISSSKEFSVRLVCPTGN 299

Query: 295 IGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQ 354
           +GGVIGKGG IINQIRQ+SGA IKVDSS+ +GDDCLIT+S+KEFFE+T S T+EA V LQ
Sbjct: 300 LGGVIGKGGGIINQIRQDSGATIKVDSSA-KGDDCLITISTKEFFEETFSPTVEAAVLLQ 358

Query: 355 PRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKI 414
           PRCSEK ERDSG+ISFTTRLLV +SRIGCLIGKGGSIITEMRRLTK+NIRIL KENLPKI
Sbjct: 359 PRCSEKSERDSGIISFTTRLLVSSSRIGCLIGKGGSIITEMRRLTKSNIRILSKENLPKI 418

Query: 415 ASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           AS+DDEMVQISGDLD+AKDAL+QV+TRLRANLFDREGAV  F+PV 
Sbjct: 419 ASDDDEMVQISGDLDVAKDALVQVLTRLRANLFDREGAVPGFLPVL 464

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531744|ref|XP_003534436.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  674 bits (1740), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/461 (73%), Positives = 394/461 (85%), Gaps = 7/461 (1%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRY-TGDDRDQFIIGPEDTVYRYLCPIRKIGSIIG 59
           M GQR+SYGKRSHS +D      NKRR    D+    +I  +DTV+RYLCP+RKIGS+IG
Sbjct: 1   MTGQRSSYGKRSHSHSDSDAGSKNKRRNPAADESSSSLITADDTVFRYLCPVRKIGSVIG 60

Query: 60  RGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKV 119
           RGG+IVKQLR DTK+KIRIG+ +PG +ERVVT++S+S+ETN F++ D  VSPAQDALF+V
Sbjct: 61  RGGDIVKQLRADTKAKIRIGDALPGCDERVVTIHSSSEETNHFDETDDLVSPAQDALFRV 120

Query: 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
           H RVIAE+ R DED +  H VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD+
Sbjct: 121 HQRVIAEDAREDEDEERNH-VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDD 179

Query: 180 HLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVG 239
            LP CAL +DELVQISGEA+VVKKAL QIA+++ DNPSRSQHLLASA+   +++ G    
Sbjct: 180 RLPPCALSTDELVQISGEAAVVKKALFQIAAQIRDNPSRSQHLLASAVPGGYATGG---- 235

Query: 240 PTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVI 299
           P A  PI+G+AP +G YGGYKGDT GDWSRSLY APRD+ S +EFS+R VCP  NIGGVI
Sbjct: 236 PGAGAPIMGVAPFVGAYGGYKGDT-GDWSRSLYPAPRDEASMREFSVRFVCPTGNIGGVI 294

Query: 300 GKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE 359
           GKGGAIINQIRQ+SGA IKVDSS+TEGDDCLI +S+KEFFED+ S TIEA VRLQPRCSE
Sbjct: 295 GKGGAIINQIRQDSGATIKVDSSATEGDDCLIIISTKEFFEDSFSPTIEAAVRLQPRCSE 354

Query: 360 KIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDD 419
           K+ERDSG++SFTTRLLVPTSRIGCLIGKGG+I+TEMRRLTKANIRIL K+NLPKIASEDD
Sbjct: 355 KVERDSGIVSFTTRLLVPTSRIGCLIGKGGTIVTEMRRLTKANIRILSKDNLPKIASEDD 414

Query: 420 EMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           EMVQISGDLD+AKDAL+Q +TRLRANLFD+E AVS F+PV 
Sbjct: 415 EMVQISGDLDVAKDALVQALTRLRANLFDKERAVSGFLPVL 455

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568682|ref|XP_003552539.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  659 bits (1699), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/461 (73%), Positives = 390/461 (84%), Gaps = 7/461 (1%)

Query: 1   MAGQRNSYGKRSHSQTDYADHGPNKRRY-TGDDRDQFIIGPEDTVYRYLCPIRKIGSIIG 59
           M GQR SYGKRSHS +D      NKRR    DD    +I  +DTV+RYLCP+RKIGS+IG
Sbjct: 1   MTGQRISYGKRSHSHSDSDAGSKNKRRNPAADDSSSSLITADDTVFRYLCPVRKIGSVIG 60

Query: 60  RGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKV 119
           RGG+IVKQLR DTK+KIRIG+ +PG +ERVVT++S+S+ETN F++    VSPAQDALF+V
Sbjct: 61  RGGDIVKQLRADTKAKIRIGDALPGCDERVVTIHSSSEETNHFDETGDLVSPAQDALFRV 120

Query: 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
           H RVIAE+ R DED +  H VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD+
Sbjct: 121 HQRVIAEDAREDEDDERNH-VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDD 179

Query: 180 HLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVG 239
            LP CAL +DELVQISGEA+VVKKAL QIA+++ DNPSRSQHLLASA+   +++ G    
Sbjct: 180 RLPPCALSNDELVQISGEAAVVKKALFQIAAQIRDNPSRSQHLLASAVPGGYAAGGP--- 236

Query: 240 PTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVI 299
             A  PI+G+AP +G YGGYKGDT GDWSRSLY APRD+ S +EFS+R VCP  NIGGVI
Sbjct: 237 -GAGAPIMGVAPFVGAYGGYKGDT-GDWSRSLYPAPRDEASMREFSVRFVCPTGNIGGVI 294

Query: 300 GKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE 359
           GKGGAIINQIRQ+SGA IKVDSS+TEGDDCLI +S KEFFED+ S TIEA VRLQPRCSE
Sbjct: 295 GKGGAIINQIRQDSGATIKVDSSATEGDDCLIIISMKEFFEDSFSPTIEAAVRLQPRCSE 354

Query: 360 KIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDD 419
           K+ERDSG++SFTTRLLVPTSRIGCLIGKGG+I+TEMRRLTKANIRIL KENLPKIASEDD
Sbjct: 355 KVERDSGIVSFTTRLLVPTSRIGCLIGKGGTIVTEMRRLTKANIRILSKENLPKIASEDD 414

Query: 420 EMVQISGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPVF 460
           EMVQISGDLD+AKDAL+Q +TRLRANLFD+E AVS F+PV 
Sbjct: 415 EMVQISGDLDVAKDALVQALTRLRANLFDKERAVSGFLPVL 455

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	462
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.969	0.817	0.632	1.2e-150
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.699	0.674	0.444	4.9e-69
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.354	0.254	0.404	2.8e-48
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.859	0.608	0.307	2.3e-46
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.352	0.262	0.353	3.4e-39
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.441	0.336	0.313	1.6e-38
TAIR|locus:2056951	153	AT2G03110 "AT2G03110" [Arabido	0.307	0.928	0.522	1.3e-34
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.374	0.273	0.309	1.1e-18
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.393	0.315	0.303	6.8e-18
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.383	0.357	0.288	2.5e-12

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

 Score = 1470 (522.5 bits), Expect = 1.2e-150, P = 1.2e-150
 Identities = 288/455 (63%), Positives = 353/455 (77%)

Query:     5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPXXXXXXXXXXXXXX 64
             R+S+ KRS  Q+DY D+G +KRRY GDDRD  +I  +DTV+RYLCP              
Sbjct:    12 RDSHRKRSRPQSDYDDNGGSKRRYRGDDRDSLVIDRDDTVFRYLCPVKKIGSVIGRGGDI 71

Query:    65 VKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124
             VKQLR DT+SKIRIGE +PG +ERV+T+YS SDETNAF DG+K +SPAQDALF++HDRV+
Sbjct:    72 VKQLRNDTRSKIRIGEAIPGCDERVITIYSPSDETNAFGDGEKVLSPAQDALFRIHDRVV 131

Query:   125 AEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSC 184
             A++ R ++  +G  QVTAKLLVPSDQIGC++G+GGQIVQNIRSETGAQIRI+KD ++P C
Sbjct:   132 ADDARSEDSPEGEKQVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPLC 191

Query:   185 ALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAXXXXXXXXXXXXLVGPTAAT 244
             AL SDEL+QISGE  +VKKAL QIASRLH+NPSRSQ+LL+            L+      
Sbjct:   192 ALNSDELIQISGEVLIVKKALLQIASRLHENPSRSQNLLSSSGGYPAGS---LMSHAGGP 248

Query:   245 PIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPXXXXXXXXXXXXX 304
              +VG+APLMG YG    D AGDWSR LY  PR+D  + EF +RLV P             
Sbjct:   249 RLVGLAPLMGSYGR---D-AGDWSRPLYQPPRNDPPATEFFIRLVSPVENIASVIGKGGA 304

Query:   305 XXXQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364
                Q+RQE+ A IKVDSS TEG+DCLIT+S++E FED  S TIEAV+RLQP+CS+K+ERD
Sbjct:   305 LINQLRQETRATIKVDSSRTEGNDCLITISAREVFEDAYSPTIEAVMRLQPKCSDKVERD 364

Query:   365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQI 424
             SGL+SFTTRLLVP+SRIGC++GKGG+IITEMRR+TKANIRIL KENLPK+AS+DDEMVQI
Sbjct:   365 SGLVSFTTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLPKVASDDDEMVQI 424

Query:   425 SGDLDLAKDALIQVMTRLRANLFDREGAVSTFVPV 459
             SG+LD+AK+ALIQ+ +RLRAN+FDREGAVS  +PV
Sbjct:   425 SGELDVAKEALIQITSRLRANVFDREGAVSALMPV 459

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 700 (251.5 bits), Expect = 4.9e-69, P = 4.9e-69
 Identities = 157/353 (44%), Positives = 210/353 (59%)

Query:     5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPXXXXXXXXXXXXXX 64
             RN +GKRS+ Q+++  +G +KRR   D+ DQ +I  EDTVYRYLCP              
Sbjct:     6 RNIHGKRSNLQSEFTGNGGSKRRNLHDETDQNVIASEDTVYRYLCPVKKTGSIIGKGGEI 65

Query:    65 VKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124
              KQ+R +TKS +RI E +PG EERVVT+YS ++E N F D  + V PA DALFKVHD V+
Sbjct:    66 AKQIRSETKSNMRINEALPGCEERVVTMYSTNEELNHFGDDGELVCPALDALFKVHDMVV 125

Query:   125 AEELRGD---EDSDGGHQ--VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
             A+  + D   +D+D G +  VT ++LVPSDQIGCVIGKGGQ++QN+R++T AQIR++KD 
Sbjct:   126 ADADQDDGTDDDNDLGEKQTVTVRMLVPSDQIGCVIGKGGQVIQNLRNDTNAQIRVIKD- 184

Query:   180 HLPSCALR--SDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAXXXXXXXXXXXXL 237
             HLP+CAL    DEL+ I GE  VV++AL Q+AS LHDNPSR QHLL             +
Sbjct:   185 HLPACALTLSHDELLLIIGEPLVVREALYQVASLLHDNPSRFQHLLLSSSSSSMHQPGAM 244

Query:   238 VGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPXXXXXX 297
             +   A T                       S   Y+  RD   ++EF +  +CP      
Sbjct:   245 LMSAALTS----------------------SHRNYAVRRDIADAREFCVCFICPAENVGG 282

Query:   298 XXXXXXXXXXQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAV 350
                       QIRQE+GA I+V++S T+ DDC+I +SSKEF+ED   A   A+
Sbjct:   283 VIGKGGGFINQIRQETGATIRVNTSETDDDDCIIFISSKEFYEDQSPAVNAAI 335

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 289 (106.8 bits), Expect = 2.8e-48, Sum P(2) = 2.8e-48
 Identities = 70/173 (40%), Positives = 105/173 (60%)

Query:   281 SKEFSLRLVCPXXXXXXXXXXXXXXXXQIRQESGAAIKV-DSSSTEGDDCLITVSSKEFF 339
             S++ +++++C                  IRQ SG+ I+V DS +   DDC+ITV++ E  
Sbjct:   314 SEKLAIKVICSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATESP 373

Query:   340 EDTLSATIEAVVRLQPRCSEKI-ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRL 398
             +D  S  +EAV+ LQ    EKI + D   +    +LLV +  IGC+IGK GSII+E+R+ 
Sbjct:   374 DDLKSMAVEAVLLLQ----EKINDEDEDKVKM--QLLVSSKVIGCIIGKSGSIISEIRKR 427

Query:   399 TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF-DRE 450
             TKA+I I    N PK A  +DE+V+ISG++   +DALIQ++ RLR ++  DRE
Sbjct:   428 TKADIHISKGNNTPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRE 480

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 486 (176.1 bits), Expect = 2.3e-46, P = 2.3e-46
 Identities = 131/426 (30%), Positives = 217/426 (50%)

Query:    43 TVYRYLCPXXXXXXXXXXXXXXVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAF 102
             T YR LC               +K +R  T + I + E VPG  ER++ +   SD     
Sbjct:    68 TTYRILCHDAKAGGVIGKSGTIIKSIRQHTGAWINVHELVPGDAERIIEI---SDNRRRD 124

Query:   103 EDGDK-FVSPAQDALFKVHDRVIAEELR-G------DEDSD------GGHQVTAKLLVPS 148
              DG     SPAQ+ALF VHDR++  E + G      +E+ D      GG +V  +L+V  
Sbjct:   125 PDGRMPSFSPAQEALFSVHDRILESEAQFGYGGPPPEEEEDYGGVRPGGGRVVTRLVVSR 184

Query:   149 DQIGCVIGKGGQIVQNIRSETGAQIRIL-KDEHLPSCALRSDELVQISGEASVVKKALCQ 207
               +GC++GKGG+I++ +R ET   IRIL ++ +LP C   S+E+VQI GE + VK AL  
Sbjct:   185 MHVGCLLGKGGKIIEQMRIETKTHIRILPRESNLPRCVSLSEEIVQIVGELNAVKNALAI 244

Query:   208 IASRLHDNPSRSQHLLAXXXXXXXXXXXXLVGPTAATPIVGIAPLMGPYGGYKGDTAGDW 267
             ++SRL ++  R +                  G      +   +    P G ++ +     
Sbjct:   245 VSSRLRESQHRDRSNFQGRSHSPERSFAA-AGDDYMPQLRRQSSDRFPRGNFRNNNFSS- 302

Query:   268 SRSLYS--APR----DDLSSKEFSLRLVCPXXXXXXXXXXXXXXXXQIRQESGAAIKVDS 321
              +S Y+  AP     +++ S+E   +++CP                 ++ E G  ++V  
Sbjct:   303 RQSNYAEEAPAVPVGENVYSEELVFQILCPADKIVRVVGESQGIIDLLQNEIGVDVRVSD 362

Query:   322 SSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRI 381
                  D+ +IT+SS+E  +D      EA++ +Q +  + I     LI  TTRLLVP+   
Sbjct:   363 PVAGSDEQIITISSEEAPDDPFFPAQEALLHIQTQIIDLIPDKDNLI--TTRLLVPSRDS 420

Query:   382 GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTR 441
              CL GK GS+ +E+ RLT  +++IL +E +P+ AS +D ++QI+G++  A++AL+++   
Sbjct:   421 ICLEGKAGSV-SEISRLTGTSVQILAREEIPRCASINDVVIQITGEIRAAREALVELTLL 479

Query:   442 LRANLF 447
             LR+++F
Sbjct:   480 LRSHMF 485

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 255 (94.8 bits), Expect = 3.4e-39, Sum P(3) = 3.4e-39
 Identities = 59/167 (35%), Positives = 95/167 (56%)

Query:   282 KEFSLRLVCPXXXXXXXXXXXXXXXXQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFED 341
             +E + RL+CP                 ++ ESGA+IKV   + + ++ +I +S++E  E 
Sbjct:   274 EEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLER 333

Query:   342 TLSATIEAVVRLQPRCSE-KIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400
               S   + V+R+  R  E   E  + +++   RLLV +  IG L+GKGG +I+EMRR T 
Sbjct:   334 RHSLAQDGVMRVHNRIVEIGFEPSAAVVA---RLLVHSPYIGRLLGKGGHLISEMRRATG 390

Query:   401 ANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447
             A+IR+  K+   K  S+ DE+VQ+ G+L   +DAL Q++ RLR  +F
Sbjct:   391 ASIRVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMF 437

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 247 (92.0 bits), Expect = 1.6e-38, Sum P(2) = 1.6e-38
 Identities = 68/217 (31%), Positives = 112/217 (51%)

Query:    10 KRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPXXXXXXXXXXXXXXVKQLR 69
             KR   Q + ++   N++R    D+   I   E  VYR LCP              +  +R
Sbjct:     6 KRKQIQRNNSESNRNQKRRISHDK---INRDELVVYRILCPIDVVGGVIGKSGKVINAIR 62

Query:    70 IDTKSKIRIGETVPGSEERVVTVYSA----SDETNAFEDGDKFVSPAQDALFKVHDRVIA 125
              +TK+KI++ + + G  +RV+T+Y +     +E    +  ++ +  AQDAL KV+D ++A
Sbjct:    63 HNTKAKIKVFDQLHGCSQRVITIYCSVKEKQEEIGFTKSENEPLCCAQDALLKVYDAIVA 122

Query:   126 --EELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL-KDEHLP 182
               EE     + D       +LLVP  Q   +IGK G+ ++ IR  T A ++++ KD   P
Sbjct:   123 SDEENNTKTNVDRDDNKECRLLVPFSQSSSLIGKAGENIKRIRRRTRASVKVVSKDVSDP 182

Query:   183 S--CALRSDELVQISGEASVVKKALCQIASRLHD-NP 216
             S  CA+  D +V ISGE   VK+AL  +++ ++  NP
Sbjct:   183 SHVCAMEYDNVVVISGEPESVKQALFAVSAIMYKINP 219

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 80/153 (52%), Positives = 110/153 (71%)

Query:    76 IRIGETVPGSEERVVTVYSASDETNAFEDGDK-FVSPAQDALFKVHDRVIAEELRGDED- 133
             +R+ E +PG +ERVVT+YS S+E N  ED ++ FV PA DALFKVHD V+ EE   D+D 
Sbjct:     1 MRVNEALPGCDERVVTIYSNSEERNRIEDDNEDFVCPAFDALFKVHDMVVVEEFDDDDDY 60

Query:   134 ------SDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR 187
                   S+G   VT ++LVPSDQIG +IGKGG I+Q +R++T AQIR+ ++++LP CAL 
Sbjct:    61 NDNDEYSEGQTVVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV-RNDNLPMCALA 119

Query:   188 --SDELVQISGEASVVKKALCQIASRLHDNPSR 218
                DEL+QI G+ S V++AL Q+A  L++NPSR
Sbjct:   120 LSHDELLQIIGDPSAVREALYQVAFLLYNNPSR 152

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 194 (73.4 bits), Expect = 1.1e-18, Sum P(2) = 1.1e-18
 Identities = 60/194 (30%), Positives = 92/194 (47%)

Query:    40 PEDTVYRYLCPXXXXXXXXXXXXXXVKQLRIDTKSKIRIGETVPGSEERVVTVYSAS--- 96
             P++T  R +C               V +LR +T +KI     V GS+  VV +  ++   
Sbjct:    22 PDETAIRVVCHASVIGGIIGSNGYVVSKLRRETGTKIHCESPVNGSDHWVVFIVGSTAVN 81

Query:    97 ------DETNAFEDGDKF------VSPAQDALFKVHDR--VIAEELRGDEDSDG-GHQVT 141
                   D    F  G+        VS AQ AL +V +R  V+     G    DG   +  
Sbjct:    82 QSILLTDRVGEFSGGEHEDWVTCEVSAAQTALIRVLERSWVVLAAKDGGGVVDGEDEEAY 141

Query:   142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVV 201
               +L   +QIG V+G GG+ V+ +R  +GA IR+L     P C  ++DEL+QI+G+   V
Sbjct:   142 CGILADRNQIGAVLGLGGKNVEWMRRNSGAMIRVLPP---PICGTKNDELIQITGDVLAV 198

Query:   202 KKALCQIASRLHDN 215
             KKAL  ++S + +N
Sbjct:   199 KKALVMVSSYIQNN 212

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 221 (82.9 bits), Expect = 6.8e-18, Sum P(3) = 6.8e-18
 Identities = 58/191 (30%), Positives = 101/191 (52%)

Query:    23 PNKRRYTGDDRDQFIIGPEDTVYRYLCPXXXXXXXXXXXXXXVKQLRIDTKSKIRIGETV 82
             P +    G +  ++   P +TV+R L P              +K++  +T+++I+I +  
Sbjct:   167 PEEDATVGGEEKRWPGWPGETVFRMLVPAQKVGSIIGRKGDVIKKIVEETRARIKILDGP 226

Query:    83 PGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD-EDSDGGHQVT 141
             PG+ ER V V       +  E+ +  + P+ D L +VH R++ + L G+   +    +V+
Sbjct:   227 PGTTERAVMV-------SGKEEPESSLPPSMDGLLRVHMRIV-DGLDGEASQAPPPSKVS 278

Query:   142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVV 201
              +LLVP+ Q G +IGK G  V+ I+  +   +R+L  E LP  AL+ D +V++ GE + V
Sbjct:   279 TRLLVPASQAGSLIGKQGGTVKAIQEASACIVRVLGSEDLPVFALQDDRVVEVVGEPTSV 338

Query:   202 KKALCQIASRL 212
              +AL  IAS L
Sbjct:   339 HRALELIASHL 349

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 193 (73.0 bits), Expect = 2.5e-12, Sum P(2) = 2.5e-12
 Identities = 54/187 (28%), Positives = 93/187 (49%)

Query:    29 TGDDRDQFIIG-PEDTVYRYLCPXXXXXXXXXXXXXXVKQLRIDTKSKIRIGETVPGSEE 87
             T D  ++   G P D V+R + P              +K++  +T+++I++ +    + +
Sbjct:    59 TNDSAEERWPGWPGDCVFRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGPVNTPD 118

Query:    88 RVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQV--TAKLL 145
             R+V + S  +E  A+      +SPA DA+ +V  RV       D+D      V  + +LL
Sbjct:   119 RIVLI-SGKEEPEAY------MSPAMDAVLRVFRRVSGLPDNDDDDVQNAGSVFSSVRLL 171

Query:   146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKAL 205
             V S Q   +IGK G ++++I   +GA +RIL +E  P  A + + +V + GEA  + KAL
Sbjct:   172 VASTQAINLIGKQGSLIKSIVENSGASVRILSEEETPFYAAQDERIVDLQGEALKILKAL 231

Query:   206 CQIASRL 212
               I   L
Sbjct:   232 EAIVGHL 238

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0048367 "shoot system development" evidence=IMP

GO:0048467 "gynoecium development" evidence=IMP

---

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	462
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	6e-19
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-17
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	8e-14
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-13
pfam00013	59	pfam00013, KH_1, KH domain	2e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-10
pfam00013	59	pfam00013, KH_1, KH domain	4e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	5e-10
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-09
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	6e-09
pfam13014	42	pfam13014, KH_3, KH domain	1e-07
pfam13014	42	pfam13014, KH_3, KH domain	2e-07
pfam00013	59	pfam00013, KH_1, KH domain	3e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-07
pfam13014	42	pfam13014, KH_3, KH domain	6e-07
pfam00013	59	pfam00013, KH_1, KH domain	9e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-06
pfam13014	42	pfam13014, KH_3, KH domain	3e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-06
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	8e-06
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	7e-05
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-04
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	8e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.001
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.001
cd02134	61	cd02134, NusA_KH, NusA_K homology RNA-binding doma	0.001
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	0.001
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.002
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.002
COG0195	190	COG0195, NusA, Transcription elongation factor [Tr	0.002
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.003
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.003

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

 Score = 80.2 bits (199), Expect = 6e-19
 Identities = 34/69 (49%), Positives = 45/69 (65%), Gaps = 4/69 (5%)

Query: 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV 200
           T +LLVPS Q G +IGKGG  ++ IR ETGA+IR+ K   LP     ++ +V ISG+ S 
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS-VLPGS---TERVVTISGKPSA 56

Query: 201 VKKALCQIA 209
           V+KAL  I 
Sbjct: 57  VQKALLLIL 65

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

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

 Score = 76.0 bits (188), Expect = 2e-17
 Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           T RLLVP+S+ G +IGKGGS I E+R  T A IR+             + +V ISG    
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSA 56

Query: 431 AKDALIQV 438
            + AL+ +
Sbjct: 57  VQKALLLI 64

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

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

 Score = 65.6 bits (161), Expect = 8e-14
 Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 7/71 (9%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEG-DDCLITVSSKEFFEDTL 343
           +LRL+ P +  G +IGKGG+ I +IR+E+GA I+V  S   G  + ++T+S K       
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK------P 54

Query: 344 SATIEAVVRLQ 354
           SA  +A++ + 
Sbjct: 55  SAVQKALLLIL 65

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

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

 Score = 65.6 bits (161), Expect = 1e-13
 Identities = 30/78 (38%), Positives = 42/78 (53%), Gaps = 14/78 (17%)

Query: 44  VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETV-PGSEERVVTVYSASDETNAF 102
             R L P  + GSIIG+GG  +K++R +T +KIR+ ++V PGS ERVVT+ S        
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTI-SGK------ 53

Query: 103 EDGDKFVSPAQDALFKVH 120
                  S  Q AL  + 
Sbjct: 54  ------PSAVQKALLLIL 65

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

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

 Score = 61.4 bits (150), Expect = 2e-12
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 9/68 (13%)

Query: 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV 200
           T ++L+P D++G +IGKGG  ++ IR ETG +IRI  D          D+ V ISG    
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR---------DDTVTISGTPEQ 51

Query: 201 VKKALCQI 208
           V+KA   I
Sbjct: 52  VEKAKELI 59

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

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

 Score = 61.0 bits (149), Expect = 4e-12
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV 200
           T ++LVPS  +G +IGKGG  ++ IR ETGA+I+I             + +V I+G    
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGS-----EERIVTITGTPEA 55

Query: 201 VKKALCQI 208
           V+KA   I
Sbjct: 56  VEKAKELI 63

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

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

 Score = 56.0 bits (136), Expect = 2e-10
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           T R+LVP+S +G +IGKGGS I E+R  T A I+I    +       ++ +V I+G  + 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEA 55

Query: 431 AKDALIQVM 439
            + A   ++
Sbjct: 56  VEKAKELIL 64

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

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

 Score = 54.9 bits (133), Expect = 4e-10
 Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           T R+L+P  ++G +IGKGGS I E+R  T   IRI           + D+ V ISG  + 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD---------DRDDTVTISGTPEQ 51

Query: 431 AKDALIQV 438
            + A   +
Sbjct: 52  VEKAKELI 59

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

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

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 18/53 (33%), Positives = 36/53 (67%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
           + R++ P + +G +IGKGG+ I +IR+E+GA IK+  S +  ++ ++T++   
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTP 53

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

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            VT ++L+P+D++G +IGKGG  ++ I  ETG +I I             + +V+I+G  
Sbjct: 2   PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-------EERVVEITGPP 54

Query: 199 SVVKKALCQIASRL 212
             V+KA   I   L
Sbjct: 55  ENVEKAAELILEIL 68

Length = 68

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

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 22/49 (44%), Positives = 34/49 (69%)

Query: 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
            R L P   +G IIG+GG  +K++R +T +KI+I ++  GSEER+VT+
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTI 49

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

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

 Score = 47.6 bits (114), Expect = 1e-07
 Identities = 14/40 (35%), Positives = 26/40 (65%)

Query: 295 IGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS 334
           +G +IGKGG  I +IR+E+GA I++        + ++T++
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

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

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 20/40 (50%), Positives = 32/40 (80%)

Query: 53 KIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
           +G+IIG+GGE +K++R +T +KI+I +  PGS ER+VT+
Sbjct: 1  LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTI 40

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

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

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 4/51 (7%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSS 335
           + R++ P   +G +IGKGG+ I +IR+E+G  I++        D  +T+S 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD----RDDTVTISG 47

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

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

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 10/72 (13%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD- 429
           T  +L+P  ++G +IGKGGS I ++   T   I I            ++ +V+I+G  + 
Sbjct: 4   TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGPPEN 56

Query: 430 --LAKDALIQVM 439
              A + +++++
Sbjct: 57  VEKAAELILEIL 68

Length = 68

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

 Score = 45.6 bits (109), Expect = 6e-07
 Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 5/47 (10%)

Query: 150 QIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG 196
            +G +IGKGG+ ++ IR ETGA+I+I             + +V I+G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQI-----PKPEPGSGERIVTITG 42

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

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

 Score = 45.6 bits (109), Expect = 9e-07
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 44  VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNA 101
             R L P  K+G IIG+GG  +K++R +T  KIRI    P   +  VT+    ++   
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRI----PDDRDDTVTISGTPEQVEK 54

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

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
              ++ ++ P   +G +IGKGG+ I +I +E+G  I +    +E     IT
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEIT 51

Length = 68

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

 Score = 43.7 bits (104), Expect = 3e-06
 Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 5/46 (10%)

Query: 381 IGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426
           +G +IGKGG  I E+R  T A I+I   E         + +V I+G
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPE-----PGSGERIVTITG 42

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

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYS 94
          +      L P  K+G IIG+GG  +K++  +T  KI I    PGSEERVV +  
Sbjct: 1  DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITG 52

Length = 68

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

 Score = 47.7 bits (115), Expect = 8e-06
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 11/66 (16%)

Query: 273 SAPRDDLSSKEFSLRLVC---PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDC 329
           S PR +LS   ++ R+     P   I  VIG GG  I +I +E+GA I ++      DD 
Sbjct: 542 SEPRAELS--PYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE------DDG 593

Query: 330 LITVSS 335
            + +++
Sbjct: 594 TVKIAA 599

Length = 693

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

 Score = 40.2 bits (95), Expect = 7e-05
 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV 200
           T ++ +P      +IGK G  ++ I  ETG +IR               + + I+G    
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS-------KSDTITITGPKEN 53

Query: 201 VKKALCQI 208
           V+KA  +I
Sbjct: 54  VEKAKEEI 61

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

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

 Score = 44.0 bits (105), Expect = 1e-04
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 11/67 (16%)

Query: 273 SAPRDDLSSKEFSLRLV---CPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDC 329
           S PR +LS   ++ R+         I  VIG GG +I +I +E+GA I ++      DD 
Sbjct: 539 SEPRAELS--PYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE------DDG 590

Query: 330 LITVSSK 336
            + +++ 
Sbjct: 591 TVKIAAS 597

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

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

 Score = 37.5 bits (88), Expect = 8e-04
 Identities = 15/33 (45%), Positives = 21/33 (63%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
           +P D+I  VIG GG+ ++ I  ETG +I I  D
Sbjct: 8   IPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD 40

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

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

 Score = 40.9 bits (97), Expect = 0.001
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175
           +  D+I  VIG GG++++ I  ETGA+I I
Sbjct: 557 INPDKIRDVIGPGGKVIREITEETGAKIDI 586

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

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

 Score = 36.7 bits (86), Expect = 0.001
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 6/47 (12%)

Query: 291 PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
           P   I  VIG GG  I +I +E+G  I ++      DD  + +++ +
Sbjct: 9   PPDKIRDVIGPGGKTIKKIIEETGVKIDIE------DDGTVYIAASD 49

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH)

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176
             +  A+++VP DQ+G  IGKGGQ V+      G +I I+
Sbjct: 22  DEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDIV 61

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. Length = 61

>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 112 AQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGA 171
           A+ A+  V    I      DE S    ++   + +P D+IG VIG  G+++  I+ ETGA
Sbjct: 554 ARLAILDVMAEAID---TPDEMSPYAPRIIT-VKIPVDKIGEVIGPKGKMINQIQDETGA 609

Query: 172 QIRILKD 178
           +I I  D
Sbjct: 610 EISIEDD 616

Sohlberg, et al present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase. Length = 719

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

 Score = 36.3 bits (85), Expect = 0.002
 Identities = 12/35 (34%), Positives = 20/35 (57%)

Query: 298 VIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
           +IGK G+ I +I +E+G  I+     ++ D   IT
Sbjct: 14  IIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITIT 48

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

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 10/55 (18%)

Query: 384 LIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG---DLDLAKDAL 435
           +IGK GS I ++   T   IR  P            + + I+G   +++ AK+ +
Sbjct: 14  IIGKKGSNIRKIMEETGVKIRF-PDPG------SKSDTITITGPKENVEKAKEEI 61

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

>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription]

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 35/123 (28%), Positives = 50/123 (40%), Gaps = 31/123 (25%)

Query: 53  KIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPA 112
            +G+ IG+ G  VK +  +   KI + E      E +          NA        +PA
Sbjct: 86  PVGACIGKRGSRVKAVSEELGEKIDVVEWSEDPAEFIK---------NAL-------APA 129

Query: 113 QDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ 172
                +V    I E+       DG     A ++VP DQ+   IGKGGQ V+     TG +
Sbjct: 130 -----EVLSVNIKED-------DGH---VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWE 174

Query: 173 IRI 175
           I I
Sbjct: 175 IDI 177

Length = 190

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

 Score = 39.6 bits (94), Expect = 0.003
 Identities = 15/30 (50%), Positives = 21/30 (70%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175
           +P D+I  VIG GG+ ++ I  ETGA+I I
Sbjct: 560 IPPDKIRDVIGPGGKTIREITEETGAKIDI 589

Length = 693

>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 11/66 (16%)

Query: 273 SAPRDDLSSKEFSLRLVC---PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDC 329
           S PR +LS   ++ R+         I  VIG GG  I  I +E+G  I ++      DD 
Sbjct: 540 SEPRKELS--PYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDG 591

Query: 330 LITVSS 335
            + +++
Sbjct: 592 TVKIAA 597

Length = 692

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	462
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.97
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.96
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.89
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.82
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.77
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.56
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.56
PRK13763	180	putative RNA-processing protein; Provisional	99.53
PRK13763	180	putative RNA-processing protein; Provisional	99.53
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.42
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.36
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.35
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.34
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.33
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.3
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.29
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.26
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.22
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.2
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.16
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.14
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.11
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.05
PF13014	43	KH_3: KH domain	98.99
smart00322	69	KH K homology RNA-binding domain.	98.98
PF13014	43	KH_3: KH domain	98.97
smart00322	69	KH K homology RNA-binding domain.	98.76
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.65
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.63
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.53
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.16
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.02
PRK08406	140	transcription elongation factor NusA-like protein;	98.01
PRK08406	140	transcription elongation factor NusA-like protein;	97.96
KOG2113	394	consensus Predicted RNA binding protein, contains	97.87
KOG2113	394	consensus Predicted RNA binding protein, contains	97.85
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.68
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.64
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.62
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.59
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.57
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.53
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.51
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.46
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.4
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.14
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.01
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.98
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.82
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.78
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.75
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.71
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.69
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.58
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.58
PRK12704	520	phosphodiesterase; Provisional	96.58
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.58
PRK00106	535	hypothetical protein; Provisional	96.56
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.52
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.45
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.42
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.36
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.34
TIGR01953	341	NusA transcription termination factor NusA. This m	96.32
TIGR01953	341	NusA transcription termination factor NusA. This m	96.28
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.15
PRK00468	75	hypothetical protein; Provisional	96.13
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.12
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.1
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.02
PRK02821	77	hypothetical protein; Provisional	95.92
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.88
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.79
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.72
PRK00468	75	hypothetical protein; Provisional	95.52
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.45
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.41
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	95.35
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.33
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.28
PRK02821	77	hypothetical protein; Provisional	95.25
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.18
PRK01064	78	hypothetical protein; Provisional	95.09
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.08
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.03
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.84
PRK12704	520	phosphodiesterase; Provisional	94.75
PRK00106	535	hypothetical protein; Provisional	94.74
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.32
PRK01064	78	hypothetical protein; Provisional	94.31
PRK12705	508	hypothetical protein; Provisional	94.05
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	92.91
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	92.75
PRK12705	508	hypothetical protein; Provisional	91.7
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	91.54
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	91.01
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.76
KOG2874	356	consensus rRNA processing protein [Translation, ri	90.45
KOG2874	356	consensus rRNA processing protein [Translation, ri	90.15
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	89.97
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	89.97
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	89.35
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	88.8
COG1855	604	ATPase (PilT family) [General function prediction	88.12
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	87.76
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	87.55
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	87.48
PRK13764	602	ATPase; Provisional	87.18
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	86.8
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	85.81
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	85.1
COG1855	604	ATPase (PilT family) [General function prediction	85.07
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	84.0
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	83.69
COG5166	657	Uncharacterized conserved protein [Function unknow	83.28
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	82.79
PRK13764	602	ATPase; Provisional	82.72
PRK06418	166	transcription elongation factor NusA-like protein;	82.67
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	81.65
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	80.8

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

Probab=100.00  E-value=1.6e-43  Score=356.69  Aligned_cols=405  Identities=40%  Similarity=0.609  Sum_probs=313.0

Q ss_pred             CCccCCCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCC
Q 012477            5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPG   84 (462)
Q Consensus         5 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~   84 (462)
                      |..-.++....+....++..+++....+..+. ..+...++|||||.+.+|.||||+|..|++|++++.++|+|.+..++
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~   84 (485)
T KOG2190|consen    6 RGLPRPKNSTTSNVGDNGSIKRPSLGDPVIST-GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPG   84 (485)
T ss_pred             ccCccccCCCcccccCCCcccccCCCCCcccC-CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCC
Confidence            44455666666676677777777777765444 33444459999999999999999999999999999999999998999


Q ss_pred             CCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhh---cc---CCCCCCCCCceEEEEEEeCCceeeeecCC
Q 012477           85 SEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEE---LR---GDEDSDGGHQVTAKLLVPSDQIGCVIGKG  158 (462)
Q Consensus        85 ~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~---~~---~~~~~~~~~~~~~~l~ip~~~~g~IIGk~  158 (462)
                      +++|+++|+|...+.        ..+.+.+|+.++++.+....   ..   ....+.....+++||+||..++|.||||+
T Consensus        85 c~eRIiti~g~~~~~--------~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~  156 (485)
T KOG2190|consen   85 CPERIITITGNRVEL--------NLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKG  156 (485)
T ss_pred             CCcceEEEecccccc--------cCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccC
Confidence            999999999962221        35557888888888776631   11   11111222368999999999999999999


Q ss_pred             chHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCC
Q 012477          159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLV  238 (462)
Q Consensus       159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~  238 (462)
                      |++||+|+++|||+|++.++ ++|.   +++|.|+|.|.+++|.+|+..|..+|.+++........+..+  |.      
T Consensus       157 G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~--y~------  224 (485)
T KOG2190|consen  157 GSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIP--YR------  224 (485)
T ss_pred             cHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCccc--CC------
Confidence            99999999999999999987 8887   899999999999999999999999999965332111111111  00      


Q ss_pred             CCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEE
Q 012477          239 GPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIK  318 (462)
Q Consensus       239 ~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~  318 (462)
                       |    ......+...+.+...         ..+.++.....+.++..++.+|...++.|+|++|..|+.|+.++++.|.
T Consensus       225 -P----~~~~~~~~~~s~~~~~---------~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~  290 (485)
T KOG2190|consen  225 -P----SASQGGPVLPSTAQTS---------PDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASIS  290 (485)
T ss_pred             -C----cccccCccccccccCC---------cccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceE
Confidence             0    0000000000000000         0111122223455667889999999999999999999999999999999


Q ss_pred             ecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecCCccceeecCCCchHHHHHHh
Q 012477          319 VDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRL  398 (462)
Q Consensus       319 i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~  398 (462)
                      +.....+   |+++++..+...+..+.++++++..+++..+....+. ...++.++.||.+++||||||+|.+|.+||+.
T Consensus       291 v~~~~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~  366 (485)
T KOG2190|consen  291 VGDSRTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQR  366 (485)
T ss_pred             eccccCc---ceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHh
Confidence            9987654   9999999999988889999999999998887766555 67899999999999999999999999999999


Q ss_pred             hCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhccCCC
Q 012477          399 TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREG  451 (462)
Q Consensus       399 sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~  451 (462)
                      |||.|+|.+.++.   ....++.++|+|...+...|++++..++.......++
T Consensus       367 tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~  416 (485)
T KOG2190|consen  367 TGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSAPKSSMGG  416 (485)
T ss_pred             cCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccccCccCCCC
Confidence            9999999987543   2567899999999999999999999888887654433

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

Probab=100.00  E-value=4.8e-43  Score=346.80  Aligned_cols=350  Identities=20%  Similarity=0.357  Sum_probs=264.2

Q ss_pred             ccccCCCCCCCcccCC-CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccc
Q 012477           25 KRRYTGDDRDQFIIGP-EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFE  103 (462)
Q Consensus        25 ~~~~~~~~~~~~~~~~-~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~  103 (462)
                      |+...+.+...+..+. ..++.+..||.+++++||||+|+.|..|.+++||+|.+.....+..+|.+.++|.++++    
T Consensus        35 ~~~~~~~~l~p~~~~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v----  110 (600)
T KOG1676|consen   35 KGPSEDTDLDPDMDPSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENV----  110 (600)
T ss_pred             cCCCCccccCcccCCcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccH----
Confidence            4444444443333333 55678899999999999999999999999999999998766667789999999999994    


Q ss_pred             CCCCcCCHHHHHHHHHHHHHHHhhc--cCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCC
Q 012477          104 DGDKFVSPAQDALFKVHDRVIAEEL--RGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHL  181 (462)
Q Consensus       104 ~~~~~v~~a~~a~~~i~~~i~~~~~--~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~  181 (462)
                               ..|- ++++.+.....  ...........++..|+||.+.+|.||||+|++||.|++.+||++.+..+...
T Consensus       111 ---------~~aK-~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~  180 (600)
T KOG1676|consen  111 ---------EVAK-QLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSI  180 (600)
T ss_pred             ---------HHHH-HhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCc
Confidence                     2222 22222322221  11122233567899999999999999999999999999999999999888654


Q ss_pred             CCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 012477          182 PSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKG  261 (462)
Q Consensus       182 p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~  261 (462)
                      ..   ..++.+.|+|+++.|+.|..+|.++|++....           .+..+++                   +++.. 
T Consensus       181 ~~---~~~KplritGdp~~ve~a~~lV~dil~e~~~~-----------~~g~~~~-------------------~g~~~-  226 (600)
T KOG1676|consen  181 AT---GADKPLRITGDPDKVEQAKQLVADILREEDDE-----------VPGSGGH-------------------AGVRG-  226 (600)
T ss_pred             CC---CCCCceeecCCHHHHHHHHHHHHHHHHhcccC-----------CCccccc-------------------cCcCc-
Confidence            43   47889999999999999999999999974211           1111000                   11100 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCC-CCCceEEEEecCCccc
Q 012477          262 DTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST-EGDDCLITVSSKEFFE  340 (462)
Q Consensus       262 ~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~~~~~~i~i~G~~~~~  340 (462)
                                         ....+++|.||...+|.||||+|++||+|+.+||++|+|-+++. .+.+|++.|.|+...-
T Consensus       227 -------------------g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~i  287 (600)
T KOG1676|consen  227 -------------------GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQI  287 (600)
T ss_pred             -------------------cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHH
Confidence                               11237899999999999999999999999999999999999765 7889999999986443


Q ss_pred             ccccHHHHHHHhhcCcccccccccCCCcce--EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCC
Q 012477          341 DTLSATIEAVVRLQPRCSEKIERDSGLISF--TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASED  418 (462)
Q Consensus       341 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~  418 (462)
                      ......+.+++........ ..-..+....  ..+|.||...||.||||||++||.|.++|||++.+++.   |+..+..
T Consensus       288 e~Aa~lI~eii~~~~~~~~-~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~  363 (600)
T KOG1676|consen  288 EHAAELINEIIAEAEAGAG-GGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPK  363 (600)
T ss_pred             HHHHHHHHHHHHHHhccCC-CCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCcc
Confidence            3334444444443211110 0001112223  78899999999999999999999999999999999875   4566788


Q ss_pred             CceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          419 DEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       419 ~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      +++|+|+|++.+|+.|+.||..++...
T Consensus       364 ektf~IrG~~~QIdhAk~LIr~kvg~~  390 (600)
T KOG1676|consen  364 EKTFVIRGDKRQIDHAKQLIRDKVGDI  390 (600)
T ss_pred             ceEEEEecCcccchHHHHHHHHHhccc
Confidence            999999999999999999999999875

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

Probab=100.00  E-value=2e-42  Score=326.51  Aligned_cols=369  Identities=22%  Similarity=0.380  Sum_probs=274.6

Q ss_pred             CCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEcCCcccccccCCCCcCCH
Q 012477           33 RDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYSASDETNAFEDGDKFVSP  111 (462)
Q Consensus        33 ~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~-~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~  111 (462)
                      ..+...-..+..+|+|||-.++|.|||+.|.+||.|.+.|.|+|+|.. ...+..|++|+|-|++|.             
T Consensus       189 G~~~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------  255 (584)
T KOG2193|consen  189 GPHHKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------  255 (584)
T ss_pred             CCcccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------
Confidence            344445567889999999999999999999999999999999999975 455888999999999999             


Q ss_pred             HHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCce
Q 012477          112 AQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL  191 (462)
Q Consensus       112 a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~  191 (462)
                      +.+|+.+|++.+..+...    +.....+.++++-++.++|++|||.|.++|+|+.+||++|.|++--++..  ...+|+
T Consensus       256 ~s~Ac~~ILeimqkEA~~----~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERT  329 (584)
T KOG2193|consen  256 TSKACKMILEIMQKEAVD----DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERT  329 (584)
T ss_pred             hHHHHHHHHHHHHHhhhc----cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccce
Confidence            467788888876655432    23346788999999999999999999999999999999999998766655  367999


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCC--CCCC-CCCCCCC
Q 012477          192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYG--GYKG-DTAGDWS  268 (462)
Q Consensus       192 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~--~~~~-~~~~~~~  268 (462)
                      ++++|+.++|..|..+|..+|++.++.+...+  ++.       ..+.|....+..++-|..+++.  .+.+ .+....+
T Consensus       330 ItVkGsiEac~~AE~eImkKlre~yEnDl~a~--s~q-------~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p  400 (584)
T KOG2193|consen  330 ITVKGSIEACVQAEAEIMKKLRECYENDLAAM--SLQ-------CHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASP  400 (584)
T ss_pred             EEecccHHHHHHHHHHHHHHHHHHHhhhHHHh--hcc-------CCCCcccCccccCCCCcccccCCCCCCCCccccCCC
Confidence            99999999999999999999999877653211  100       0011111000000000000000  0000 0010111


Q ss_pred             CCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCC-CCCCceEEEEecCCcccccccHHH
Q 012477          269 RSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS-TEGDDCLITVSSKEFFEDTLSATI  347 (462)
Q Consensus       269 ~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~-~~~~~~~i~i~G~~~~~~~~~~~~  347 (462)
                      +.++.     .....-.+++.||...+|+|||++|.+||.|...+||+|+|.++. ++..+|.|+|+|.+          
T Consensus       401 ~~~~h-----q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp----------  465 (584)
T KOG2193|consen  401 YPLFH-----QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP----------  465 (584)
T ss_pred             chhhh-----cCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh----------
Confidence            11111     111234789999999999999999999999999999999998864 56789999999975          


Q ss_pred             HHHHhhcCcccccccc-----cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceE
Q 012477          348 EAVVRLQPRCSEKIER-----DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMV  422 (462)
Q Consensus       348 ~a~~~~~~~~~~~~~~-----~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v  422 (462)
                      ++.+..+.+++.++..     +.....+.+.+.||...+|+||||||.+++++++.|+|-+.|+++. .|.  ..+.-+|
T Consensus       466 eaqfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdq-tpd--End~viv  542 (584)
T KOG2193|consen  466 EAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ-TPD--ENDQVIV  542 (584)
T ss_pred             HHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccC-CCC--ccceeee
Confidence            3455555555544432     2234567889999999999999999999999999999999997654 443  2334568


Q ss_pred             EEEcCHHHHHHHHHHHHHHHHhhhc
Q 012477          423 QISGDLDLAKDALIQVMTRLRANLF  447 (462)
Q Consensus       423 ~I~G~~~~v~~A~~~I~~~l~~~~~  447 (462)
                      .|.|.+-+.+.|+..|.+.+.+...
T Consensus       543 riiGhfyatq~aQrki~~iv~qvkq  567 (584)
T KOG2193|consen  543 RIIGHFYATQNAQRKIAHIVNQVKQ  567 (584)
T ss_pred             eeechhhcchHHHHHHHHHHHHHHH
Confidence            8999999999999999998887754

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

Probab=100.00  E-value=2.5e-38  Score=282.63  Aligned_cols=366  Identities=19%  Similarity=0.273  Sum_probs=235.1

Q ss_pred             CCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceE
Q 012477           10 KRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERV   89 (462)
Q Consensus        10 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~erv   89 (462)
                      +|.|+..+++.   ..+|..++. +..++....+.++||+.++.+|+||||+|++||+|+.+++++|.|++.  ..++|+
T Consensus        19 ~~~~~~e~g~~---~gkrp~~d~-~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri   92 (390)
T KOG2192|consen   19 ETFPNTETGGE---FGKRPAEDM-EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERI   92 (390)
T ss_pred             hcCCCCccccc---ccCCcchhh-HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCcee
Confidence            45555444322   333333333 445566788999999999999999999999999999999999999987  788999


Q ss_pred             EEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhc
Q 012477           90 VTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET  169 (462)
Q Consensus        90 i~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~t  169 (462)
                      ++|+...+-             +-+-|++++..|.+. +      ...+.|.+||||+.+++|.|||++|++||+|++++
T Consensus        93 ~tisad~~t-------------i~~ilk~iip~lee~-f------~~~~pce~rllihqs~ag~iigrngskikelrekc  152 (390)
T KOG2192|consen   93 LTISADIET-------------IGEILKKIIPTLEEG-F------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKC  152 (390)
T ss_pred             EEEeccHHH-------------HHHHHHHHhhhhhhC-C------CCCCchhhhhhhhhhhccceecccchhHHHHHHhh
Confidence            999988544             344555555555322 1      34567999999999999999999999999999999


Q ss_pred             CceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccc--cCCCCCCCCCCCCCCCCCCCc
Q 012477          170 GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASA--ISNSHSSSGSLVGPTAATPIV  247 (462)
Q Consensus       170 ga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~--~~~~~~~~g~~~~p~~~~~~~  247 (462)
                      .|++.|...    .|+++++|+|.|.|.+.+|..+++.|.+.|.+.|.+.....+..  ....|.+||..|.-...+.-.
T Consensus       153 sarlkift~----c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~p  228 (390)
T KOG2192|consen  153 SARLKIFTE----CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRP  228 (390)
T ss_pred             hhhhhhhhc----cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCC
Confidence            999999876    67889999999999999999999999999999988876655433  223455666432211000000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCC
Q 012477          248 GIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGD  327 (462)
Q Consensus       248 ~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~  327 (462)
                      +.+|..++++-.+              |+..       .-+.+..      -|+-|..       +--.+.|....... 
T Consensus       229 gpapqrggqgpp~--------------~~~s-------dlmay~r------~GrpG~r-------ydg~vdFs~detw~-  273 (390)
T KOG2192|consen  229 GPAPQRGGQGPPP--------------PRGS-------DLMAYDR------RGRPGDR-------YDGMVDFSADETWP-  273 (390)
T ss_pred             CCCCCCCCCCCCC--------------CCcc-------ccceecc------CCCCCcc-------ccccccccccccCC-
Confidence            0011111111000              0000       0000000      0110111       00011111111100 


Q ss_pred             ceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          328 DCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       328 ~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                      ..+-+..-++ |...+.+..-.-..........+..+.+.+..|..|.||.++-|.||||||++|++|++++||.|+|.+
T Consensus       274 saidtw~~Se-wqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide  352 (390)
T KOG2192|consen  274 SAIDTWSPSE-WQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE  352 (390)
T ss_pred             CcCCCcCccc-cccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC
Confidence            0000000000 000000000000000000001112334567889999999999999999999999999999999999976


Q ss_pred             CCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          408 KENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       408 ~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      +     .+++.+|.++|+|+.++++.|++|+.+.++++.
T Consensus       353 p-----leGsedrIitItGTqdQIqnAQYLlQn~Vkq~r  386 (390)
T KOG2192|consen  353 P-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQYR  386 (390)
T ss_pred             c-----CCCCCceEEEEeccHHHHhhHHHHHHHHHHhhh
Confidence            4     357889999999999999999999999988653

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

Probab=99.97  E-value=1.9e-29  Score=250.49  Aligned_cols=243  Identities=26%  Similarity=0.419  Sum_probs=186.7

Q ss_pred             ccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC--CCCCCCceEEEEEcCCcccccccCCCCcCCHHHH
Q 012477           37 IIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE--TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQD  114 (462)
Q Consensus        37 ~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~--~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~  114 (462)
                      ..+...++.+|+||.+.+|+||||+|++||+|++.+||++.+-+  .......+.+.|+|.++.+             +.
T Consensus       133 ~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~  199 (600)
T KOG1676|consen  133 NQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQ  199 (600)
T ss_pred             cCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HH
Confidence            34467899999999999999999999999999999999998753  2333467899999999883             55


Q ss_pred             HHHHHHHHHHHhhccCCC-----CCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCC
Q 012477          115 ALFKVHDRVIAEELRGDE-----DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSD  189 (462)
Q Consensus       115 a~~~i~~~i~~~~~~~~~-----~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~  189 (462)
                      |..++++.|.++.-....     ........++++.||.+.||.||||+|++||+|+.+||+||+|.++++ |   .+.+
T Consensus       200 a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~spe  275 (600)
T KOG1676|consen  200 AKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPE  275 (600)
T ss_pred             HHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCcc
Confidence            666666666543311111     112233458999999999999999999999999999999999988743 4   3889


Q ss_pred             ceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCC
Q 012477          190 ELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSR  269 (462)
Q Consensus       190 r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~  269 (462)
                      |.+.|.|+.+.|..|.++|.++|.+.....          .   +++.                   +|.          
T Consensus       276 R~~~IiG~~d~ie~Aa~lI~eii~~~~~~~----------~---~~~~-------------------~G~----------  313 (600)
T KOG1676|consen  276 RPAQIIGTVDQIEHAAELINEIIAEAEAGA----------G---GGMG-------------------GGA----------  313 (600)
T ss_pred             ceeeeecCHHHHHHHHHHHHHHHHHHhccC----------C---CCcC-------------------CCC----------
Confidence            999999999999999999999998842110          0   0000                   000          


Q ss_pred             CCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCC--CCCCceEEEEecCCcccccccHHH
Q 012477          270 SLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS--TEGDDCLITVSSKEFFEDTLSATI  347 (462)
Q Consensus       270 ~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~--~~~~~~~i~i~G~~~~~~~~~~~~  347 (462)
                           |.     ....+.+.||...+|+||||+|++||.|..+|||++.+.+..  .+..+++++|.|.+...+.....+
T Consensus       314 -----P~-----~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LI  383 (600)
T KOG1676|consen  314 -----PG-----LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLI  383 (600)
T ss_pred             -----cc-----ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHH
Confidence                 00     001678999999999999999999999999999999999873  345789999999876554444443


Q ss_pred             H
Q 012477          348 E  348 (462)
Q Consensus       348 ~  348 (462)
                      +
T Consensus       384 r  384 (600)
T KOG1676|consen  384 R  384 (600)
T ss_pred             H
Confidence            3

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

Probab=99.96  E-value=4.8e-29  Score=236.06  Aligned_cols=241  Identities=23%  Similarity=0.397  Sum_probs=190.4

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS  217 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  217 (462)
                      ....+|++||..++|.||||.|+|||.|...|-|+|+|...+.-    +..|+.++|-|+++...+|+++|.+++..+..
T Consensus       197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~----Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~  272 (584)
T KOG2193|consen  197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA----GAAEKIITVHSTPEGTSKACKMILEIMQKEAV  272 (584)
T ss_pred             cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC----CcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence            34679999999999999999999999999999999999987653    57899999999999999999999999987532


Q ss_pred             CcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCcccc
Q 012477          218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG  297 (462)
Q Consensus       218 ~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~  297 (462)
                      ..                                                           ....++.++++-.+.++|+
T Consensus       273 ~~-----------------------------------------------------------k~~~e~pLk~lAHN~lvGR  293 (584)
T KOG2193|consen  273 DD-----------------------------------------------------------KVAEEIPLKILAHNNLVGR  293 (584)
T ss_pred             cc-----------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence            11                                                           1234567889999999999


Q ss_pred             ccccCChhHHhHHhhhCCeEEecCCC---CCCCceEEEEecCCcccccc----------cHHHHHH---HhhcCcccccc
Q 012477          298 VIGKGGAIINQIRQESGAAIKVDSSS---TEGDDCLITVSSKEFFEDTL----------SATIEAV---VRLQPRCSEKI  361 (462)
Q Consensus       298 IIGk~G~~Ik~I~~~sga~I~i~~~~---~~~~~~~i~i~G~~~~~~~~----------~~~~~a~---~~~~~~~~~~~  361 (462)
                      +|||.|.++|+|+++||++|.|.+--   ....+|+|++.|+  ++..+          ..+.+..   +.++..+...+
T Consensus       294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGs--iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l  371 (584)
T KOG2193|consen  294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS--IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGL  371 (584)
T ss_pred             hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEeccc--HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCccc
Confidence            99999999999999999999999842   2346899999994  22211          1112211   12221111000


Q ss_pred             --------------cc----c-------------CCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCC
Q 012477          362 --------------ER----D-------------SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN  410 (462)
Q Consensus       362 --------------~~----~-------------~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~  410 (462)
                                    .+    +             .........|.||...+|+|||++|.+||.|.+.+||+|+|..+  
T Consensus       372 ~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp--  449 (584)
T KOG2193|consen  372 NLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP--  449 (584)
T ss_pred             CccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC--
Confidence                          00    0             01134567899999999999999999999999999999999764  


Q ss_pred             CCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhc
Q 012477          411 LPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF  447 (462)
Q Consensus       411 ~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~  447 (462)
                        ..++..+|+|+|+|++++..+|+-.|+.+|++..+
T Consensus       450 --E~pdvseRMViItGppeaqfKAQgrifgKikEenf  484 (584)
T KOG2193|consen  450 --EIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF  484 (584)
T ss_pred             --CCCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence              34467899999999999999999999999998854

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

Probab=99.95  E-value=2.2e-26  Score=212.11  Aligned_cols=237  Identities=25%  Similarity=0.416  Sum_probs=176.8

Q ss_pred             CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC---CCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHH
Q 012477           41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE---TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF  117 (462)
Q Consensus        41 ~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~---~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~  117 (462)
                      ..+.+++|||+..+|.||||+|++|.+|+++|||+|++++   ..|+++||+|.|.|+.+++             ...++
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai-------------~av~e  103 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEAL-------------NAVHE  103 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHH-------------HHHHH
Confidence            4599999999999999999999999999999999999974   6999999999999997773             44566


Q ss_pred             HHHHHHHHhhccCCC-CC-----CCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCce
Q 012477          118 KVHDRVIAEELRGDE-DS-----DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL  191 (462)
Q Consensus       118 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~  191 (462)
                      .|+++|.+....... .+     ..+..-.++++||++.+|.||||+|.+||.|++++||-|+|++..  |....-.+|+
T Consensus       104 fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqerv  181 (402)
T KOG2191|consen  104 FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERV  181 (402)
T ss_pred             HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEE
Confidence            677787765432222 11     222334599999999999999999999999999999999999421  2233468999


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCC
Q 012477          192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSL  271 (462)
Q Consensus       192 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~  271 (462)
                      |++.|.+++..+|+.+|.+++.++|.....+..     .|....   +|     ..-..|-+++|... .+         
T Consensus       182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~-----sya~vs---Gp-----vaNsnPtGspya~~-~~---------  238 (402)
T KOG2191|consen  182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNI-----SYANVS---GP-----VANSNPTGSPYAYQ-AH---------  238 (402)
T ss_pred             EEecCCHHHHHHHHHHHHHHhhcCCcccceecc-----chhccc---Cc-----ccccCCCCCCCCCC-Cc---------
Confidence            999999999999999999999999877665442     122111   00     00111111111110 01         


Q ss_pred             CCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCC
Q 012477          272 YSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSS  322 (462)
Q Consensus       272 ~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~  322 (462)
                             ..+...+....++....|..-|.+|.++-.|-.-+|+.+.++..
T Consensus       239 -------~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~  282 (402)
T KOG2191|consen  239 -------VLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA  282 (402)
T ss_pred             -------cccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence                   01222345677888899999999999999999999998888774

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

Probab=99.89  E-value=6.6e-22  Score=182.71  Aligned_cols=246  Identities=24%  Similarity=0.339  Sum_probs=181.5

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCC-CCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH-LPSCALRSDELVQISGEASVVKKALCQIASRLHDNP  216 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  216 (462)
                      ..+.+++|||...+|.||||+|++|.+|+.+|||+|++++..+ +|   +.+||+|.|+|+.+++......|.++|++.+
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP---GTTeRvcli~Gt~eai~av~efI~dKire~p  113 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP---GTTERVCLIQGTVEALNAVHEFIADKIREKP  113 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC---CccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence            4489999999999999999999999999999999999998654 44   6999999999999999999999999999965


Q ss_pred             CCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccc
Q 012477          217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG  296 (462)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g  296 (462)
                      .....                                              +...+++..   .+..-.+++++|+..+|
T Consensus       114 ~~~~k----------------------------------------------~v~~~~pqt---~~r~kqikivvPNstag  144 (402)
T KOG2191|consen  114 QAVAK----------------------------------------------PVDILQPQT---PDRIKQIKIVVPNSTAG  144 (402)
T ss_pred             HhhcC----------------------------------------------CccccCCCC---ccccceeEEeccCCccc
Confidence            32110                                              000000000   01112579999999999


Q ss_pred             cccccCChhHHhHHhhhCCeEEecCCCC---CCCceEEEEecCCcccccccHHHHHHHhhc------Cc----cccc---
Q 012477          297 GVIGKGGAIINQIRQESGAAIKVDSSST---EGDDCLITVSSKEFFEDTLSATIEAVVRLQ------PR----CSEK---  360 (462)
Q Consensus       297 ~IIGk~G~~Ik~I~~~sga~I~i~~~~~---~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~------~~----~~~~---  360 (462)
                      .||||+|.+||.|++++||.|+|.+..+   .-.+|++|+.|...      ....|+-.+.      |+    +...   
T Consensus       145 ~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e------~~~~A~~~IL~Ki~eDpqs~scln~sya~  218 (402)
T KOG2191|consen  145 MIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPE------QNMKAVSLILQKIQEDPQSGSCLNISYAN  218 (402)
T ss_pred             ceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHH------HHHHHHHHHHHHhhcCCcccceeccchhc
Confidence            9999999999999999999999996433   35789999999632      1222221111      11    1000   


Q ss_pred             ----c------------cccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEE
Q 012477          361 ----I------------ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQI  424 (462)
Q Consensus       361 ----~------------~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I  424 (462)
                          .            .........+....|+....|..-|.+|.++-.|...+|+.+.+++..++-.  +...+ .-+
T Consensus       219 vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~--g~gy~-~n~  295 (402)
T KOG2191|consen  219 VSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMA--GYGYN-TNI  295 (402)
T ss_pred             ccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeecccccccc--ccccc-ccc
Confidence                0            0111123455667899999999999999999999999999999987765322  33444 778


Q ss_pred             EcCHHHHHHHHHHHHHHHHh
Q 012477          425 SGDLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       425 ~G~~~~v~~A~~~I~~~l~~  444 (462)
                      .|.+-++..|-.+|..+...
T Consensus       296 ~g~~ls~~aa~g~L~~~~~~  315 (402)
T KOG2191|consen  296 LGLGLSILAAEGVLAAKVAS  315 (402)
T ss_pred             cchhhhhhhhhhHHHHhhcc
Confidence            88888888888777665543

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

Probab=99.82  E-value=4.9e-19  Score=179.43  Aligned_cols=171  Identities=36%  Similarity=0.560  Sum_probs=136.8

Q ss_pred             ceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc
Q 012477          283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE  362 (462)
Q Consensus       283 ~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~  362 (462)
                      +.+++++++...+|.|||++|..|++|+.++.++|+|.....++.+|+++|+|.. .+...+++.+++++.+..+.....
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~-~~~~~~~~~~al~ka~~~iv~~~~  120 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNR-VELNLSPATDALFKAFDMIVFKLE  120 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccc-ccccCCchHHHHHHHHHHHhhccc
Confidence            3458999999999999999999999999999999999998888899999999941 122345566666666655443221


Q ss_pred             ----------ccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHH
Q 012477          363 ----------RDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAK  432 (462)
Q Consensus       363 ----------~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~  432 (462)
                                .+.....++.+|+||..++|+||||+|+.|++|++.|||+|+|..+ .+|   ..++|.|+|.|.+++|.
T Consensus       121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP---~ster~V~IsG~~~av~  196 (485)
T KOG2190|consen  121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLP---NSTERAVTISGEPDAVK  196 (485)
T ss_pred             ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCC---cccceeEEEcCchHHHH
Confidence                      0111225789999999999999999999999999999999999876 556   47889999999999999


Q ss_pred             HHHHHHHHHHHhhh---ccCCCCCCCCCC
Q 012477          433 DALIQVMTRLRANL---FDREGAVSTFVP  458 (462)
Q Consensus       433 ~A~~~I~~~l~~~~---~~~~~~~~~~~p  458 (462)
                      +|+..|...|.+..   ...-+....|.|
T Consensus       197 ~al~~Is~~L~~~~~~~~~~~~st~~y~P  225 (485)
T KOG2190|consen  197 KALVQISSRLLENPPRSPPPLVSTIPYRP  225 (485)
T ss_pred             HHHHHHHHHHHhcCCcCCCCCCCcccCCC
Confidence            99999999999974   223444444444

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

Probab=99.77  E-value=2.7e-18  Score=154.44  Aligned_cols=158  Identities=28%  Similarity=0.460  Sum_probs=133.4

Q ss_pred             CCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEc-CCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHH
Q 012477           39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF  117 (462)
Q Consensus        39 ~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~-~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~  117 (462)
                      .++.+.+||||+.+++|.|||++|++||+|++++.++++|- ...|++++|+|.+.|.+.+             ++..++
T Consensus       119 ~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~-------------v~~~i~  185 (390)
T KOG2192|consen  119 LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKR-------------VVECIK  185 (390)
T ss_pred             CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcch-------------HHHHHH
Confidence            46679999999999999999999999999999999999875 5788999999999999988             577888


Q ss_pred             HHHHHHHHhhccC--------------------------------------------------------CC---------
Q 012477          118 KVHDRVIAEELRG--------------------------------------------------------DE---------  132 (462)
Q Consensus       118 ~i~~~i~~~~~~~--------------------------------------------------------~~---------  132 (462)
                      .+++.+.+..+.+                                                        ++         
T Consensus       186 ~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vd  265 (390)
T KOG2192|consen  186 IILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVD  265 (390)
T ss_pred             HHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccccc
Confidence            8877776632211                                                        00         


Q ss_pred             ------------------------------------------CCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcC
Q 012477          133 ------------------------------------------DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG  170 (462)
Q Consensus       133 ------------------------------------------~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tg  170 (462)
                                                                .+-....++..+.||.++-|.||||+|+.|++|+.++|
T Consensus       266 Fs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esG  345 (390)
T KOG2192|consen  266 FSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESG  345 (390)
T ss_pred             ccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccC
Confidence                                                      00123457899999999999999999999999999999


Q ss_pred             ceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          171 AQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       171 a~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      |.|.+...     ..++.+|+++|+|+.++++.|..++...+++
T Consensus       346 A~Ikidep-----leGsedrIitItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  346 ASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             ceEEecCc-----CCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence            99999653     3368999999999999999999999888875

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.56  E-value=9.9e-15  Score=129.75  Aligned_cols=138  Identities=22%  Similarity=0.214  Sum_probs=96.4

Q ss_pred             EEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEE---EcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477           47 YLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV---YSASDETNAFEDGDKFVSPAQDALFKVHDRV  123 (462)
Q Consensus        47 ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I---~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i  123 (462)
                      +.||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|   +++++.             +..|...+....
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~i~   63 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKAIG   63 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHHHH
Confidence            56899999999999999999999999999999753     245777   444443             233333332211


Q ss_pred             HHhhccCCCC-CCCCCceEEEEEEeC---------CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEE
Q 012477          124 IAEELRGDED-SDGGHQVTAKLLVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQ  193 (462)
Q Consensus       124 ~~~~~~~~~~-~~~~~~~~~~l~ip~---------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~  193 (462)
                      ....+. +.. ...+......+-|+.         ...|+|||++|++++.|++.|||+|.|..            ..|.
T Consensus        64 ~gf~~e-~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~  130 (172)
T TIGR03665        64 RGFSPE-KALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVG  130 (172)
T ss_pred             cCCCHH-HHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEE
Confidence            100000 000 001111222234443         36899999999999999999999999842            5799


Q ss_pred             EEcCHHHHHHHHHHHHHHHhcC
Q 012477          194 ISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       194 I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      |.|+++++..|...|.+++...
T Consensus       131 i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       131 IIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             EECCHHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999664

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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.56  E-value=1.4e-14  Score=128.87  Aligned_cols=138  Identities=21%  Similarity=0.269  Sum_probs=91.9

Q ss_pred             EeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEe--cCC-cccccccHHHHHHHhhcCccccccccc
Q 012477          288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS--SKE-FFEDTLSATIEAVVRLQPRCSEKIERD  364 (462)
Q Consensus       288 v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~--G~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~  364 (462)
                      +.||.+.+|.|||++|++|+.|+++||++|.+...     +..|.|.  +.+ .........+.++.+-++  .+....-
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~--~e~A~~l   74 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS--PEKALKL   74 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC--HHHHHHh
Confidence            56899999999999999999999999999999973     2356662  221 111111111222211100  0000000


Q ss_pred             CCCcceEEEEEecC---------CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHH
Q 012477          365 SGLISFTTRLLVPT---------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL  435 (462)
Q Consensus       365 ~~~~~~t~~i~Vp~---------~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~  435 (462)
                      .+....-.-+.|+.         ...|+|||++|++++.|+..|||+|.|..            +.|.|.|++++++.|.
T Consensus        75 ~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~~~A~  142 (172)
T TIGR03665        75 LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQVQIAR  142 (172)
T ss_pred             cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHHHHHH
Confidence            01111112233443         36899999999999999999999999941            5899999999999999


Q ss_pred             HHHHHHHHh
Q 012477          436 IQVMTRLRA  444 (462)
Q Consensus       436 ~~I~~~l~~  444 (462)
                      .+|...|+.
T Consensus       143 ~~i~~li~~  151 (172)
T TIGR03665       143 EAIEMLIEG  151 (172)
T ss_pred             HHHHHHHcC
Confidence            999887743

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.53  E-value=6.9e-14  Score=125.20  Aligned_cols=141  Identities=21%  Similarity=0.270  Sum_probs=93.9

Q ss_pred             eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEe---cCC-cccccccHHHHHHHhhcCcccc
Q 012477          284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS---SKE-FFEDTLSATIEAVVRLQPRCSE  359 (462)
Q Consensus       284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~---G~~-~~~~~~~~~~~a~~~~~~~~~~  359 (462)
                      +...+.||.+.++.|||++|++|+.|+++||++|.+...     +..|.|.   +.+ .........++++..-.+  .+
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~--~e   75 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS--PE   75 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC--HH
Confidence            367899999999999999999999999999999999974     2455665   222 111111111222222100  00


Q ss_pred             cccccCCCcceEEE-EEec---------CCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 012477          360 KIERDSGLISFTTR-LLVP---------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD  429 (462)
Q Consensus       360 ~~~~~~~~~~~t~~-i~Vp---------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~  429 (462)
                      ....-.+ ..+..+ +.|.         ...+|.|||++|++++.|++.|||+|.|..            +.|.|.|+++
T Consensus        76 ~A~~l~g-d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~~  142 (180)
T PRK13763         76 KALRLLD-DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDPE  142 (180)
T ss_pred             HHHHHhC-CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCHH
Confidence            0000000 111111 1121         137899999999999999999999999942            3599999999


Q ss_pred             HHHHHHHHHHHHHHh
Q 012477          430 LAKDALIQVMTRLRA  444 (462)
Q Consensus       430 ~v~~A~~~I~~~l~~  444 (462)
                      +++.|...|...++.
T Consensus       143 ~~~~A~~~I~~li~g  157 (180)
T PRK13763        143 QVEIAREAIEMLIEG  157 (180)
T ss_pred             HHHHHHHHHHHHHcC
Confidence            999999999887743

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.53  E-value=5.3e-14  Score=125.93  Aligned_cols=143  Identities=20%  Similarity=0.174  Sum_probs=99.0

Q ss_pred             ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEE----cCCcccccccCCCCcCCHHHHHHH
Q 012477           42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY----SASDETNAFEDGDKFVSPAQDALF  117 (462)
Q Consensus        42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~----G~~e~~~~~~~~~~~v~~a~~a~~  117 (462)
                      .+...+.||.+.++.|||++|++|+.|+++|||+|++.+.     +..|.|.    ++++.             +.+|..
T Consensus         2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-------------i~kA~~   63 (180)
T PRK13763          2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-------------VLKARD   63 (180)
T ss_pred             CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-------------HHHHHH
Confidence            3567899999999999999999999999999999999754     2467775    44433             233333


Q ss_pred             HHHHHHHHhhccCCCCCCCCCceEEEE-EEeC---------CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477          118 KVHDRVIAEELRGDEDSDGGHQVTAKL-LVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR  187 (462)
Q Consensus       118 ~i~~~i~~~~~~~~~~~~~~~~~~~~l-~ip~---------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  187 (462)
                      .+...+..-.+. +........+...+ -+..         ..+|+|||++|++++.|++.|||+|.|..          
T Consensus        64 ~I~ai~~gf~~e-~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------  132 (180)
T PRK13763         64 IVKAIGRGFSPE-KALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------  132 (180)
T ss_pred             HHHHHhcCCCHH-HHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------
Confidence            332211100000 00000011122221 1111         36899999999999999999999999853          


Q ss_pred             CCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          188 SDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       188 ~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                        ..|.|.|+++++..|...|.++++..
T Consensus       133 --~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        133 --KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             --CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence              24999999999999999999999664

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.42  E-value=5.3e-13  Score=99.02  Aligned_cols=63  Identities=41%  Similarity=0.627  Sum_probs=57.2

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV  438 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I  438 (462)
                      .+|.||...+|+|||++|++|++|+++|||+|++.+...    .+.++|.|+|+|++++++.|+.||
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence            579999999999999999999999999999999976532    257789999999999999999987

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

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.36  E-value=1.6e-12  Score=139.48  Aligned_cols=305  Identities=21%  Similarity=0.257  Sum_probs=199.7

Q ss_pred             eEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHH-
Q 012477           43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD-  121 (462)
Q Consensus        43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~-  121 (462)
                      +..++.+....+.++||++|.++..++.++.+.++|+.....  .....+.|...++.-      ...-.+.++.++-. 
T Consensus       201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~--~~~~~i~~~~~~~~~------~~~~i~~~~~~le~~  272 (753)
T KOG2208|consen  201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKS--SPSNKIDGRLNSSSS------INVEIQEALTRLESE  272 (753)
T ss_pred             EEEEeeccccchhhhccccccccccccccceeEEEccccccc--chhhhhcccccccee------hhhhhHHHHHHhcCh
Confidence            667899999999999999999999999999999999864222  223344554333210      00001111111100 


Q ss_pred             ----------------------------HHHHhh-ccCC-C--------------------------CCCCCCceEEEEE
Q 012477          122 ----------------------------RVIAEE-LRGD-E--------------------------DSDGGHQVTAKLL  145 (462)
Q Consensus       122 ----------------------------~i~~~~-~~~~-~--------------------------~~~~~~~~~~~l~  145 (462)
                                                  ...... ...+ +                          ...........+-
T Consensus       273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~  352 (753)
T KOG2208|consen  273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKRE  352 (753)
T ss_pred             hhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEe
Confidence                                        000000 0000 0                          0012234778888


Q ss_pred             EeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccc
Q 012477          146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAS  225 (462)
Q Consensus       146 ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~  225 (462)
                      +...++..++||+|.++.+|++++.|.+.+...       ++.+..+.++|...++.+|...+...+.+...        
T Consensus       353 i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n--------  417 (753)
T KOG2208|consen  353 IFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN--------  417 (753)
T ss_pred             ecHHhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc--------
Confidence            999999999999999999999999999999763       26688999999999999999999999887421        


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChh
Q 012477          226 AISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAI  305 (462)
Q Consensus       226 ~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~  305 (462)
                                                                              +.....+.+|..++.+|||.+|..
T Consensus       418 --------------------------------------------------------~~~~~~~~iP~k~~~~iig~~g~~  441 (753)
T KOG2208|consen  418 --------------------------------------------------------SIVKEEVQIPTKSHKRIIGTKGAL  441 (753)
T ss_pred             --------------------------------------------------------ccccceeecCccchhhhhcccccc
Confidence                                                                    013446889999999999999999


Q ss_pred             HHhHHhhhC-CeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecCCcccee
Q 012477          306 INQIRQESG-AAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCL  384 (462)
Q Consensus       306 Ik~I~~~sg-a~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~~~~g~I  384 (462)
                      |+.|+.+++ ..|++.+......  ..++.+.-...   ..+..-...+. .   ...........+.+...|..+.+..
T Consensus       442 i~~I~~k~~~v~i~f~~~~~~~~--~~~~~~~~~dv---~~~~~~~~~~~-~---~a~~~~~~~~~~~d~~~~~~~~~~~  512 (753)
T KOG2208|consen  442 INYIMGKHGGVHIKFQNNNNSSD--MVTIRGISKDV---EKSVSLLKALK-A---DAKNLKFRDVVTKDKLLPVKYIGKE  512 (753)
T ss_pred             HHHHHhhcCcEEEecCCCCcccc--cceEecccccc---chhHHHHHhhh-h---hhhcchhhhhhhccccchHHhhccc
Confidence            999999998 7777777654333  33444421110   01111011110 0   0001111234556677777777777


Q ss_pred             ecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          385 IGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       385 IGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      +|+.|..++...+.....+          ....++..++|.|..+.|..|.+.+...++..
T Consensus       513 ~g~~~~i~d~~~~~~i~~~----------~~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~  563 (753)
T KOG2208|consen  513 IGKNGTIRDSLGDKSIFPP----------NEDEDHEKITIEGKLELVLEAPAELKALIEAL  563 (753)
T ss_pred             ccCceeeeccCCceeeccc----------ccccccceeeecccccchhhhHHHHHhcchhh
Confidence            7777776665555553322          23456678999999999999999998877666

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.35  E-value=2.3e-12  Score=95.56  Aligned_cols=64  Identities=50%  Similarity=0.740  Sum_probs=58.1

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI  208 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  208 (462)
                      +++|+||...+|+|||++|.+|++|+++|||+|.+.+...    .+..+|+|+|+|+++++.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence            3789999999999999999999999999999999987643    247899999999999999999987

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.34  E-value=1.7e-12  Score=95.54  Aligned_cols=61  Identities=21%  Similarity=0.330  Sum_probs=54.7

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM  439 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~  439 (462)
                      .++.||..++++|||++|++|++|+++|||+|.+++.       .+.++.|+|+|++++|..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-------GSKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC-------CCCCCEEEEEcCHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999643       245689999999999999998873

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

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

Probab=99.33  E-value=5.4e-12  Score=125.02  Aligned_cols=271  Identities=22%  Similarity=0.285  Sum_probs=173.6

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHH
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKV  119 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i  119 (462)
                      ++++..++.||..++..+|||.|++|+.|++.++++|.+.+.. ..+++...+.|.+..          +.++..++-  
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~----------v~~a~a~~~--  131 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ----------VCKAKAAIH--  131 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC----------CChHHHHHH--
Confidence            5789999999999999999999999999999999999997542 334566666666554          344444433  


Q ss_pred             HHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHH
Q 012477          120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS  199 (462)
Q Consensus       120 ~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~  199 (462)
                       .++.           ....+...+.+|...++.|+|++|++++.|+.-++|+|.+..+.  .   ....+...|.|...
T Consensus       132 -~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng--r---~g~~~~~~i~~qqk  194 (608)
T KOG2279|consen  132 -QILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG--R---LGLSRLIKISGQQK  194 (608)
T ss_pred             -HHHh-----------cCCcccccccchhhhcccccccchhhhcchhccccccccccccc--c---cccccceecccccc
Confidence             3332           33567888999999999999999999999999999999986542  1   25688889999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCccccccc------------cc-CCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCC-C
Q 012477          200 VVKKALCQIASRLHDNPSRSQHLLAS------------AI-SNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTA-G  265 (462)
Q Consensus       200 ~v~~A~~~I~~~l~~~~~~~~~~~~~------------~~-~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~-~  265 (462)
                      -++.|..++.+.+.++...-......            .. ...+..++...+.-++.-...++|-.......+.++. .
T Consensus       195 ~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~  274 (608)
T KOG2279|consen  195 EVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVV  274 (608)
T ss_pred             hHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeE
Confidence            99999999999887753221110000            00 0011111111111111101111111111111111110 0


Q ss_pred             CCCCCCCCCCCCCC---CCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCc---eEEEEecCCcc
Q 012477          266 DWSRSLYSAPRDDL---SSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD---CLITVSSKEFF  339 (462)
Q Consensus       266 ~~~~~~~~~p~~~~---~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~---~~i~i~G~~~~  339 (462)
                      -.....++.|.+++   .....-..|.+|+..+|.+||..|+++..+...+++.+.|......+.-   .+..+.|+...
T Consensus       275 vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~  354 (608)
T KOG2279|consen  275 VSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHY  354 (608)
T ss_pred             EecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHH
Confidence            01112233333322   1223356789999999999999999999999999999999876544322   34556776543


Q ss_pred             c
Q 012477          340 E  340 (462)
Q Consensus       340 ~  340 (462)
                      .
T Consensus       355 ~  355 (608)
T KOG2279|consen  355 E  355 (608)
T ss_pred             H
Confidence            3

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

Probab=99.30  E-value=1e-11  Score=90.51  Aligned_cols=58  Identities=26%  Similarity=0.342  Sum_probs=52.6

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHH
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQV  438 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I  438 (462)
                      .+..+.||.+++|+|||++|++|++|+++|||+|.|++           ++.|+|+|+ +++++.|+.+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence            35679999999999999999999999999999999942           358999999 99999999887

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.29  E-value=2.2e-12  Score=94.26  Aligned_cols=60  Identities=35%  Similarity=0.511  Sum_probs=54.1

Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV  438 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I  438 (462)
                      |.+|.||.+++|+|||++|++|++|+++|||+|.++++       + +...|+|+|++++|+.|+.+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------C-CcEEEEEEeCHHHHHHHHhhC
Confidence            67899999999999999999999999999999999642       2 345999999999999999886

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.26  E-value=3.3e-11  Score=129.50  Aligned_cols=316  Identities=16%  Similarity=0.214  Sum_probs=184.6

Q ss_pred             ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHH
Q 012477           42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD  121 (462)
Q Consensus        42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~  121 (462)
                      .+...+.+-..++..|+||+|.+|.+|++++.|.|.+...  +..+..+.++|...++          .++.+.+..+..
T Consensus       346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~----------~ka~~~v~~~~~  413 (753)
T KOG2208|consen  346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND----------EKAVEDVEKIIA  413 (753)
T ss_pred             ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch----------hHHHHHHHHHHH
Confidence            3667788889999999999999999999999999999874  5667789999998773          334555554443


Q ss_pred             HHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcC-ceEEEecCCCCCC-----------------
Q 012477          122 RVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG-AQIRILKDEHLPS-----------------  183 (462)
Q Consensus       122 ~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~-----------------  183 (462)
                      .+..            +.....+.+|...+.++||.+|..|..|.++++ ..|++........                 
T Consensus       414 ei~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~  481 (753)
T KOG2208|consen  414 EILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMVTIRGISKDVEKSVSL  481 (753)
T ss_pred             hhhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccceEeccccccchhHHH
Confidence            3321            145677999999999999999999999999999 5665543211100                 


Q ss_pred             --------------------------------------------------cCCCCCceEEEEcCHHHHHHHHHHHHHHHh
Q 012477          184 --------------------------------------------------CALRSDELVQISGEASVVKKALCQIASRLH  213 (462)
Q Consensus       184 --------------------------------------------------~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~  213 (462)
                                                                        -.......++|.|..+.|..|...+...+.
T Consensus       482 ~~~~~~~a~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~~~~~i~i~gk~~~v~~a~~~L~~~~~  561 (753)
T KOG2208|consen  482 LKALKADAKNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDEDHEKITIEGKLELVLEAPAELKALIE  561 (753)
T ss_pred             HHhhhhhhhcchhhhhhhccccchHHhhcccccCceeeeccCCceeecccccccccceeeecccccchhhhHHHHHhcch
Confidence                                                              000111133444444444444444433333


Q ss_pred             cCCCCcccccccccCCCCCCC--CCCCCCCCC-----CC-CcCCCCCCCCCCCCCCCCC-CCCC--CCCCCC---C---C
Q 012477          214 DNPSRSQHLLASAISNSHSSS--GSLVGPTAA-----TP-IVGIAPLMGPYGGYKGDTA-GDWS--RSLYSA---P---R  276 (462)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~--g~~~~p~~~-----~~-~~~~~p~~~~~~~~~~~~~-~~~~--~~~~~~---p---~  276 (462)
                      ........ .     ..++.+  -.+....+.     .. ..+.   ..++.....+.. ..|.  ...+..   .   .
T Consensus       562 ~~~~~~~~-~-----v~~~~~~~~~~l~~~~~~~~~~~e~~~gv---~~~fp~~~~~~~e~~i~g~~~~v~aa~~~~~~i  632 (753)
T KOG2208|consen  562 ALIKATLL-E-----VNNPPGQHRPFLIGKGIENRTYVEVFGGV---VVPFPRSPTSSDEVSIKGAKDEVKAAKGRLEEI  632 (753)
T ss_pred             hhhhhhhh-h-----ccCcchheeeeeeccccccccceeecCcc---cccCCCCCCchhhhccchhHHHHHHhhccchhh
Confidence            32110000 0     000000  000000000     00 0000   000000000000 0000  000000   0   0


Q ss_pred             CCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCc
Q 012477          277 DDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPR  356 (462)
Q Consensus       277 ~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~  356 (462)
                      ........+..+.+|..++..+.|.+|..+++++..++..+.++..........+.+.|..        ....   .   
T Consensus       633 ~~~~~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~~~~~~~~--------~~~e---~---  698 (753)
T KOG2208|consen  633 VEYLSAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNTIHVSGEK--------MQSE---I---  698 (753)
T ss_pred             hhhcccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCcchhhhhh--------hhhh---h---
Confidence            0122444566799999999999999999999999999999999986543222112222210        0000   0   


Q ss_pred             ccccccccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          357 CSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       357 ~~~~~~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                         ..........++.++.+|..+|+.+||++|++++.+..++++.+.+.+
T Consensus       699 ---~~~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~  746 (753)
T KOG2208|consen  699 ---AKIALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN  746 (753)
T ss_pred             ---cccccccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence               001112234688999999999999999999999999999999999854

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

Probab=99.22  E-value=4.4e-11  Score=88.49  Aligned_cols=62  Identities=37%  Similarity=0.600  Sum_probs=55.4

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV  438 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I  438 (462)
                      .++.||.+++++|||++|++|++|++.|||+|.|.+..     .+.+++.|+|.|+.++++.|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-----~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-----SGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC-----CCCCceEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999997542     135678999999999999999886

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

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

Probab=99.20  E-value=2.6e-11  Score=120.26  Aligned_cols=229  Identities=22%  Similarity=0.327  Sum_probs=167.6

Q ss_pred             CCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477          137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP  216 (462)
Q Consensus       137 ~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  216 (462)
                      ...+.+.++|+...+..++|++|++|+.|+..+++||.+-.+ +.     ..++...+.|.+.++-.|...+..++.++.
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~  138 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DV-----GDERVLLISGFPVQVCKAKAAIHQILTENT  138 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cC-----CcccchhhccCCCCCChHHHHHHHHHhcCC
Confidence            356789999999999999999999999999999999998655 32     346667777799999999999999988742


Q ss_pred             CCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccc
Q 012477          217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG  296 (462)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g  296 (462)
                                                                                        .+.....+|...++
T Consensus       139 ------------------------------------------------------------------pvk~~lsvpqr~~~  152 (608)
T KOG2279|consen  139 ------------------------------------------------------------------PVSEQLSVPQRSVG  152 (608)
T ss_pred             ------------------------------------------------------------------cccccccchhhhcc
Confidence                                                                              24667789999999


Q ss_pred             cccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHH-------HHHHHhhcCccc-----------
Q 012477          297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSAT-------IEAVVRLQPRCS-----------  358 (462)
Q Consensus       297 ~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~-------~~a~~~~~~~~~-----------  358 (462)
                      +|+|++|++++.|+.-++++|.+..+......+.+.|.+...........       -+...+-.++..           
T Consensus       153 ~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n  232 (608)
T KOG2279|consen  153 RIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPIN  232 (608)
T ss_pred             cccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCcc
Confidence            99999999999999999999999998666666777777643211100000       000000000000           


Q ss_pred             ---c------------------cccc-------------------------------cCCCcceEEEEEecCCccceeec
Q 012477          359 ---E------------------KIER-------------------------------DSGLISFTTRLLVPTSRIGCLIG  386 (462)
Q Consensus       359 ---~------------------~~~~-------------------------------~~~~~~~t~~i~Vp~~~~g~IIG  386 (462)
                         +                  .+..                               ........-+|.+|.-.+|.+||
T Consensus       233 ~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig  312 (608)
T KOG2279|consen  233 VRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIG  312 (608)
T ss_pred             ccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhh
Confidence               0                  0000                               01123455678999999999999


Q ss_pred             CCCchHHHHHHhhCceEEEecCCCCCCCCC-CCCceEEEEcCHHHHHHHHHHHHH
Q 012477          387 KGGSIITEMRRLTKANIRILPKENLPKIAS-EDDEMVQISGDLDLAKDALIQVMT  440 (462)
Q Consensus       387 k~G~~I~~I~~~sga~I~i~~~~~~P~~~~-~~~~~v~I~G~~~~v~~A~~~I~~  440 (462)
                      +.|+.+..+...|++.+.|..-   |-... -...++.+.|+..-+.+|..|+..
T Consensus       313 ~~gey~s~yssasn~~~hi~t~---pyt~~v~~~qic~~egkqh~~n~vl~ml~~  364 (608)
T KOG2279|consen  313 HAGEYLSVYSSASNHPNHIWTQ---PYTSRVLQLQICVNEGKQHYENSVLEMLTV  364 (608)
T ss_pred             hhhhhhhhhhhccCccceEEec---cccchhhhhhhheecchhHHHHHHHhhhhc
Confidence            9999999999999999888653   32110 112568899999999999999983

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.16  E-value=3.8e-11  Score=87.65  Aligned_cols=60  Identities=40%  Similarity=0.613  Sum_probs=54.2

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI  208 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  208 (462)
                      |.+|.||.+++++|||++|++|++|+++|||+|.|+.+        .....|+|+|++++|.+|+.+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--------~~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999764        1245999999999999999876

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.14  E-value=6.8e-11  Score=86.90  Aligned_cols=60  Identities=28%  Similarity=0.441  Sum_probs=55.0

Q ss_pred             EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477          142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI  208 (462)
Q Consensus       142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  208 (462)
                      ..|.||..++++|||++|++|++|+++|||+|.|+..+       +.++.|+|+|+.++|..|..+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999997753       4688999999999999999876

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

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

Probab=99.11  E-value=3.1e-10  Score=82.74  Aligned_cols=58  Identities=34%  Similarity=0.488  Sum_probs=52.5

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC-HHHHHHHHHHH
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQI  208 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I  208 (462)
                      ....+.||.+++++|||++|++|+.|+++|||+|.+..           ++.|.|+|+ ++++..|..+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence            35678999999999999999999999999999999854           457999998 99999999886

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

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

Probab=99.05  E-value=7e-10  Score=82.01  Aligned_cols=62  Identities=40%  Similarity=0.657  Sum_probs=55.9

Q ss_pred             EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477          142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI  208 (462)
Q Consensus       142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  208 (462)
                      .++.||..++++|||++|++|++|+++|||+|.|.....     ...++.|.|.|+.+++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence            579999999999999999999999999999999987532     25789999999999999998876

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

>PF13014 KH_3: KH domain

Probab=98.99  E-value=9.1e-10  Score=74.34  Aligned_cols=42  Identities=48%  Similarity=0.794  Sum_probs=39.0

Q ss_pred             ccceeecCCchHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEc
Q 012477           53 KIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYS   94 (462)
Q Consensus        53 ~~g~IIGk~G~~Ik~i~~~tg~~I~v~~-~~~~~~ervi~I~G   94 (462)
                      +||+|||++|++|++|+++|+|+|+|++ ..++..++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999999997 66788899999997

>smart00322 KH K homology RNA-binding domain

Probab=98.98  E-value=3.3e-09  Score=79.10  Aligned_cols=67  Identities=28%  Similarity=0.519  Sum_probs=59.2

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL  442 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  442 (462)
                      ..+.++.||..+++++||++|++|++|++.||++|.+...       ..+...|+|.|+.++++.|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~-------~~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED-------GSEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC-------CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            3578899999999999999999999999999999999532       125678999999999999999998876

>PF13014 KH_3: KH domain

Probab=98.97  E-value=1.1e-09  Score=73.99  Aligned_cols=43  Identities=47%  Similarity=0.741  Sum_probs=37.4

Q ss_pred             ccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc
Q 012477          380 RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG  426 (462)
Q Consensus       380 ~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G  426 (462)
                      +||+|||++|++|++|+++|||+|+|++ +.   ..+.+++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~---~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP-EN---EPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC-cc---CCCCCceEEEEEC
Confidence            5899999999999999999999999987 22   2357889999998

>smart00322 KH K homology RNA-binding domain

Probab=98.76  E-value=5.2e-08  Score=72.55  Aligned_cols=67  Identities=39%  Similarity=0.655  Sum_probs=59.6

Q ss_pred             ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      ..+.++.||...++.+||++|.+|++|++.||++|.+....       .....+.|.|+.+++..|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999999999986541       25789999999999999999998876

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

Probab=98.65  E-value=1.1e-07  Score=83.82  Aligned_cols=141  Identities=23%  Similarity=0.308  Sum_probs=93.5

Q ss_pred             eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCccccccc-----HHHHHHHhhcC-cc
Q 012477          284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS-----ATIEAVVRLQP-RC  357 (462)
Q Consensus       284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~-----~~~~a~~~~~~-~~  357 (462)
                      .+..+.||..-.+.+||+.|+.-+.|.+.+++++.++..     +..|+|...+...+.+.     ..+.|+-+-++ ..
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~   82 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK   82 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence            366799999999999999999999999999999999874     34566665432222211     11111111110 00


Q ss_pred             cccccccCCCcceEEEEEe------c----CCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC
Q 012477          358 SEKIERDSGLISFTTRLLV------P----TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD  427 (462)
Q Consensus       358 ~~~~~~~~~~~~~t~~i~V------p----~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~  427 (462)
                      .-.+-.+   ...-..+.+      +    ....|+|||++|.+-+-|++.|||+|.|..            .+|.|.|.
T Consensus        83 A~~LL~d---~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVaiiG~  147 (194)
T COG1094          83 ALKLLED---DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVAIIGG  147 (194)
T ss_pred             HHHHhcC---CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEEEecC
Confidence            0000000   000001111      1    224599999999999999999999999953            38999999


Q ss_pred             HHHHHHHHHHHHHHHHh
Q 012477          428 LDLAKDALIQVMTRLRA  444 (462)
Q Consensus       428 ~~~v~~A~~~I~~~l~~  444 (462)
                      +++|+.|...|...|+.
T Consensus       148 ~~~v~iAr~AVemli~G  164 (194)
T COG1094         148 FEQVEIAREAVEMLING  164 (194)
T ss_pred             hhhhHHHHHHHHHHHcC
Confidence            99999999998776643

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

Probab=98.63  E-value=8.9e-07  Score=78.18  Aligned_cols=149  Identities=21%  Similarity=0.282  Sum_probs=99.2

Q ss_pred             CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHH
Q 012477           41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH  120 (462)
Q Consensus        41 ~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~  120 (462)
                      ......+.||.+..+.+||+.|+..+.|.+.+++++.++..     +..|.|......-+.     -.+-+|.+-+..+ 
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp-----~~~~ka~d~VkAI-   74 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDP-----LALLKARDVVKAI-   74 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCCh-----HHHHHHHHHHHHH-
Confidence            45567799999999999999999999999999999999643     456788776221110     0011122211111 


Q ss_pred             HHHHHhhccCCCCC-CCCCceEEE-E----EEe--C----CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCC
Q 012477          121 DRVIAEELRGDEDS-DGGHQVTAK-L----LVP--S----DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRS  188 (462)
Q Consensus       121 ~~i~~~~~~~~~~~-~~~~~~~~~-l----~ip--~----~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~  188 (462)
                          ..++..+.+. -....+.+. +    ++.  .    ...|+|||++|.+-+.|++-|+|.|.|..+          
T Consensus        75 ----grGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~----------  140 (194)
T COG1094          75 ----GRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK----------  140 (194)
T ss_pred             ----hcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc----------
Confidence                1111100000 000111111 1    111  1    235999999999999999999999999654          


Q ss_pred             CceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477          189 DELVQISGEASVVKKALCQIASRLHDNP  216 (462)
Q Consensus       189 ~r~v~I~G~~~~v~~A~~~I~~~l~~~~  216 (462)
                        .|.|-|.+++|..|...|..++...+
T Consensus       141 --tVaiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         141 --TVAIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             --EEEEecChhhhHHHHHHHHHHHcCCC
Confidence              79999999999999999999998753

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

Probab=98.53  E-value=3.3e-07  Score=76.04  Aligned_cols=67  Identities=21%  Similarity=0.308  Sum_probs=51.8

Q ss_pred             CCccceeecCCCchHHHHHHhhCceEEEecCCCCC-----------CCC-CCCCceEEEEcCH---HHHHHHHHHHHHHH
Q 012477          378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP-----------KIA-SEDDEMVQISGDL---DLAKDALIQVMTRL  442 (462)
Q Consensus       378 ~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P-----------~~~-~~~~~~v~I~G~~---~~v~~A~~~I~~~l  442 (462)
                      .+++|.|||++|++||+|+++|||+|.|..+...-           ... .++.-.|.|+++.   ++++.|+.+|...|
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            56889999999999999999999999997653210           000 1223579999964   99999999999877


Q ss_pred             Hh
Q 012477          443 RA  444 (462)
Q Consensus       443 ~~  444 (462)
                      ..
T Consensus        94 ~~   95 (120)
T cd02395          94 KP   95 (120)
T ss_pred             cc
Confidence            63

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

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

Probab=98.16  E-value=6.9e-06  Score=68.22  Aligned_cols=67  Identities=25%  Similarity=0.391  Sum_probs=52.3

Q ss_pred             CceeeeecCCchHHHHHHhhcCceEEEecCCCCCC------------cCCCCCceEEEEcCH---HHHHHHHHHHHHHHh
Q 012477          149 DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPS------------CALRSDELVQISGEA---SVVKKALCQIASRLH  213 (462)
Q Consensus       149 ~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~------------~~~~~~r~v~I~G~~---~~v~~A~~~I~~~l~  213 (462)
                      +++|.|||++|.++|.|+++|||+|.|..+.....            ......-.|.|++..   +++.+|..+|..++.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999976521100            001233578999964   999999999999998


Q ss_pred             cC
Q 012477          214 DN  215 (462)
Q Consensus       214 ~~  215 (462)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            64

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

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.02  E-value=1.9e-05  Score=83.85  Aligned_cols=96  Identities=25%  Similarity=0.327  Sum_probs=78.1

Q ss_pred             CcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCC
Q 012477          107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL  186 (462)
Q Consensus       107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  186 (462)
                      +++..|.+++.++++.+.+....+ .+.....+....+.||.+.++.|||++|.+||.|.++|||+|.+..         
T Consensus       546 ~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------  615 (719)
T TIGR02696       546 SALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------  615 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------
Confidence            456678888888888765544333 3344556778899999999999999999999999999999999843         


Q ss_pred             CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477          187 RSDELVQISG-EASVVKKALCQIASRLHD  214 (462)
Q Consensus       187 ~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  214 (462)
                        +..|.|.+ ..+++.+|+.+|..++..
T Consensus       616 --~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       616 --DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             --CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence              56899988 489999999999998885

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.01  E-value=2.8e-05  Score=66.56  Aligned_cols=103  Identities=21%  Similarity=0.309  Sum_probs=71.4

Q ss_pred             eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccc
Q 012477          284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER  363 (462)
Q Consensus       284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~  363 (462)
                      -.+.+.|+...+|..||++|++|+.|++..|-+|.+-.-+.+.                 ..-+..++  .|.-.....-
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d~-----------------~~fI~n~l--~Pa~V~~v~I   92 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDDP-----------------EEFIKNIF--APAAVRSVTI   92 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCCH-----------------HHHHHHHc--CCCEEEEEEE
Confidence            3778899999999999999999999999999888776632221                 00111111  1111000000


Q ss_pred             cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEE
Q 012477          364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI  405 (462)
Q Consensus       364 ~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i  405 (462)
                      ..........+.|+....|..|||+|++|+.++..+|-.+.|
T Consensus        93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            001123456788999999999999999999999999998877

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.96  E-value=1.1e-05  Score=69.00  Aligned_cols=102  Identities=19%  Similarity=0.277  Sum_probs=68.2

Q ss_pred             EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477           44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV  123 (462)
Q Consensus        44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i  123 (462)
                      .+.++|+...+|..||++|++|+.|++..|-+|.|-+           .+-.+                ..-+..++.-.
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~s~d~----------------~~fI~n~l~Pa   85 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------YSDDP----------------EEFIKNIFAPA   85 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------cCCCH----------------HHHHHHHcCCC
Confidence            4567889999999999999999999999988887532           11111                11111111100


Q ss_pred             HHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEE
Q 012477          124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI  175 (462)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i  175 (462)
                      .-.++.   -........+.+.|+....|.+|||+|.+++.++.-++-.+.+
T Consensus        86 ~V~~v~---I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         86 AVRSVT---IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EEEEEE---EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            000000   0011223466778999999999999999999999999988766

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

Probab=97.87  E-value=2.6e-05  Score=72.89  Aligned_cols=140  Identities=21%  Similarity=0.347  Sum_probs=99.7

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS  217 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  217 (462)
                      ..++..+.||..+++.+.|++|.+||.|+.+|...|.-+....        +-++.++|..+.|..|++.|...-+..- 
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~saaeH~~-   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPSAAEHFG-   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCccccceee-
Confidence            6788889999999999999999999999999999998766543        3478899999999999988754322210 


Q ss_pred             CcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCcccc
Q 012477          218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG  297 (462)
Q Consensus       218 ~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~  297 (462)
                          +..      +                     ..++.+..    ..     |+      .+.+.+..+.+|...+|.
T Consensus        95 ----l~~------~---------------------s~s~Sgg~----~~-----~s------~s~qt~sy~svP~rvvgl  128 (394)
T KOG2113|consen   95 ----LIR------A---------------------SRSFSGGT----NG-----AS------ASGQTTSYVSVPLRVVGL  128 (394)
T ss_pred             ----eee------e---------------------cccccCCC----cc-----cc------ccCCCceeeeccceeeee
Confidence                000      0                     00000000    00     00      123346678899999999


Q ss_pred             ccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEec
Q 012477          298 VIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSS  335 (462)
Q Consensus       298 IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G  335 (462)
                      +.|..|.+|+.|++.+...|.-+-..   .+.++.++|
T Consensus       129 vv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg  163 (394)
T KOG2113|consen  129 VVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTG  163 (394)
T ss_pred             ccccccCccchheecccceEeeeccC---CCceEEEec
Confidence            99999999999999999988776644   334555555

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

Probab=97.85  E-value=1.5e-05  Score=74.40  Aligned_cols=136  Identities=18%  Similarity=0.311  Sum_probs=98.0

Q ss_pred             cceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccc--
Q 012477          282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE--  359 (462)
Q Consensus       282 ~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~--  359 (462)
                      ..++..+.+|..+++.|.|++|.+||.|+.+|.+.|+-+...   .+.++.++|...       ..+.+.+..+...+  
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~e-------dv~~aRrei~saaeH~   93 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHE-------DVRRARREIPSAAEHF   93 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCch-------hHHHHhhcCcccccee
Confidence            456788899999999999999999999999999999877643   446777888532       11122211111000  


Q ss_pred             ----ccc------ccC-CCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH
Q 012477          360 ----KIE------RDS-GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL  428 (462)
Q Consensus       360 ----~~~------~~~-~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~  428 (462)
                          ++.      ... ...+.+..+.+|-..+|.|.|..|.+|+.|++.+...|.-.-+        ..+.++-++|.+
T Consensus        94 ~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~  165 (394)
T KOG2113|consen   94 GLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAP  165 (394)
T ss_pred             eeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCC
Confidence                000      000 1246778899999999999999999999999999999876432        345689999998


Q ss_pred             HH-HHHHH
Q 012477          429 DL-AKDAL  435 (462)
Q Consensus       429 ~~-v~~A~  435 (462)
                      .+ +++|.
T Consensus       166 ~nC~kra~  173 (394)
T KOG2113|consen  166 KNCVKRAR  173 (394)
T ss_pred             cchhhhcc
Confidence            88 55554

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.68  E-value=8.7e-05  Score=80.15  Aligned_cols=96  Identities=21%  Similarity=0.295  Sum_probs=73.1

Q ss_pred             cCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477          108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR  187 (462)
Q Consensus       108 ~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  187 (462)
                      .+..|.++..+|++.+.+.............+....+.||.+.++.|||++|.+||.|+++|||+|.|..          
T Consensus       519 al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d----------  588 (684)
T TIGR03591       519 ALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED----------  588 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec----------
Confidence            4455677777777765543333333334455678889999999999999999999999999999999954          


Q ss_pred             CCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477          188 SDELVQISG-EASVVKKALCQIASRLHD  214 (462)
Q Consensus       188 ~~r~v~I~G-~~~~v~~A~~~I~~~l~~  214 (462)
                       +..|.|.+ ..+.+.+|..+|..+...
T Consensus       589 -dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       589 -DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             -CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence             45677776 588889999999888653

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

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.64  E-value=0.00018  Score=61.41  Aligned_cols=103  Identities=23%  Similarity=0.283  Sum_probs=70.9

Q ss_pred             EEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccccc
Q 012477          285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD  364 (462)
Q Consensus       285 ~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  364 (462)
                      .+-|.|....+|..||++|++|+.|++..|-+|.+-.-+++.             .    .-+..+  +.|.-.....-.
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~-------------~----~fI~N~--l~PA~V~~V~i~   94 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENL-------------E----EFVANK--LAPAEVKNVTVS   94 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCH-------------H----HHHHHc--CCCceEEEEEEE
Confidence            677889999999999999999999988888888776632221             0    000111  111111111000


Q ss_pred             CCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEe
Q 012477          365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRIL  406 (462)
Q Consensus       365 ~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~  406 (462)
                      .........+.||.+..+..|||+|++|+..++.+|-++.|.
T Consensus        95 ~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        95 EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            011235677889999999999999999999999999988773

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

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

Probab=97.62  E-value=0.0005  Score=68.52  Aligned_cols=77  Identities=22%  Similarity=0.342  Sum_probs=58.3

Q ss_pred             ceEEEEEec------CCccceeecCCCchHHHHHHhhCceEEEecCCCC----------CCCC-CCCCceEEEEcC-HHH
Q 012477          369 SFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENL----------PKIA-SEDDEMVQISGD-LDL  430 (462)
Q Consensus       369 ~~t~~i~Vp------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~----------P~~~-~~~~~~v~I~G~-~~~  430 (462)
                      .++.+|.||      .+++|.|||..|.|.|+|+++|||+|.|-.+...          .... ..++=-+.|+++ .|.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            567788888      6789999999999999999999999999752211          0001 112234778876 588


Q ss_pred             HHHHHHHHHHHHHhh
Q 012477          431 AKDALIQVMTRLRAN  445 (462)
Q Consensus       431 v~~A~~~I~~~l~~~  445 (462)
                      |++|+.+|...|++-
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999998863

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.59  E-value=0.00014  Score=77.46  Aligned_cols=65  Identities=25%  Similarity=0.287  Sum_probs=57.3

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRA  444 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~  444 (462)
                      .....+.||.+.+|.|||+||.+||.|.++|||+|.|.+           +..|.|.+. .+.+++|+.+|...+..
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            456789999999999999999999999999999999942           468999984 79999999999887774

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.57  E-value=0.00011  Score=62.58  Aligned_cols=102  Identities=22%  Similarity=0.273  Sum_probs=68.0

Q ss_pred             EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477           44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV  123 (462)
Q Consensus        44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i  123 (462)
                      .+-++|....+|..||++|++|+.|++..|-+|.|-           ..+..+++.            +.++       +
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV-----------eys~D~~~f------------I~N~-------l   83 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI-----------EYSENLEEF------------VANK-------L   83 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE-----------EcCCCHHHH------------HHHc-------C
Confidence            566789999999999999999999988888888752           222222110            0000       0


Q ss_pred             HHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEE
Q 012477          124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI  175 (462)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i  175 (462)
                      .--......-..........+.||....+..|||+|.+++....-++-.+.+
T Consensus        84 ~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952        84 APAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI  135 (141)
T ss_pred             CCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence            0000000000011233567788999999999999999999999999888766

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

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

Probab=97.53  E-value=0.00012  Score=71.55  Aligned_cols=64  Identities=28%  Similarity=0.467  Sum_probs=52.1

Q ss_pred             CCCCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCc
Q 012477           31 DDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASD   97 (462)
Q Consensus        31 ~~~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e   97 (462)
                      +.+...+...+++.+++.+-++++|.|||++|++|++|+..|+++|++.+.   ..+-.|+|.|...
T Consensus        35 ~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~   98 (629)
T KOG0336|consen   35 DSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH   98 (629)
T ss_pred             CCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence            333444556778999999999999999999999999999999999999754   2355688888743

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

Probab=97.51  E-value=0.00015  Score=75.61  Aligned_cols=99  Identities=23%  Similarity=0.256  Sum_probs=78.6

Q ss_pred             CCCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCc
Q 012477          105 GDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSC  184 (462)
Q Consensus       105 ~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  184 (462)
                      +..++.+|..+..+++..+.+..-..+.......+-...+.|+...+..+||++|.+|++|.++|||+|++..       
T Consensus       517 m~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied-------  589 (692)
T COG1185         517 MKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED-------  589 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC-------
Confidence            3345667888888888876554333333444556667889999999999999999999999999999999952       


Q ss_pred             CCCCCceEEEEcC-HHHHHHHHHHHHHHHhc
Q 012477          185 ALRSDELVQISGE-ASVVKKALCQIASRLHD  214 (462)
Q Consensus       185 ~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~  214 (462)
                          +..|.|.++ .+.+.+|+..|..+.++
T Consensus       590 ----dGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         590 ----DGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             ----CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence                557999987 48889999999999966

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

Probab=97.46  E-value=0.00095  Score=66.56  Aligned_cols=77  Identities=25%  Similarity=0.381  Sum_probs=58.5

Q ss_pred             CceEEEEEEeC------CceeeeecCCchHHHHHHhhcCceEEEecCCC----------CCCcC-CCCCceEEEEcC-HH
Q 012477          138 HQVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEH----------LPSCA-LRSDELVQISGE-AS  199 (462)
Q Consensus       138 ~~~~~~l~ip~------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------~p~~~-~~~~r~v~I~G~-~~  199 (462)
                      ..++.++.||.      +++|+|||.+|.|.|+|+++|||||.|-.+..          +.... ...+=-|.|++. -+
T Consensus       136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e  215 (554)
T KOG0119|consen  136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE  215 (554)
T ss_pred             cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence            36778888886      58899999999999999999999999976211          11111 122335778875 78


Q ss_pred             HHHHHHHHHHHHHhc
Q 012477          200 VVKKALCQIASRLHD  214 (462)
Q Consensus       200 ~v~~A~~~I~~~l~~  214 (462)
                      .|.+|+..|..+|.+
T Consensus       216 ki~~Ai~vienli~~  230 (554)
T KOG0119|consen  216 KIKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            899999999999986

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.40  E-value=0.00021  Score=77.81  Aligned_cols=98  Identities=20%  Similarity=0.249  Sum_probs=78.7

Q ss_pred             CCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCce-EEEecCCCCCCc
Q 012477          106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ-IRILKDEHLPSC  184 (462)
Q Consensus       106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~  184 (462)
                      .+++..|.+++.++++.+.+....+........+....+.||.+.++.|||.+|.+||.|.++||++ |.+.        
T Consensus       651 ~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~--------  722 (891)
T PLN00207        651 ERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ--------  722 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC--------
Confidence            3456678888888888766544444444455667889999999999999999999999999999999 8763        


Q ss_pred             CCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477          185 ALRSDELVQISG-EASVVKKALCQIASRLHD  214 (462)
Q Consensus       185 ~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  214 (462)
                         .+..|.|.+ ..+.+.+|+.+|..++.+
T Consensus       723 ---ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        723 ---DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             ---CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence               256788888 589999999999998874

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.14  E-value=0.00061  Score=73.69  Aligned_cols=65  Identities=26%  Similarity=0.326  Sum_probs=55.0

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~  444 (462)
                      .....+.||.+.++.|||+||++||.|.++|||+|.|..           +..|.|.+ ..+.+++|+.+|......
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            456789999999999999999999999999999999942           34677777 468899999999876553

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

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

Probab=97.01  E-value=0.00083  Score=65.81  Aligned_cols=64  Identities=25%  Similarity=0.354  Sum_probs=53.2

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHH
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT  440 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~  440 (462)
                      .+...+.|.++++|.|||++|++|+.|+..|.++|+|.+.        +.+-.|+|-|...--.+|+..|..
T Consensus        46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~  109 (629)
T KOG0336|consen   46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDR  109 (629)
T ss_pred             CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhh
Confidence            3556677889999999999999999999999999999764        445789999998777777666643

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.98  E-value=0.0022  Score=57.53  Aligned_cols=100  Identities=24%  Similarity=0.337  Sum_probs=66.5

Q ss_pred             EeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCC
Q 012477          288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGL  367 (462)
Q Consensus       288 v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  367 (462)
                      +.+-...+|..||++|.+|+.|.++.|=+|.|-.-+++.             ..   -..+++ .  |.-.....-... 
T Consensus        80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d~-------------~~---fI~nal-~--Pa~v~~V~~~~~-  139 (190)
T COG0195          80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSEDP-------------AE---FIKNAL-A--PAEVLSVNIKED-  139 (190)
T ss_pred             eecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCCH-------------HH---HHHHhc-C--cceEeEEEEEeC-
Confidence            334456789999999999999999999666665533221             00   011111 1  111111110000 


Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                      +.-...+.||.+..+..|||+|.+++-+.+.||-++.|..
T Consensus       140 d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         140 DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            1126788899999999999999999999999999999953

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.82  E-value=0.0032  Score=56.57  Aligned_cols=104  Identities=30%  Similarity=0.352  Sum_probs=68.0

Q ss_pred             EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477           44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV  123 (462)
Q Consensus        44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i  123 (462)
                      .+-..+-.+.+|..||++|++|+.|.++.|=+|.|-+-           +-.+.+.            +.+++.      
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s~d~~~f------------I~nal~------  127 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------SEDPAEF------------IKNALA------  127 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------CCCHHHH------------HHHhcC------
Confidence            44555667788999999999999999999977765221           1111110            111111      


Q ss_pred             HHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                       --...+-.-...+.. ...+.||.+..+.+|||+|.+++-+..-||-++.|...
T Consensus       128 -Pa~v~~V~~~~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~  180 (190)
T COG0195         128 -PAEVLSVNIKEDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI  180 (190)
T ss_pred             -cceEeEEEEEeCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence             000000000011112 78888999999999999999999999999999998654

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

Probab=96.78  E-value=0.0025  Score=46.25  Aligned_cols=37  Identities=30%  Similarity=0.421  Sum_probs=33.9

Q ss_pred             ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEE
Q 012477           42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI   78 (462)
Q Consensus        42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v   78 (462)
                      .-...+.|+.+..|..|||+|.+|+.+++.++-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3578899999999999999999999999999988875

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.75  E-value=0.0015  Score=70.99  Aligned_cols=96  Identities=22%  Similarity=0.318  Sum_probs=72.7

Q ss_pred             cCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477          108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR  187 (462)
Q Consensus       108 ~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  187 (462)
                      .+..|.++..+|++.+.+....+........+....+.||.+.++.+||.+|.+||.|.++||++|.+.           
T Consensus       522 al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------  590 (693)
T PRK11824        522 ALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------  590 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------
Confidence            455677888888877655433333333334455667778999999999999999999999999998872           


Q ss_pred             CCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477          188 SDELVQISG-EASVVKKALCQIASRLHD  214 (462)
Q Consensus       188 ~~r~v~I~G-~~~~v~~A~~~I~~~l~~  214 (462)
                      .+..|.|.+ ..+.+.+|..+|..+..+
T Consensus       591 d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        591 DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            256788888 588899999999887754

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

Probab=96.71  E-value=0.0021  Score=59.62  Aligned_cols=39  Identities=33%  Similarity=0.569  Sum_probs=35.2

Q ss_pred             CCceEEEEEeeCC------ccceeecCCchHHHHHHHHhCCeEEE
Q 012477           40 PEDTVYRYLCPIR------KIGSIIGRGGEIVKQLRIDTKSKIRI   78 (462)
Q Consensus        40 ~~~~~~~ilvp~~------~~g~IIGk~G~~Ik~i~~~tg~~I~v   78 (462)
                      .-.++.+|+||.+      ++|.|+|.+|.++|+|+++|+|+|.|
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~I  133 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMI  133 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEE
Confidence            4467889999988      79999999999999999999999875

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

Probab=96.69  E-value=0.0029  Score=45.94  Aligned_cols=36  Identities=33%  Similarity=0.570  Sum_probs=33.6

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEE
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI  405 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i  405 (462)
                      ....+.||....|..|||+|++|+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            577899999999999999999999999999988876

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

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

Probab=96.58  E-value=0.008  Score=53.35  Aligned_cols=42  Identities=26%  Similarity=0.590  Sum_probs=36.5

Q ss_pred             cceEEEEEec------CCccceeecCCCchHHHHHHhhCceEEEecCC
Q 012477          368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKE  409 (462)
Q Consensus       368 ~~~t~~i~Vp------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~  409 (462)
                      ..++.+++||      .+++|.|||+.|++.+++++.|+|+|.|-.+.
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            3567778888      78999999999999999999999999996543

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.58  E-value=0.0055  Score=64.06  Aligned_cols=68  Identities=22%  Similarity=0.277  Sum_probs=53.7

Q ss_pred             cceEEEEEecC-CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~-~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~  445 (462)
                      ...+..|.+|+ ++-|.|||+.|.+|+-+...||+.|.|+          ++...|+|+| +|---+.|...+...|.+.
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~fdp~rreia~~~l~~li~dg  271 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPVRREIARMALEKLIQDG  271 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc----------CCCCeEEecCCchHHHHHHHHHHHHHHHcC
Confidence            35667788998 5669999999999999999999999994          3345899999 6766677776666655543

>PRK12704 phosphodiesterase; Provisional

Probab=96.58  E-value=0.0057  Score=64.04  Aligned_cols=68  Identities=22%  Similarity=0.269  Sum_probs=52.8

Q ss_pred             cceEEEEEecC-CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~-~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~  445 (462)
                      ...+..|.+|+ ++-|.|||+.|.+|+-+...||+.|.|+          ++...|+|+| +|---+.|...+...+.+.
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc----------CCCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            35667788998 5669999999999999999999999994          3345899999 6666567766665555443

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

Probab=96.58  E-value=0.0031  Score=66.00  Aligned_cols=65  Identities=26%  Similarity=0.305  Sum_probs=57.0

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH-HHHHHHHHHHHHHHHhh
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL-DLAKDALIQVMTRLRAN  445 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~l~~~  445 (462)
                      -..++.|+.+.++-+||+||.+|++|.++|||.|+|.           ++.+|.|.++. +.++.|+.+|.+..++.
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence            4567889999999999999999999999999999994           33579999986 88999999999887665

>PRK00106 hypothetical protein; Provisional

Probab=96.56  E-value=0.0065  Score=63.29  Aligned_cols=68  Identities=24%  Similarity=0.306  Sum_probs=53.7

Q ss_pred             cceEEEEEecC-CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~-~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~  445 (462)
                      ...+..|.+|+ ++-|.|||+.|.+|+-+...||+.+.|+          ++...|+|+| +|---+.|...+...|.+.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~dg  292 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIKDG  292 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence            45677788998 5669999999999999999999999994          3445899999 7777777766666555443

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

Probab=96.52  E-value=0.0031  Score=60.12  Aligned_cols=71  Identities=27%  Similarity=0.391  Sum_probs=58.9

Q ss_pred             ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      .....++++..+.++|||++|.|-++|+++|+++|.++...+      ..+.+..+.+..++|.+|...|.-++...
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            456778999999999999999999999999999999977531      33444455557999999999999998775

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

Probab=96.45  E-value=0.0034  Score=58.26  Aligned_cols=42  Identities=24%  Similarity=0.458  Sum_probs=37.0

Q ss_pred             cceEEEEEec------CCccceeecCCCchHHHHHHhhCceEEEecCC
Q 012477          368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKE  409 (462)
Q Consensus       368 ~~~t~~i~Vp------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~  409 (462)
                      ...+.+|+||      .++||.|+|+.|.++|+|+++|||+|-|-.+.
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg  137 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG  137 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence            4577888888      56899999999999999999999999997654

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.42  E-value=0.0031  Score=68.99  Aligned_cols=64  Identities=20%  Similarity=0.307  Sum_probs=55.2

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCce-EEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN-IRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR  443 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~-I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~  443 (462)
                      .....+.||.+.++.|||.||.+||.|.++||+. |.+.           ++-.|.|.+ +.+.+++|+.+|.+...
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4667899999999999999999999999999999 8873           235788888 57899999999887764

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.36  E-value=0.0068  Score=56.91  Aligned_cols=63  Identities=21%  Similarity=0.239  Sum_probs=52.5

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH-HHHHHHHHHHHHHHHhh
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL-DLAKDALIQVMTRLRAN  445 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~l~~~  445 (462)
                      ..+.||..+++.+||++|.+|+.|.+.+++.|.|.           .+-.|.|.++. +++..|+.+|.+.-++.
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            45889999999999999999999999999999983           23589999975 58889988887644433

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.34  E-value=0.013  Score=57.92  Aligned_cols=96  Identities=21%  Similarity=0.192  Sum_probs=64.7

Q ss_pred             CccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceE
Q 012477          293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT  371 (462)
Q Consensus       293 ~~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t  371 (462)
                      +-+|..||++|.+|+.|.++. |=+|.|-.-+++..             ..   ..+++   .|.-.......  .....
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~-------------~f---I~Nal---~Pa~V~~V~i~--~~~~~  309 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPE-------------IF---IARAL---APAIISSVKIE--EEEKK  309 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH-------------HH---HHHhC---CCceeeEEEEc--CCCcE
Confidence            357999999999999999998 76776655332210             00   00111   11111011001  11246


Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCC
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKE  409 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~  409 (462)
                      ..+.||.+..+..|||+|++++-..+.||.+|.|-.-+
T Consensus       310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            78899999999999999999999999999999997644

>TIGR01953 NusA transcription termination factor NusA

Probab=96.32  E-value=0.011  Score=58.37  Aligned_cols=93  Identities=26%  Similarity=0.403  Sum_probs=63.2

Q ss_pred             ccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc-ccCCCcceE
Q 012477          294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE-RDSGLISFT  371 (462)
Q Consensus       294 ~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~t  371 (462)
                      -+|..||++|++|+.|.++. |=+|.|-.-+++..             ..   ..+++   .|.-..... .+.  ....
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~-------------~f---i~nal---~Pa~v~~v~i~~~--~~~~  302 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPA-------------EF---IANAL---SPAKVISVEVLDE--DKHS  302 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHH-------------HH---HHHhc---CCceEEEEEEEcC--CCcE
Confidence            57999999999999999998 76776655332210             00   00111   111111110 011  1246


Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                      ..+.||.+..+..|||+|++++-..+.||.+|.|..
T Consensus       303 ~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       303 AEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            789999999999999999999999999999999953

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

>TIGR01953 NusA transcription termination factor NusA

Probab=96.28  E-value=0.013  Score=57.97  Aligned_cols=96  Identities=29%  Similarity=0.406  Sum_probs=62.7

Q ss_pred             CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477           52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG  130 (462)
Q Consensus        52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~  130 (462)
                      +-+|+.||++|++|+.|.++. |=+|+|-.-           +-.++..            +.+|+.=.  .+..-.+  
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~f------------i~nal~Pa--~v~~v~i--  295 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEY-----------SDDPAEF------------IANALSPA--KVISVEV--  295 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eEEEEEE--
Confidence            348999999999999999998 777776221           1111100            00000000  0000000  


Q ss_pred             CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                          .....-...+.||....+..|||+|.+++-...-||.+|.|...
T Consensus       296 ----~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       296 ----LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             ----EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence                00112478899999999999999999999999999999999764

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

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.15  E-value=0.013  Score=58.21  Aligned_cols=94  Identities=26%  Similarity=0.324  Sum_probs=63.4

Q ss_pred             ccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEE
Q 012477          294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT  372 (462)
Q Consensus       294 ~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~  372 (462)
                      -+|..||++|.+|+.|..+. |-+|.+-.-+++..             .    -+..+  +.|.-.....-.. ......
T Consensus       246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~-------------~----fi~na--l~Pa~v~~v~i~~-~~~~~~  305 (362)
T PRK12327        246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA-------------E----FVANA--LSPAKVVSVEVDD-EEEKAA  305 (362)
T ss_pred             chheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH-------------H----HHHHh--CCCceEEEEEEEc-CCCcEE
Confidence            57999999999999999998 76776665332210             0    00000  1111111110000 112467


Q ss_pred             EEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       373 ~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                      .+.||.+..+..|||+|.+++--.+.||.+|.|..
T Consensus       306 ~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        306 RVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             EEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            89999999999999999999999999999999964

>PRK00468 hypothetical protein; Provisional

Probab=96.13  E-value=0.0066  Score=45.85  Aligned_cols=33  Identities=21%  Similarity=0.450  Sum_probs=29.6

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHh
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT   72 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~t   72 (462)
                      .+.+.+++.|..+..|.||||+|.+|+.||.--
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            356889999999999999999999999999764

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.12  E-value=0.016  Score=57.29  Aligned_cols=96  Identities=20%  Similarity=0.154  Sum_probs=63.0

Q ss_pred             CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477           52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG  130 (462)
Q Consensus        52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~  130 (462)
                      +-+|+.||++|++|+.|.++. |=+|+|-.-           +-.+...            +.+|+.       --.+..
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~-----------s~D~~~f------------I~Nal~-------Pa~V~~  300 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEY-----------SNVPEIF------------IARALA-------PAIISS  300 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhCC-------CceeeE
Confidence            358999999999999999998 777776321           1111000            000000       000000


Q ss_pred             CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCC
Q 012477          131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE  179 (462)
Q Consensus       131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~  179 (462)
                      .  ......-...+.||....+..|||+|.+++-...-||.+|.|..-+
T Consensus       301 V--~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        301 V--KIEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             E--EEcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            0  0001223678899999999999999999999999999999997653

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.10  E-value=0.022  Score=56.62  Aligned_cols=96  Identities=25%  Similarity=0.313  Sum_probs=62.9

Q ss_pred             CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477           52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG  130 (462)
Q Consensus        52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~  130 (462)
                      +-+|+.||++|.+|+.|.++. |=+|+|-.-           +-.++..            +.+|+.       --....
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~-----------s~d~~~f------------i~nal~-------Pa~v~~  294 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW-----------SEDPAEF------------VANALS-------PAKVVS  294 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhCC-------CceEEE
Confidence            358999999999999999998 778876221           1111100            000000       000000


Q ss_pred             CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                      . .......-.+.+.||....+..|||+|.+++-...-||.+|.|...
T Consensus       295 v-~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        295 V-EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             E-EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            0 0000122468899999999999999999999999999999999765

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

Probab=96.02  E-value=0.01  Score=56.76  Aligned_cols=71  Identities=27%  Similarity=0.405  Sum_probs=57.8

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhhh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~~  446 (462)
                      .+...+.|++.+.|.|||++|.+-++|+++|+++|.++.+       .++...|+|+| +.++|.+|...|...|....
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-------~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-------NTNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-------CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            4566789999999999999999999999999999999653       34445566666 57899999988877776654

>PRK02821 hypothetical protein; Provisional

Probab=95.92  E-value=0.0088  Score=45.33  Aligned_cols=34  Identities=24%  Similarity=0.381  Sum_probs=30.2

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK   73 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg   73 (462)
                      .+.+.+++.|..+..|.||||+|.+|+.||.--.
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            3457899999999999999999999999998754

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.88  E-value=0.017  Score=58.06  Aligned_cols=94  Identities=28%  Similarity=0.363  Sum_probs=62.9

Q ss_pred             CccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc-ccCCCcce
Q 012477          293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE-RDSGLISF  370 (462)
Q Consensus       293 ~~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~  370 (462)
                      +-+|..||.+|.+|+.|..+. |=+|.|-.-+++.             ..    -+..+  +.|.-..... .+  ....
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp-------------~~----fI~Na--LsPA~V~~V~i~~--~~~k  335 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP-------------AT----YIANA--LSPARVDEVRLVD--PEGR  335 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCH-------------HH----HHHHh--cCCceeeEEEEEc--CCCc
Confidence            357999999999999999998 7677665533221             00    00000  1111111110 01  1124


Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                      ...+.||.+..+.-|||+|++++--.+.||.+|.|..
T Consensus       336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            5679999999999999999999999999999999953

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.79  E-value=0.022  Score=58.75  Aligned_cols=94  Identities=24%  Similarity=0.373  Sum_probs=63.6

Q ss_pred             ccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEE
Q 012477          294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT  372 (462)
Q Consensus       294 ~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~  372 (462)
                      -+|..||.+|++|+.|..+. |=+|.|-.-+++.             ...   ..+++   .|.-.....-+.  ..-..
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-------------~~f---i~nal---~pa~v~~v~~~~--~~~~~  304 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDDP-------------AQF---IINAL---SPAEVSSVVVDE--DEHSA  304 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH-------------HHH---HHHhC---CCCEEEEEEEeC--CCCEE
Confidence            47999999999999999998 7677666533221             000   01111   111100110001  12377


Q ss_pred             EEEecCCccceeecCCCchHHHHHHhhCceEEEecC
Q 012477          373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK  408 (462)
Q Consensus       373 ~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~  408 (462)
                      .+.||....+.-|||+|++|+..++.||.+|.|...
T Consensus       305 ~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        305 DVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            899999999999999999999999999999999653

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.72  E-value=0.021  Score=57.44  Aligned_cols=96  Identities=28%  Similarity=0.302  Sum_probs=62.0

Q ss_pred             CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477           52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG  130 (462)
Q Consensus        52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~  130 (462)
                      +-+|+.||++|++|+.|.++. |=+|+|-.-           +-.++..            +.+|+.=.  ++..-.+  
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y-----------s~Dp~~f------------I~NaLsPA--~V~~V~i--  329 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW-----------SPDPATY------------IANALSPA--RVDEVRL--  329 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eeeEEEE--
Confidence            458999999999999999998 777776221           1111100            00000000  0000000  


Q ss_pred             CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                          .....-.+.+.||....+..|||+|.+++-...-||.+|.|...
T Consensus       330 ----~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~  373 (449)
T PRK12329        330 ----VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS  373 (449)
T ss_pred             ----EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence                00112357899999999999999999999999999999998543

>PRK00468 hypothetical protein; Provisional

Probab=95.52  E-value=0.017  Score=43.68  Aligned_cols=34  Identities=35%  Similarity=0.486  Sum_probs=29.8

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCc
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKA  401 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga  401 (462)
                      ..+..++.+..+-+|.||||+|.+|+.||..-.+
T Consensus        28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~a   61 (75)
T PRK00468         28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKA   61 (75)
T ss_pred             CeEEEEEEEChhhCcceecCCChhHHHHHHHHHH
Confidence            4578889999999999999999999999987543

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

Probab=95.45  E-value=0.019  Score=43.17  Aligned_cols=33  Identities=15%  Similarity=0.343  Sum_probs=29.7

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHh
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT   72 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~t   72 (462)
                      ...+.+++-+..+..|.||||+|.+|+.||.--
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            456789999999999999999999999999763

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.41  E-value=0.03  Score=52.58  Aligned_cols=65  Identities=20%  Similarity=0.271  Sum_probs=54.8

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC-HHHHHHHHHHHHHHHhcCC
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHDNP  216 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~~  216 (462)
                      -+.+.||..+++.+||++|.+|+.|.++|+++|.+-.           +..|.|.+. .+++.+|..+|..+-++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            4668899999999999999999999999999998833           457899887 6688888888887776643

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

Probab=95.35  E-value=0.03  Score=57.09  Aligned_cols=114  Identities=18%  Similarity=0.209  Sum_probs=82.2

Q ss_pred             EEEEcCCccccccc----CCCCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHH
Q 012477           90 VTVYSASDETNAFE----DGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI  165 (462)
Q Consensus        90 i~I~G~~e~~~~~~----~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I  165 (462)
                      +.|.|+.+.+-|+.    -..+++.+|.+|..+|++.+....-.+.........+...+.++.+....+||.+|...|+|
T Consensus       543 FKiAGt~dGvTA~gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki  622 (760)
T KOG1067|consen  543 FKIAGTNDGVTALGIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKI  622 (760)
T ss_pred             eeeccccCcceecCCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeE
Confidence            34566666655542    12234556777777777766554444455556667889999999999999999999999999


Q ss_pred             HhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012477          166 RSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHDN  215 (462)
Q Consensus       166 ~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~  215 (462)
                      ..+||+.-.+            ++..++|-. +..+.++|...|..++...
T Consensus       623 ~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  623 EVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             eeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            9999955544            245677766 5778899999998888663

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.33  E-value=0.27  Score=45.26  Aligned_cols=131  Identities=17%  Similarity=0.166  Sum_probs=87.7

Q ss_pred             EEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccccc
Q 012477          285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD  364 (462)
Q Consensus       285 ~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  364 (462)
                      .+.+.++....-.+...+|..++.|....|++|.+..     ....+.|+|++.....+...++.++.            
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~i~~~i~~~l~------------   89 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEYIEASINEILS------------   89 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHHHHHHHHHHHh------------
Confidence            3445556777888899999999999888899999988     34688999986433322222222222            


Q ss_pred             CCCcceEEEEEecCCccceeec----CCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-----CHHHHHHHH
Q 012477          365 SGLISFTTRLLVPTSRIGCLIG----KGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-----DLDLAKDAL  435 (462)
Q Consensus       365 ~~~~~~t~~i~Vp~~~~g~IIG----k~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-----~~~~v~~A~  435 (462)
                         ...+.++.++.-..-.-.+    .....+++|++.|++.|.....          ...+.|+.     ....++.|+
T Consensus        90 ---~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~~~~a~  156 (210)
T PF14611_consen   90 ---NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKRADRAK  156 (210)
T ss_pred             ---hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccchHHHHH
Confidence               1245566666432211221    2467899999999999998432          23455554     568899999


Q ss_pred             HHHHHHHHhh
Q 012477          436 IQVMTRLRAN  445 (462)
Q Consensus       436 ~~I~~~l~~~  445 (462)
                      ++++-.+...
T Consensus       157 RlL~~a~~~~  166 (210)
T PF14611_consen  157 RLLLWALDYN  166 (210)
T ss_pred             HHHHHhccCC
Confidence            9999888533

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.28  E-value=0.044  Score=56.52  Aligned_cols=94  Identities=23%  Similarity=0.324  Sum_probs=62.3

Q ss_pred             ccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccCC
Q 012477           53 KIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD  131 (462)
Q Consensus        53 ~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~  131 (462)
                      -+|+.||++|++|+.|.++. |=+|.|-.-           +-.+..                   .+.+.+..-.+...
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~-------------------fi~nal~pa~v~~v  295 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILW-----------SDDPAQ-------------------FIINALSPAEVSSV  295 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHH-------------------HHHHhCCCCEEEEE
Confidence            48999999999999999998 777776221           111110                   00000000000000


Q ss_pred             CCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          132 EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       132 ~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                        ......-.+.+.||....+..|||+|.+++.....||.+|.|...
T Consensus       296 --~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        296 --VVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             --EEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence              000012378899999999999999999999999999999999764

>PRK02821 hypothetical protein; Provisional

Probab=95.25  E-value=0.021  Score=43.24  Aligned_cols=34  Identities=29%  Similarity=0.447  Sum_probs=29.7

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCc
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKA  401 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga  401 (462)
                      ......+.|..+-+|.||||+|.+|+.||..-.+
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            3577889999999999999999999999987544

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

Probab=95.18  E-value=0.052  Score=48.32  Aligned_cols=44  Identities=20%  Similarity=0.360  Sum_probs=36.5

Q ss_pred             CCCCceEEEEEEeC------CceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          135 DGGHQVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       135 ~~~~~~~~~l~ip~------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                      .....++-++.||-      +++|.|||..|.|.|.|++.|+|+|.|-..
T Consensus       143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            34455667777774      589999999999999999999999999654

>PRK01064 hypothetical protein; Provisional

Probab=95.09  E-value=0.03  Score=42.61  Aligned_cols=33  Identities=27%  Similarity=0.496  Sum_probs=29.5

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHh
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT   72 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~t   72 (462)
                      ...+.+++.|..+..|.+|||+|.+|+.|+.-.
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            356889999999999999999999999999764

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.08  E-value=0.016  Score=62.94  Aligned_cols=64  Identities=30%  Similarity=0.366  Sum_probs=53.6

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~  444 (462)
                      ....+.||.+.++.+||.||.+||+|.++||+.|.+.           ++-.|.|.+ ..+.+++|+.+|......
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            4556778999999999999999999999999988772           235788888 478899999999887654

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

Probab=95.03  E-value=0.03  Score=42.11  Aligned_cols=34  Identities=32%  Similarity=0.442  Sum_probs=30.3

Q ss_pred             CcceEEEEEecCCccceeecCCCchHHHHHHhhC
Q 012477          367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK  400 (462)
Q Consensus       367 ~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sg  400 (462)
                      ......++.|...-.|.||||+|.+|+.||..-.
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~   60 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS   60 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence            4578899999999999999999999999997743

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.84  E-value=0.13  Score=53.90  Aligned_cols=66  Identities=21%  Similarity=0.367  Sum_probs=51.4

Q ss_pred             ceEEEEEEeC-CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477          139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD  214 (462)
Q Consensus       139 ~~~~~l~ip~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  214 (462)
                      .+.-.+.+|+ .+-|+|||+.|.+|+.++..||+.+-|..          +...|.|+| .|-.-+-|...+..++.+
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            4455567777 67799999999999999999999999843          234688888 566667777777777765

>PRK12704 phosphodiesterase; Provisional

Probab=94.75  E-value=0.14  Score=53.88  Aligned_cols=66  Identities=21%  Similarity=0.355  Sum_probs=49.3

Q ss_pred             ceEEEEEEeC-CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477          139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD  214 (462)
Q Consensus       139 ~~~~~l~ip~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  214 (462)
                      .+.-.+.+|+ .+-|+|||+.|.+|+.++.-||+.|-|..          +...|.|+| .+-.-+.|...+..++.+
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            3445566676 67799999999999999999999999843          244788998 455555666666666654

>PRK00106 hypothetical protein; Provisional

Probab=94.74  E-value=0.16  Score=53.16  Aligned_cols=68  Identities=25%  Similarity=0.404  Sum_probs=52.8

Q ss_pred             CceEEEEEEeC-CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012477          138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHDN  215 (462)
Q Consensus       138 ~~~~~~l~ip~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~  215 (462)
                      ..+.-.+.+|+ .+-|+|||+.|.+|+.++.-||+.+-|..          +...|.|+| .|-.-+-|...+..++.+.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~dg  292 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIKDG  292 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence            34455667777 67799999999999999999999999843          234688998 5777777777777777653

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.32  E-value=0.98  Score=41.55  Aligned_cols=86  Identities=15%  Similarity=0.249  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEE
Q 012477          115 ALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQI  194 (462)
Q Consensus       115 a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I  194 (462)
                      .+..|+..++.-.+.+.    -+..-.+.+.++......+...+|..++.|....||+|.+..+          +..+.|
T Consensus         5 l~~~Il~d~W~l~v~e~----v~~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~I   70 (210)
T PF14611_consen    5 LAERILRDCWNLEVSEE----VDELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIRI   70 (210)
T ss_pred             HHHHHHHHhcCCcccce----eeccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEEE
Confidence            45566666655333211    1122345555668888999999999999998889999999764          568999


Q ss_pred             EcCHHHHHHHHHHHHHHHhc
Q 012477          195 SGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       195 ~G~~~~v~~A~~~I~~~l~~  214 (462)
                      +|+...+..+...|.+.+..
T Consensus        71 ~g~k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   71 TGTKSTAEYIEASINEILSN   90 (210)
T ss_pred             EccHHHHHHHHHHHHHHHhh
Confidence            99999999999999999876

>PRK01064 hypothetical protein; Provisional

Probab=94.31  E-value=0.055  Score=41.17  Aligned_cols=34  Identities=32%  Similarity=0.442  Sum_probs=29.8

Q ss_pred             CcceEEEEEecCCccceeecCCCchHHHHHHhhC
Q 012477          367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK  400 (462)
Q Consensus       367 ~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sg  400 (462)
                      ...+..++.|...-.|.+|||+|.+|+.||....
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~   60 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV   60 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence            3567888999999999999999999999998643

>PRK12705 hypothetical protein; Provisional

Probab=94.05  E-value=0.067  Score=55.54  Aligned_cols=65  Identities=25%  Similarity=0.247  Sum_probs=45.8

Q ss_pred             cceEEEEEecCC-ccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHH
Q 012477          368 ISFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRL  442 (462)
Q Consensus       368 ~~~t~~i~Vp~~-~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l  442 (462)
                      ......+.+|++ +-|.|||+.|.+|+.+...||+.|.|++   .|       +.|+|++ +|.--+.|...+...|
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---tp-------~~V~ls~fdp~rreia~~~l~~Li  262 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD---TP-------EAVVISSFNPIRREIARLTLEKLL  262 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC---Cc-------cchhhcccCccchHHHHHHHHHHH
Confidence            345667788874 5599999999999999999999999942   23       3566766 3444444544444443

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=92.91  E-value=0.058  Score=40.62  Aligned_cols=34  Identities=15%  Similarity=0.214  Sum_probs=29.3

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK   73 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg   73 (462)
                      .+...+.+-+..+..|.||||+|.+++.||.-.+
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            3566778888999999999999999999997654

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

Probab=92.75  E-value=0.041  Score=60.47  Aligned_cols=70  Identities=19%  Similarity=0.129  Sum_probs=57.1

Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  444 (462)
                      ...+.+|.....+|||+||++|+.+|..|||.|.|.+--  |.  ...+|.+++.|.++.+..|...|.-.|.+
T Consensus      1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence            345778888899999999999999999999999996521  21  25689999999999999998887655433

>PRK12705 hypothetical protein; Provisional

Probab=91.70  E-value=0.14  Score=53.32  Aligned_cols=43  Identities=26%  Similarity=0.288  Sum_probs=36.8

Q ss_pred             CCCceEEEEEeeC-CccceeecCCchHHHHHHHHhCCeEEEcCC
Q 012477           39 GPEDTVYRYLCPI-RKIGSIIGRGGEIVKQLRIDTKSKIRIGET   81 (462)
Q Consensus        39 ~~~~~~~~ilvp~-~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~   81 (462)
                      ..+.++-.+-+|+ ++-|+||||.|.||+.++..||+.|-|++.
T Consensus       194 ~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt  237 (508)
T PRK12705        194 ASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT  237 (508)
T ss_pred             hhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence            3556666777887 689999999999999999999999999764

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

Probab=91.54  E-value=0.12  Score=45.72  Aligned_cols=53  Identities=23%  Similarity=0.337  Sum_probs=47.3

Q ss_pred             CCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL  442 (462)
Q Consensus       378 ~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  442 (462)
                      +..+|.|+||+|.+---|.+.|.++|.+..            ..|-|-|..++++.|...|+..|
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLI  229 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLI  229 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhh
Confidence            456799999999999999999999999842            37999999999999999998765

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

Probab=91.01  E-value=0.38  Score=34.98  Aligned_cols=35  Identities=14%  Similarity=0.214  Sum_probs=27.7

Q ss_pred             ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeE
Q 012477           42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI   76 (462)
Q Consensus        42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I   76 (462)
                      .....+.+.....|.+||++|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35555666666789999999999999999987443

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

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

Probab=90.76  E-value=0.22  Score=37.05  Aligned_cols=37  Identities=27%  Similarity=0.436  Sum_probs=30.0

Q ss_pred             EEEEEecCCc-----cceeecCCCchHHHHHHhh-CceEEEec
Q 012477          371 TTRLLVPTSR-----IGCLIGKGGSIITEMRRLT-KANIRILP  407 (462)
Q Consensus       371 t~~i~Vp~~~-----~g~IIGk~G~~I~~I~~~s-ga~I~i~~  407 (462)
                      ...+.|-+..     +|..||++|++|+.|+++. |-+|.|-.
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            4556777777     8999999999999999999 99999864

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=90.45  E-value=0.47  Score=44.36  Aligned_cols=51  Identities=16%  Similarity=0.193  Sum_probs=46.7

Q ss_pred             eeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       152 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      -++||.+|+|++.|+-.|.|-|-|...            +|.+.|....+..+...+.+++.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhc
Confidence            579999999999999999999998654            799999999999999999999977

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=90.15  E-value=0.56  Score=43.91  Aligned_cols=51  Identities=24%  Similarity=0.261  Sum_probs=44.2

Q ss_pred             ceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477          382 GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       382 g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  444 (462)
                      -++||.+|++++.|+-.|.|.|-|+.            .+|.+.|....++.+...+.+.++.
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            57899999999999999999999953            3899999999999998887765543

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

Probab=89.97  E-value=0.6  Score=33.93  Aligned_cols=34  Identities=24%  Similarity=0.426  Sum_probs=27.8

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceE
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANI  403 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I  403 (462)
                      ....+.+.....|.+||++|++++.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            5556666666789999999999999999988544

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

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

Probab=89.97  E-value=0.7  Score=42.73  Aligned_cols=47  Identities=21%  Similarity=0.408  Sum_probs=40.3

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD  429 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~  429 (462)
                      .-+.||...+..+||++|+.++.+.+.|+|+|-|-.+           -.|=|.|..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-----------G~IWV~~~~~  194 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-----------GRIWVDGENE  194 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-----------CEEEecCCCc
Confidence            4578999999999999999999999999999999533           4777888765

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=89.35  E-value=0.22  Score=37.46  Aligned_cols=33  Identities=18%  Similarity=0.297  Sum_probs=28.2

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcC
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG  170 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tg  170 (462)
                      ....+.+-+.....|.||||+|.+++.|+.-.+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            455788888999999999999999999986544

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

Probab=88.80  E-value=0.92  Score=41.97  Aligned_cols=60  Identities=22%  Similarity=0.364  Sum_probs=46.8

Q ss_pred             EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHH-HHHHHHHHHHHH
Q 012477          142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV-VKKALCQIASRL  212 (462)
Q Consensus       142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~-v~~A~~~I~~~l  212 (462)
                      .-+.|+...+.++||++|+.++.|.+.|+|+|-+-.+           ..|-|.|..+. ...|...|..+=
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-----------G~IWV~~~~~~~e~~~~~aI~~ie  208 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-----------GRIWVDGENESLEELAIEAIRKIE  208 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-----------CEEEecCCCcchHHHHHHHHHHHh
Confidence            5578999999999999999999999999999998553           46888887764 444555554433

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

Probab=88.12  E-value=1.1  Score=45.44  Aligned_cols=41  Identities=34%  Similarity=0.471  Sum_probs=36.8

Q ss_pred             ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCC
Q 012477          139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE  179 (462)
Q Consensus       139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~  179 (462)
                      .-...+.||..+++.+|||+|.+|++|++..|-+|.|...+
T Consensus       485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            34577899999999999999999999999999999997653

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=87.76  E-value=0.6  Score=35.47  Aligned_cols=33  Identities=18%  Similarity=0.247  Sum_probs=26.6

Q ss_pred             EEEEEeeCCccceeecCCchHHHHHHHHhCCeE
Q 012477           44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI   76 (462)
Q Consensus        44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I   76 (462)
                      .+.+-+..+..|.+|||+|+++..||--.+.-+
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            345666778899999999999999998766443

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

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

Probab=87.55  E-value=0.38  Score=42.75  Aligned_cols=57  Identities=28%  Similarity=0.394  Sum_probs=50.2

Q ss_pred             CCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477          148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP  216 (462)
Q Consensus       148 ~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  216 (462)
                      ...+|+|+||+|.+--.|+.-|-.+|.+.            +..+.|-|..+++.-|...|+.++...+
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGsp  233 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGSP  233 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccCC
Confidence            35679999999999999999999999874            3479999999999999999999998754

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

Probab=87.48  E-value=0.37  Score=35.82  Aligned_cols=34  Identities=21%  Similarity=0.378  Sum_probs=27.1

Q ss_pred             EEEEeeCCc-----cceeecCCchHHHHHHHHh-CCeEEE
Q 012477           45 YRYLCPIRK-----IGSIIGRGGEIVKQLRIDT-KSKIRI   78 (462)
Q Consensus        45 ~~ilvp~~~-----~g~IIGk~G~~Ik~i~~~t-g~~I~v   78 (462)
                      ..+.|-+..     +|..||++|+.|+.|.++. |-+|+|
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv   44 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDV   44 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence            356666666     9999999999999999999 888875

>PRK13764 ATPase; Provisional

Probab=87.18  E-value=0.67  Score=49.41  Aligned_cols=44  Identities=27%  Similarity=0.463  Sum_probs=39.2

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCC
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP  412 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P  412 (462)
                      .-+..+.||..+++.+|||+|.+|++|.+..|.+|.|-..++.|
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            35678999999999999999999999999999999998776544

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=86.80  E-value=0.34  Score=36.83  Aligned_cols=34  Identities=18%  Similarity=0.370  Sum_probs=28.4

Q ss_pred             eEEEEEeeCCccceeecCCchHHHHHHHHhCCeE
Q 012477           43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI   76 (462)
Q Consensus        43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I   76 (462)
                      -...+.+.....+.|||++|++|++|.+...-.+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            3457889999999999999999999998765444

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

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

Probab=85.81  E-value=0.57  Score=36.03  Aligned_cols=38  Identities=13%  Similarity=0.270  Sum_probs=31.3

Q ss_pred             eEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC
Q 012477           43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE   80 (462)
Q Consensus        43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~   80 (462)
                      ...++.|....-|.|||++|+.|++|+++-.-...+++
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~   67 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE   67 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence            34788899999999999999999999998765555543

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

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

Probab=85.10  E-value=0.32  Score=53.90  Aligned_cols=72  Identities=26%  Similarity=0.247  Sum_probs=59.7

Q ss_pred             ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ....++.+|.....+|||++|.+|+.++..|||-|.+.+-.  +.  .-.||.+.+.|.++.+..|...|.-.+.+
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence            34577889999999999999999999999999999996521  11  25689999999999999998888666544

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

Probab=85.07  E-value=0.7  Score=46.75  Aligned_cols=41  Identities=32%  Similarity=0.421  Sum_probs=36.7

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCC
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN  410 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~  410 (462)
                      -...+.||..+++.+|||+|.+|++|.+..|-+|.|-..+.
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            35678899999999999999999999999999999976554

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=84.00  E-value=1.3  Score=33.57  Aligned_cols=34  Identities=26%  Similarity=0.459  Sum_probs=28.0

Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEE
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIR  404 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~  404 (462)
                      ...+.|..+..|.+|||.|++++.|+-.+..-+.
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            4557777888999999999999999988766544

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

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=83.69  E-value=0.59  Score=35.52  Aligned_cols=34  Identities=29%  Similarity=0.474  Sum_probs=28.6

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceE
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQI  173 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I  173 (462)
                      ....+.+.....+.+||++|++|++|.....-.+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            4577889999999999999999999987655444

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

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=83.28  E-value=2.2  Score=43.55  Aligned_cols=136  Identities=14%  Similarity=0.102  Sum_probs=86.8

Q ss_pred             EEeeeCCccccccccCChhHHhHHhhhCCe--EEecCCCCCCCceEEE-EecCCcccccccHHHHHHHhhcCcccccccc
Q 012477          287 RLVCPVANIGGVIGKGGAIINQIRQESGAA--IKVDSSSTEGDDCLIT-VSSKEFFEDTLSATIEAVVRLQPRCSEKIER  363 (462)
Q Consensus       287 ~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~--I~i~~~~~~~~~~~i~-i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~  363 (462)
                      ++.+| +.-.++-|++.-++.+|++.+.|.  +.+.... + . ++.+ +.|.       .......+...+.-      
T Consensus       384 q~~~e-d~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~-g-s-~~~~~~~g~-------~~~F~k~~~~~~~E------  446 (657)
T COG5166         384 QFGVE-DNEDFLRGKKNGKATRIMKGVSCSELSSIVSST-G-S-IVETNGIGE-------KMSFSKKLSIPPTE------  446 (657)
T ss_pred             eecCC-chHHHhccccCcchhhhhhhcccceeeEEEecC-C-c-EEEEeccCc-------chhhHHHhcCCccc------
Confidence            33344 334477888888899999998887  4444432 1 1 3222 2232       11222233322111      


Q ss_pred             cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCc-eEEEEcCH---HHHHHHHHHHH
Q 012477          364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDE-MVQISGDL---DLAKDALIQVM  439 (462)
Q Consensus       364 ~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~-~v~I~G~~---~~v~~A~~~I~  439 (462)
                          -.-...+.+|...|..|||.||..|.+++..-++.|+....-.+|.   +..+ -|.|.-+.   +++-.++.-++
T Consensus       447 ----Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s~~~dNV~I~~PrKn~~ni~~~KNd~~  519 (657)
T COG5166         447 ----FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---SQWHDNVLIEAPRKNQDNISGKKNDKL  519 (657)
T ss_pred             ----CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---hhhhcceEEECCccCccchhcccccHH
Confidence                1134568899999999999999999999999999999876655553   2222 27777765   55667777777


Q ss_pred             HHHHhhh
Q 012477          440 TRLRANL  446 (462)
Q Consensus       440 ~~l~~~~  446 (462)
                      +++.++-
T Consensus       520 ~~V~~~c  526 (657)
T COG5166         520 DKVKQQC  526 (657)
T ss_pred             HHHhhhc
Confidence            8877653

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

Probab=82.79  E-value=3.6  Score=35.09  Aligned_cols=38  Identities=32%  Similarity=0.646  Sum_probs=32.7

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                      +-.+.|-...-|.+||++|.++++|..+||-+-.+.+.
T Consensus        77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            44567778888999999999999999999988887665

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PRK13764 ATPase; Provisional

Probab=82.72  E-value=3.2  Score=44.42  Aligned_cols=45  Identities=31%  Similarity=0.499  Sum_probs=39.4

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCC
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLP  182 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p  182 (462)
                      ..-...+.||...++.+|||+|.+|++|+++.|.+|.|-..++.+
T Consensus       479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            445788899999999999999999999999999999998765433

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=82.67  E-value=1.5  Score=38.51  Aligned_cols=33  Identities=30%  Similarity=0.386  Sum_probs=28.2

Q ss_pred             EEEeeCCccceeecCCchHHHHHHHHhCCeEEEc
Q 012477           46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG   79 (462)
Q Consensus        46 ~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~   79 (462)
                      -++|-... |.-||++|++|++|++..|-+|.+-
T Consensus        64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV   96 (166)
T PRK06418         64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV   96 (166)
T ss_pred             EEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence            35666666 9999999999999999999988763

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

Probab=81.65  E-value=2.3  Score=44.02  Aligned_cols=66  Identities=20%  Similarity=0.202  Sum_probs=54.9

Q ss_pred             CcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHh
Q 012477          367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRA  444 (462)
Q Consensus       367 ~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~  444 (462)
                      ...+...+.|+.+....+||.+|-..|+|..+||+.-.+            ++.+|+|.-. +...++|+.+|...+..
T Consensus       594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             cCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            346778899999999999999999999999999965554            2347877774 78899999999887766

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

Probab=80.80  E-value=2.2  Score=36.43  Aligned_cols=94  Identities=18%  Similarity=0.322  Sum_probs=60.6

Q ss_pred             cccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecC
Q 012477          299 IGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPT  378 (462)
Q Consensus       299 IGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~  378 (462)
                      +-..|..|+.|..+..-+|.|-.+...-              ..-..+.+.+..+.|.-.+ + .+-.-+..|.++.|-.
T Consensus        21 ~~~~~dli~~lAk~lrKRIvvR~dps~l--------------~~~e~A~~~I~~ivP~ea~-i-~di~Fd~~tGEV~Iea   84 (145)
T cd02410          21 FAEDGDLVKDLAKDLRKRIVIRPDPSVL--------------KPPEEAIKIILEIVPEEAG-I-TDIYFDDDTGEVIIEA   84 (145)
T ss_pred             HhcccHHHHHHHHHHhceEEEcCChhhc--------------CCHHHHHHHHHHhCCCccC-c-eeeEecCCCcEEEEEE
Confidence            4456788999999888888876532110              0001233344444432111 0 0011123567888999


Q ss_pred             CccceeecCCCchHHHHHHhhCceEEEecC
Q 012477          379 SRIGCLIGKGGSIITEMRRLTKANIRILPK  408 (462)
Q Consensus       379 ~~~g~IIGk~G~~I~~I~~~sga~I~i~~~  408 (462)
                      ..-|.+||++|.++++|..+||-.-.|-+.
T Consensus        85 eKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          85 EKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             cCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            999999999999999999999999888664

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	462
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		8e-05
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		9e-05
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		2e-04
1wvn_A	82	Crsytal Structure Of Domain 3 Of Human Alpha Polyc		2e-04
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		2e-04
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		3e-04
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		3e-04
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		7e-04

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 5/69 (7%)
Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
           GG  +T ++ +P D  G +IGKGGQ ++ IR E+GA I+I  DE L       D ++ I+
Sbjct: 10  GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGS---EDRIITIT 64
Query: 196 GEASVVKKA 204
           G    ++ A
Sbjct: 65  GTQDQIQNA 73

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 65/131 (49%), Gaps = 28/131 (21%)
Query: 65  VKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124
           VK++R ++ ++I I E      ER++T+   ++                 A+FK    +I
Sbjct: 27  VKKMREESGARINISEG--NCPERIITLAGPTN-----------------AIFKAFAMII 67
Query: 125 AEELRGDEDSDGGHQ-------VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK 177
            ++L  D  S   +        VT +L+VP+ Q G +IGKGG  ++ IR  TGAQ+++  
Sbjct: 68  -DKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG 126
Query: 178 DEHLPSCALRS 188
           D  LP+   R+
Sbjct: 127 D-MLPNSTERA 136

>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of Poly(C)-Binding Protein 1 To Its Affinity And Specificity For C-Rich Oligonucleotides Length = 76

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE 197
           H +T +LL+   ++G +IGK G+ V+ IR E+GA+I I       S     + ++ ++G 
Sbjct: 1   HMLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI-------SEGNSPERIITLTGP 53
Query: 198 ASVVKKALCQIASRLHDNPSRS 219
            + + KA   I  +L ++ + S
Sbjct: 54  TNAIFKAFAMIIDKLEEDINSS 75

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG 196
           G Q T +L +P++ IGC+IG+ G  +  IR  +GAQI+I            S   V I+G
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN-----PVEGSSGRQVTITG 57
Query: 197 EASVVKKALCQIASRL 212
            A+ +  A   I +RL
Sbjct: 58  SAASISLAQYLINARL 73

>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25NT RNA Hairpin Length = 178

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 78/157 (49%), Gaps = 12/157 (7%)
Query: 65  VKQLRIDTKSKIRIGET---VPGSEERVVTVYSASDETNAFED--GDKFVSPAQDALFKV 119
           + QL+ +T + I++ ++    PG+ ERV  +    +  NA      +K     Q+ + K 
Sbjct: 28  IVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREXPQN-VAKT 86
Query: 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
               I +  +   + D  +QV  K++VP+   G +IGKGG  V+ I  ++GA +++ +  
Sbjct: 87  EPVSILQP-QTTVNPDRANQV--KIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQK- 142
Query: 180 HLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216
             P      + +V +SGE    +KA+  I  ++ ++P
Sbjct: 143 --PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP 177

>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25 NT RNA Hairpin Length = 178

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 78/157 (49%), Gaps = 12/157 (7%)
Query: 65  VKQLRIDTKSKIRIGET---VPGSEERVVTVYSASDETNAFED--GDKFVSPAQDALFKV 119
           + QL+ +T + I++ ++    PG+ ERV  +    +  NA      +K     Q+ + K 
Sbjct: 28  IVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQN-VAKT 86
Query: 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
               I +  +   + D  +QV  K++VP+   G +IGKGG  V+ I  ++GA +++ +  
Sbjct: 87  EPVSILQP-QTTVNPDRANQV--KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQK- 142
Query: 180 HLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216
             P      + +V +SGE    +KA+  I  ++ ++P
Sbjct: 143 --PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP 177

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
           +T ++ +P D  G +IGKGGQ ++ IR E+GA I+I  DE L       D ++ I+G   
Sbjct: 7   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGS---EDRIITITGTQD 61
Query: 200 VVKKA 204
            ++ A
Sbjct: 62  QIQNA 66

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
           GG  +T ++ +P D    +IGKGGQ ++ IR E+GA I+I  DE L       D ++ I+
Sbjct: 10  GGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI--DEPLEGS---EDRIITIT 64
Query: 196 GEASVVKKA 204
           G    ++ A
Sbjct: 65  GTQDQIQNA 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	462
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-41
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-31
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-22
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-38
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-29
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-37
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	9e-33
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-07
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-06
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-36
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-31
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-17
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-33
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	5e-25
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-21
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-08
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-17
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-10
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-16
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	5e-11
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	5e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-16
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-11
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	5e-09
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-08
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-16
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-11
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-16
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	7e-09
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	4e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	7e-16
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	4e-08
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	8e-16
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-10
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-10
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-15
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-08
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-07
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-15
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	7e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-09
1we8_A	104	Tudor and KH domain containing protein; structural	7e-13
1we8_A	104	Tudor and KH domain containing protein; structural	8e-08
1we8_A	104	Tudor and KH domain containing protein; structural	4e-07
1we8_A	104	Tudor and KH domain containing protein; structural	2e-06
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	8e-13
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-06
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	9e-12
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	9e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-06
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-10
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	4e-08
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	6e-10
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	6e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-05
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	1e-09
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	9e-08
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	3e-08
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	1e-06
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	5e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	4e-08
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	4e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	7e-04
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	6e-07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	8e-07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	9e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	9e-06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	8e-04
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	6e-04
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	7e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	3e-04
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	4e-06
2cxc_A	144	NUSA; transcription termination, RNA binding prote	7e-06
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	8e-06
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	3e-04
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	9e-06
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	3e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	2e-05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	3e-04
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-05
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	1e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	7e-04

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score =  144 bits (364), Expect = 3e-41
 Identities = 43/185 (23%), Positives = 83/185 (44%), Gaps = 16/185 (8%)

Query: 39  GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI---GETVPGSEERVVTVYSA 95
                  + L P    GSIIG+GG+ + QL+ +T + I++    +  PG+ ERV  +   
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 96  SDETNAFEDGDKFVSPAQDALFKVHDRVIAEE----LRGDEDSDGGHQVTAKLLVPSDQI 151
            +        +       + + ++   V   E    L+     +       K++VP+   
Sbjct: 62  IEAL------NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTA 115

Query: 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASR 211
           G +IGKGG  V+ I  ++GA +++ +    P      + +V +SGE    +KA+  I  +
Sbjct: 116 GLIIGKGGATVKAIMEQSGAWVQLSQK---PDGINLQNRVVTVSGEPEQNRKAVELIIQK 172

Query: 212 LHDNP 216
           + ++P
Sbjct: 173 IQEDP 177

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score =  117 bits (294), Expect = 3e-31
 Identities = 38/175 (21%), Positives = 82/175 (46%), Gaps = 15/175 (8%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTE---GDDCLITVSSKE 337
             ++ L+++ P    G +IGKGG  I Q+++E+GA IK+  S        + +  +    
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 338 FFEDTLSATIEAVVRLQPRCSEKIERDSGL---------ISFTTRLLVPTSRIGCLIGKG 388
              + +   I   +R  P+   K E  S L          +   +++VP S  G +IGKG
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122

Query: 389 GSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443
           G+ +  +   + A +++  K +     +  + +V +SG+ +  + A+  ++ +++
Sbjct: 123 GATVKAIMEQSGAWVQLSQKPDGI---NLQNRVVTVSGEPEQNRKAVELIIQKIQ 174

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 92.2 bits (229), Expect = 5e-22
 Identities = 42/202 (20%), Positives = 75/202 (37%), Gaps = 50/202 (24%)

Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD-EHLPSCALRSDELVQI 194
            G Q   K+L+PS   G +IGKGGQ +  ++ ETGA I++ K  +  P    R   +  I
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTER---VCLI 58

Query: 195 SGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMG 254
            G    +      IA ++ + P         +I    ++                     
Sbjct: 59  QGTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNP------------------ 100

Query: 255 PYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESG 314
                                      +   ++++ P +  G +IGKGGA +  I ++SG
Sbjct: 101 --------------------------DRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSG 134

Query: 315 AAIKVDSSSTEG--DDCLITVS 334
           A +++          + ++TVS
Sbjct: 135 AWVQLSQKPDGINLQNRVVTVS 156

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

 Score =  136 bits (343), Expect = 3e-38
 Identities = 37/175 (21%), Positives = 72/175 (41%), Gaps = 6/175 (3%)

Query: 42  DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY-SASDETN 100
             +     P   +G +IGR GE++K+++ D   +I+       + ER+  +        +
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 101 AFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGG---HQVTAKLLVPSDQIGCVIGK 157
           A E     +   Q               RG  + + G          +VP+ + G +IGK
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 158 GGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212
           GG+ +++I  ++GA+I +    + P  A  + +L  I G    +  A   I  ++
Sbjct: 122 GGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score =  112 bits (281), Expect = 2e-29
 Identities = 30/175 (17%), Positives = 60/175 (34%), Gaps = 17/175 (9%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSK------ 336
              + +  P   +G VIG+ G +I +I+ ++G  I+         + +  ++        
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 337 ---------EFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGK 387
                       +           R + R                  +VPT + G +IGK
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 388 GGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442
           GG  I  + + + A I +  + N P  A  + ++  I G       A   +  ++
Sbjct: 122 GGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 52.6 bits (126), Expect = 2e-08
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 3/86 (3%)

Query: 10  KRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLR 69
           +   +          + R  G              + ++ P  K G IIG+GGE +K + 
Sbjct: 71  RSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSIS 130

Query: 70  IDTKSKIRIGETVP---GSEERVVTV 92
             + ++I +    P       ++ T+
Sbjct: 131 QQSGARIELQRNPPPNADPNMKLFTI 156

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

 Score =  134 bits (338), Expect = 1e-37
 Identities = 39/181 (21%), Positives = 78/181 (43%), Gaps = 20/181 (11%)

Query: 41  EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET-VPGSEERVVTVYSASDET 99
           E  + +   P + +G+IIG+ G+ +KQL     + I+I     P S+ R+V +    +  
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA- 59

Query: 100 NAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGG 159
                          A  +++ ++  E   G ++     ++   + VP+   G VIGKGG
Sbjct: 60  ------------QFKAQGRIYGKLKEENFFGPKEEV---KLETHIRVPASAAGRVIGKGG 104

Query: 160 QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRS 219
           + V  +++ T A++ + +D+           +V+I G     + A  +I   L     + 
Sbjct: 105 KTVNELQNLTAAEVVVPRDQTPDE---NDQVIVKIIGHFYASQMAQRKIRDILAQVKQQH 161

Query: 220 Q 220
           Q
Sbjct: 162 Q 162

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

 Score =  121 bits (304), Expect = 9e-33
 Identities = 39/166 (23%), Positives = 74/166 (44%), Gaps = 17/166 (10%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDT 342
           +  +++  P   +G +IGK G  I Q+ + + A+IK+    T      +           
Sbjct: 2   QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMV---------I 52

Query: 343 LSATIEAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGCLIGKGGSIITEMRR 397
           ++   EA  + Q R   K++ ++       +   T + VP S  G +IGKGG  + E++ 
Sbjct: 53  ITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQN 112

Query: 398 LTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443
           LT A + + P++  P     D  +V+I G    ++ A  ++   L 
Sbjct: 113 LTAAEVVV-PRDQTP--DENDQVIVKIIGHFYASQMAQRKIRDILA 155

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

 Score = 49.8 bits (119), Expect = 2e-07
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 280 SSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKV--DSSSTEGDDCLITVS 334
              +    +  P +  G VIGKGG  +N+++  + A + V  D +  E D  ++ + 
Sbjct: 81  EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKII 137

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

 Score = 47.1 bits (112), Expect = 2e-06
 Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 39  GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI-GETVPGS-EERVVTV 92
                      P    G +IG+GG+ V +L+  T +++ +  +  P   ++ +V +
Sbjct: 81  EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKI 136

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

 Score =  129 bits (325), Expect = 7e-36
 Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 21/177 (11%)

Query: 40  PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDET 99
                 R L   +++GSIIG+ GE VK++R ++ ++I I E      ER++T+   ++  
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTN-- 57

Query: 100 NAFEDGDKFVSPAQDALFKVHDRV--IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGK 157
                          A   + D++         +  +     VT +L+VP+ Q G +IGK
Sbjct: 58  -----------AIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGK 106

Query: 158 GGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214
           GG  ++ IR  TGAQ+++  D         ++  + I+G    + + + QI   + +
Sbjct: 107 GGCKIKEIRESTGAQVQVAGDM----LPNSTERAITIAGIPQSIIECVKQICVVMLE 159

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

 Score =  117 bits (296), Expect = 1e-31
 Identities = 39/163 (23%), Positives = 71/163 (43%), Gaps = 6/163 (3%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFE 340
           +   ++RL+     +G +IGK G  + ++R+ESGA I +   +    + +IT++      
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAI 59

Query: 341 DTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400
               A I   +      S      +     T RL+VP S+ G LIGKGG  I E+R  T 
Sbjct: 60  FKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTG 119

Query: 401 ANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443
           A +++          +  +  + I+G      + + Q+   + 
Sbjct: 120 AQVQVAGDML----PNSTERAITIAGIPQSIIECVKQICVVML 158

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

 Score = 78.3 bits (193), Expect = 2e-17
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 61/196 (31%)

Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
           +T +LL+   ++G +IGK G+ V+ +R E+GA+I I +           + ++ ++G  +
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC-------PERIITLAGPTN 57

Query: 200 VVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGY 259
            + KA                 ++   +    SSS +     +  P+             
Sbjct: 58  AIFKAF---------------AMIIDKLEEDISSSMTNSTAASRPPV------------- 89

Query: 260 KGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKV 319
                                    +LRLV P +  G +IGKGG  I +IR+ +GA ++V
Sbjct: 90  -------------------------TLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV 124

Query: 320 DSSSTEG-DDCLITVS 334
                    +  IT++
Sbjct: 125 AGDMLPNSTERAITIA 140

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

 Score = 52.1 bits (125), Expect = 3e-08
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 30  GDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI-GETVPGSEER 88
               +           R + P  + GS+IG+GG  +K++R  T +++++ G+ +P S ER
Sbjct: 76  SSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTER 135

Query: 89  VVTV 92
            +T+
Sbjct: 136 AITI 139

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

 Score =  122 bits (307), Expect = 4e-33
 Identities = 31/174 (17%), Positives = 65/174 (37%), Gaps = 17/174 (9%)

Query: 43  TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI--GETVPGSEERVVTVYSASDETN 100
           TV   + P  K G +IG+GGE +KQL+     K+ +    +   + ++ + +     +  
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK-- 59

Query: 101 AFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQ 160
                   V  A + +  +             +          + VP   +G VIG+ G+
Sbjct: 60  --------VQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGE 111

Query: 161 IVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214
           +++ I+++ G +I+              +++  I G     + A   I   L  
Sbjct: 112 MIKKIQNDAGVRIQF-----KQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

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

 Score = 99.9 bits (249), Expect = 5e-25
 Identities = 30/163 (18%), Positives = 65/163 (39%), Gaps = 8/163 (4%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKV--DSSSTEGDDCLITVSSKEFFEDT 342
              ++ P    G VIGKGG  I Q+++ +G  + +  D S     D  + +    +    
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 343 LSATIEAVVRLQPRCSEKIERDSG-LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKA 401
               +  ++R + +       + G  I     + VP   +G +IG+ G +I +++     
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGV 122

Query: 402 NIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444
            I+    +      +  +++  I G  D  + A   +   L++
Sbjct: 123 RIQFKQDDG-----TGPEKIAHIMGPPDRCEHAARIINDLLQS 160

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

 Score = 90.2 bits (224), Expect = 1e-21
 Identities = 28/194 (14%), Positives = 69/194 (35%), Gaps = 55/194 (28%)

Query: 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV 200
             ++++P+ + G VIGKGG+ ++ ++   G ++ +++D    +     D+ ++I G+   
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTN---VDKPLRIIGDPYK 59

Query: 201 VKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYK 260
           V++A   +   L +                                           G +
Sbjct: 60  VQQACEMVMDILRERDQ-------------------------------------GGFGDR 82

Query: 261 GDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVD 320
            +        +                +  P  ++G VIG+ G +I +I+ ++G  I+  
Sbjct: 83  NEYGSRIGGGI---------------DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFK 127

Query: 321 SSSTEGDDCLITVS 334
                G + +  + 
Sbjct: 128 QDDGTGPEKIAHIM 141

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

 Score = 55.9 bits (135), Expect = 1e-09
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
              +++P  + G +IGKGG  I +++      + ++   +     +  D+ ++I GD   
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYK 59

Query: 431 AKDALIQVMTRLRAN 445
            + A   VM  LR  
Sbjct: 60  VQQACEMVMDILRER 74

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

 Score = 52.1 bits (125), Expect = 3e-08
 Identities = 11/54 (20%), Positives = 24/54 (44%)

Query: 39  GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
                      P   +G +IGR GE++K+++ D   +I+  +      E++  +
Sbjct: 87  SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 140

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

 Score = 76.6 bits (189), Expect = 1e-17
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 5/90 (5%)

Query: 129 RGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRS 188
                  GG  +T ++ +P D  G +IGKGGQ ++ IR E+GA I+I  DE L     R 
Sbjct: 3   HMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDR- 59

Query: 189 DELVQISGEASVVKKALCQIASRLHDNPSR 218
             ++ I+G    ++ A   + + +     +
Sbjct: 60  --IITITGTQDQIQNAQYLLQNSVKQYSGK 87

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

 Score = 58.1 bits (141), Expect = 5e-11
 Identities = 21/64 (32%), Positives = 37/64 (57%)

Query: 38  IGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASD 97
           +G      +   P    GSIIG+GG+ +KQ+R ++ + I+I E + GSE+R++T+    D
Sbjct: 9   LGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 68

Query: 98  ETNA 101
           +   
Sbjct: 69  QIQN 72

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

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 10/93 (10%)

Query: 274 APRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITV 333
               DL     + ++  P    G +IGKGG  I QIR ESGA+IK+D      +D +IT+
Sbjct: 4   MSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63

Query: 334 SSKEFFEDTLSATIEAVVRLQPRCSEKIERDSG 366
           +           T + +   Q      +++ SG
Sbjct: 64  TG----------TQDQIQNAQYLLQNSVKQYSG 86

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

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           TT++ +P    G +IGKGG  I ++R  + A+I+I            +D ++ I+G  D 
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-----GSEDRIITITGTQDQ 69

Query: 431 AKDALIQVMTRLRAN 445
            ++A   +   ++  
Sbjct: 70  IQNAQYLLQNSVKQY 84

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 73.5 bits (181), Expect = 1e-16
 Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 7/77 (9%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            +T +LL+   ++G +IGK G+ V+ +R E+GA+I I  + + P      + ++ ++G  
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGPT 56

Query: 199 SVVKKALCQIASRLHDN 215
           + + KA   I  +L ++
Sbjct: 57  NAIFKAFAMIIDKLEED 73

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427
           ++ T RLL+    +G +IGK G  + +MR  + A I I  + N P      + ++ ++G 
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGP 55

Query: 428 LDLAKDALIQVMTRLRAN 445
            +    A   ++ +L  +
Sbjct: 56  TNAIFKAFAMIIDKLEED 73

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 12/84 (14%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFE 340
           +   ++RL+     +G +IGK G  + ++R+ESGA I +   +    + +IT+       
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITL------- 52

Query: 341 DTLSATIEAVVRLQPRCSEKIERD 364
              +    A+ +      +K+E D
Sbjct: 53  ---AGPTNAIFKAFAMIIDKLEED 73

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 54.6 bits (132), Expect = 5e-10
 Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
               R L   +++GSIIG+ GE VK++R ++ ++I I E      ER++T+
Sbjct: 3  VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITL 52

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 73.5 bits (181), Expect = 1e-16
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
           +   ++ VP + +G ++GKGG+ +   +  TGA+I+I K           +  V I+G  
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT--RNRRVTITGSP 59

Query: 199 SVVKKALCQIASRLHD 214
           +  + A   I+ R+  
Sbjct: 60  AATQAAQYLISQRVTY 75

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427
           +     + VP + +G ++GKGG  + E + LT A I+I  K             V I+G 
Sbjct: 1   MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRN--RRVTITGS 58

Query: 428 LDLAKDALIQVMTRLRA 444
               + A   +  R+  
Sbjct: 59  PAATQAAQYLISQRVTY 75

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 51.9 bits (125), Expect = 5e-09
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI---GETVPGSEERVVTV 92
           +     P   +G+I+G+GG+ + + +  T ++I+I   GE +PG+  R VT+
Sbjct: 3  ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 9/41 (21%), Positives = 22/41 (53%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS 323
           +  + +  P   +G ++GKGG  + + ++ +GA I++    
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG 42

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
            G  +T ++ +P D  G +IGKGGQ ++ IR E+GA I+I  DE L     R   ++ I+
Sbjct: 3   MGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDR---IITIT 57

Query: 196 GEASVVKKALCQIASRLHDNPSR 218
           G    ++ A   + + +     +
Sbjct: 58  GTQDQIQNAQYLLQNSVKQYSGK 80

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 39  GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE 98
           GP  T  +   P    GSIIG+GG+ +KQ+R ++ + I+I E + GSE+R++T+    D+
Sbjct: 4   GPIITT-QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 62

Query: 99  TNA 101
              
Sbjct: 63  IQN 65

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 10/82 (12%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS 344
           + ++  P    G +IGKGG  I QIR ESGA+IK+D      +D +IT++       T  
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG------TQD 61

Query: 345 ATIEAVVRLQPRCSEKIERDSG 366
               A   LQ      +++ SG
Sbjct: 62  QIQNAQYLLQ----NSVKQYSG 79

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           TT++ +P    G +IGKGG  I ++R  + A+I+I            +D ++ I+G  D 
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-----GSEDRIITITGTQDQ 62

Query: 431 AKDALIQVMTRLRAN 445
            ++A   +   ++  
Sbjct: 63  IQNAQYLLQNSVKQY 77

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 73.5 bits (181), Expect = 2e-16
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
           +   ++ VP + +G ++GKGG+ +   +  TGA+I+I K           +  V I+G  
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT--RNRRVTITGSP 59

Query: 199 SVVKKALCQIASRLHDNPSRSQ 220
           +  + A   I+ R+        
Sbjct: 60  AATQAAQYLISQRVTYEQGVRA 81

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427
           +     + VP + +G ++GKGG  + E + LT A I+I  K          +  V I+G 
Sbjct: 1   MKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGS 58

Query: 428 LDLAKDALIQVMTRLRANLFDREG 451
               + A   +  R+      R  
Sbjct: 59  PAATQAAQYLISQRVTYEQGVRAS 82

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 52.0 bits (125), Expect = 7e-09
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI---GETVPGSEERVVTV 92
           +     P   +G+I+G+GG+ + + +  T ++I+I   GE +PG+  R VT+
Sbjct: 3  ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 9/41 (21%), Positives = 22/41 (53%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS 323
           +  + +  P   +G ++GKGG  + + ++ +GA I++    
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG 42

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

 Score = 71.6 bits (176), Expect = 7e-16
 Identities = 17/84 (20%), Positives = 44/84 (52%), Gaps = 3/84 (3%)

Query: 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDE 190
           D  + G +    ++++P+ + G VIGKGG+ ++ ++   G ++ +++D    +   +   
Sbjct: 5   DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDK--- 61

Query: 191 LVQISGEASVVKKALCQIASRLHD 214
            ++I G+   V++A   +   L +
Sbjct: 62  PLRIIGDPYKVQQACEMVMDILRE 85

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

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
              +++P  + G +IGKGG  I +++      + ++   +     +  D+ ++I GD   
Sbjct: 15  VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYK 71

Query: 431 AKDALIQVMTRLR 443
            + A   VM  LR
Sbjct: 72  VQQACEMVMDILR 84

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKV--DSSSTEGDDCLITVS 334
                ++ P    G VIGKGG  I Q+++ +G  + +  D S     D  + + 
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII 66

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

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI--GETVPGSEERVVTV 92
          G   TV   + P  K G +IG+GGE +KQL+     K+ +    +   + ++ + +
Sbjct: 10 GQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRI 65

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

 Score = 71.5 bits (176), Expect = 8e-16
 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
            G Q T +L +P++ IGC+IG+ G  +  IR  +GAQI+I            S   V I+
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTIT 56

Query: 196 GEASVVKKALCQIASRLHDNPSRSQ 220
           G A+ +  A   I +RL        
Sbjct: 57  GSAASISLAQYLINARLSSEKGMGC 81

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

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           T  L +P + IGC+IG+ G+ I E+R+++ A I+I                V I+G    
Sbjct: 7   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE-----GSSGRQVTITGSAAS 61

Query: 431 AKDALIQVMTRLRA 444
              A   +  RL +
Sbjct: 62  ISLAQYLINARLSS 75

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

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 19/50 (38%), Positives = 28/50 (56%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS 334
           +  L  P   IG +IG+ GA IN+IRQ SGA IK+ +         +T++
Sbjct: 7   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 56

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 18/54 (33%), Positives = 27/54 (50%)

Query: 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
              T +    P   IG IIGR G  + ++R  + ++I+I   V GS  R VT+
Sbjct: 2  LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 55

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

 Score = 70.5 bits (173), Expect = 2e-15
 Identities = 19/86 (22%), Positives = 45/86 (52%), Gaps = 3/86 (3%)

Query: 133 DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELV 192
             DG      ++++P+ + G VIGKGG+ ++ ++   G ++ +++D    + A +    +
Sbjct: 8   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADK---PL 64

Query: 193 QISGEASVVKKALCQIASRLHDNPSR 218
           +I+G+   V++A   +   + D  S 
Sbjct: 65  RITGDPYKVQQAKEMVLELIRDQGSG 90

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

 Score = 52.0 bits (125), Expect = 7e-09
 Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
              +++P S+ G +IGKGG  I +++      + ++         +  D+ ++I+GD   
Sbjct: 16  VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYK 72

Query: 431 AKDALIQVMTRLR 443
            + A   V+  +R
Sbjct: 73  VQQAKEMVLELIR 85

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

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKV--DSSSTEGDDCLITVS 334
                ++ P +  G VIGKGG  I Q+++ +G  + +  D     G D  + ++
Sbjct: 14  NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 67

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

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE--TVPGSEERVVTV 92
          GP + V   + P  K G +IG+GGE +KQL+     K+ + +        ++ + +
Sbjct: 11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRI 66

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

 Score = 68.5 bits (168), Expect = 6e-15
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG 196
               + +L +P+D IGC+IG+ G  +  IR  +GAQI+I            +D  V I+G
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV-----EGSTDRQVTITG 56

Query: 197 EASVVKKALCQIASRL 212
            A+ +  A   I  RL
Sbjct: 57  SAASISLAQYLINVRL 72

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

 Score = 54.6 bits (132), Expect = 6e-10
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 10/85 (11%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFE 340
           ++  S  L  P   IG +IG+ GA IN+IRQ SGA IK+ +      D  +T++      
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITG----- 56

Query: 341 DTLSATIEAVVRLQPRCSEKIERDS 365
            + ++   A   +      ++  ++
Sbjct: 57  -SAASISLAQYLIN----VRLSSET 76

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

 Score = 54.2 bits (131), Expect = 7e-10
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL 428
           + +  L +P   IGC+IG+ G+ I E+R+++ A I+I             D  V I+G  
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV-----EGSTDRQVTITGSA 58

Query: 429 DLAKDALIQVMTRLRA 444
                A   +  RL +
Sbjct: 59  ASISLAQYLINVRLSS 74

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
           + T +    P   IG IIGR G  + ++R  + ++I+I   V GS +R VT+
Sbjct: 2  AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTI 54

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 63.7 bits (155), Expect = 7e-13
 Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 3/94 (3%)

Query: 133 DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELV 192
                  V  +L VP   +G +IG+GG+ +++I   +GA+I   K+        R   L+
Sbjct: 8   ILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR---LI 64

Query: 193 QISGEASVVKKALCQIASRLHDNPSRSQHLLASA 226
           +ISG    V  A   I  ++ ++    + +  SA
Sbjct: 65  KISGTQKEVAAAKHLILEKVSEDEELRKRIAHSA 98

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 49.4 bits (118), Expect = 8e-08
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 273 SAPRDDLSSKE-FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS--TEGDDC 329
           S     L+       +L  P  ++G +IG+GG  I  I + SGA I  D  S  T     
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR 62

Query: 330 LITVS 334
           LI +S
Sbjct: 63  LIKIS 67

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
             +L VP   +G +IG+GG  I  + + + A I    +    +       +++ISG    
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE---SEGTLLLSRLIKISGTQKE 72

Query: 431 AKDALIQVMTRLR 443
              A   ++ ++ 
Sbjct: 73  VAAAKHLILEKVS 85

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 48  LCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGS--EERVVTVYSASDETNA 101
             P R +G IIGRGGE ++ +   + +KI   +   G+    R++ +     E  A
Sbjct: 20  SVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAA 75

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

 Score = 63.7 bits (155), Expect = 8e-13
 Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
                     +P+ + G VIG+GG+ V+ I  +TGA + I     LP     + +L  I 
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFIIR 60

Query: 196 GEASVVKKALCQIASRLHDNPSRSQ 220
           G    +  A   I  ++        
Sbjct: 61  GSPQQIDHAKQLIEEKIEGPLCPVG 85

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

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 2/75 (2%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
                +PT + G +IG+GG  +  + + T A + I     LP     + ++  I G    
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFIIRGSPQQ 65

Query: 431 AKDALIQVMTRLRAN 445
              A   +  ++   
Sbjct: 66  IDHAKQLIEEKIEGP 80

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

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS 344
            +    P    G VIG+GG  +  I Q++GA +++        D     + K F    + 
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDP----NFKLF---IIR 60

Query: 345 ATIEAVVRLQPRCSEKIERD 364
            + + +   +    EKIE  
Sbjct: 61  GSPQQIDHAKQLIEEKIEGP 80

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

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVP---GSEERVVTV 92
           P   +  +  P  K G +IGRGGE VK +   T + + I   +P       ++  +
Sbjct: 4  APGGEM-TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFII 59

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

 Score = 60.6 bits (147), Expect = 9e-12
 Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 5/91 (5%)

Query: 130 GDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSD 189
           G   +         + VP   +G VIG+ G++++ I+++ G +I+  +D+   +   +  
Sbjct: 1   GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--GTGPEK-- 56

Query: 190 ELVQISGEASVVKKALCQIASRLHDNPSRSQ 220
            +  I G     + A   I   L    S   
Sbjct: 57  -IAHIMGPPDRCEHAARIINDLLQSLRSGPP 86

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

 Score = 52.1 bits (125), Expect = 1e-08
 Identities = 16/110 (14%), Positives = 37/110 (33%), Gaps = 11/110 (10%)

Query: 280 SSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFF 339
           S     + +  P  ++G VIG+ G +I +I+ ++G  I+       G + +  +      
Sbjct: 7   SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI------ 60

Query: 340 EDTLSATIEAVVRLQPRCSEKIERDSGLISFT-TRLLVPTSRIGCLIGKG 388
                   +         ++ ++              +P    G   G+G
Sbjct: 61  ----MGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQG 106

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

 Score = 49.4 bits (118), Expect = 9e-08
 Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 20/111 (18%)

Query: 48  LCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDK 107
             P   +G +IGR GE++K+++ D   +I+  +      E++  +    D          
Sbjct: 16  PVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDR--------- 66

Query: 108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKG 158
               A         R+I + L+       G        +P    G   G+G
Sbjct: 67  -CEHAA--------RIINDLLQSLRSGPPGPPGGP--GMPPGGRGRGRGQG 106

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

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 8/83 (9%)

Query: 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQI 424
              I     + VP   +G +IG+ G +I +++      I+    +      +  +++  I
Sbjct: 6   GSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHI 60

Query: 425 SGDLD---LAKDALIQVMTRLRA 444
            G  D    A   +  ++  LR+
Sbjct: 61  MGPPDRCEHAARIINDLLQSLRS 83

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 56.7 bits (137), Expect = 2e-10
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 134 SDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQ 193
                 +T +  VP   +G +IG+GG+ +  I+ E+G +I+I  D        RS     
Sbjct: 9   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--GGLPERS---CM 63

Query: 194 ISGEASVVKKALCQIASRLHDNPSRSQ 220
           ++G    V+ A   +   +    S   
Sbjct: 64  LTGTPESVQSAKRLLDQIVEKGRSGPS 90

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 51.3 bits (123), Expect = 1e-08
 Identities = 14/62 (22%), Positives = 27/62 (43%)

Query: 273 SAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
            +          +     P   +G +IG+GG  I++I+QESG  I++   S    +    
Sbjct: 4   GSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCM 63

Query: 333 VS 334
           ++
Sbjct: 64  LT 65

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL 428
             T    VP   +G +IG+GG  I+ +++ +   I+I P           +    ++G  
Sbjct: 14  VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLTGTP 68

Query: 429 D---LAKDALIQVMTRLRAN 445
           +    AK  L Q++ + R+ 
Sbjct: 69  ESVQSAKRLLDQIVEKGRSG 88

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 16/63 (25%), Positives = 27/63 (42%)

Query: 39  GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE 98
                   Y  P   +G IIGRGGE + +++ ++  KI+I     G  ER   +    + 
Sbjct: 11  QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES 70

Query: 99  TNA 101
             +
Sbjct: 71  VQS 73

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 55.1 bits (133), Expect = 6e-10
 Identities = 20/91 (21%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 129 RGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRS 188
            GD  +    Q +A + +P +    VIGK G+ +Q++  +T  +I+I + +         
Sbjct: 6   SGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DP 58

Query: 189 DELVQISGEASVVKKALCQIASRLHDNPSRS 219
              ++I+G    ++KA  ++     +   RS
Sbjct: 59  SNQIKITGTKEGIEKARHEVLLISAEQDKRS 89

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 10/52 (19%), Positives = 20/52 (38%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
             + S  +  P  +   VIGK G  +  +  ++   I++       +   IT
Sbjct: 14  QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKIT 65

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 43.6 bits (103), Expect = 6e-06
 Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 7/59 (11%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427
             +  + +P      +IGK G  + ++   T   I+I   +       +    ++I+G 
Sbjct: 16  QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGT 67

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 50 PIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
          P      +IG+ GE ++ L + T +KI+I    P      + +
Sbjct: 24 PKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKI 64

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 55.8 bits (134), Expect = 1e-09
 Identities = 32/156 (20%), Positives = 54/156 (34%), Gaps = 26/156 (16%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAA-IKVDSSSTEGDDCLITVSSKEFF 339
           +  F  + +     +G  IG  GA I Q R+  G   I +D      D C   +      
Sbjct: 1   ASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE-----DTCTFHIYG---- 51

Query: 340 EDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLT 399
            +   A  +A   L+                   + VP + +G +IGK G +I E+   +
Sbjct: 52  -EDQDAVKKARSFLEF--------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKS 96

Query: 400 KANIRILPKENLPKIASEDDEM-VQISGDLDLAKDA 434
                 +  EN   +  E+  +     G  D   +A
Sbjct: 97  GVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANA 132

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 50.4 bits (120), Expect = 9e-08
 Identities = 26/161 (16%), Positives = 52/161 (32%), Gaps = 37/161 (22%)

Query: 46  RYLCPIRKIGSIIGRGGEIVKQLRIDTK-SKIRIGETVPGSEERVVTVYSASDETNAFED 104
           +++     +G  IG  G  ++Q R     + I + E     +     +Y    +      
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE-----DTCTFHIYGEDQDA----- 56

Query: 105 GDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQN 164
               V  A+  L                           + VP + +G VIGK G+++Q 
Sbjct: 57  ----VKKARSFL---------------------EFAEDVIQVPRNLVGKVIGKNGKLIQE 91

Query: 165 IRSETGAQIRILKDEHLPSCALRSDEL-VQISGEASVVKKA 204
           I  ++G     ++ E+  +       +     G    +  A
Sbjct: 92  IVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANA 132

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 14/68 (20%), Positives = 20/68 (29%), Gaps = 9/68 (13%)

Query: 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV 200
             + +V  D +G  IG  G  +Q  R   G     L ++              I GE   
Sbjct: 5   HEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDED---------TCTFHIYGEDQD 55

Query: 201 VKKALCQI 208
             K     
Sbjct: 56  AVKKARSF 63

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 53.2 bits (127), Expect = 3e-08
 Identities = 32/164 (19%), Positives = 58/164 (35%), Gaps = 28/164 (17%)

Query: 48  LCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI---GETVPGSEERVVT----VYSASDETN 100
             P  +I  +IG+ G+  K++   TK+KI I      V  +  +       V+ A D   
Sbjct: 39  KIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVL 98

Query: 101 AFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQ 160
           A   G       + A      R++ E    +  +     +  +        G +IG+ G+
Sbjct: 99  AIGRGF----SPERAF-----RLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGR 149

Query: 161 IVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKA 204
             Q I   +GA + +              + V I G    ++ A
Sbjct: 150 TRQIIEEMSGASVSV------------YGKTVAIIGNPIQIEIA 181

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 48.5 bits (115), Expect = 1e-06
 Identities = 25/157 (15%), Positives = 51/157 (32%), Gaps = 24/157 (15%)

Query: 295 IGGVIGKGGAIINQIRQESGAAIKVDSSS---------TEGDDCLITVSSKEFFEDTLSA 345
           I  +IGK G    +I + +   I +DS +            D   +  +           
Sbjct: 45  IAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGF 104

Query: 346 TIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405
           + E   RL          +   I             G +IG+ G     +  ++ A++ +
Sbjct: 105 SPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV 164

Query: 406 LPKENLPKIASEDDEMVQISGD---LDLAKDALIQVM 439
                         + V I G+   +++AK A+ ++ 
Sbjct: 165 ------------YGKTVAIIGNPIQIEIAKTAIEKLA 189

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 40.5 bits (94), Expect = 5e-04
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
           +     E +  +++ +   +    + +P D+I  +IGK GQ  + I   T  +I I  + 
Sbjct: 14  NVNKDGEIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSET 73

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

 Score = 50.2 bits (120), Expect = 4e-08
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            VT ++ VP D    VIG+ G  ++ +  E    I +      P+  L+SD  + I+G A
Sbjct: 16  PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV------PAPELQSDI-IAITGLA 68

Query: 199 SVVKKALCQIASRLHDNPSRSQH 221
           + + +A   +  R+ +  +  + 
Sbjct: 69  ANLDRAKAGLLERVKELQAEQED 91

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 10/97 (10%)

Query: 357 CSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIAS 416
            S   E    L+  T  + VP      +IG+ GS I +M    + NI +   E       
Sbjct: 4   GSSGKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE------- 56

Query: 417 EDDEMVQISG---DLDLAKDALIQVMTRLRANLFDRE 450
              +++ I+G   +LD AK  L++ +  L+A   DR 
Sbjct: 57  LQSDIIAITGLAANLDRAKAGLLERVKELQAEQEDRA 93

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

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 12/42 (28%), Positives = 18/42 (42%)

Query: 291 PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
           P      VIG+ G+ I ++  E    I V +   + D   IT
Sbjct: 24  PFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAIT 65

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

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 6/43 (13%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 50 PIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
          P      +IG+ G  ++++  + +  I +    P  +  ++ +
Sbjct: 24 PFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAI 64

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 6/83 (7%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            V+  + +       +IG  G+ ++ I  E    IR       P         V ++G  
Sbjct: 16  MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLP 69

Query: 199 SVVKKALCQIASRLHDNPSRSQH 221
             V++A+  I +   +  + S  
Sbjct: 70  ENVEEAIDHILNLEEEYLADSGP 92

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

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 9/72 (12%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-- 426
             +  + +       +IG  G  I ++    K +IR       P+  + D   V ++G  
Sbjct: 16  MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLP 69

Query: 427 -DLDLAKDALIQ 437
            +++ A D ++ 
Sbjct: 70  ENVEEAIDHILN 81

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 46.4 bits (110), Expect = 6e-07
 Identities = 12/76 (15%), Positives = 25/76 (32%), Gaps = 4/76 (5%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
                + V       +IG+ G ++  IR E    I+    +          + + I+G  
Sbjct: 16  SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQ----PQDQITITGYE 71

Query: 199 SVVKKALCQIASRLHD 214
              + A   I   + +
Sbjct: 72  KNTEAARDAILRIVGE 87

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 21/91 (23%), Positives = 45/91 (49%), Gaps = 7/91 (7%)

Query: 358 SEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASE 417
           S   + D  L SF   + V       +IG+ G++IT++R     NI+   K++     ++
Sbjct: 5   SSGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQ 60

Query: 418 DDEMVQISG---DLDLAKDALIQVMTRLRAN 445
             + + I+G   + + A+DA+++++  L   
Sbjct: 61  PQDQITITGYEKNTEAARDAILRIVGELEQM 91

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 14/56 (25%), Positives = 23/56 (41%)

Query: 273 SAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD 328
           S  ++D + + F L +         +IG+ GA+I QIR E    I+          
Sbjct: 6   SGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQP 61

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 48.5 bits (115), Expect = 9e-07
 Identities = 28/168 (16%), Positives = 58/168 (34%), Gaps = 23/168 (13%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDT 342
           +  + +      +G VIG  G +  +I + +G  I VD+ ++                  
Sbjct: 3   KPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMK 62

Query: 343 LSATIEAVVR-LQPRCSEKIERD-SGLISFTTRLLV------PTSRIGCLIGKGGSIITE 394
            +  ++A+     P  + ++  +   L+    + +V           G +IG+GG     
Sbjct: 63  AAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRT 122

Query: 395 MRRLTKANIRILPKENLPKIASEDDEMVQISGD---LDLAKDALIQVM 439
           +  +T   I +             +  V I GD      AK A+  + 
Sbjct: 123 IEEMTDTYINV------------GEYEVAIIGDYERAMAAKQAIEMLA 158

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 45.4 bits (107), Expect = 9e-06
 Identities = 28/159 (17%), Positives = 48/159 (30%), Gaps = 21/159 (13%)

Query: 49  CPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKF 108
               ++G++IG  GE+  ++   T + I +      +E  +V V     E     +  K 
Sbjct: 10  VKPERLGAVIGPRGEVKAEIMRRTGTVITV-----DTENSMVIVEP-EAEGIPPVNLMKA 63

Query: 109 VSPAQDALFKVHDRVIAEELRGD---EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI 165
               +              L  D      D    V           G +IG+GG+  + I
Sbjct: 64  AEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTI 123

Query: 166 RSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKA 204
              T   I +             +  V I G+      A
Sbjct: 124 EEMTDTYINV------------GEYEVAIIGDYERAMAA 150

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 39.6 bits (92), Expect = 8e-04
 Identities = 11/52 (21%), Positives = 23/52 (44%)

Query: 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDD 419
           +     + V   R+G +IG  G +  E+ R T   I +  + ++  +  E +
Sbjct: 2   MKPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAE 53

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
           Q T ++ VP   +G V+G  G  ++ I+  T   I     +  P           ++G  
Sbjct: 9   QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVF--------AVTGMP 60

Query: 199 SVVKKALCQIASRLHDNPSRS 219
             V +A  +I + +      S
Sbjct: 61  ENVDRAREEIEAHITLRSGPS 81

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 11/35 (31%), Positives = 16/35 (45%)

Query: 291 PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTE 325
           P   +G V+G  GA I +I+Q +   I       E
Sbjct: 17  PYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKE 51

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 7/65 (10%)

Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
              ++ +       +IGK G  +  I+ +    +RI  D            L++I G+  
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQ 57

Query: 200 VVKKA 204
            V++A
Sbjct: 58  GVQQA 62

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 10/52 (19%), Positives = 24/52 (46%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
           ++   + +         +IGK GA IN+I+ +   ++++   S + +   I 
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIE 53

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 10/73 (13%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD--- 427
              + +       LIGK G+ I  ++   K ++RI P ++      E   +++I GD   
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI-PPDS------EKSNLIRIEGDPQG 58

Query: 428 LDLAKDALIQVMT 440
           +  AK  L+++ +
Sbjct: 59  VQQAKRELLELAS 71

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

 Score = 47.6 bits (112), Expect = 4e-06
 Identities = 33/296 (11%), Positives = 74/296 (25%), Gaps = 27/296 (9%)

Query: 138 HQVTAKLLVPSDQIGCVIGKGGQI--VQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
            +VT  +   S     +    G    V +I +ET   I++       +      + V I+
Sbjct: 28  TRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTIT 87

Query: 196 GEASVVKKALCQIASR--------LHDNPSRSQHLLASAISNSHSSSGSLV--GPTAATP 245
           G    V +A   +           L         L A    N   +        P     
Sbjct: 88  GYFGDVDRARMLMRRNCHFTVFMALSKMKMPLHELQAHVRQNPIQNVEMSFVDAPEKNGI 147

Query: 246 IVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGA- 304
           +     +                 +             F+L        +  V+G     
Sbjct: 148 VTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLSTYYVDQVLGSSSTA 207

Query: 305 -IINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363
            ++  I +E+   I     +   +           +E  +   I+ V+       +    
Sbjct: 208 QLMPVIERETTTIISYPCYNNRNETRG------NIYEIKVVGNIDNVL-------KARRY 254

Query: 364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDD 419
              L+  +    +  + +          I  +   +   +++ P    P      +
Sbjct: 255 IMDLLPISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGE 310

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 45.0 bits (107), Expect = 7e-06
 Identities = 26/128 (20%), Positives = 38/128 (29%), Gaps = 30/128 (23%)

Query: 52  RKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSP 111
            + G  IGRGG ++K LR      I +   V  S +    V +                 
Sbjct: 45  GEAGRAIGRGGRLIKLLREALGKNIEV---VEYSSDLERIVKNL-------------FPG 88

Query: 112 AQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGA 171
                 K+    + E                 + V  D  G  IGKGG+ V+  R     
Sbjct: 89  V-----KIESINVRER---------NGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSK 134

Query: 172 QIRILKDE 179
              + K  
Sbjct: 135 LFGVEKVV 142

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 47.5 bits (114), Expect = 8e-06
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 11/66 (16%)

Query: 273 SAPRDDLSSKEFSLRLVC---PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDC 329
           +APR D+S  EF+ R+         I  VIGKGG++I  + +E+G  I+++      DD 
Sbjct: 548 NAPRGDIS--EFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE------DDG 599

Query: 330 LITVSS 335
            + +++
Sbjct: 600 TVKIAA 605

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 13/30 (43%), Positives = 19/30 (63%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175
           +  D+I  VIGKGG +++ +  ETG  I I
Sbjct: 566 INPDKIKDVIGKGGSVIRALTEETGTTIEI 595

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 47.1 bits (113), Expect = 9e-06
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 11/66 (16%)

Query: 273 SAPRDDLSSKEFSLRLVC---PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDC 329
            APR D+   +F+ ++     P   I  VIG GG +I +I   +GA + ++      DD 
Sbjct: 558 DAPRADVG--DFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN------DDG 609

Query: 330 LITVSS 335
           ++ VS+
Sbjct: 610 VVKVSA 615

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 42.5 bits (101), Expect = 3e-04
 Identities = 13/30 (43%), Positives = 23/30 (76%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175
           +P+D+I  VIG GG++++ I + TGA++ I
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDI 605

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 46.0 bits (110), Expect = 2e-05
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 14/85 (16%)

Query: 273 SAPRDDLSSKEFSLRLVC---PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDC 329
           S PR      E    +     P++     +G GG  + +++ E+G  I         D+ 
Sbjct: 555 SKPRASRK--ENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV------DEE 606

Query: 330 LITVSS--KEFFEDTLSATIEAVVR 352
             +V +       +     I  + +
Sbjct: 607 TFSVFAPTPSAMHEAR-DFITEICK 630

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 42.5 bits (101), Expect = 3e-04
 Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 12/64 (18%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKA 204
           VP  +    +G GG  ++ +++ETG  I     +         +E   +     S + +A
Sbjct: 573 VPLSKRAKFVGPGGYNLKKLQAETGVTISQ--VD---------EETFSVFAPTPSAMHEA 621

Query: 205 LCQI 208
              I
Sbjct: 622 RDFI 625

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

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
               ++ +P+     +IG  G+++++I  E G  + I    H P     SD  V I G +
Sbjct: 16  IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGG-VHI----HFPVEGSGSDT-VVIRGPS 69

Query: 199 SVVKKALCQIASRLHDNPSRSQH 221
           S V+KA  Q+     +  ++S  
Sbjct: 70  SDVEKAKKQLLHLAEEKQTKSGP 92

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 43.7 bits (104), Expect = 1e-04
 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 6/45 (13%)

Query: 291 PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSS 335
           PV  IG VIG    +INQI++++GA I ++      DD  I + +
Sbjct: 605 PVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGA 643

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 41.0 bits (97), Expect = 7e-04
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175
           +P D+IG VIG   Q++  I+ +TGA+I I
Sbjct: 604 IPVDKIGEVIGPKRQMINQIQEDTGAEITI 633

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	462
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.93
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.92
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.91
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.91
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.9
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.9
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.9
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.88
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.88
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.87
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.85
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.76
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.75
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.6
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.57
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.56
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.56
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.55
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.55
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.54
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.52
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.51
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.5
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.5
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.48
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.47
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.46
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.46
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.45
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.45
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.45
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.45
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.44
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.44
1we8_A	104	Tudor and KH domain containing protein; structural	99.43
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.41
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.41
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.4
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.4
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.39
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.39
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.38
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.38
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.38
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.37
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.36
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.36
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.33
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.33
1we8_A	104	Tudor and KH domain containing protein; structural	99.33
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.31
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.26
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.26
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.23
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.19
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.15
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.09
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.07
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.96
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.71
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.61
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.57
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.47
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.43
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.13
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.1
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.03
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.94
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.69
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.64
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.46
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.44
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.35
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.84
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.16
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.86
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.81
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.6
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.56
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.73
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.69
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.18
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	92.82
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.85

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.93  E-value=4.3e-26  Score=204.45  Aligned_cols=161  Identities=24%  Similarity=0.421  Sum_probs=129.6

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCC---CCCCCceEEEEEcCCcccccccCCCCcCCHHHHHH
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET---VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDAL  116 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~---~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~  116 (462)
                      ++.++++|+||.+++|.||||+|++|++|+++|||+|+|++.   .+++++|+|+|+|++++             +.+|.
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~-------------v~~A~   69 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA-------------LNAVH   69 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHH-------------HHHHH
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHH-------------HHHHH
Confidence            468999999999999999999999999999999999999853   46788999999999777             34555


Q ss_pred             HHHHHHHHHhhccC-----------CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcC
Q 012477          117 FKVHDRVIAEELRG-----------DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCA  185 (462)
Q Consensus       117 ~~i~~~i~~~~~~~-----------~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~  185 (462)
                      ..+.+.+.+.....           ..........+++|+||.+++|.|||++|++|++|+++|||+|+|.+....+   
T Consensus        70 ~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~---  146 (178)
T 2anr_A           70 GFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGI---  146 (178)
T ss_dssp             HHHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC------
T ss_pred             HHHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCC---
Confidence            55555443221000           0000122357899999999999999999999999999999999998764333   


Q ss_pred             CCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477          186 LRSDELVQISGEASVVKKALCQIASRLHDNP  216 (462)
Q Consensus       186 ~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  216 (462)
                      .+.++.|+|+|++++|.+|+.+|.++++++|
T Consensus       147 ~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          147 NLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             -CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            3688999999999999999999999999875

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

Probab=99.93  E-value=2.1e-25  Score=197.05  Aligned_cols=155  Identities=24%  Similarity=0.393  Sum_probs=130.6

Q ss_pred             ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCC-CCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHH
Q 012477           42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET-VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH  120 (462)
Q Consensus        42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~-~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~  120 (462)
                      +-+++|+||.+++|.|||++|++|++|+++|||+|+|++. .+++.+|+|+|+|++++             +..|...++
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~-------------v~~A~~~I~   68 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA-------------QFKAQGRIY   68 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHH-------------HHHHHHHHH
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHH-------------HHHHHHHHH
Confidence            4578999999999999999999999999999999999874 67889999999999877             567777787


Q ss_pred             HHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHH
Q 012477          121 DRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV  200 (462)
Q Consensus       121 ~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~  200 (462)
                      +.+.+....   ........+.+|+||..++|+|||++|++|++|+++|||+|.|.++ ..|.  ...++.|+|+|++++
T Consensus        69 ~~~~e~~~~---~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~-~~~~--~~~~~~v~I~G~~~~  142 (163)
T 3krm_A           69 GKLKEENFF---GPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRD-QTPD--ENDQVIVKIIGHFYA  142 (163)
T ss_dssp             HHHHHTTSS---CSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTT-CCCC--TTSEEEEEEEECHHH
T ss_pred             HHHhccccc---ccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCC-CCCC--CCCceEEEEEeCHHH
Confidence            776654321   1123456788999999999999999999999999999999999764 3443  233458999999999


Q ss_pred             HHHHHHHHHHHHhcC
Q 012477          201 VKKALCQIASRLHDN  215 (462)
Q Consensus       201 v~~A~~~I~~~l~~~  215 (462)
                      |.+|..+|.+++++.
T Consensus       143 v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          143 SQMAQRKIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999874

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

Probab=99.92  E-value=2.6e-25  Score=195.83  Aligned_cols=155  Identities=29%  Similarity=0.471  Sum_probs=130.3

Q ss_pred             CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHH
Q 012477           41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH  120 (462)
Q Consensus        41 ~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~  120 (462)
                      ..++++|+||.+++|.|||++|++|++|+++|||+|+|++.  ++++|.|+|+|++++             +.+|...++
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~-------------v~~A~~~I~   67 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNA-------------IFKAFAMII   67 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHH-------------HHHHHHHHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHH-------------HHHHHHHHH
Confidence            46899999999999999999999999999999999999875  677999999999776             466777777


Q ss_pred             HHHHHhhccCCC--CCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCH
Q 012477          121 DRVIAEELRGDE--DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA  198 (462)
Q Consensus       121 ~~i~~~~~~~~~--~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~  198 (462)
                      +.+.+......+  ........+++|+||.+++|+|||++|.+|++|+++|||+|+|.++ ..|   .+.++.|+|+|++
T Consensus        68 ~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~-~~~---~~~~~~v~I~G~~  143 (160)
T 2jzx_A           68 DKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD-MLP---NSTERAITIAGIP  143 (160)
T ss_dssp             HHHHHHHTSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC-CST---TCCEEEEEEEECH
T ss_pred             HHHHhhccccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC-CCC---CCCceEEEEEcCH
Confidence            666554321111  1123346899999999999999999999999999999999999764 344   3789999999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q 012477          199 SVVKKALCQIASRLHD  214 (462)
Q Consensus       199 ~~v~~A~~~I~~~l~~  214 (462)
                      ++|.+|+.+|.+++.+
T Consensus       144 ~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          144 QSIIECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999999999876

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

Probab=99.91  E-value=2.1e-24  Score=192.62  Aligned_cols=156  Identities=24%  Similarity=0.401  Sum_probs=123.3

Q ss_pred             ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHH
Q 012477           42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD  121 (462)
Q Consensus        42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~  121 (462)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|++..++.++|+|+|+|++++             +..|+..+.+
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~-------------v~~A~~~I~~   68 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR-------------AQHAAEIITD   68 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHH-------------HHHHHHHHHH
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHH-------------HHHHHHHHHH
Confidence            468899999999999999999999999999999999987666788999999999877             3455555544


Q ss_pred             HHHHhhccCC--C------------C---CCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCc
Q 012477          122 RVIAEELRGD--E------------D---SDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSC  184 (462)
Q Consensus       122 ~i~~~~~~~~--~------------~---~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  184 (462)
                      .+.+......  +            .   .......+++|+||.+++|.||||+|++|++|+++|||+|+|.++.  +.+
T Consensus        69 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~--~~~  146 (174)
T 1j4w_A           69 LLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPN  146 (174)
T ss_dssp             HHHHHC-----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC--TTT
T ss_pred             HHHhcccCCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC--CCC
Confidence            4433210000  0            0   0012346899999999999999999999999999999999998652  233


Q ss_pred             CCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          185 ALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       185 ~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      ..+.++.|+|+|++++|.+|..+|.++|
T Consensus       147 ~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          147 ADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             SCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             CCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            4577899999999999999999998864

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

Probab=99.91  E-value=2e-24  Score=191.02  Aligned_cols=154  Identities=23%  Similarity=0.376  Sum_probs=124.3

Q ss_pred             eEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCC--CCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHH
Q 012477           43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET--VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH  120 (462)
Q Consensus        43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~--~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~  120 (462)
                      ++++|+||.+++|+|||++|++|++|+++|||+|+|++.  .++..+|+|+|+|++++             +..|+..+.
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~-------------v~~A~~~I~   68 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK-------------VQQACEMVM   68 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHH-------------HHHHHHHHH
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHH-------------HHHHHHHHH
Confidence            688999999999999999999999999999999999753  35677899999998777             456666666


Q ss_pred             HHHHHhhccC---CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC
Q 012477          121 DRVIAEELRG---DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE  197 (462)
Q Consensus       121 ~~i~~~~~~~---~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~  197 (462)
                      +.+.+....+   ..+.......+++|.||..++|+|||++|.+|++|+++|||+|.|.+...     .+.++.|+|+|+
T Consensus        69 ~ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~-----~~~~~~v~I~G~  143 (164)
T 2jvz_A           69 DILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAHIMGP  143 (164)
T ss_dssp             HHTTCSSSCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCT-----TSSEEEEEEESC
T ss_pred             HHHHhccCCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCC-----CCCcEEEEEEcC
Confidence            6554322111   00111111346889999999999999999999999999999999986532     356899999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 012477          198 ASVVKKALCQIASRLHD  214 (462)
Q Consensus       198 ~~~v~~A~~~I~~~l~~  214 (462)
                      +++|..|..+|.+++++
T Consensus       144 ~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A          144 PDRCEHAARIINDLLQS  160 (164)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhh
Confidence            99999999999999875

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.90  E-value=6.7e-24  Score=190.13  Aligned_cols=159  Identities=21%  Similarity=0.380  Sum_probs=120.0

Q ss_pred             CcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCC---CCCCceEEEEecCCcccccccHHHHHHHhhcCcc
Q 012477          281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS---TEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRC  357 (462)
Q Consensus       281 ~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~---~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~  357 (462)
                      ..+++++|.||.+++|.|||++|++|++|+++|||+|+|++..   +.+.+|+++|+|...   .+..+...+.......
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~---~v~~A~~~I~~~~~~~   79 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE---ALNAVHGFIAEKIREM   79 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHH---HHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHH---HHHHHHHHHHHHHhcc
Confidence            3568999999999999999999999999999999999998753   346789999999732   1222222222221111


Q ss_pred             cccc------------cccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEE
Q 012477          358 SEKI------------ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQIS  425 (462)
Q Consensus       358 ~~~~------------~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~  425 (462)
                      ....            .........+.+|.||.+++|+|||++|++|++|++.|||+|+|.+...   ....+++.|+|+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~---~~~~~~~~v~I~  156 (178)
T 2anr_A           80 PQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD---GINLQNRVVTVS  156 (178)
T ss_dssp             CCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-------CCEEEEEEE
T ss_pred             CCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCC---CCCCCceEEEEE
Confidence            0000            0001123478899999999999999999999999999999999976532   224567999999


Q ss_pred             cCHHHHHHHHHHHHHHHHhh
Q 012477          426 GDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       426 G~~~~v~~A~~~I~~~l~~~  445 (462)
                      |++++|+.|+.+|.++|+++
T Consensus       157 G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          157 GEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             SSHHHHHHHHHHHHHHHHSC
T ss_pred             cCHHHHHHHHHHHHHHHHhC
Confidence            99999999999999999875

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

Probab=99.90  E-value=2.1e-23  Score=184.20  Aligned_cols=155  Identities=21%  Similarity=0.311  Sum_probs=118.4

Q ss_pred             eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCC-CCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc
Q 012477          284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSS-STEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE  362 (462)
Q Consensus       284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~-~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~  362 (462)
                      .+++|.||.+++|.|||++|++|++|+++|||+|+|++. .+++.+++|+|+|+...   +..+...++......  ...
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~---v~~A~~~I~~~~~e~--~~~   77 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA---QFKAQGRIYGKLKEE--NFF   77 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHH---HHHHHHHHHHHHHHT--TSS
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHH---HHHHHHHHHHHHhcc--ccc
Confidence            378999999999999999999999999999999999986 35678999999996421   111222222211000  011


Q ss_pred             ccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          363 RDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL  442 (462)
Q Consensus       363 ~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  442 (462)
                      .+......+.+|.||.+++|+|||++|++|++|++.|||+|.|.+.. .|.  ..+++.|+|+|++++|+.|+.+|.+.|
T Consensus        78 ~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~-~~~--~~~~~~v~I~G~~~~v~~A~~~I~~~i  154 (163)
T 3krm_A           78 GPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ-TPD--ENDQVIVKIIGHFYASQMAQRKIRDIL  154 (163)
T ss_dssp             CSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTC-CCC--TTSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             ccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCC-CCC--CCCceEEEEEeCHHHHHHHHHHHHHHH
Confidence            11223457889999999999999999999999999999999997542 232  233458999999999999999999998


Q ss_pred             Hhhh
Q 012477          443 RANL  446 (462)
Q Consensus       443 ~~~~  446 (462)
                      ++..
T Consensus       155 ~~~~  158 (163)
T 3krm_A          155 AQVK  158 (163)
T ss_dssp             HHHT
T ss_pred             HHHH
Confidence            8753

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

Probab=99.90  E-value=2.2e-23  Score=202.78  Aligned_cols=229  Identities=16%  Similarity=0.136  Sum_probs=156.0

Q ss_pred             CCCCceEEEEEEeCCceeeeecCCc--hHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          135 DGGHQVTAKLLVPSDQIGCVIGKGG--QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       135 ~~~~~~~~~l~ip~~~~g~IIGk~G--~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      ...+.+++.+.||..+|++||||+|  ++|++|+++|||+|+|+..+.-..........|+|+|.+++|++|+..|.+++
T Consensus        25 ~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~  104 (376)
T 3n89_A           25 INPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC  104 (376)
T ss_dssp             CCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSC
T ss_pred             ecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcC
Confidence            3467899999999999999999999  99999999999999997653000001245678999999999999999987643


Q ss_pred             hcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeC
Q 012477          213 HDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPV  292 (462)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~  292 (462)
                      -                                                                      +++.+.+|.
T Consensus       105 P----------------------------------------------------------------------l~i~~elp~  114 (376)
T 3n89_A          105 H----------------------------------------------------------------------FTVFMALSK  114 (376)
T ss_dssp             E----------------------------------------------------------------------EEEEEECTT
T ss_pred             C----------------------------------------------------------------------ceEEEEccc
Confidence            1                                                                      234444544


Q ss_pred             CccccccccCChhHHhHHhhhCCeEEecCCCCC--CCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcce
Q 012477          293 ANIGGVIGKGGAIINQIRQESGAAIKVDSSSTE--GDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISF  370 (462)
Q Consensus       293 ~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~--~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  370 (462)
                      ..++.  ...+..|.+ ++.++++|.|+.....  .....|+|+|.+...+   .+.+|+..+...+.+.  .......+
T Consensus       115 ~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~---~akeA~~~Ll~~l~~~--e~~~~~~~  186 (376)
T 3n89_A          115 MKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQH---ELIEAAKRLNEILFRE--SPAPENNF  186 (376)
T ss_dssp             CSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEGGGHH---HHHHHHHHHHHHHCC----CCCSSCE
T ss_pred             cccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcChhhHH---HHHHHHHHHHHHHHhh--hcccccce
Confidence            32221  111234444 5678999999664321  1256899999764332   2334433332222111  11123468


Q ss_pred             EEEEEecCCccceeecCCC--chHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          371 TTRLLVPTSRIGCLIGKGG--SIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL  442 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G--~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  442 (462)
                      +.+|.|+..+|..|||++|  ..|++|+++|||+|.+++..+ +.....+...|+|+|+.++|+.|+.+|++.|
T Consensus       187 s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d-~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          187 TLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNN-RNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             EEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC----------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             EEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCC-cccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            9999999999999999999  566999999999999864322 1100123468999999999999999998764

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

Probab=99.88  E-value=5.3e-23  Score=183.53  Aligned_cols=157  Identities=18%  Similarity=0.280  Sum_probs=115.8

Q ss_pred             eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCc-ccccc-
Q 012477          284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPR-CSEKI-  361 (462)
Q Consensus       284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~-~~~~~-  361 (462)
                      .+++|.||.+++|.|||++|++|++|+++|||+|+|.+..+.+.+++|+|.|+..........+...+..... ..... 
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~~~   82 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPGGPG   82 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC--------
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCCCCCC
Confidence            5789999999999999999999999999999999998766567789999999742111111112222221110 00000 


Q ss_pred             -------------cccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH
Q 012477          362 -------------ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL  428 (462)
Q Consensus       362 -------------~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~  428 (462)
                                   .........+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..  |+..+.+++.|+|+|++
T Consensus        83 p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~--~~~~~~~~~~v~I~G~~  160 (174)
T 1j4w_A           83 PGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLFTIRGTP  160 (174)
T ss_dssp             ---------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC--TTTSCTTEEEEEEECCH
T ss_pred             CCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC--CCCCCCCceEEEEECCH
Confidence                         000001246889999999999999999999999999999999997642  33345678999999999


Q ss_pred             HHHHHHHHHHHHHH
Q 012477          429 DLAKDALIQVMTRL  442 (462)
Q Consensus       429 ~~v~~A~~~I~~~l  442 (462)
                      ++|+.|+.+|.++|
T Consensus       161 ~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          161 QQIDYARQLIEEKI  174 (174)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999998864

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

Probab=99.88  E-value=5.9e-23  Score=180.72  Aligned_cols=153  Identities=25%  Similarity=0.438  Sum_probs=117.3

Q ss_pred             ceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCc-ccccc
Q 012477          283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPR-CSEKI  361 (462)
Q Consensus       283 ~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~-~~~~~  361 (462)
                      +++++|.||..++|.|||++|++|++|+++|||+|+|++.  ++.+++|+|.|+..   .+..+...+...... .....
T Consensus         4 ~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~---~v~~A~~~I~~~i~e~~~~~~   78 (160)
T 2jzx_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN---AIFKAFAMIIDKLEEDISSSM   78 (160)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHH---HHHHHHHHHHHHHHHHHTSCC
T ss_pred             cEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHH---HHHHHHHHHHHHHHhhccccC
Confidence            4789999999999999999999999999999999999985  34689999999731   112222222111100 00000


Q ss_pred             cc--cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 012477          362 ER--DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM  439 (462)
Q Consensus       362 ~~--~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~  439 (462)
                      ..  .......+.++.||.+++|+|||++|++|++|++.|||+|+|.+. ..|   +.+++.|+|+|++++|+.|+.+|.
T Consensus        79 ~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~-~~~---~~~~~~v~I~G~~~~v~~A~~~I~  154 (160)
T 2jzx_A           79 TNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD-MLP---NSTERAITIAGIPQSIIECVKQIC  154 (160)
T ss_dssp             CSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC-CST---TCCEEEEEEEECHHHHHHHHHHHH
T ss_pred             CCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC-CCC---CCCceEEEEEcCHHHHHHHHHHHH
Confidence            00  012235889999999999999999999999999999999999653 223   467899999999999999999999


Q ss_pred             HHHHh
Q 012477          440 TRLRA  444 (462)
Q Consensus       440 ~~l~~  444 (462)
                      +.|.+
T Consensus       155 ~~i~e  159 (160)
T 2jzx_A          155 VVMLE  159 (160)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            98876

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

Probab=99.87  E-value=5.3e-22  Score=175.40  Aligned_cols=143  Identities=20%  Similarity=0.437  Sum_probs=116.0

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCc
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRS  219 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~  219 (462)
                      ++.+|+||.+++|.|||++|++|++|+++|||+|++.++...+   ...+|.|+|+|++++|.+|+.+|.+++.+.....
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~~   78 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYKVQQACEMVMDILRERDQGG   78 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSS---SSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSCC
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhccCCC
Confidence            5789999999999999999999999999999999997653322   4678999999999999999999999998742100


Q ss_pred             ccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCcccccc
Q 012477          220 QHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVI  299 (462)
Q Consensus       220 ~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~II  299 (462)
                                 |..                  .            ..     |. +     ...+++++.||..++|+||
T Consensus        79 -----------~~~------------------~------------~~-----~~-~-----~~~~~~~i~vp~~~~g~iI  106 (164)
T 2jvz_A           79 -----------FGD------------------R------------NE-----YG-S-----RIGGGIDVPVPRHSVGVVI  106 (164)
T ss_dssp             -----------CSS------------------C------------SS-----CT-T-----SCSSSBCCEEETTTHHHHH
T ss_pred             -----------CCC------------------c------------cc-----cC-C-----CCCceEEEEEChhhccccC
Confidence                       000                  0            00     00 0     0123568899999999999


Q ss_pred             ccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCC
Q 012477          300 GKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKE  337 (462)
Q Consensus       300 Gk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~  337 (462)
                      |++|.+|++|+++|||+|.|++..+.+.+++|+|.|+.
T Consensus       107 Gk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~  144 (164)
T 2jvz_A          107 GRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPP  144 (164)
T ss_dssp             CSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCH
T ss_pred             CCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCH
Confidence            99999999999999999999987666678999999974

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

Probab=99.85  E-value=1.1e-20  Score=183.79  Aligned_cols=291  Identities=11%  Similarity=0.088  Sum_probs=181.2

Q ss_pred             CCceEEEEEeeCCccceeecCCc--hHHHHHHHHhCCeEEEcCCC-----CCCCceEEEEEcCCcccccccCCCCcCCHH
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGG--EIVKQLRIDTKSKIRIGETV-----PGSEERVVTVYSASDETNAFEDGDKFVSPA  112 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G--~~Ik~i~~~tg~~I~v~~~~-----~~~~ervi~I~G~~e~~~~~~~~~~~v~~a  112 (462)
                      ...+++++.||..+|++||||+|  ++|++|+++|||+|+|++..     +......|+|+|.+++|             
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enV-------------   93 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDV-------------   93 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHH-------------
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHH-------------
Confidence            56899999999999999999999  99999999999999998754     12345789999999995             


Q ss_pred             HHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceE
Q 012477          113 QDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELV  192 (462)
Q Consensus       113 ~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v  192 (462)
                      +.|...+.+.               ..+.+.+-+|...++.  ..-+..|.+ ++.++++|.|.......   +.....|
T Consensus        94 E~AR~~I~~l---------------~Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~---~~~sd~V  152 (376)
T 3n89_A           94 DRARMLMRRN---------------CHFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKN---GIVTTYL  152 (376)
T ss_dssp             HHHHHHHHHS---------------CEEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC--------CEEEE
T ss_pred             HHHHHHHHhc---------------CCceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCccccc---CCCCCEE
Confidence            3444444331               1334555555433221  111334544 67899999986642211   1235689


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCC
Q 012477          193 QISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLY  272 (462)
Q Consensus       193 ~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~  272 (462)
                      +|+|...++..|...+..+++......                                                     
T Consensus       153 ~IrG~~~nv~~akeA~~~Ll~~l~~~e-----------------------------------------------------  179 (376)
T 3n89_A          153 RITAREKNQHELIEAAKRLNEILFRES-----------------------------------------------------  179 (376)
T ss_dssp             EEEEEGGGHHHHHHHHHHHHHHHCC-------------------------------------------------------
T ss_pred             EEEcChhhHHHHHHHHHHHHHHHHhhh-----------------------------------------------------
Confidence            999999777766655555554311000                                                     


Q ss_pred             CCCCCCCCCcceEEEEeeeCCccccccccCC--hhHHhHHhhhCCeEEecCCCCC----CCceEEEEecCCcccccccHH
Q 012477          273 SAPRDDLSSKEFSLRLVCPVANIGGVIGKGG--AIINQIRQESGAAIKVDSSSTE----GDDCLITVSSKEFFEDTLSAT  346 (462)
Q Consensus       273 ~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G--~~Ik~I~~~sga~I~i~~~~~~----~~~~~i~i~G~~~~~~~~~~~  346 (462)
                           ......+++.+.|+..+|..|||++|  ..|++|+++|||+|.|++..+.    .....|+|+|+..   .+..+
T Consensus       180 -----~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e---~V~~A  251 (376)
T 3n89_A          180 -----PAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNID---NVLKA  251 (376)
T ss_dssp             -----CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHH---HHHHH
T ss_pred             -----cccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHH---HHHHH
Confidence                 00123478999999999999999999  5679999999999999975432    2356899999752   23334


Q ss_pred             HHHHHhhcCcccccccccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCC---CceEE
Q 012477          347 IEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASED---DEMVQ  423 (462)
Q Consensus       347 ~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~---~~~v~  423 (462)
                      .+.+..+.|              +...+.++.+..-.-.-.--..|..+.++.++.|.|.++..-|..--++   -..|+
T Consensus       252 rk~I~~lLP--------------v~l~Fd~~~~d~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~  317 (376)
T 3n89_A          252 RRYIMDLLP--------------ISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVPLNCAS  317 (376)
T ss_dssp             HHHHHHTSE--------------EEEEEEEEGGGBC--------CBEEEECTTSCEEEEEEEEECCSSSSCCCEEEEEEE
T ss_pred             HHHHHhhCC--------------EEEEEecCCcccccccccchhHHHHHHHhcCeEEEEeecCCCchhhcccccccceEE
Confidence            445555443              4444555544332222333344556778899999997653222100011   14577


Q ss_pred             EEcCH---HHHHHHHHHHH
Q 012477          424 ISGDL---DLAKDALIQVM  439 (462)
Q Consensus       424 I~G~~---~~v~~A~~~I~  439 (462)
                      |++-.   .++..|...++
T Consensus       318 ~~s~e~n~~~~y~~~~~~l  336 (376)
T 3n89_A          318 LRSKEFNIKKLYTAYQKVL  336 (376)
T ss_dssp             EEEEGGGHHHHHHHHHHHB
T ss_pred             EEEEeccHHHHHHHHHHHh
Confidence            77754   45555555544

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.76  E-value=2.1e-18  Score=147.86  Aligned_cols=137  Identities=20%  Similarity=0.318  Sum_probs=99.0

Q ss_pred             ceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc
Q 012477          283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE  362 (462)
Q Consensus       283 ~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~  362 (462)
                      .++.+|.||++.+|.+||++|++|+.|++++|  |.+....++ . ..+.+.+..      ...+..+..+.    .   
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~~-~-~~~i~~~~~------p~~v~~~~~~l----~---   65 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDED-T-CTFHIYGED------QDAVKKARSFL----E---   65 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEETT-T-TEEEEEESS------HHHHHHHHHHH----C---
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCCC-c-hheeeccCC------HHHHHHHHHhh----h---
Confidence            36889999999999999999999999999999  444332222 2 234444421      11121111110    0   


Q ss_pred             ccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCc-eEEEecCCCCCCCCCCCCc--eEEEEcCHHHHHHHHHHHH
Q 012477          363 RDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKA-NIRILPKENLPKIASEDDE--MVQISGDLDLAKDALIQVM  439 (462)
Q Consensus       363 ~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga-~I~i~~~~~~P~~~~~~~~--~v~I~G~~~~v~~A~~~I~  439 (462)
                            ....++.||.+++|++|||+|++|+.|++.||| +|.|...++...  ..+++  .|+|+|++++|+.|+.||.
T Consensus        66 ------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~--~~~~~~~~vtI~G~~~~v~~Ak~li~  137 (144)
T 2qnd_A           66 ------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPFVFVGTKDSIANATVLLD  137 (144)
T ss_dssp             ------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC--CCCTTEEEEEEEEEHHHHHHHHHHHH
T ss_pred             ------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc--cccCCeeEEEEEeCHHHHHHHHHHHH
Confidence                  113789999999999999999999999999997 999987543210  12233  5899999999999999999


Q ss_pred             HHHHh
Q 012477          440 TRLRA  444 (462)
Q Consensus       440 ~~l~~  444 (462)
                      ++|+.
T Consensus       138 ~~l~~  142 (144)
T 2qnd_A          138 YHLNY  142 (144)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            99875

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.75  E-value=4.6e-18  Score=145.80  Aligned_cols=137  Identities=18%  Similarity=0.230  Sum_probs=101.3

Q ss_pred             ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHH
Q 012477           42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD  121 (462)
Q Consensus        42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~  121 (462)
                      .++.+++||.+.+|++||++|++|++|++++|  |++.+.. ..++..+...+.++.|             ..+ ..++.
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~~i~~~~~p~~v-------------~~~-~~~l~   65 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCTFHIYGEDQDAV-------------KKA-RSFLE   65 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTEEEEEESSHHHH-------------HHH-HHHHC
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchheeeccCCHHHH-------------HHH-HHhhh
Confidence            56889999999999999999999999999999  5443221 2234443333444442             122 11111


Q ss_pred             HHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCc-eEEEecCCCCCCcCCCCCc--eEEEEcCH
Q 012477          122 RVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGA-QIRILKDEHLPSCALRSDE--LVQISGEA  198 (462)
Q Consensus       122 ~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga-~I~i~~~~~~p~~~~~~~r--~v~I~G~~  198 (462)
                                       .....+.||.+++|++|||+|.+|+.|++.||| +|+|.++++...  ...++  .|+|+|++
T Consensus        66 -----------------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~--~~~~~~~~vtI~G~~  126 (144)
T 2qnd_A           66 -----------------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPFVFVGTK  126 (144)
T ss_dssp             -----------------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC--CCCTTEEEEEEEEEH
T ss_pred             -----------------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc--cccCCeeEEEEEeCH
Confidence                             114889999999999999999999999999997 999987643211  12344  58999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q 012477          199 SVVKKALCQIASRLHD  214 (462)
Q Consensus       199 ~~v~~A~~~I~~~l~~  214 (462)
                      ++|..|..+|.++|.+
T Consensus       127 ~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          127 DSIANATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999875

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

Probab=99.60  E-value=1.3e-15  Score=138.83  Aligned_cols=144  Identities=20%  Similarity=0.189  Sum_probs=102.1

Q ss_pred             eEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHH
Q 012477           43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDR  122 (462)
Q Consensus        43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~  122 (462)
                      -..++.||.+.+|.|||++|++|+.|+++|||+|+++..     ++.|+|+|+..--     +   ...+++|...+...
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~-----~g~V~I~~~~~t~-----d---~~~i~kA~~~I~~i  100 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETE-----D---PLAVWKARDIVLAI  100 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCC-----S---HHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCC-----C---HHHHHHHHHHHHHH
Confidence            356899999999999999999999999999999999732     4678999874110     0   01134444444332


Q ss_pred             HH----HhhccCCCCCCCCCceEEEEEEeC-----------CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477          123 VI----AEELRGDEDSDGGHQVTAKLLVPS-----------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR  187 (462)
Q Consensus       123 i~----~~~~~~~~~~~~~~~~~~~l~ip~-----------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  187 (462)
                      +.    +....-    ..+......+-++.           ..+|+||||+|.+|+.|++.|||+|.|.           
T Consensus       101 ~rg~~~e~g~~l----l~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~-----------  165 (219)
T 2e3u_A          101 GRGFSPERAFRL----LNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY-----------  165 (219)
T ss_dssp             HTTCCHHHHGGG----GSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE-----------
T ss_pred             hccCCcccccee----ccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC-----------
Confidence            21    000000    00111122233332           2689999999999999999999999994           


Q ss_pred             CCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          188 SDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       188 ~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                       ++.|+|.|+.++|..|...|.+++...
T Consensus       166 -~~~v~i~G~~~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          166 -GKTVAIIGNPIQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             -TTEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             -CeEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence             347999999999999999999999764

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.57  E-value=2.9e-15  Score=114.02  Aligned_cols=73  Identities=26%  Similarity=0.413  Sum_probs=64.1

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  444 (462)
                      .+.++.||.+++|+|||++|++|++|++.|||+|+|.+..+..  +++.++.|+|+|++++++.|+.+|.+.+++
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCC--CCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999998753322  256789999999999999999999998765

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.56  E-value=2.5e-15  Score=113.08  Aligned_cols=71  Identities=24%  Similarity=0.468  Sum_probs=64.2

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|+|++.       +..+|.|+|+|+++++.+|+.+|.++|+++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-------CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            35789999999999999999999999999999999999753       356799999999999999999999999863

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.56  E-value=8.4e-15  Score=112.96  Aligned_cols=73  Identities=26%  Similarity=0.467  Sum_probs=65.7

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      +.++.+|.||.+++|+||||+|++|++|+++|||+|+|++.     .++.+++.|+|+|++++++.|+.+|.+.+++.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC-----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999999999999999999753     12567799999999999999999999998864

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

Probab=99.55  E-value=3.2e-15  Score=113.64  Aligned_cols=73  Identities=29%  Similarity=0.505  Sum_probs=65.9

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|+|.+.     .++.+++.|+|+|++++++.|+.+|.+.++++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-----VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC-----CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            35789999999999999999999999999999999999753     23567899999999999999999999998764

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

Probab=99.55  E-value=8.4e-15  Score=133.42  Aligned_cols=140  Identities=19%  Similarity=0.207  Sum_probs=98.7

Q ss_pred             EEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccc--cccHHH---HHHHhhc-Cccc
Q 012477          285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFED--TLSATI---EAVVRLQ-PRCS  358 (462)
Q Consensus       285 ~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~--~~~~~~---~a~~~~~-~~~~  358 (462)
                      ..++.||.+.++.|||++|.+|+.|+++||++|.|+..     +..|+|.+++...+  .+..+.   .++.+-+ +...
T Consensus        35 i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~-----~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~g  109 (219)
T 2e3u_A           35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERA  109 (219)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             EEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCcccc
Confidence            66899999999999999999999999999999999852     35678887642211  111122   2221100 0000


Q ss_pred             ccccccCCCcceEEEEEecC-----------CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC
Q 012477          359 EKIERDSGLISFTTRLLVPT-----------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD  427 (462)
Q Consensus       359 ~~~~~~~~~~~~t~~i~Vp~-----------~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~  427 (462)
                      ..+..+   ...-..+.++.           ..+|+||||+|++|+.|++.|||+|.|..            +.|+|.|+
T Consensus       110 ~~ll~d---d~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~------------~~v~i~G~  174 (219)
T 2e3u_A          110 FRLLNE---GEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG------------KTVAIIGN  174 (219)
T ss_dssp             GGGGST---TCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET------------TEEEEEEC
T ss_pred             ceeccC---CccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC------------eEEEEEeC
Confidence            011111   11222233331           26899999999999999999999999952            47999999


Q ss_pred             HHHHHHHHHHHHHHHHh
Q 012477          428 LDLAKDALIQVMTRLRA  444 (462)
Q Consensus       428 ~~~v~~A~~~I~~~l~~  444 (462)
                      +++++.|+.+|++.|..
T Consensus       175 ~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          175 PIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHcC
Confidence            99999999999999854

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

Probab=99.54  E-value=5.7e-15  Score=113.97  Aligned_cols=73  Identities=29%  Similarity=0.487  Sum_probs=64.9

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|+|.+.     .++++++.|+|+|+++++++|+.+|.+.+++.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~-----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC-----CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            46889999999999999999999999999999999999753     23567899999999999999999999998776

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.52  E-value=6.6e-15  Score=114.97  Aligned_cols=77  Identities=25%  Similarity=0.354  Sum_probs=67.5

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhcc
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFD  448 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~~  448 (462)
                      .+.+|.||.+++|+|||++|++|++|++.|||+|+|.+..++.  +++.++.|+|+|++++++.|+.+|.+.|.+....
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~--~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~   79 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTYEQGV   79 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBS--TTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhccccc
Confidence            5788999999999999999999999999999999998653321  2567899999999999999999999999887544

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.51  E-value=1.9e-14  Score=108.27  Aligned_cols=70  Identities=29%  Similarity=0.571  Sum_probs=65.2

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ..+.++|+||.+.+|.|||++|++|++|+++|||+|+++++       +..+|+|+|.|+++++.+|..+|.++|++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-------CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            46799999999999999999999999999999999999865       25689999999999999999999999986

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

Probab=99.50  E-value=1.5e-14  Score=113.28  Aligned_cols=75  Identities=27%  Similarity=0.465  Sum_probs=67.0

Q ss_pred             CCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          366 GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       366 ~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ....++.+|.||.+++|+||||+|++|++|+++|||+|+|++.     .++.+++.|+|+|+++++++|+.+|.+.+++.
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~-----~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC-----CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC-----CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3467899999999999999999999999999999999999753     12467899999999999999999999998874

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.50  E-value=3.4e-14  Score=111.98  Aligned_cols=74  Identities=19%  Similarity=0.338  Sum_probs=66.5

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|+|.+..     ++..++.|+|+|++++|++|+.+|.+.|++..
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~-----~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----GGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC-----CCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            468899999999999999999999999999999999997542     24568999999999999999999999998764

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=2e-14  Score=110.42  Aligned_cols=68  Identities=16%  Similarity=0.275  Sum_probs=60.7

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR  443 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  443 (462)
                      ..++.+|.||.+++|+||||+|++||+|+++|||+|+|++.        ++++.|+|+|+++++++|+.+|.+.+.
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~--------~~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR--------DKEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS--------SSCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC--------CCCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            45889999999999999999999999999999999999643        235789999999999999999998644

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

Probab=99.47  E-value=9.6e-14  Score=107.78  Aligned_cols=73  Identities=23%  Similarity=0.402  Sum_probs=64.1

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR  443 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  443 (462)
                      ...+.+|.||.+++|.||||+|++|++|+++|||+|.|.+....   ....+|.|+|+|++++++.|+.+|.+.++
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~---~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---NTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCS---STTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            45778999999999999999999999999999999999764321   24568899999999999999999998875

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

Probab=99.46  E-value=6.7e-14  Score=113.43  Aligned_cols=74  Identities=20%  Similarity=0.334  Sum_probs=65.2

Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|.+... | ..+.+++.|+|+|++++|++|+.+|.++|++..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~-~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLP-P-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCC-T-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccC-C-CCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            7789999999999999999999999999999999976532 2 234567999999999999999999999988764

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.46  E-value=1.1e-13  Score=105.27  Aligned_cols=73  Identities=26%  Similarity=0.443  Sum_probs=64.6

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      .+++|+||.+++|.|||++|++|++|+++|||+|+|.++++.  ++++.+|.|+|+|+++++.+|..+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCC--STTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCC--CCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999875332  2247899999999999999999999998865

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

Probab=99.45  E-value=1.1e-13  Score=111.61  Aligned_cols=73  Identities=18%  Similarity=0.291  Sum_probs=64.0

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhc
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF  447 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~  447 (462)
                      .+.+|.||.+++++||||+|++|++|+++|||+|+|.+++     ....+|.|+|+|+++++++|+.+|.+.+++...
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~-----~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~   83 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHIMGPPDRCEHAARIINDLLQSLRS   83 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC-----SSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC-----CCCceeEEEEEeCHHHHHHHHHHHHHHHhcccc
Confidence            4678999999999999999999999999999999997542     235678999999999999999999999887654

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

Probab=99.45  E-value=1.2e-13  Score=106.46  Aligned_cols=74  Identities=36%  Similarity=0.593  Sum_probs=65.9

Q ss_pred             CCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       137 ~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ...++.+|+||.+++|.|||++|++|++|+++|||+|+|.+.     +.++.+|.|+|+|+++++.+|..+|.+++.+.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~-----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC-----CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            356899999999999999999999999999999999999764     22478999999999999999999999999875

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.45  E-value=2.2e-13  Score=104.95  Aligned_cols=73  Identities=30%  Similarity=0.553  Sum_probs=66.1

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ..++.+|+||.+++|.||||+|++|++|+++|||+|+|.+.  .|   ++.+|.|+|+|++++|.+|..+|.+++.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~--~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT--TS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC--CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999753  22   467899999999999999999999999873

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

Probab=99.45  E-value=7.4e-14  Score=110.48  Aligned_cols=75  Identities=21%  Similarity=0.392  Sum_probs=66.1

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+....   ...+++.|+|+|++++++.|+.+|.+.|++.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ---NTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC---SSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            46889999999999999999999999999999999999765321   1346899999999999999999999998764

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

Probab=99.44  E-value=1e-13  Score=105.28  Aligned_cols=73  Identities=34%  Similarity=0.584  Sum_probs=66.3

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ..++.+|+||.+++|.|||++|++|++|+++|||+|++.+.     ++++.+|.|+|+|+++++.+|..+|.+++.++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-----VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC-----CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            46789999999999999999999999999999999999763     23578999999999999999999999999763

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.44  E-value=4.4e-13  Score=118.96  Aligned_cols=65  Identities=20%  Similarity=0.245  Sum_probs=59.1

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEE-----cCHHHHHHHHHHHHHHHhcC
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS-----GEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ..+++||...+|.|||++|++++.|++.+|++|++..          .++.++|.     |++.++.+|..+|..+.+..
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~----------~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf   74 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT----------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   74 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET----------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc----------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCC
Confidence            3689999999999999999999999999999999964          36788888     99999999999999988764

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.43  E-value=2.2e-13  Score=109.86  Aligned_cols=76  Identities=20%  Similarity=0.298  Sum_probs=65.7

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ...+.+|.||.+++|+|||++|++|++|+++|||+|+|.+...   ....+++.|+|+|++++++.|+.+|.+.+++..
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~---~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC---CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC---CCCCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            3578899999999999999999999999999999999976422   112357999999999999999999999997663

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.41  E-value=2e-13  Score=121.11  Aligned_cols=143  Identities=19%  Similarity=0.177  Sum_probs=99.6

Q ss_pred             EEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHH
Q 012477           45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI  124 (462)
Q Consensus        45 ~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~  124 (462)
                      ++++||.+.+|.|||++|++++.|++.++++|.++.     .++.++|+.+....+        ....+.|...+.....
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~d--------p~~i~KA~dlI~ai~r   72 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIP--------PVNLMKAAEVVKAISL   72 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSC--------HHHHHHHHHHHHHHHH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCC--------HHHHHHHHHHHHHHHc
Confidence            689999999999999999999999999999999964     367788883322210        0012333333321111


Q ss_pred             H---hhccCCCCCCCCCceEEEEEEeC----------CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCce
Q 012477          125 A---EELRGDEDSDGGHQVTAKLLVPS----------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL  191 (462)
Q Consensus       125 ~---~~~~~~~~~~~~~~~~~~l~ip~----------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~  191 (462)
                      .   ++...   ...+..+...+-++.          ...|+|||++|.+++.|+..|||+|.|.            ++.
T Consensus        73 gf~~e~A~~---Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~------------~~~  137 (191)
T 1tua_A           73 GFPPEKAFR---LLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG------------EYE  137 (191)
T ss_dssp             TCCHHHHGG---GGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC------------SSE
T ss_pred             CCCHHHhhh---cccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc------------CCE
Confidence            0   00000   001122233333442          3579999999999999999999999984            338


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          192 VQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       192 v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      |.|.|+.+++..|...|.+++...
T Consensus       138 v~i~G~~~~i~~Ar~~i~~li~g~  161 (191)
T 1tua_A          138 VAIIGDYERAMAAKQAIEMLAEGR  161 (191)
T ss_dssp             EEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             EEEEeChHHHHHHHHHHHHHHcCC
Confidence            999999999999999999999753

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

Probab=99.41  E-value=1.8e-13  Score=102.30  Aligned_cols=66  Identities=24%  Similarity=0.341  Sum_probs=59.3

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHH
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTR  441 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~  441 (462)
                      ..+.+|.||.++||.|||+||++|++|+++|||+|+|+++       ++.++.|+|+|+++++++|+.+|.+.
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~-------g~~~~~V~I~G~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC-------CCcccEEEEEcCHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999643       23568999999999999999999874

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

Probab=99.40  E-value=6.7e-13  Score=104.86  Aligned_cols=74  Identities=16%  Similarity=0.199  Sum_probs=64.8

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhc
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF  447 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~  447 (462)
                      ..++.+|.||.++||.|||++|++|++|+++|||+|+|+++.      +.+++.|+|+|++++++.|+.+|...+++...
T Consensus        15 ~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g------~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC------CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999996431      23467999999999999999999998777654

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

Probab=99.40  E-value=7.4e-13  Score=102.72  Aligned_cols=75  Identities=21%  Similarity=0.475  Sum_probs=66.1

Q ss_pred             CCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       137 ~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ......+|.||.+.+|.||||+|++|++|+++|||+|.+.++...+   .+.+|.|+|+|+++++.+|..+|.+++.+
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~---~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSS---TTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            3457889999999999999999999999999999999998753322   37899999999999999999999998864

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

Probab=99.39  E-value=3.6e-13  Score=106.45  Aligned_cols=72  Identities=17%  Similarity=0.254  Sum_probs=63.6

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ..++.+|.||.+++|.|||+||++|++|+++|||+|+|++.       ++.++.|+|+|+++++++|+.+|.+.+++..
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~-------~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC-------CCCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            35889999999999999999999999999999999999643       2235799999999999999999999887653

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.39  E-value=2.9e-13  Score=105.57  Aligned_cols=74  Identities=26%  Similarity=0.441  Sum_probs=65.9

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      .+++|+||.+++|.|||++|++|++|+++|||+|+|.++++.  .+++.+|.|+|+|+++++..|..+|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~--~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCB--STTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            478999999999999999999999999999999999875331  22478999999999999999999999999763

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

Probab=99.38  E-value=8.8e-13  Score=104.68  Aligned_cols=74  Identities=20%  Similarity=0.277  Sum_probs=64.1

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..++..|.||.++|+.|||++|++|++|+++|||+|+|++... |   +..++.|+|+|++++++.|+.+|...+++.
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~-~---~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999975432 1   236789999999999999999999877654

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.38  E-value=8.7e-13  Score=103.85  Aligned_cols=59  Identities=27%  Similarity=0.436  Sum_probs=54.8

Q ss_pred             CCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcc
Q 012477           40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE   98 (462)
Q Consensus        40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~   98 (462)
                      ...++++|+||.+++|+||||+|++|++|+++|||+|+|++..++..+|.|+|+|++++
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~   70 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES   70 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHH
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHH
Confidence            45789999999999999999999999999999999999998766788999999999877

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

Probab=99.38  E-value=3.9e-13  Score=105.23  Aligned_cols=75  Identities=32%  Similarity=0.597  Sum_probs=67.5

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ....++.+|.||.+++|.||||+|++|++|+++|||+|+|.+.  .|   ++.+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~--~~---~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC--CS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC--CC---CCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3567899999999999999999999999999999999999753  22   477999999999999999999999999874

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

Probab=99.37  E-value=6.6e-13  Score=107.54  Aligned_cols=73  Identities=26%  Similarity=0.419  Sum_probs=64.7

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      +++|+||.++++.||||+|++|++|+++|||+|+|.++.. + .....+|.|+|+|+.++|.+|+.+|.+++.+.
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~-~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLP-P-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCC-T-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccC-C-CCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            7899999999999999999999999999999999987532 1 12356899999999999999999999999875

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=3e-13  Score=103.83  Aligned_cols=71  Identities=23%  Similarity=0.346  Sum_probs=64.3

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      .....+.+|.||.+++|.||||+|++||+|+++|||+|++++.        ..+++++|+|++++|.+|..+|.+++..
T Consensus         6 ~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~--------~~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR--------DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             SCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS--------SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC--------CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            3466899999999999999999999999999999999999764        2368999999999999999999998765

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

Probab=99.36  E-value=5.7e-13  Score=105.36  Aligned_cols=77  Identities=22%  Similarity=0.502  Sum_probs=68.2

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ....++.+|+||.+.++.||||+|++|++|+++|||+|+|.++....   ...+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            34678999999999999999999999999999999999998753221   257999999999999999999999999874

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

Probab=99.33  E-value=1.3e-12  Score=104.99  Aligned_cols=71  Identities=21%  Similarity=0.245  Sum_probs=62.8

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ..+.+|.||.++||.|||+||++|++|+++|||+|+|++.       +...+.|+|+|++++++.|+.+|.+.+++..
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~-------g~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            4788999999999999999999999999999999999643       2234699999999999999999999877653

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

Probab=99.33  E-value=1.6e-12  Score=104.70  Aligned_cols=71  Identities=23%  Similarity=0.453  Sum_probs=64.0

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      .+++|+||.++++.||||+|++|++|+++|||+|+|.+++.     .+.+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~-----~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCS-----SSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCC-----CCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            47899999999999999999999999999999999976532     356899999999999999999999999873

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.33  E-value=3.1e-12  Score=103.13  Aligned_cols=79  Identities=28%  Similarity=0.445  Sum_probs=68.5

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      .....+.+|+||.+.+|.|||++|++|++|+++|||+|+|.+.....   .+.++.|+|+|+.+++.+|+.+|.+++.+.
T Consensus        11 ~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~---~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT---LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC---CCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            44668899999999999999999999999999999999998653211   246899999999999999999999999875


Q ss_pred             CC
Q 012477          216 PS  217 (462)
Q Consensus       216 ~~  217 (462)
                      +.
T Consensus        88 ~~   89 (104)
T 1we8_A           88 EE   89 (104)
T ss_dssp             HH
T ss_pred             hH
Confidence            44

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

Probab=99.31  E-value=1.7e-12  Score=96.88  Aligned_cols=68  Identities=19%  Similarity=0.301  Sum_probs=61.1

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      ...+..|.||.++++.|||++|.+|++|+++|||+|+|+++.       ..++.|+|+|+.+++.+|+.+|.+++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            456889999999999999999999999999999999997652       35789999999999999999998764

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

Probab=99.26  E-value=5.3e-12  Score=99.67  Aligned_cols=74  Identities=18%  Similarity=0.245  Sum_probs=65.8

Q ss_pred             CCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       135 ~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      .....++..|.||..+++.|||++|.+|++|+++|||+|+|+.+..      ..++.|+|+|++++|.+|+.+|..++.+
T Consensus        12 ~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC------CCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999999999999999976522      3478999999999999999999999876

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

Probab=99.26  E-value=7.7e-12  Score=99.23  Aligned_cols=73  Identities=16%  Similarity=0.248  Sum_probs=64.7

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ..+++.|.||..+++.|||++|++|++|+++|||+|+|+++.. +   ...++.|+|+|+.+++.+|+.+|..++.+
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~-~---~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            3568999999999999999999999999999999999987532 2   24689999999999999999999998865

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

Probab=99.25  E-value=5.5e-12  Score=99.61  Aligned_cols=73  Identities=22%  Similarity=0.372  Sum_probs=65.3

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ....++..|.||...++.|||++|.+|++|+++|||+|+|++.+       ..++.|+|+|+++++.+|..+|.+++.+.
T Consensus        13 l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           13 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             hCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            34678999999999999999999999999999999999997642       23679999999999999999999999774

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

Probab=99.23  E-value=9.2e-12  Score=98.08  Aligned_cols=72  Identities=17%  Similarity=0.190  Sum_probs=63.9

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhh-CceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLT-KANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~s-ga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ..++.+|.||.++|+.|||++|.+|++|+++| ||+|+|++.       ++..+.|+|+|+.+++++|+.+|.+.+++..
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-------g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e   87 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            46889999999999999999999999999999 999999542       3455699999999999999999999887654

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

Probab=99.19  E-value=4.2e-11  Score=95.70  Aligned_cols=70  Identities=14%  Similarity=0.200  Sum_probs=61.3

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHh-hCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhc
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRL-TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF  447 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~-sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~  447 (462)
                      .++.+|.||.++|++|||++|++|++|+++ ++++|++++          +++.|+|+|+++.|++|+.+|...+++..-
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999999999997 599998842          346899999999999999999988876644


Q ss_pred             c
Q 012477          448 D  448 (462)
Q Consensus       448 ~  448 (462)
                      .
T Consensus        96 ~   96 (102)
T 2ctf_A           96 R   96 (102)
T ss_dssp             H
T ss_pred             h
Confidence            3

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

Probab=99.15  E-value=2.9e-11  Score=97.07  Aligned_cols=70  Identities=24%  Similarity=0.369  Sum_probs=63.0

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      .+....|.||..+++.|||++|++|++|+++|||+|+|+++.       ...+.|+|+|+.+++.+|+.+|..++.+
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            357899999999999999999999999999999999997652       2356999999999999999999999876

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

Probab=99.09  E-value=7.3e-11  Score=92.92  Aligned_cols=73  Identities=23%  Similarity=0.343  Sum_probs=65.9

Q ss_pred             CCCCceEEEEEEeCCceeeeecCCchHHHHHHhhc-CceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHh
Q 012477          135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET-GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLH  213 (462)
Q Consensus       135 ~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~  213 (462)
                      ...+.++..|.||..+++.|||++|.+|++|+++| ||+|+|+.+       ++..+.|+|.|+.++|.+|+.+|.+++.
T Consensus        12 e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-------g~~~~~V~I~G~~~~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           12 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAE   84 (95)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            45677899999999999999999999999999999 999999764       2457799999999999999999999997


Q ss_pred             c
Q 012477          214 D  214 (462)
Q Consensus       214 ~  214 (462)
                      +
T Consensus        85 e   85 (95)
T 2ctj_A           85 E   85 (95)
T ss_dssp             H
T ss_pred             h
Confidence            6

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

Probab=99.07  E-value=1.8e-10  Score=91.93  Aligned_cols=65  Identities=23%  Similarity=0.318  Sum_probs=59.8

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhc-CceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSET-GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ++..|.||..+|++|||++|++|++|++++ +++|+|+..          ++.|+|+|+++.|.+|..+|..++.+
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~~----------~~~ItI~G~~~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG----------EDKITLEGPTEDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS----------SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCCC----------CCEEEEECCHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999999974 899998652          56899999999999999999998876

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.96  E-value=4.4e-10  Score=86.71  Aligned_cols=64  Identities=25%  Similarity=0.308  Sum_probs=57.2

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCce-EEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHH
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN-IRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTR  441 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~-I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~  441 (462)
                      ..+..++.||.+++|.|||++|.+|++|+++|||. |.|.+          ++.+|+|.| +.+++++|+.+|...
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e----------ddG~V~I~g~~~ea~~~A~~~I~~i   78 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----------DTGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----------TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc----------CCCEEEEEECCHHHHHHHHHHHHhh
Confidence            46889999999999999999999999999999998 99942          347999999 899999999998663

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.71  E-value=1.5e-08  Score=78.19  Aligned_cols=66  Identities=27%  Similarity=0.335  Sum_probs=57.9

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCce-EEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHH
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ-IRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASR  211 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~  211 (462)
                      ....+...|.||.+.++.|||++|.+|++|+++|||+ |.+..+          +..|+|.| +.+++.+|+.+|..+
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed----------dG~V~I~g~~~ea~~~A~~~I~~i   78 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED----------TGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT----------TTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC----------CCEEEEEECCHHHHHHHHHHHHhh
Confidence            4466889999999999999999999999999999998 999532          57999999 799999999888543

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.61  E-value=8.8e-08  Score=79.75  Aligned_cols=76  Identities=18%  Similarity=0.361  Sum_probs=61.1

Q ss_pred             ceEEEEEecCC------ccceeecCCCchHHHHHHhhCceEEEecCCCCCC-----------CCCCCCceEEEEc-CHHH
Q 012477          369 SFTTRLLVPTS------RIGCLIGKGGSIITEMRRLTKANIRILPKENLPK-----------IASEDDEMVQISG-DLDL  430 (462)
Q Consensus       369 ~~t~~i~Vp~~------~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~-----------~~~~~~~~v~I~G-~~~~  430 (462)
                      .++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|..+.....           ....++-.|.|++ +.+.
T Consensus         6 k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~   85 (131)
T 1k1g_A            6 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   85 (131)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             eEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHH
Confidence            47889999987      8899999999999999999999999976432110           0112356789999 5799


Q ss_pred             HHHHHHHHHHHHHh
Q 012477          431 AKDALIQVMTRLRA  444 (462)
Q Consensus       431 v~~A~~~I~~~l~~  444 (462)
                      +++|+.+|...|..
T Consensus        86 ~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           86 VKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999998865

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.57  E-value=1.9e-07  Score=76.13  Aligned_cols=78  Identities=15%  Similarity=0.019  Sum_probs=58.5

Q ss_pred             cceEEEEEecCC-------ccceeecCCCchHHHHHHhhCceEEEecCCCC----CCC-CCCCCceEEEEc-CHHHHHHH
Q 012477          368 ISFTTRLLVPTS-------RIGCLIGKGGSIITEMRRLTKANIRILPKENL----PKI-ASEDDEMVQISG-DLDLAKDA  434 (462)
Q Consensus       368 ~~~t~~i~Vp~~-------~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~----P~~-~~~~~~~v~I~G-~~~~v~~A  434 (462)
                      ..++.+|.||-+       ++|.|||++|.+||+|+++|||+|.|..+...    ... ...++-.|.|++ +++++++|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            457788888865       67999999999999999999999999643210    000 112334677876 58999999


Q ss_pred             HHHHHHHHHhh
Q 012477          435 LIQVMTRLRAN  445 (462)
Q Consensus       435 ~~~I~~~l~~~  445 (462)
                      +.+|.+.|...
T Consensus        90 ~~~Ie~Ll~~v  100 (119)
T 2yqr_A           90 KKLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHhhch
Confidence            99999887653

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.47  E-value=4.5e-07  Score=75.45  Aligned_cols=77  Identities=27%  Similarity=0.374  Sum_probs=61.8

Q ss_pred             CceEEEEEEeCC------ceeeeecCCchHHHHHHhhcCceEEEecCCCCCC-----------cCCCCCceEEEEc-CHH
Q 012477          138 HQVTAKLLVPSD------QIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPS-----------CALRSDELVQISG-EAS  199 (462)
Q Consensus       138 ~~~~~~l~ip~~------~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~-----------~~~~~~r~v~I~G-~~~  199 (462)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|........           .....+-.|.|++ +.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            357889999988      7889999999999999999999999976421110           0012366888999 589


Q ss_pred             HHHHHHHHHHHHHhc
Q 012477          200 VVKKALCQIASRLHD  214 (462)
Q Consensus       200 ~v~~A~~~I~~~l~~  214 (462)
                      .+.+|+.+|..+|..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999976

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.43  E-value=3.4e-07  Score=74.59  Aligned_cols=77  Identities=25%  Similarity=0.202  Sum_probs=58.3

Q ss_pred             CceEEEEEEeCC-------ceeeeecCCchHHHHHHhhcCceEEEecCCCC---C--CcCCCCCceEEEEc-CHHHHHHH
Q 012477          138 HQVTAKLLVPSD-------QIGCVIGKGGQIVQNIRSETGAQIRILKDEHL---P--SCALRSDELVQISG-EASVVKKA  204 (462)
Q Consensus       138 ~~~~~~l~ip~~-------~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~---p--~~~~~~~r~v~I~G-~~~~v~~A  204 (462)
                      ..++.+|.||.+       +++.|||++|.+||+|+++|||+|.|..+...   +  ......+-.|.|.+ +.+++.+|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            356778888875       67999999999999999999999999643110   0  00011344677876 59999999


Q ss_pred             HHHHHHHHhc
Q 012477          205 LCQIASRLHD  214 (462)
Q Consensus       205 ~~~I~~~l~~  214 (462)
                      +.+|.+++..
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999999975

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.13  E-value=2.5e-06  Score=71.26  Aligned_cols=76  Identities=26%  Similarity=0.399  Sum_probs=56.5

Q ss_pred             eEEEEEEeCCc------eeeeecCCchHHHHHHhhcCceEEEecCCCCC------------Cc-CCCCCceEEEEcC-H-
Q 012477          140 VTAKLLVPSDQ------IGCVIGKGGQIVQNIRSETGAQIRILKDEHLP------------SC-ALRSDELVQISGE-A-  198 (462)
Q Consensus       140 ~~~~l~ip~~~------~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p------------~~-~~~~~r~v~I~G~-~-  198 (462)
                      ++.++.||.+.      +|.|||++|.++|+|+++|||+|.|-.+...-            .. ....+--|.|++. . 
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            46788888655      89999999999999999999999998653210            00 0112237889985 3 


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 012477          199 ----SVVKKALCQIASRLHDN  215 (462)
Q Consensus       199 ----~~v~~A~~~I~~~l~~~  215 (462)
                          ..+.+|+.+|..+|...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             hhHHHHHHHHHHHHHHHCCCC
Confidence                27999999999998754

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.10  E-value=2.5e-06  Score=71.28  Aligned_cols=74  Identities=22%  Similarity=0.276  Sum_probs=54.2

Q ss_pred             eEEEEEecC------CccceeecCCCchHHHHHHhhCceEEEecCCCCC------------CC-CCCCCceEEEEcC-HH
Q 012477          370 FTTRLLVPT------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLP------------KI-ASEDDEMVQISGD-LD  429 (462)
Q Consensus       370 ~t~~i~Vp~------~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P------------~~-~~~~~~~v~I~G~-~~  429 (462)
                      ++.+|.||-      +++|.|||++|+++|+|+++|||+|.|-.+...-            .. ...+.=-|.|++. ++
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            467788884      4589999999999999999999999997653210            00 0111226889984 43


Q ss_pred             -----HHHHHHHHHHHHHH
Q 012477          430 -----LAKDALIQVMTRLR  443 (462)
Q Consensus       430 -----~v~~A~~~I~~~l~  443 (462)
                           .++.|+.+|...|.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                 79999999988765

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.03  E-value=3.3e-06  Score=88.40  Aligned_cols=93  Identities=17%  Similarity=0.199  Sum_probs=71.7

Q ss_pred             CCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCC
Q 012477          109 VSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRS  188 (462)
Q Consensus       109 v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~  188 (462)
                      +..|.++..++++.+.+.............+....+.||.+.++.|||++|.+||.|+++|||+|.|..           
T Consensus       536 L~~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d-----------  604 (630)
T 3u1k_A          536 IQQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD-----------  604 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS-----------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC-----------
Confidence            456777777777766543333333334455678899999999999999999999999999999999842           


Q ss_pred             CceEEEEcC-HHHHHHHHHHHHHHH
Q 012477          189 DELVQISGE-ASVVKKALCQIASRL  212 (462)
Q Consensus       189 ~r~v~I~G~-~~~v~~A~~~I~~~l  212 (462)
                      +..|.|.|+ .+++.+|+.+|..++
T Consensus       605 ~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          605 EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            568999997 688999999887654

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.94  E-value=1.9e-05  Score=64.49  Aligned_cols=68  Identities=18%  Similarity=0.179  Sum_probs=59.8

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..+.|....++.|+|++|+.|+.|+..|++.|+|..-+      .++...|+|.|++..-..|+.+|....+-+
T Consensus        58 lVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~------s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           58 KRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG------PERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             EEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC------TTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC------CCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            56889999999999999999999999999999997542      245678999999999999999998876655

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.69  E-value=1.2e-05  Score=84.11  Aligned_cols=63  Identities=17%  Similarity=0.231  Sum_probs=53.9

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHH
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRL  442 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l  442 (462)
                      .....+.||.+.+|.|||+||++||.|+++|||+|.|.           ++..|.|.|+ .+.+++|+.+|.+.+
T Consensus       566 p~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~-----------d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          566 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV-----------DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC-----------SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc-----------CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            35678999999999999999999999999999999994           2368999997 688999999886543

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.64  E-value=2.5e-05  Score=65.71  Aligned_cols=104  Identities=21%  Similarity=0.269  Sum_probs=74.5

Q ss_pred             eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccc
Q 012477          284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER  363 (462)
Q Consensus       284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~  363 (462)
                      -.+.+.|+...+|..||++|++|+.|+++.|-+|.+-.-+++.                 ..-+..+  +.|.-.....-
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~d~-----------------~~fI~na--LsPA~V~~V~i   96 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSDL-----------------ERIVKNL--FPGVKIESINV   96 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCSSH-----------------HHHHHHH--STTSCEEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCCCH-----------------HHHHHHh--cCCceEEEEEE
Confidence            3788999999999999999999999999999999877643321                 0011111  11211111110


Q ss_pred             cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEe
Q 012477          364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRIL  406 (462)
Q Consensus       364 ~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~  406 (462)
                      ..........+.||.+..+..|||+|++++-..+.||.+|.|.
T Consensus        97 ~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           97 RERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             EEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             eecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            0001246778999999999999999999999999999998873

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.46  E-value=3.8e-05  Score=81.27  Aligned_cols=96  Identities=23%  Similarity=0.326  Sum_probs=28.9

Q ss_pred             cCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477          108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR  187 (462)
Q Consensus       108 ~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  187 (462)
                      .+..|.++..+|++.+.+.............+....+.||.+.++.|||++|.+||.|.++||++|.+..          
T Consensus       538 aL~~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d----------  607 (726)
T 4aid_A          538 ALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND----------  607 (726)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSSCCSSCCSSCCC-----------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC----------
Confidence            3556777777777765443322223333344567889999999999999999999999999999999843          


Q ss_pred             CCceEEEEcC-HHHHHHHHHHHHHHHhc
Q 012477          188 SDELVQISGE-ASVVKKALCQIASRLHD  214 (462)
Q Consensus       188 ~~r~v~I~G~-~~~v~~A~~~I~~~l~~  214 (462)
                       +..|.|.+. .+++.+|+.+|..++.+
T Consensus       608 -dG~v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          608 -DGVVKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             -------CCSCHHHHHHHHHC-------
T ss_pred             -CceEEEEeCCHHHHHHHHHHHHHHhhh
Confidence             456788775 88999999999888764

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.44  E-value=5.1e-05  Score=63.76  Aligned_cols=104  Identities=22%  Similarity=0.282  Sum_probs=71.0

Q ss_pred             eEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHH
Q 012477           43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDR  122 (462)
Q Consensus        43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~  122 (462)
                      =.+.++|+...+|+.||++|++|+.|.++.|-+|+|-+-           +..++.                -+.   +.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~-----------s~d~~~----------------fI~---na   85 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEY-----------SSDLER----------------IVK---NL   85 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEEC-----------CSSHHH----------------HHH---HH
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEc-----------CCCHHH----------------HHH---Hh
Confidence            456789999999999999999999999999999986321           111111                000   00


Q ss_pred             HHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEe
Q 012477          123 VIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL  176 (462)
Q Consensus       123 i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~  176 (462)
                      +.--.+.+..-...+......+.||....+..|||+|.+++-...-||.+|.|.
T Consensus        86 LsPA~V~~V~i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           86 FPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             STTSCEEEEEEEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             cCCceEEEEEEeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            000000000000002345788999999999999999999999999999988774

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.35  E-value=0.00038  Score=56.85  Aligned_cols=68  Identities=15%  Similarity=0.151  Sum_probs=60.3

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      .+.+.+...+++.|+|++|+.|+.|+..|++.|++..-+.      +..-.|+|.|++..=..|..+|..+..-
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s------~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP------ERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT------TSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC------CCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            6789999999999999999999999999999999976522      4577899999999999999999887754

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.84  E-value=0.00022  Score=75.50  Aligned_cols=65  Identities=28%  Similarity=0.358  Sum_probs=11.7

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHhh
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~~  445 (462)
                      ....+.||.+.++.|||+||.+||.|.++||++|.|.           ++..|.|.+. .+++++|+.+|...+.+.
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~-----------ddG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN-----------DDGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             C------------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE-----------CCceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            4567899999999999999999999999999999983           2346788776 788999999988776544

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=96.16  E-value=0.004  Score=56.88  Aligned_cols=97  Identities=23%  Similarity=0.294  Sum_probs=65.3

Q ss_pred             CccccccccCChhHHhH-HhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc-ccCCCcce
Q 012477          293 ANIGGVIGKGGAIINQI-RQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE-RDSGLISF  370 (462)
Q Consensus       293 ~~~g~IIGk~G~~Ik~I-~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~  370 (462)
                      +-+|.-||++|++|+.| ++..|=+|.|-.-+++.                 ..-+..+  +.|.-..... .+.  ...
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~dp-----------------~~fi~na--lsPA~V~~V~i~~~--~~~  184 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDP-----------------ARFVANA--LSPAKVVSVSVIDQ--TAR  184 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSSH-----------------HHHHHHH--TTTSCCSEEEEEET--TTT
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCCH-----------------HHHHHhc--cCCcceEEEEEEcC--CCc
Confidence            35799999999999999 55568788776643221                 0011111  1121111111 011  124


Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCC
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN  410 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~  410 (462)
                      ...+.||.+..+.-|||+|++++--.+.||.+|.|....+
T Consensus       185 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          185 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             EEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            6889999999999999999999999999999999976543

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.86  E-value=0.0062  Score=55.64  Aligned_cols=98  Identities=23%  Similarity=0.223  Sum_probs=63.5

Q ss_pred             CccceeecCCchHHHHH-HHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477           52 RKIGSIIGRGGEIVKQL-RIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG  130 (462)
Q Consensus        52 ~~~g~IIGk~G~~Ik~i-~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~  130 (462)
                      +-+|+-||++|++|+.| ++-.|=+|+|-+-           +-.++.                   .+.+.+.-..+..
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~-----------s~dp~~-------------------fi~nalsPA~V~~  175 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDY-----------DDDPAR-------------------FVANALSPAKVVS  175 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC-----------CSSHHH-------------------HHHHHTTTSCCSE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEe-----------cCCHHH-------------------HHHhccCCcceEE
Confidence            45899999999999999 5667888876321           111111                   0111110000000


Q ss_pred             CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCC
Q 012477          131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH  180 (462)
Q Consensus       131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~  180 (462)
                      .. ......-...+.||....+..|||+|.+++-....||.+|.|...++
T Consensus       176 V~-i~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          176 VS-VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             EE-EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             EE-EEcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            00 00011236889999999999999999999999999999999977643

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.81  E-value=0.0072  Score=58.44  Aligned_cols=103  Identities=21%  Similarity=0.274  Sum_probs=69.9

Q ss_pred             EEEEeeeC-----CccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccc
Q 012477          285 SLRLVCPV-----ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCS  358 (462)
Q Consensus       285 ~~~v~ip~-----~~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~  358 (462)
                      ..++.|-.     +-+|..||++|++|+.|.++. |=+|.|-.-+++.                 ..-+..+  +.|.-.
T Consensus       236 RaKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~dp-----------------~~fi~na--lsPA~V  296 (366)
T 1k0r_A          236 RSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDP-----------------ARFVANA--LSPAKV  296 (366)
T ss_dssp             EEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSSH-----------------HHHHHHH--TTTSCC
T ss_pred             eEEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHh--cCCcce
Confidence            44555543     457999999999999999999 7777776633221                 0011111  112111


Q ss_pred             ccc-cccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecC
Q 012477          359 EKI-ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK  408 (462)
Q Consensus       359 ~~~-~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~  408 (462)
                      ... ..+.  ......+.||....+..|||+|++++-..+.||.+|.|...
T Consensus       297 ~~V~~~~~--~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          297 VSVSVIDQ--TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             SEEEEEET--TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             eEEEEEcC--CCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            111 0011  13578899999999999999999999999999999999654

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.60  E-value=0.016  Score=56.03  Aligned_cols=98  Identities=23%  Similarity=0.234  Sum_probs=65.0

Q ss_pred             CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477           52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG  130 (462)
Q Consensus        52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~  130 (462)
                      +-+|+.||++|++|+.|.++. |=+|+|-+-           +-.++.                   .+.+.+.--.+..
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~-----------s~dp~~-------------------fi~nalsPA~V~~  298 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDY-----------DDDPAR-------------------FVANALSPAKVVS  298 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC-----------CSSHHH-------------------HHHHHTTTSCCSE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEc-----------CCCHHH-------------------HHHHhcCCcceeE
Confidence            568999999999999999998 888876321           101110                   0111110000000


Q ss_pred             CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCC
Q 012477          131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH  180 (462)
Q Consensus       131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~  180 (462)
                      .. ..........+.||....+..|||+|.+++-...-||.+|.|...++
T Consensus       299 V~-~~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  347 (366)
T 1k0r_A          299 VS-VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  347 (366)
T ss_dssp             EE-EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESSC
T ss_pred             EE-EEcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHHH
Confidence            00 00011347889999999999999999999999999999999977643

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.56  E-value=0.0028  Score=67.41  Aligned_cols=95  Identities=23%  Similarity=0.277  Sum_probs=12.0

Q ss_pred             cCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477          108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR  187 (462)
Q Consensus       108 ~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  187 (462)
                      .+..|.++..++++.+.+.............+....+.||...++.+||++|.+|+.|.++||+.|.+..          
T Consensus       528 ~l~~A~~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~----------  597 (723)
T 3cdi_A          528 ALNQAKGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED----------  597 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCC-----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC----------
Confidence            3455667777777765443222222223334566788999999999999999999999999999998742          


Q ss_pred             CCceEEEEcC-HHHHHHHHHHHHHHHh
Q 012477          188 SDELVQISGE-ASVVKKALCQIASRLH  213 (462)
Q Consensus       188 ~~r~v~I~G~-~~~v~~A~~~I~~~l~  213 (462)
                       +..+.|.+. .+.+.+|..+|..++.
T Consensus       598 -dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          598 -DGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ---------------------------
T ss_pred             -CccEEEecCCHHHHHHHHHHHHHHhh
Confidence             456777664 6677778777766553

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=94.73  E-value=0.0027  Score=67.76  Aligned_cols=93  Identities=24%  Similarity=0.333  Sum_probs=36.9

Q ss_pred             cCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477          108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR  187 (462)
Q Consensus       108 ~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  187 (462)
                      .+..|.++..+|++.+.+..... .......+....+.||.+.++.+||++|.+||.|.++||+.|.+..          
T Consensus       567 aL~~A~~~~~~I~~~m~~al~~~-~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~----------  635 (757)
T 1e3p_A          567 ALKQARDARLHILDVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----------  635 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSSC-CCCCTTSCBCCCC------------------CTTCCCCCSCC--------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhccc-ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC----------
Confidence            44567777777777654432222 2222333445678899999999999999999999999999998843          


Q ss_pred             CCceEEEEcC-HHHHHHHHHHHHHHH
Q 012477          188 SDELVQISGE-ASVVKKALCQIASRL  212 (462)
Q Consensus       188 ~~r~v~I~G~-~~~v~~A~~~I~~~l  212 (462)
                       +..|.|.+. .....+|...|..+.
T Consensus       636 -dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          636 -DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             -----CCCBSSHHHHCC---------
T ss_pred             -CceEEEecCCHHHHHHHHHHHHHhc
Confidence             445666664 677777766665544

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=94.69  E-value=0.034  Score=53.54  Aligned_cols=93  Identities=32%  Similarity=0.449  Sum_probs=63.7

Q ss_pred             ccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccc-cCCCcceE
Q 012477          294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER-DSGLISFT  371 (462)
Q Consensus       294 ~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~t  371 (462)
                      -+|+.||.+|.+|+.|..+. |-+|.+-.-+++.                 ..-+..++  .|.-.....- +  .....
T Consensus       246 pvGacvg~~G~ri~~i~~el~ge~Idii~~s~d~-----------------~~fi~nal--~Pa~v~~v~~~d--~~~~~  304 (344)
T 1hh2_P          246 PIGACIGEGGSRIAAILKELKGEKLDVLKWSDDP-----------------KQLIANAL--APATVIEVEILD--KENKA  304 (344)
T ss_dssp             HHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSSH-----------------HHHHHHHT--CSSCCSEEEEEE--TTTTE
T ss_pred             ccceeeccCCcEeHHHHHHhCCCeeeEEecCCCH-----------------HHHHHHhc--CccEEEEEEEEc--CCCCE
Confidence            57999999999999999998 6676665533221                 00111111  1211111111 1  11356


Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                      ..+.||....+.-|||+|++++--.+.||.+|.|..
T Consensus       305 ~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          305 ARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             EEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            889999999999999999999999999999999953

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=94.18  E-value=0.043  Score=52.83  Aligned_cols=96  Identities=23%  Similarity=0.304  Sum_probs=63.0

Q ss_pred             CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477           52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG  130 (462)
Q Consensus        52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~  130 (462)
                      +-+|+.||.+|.+|+.+.++. |=+|.|-+-           +-.++.                   .+.+.|.--.+..
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~-----------s~d~~~-------------------fi~nal~Pa~v~~  294 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKW-----------SDDPKQ-------------------LIANALAPATVIE  294 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC-----------CSSHHH-------------------HHHHHTCSSCCSE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEec-----------CCCHHH-------------------HHHHhcCccEEEE
Confidence            458999999999999999998 777765221           111100                   0001000000000


Q ss_pred             CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                      . .......-...+.||....+..|||+|.+++-....||.+|.|...
T Consensus       295 v-~~~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          295 V-EILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             E-EEEETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             E-EEEcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            0 0001123478899999999999999999999999999999999765

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=92.82  E-value=0.019  Score=60.97  Aligned_cols=62  Identities=29%  Similarity=0.378  Sum_probs=0.0

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHH
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRL  442 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l  442 (462)
                      ....+.||.+.++.|||+||.+|+.|.++||+.|.|.           .+..|.|.+. .+.+++|..+|...+
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~-----------~dg~v~I~~~~~~~~~~a~~~i~~i~  622 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE-----------DDGTVKIAATDGEKAKHAIRRIEEIT  622 (723)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEec-----------CCccEEEecCCHHHHHHHHHHHHHHh
Confidence            4567889999999999999999999999999999883           2356777775 467788877776544

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=90.85  E-value=0.014  Score=62.42  Aligned_cols=61  Identities=23%  Similarity=0.273  Sum_probs=20.8

Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHH
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRL  442 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l  442 (462)
                      ...+.||.+.+|.+||++|.+||.|.+.||+.|.|..           +..|.|+.. .+..+.|..+|....
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-----------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC-------------------CCCBSSHHHHCC---------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-----------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3468899999999999999999999999999999842           356778775 566677766665543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	462
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-15
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-05
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-04
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-14
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	9e-13
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	9e-09
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-07
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-14
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-11
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-08
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	7e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-14
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	5e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-06
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	9e-14
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-10
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-07
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-05
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	4e-13
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-12
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-07
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	6e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-11
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	6e-08
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-05
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-11
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-05
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	4e-10
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-09
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-06
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-05
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	5e-10
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-09
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-04
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	9e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-07
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-08
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	9e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	8e-04
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-08
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.002
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	6e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	5e-06
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-05
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	5e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	0.002
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	3e-06
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	5e-05
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.004
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	5e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	4e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	5e-05
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	8e-05
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.001
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.001
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.002
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.002

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.1 bits (166), Expect = 7e-15
 Identities = 28/97 (28%), Positives = 47/97 (48%), Gaps = 6/97 (6%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            V  +L VP   +G +IG+GG+ +++I   +GA+I   K+       L    L++ISG  
Sbjct: 14  PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE---SEGTLLLSRLIKISGTQ 70

Query: 199 SVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSG 235
             V  A   I  ++ ++    + +  SA   S  SSG
Sbjct: 71  KEVAAAKHLILEKVSEDEELRKRIAHSA---SGPSSG 104

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.1 bits (127), Expect = 1e-09
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
             +L VP   +G +IG+GG  I  + + + A I    +    +       +++ISG    
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE---SEGTLLLSRLIKISGTQKE 72

Query: 431 AKDALIQVMTRLR 443
              A   ++ ++ 
Sbjct: 73  VAAAKHLILEKVS 85

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 9/93 (9%)

Query: 273 SAPRDDLSSK-EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLI 331
           S     L+       +L  P  ++G +IG+GG  I  I + SGA I  D  S        
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR 62

Query: 332 TVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364
            +         +S T + V   +    EK+  D
Sbjct: 63  LI--------KISGTQKEVAAAKHLILEKVSED 87

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPG--SEERVVTV 92
            +   P R +G IIGRGGE ++ +   + +KI   +   G     R++ +
Sbjct: 16 FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKI 66

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.3 bits (162), Expect = 1e-14
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
           +T +LL+   ++G +IGK G+ V+ +R E+GA+I I +           + ++ ++G  +
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTN 56

Query: 200 VVKKALCQIASRLHD 214
            + KA   I  +L +
Sbjct: 57  AIFKAFAMIIDKLEE 71

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (148), Expect = 9e-13
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 7/76 (9%)

Query: 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427
           ++ T RLL+    +G +IGK G  + +MR  + A I I          +  + ++ ++G 
Sbjct: 2   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGP 54

Query: 428 LDLAKDALIQVMTRLR 443
            +    A   ++ +L 
Sbjct: 55  TNAIFKAFAMIIDKLE 70

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (119), Expect = 9e-09
 Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 2/50 (4%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS 334
           ++RL+     +G +IGK G  + ++R+ESGA I +   +    + +IT++
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLA 52

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)

Query: 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
             R L   +++GSIIG+ GE VK++R ++ ++I I E      ER++T+
Sbjct: 4  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITL 51

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.0 bits (161), Expect = 2e-14
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
           Q T +L +P++ IGC+IG+ G  +  IR  +GAQI+I            S   V I+G A
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSA 55

Query: 199 SVVKKALCQIASRL 212
           + +  A   I +RL
Sbjct: 56  ASISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 4e-11
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           T  L +P + IGC+IG+ G+ I E+R+++ A I+I                V I+G    
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-----EGSSGRQVTITGSAAS 57

Query: 431 AKDALIQVMTRL 442
              A   +  RL
Sbjct: 58  ISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
          T +    P   IG IIGR G  + ++R  + ++I+I   V GS  R VT+
Sbjct: 2  TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 51

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 7e-08
 Identities = 19/50 (38%), Positives = 28/50 (56%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS 334
           +  L  P   IG +IG+ GA IN+IRQ SGA IK+ +         +T++
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 52

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.5 bits (157), Expect = 6e-14
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
           +   ++ VP + +G ++GKGG+ +   +  TGA+I+I K           +  V I+G  
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT--RNRRVTITGSP 59

Query: 199 SVVKKALCQIASRL 212
           +  + A   I+ R+
Sbjct: 60  AATQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.9 bits (140), Expect = 1e-11
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
              + VP + +G ++GKGG  + E + LT A I+I  K          +  V I+G    
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAA 61

Query: 431 AKDALIQVMTRL 442
            + A   +  R+
Sbjct: 62  TQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (113), Expect = 5e-08
 Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 3/52 (5%)

Query: 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI---GETVPGSEERVVTV 92
          +     P   +G+I+G+GG+ + + +  T ++I+I   GE +PG+  R VT+
Sbjct: 4  LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 9/44 (20%), Positives = 21/44 (47%)

Query: 286 LRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDC 329
           + +  P   +G ++GKGG  + + ++ +GA I++          
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT 48

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.2 bits (156), Expect = 9e-14
 Identities = 18/81 (22%), Positives = 45/81 (55%), Gaps = 3/81 (3%)

Query: 134 SDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQ 193
            DG      ++++P+ + G VIGKGG+ ++ ++   G ++ +++D    +    +D+ ++
Sbjct: 2   GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTG---ADKPLR 58

Query: 194 ISGEASVVKKALCQIASRLHD 214
           I+G+   V++A   +   + D
Sbjct: 59  ITGDPYKVQQAKEMVLELIRD 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.6 bits (131), Expect = 2e-10
 Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL 428
           +    +++P S+ G +IGKGG  I +++      + ++         +  D+ ++I+GD 
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDP 63

Query: 429 DLAKDALIQVMTRLR 443
              + A   V+  +R
Sbjct: 64  YKVQQAKEMVLELIR 78

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.3 bits (107), Expect = 4e-07
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE--TVPGSEERVVTV 92
          GP + V   + P  K G +IG+GGE +KQL+     K+ + +        ++ + +
Sbjct: 4  GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRI 59

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDT 342
                ++ P +  G VIGKGG  I Q+++ +G  + +     +       +         
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPL--------R 58

Query: 343 LSATIEAVVRLQPRCSEKIERDSG 366
           ++     V + +    E I RD G
Sbjct: 59  ITGDPYKVQQAKEMVLELI-RDQG 81

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.5 bits (152), Expect = 4e-13
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            +T +  VP   +G +IG+GG+ +  I+ E+G +I+I  D          +    ++G  
Sbjct: 7   VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD-----SGGLPERSCMLTGTP 61

Query: 199 SVVKKALCQIASRLHDN 215
             V+ A   +   +   
Sbjct: 62  ESVQSAKRLLDQIVEKG 78

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.7 bits (129), Expect = 5e-10
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL 428
             T    VP   +G +IG+GG  I+ +++ +   I+I P           +    ++G  
Sbjct: 7   VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLTGTP 61

Query: 429 DLAKDALIQVMTRLR 443
           +  + A   +   + 
Sbjct: 62  ESVQSAKRLLDQIVE 76

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 10/80 (12%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS 344
           +     P   +G +IG+GG  I++I+QESG  I++   S    +    +          +
Sbjct: 9   TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCML----------T 58

Query: 345 ATIEAVVRLQPRCSEKIERD 364
            T E+V   +    + +E+ 
Sbjct: 59  GTPESVQSAKRLLDQIVEKG 78

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 16/47 (34%), Positives = 25/47 (53%)

Query: 46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
           Y  P   +G IIGRGGE + +++ ++  KI+I     G  ER   +
Sbjct: 11 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCML 57

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.7 bits (147), Expect = 1e-12
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG 196
           G  +T ++ +P D  G +IGKGGQ ++ IR E+GA I+I +           D ++ I+G
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITG 55

Query: 197 EASVVKKALCQIASRLH 213
               ++ A   + + + 
Sbjct: 56  TQDQIQNAQYLLQNSVK 72

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.1 bits (130), Expect = 2e-10
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           TT++ +P    G +IGKGG  I ++R  + A+I+I            +D ++ I+G  D 
Sbjct: 5   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQ 59

Query: 431 AKDALIQVMTRLR 443
            ++A   +   ++
Sbjct: 60  IQNAQYLLQNSVK 72

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 22/54 (40%), Positives = 36/54 (66%), Gaps = 1/54 (1%)

Query: 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
          GP  T  +   P    GSIIG+GG+ +KQ+R ++ + I+I E + GSE+R++T+
Sbjct: 1  GPIITT-QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 53

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.5 bits (105), Expect = 6e-07
 Identities = 21/50 (42%), Positives = 31/50 (62%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS 334
           + ++  P    G +IGKGG  I QIR ESGA+IK+D      +D +IT++
Sbjct: 5   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT 54

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.0 bits (140), Expect = 1e-11
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVK 202
             +VP+ + G +IGKGG+ +++I  ++GA+I +    + P  A  + +L  I G    + 
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQID 61

Query: 203 KALCQIASRL 212
            A   I  ++
Sbjct: 62  YARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 1e-09
 Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAK 432
             +VPT + G +IGKGG  I  + + + A I +      P  A  + ++  I G      
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLFTIRGTPQQID 61

Query: 433 DALIQVMTRL 442
            A   +  ++
Sbjct: 62  YARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 6e-08
 Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI---GETVPGSEERVVTV 92
          + ++ P  K G IIG+GGE +K +   + ++I +            ++ T+
Sbjct: 3  FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTI 53

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 286 LRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSA 345
              + P    G +IGKGG  I  I Q+SGA I++  +     D  + +        T+  
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLF-------TIRG 55

Query: 346 TIEAVVRLQPRCSEKI 361
           T + +   +    EKI
Sbjct: 56  TPQQIDYARQLIEEKI 71

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (137), Expect = 4e-11
 Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 7/70 (10%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
           Q +A + +P +    VIGK G+ +Q++  +T  +I+I + +            ++I+G  
Sbjct: 9   QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-------PSNQIKITGTK 61

Query: 199 SVVKKALCQI 208
             ++KA  ++
Sbjct: 62  EGIEKARHEV 71

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 10/52 (19%), Positives = 20/52 (38%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
             + S  +  P  +   VIGK G  +  +  ++   I++       +   IT
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKIT 58

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (107), Expect = 5e-07
 Identities = 12/69 (17%), Positives = 29/69 (42%), Gaps = 7/69 (10%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
           +  + +P      +IGK G  + ++   T   I+I   +       +    ++I+G  + 
Sbjct: 11  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEG 63

Query: 431 AKDALIQVM 439
            + A  +V+
Sbjct: 64  IEKARHEVL 72

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 49 CPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
           P      +IG+ GE ++ L + T +KI+I    P      + +
Sbjct: 16 IPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKI 57

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.1 bits (130), Expect = 4e-10
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            VT ++ VP D    VIG+ G  ++ +  E    I +   E          +++ I+G A
Sbjct: 9   PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLA 61

Query: 199 SVVKKALCQIASRLHD 214
           + + +A   +  R+ +
Sbjct: 62  ANLDRAKAGLLERVKE 77

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.0 bits (122), Expect = 5e-09
 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 10/89 (11%)

Query: 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQI 424
             L+  T  + VP      +IG+ GS I +M    + NI +   E          +++ I
Sbjct: 5   EALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAI 57

Query: 425 SGD---LDLAKDALIQVMTRLRANLFDRE 450
           +G    LD AK  L++ +  L+A   DR 
Sbjct: 58  TGLAANLDRAKAGLLERVKELQAEQEDRA 86

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (100), Expect = 5e-06
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 276 RDDLSSK-EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
           ++ L +    ++ +  P      VIG+ G+ I ++  E    I V +   + D   IT
Sbjct: 1   KEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAIT 58

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (92), Expect = 7e-05
 Identities = 6/43 (13%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 50 PIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV 92
          P      +IG+ G  ++++  + +  I +    P  +  ++ +
Sbjct: 17 PFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAI 57

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.7 bits (129), Expect = 5e-10
 Identities = 12/76 (15%), Positives = 25/76 (32%), Gaps = 4/76 (5%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
                + V       +IG+ G ++  IR E    I+    +          + + I+G  
Sbjct: 9   SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQ----PQDQITITGYE 64

Query: 199 SVVKKALCQIASRLHD 214
              + A   I   + +
Sbjct: 65  KNTEAARDAILRIVGE 80

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 362 ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEM 421
           + D  L SF   + V       +IG+ G++IT++R     NI+   K++     ++  + 
Sbjct: 2   QEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQ 57

Query: 422 VQISGDLDLAKDALIQVMTRLR 443
           + I+G     + A   ++  + 
Sbjct: 58  ITITGYEKNTEAARDAILRIVG 79

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (110), Expect = 2e-07
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 276 RDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEG-DDCLITVS 334
           ++D + + F L +         +IG+ GA+I QIR E    I+             IT++
Sbjct: 2   QEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITIT 61

Query: 335 SKEFFEDTLSATIEAVVR 352
             E   +     I  +V 
Sbjct: 62  GYEKNTEAARDAILRIVG 79

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 50 PIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTV 92
            +    IIGR G ++ Q+R++    I+   +      +  +T+
Sbjct: 17 DPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITI 60

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 1e-09
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
           G H +   + +P   +G VIG+ G++++ I+++ G +I+       P      + + QI+
Sbjct: 1   GSHMI--DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQ-----FKPDDGTTPERIAQIT 53

Query: 196 GEASVVKKALCQIASRLHD 214
           G     + A   I   L  
Sbjct: 54  GPPDRAQHAAEIITDLLRS 72

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 9e-09
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL 428
           S    + +P   +G +IG+ G +I +++      I+  P +      +  + + QI+G  
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPP 56

Query: 429 DLAKDALIQVMTRLR 443
           D A+ A   +   LR
Sbjct: 57  DRAQHAAEIITDLLR 71

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 13/55 (23%), Positives = 26/55 (47%)

Query: 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASD 97
           +     P   +G +IGR GE++K+++ D   +I+       + ER+  +    D
Sbjct: 3  HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPD 57

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 10/50 (20%), Positives = 24/50 (48%)

Query: 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS 334
            + +  P   +G VIG+ G +I +I+ ++G  I+         + +  ++
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQIT 53

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 7/70 (10%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
               ++ +       +IGK G  +  I+ +    +RI  D            L++I G+ 
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-------KSNLIRIEGDP 56

Query: 199 SVVKKALCQI 208
             V++A  ++
Sbjct: 57  QGVQQAKREL 66

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 7/69 (10%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430
              + +       LIGK G+ I  ++   K ++RI P         E   +++I GD   
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQG 58

Query: 431 AKDALIQVM 439
            + A  +++
Sbjct: 59  VQQAKRELL 67

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (90), Expect = 9e-05
 Identities = 10/52 (19%), Positives = 24/52 (46%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLIT 332
           ++   + +         +IGK GA IN+I+ +   ++++   S + +   I 
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIE 53

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (83), Expect = 8e-04
 Identities = 6/48 (12%), Positives = 18/48 (37%), Gaps = 2/48 (4%)

Query: 50 PIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASD 97
            +    +IG+ G  + +++   K  +RI       +  ++ +     
Sbjct: 12 DHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGDPQ 57

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 6/76 (7%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
            V+  + +       +IG  G+ ++ I  E    IR       P         V ++G  
Sbjct: 9   MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLP 62

Query: 199 SVVKKALCQIASRLHD 214
             V++A+  I +   +
Sbjct: 63  ENVEEAIDHILNLEEE 78

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 1e-05
 Identities = 11/57 (19%), Positives = 18/57 (31%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
            +  S  +         +IG  G  I +I  E    I+   S     +C+      E
Sbjct: 7   EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPE 63

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 6/70 (8%)

Query: 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429
            +  + +       +IG  G  I ++    K +IR       P+  + D   V ++G  +
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLPE 63

Query: 430 LAKDALIQVM 439
             ++A+  ++
Sbjct: 64  NVEEAIDHIL 73

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 9/42 (21%), Positives = 17/42 (40%)

Query: 50 PIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVT 91
            R    IIG  G+ ++++  + K  IR  ++       V  
Sbjct: 17 DHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTV 58

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 47.0 bits (112), Expect = 6e-08
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
               + +P D+IG VIG   Q++  I+ +TGA+I I  D
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD 41

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 45.0 bits (107), Expect = 2e-07
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 6/51 (11%)

Query: 287 RLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
            +  PV  IG VIG    +INQI++++GA I ++      DD  I + + +
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAAD 50

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 41.6 bits (98), Expect = 5e-06
 Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 6/55 (10%)

Query: 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE 98
          +     P+ KIG +IG   +++ Q++ DT ++I I       ++  + + +A   
Sbjct: 4  IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI------EDDGTIYIGAADGP 52

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 40.0 bits (94), Expect = 2e-05
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 11/56 (19%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426
              + +P  +IG +IG    +I +++  T A I I           EDD  + I  
Sbjct: 4   IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI-----------EDDGTIYIGA 48

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSE-TGAQIRILKDEHLPSCALRSDELVQISGE 197
               ++ +P+     +IG  G+++++I  E  G  I    +           + V I G 
Sbjct: 9   IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-------GSDTVVIRGP 61

Query: 198 ASVVKKALCQIASRLHDNPSR 218
           +S V+KA  Q+     +  ++
Sbjct: 62  SSDVEKAKKQLLHLAEEKQTK 82

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 10/57 (17%), Positives = 18/57 (31%)

Query: 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
           +    + +  P      +IG  G +I  I +E G           G D ++      
Sbjct: 7   ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSS 63

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 13/74 (17%), Positives = 23/74 (31%), Gaps = 8/74 (10%)

Query: 371 TTRLLVPTSRIGCLIGKGGSIITE-MRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429
              + +P      LIG  G +I   M      +I    + +         + V I G   
Sbjct: 11  EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-------GSDTVVIRGPSS 63

Query: 430 LAKDALIQVMTRLR 443
             + A  Q++    
Sbjct: 64  DVEKAKKQLLHLAE 77

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 10/42 (23%), Positives = 16/42 (38%)

Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180
               + +V  D +G  IG  G  +Q  R   G     L ++ 
Sbjct: 7   AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDT 48

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN-LPKIASEDDEMVQ 423
           +F    +V    +G  IG  GS I + R++       L ++    +I  E  + V+
Sbjct: 7   AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVK 62

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.7 bits (77), Expect = 0.004
 Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 4/44 (9%)

Query: 281 SKEFSLRLVC----PVANIGGVIGKGGAIINQIRQESGAAIKVD 320
           +K+ +             +G  IG  G+ I Q R+  G      
Sbjct: 1   TKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIEL 44

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 42.5 bits (100), Expect = 5e-06
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
           V  +++G VIG  G++   I   TG  I +  + 
Sbjct: 9   VKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN 42

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 13/66 (19%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 376 VPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435
           V   R+G +IG  G +  E+ R T   I +  + ++  +  E + +  ++  L  A + +
Sbjct: 9   VKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVN--LMKAAE-V 65

Query: 436 IQVMTR 441
           ++ ++ 
Sbjct: 66  VKAISL 71

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 11/67 (16%), Positives = 25/67 (37%)

Query: 286 LRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSA 345
           + +      +G VIG  G +  +I + +G  I VD+ ++                   + 
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAE 64

Query: 346 TIEAVVR 352
            ++A+  
Sbjct: 65  VVKAISL 71

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 11/63 (17%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKAL 205
           +   ++  VIGK G +++ ++SE   QI + +           + L+ ++G+   V  A 
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIWVNGDRRKVSIAE 55

Query: 206 CQI 208
             I
Sbjct: 56  EAI 58

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 291 PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAV 350
             A +  VIGK G++I  ++ E    I V        + LI V+            I  +
Sbjct: 8   NPARVPRVIGKKGSMIKLLKSELDVQIVVG------QNGLIWVNGDRRKVSIAEEAIYLI 61

Query: 351 VR 352
            +
Sbjct: 62  EQ 63

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 13/74 (17%)

Query: 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429
           F   + +  +R+  +IGK GS+I  ++      I +             + ++ ++GD  
Sbjct: 1   FGRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVV-----------GQNGLIWVNGDRR 49

Query: 430 LAKDA--LIQVMTR 441
               A   I ++ +
Sbjct: 50  KVSIAEEAIYLIEQ 63

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 38.9 bits (91), Expect = 8e-05
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 16/83 (19%)

Query: 291 PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAV 350
             A +  VIG+  +++  + +++   I V        +  I +      ED  +  + A+
Sbjct: 8   SPAKVPRVIGRKMSMLKTLEEKTECKIFVA------RNGRIHLECPN--EDLEAIAVMAI 59

Query: 351 VRLQPRCSEKIERDSGLISFTTR 373
                   + I+ ++     T R
Sbjct: 60  --------KIIDEEAYTSGLTKR 74

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 5/33 (15%), Positives = 18/33 (54%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
           +   ++  VIG+   +++ +  +T  +I + ++
Sbjct: 7   ISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN 39

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 7/33 (21%), Positives = 17/33 (51%)

Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
           +   ++  VIGK   + + + S++G  I +  +
Sbjct: 7   IMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN 39

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 16/75 (21%)

Query: 291 PVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAV 350
               +  VIGK  ++   +  +SG +I V       ++  I  +       +    IEA+
Sbjct: 8   MPVKVPRVIGKNKSMYETLTSKSGCSIFVA------NNGRIWATCPS--RFSEEILIEAI 59

Query: 351 VRLQPRCSEKIERDS 365
                    KIE +S
Sbjct: 60  --------RKIENES 66

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 6/49 (12%), Positives = 16/49 (32%), Gaps = 1/49 (2%)

Query: 376 VPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQI 424
           +   ++  +IGK  S+   +   +  +I +                 +I
Sbjct: 7   IMPVKVPRVIGKNKSMYETLTSKSGCSIFV-ANNGRIWATCPSRFSEEI 54

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	462
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.62
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.61
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.61
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.61
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.58
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.58
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.55
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.55
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.51
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.51
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.51
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.51
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.51
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.51
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.49
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.45
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.44
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.41
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.3
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.29
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.25
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.16
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.13
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.08
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.94
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.86
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.83
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.74
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.68
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.66
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.61
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.57
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.5
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.38
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.16
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.95
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.86
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.6
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.31
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.16
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.08
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.0
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	91.41
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	86.81
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	83.83

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.1e-16  Score=118.17  Aligned_cols=73  Identities=26%  Similarity=0.467  Sum_probs=66.2

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      +.+|.+|.||.+++|+|||++|++|++|+++|||+|+|.++     .++.+++.|+|+|++++|+.|+.+|.++|+++
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~-----~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC-----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999999999999654     23567899999999999999999999999875

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.3e-16  Score=115.90  Aligned_cols=68  Identities=31%  Similarity=0.522  Sum_probs=62.0

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL  442 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  442 (462)
                      .|.+|.||..++|+|||++|++|++|+++|||+|.|++.     .++.++|.|+|+|++++|+.|+.+|.++|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~-----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCC-----CCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            688999999999999999999999999999999999754     23567799999999999999999999876

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=4.5e-16  Score=115.77  Aligned_cols=71  Identities=27%  Similarity=0.436  Sum_probs=63.1

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL  442 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  442 (462)
                      .+.+|.||.+++|+|||++|++|++|++.|||+|+|.+.++..  .+.++|.|+|+|++++|+.|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            3578999999999999999999999999999999998765432  3567899999999999999999999875

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2.6e-16  Score=116.05  Aligned_cols=69  Identities=25%  Similarity=0.456  Sum_probs=63.4

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  444 (462)
                      .++.+|.||.+++|+|||++|++|++|++.|||+|++++.       +..+|.|+|+|++++|.+|+.+|.++|++
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            5889999999999999999999999999999999999643       34579999999999999999999999875

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=4.1e-16  Score=115.01  Aligned_cols=70  Identities=23%  Similarity=0.367  Sum_probs=61.8

Q ss_pred             EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL  442 (462)
Q Consensus       371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  442 (462)
                      +.+|.||..++|+|||++|++|++|++.|||+|+|++...  +..+.++|.|+|+|++++|+.|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~--~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP--PNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT--TTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC--CCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4579999999999999999999999999999999976543  234567899999999999999999999874

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=7.5e-16  Score=116.70  Aligned_cols=74  Identities=22%  Similarity=0.391  Sum_probs=66.5

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  444 (462)
                      ..++.+|.||..++|+|||++|++|++|+++|||+|.|.+.+..|   .+.+|.|+|+|++++|+.|+.+|.+.|++
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999998754322   46789999999999999999999998865

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=8.5e-16  Score=114.36  Aligned_cols=72  Identities=24%  Similarity=0.424  Sum_probs=64.6

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..+.+|.||.+++|+|||++|++|++|+++|||+|+|.+.+     ++..++.|+|+|++++|+.|+.+|.+.|++.
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-----GTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT-----TSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC-----CCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            35788999999999999999999999999999999997653     2456789999999999999999999999864

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.9e-15  Score=111.27  Aligned_cols=70  Identities=29%  Similarity=0.571  Sum_probs=64.4

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ..++++|+||.+++|+|||++|++|++|+++|||+|++++.       ..++|+|+|+|++++|.+|..+|.++|++
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            35799999999999999999999999999999999999764       25689999999999999999999999875

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=2.8e-15  Score=112.98  Aligned_cols=73  Identities=19%  Similarity=0.353  Sum_probs=66.2

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..++.+|.||..++|+|||++|.+|++|++.|||+|.|++.+     ++.+++.|+|+|++++|+.|+.+|.+.|++.
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            468899999999999999999999999999999999997642     2567899999999999999999999999874

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=5.6e-15  Score=111.74  Aligned_cols=73  Identities=16%  Similarity=0.212  Sum_probs=64.6

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ..++.++.||..+|++|||++|++|++|+++|||+|++++.+      +.+++.|+|+|++++|++|+.+|++.++++.
T Consensus         8 ~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~------~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           8 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc------CCCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            467889999999999999999999999999999999996432      3345789999999999999999999888764

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=5.7e-15  Score=111.75  Aligned_cols=76  Identities=22%  Similarity=0.506  Sum_probs=68.8

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ....++.+|+||.+++|.|||++|++|++|+++|||+|.|+++...+   .+.+|+|+|+|++++|.+|..+|.++|++
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            34678999999999999999999999999999999999998764433   47899999999999999999999999976

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=1.1e-14  Score=115.57  Aligned_cols=76  Identities=20%  Similarity=0.298  Sum_probs=67.1

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ..++.+|.||..++|+|||++|++|++|+++|||+|.|.+....   ....+|.|+|+|++++|+.|+.+|.++|++..
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            46889999999999999999999999999999999999765432   24567899999999999999999999997653

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.8e-14  Score=107.43  Aligned_cols=72  Identities=29%  Similarity=0.538  Sum_probs=65.4

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      +.++.++.||.+++|+|||++|++|++|+++|||+|+|....     .++.+|+|+|+|++++|.+|..+|.+++++
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~-----~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT-----SCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999999997542     246799999999999999999999999986

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.3e-14  Score=107.65  Aligned_cols=70  Identities=27%  Similarity=0.481  Sum_probs=63.0

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      .++|+||.+++|.|||++|++|++|+++|||+|+|.++++..  +.+.+|+|+|+|++++|.+|..+|.++|
T Consensus         4 ~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            578999999999999999999999999999999998765422  2478999999999999999999999876

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.3e-14  Score=106.81  Aligned_cols=70  Identities=26%  Similarity=0.482  Sum_probs=61.9

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      ++.|+||.+++|+|||++|++|++|+++|||+|+|+++..  ....+.+|.|+|+|++++|.+|..+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~--~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP--PNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT--TTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC--CCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4689999999999999999999999999999999987533  223467899999999999999999998874

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1e-14  Score=106.93  Aligned_cols=68  Identities=37%  Similarity=0.586  Sum_probs=62.0

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      .+.+|.||.+++|+|||++|.+|++|+++|||+|.|++..     .++.+|+|+|+|++++|..|..+|.++|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-----EGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC-----CCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5889999999999999999999999999999999997642     2467899999999999999999999876

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2.3e-14  Score=109.18  Aligned_cols=73  Identities=21%  Similarity=0.301  Sum_probs=65.2

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      .++.+|.||..+|++|||++|++|++|++.|||+|++++...    .+.+++.|+|+|++++|+.|+.+|++.+++.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~----~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT----CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC----CCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            578899999999999999999999999999999999965422    2466789999999999999999999998875

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.3e-14  Score=109.67  Aligned_cols=71  Identities=17%  Similarity=0.277  Sum_probs=64.0

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..++.+|.||..+||+|||++|++|++|+++|||+|.+++.       ++.++.|+|+|++++|++|+.+|++.+++.
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-------CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999543       345679999999999999999999988875

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.3e-14  Score=107.75  Aligned_cols=71  Identities=23%  Similarity=0.455  Sum_probs=64.7

Q ss_pred             ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ...++|.||.+++|+|||++|++|++|+++|||+|+|...+.     .+.+|.|+|+|++++|.+|..+|.++|++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT-----SCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC-----CCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999999987532     36789999999999999999999999875

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=3.7e-14  Score=104.19  Aligned_cols=66  Identities=24%  Similarity=0.341  Sum_probs=59.3

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHH
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTR  441 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~  441 (462)
                      ..+.+|.||.++|++|||++|++|++|+++|||+|+++++       +++++.|+|+|++++|+.|+.+|++.
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-------CCCCCEEEEECCHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999999999999543       35568999999999999999999874

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=5.1e-14  Score=105.96  Aligned_cols=74  Identities=23%  Similarity=0.418  Sum_probs=67.1

Q ss_pred             CCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       137 ~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ...++.+|.||.+++|+|||++|.+|++|+++|||+|.|++.+.     ++.++.|+|+|++++|..|..+|.++|.+.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT-----TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCC-----CCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            45789999999999999999999999999999999999976532     367899999999999999999999999863

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=3.3e-14  Score=107.79  Aligned_cols=72  Identities=17%  Similarity=0.188  Sum_probs=63.2

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHh-hCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRL-TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL  446 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~-sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~  446 (462)
                      ..++.+|.||..+||+|||++|++|++|+++ ++|+|.+++.       ++.++.|+|+|++++|+.|+.+|++.+++..
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-------CCCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            3578999999999999999999999999987 5999988532       4566899999999999999999999998753

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=9.5e-14  Score=110.17  Aligned_cols=78  Identities=28%  Similarity=0.451  Sum_probs=68.9

Q ss_pred             CCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       135 ~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      .....++.+|+||..++++|||++|.+|++|+++|||+|.|.+.....   ...+|+|+|+|++++|.+|..+|.++|.+
T Consensus        10 ~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          10 TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT---LLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             SSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCC---CCCccEEEEEeCHHHHHHHHHHHHHHHhC
Confidence            445678899999999999999999999999999999999997764322   35789999999999999999999999976


Q ss_pred             C
Q 012477          215 N  215 (462)
Q Consensus       215 ~  215 (462)
                      .
T Consensus        87 ~   87 (104)
T d1we8a_          87 D   87 (104)
T ss_dssp             H
T ss_pred             c
Confidence            4

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=9.4e-14  Score=107.37  Aligned_cols=70  Identities=21%  Similarity=0.256  Sum_probs=63.3

Q ss_pred             ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      .++.++.||..+|++|||++|++|++|+++|||+|.+++.       +++++.|+|+|++++|+.|+.+|++.+++.
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-------CCCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            5889999999999999999999999999999999999543       345679999999999999999999988764

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=2.6e-13  Score=102.39  Aligned_cols=73  Identities=18%  Similarity=0.236  Sum_probs=64.9

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ....++..+.||..+|++|||++|++|++|+++|||+|+|+..++      ..++.|+|+|++++|.+|..+|.+++++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~------~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           6 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC------CCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            345678899999999999999999999999999999999976532      3457899999999999999999999886

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=3.8e-13  Score=102.27  Aligned_cols=72  Identities=17%  Similarity=0.259  Sum_probs=64.8

Q ss_pred             ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ..++.|.||..++++|||++|++|++|+++|||+|+|++.+.    ....++.|+|+|+.++|.+|..+|.+++.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~----~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT----CSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC----CCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            468899999999999999999999999999999999976532    236789999999999999999999999876

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=4.9e-13  Score=100.79  Aligned_cols=71  Identities=23%  Similarity=0.368  Sum_probs=65.1

Q ss_pred             CCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       137 ~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ...++..|.||..++++|||++|.+|++|+++|||+|.|++.       ++.++.|+|+|++++|.+|..+|.+++.+
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-------CCCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            456799999999999999999999999999999999999764       25678999999999999999999999876

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=1.4e-12  Score=100.09  Aligned_cols=68  Identities=15%  Similarity=0.200  Sum_probs=61.0

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHh-hCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRL-TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~-sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..+|.+|.||..+|++|||++|++|++|+++ +|++|.+++          ++..|+|+|++++|+.|+.+|.+.+++.
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~----------~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC----------CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999 489999842          2458999999999999999999988875

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=6.9e-13  Score=97.26  Aligned_cols=68  Identities=19%  Similarity=0.289  Sum_probs=61.3

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL  212 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  212 (462)
                      ......|.||..++++|||++|++|++|+++|||+|+|++.       .+.++.|+|+|++++|.+|..+|.++.
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-------CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            45688999999999999999999999999999999999764       256789999999999999999998764

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=7.2e-13  Score=98.45  Aligned_cols=63  Identities=27%  Similarity=0.326  Sum_probs=56.5

Q ss_pred             cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHH
Q 012477          368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVM  439 (462)
Q Consensus       368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~  439 (462)
                      ..++.++.||.+++|+|||+||++|++|++.|||+|.+..         ++++.|+|.| +++++++|+.||.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~---------~~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD---------EDTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHS
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec---------CCCceEEEEECCHHHHHHHHHHHH
Confidence            4688999999999999999999999999999999998853         3446899999 6999999999984

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=8.5e-13  Score=99.81  Aligned_cols=73  Identities=22%  Similarity=0.322  Sum_probs=64.8

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhh-cCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSE-TGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ..+.++..|.||..+|++|||++|++|++|+++ ++|+|+++..       ++.++.|+|+|++++|.+|..+|.+++++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e   78 (82)
T d2ctja1           6 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEE   78 (82)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-------CCCCceEEEeCCHHHHHHHHHHHHHHHhh
Confidence            445678999999999999999999999999987 5899998654       25688999999999999999999999986


Q ss_pred             C
Q 012477          215 N  215 (462)
Q Consensus       215 ~  215 (462)
                      .
T Consensus        79 ~   79 (82)
T d2ctja1          79 K   79 (82)
T ss_dssp             H
T ss_pred             h
Confidence            3

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.29  E-value=1.2e-12  Score=98.59  Aligned_cols=63  Identities=17%  Similarity=0.221  Sum_probs=56.6

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~  445 (462)
                      ..+.||.+++|.|||++|++|++|+++|||+|+|.+           +..|+|+|++++++.|+.+|...+++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-----------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-----------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            468899999999999999999999999999999942           358999999999999999998877664

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=2.4e-12  Score=99.28  Aligned_cols=70  Identities=23%  Similarity=0.339  Sum_probs=64.1

Q ss_pred             CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ..++..|.||..+|++|||++|.+|++|+++|||+|.|+..       ++.++.|+|+|+.++|.+|..+|.+++.+
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-------CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999999765       25678999999999999999999999875

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=2.5e-11  Score=92.90  Aligned_cols=69  Identities=22%  Similarity=0.291  Sum_probs=62.1

Q ss_pred             CCCceEEEEEEeCCceeeeecCCchHHHHHHhhc-CceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET-GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      ..+.++..+.||..+|++|||++|++|++|++++ |++|.|+.+          +..|+|+|++++|.+|..+|.+++.+
T Consensus        17 ~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~----------~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          17 ANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG----------EDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS----------SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC----------CceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            3457899999999999999999999999999995 799999643          56899999999999999999999876

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.13  E-value=3e-11  Score=90.83  Aligned_cols=63  Identities=22%  Similarity=0.296  Sum_probs=57.6

Q ss_pred             EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477          142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      ..+.||.++++.|||++|++|++|+++|||+|+|.+           ++.|+|.|+++++..|..+|..++++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-----------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-----------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            358899999999999999999999999999999953           457999999999999999999998874

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=4.5e-11  Score=88.53  Aligned_cols=64  Identities=27%  Similarity=0.355  Sum_probs=57.1

Q ss_pred             CCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHH
Q 012477          137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIA  209 (462)
Q Consensus       137 ~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~  209 (462)
                      ...++..|.||.+++|+|||++|++|++|+++|||+|.+..+         .++.|+|.| ++++|.+|..+|.
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~---------~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC---------CCceEEEEECCHHHHHHHHHHHH
Confidence            356788999999999999999999999999999999988653         357899999 6999999999984

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.94  E-value=1.2e-11  Score=89.39  Aligned_cols=60  Identities=8%  Similarity=0.020  Sum_probs=45.8

Q ss_pred             EEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHH
Q 012477          373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLR  443 (462)
Q Consensus       373 ~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~  443 (462)
                      .+.||.+++|.|||++|++|+.|+++|||+|.|.+           +..|+|+|. +++++.|..+|....+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~-----------~g~v~I~g~~~~~v~~A~~~I~~i~~   64 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-----------NGRIWATCPSRFSEEILIEAIRKIEN   64 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT-----------TSEEEC-----CTTCCTHHHHTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC-----------CCEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999942           247999996 6899999999966443

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.86  E-value=9.6e-10  Score=82.09  Aligned_cols=62  Identities=23%  Similarity=0.185  Sum_probs=51.2

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEE-----cCHHHHHHHHHHHHHHHH
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQIS-----GDLDLAKDALIQVMTRLR  443 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~l~  443 (462)
                      .++.||.+.+|.|||++|++|++|+++|||+|+|.+.          +..+.+.     |.+.++++|..+|.+..+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d----------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC----------CCeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            3589999999999999999999999999999999532          2355554     468899999999987543

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.83  E-value=2.3e-09  Score=80.12  Aligned_cols=62  Identities=13%  Similarity=0.200  Sum_probs=53.8

Q ss_pred             EEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHhh
Q 012477          373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRAN  445 (462)
Q Consensus       373 ~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~~  445 (462)
                      .+.||.+.+|.|||+||++|+.|+.+|||+|.|.+           +..|.|.|+ .+.+..|+.+|....++-
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-----------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-----------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999953           248999995 789999999998765543

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.74  E-value=2.2e-10  Score=82.63  Aligned_cols=61  Identities=13%  Similarity=0.144  Sum_probs=47.4

Q ss_pred             EEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC-HHHHHHHHHHHHHHHhc
Q 012477          143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHD  214 (462)
Q Consensus       143 ~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~  214 (462)
                      .+.||.+.++.|||++|++|+.|+++|||+|.+.+           +..|+|.|. .+++..|..+|..+.++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~-----------~g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-----------NGRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT-----------TSEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC-----------CCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999943           347999996 78999999999776665

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.68  E-value=1.3e-08  Score=75.90  Aligned_cols=64  Identities=20%  Similarity=0.264  Sum_probs=53.8

Q ss_pred             EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEE-----EcCHHHHHHHHHHHHHHHhcC
Q 012477          142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQI-----SGEASVVKKALCQIASRLHDN  215 (462)
Q Consensus       142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I-----~G~~~~v~~A~~~I~~~l~~~  215 (462)
                      +.+.||.+.+|.|||++|++|++|+++|||+|+|..+          +..+.+     .|.+.++.+|...|.++.+.+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d----------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC----------CCeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            3589999999999999999999999999999999654          234554     457899999999998887654

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.66  E-value=1.7e-08  Score=75.32  Aligned_cols=62  Identities=11%  Similarity=0.200  Sum_probs=55.2

Q ss_pred             EEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC-HHHHHHHHHHHHHHHhcC
Q 012477          143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHDN  215 (462)
Q Consensus       143 ~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  215 (462)
                      .+.||.+.++.|||++|++|+.|+++|||+|.|..           +..|.|.|. .+.+..|..+|..+.++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-----------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-----------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999954           347999995 899999999999887763

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.61  E-value=1.2e-09  Score=73.93  Aligned_cols=45  Identities=29%  Similarity=0.468  Sum_probs=14.0

Q ss_pred             EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC
Q 012477          372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD  427 (462)
Q Consensus       372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~  427 (462)
                      ..|.||.+++|.|||+||++||+|+++|||+|.|.           ++..|+|.|+
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~-----------ddg~v~I~a~   49 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE-----------DDGTIYIGAA   49 (54)
T ss_dssp             C---------------------CHHHHSCCCC-------------------CCCCB
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe-----------CCeEEEEEec
Confidence            46889999999999999999999999999999994           2457887775

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.57  E-value=1.8e-08  Score=77.82  Aligned_cols=53  Identities=25%  Similarity=0.280  Sum_probs=47.1

Q ss_pred             ccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477          380 RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA  444 (462)
Q Consensus       380 ~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~  444 (462)
                      +.|.|||++|.+|+.|++.|||.|.|..            ..|.|.|++++++.|+.+|...+..
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d------------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE------------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS------------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC------------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            4799999999999999999999999932            3688999999999999999887754

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.50  E-value=4.1e-09  Score=71.18  Aligned_cols=49  Identities=24%  Similarity=0.471  Sum_probs=16.3

Q ss_pred             EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcc
Q 012477           44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE   98 (462)
Q Consensus        44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~   98 (462)
                      ..+|.||.+.+|.|||++|++||.|+++|||+|.+.+      +..|+|.|..+.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~~~~   52 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGP   52 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBSSC
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEecCcc
Confidence            3478899999999999999999999999999999864      467888887543

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.38  E-value=1.3e-07  Score=73.00  Aligned_cols=52  Identities=25%  Similarity=0.260  Sum_probs=46.7

Q ss_pred             eeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477          151 IGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD  214 (462)
Q Consensus       151 ~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  214 (462)
                      .|+|||++|.+|+.|++.|||+|.|..            ..|.|.|+++++..|..+|.+++.+
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d------------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGE------------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECS------------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeC------------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            488999999999999999999999843            2577889999999999999999976

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.16  E-value=3.5e-06  Score=67.00  Aligned_cols=76  Identities=21%  Similarity=0.399  Sum_probs=57.2

Q ss_pred             eEEEEEecCC------ccceeecCCCchHHHHHHhhCceEEEecCCCC----------CCCCCCC-CceEEEEcC-HHHH
Q 012477          370 FTTRLLVPTS------RIGCLIGKGGSIITEMRRLTKANIRILPKENL----------PKIASED-DEMVQISGD-LDLA  431 (462)
Q Consensus       370 ~t~~i~Vp~~------~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~----------P~~~~~~-~~~v~I~G~-~~~v  431 (462)
                      ++.+|.||-+      ++|.|||++|+++|+|+++|||+|.|-.+...          +...+.+ .=-|.|+++ ++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            6778899865      58999999999999999999999999765321          1001112 224777885 6899


Q ss_pred             HHHHHHHHHHHHhh
Q 012477          432 KDALIQVMTRLRAN  445 (462)
Q Consensus       432 ~~A~~~I~~~l~~~  445 (462)
                      ..|+.+|...|...
T Consensus        83 ~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          83 KKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999988653

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.95  E-value=1.5e-05  Score=63.22  Aligned_cols=77  Identities=27%  Similarity=0.399  Sum_probs=58.2

Q ss_pred             ceEEEEEEeCCc------eeeeecCCchHHHHHHhhcCceEEEecCCCC-------C---CcC-CCCCceEEEEcC-HHH
Q 012477          139 QVTAKLLVPSDQ------IGCVIGKGGQIVQNIRSETGAQIRILKDEHL-------P---SCA-LRSDELVQISGE-ASV  200 (462)
Q Consensus       139 ~~~~~l~ip~~~------~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-------p---~~~-~~~~r~v~I~G~-~~~  200 (462)
                      .++.+++||.+.      +|.|||++|+++|+|+++|||+|.|-.....       +   ... ...+=-|.|++. .+.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            357789999875      8999999999999999999999999754221       0   000 112235677775 789


Q ss_pred             HHHHHHHHHHHHhcC
Q 012477          201 VKKALCQIASRLHDN  215 (462)
Q Consensus       201 v~~A~~~I~~~l~~~  215 (462)
                      +..|+.+|..+|...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999763

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.86  E-value=4.4e-06  Score=67.16  Aligned_cols=73  Identities=22%  Similarity=0.265  Sum_probs=52.3

Q ss_pred             eEEEEEec------CCccceeecCCCchHHHHHHhhCceEEEecCCCCC--------C----CCC-CCCceEEEEcCH--
Q 012477          370 FTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP--------K----IAS-EDDEMVQISGDL--  428 (462)
Q Consensus       370 ~t~~i~Vp------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P--------~----~~~-~~~~~v~I~G~~--  428 (462)
                      +..+|+||      .+++|.|||++|+++|+|+++|||+|.|-.+...-        .    ..+ .++=-|.|+++.  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            45678888      35789999999999999999999999997764310        0    001 122347787752  


Q ss_pred             ----HHHHHHHHHHHHHH
Q 012477          429 ----DLAKDALIQVMTRL  442 (462)
Q Consensus       429 ----~~v~~A~~~I~~~l  442 (462)
                          ..+..|+.+|...|
T Consensus        82 ~~a~~kl~~A~~~I~~lL   99 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLL   99 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHc
Confidence                35788888887766

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.60  E-value=4e-05  Score=61.38  Aligned_cols=76  Identities=25%  Similarity=0.366  Sum_probs=55.7

Q ss_pred             eEEEEEEeC------CceeeeecCCchHHHHHHhhcCceEEEecCCCCCC-------------cCCCCCceEEEEcCH--
Q 012477          140 VTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPS-------------CALRSDELVQISGEA--  198 (462)
Q Consensus       140 ~~~~l~ip~------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~-------------~~~~~~r~v~I~G~~--  198 (462)
                      ++.+++||.      +++|.|||++|.++|+|+++|||+|.|-.......             .....+=-|.|++..  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            456788885      47899999999999999999999999976532100             001234467888752  


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 012477          199 ----SVVKKALCQIASRLHDN  215 (462)
Q Consensus       199 ----~~v~~A~~~I~~~l~~~  215 (462)
                          ..+.+|+.+|..+|...
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p~  102 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVPA  102 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHHHcCCC
Confidence                35888999999988654

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.31  E-value=0.0058  Score=42.31  Aligned_cols=39  Identities=38%  Similarity=0.471  Sum_probs=36.0

Q ss_pred             EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCC
Q 012477          141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE  179 (462)
Q Consensus       141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~  179 (462)
                      .+.+.||....+..|||+|.+++-...-||.+|.|...+
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~~   66 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIM   66 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEECC
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEcc
Confidence            678899999999999999999999999999999997653

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.16  E-value=0.0064  Score=42.09  Aligned_cols=38  Identities=37%  Similarity=0.534  Sum_probs=35.0

Q ss_pred             eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477          370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP  407 (462)
Q Consensus       370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~  407 (462)
                      -...+.||.+..+..|||+|.+++-..+.||.+|.|..
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            35779999999999999999999999999999999954

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.08  E-value=0.005  Score=42.48  Aligned_cols=39  Identities=21%  Similarity=0.204  Sum_probs=35.3

Q ss_pred             CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEc
Q 012477           41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG   79 (462)
Q Consensus        41 ~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~   79 (462)
                      +.-...+.||.+..+..|||+|.|++-..+-||.+|+|-
T Consensus        24 ~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~   62 (67)
T d2asba3          24 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR   62 (67)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CCcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEE
Confidence            445678999999999999999999999999999999984

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.00  E-value=0.0063  Score=41.98  Aligned_cols=39  Identities=36%  Similarity=0.417  Sum_probs=36.3

Q ss_pred             eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477          140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD  178 (462)
Q Consensus       140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~  178 (462)
                      -.+.+.||....+..|||+|.+++-..+-||.+|.|..+
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            378899999999999999999999999999999999775

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=91.41  E-value=0.099  Score=37.63  Aligned_cols=56  Identities=13%  Similarity=0.052  Sum_probs=44.0

Q ss_pred             EEEecCCccceeecCCCc-hHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHH
Q 012477          373 RLLVPTSRIGCLIGKGGS-IITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVM  439 (462)
Q Consensus       373 ~i~Vp~~~~g~IIGk~G~-~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~  439 (462)
                      -+.||..++..++|++++ .++.|.+.+++.|.|-.           +..|-|.|. ++....+...|.
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~-----------NGrIWi~~~~~~~~i~i~~aI~   61 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-----------NGKIWVKCEELSNTLACYRTIM   61 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-----------TTEEEEECSSHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec-----------CcEEEEECCCHHHHHHHHHHHH
Confidence            367899999999999998 79999999999999943           358999995 555544444443

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=86.81  E-value=0.33  Score=34.74  Aligned_cols=61  Identities=10%  Similarity=0.000  Sum_probs=47.3

Q ss_pred             EEEEeCCceeeeecCCch-HHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC-HHHHHHHHHHHHHHHhc
Q 012477          143 KLLVPSDQIGCVIGKGGQ-IVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHD  214 (462)
Q Consensus       143 ~l~ip~~~~g~IIGk~G~-~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~  214 (462)
                      .+-||..++.++||++++ .++.|.+.++++|-|-.           ...|-|.|. .+....+...|...-++
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~-----------NGrIWi~~~~~~~~i~i~~aI~~~e~~   66 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-----------NGKIWVKCEELSNTLACYRTIMECCQK   66 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-----------TTEEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec-----------CcEEEEECCCHHHHHHHHHHHHHHHHh
Confidence            467888999999999998 89999999999999844           346889995 66666655555544443

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.83  E-value=0.17  Score=36.87  Aligned_cols=31  Identities=10%  Similarity=0.236  Sum_probs=26.8

Q ss_pred             EEEEEeeCCccceeecCCchHHHHHHHHhCC
Q 012477           44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKS   74 (462)
Q Consensus        44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~   74 (462)
                      ..++.|....-|.|||++|+.|++|++.-.-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k   66 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQK   66 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHH
Confidence            4678899999999999999999999977543