Citrus Sinensis ID: 022800

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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--
Protein Sequence
MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNKKKCC
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHcHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHccccccccccccccEEEEEEccccccccHHHHHHHHcccccEEEEEEEccccccEEEEEEccHHHHHHHHHHHccccccccEEEEccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHccccHHHHHccccccccccccHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEcccccccHHHHHHHHHHcccEEEEEEEccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mdvdhvdhyrvlglpsgeegakLTEKEISKAYKWKALelhpdkrpddpdahdnfQKLKSSYEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEEREraafapdpavkaRQEEEKIARQLKEEIERIRAMHenkrtpaafasvketkqsgsggvgldkeKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSaagaatgsvcgnlsnpllvlplqpavatqipsapkpvetesiNNLVGAGYQAHEDAILEKLREKAKEKNKKKCC
Flexible Loop (DISEMBL)
mdvdhvdhyrvlglpsgeegaklteKEISKAYKWKALElhpdkrpddpdAHDNFQKLKSSYEILKDEKARKLFDDLLKIkrekqqrqsqqdgkrrkmMSDLEEreraafapdpavkarqeEEKIARQLKEEIERIRAmhenkrtpaafasvketkqsgsggvgldkekVLKVSWEKFGEDYTAERLREIFsefgkvedvviksskkkgsaLVVMATKSAAGAATGSVCGNLSNPLLVLPLQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREkakeknkkkcc
Low Complexity Region (SEG)
MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMatksaagaatgsVCGNLSNpllvlplqpavaTQIPSAPKPVETESINNLVGAGYQAHEDAILeklrekakeknkkkCC
Disordered region (IsUnstruct)
*******************************YKW************************************************************************************************************************************EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQPAVAT***************NLVGAGYQ***********************
Disordered Region (DISOPRED)
***DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKI********************************************************************************************VSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVL**********************************DAILE***************
Disordered Region (DISEMBL)
MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKR*****************************************KIARQLKEEIERIRAMHENKRTPAAFA************VGLDKEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLRE***********
Disordered Region (DISPRO)
*DVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPD***KARQEEEKIARQLKEEIERIRAMHENKRT*********************KEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP**************************QAHEDAILEKLREKAKEK*****C
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPxxxxxxxxxxxxxxxxxxxxxxxxxHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNKKKCC
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	292	2.2.26 [Sep-21-2011]
Q2KI83	304	DnaJ homolog subfamily C	yes	no	0.760	0.730	0.345	1e-20
Q9NVM6	304	DnaJ homolog subfamily C	yes	no	0.760	0.730	0.337	2e-18
Q9P7C6	289	Pre-mRNA-splicing factor	yes	no	0.732	0.740	0.297	2e-18
Q91WT4	303	DnaJ homolog subfamily C	yes	no	0.773	0.745	0.329	2e-17
Q6TUG0	358	DnaJ homolog subfamily B	no	no	0.215	0.175	0.455	2e-10
Q99KV1	358	DnaJ homolog subfamily B	no	no	0.215	0.175	0.455	2e-10
Q5RAJ6	358	DnaJ homolog subfamily B	no	no	0.215	0.175	0.455	2e-10
Q9UBS4	358	DnaJ homolog subfamily B	no	no	0.215	0.175	0.455	2e-10
P81999	358	DnaJ homolog subfamily B	no	no	0.215	0.175	0.455	3e-10
Q3ZBA6	358	DnaJ homolog subfamily B	no	no	0.215	0.175	0.455	3e-10

>sp|Q2KI83|DJC17_BOVIN DnaJ homolog subfamily C member 17 OS=Bos taurus GN=DNAJC17 PE=2 SV=1

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/243 (34%), Positives = 131/243 (53%), Gaps = 21/243 (8%)

Query: 5   HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEIL 64
            +D Y +LG+   EE A+  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L
Sbjct: 9   QMDLYALLGI---EEKAE--DKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVL 63

Query: 65  KDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKI 124
            D  AR  +D + K K++  +R  + D +R+K+  DLE RER A A        +EE   
Sbjct: 64  TDAAARAAYDKVRKAKKQAAERTQKLDERRKKVKLDLEARERQAQA---LGSEEEEESGS 120

Query: 125 ARQLKEEIERI-----RAMHENKR-TPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFG 178
           AR L++EIER+     R + E +R         +E + +G      +KE        K  
Sbjct: 121 ARTLEQEIERLREEGSRQLEEQQRLIREQIRQEQEQRLTGMAKNPENKETPKLKLKWKSK 180

Query: 179 ED------YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLS 232
           ++      Y+ + L ++F ++G+V ++V+ SSKK G+A+V  AT  AA  A  +  G + 
Sbjct: 181 KEAESQGGYSRDVLLQLFQKYGEVLNLVL-SSKKAGTAVVEFATVKAAELAVQNEVGLVD 239

Query: 233 NPL 235
           NPL
Sbjct: 240 NPL 242

Bos taurus (taxid: 9913)

>sp|Q9NVM6|DJC17_HUMAN DnaJ homolog subfamily C member 17 OS=Homo sapiens GN=DNAJC17 PE=1 SV=1

 Score = 93.2 bits (230), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 82/243 (33%), Positives = 125/243 (51%), Gaps = 21/243 (8%)

Query: 5   HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEIL 64
            +D Y +LG+       K  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L
Sbjct: 9   QMDLYALLGIEE-----KAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVL 63

Query: 65  KDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKAR------ 118
            D  AR  +D + K K++  +R  + D KR+K+  DLE RER A A +   +        
Sbjct: 64  TDAAARAAYDKVRKAKKQAAERTQKLDEKRKKVKLDLEARERQAQAQESEEEEESRSTRT 123

Query: 119 --QEEEKI----ARQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKV 172
             QE E++    +RQL+E+   IR     +R        + T+  G G   L  +   K 
Sbjct: 124 LEQEIERLREEGSRQLEEQQRLIREQIRQERDQRLRGKAENTE--GQGTPKLKLKWKCKK 181

Query: 173 SWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLS 232
             E  G  Y+ + L  +  ++G+V ++V+ SSKK G+A+V  AT  AA  A  +  G + 
Sbjct: 182 EDESKG-GYSKDVLLRLLQKYGEVLNLVL-SSKKPGTAVVEFATVKAAELAVQNEVGLVD 239

Query: 233 NPL 235
           NPL
Sbjct: 240 NPL 242

Homo sapiens (taxid: 9606)

>sp|Q9P7C6|CWC23_SCHPO Pre-mRNA-splicing factor cwf23 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cwf23 PE=1 SV=2

 Score = 93.2 bits (230), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 125/232 (53%), Gaps = 18/232 (7%)

Query: 4   DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEI 63
           D +D+Y +LG+    E A+  ++EI +A++  +L+ HPDK P+DP A + F  L+ +Y  
Sbjct: 6   DSIDYYELLGI---NEDAQ--DQEIHRAWRKTSLKYHPDKNPNDPKAAEKFHMLQLAYNA 60

Query: 64  LKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEK 123
           L D + RK +D     K  +++R+   + +R+ M+ DL ERER  +  D   K   E ++
Sbjct: 61  LIDVQLRKAYDSERFAKLARKRREEAFNFQRKSMVDDLRERERQFY--DSLEKKENERDR 118

Query: 124 IA---RQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVG-LDKEKVLKVSWE-KFG 178
           +    R L+EE   +R   EN+       S +  +++ S  +  LD+   +++ W+ K+ 
Sbjct: 119 LQEKLRALQEESANLRRQRENRLREEQEQSKRRKQETPSSKISELDRS--IRIRWKRKYA 176

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSS----KKKGSALVVMATKSAAGAATGS 226
           +      LR I+S FG +++VVI+      KK   +++V  T S+A +A  +
Sbjct: 177 DQVNDAYLRSIYSSFGTLQNVVIQKDISKEKKYVYSIIVFETLSSAYSAINA 228

Involved in pre-mRNA splicing. May be involved in endoplasmic reticulum-associated protein degradation (ERAD) and required for growth at low and high temperatures.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q91WT4|DJC17_MOUSE DnaJ homolog subfamily C member 17 OS=Mus musculus GN=Dnajc17 PE=2 SV=2

 Score = 89.7 bits (221), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 121/243 (49%), Gaps = 17/243 (6%)

Query: 5   HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEIL 64
            +D Y +LG+       K  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L
Sbjct: 9   QMDLYALLGIEE-----KAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVL 63

Query: 65  KDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVK-----ARQ 119
            D  AR  +D + K K++  +R  + D  R+K+  DLE RER A A     +     A  
Sbjct: 64  TDAAARAAYDKVRKAKKQAAERTQRLDENRKKVKLDLEARERQAQAHGSEEEEESRSATT 123

Query: 120 EEEKIARQLKEEI-----ERIRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSW 174
            E++IAR L+EE      E+ R + E  R          T+ +   G    K K      
Sbjct: 124 LEQEIAR-LREEGSRQLEEQQRLIQEQIRQDREQRLRGRTENTEGKGTPKLKLKWKCKKE 182

Query: 175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNP 234
           ++    Y+ + L  +  ++G+V ++V+ S KK G+A+V  AT  AA  A  +  G   NP
Sbjct: 183 DESQGGYSRDVLLRLLQKYGEVLNLVL-SRKKAGNAIVEFATVRAAELAVRNEVGLADNP 241

Query: 235 LLV 237
           L V
Sbjct: 242 LKV 244

Mus musculus (taxid: 10090)

>sp|Q6TUG0|DJB11_RAT DnaJ homolog subfamily B member 11 OS=Rattus norvegicus GN=Dnajb11 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D Y++LG+P        + K+I KAY+  AL+LHPD+ PDDP A + FQ L ++YE+L D
Sbjct: 25 DFYKILGVPRSA-----SIKDIKKAYRKLALQLHPDRNPDDPQAQEKFQDLGAAYEVLSD 79

Query: 67 EKARKLFD 74
           + RK +D
Sbjct: 80 SEKRKQYD 87

Serves as a co-chaperone for HSPA5. Binds directly to both unfolded proteins that are substrates for ERAD and nascent unfolded peptide chains, but dissociates from the HSPA5-unfolded protein complex before folding is completed. May help recruiting HSPA5 and other chaperones to the substrate. Stimulates HSPA5 ATPase activity.

Rattus norvegicus (taxid: 10116)

>sp|Q99KV1|DJB11_MOUSE DnaJ homolog subfamily B member 11 OS=Mus musculus GN=Dnajb11 PE=1 SV=1

 Score = 66.6 bits (161), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D Y++LG+P        + K+I KAY+  AL+LHPD+ PDDP A + FQ L ++YE+L D
Sbjct: 25 DFYKILGVPRSA-----SIKDIKKAYRKLALQLHPDRNPDDPQAQEKFQDLGAAYEVLSD 79

Query: 67 EKARKLFD 74
           + RK +D
Sbjct: 80 SEKRKQYD 87

Serves as a co-chaperone for HSPA5. Binds directly to both unfolded proteins that are substrates for ERAD and nascent unfolded peptide chains, but dissociates from the HSPA5-unfolded protein complex before folding is completed. May help recruiting HSPA5 and other chaperones to the substrate. Stimulates HSPA5 ATPase activity.

Mus musculus (taxid: 10090)

>sp|Q5RAJ6|DJB11_PONAB DnaJ homolog subfamily B member 11 OS=Pongo abelii GN=DNAJB11 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D Y++LG+P        + K+I KAY+  AL+LHPD+ PDDP A + FQ L ++YE+L D
Sbjct: 25 DFYKILGVPRSA-----SIKDIKKAYRKLALQLHPDRNPDDPQAQEKFQDLGAAYEVLSD 79

Query: 67 EKARKLFD 74
           + RK +D
Sbjct: 80 SEKRKQYD 87

Serves as a co-chaperone for HSPA5. Binds directly to both unfolded proteins that are substrates for ERAD and nascent unfolded peptide chains, but dissociates from the HSPA5-unfolded protein complex before folding is completed. May help recruiting HSPA5 and other chaperones to the substrate. Stimulates HSPA5 ATPase activity.

Pongo abelii (taxid: 9601)

>sp|Q9UBS4|DJB11_HUMAN DnaJ homolog subfamily B member 11 OS=Homo sapiens GN=DNAJB11 PE=1 SV=1

 Score = 66.6 bits (161), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D Y++LG+P        + K+I KAY+  AL+LHPD+ PDDP A + FQ L ++YE+L D
Sbjct: 25 DFYKILGVPRSA-----SIKDIKKAYRKLALQLHPDRNPDDPQAQEKFQDLGAAYEVLSD 79

Query: 67 EKARKLFD 74
           + RK +D
Sbjct: 80 SEKRKQYD 87

Serves as a co-chaperone for HSPA5. Binds directly to both unfolded proteins that are substrates for ERAD and nascent unfolded peptide chains, but dissociates from the HSPA5-unfolded protein complex before folding is completed. May help recruiting HSPA5 and other chaperones to the substrate. Stimulates HSPA5 ATPase activity.

Homo sapiens (taxid: 9606)

>sp|P81999|DJB11_CANFA DnaJ homolog subfamily B member 11 OS=Canis familiaris GN=DNAJB11 PE=1 SV=2

 Score = 65.9 bits (159), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D Y++LG+P        + K+I KAY+  AL+LHPD+ PDDP A + FQ L ++YE+L D
Sbjct: 25 DFYKILGVPR-----SASIKDIKKAYRKLALQLHPDRNPDDPRAQEKFQDLGAAYEVLSD 79

Query: 67 EKARKLFD 74
           + RK +D
Sbjct: 80 SEKRKQYD 87

Serves as a co-chaperone for HSPA5. Binds directly to both unfolded proteins that are substrates for ERAD and nascent unfolded peptide chains, but dissociates from the HSPA5-unfolded protein complex before folding is completed. May help recruiting HSPA5 and other chaperones to the substrate. Stimulates HSPA5 ATPase activity.

Canis familiaris (taxid: 9615)

>sp|Q3ZBA6|DJB11_BOVIN DnaJ homolog subfamily B member 11 OS=Bos taurus GN=DNAJB11 PE=2 SV=1

 Score = 65.9 bits (159), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D Y++LG+P        + K+I KAY+  AL+LHPD+ PDDP A + FQ L ++YE+L D
Sbjct: 25 DFYKILGVPR-----SASIKDIKKAYRKLALQLHPDRNPDDPRAQEKFQDLGAAYEVLSD 79

Query: 67 EKARKLFD 74
           + RK +D
Sbjct: 80 SEKRKQYD 87

Serves as a co-chaperone for HSPA5. Binds directly to both unfolded proteins that are substrates for ERAD and nascent unfolded peptide chains, but dissociates from the HSPA5-unfolded protein complex before folding is completed. May help recruiting HSPA5 and other chaperones to the substrate. Stimulates HSPA5 ATPase activity.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	292
225429187	286	PREDICTED: dnaJ homolog subfamily C memb	0.972	0.993	0.7	1e-107
297736401	341	unnamed protein product [Vitis vinifera]	0.972	0.832	0.7	1e-107
255563542	289	Pre-mRNA-splicing factor cwc23, putative	0.986	0.996	0.693	1e-106
449454237	290	PREDICTED: dnaJ homolog subfamily C memb	0.969	0.975	0.685	1e-106
449508808	290	PREDICTED: LOW QUALITY PROTEIN: dnaJ hom	0.969	0.975	0.681	1e-105
356575456	284	PREDICTED: dnaJ homolog subfamily C memb	0.958	0.985	0.692	1e-103
30689058	296	DNAJ heat shock N-terminal domain-contai	0.972	0.959	0.655	1e-101
356536396	287	PREDICTED: dnaJ homolog subfamily C memb	0.965	0.982	0.679	1e-100
8809700	349	unnamed protein product [Arabidopsis tha	0.938	0.785	0.671	1e-100
297812513	302	DNAJ heat shock N-terminal domain-contai	0.972	0.940	0.641	8e-99

>gi|225429187|ref|XP_002275857.1| PREDICTED: dnaJ homolog subfamily C member 17-like [Vitis vinifera]

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 203/290 (70%), Positives = 243/290 (83%), Gaps = 6/290 (2%)

Query: 1   MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSS 60
           MD++ VDHY VLGLPSGEEGAKL+EKEISKAY+ KALELHPDKRPDDP AH NFQKLK+S
Sbjct: 1   MDMN-VDHYNVLGLPSGEEGAKLSEKEISKAYRVKALELHPDKRPDDPQAHANFQKLKTS 59

Query: 61  YEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQE 120
           YEILKDEKARKLFDDLL++KRE+  RQ+Q D KRR+M+SDLEERERAA APDPA KAR+E
Sbjct: 60  YEILKDEKARKLFDDLLRVKREQFHRQAQYDVKRRRMVSDLEERERAANAPDPASKAREE 119

Query: 121 EEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQS--GSGGVGLDKEKVLKVSWEKFG 178
           EE+I ++LKEEI RIRAMH NK    +      T++     GG GL+KEKVLKVSWEK G
Sbjct: 120 EERITKKLKEEIARIRAMHANKGASGSRKEAPGTRKESVADGGGGLNKEKVLKVSWEKGG 179

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVL 238
           EDYTAE LRE+F++FG+VEDVV+KSS+KKGSALVVMA+K AA AATG+VCG++SNPLLVL
Sbjct: 180 EDYTAEGLREVFAKFGEVEDVVLKSSRKKGSALVVMASKEAAVAATGNVCGHISNPLLVL 239

Query: 239 PLQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNK 288
           PL+PAV  + P  P+ +E E  +NLVGAGYQ+ E+++L+KL +KA EK K
Sbjct: 240 PLEPAVVMEFP--PRSMEPEPSSNLVGAGYQSFEESVLKKL-QKAAEKQK 286

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736401|emb|CBI25124.3| unnamed protein product [Vitis vinifera]

 Score =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 203/290 (70%), Positives = 243/290 (83%), Gaps = 6/290 (2%)

Query: 1   MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSS 60
           MD++ VDHY VLGLPSGEEGAKL+EKEISKAY+ KALELHPDKRPDDP AH NFQKLK+S
Sbjct: 56  MDMN-VDHYNVLGLPSGEEGAKLSEKEISKAYRVKALELHPDKRPDDPQAHANFQKLKTS 114

Query: 61  YEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQE 120
           YEILKDEKARKLFDDLL++KRE+  RQ+Q D KRR+M+SDLEERERAA APDPA KAR+E
Sbjct: 115 YEILKDEKARKLFDDLLRVKREQFHRQAQYDVKRRRMVSDLEERERAANAPDPASKAREE 174

Query: 121 EEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQS--GSGGVGLDKEKVLKVSWEKFG 178
           EE+I ++LKEEI RIRAMH NK    +      T++     GG GL+KEKVLKVSWEK G
Sbjct: 175 EERITKKLKEEIARIRAMHANKGASGSRKEAPGTRKESVADGGGGLNKEKVLKVSWEKGG 234

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVL 238
           EDYTAE LRE+F++FG+VEDVV+KSS+KKGSALVVMA+K AA AATG+VCG++SNPLLVL
Sbjct: 235 EDYTAEGLREVFAKFGEVEDVVLKSSRKKGSALVVMASKEAAVAATGNVCGHISNPLLVL 294

Query: 239 PLQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNK 288
           PL+PAV  + P  P+ +E E  +NLVGAGYQ+ E+++L+KL +KA EK K
Sbjct: 295 PLEPAVVMEFP--PRSMEPEPSSNLVGAGYQSFEESVLKKL-QKAAEKQK 341

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563542|ref|XP_002522773.1| Pre-mRNA-splicing factor cwc23, putative [Ricinus communis] gi|223538011|gb|EEF39624.1| Pre-mRNA-splicing factor cwc23, putative [Ricinus communis]

 Score =  392 bits (1007), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 201/290 (69%), Positives = 237/290 (81%), Gaps = 2/290 (0%)

Query: 1   MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSS 60
           MD+D +DHY VLGL SGEEGAKLTE EISKAYK KALELHPDKR DDPDAH NFQKLKSS
Sbjct: 1   MDID-IDHYEVLGLASGEEGAKLTENEISKAYKKKALELHPDKRRDDPDAHANFQKLKSS 59

Query: 61  YEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQE 120
           YEILKDEKARKLFDDLL++KRE+     Q+D KR+KM+SDLE RERAAFAPDP  KAR+E
Sbjct: 60  YEILKDEKARKLFDDLLRVKRERYVHSFQRDSKRQKMVSDLEARERAAFAPDPVAKAREE 119

Query: 121 EEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGV-GLDKEKVLKVSWEKFGE 179
           E+ IAR+LKEEIERIRAMH NK   A  AS +E        V   D+EK+LKVSWEK GE
Sbjct: 120 EDMIARKLKEEIERIRAMHANKGAHATSASKREAVGVARESVNNTDREKMLKVSWEKGGE 179

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLP 239
           DY+AERL+E+FS+FG+VEDVVI SSKKK SALV MATK AA AATGSV G+L+NPLLVLP
Sbjct: 180 DYSAERLKELFSKFGEVEDVVISSSKKKRSALVQMATKEAAVAATGSVSGDLNNPLLVLP 239

Query: 240 LQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNKK 289
           ++PA+AT+ PS  +  E+  +NNLVG GY+A+ED+ILEKL++ A  +++K
Sbjct: 240 VKPAIATEFPSFQQQSESAHVNNLVGTGYKAYEDSILEKLQKAAAARSQK 289

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454237|ref|XP_004144862.1| PREDICTED: dnaJ homolog subfamily C member 17-like [Cucumis sativus]

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 198/289 (68%), Positives = 239/289 (82%), Gaps = 6/289 (2%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           VDHY +LGLPSGE+GAKLTEKEISKAY+ KALELHPDKRPDDP+AH NFQ LKSSYEILK
Sbjct: 3   VDHYAILGLPSGEQGAKLTEKEISKAYRAKALELHPDKRPDDPNAHANFQTLKSSYEILK 62

Query: 66  DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           DEKARKLFDDLL++KRE+ +RQS++D KR+KMM+DLE RER+AFAPDPA K  +EEEKIA
Sbjct: 63  DEKARKLFDDLLRVKREQHRRQSERDSKRQKMMTDLEARERSAFAPDPAAKELEEEEKIA 122

Query: 126 RQLKEEIERIRAMHENKRTPAAFASVKET-----KQSGSGGVGLDKEKVLKVSWEKFGED 180
           R+LKEEI RIRAMH  K  P  F   KET     K  G  G  +DKE++LKVSWEK GED
Sbjct: 123 RKLKEEIARIRAMHAKKGAPTTFPPKKETGGVGKKSDGDAGPTMDKERMLKVSWEKIGED 182

Query: 181 YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPL 240
           YTAE+LRE+FS+FG+VEDVVI+ +KKKGSA++VM++K AA A+T +V G+LSNPLLVLPL
Sbjct: 183 YTAEKLREMFSKFGEVEDVVIRHNKKKGSAVIVMSSKDAAVASTRAVLGDLSNPLLVLPL 242

Query: 241 QPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNKK 289
           QP  + ++PSA +  E   ++NLVGAGYQA ED+IL+KL +KA EK K+
Sbjct: 243 QPVSSVEMPSAERSPEHNRLDNLVGAGYQAFEDSILKKL-QKAGEKQKQ 290

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449508808|ref|XP_004163417.1| PREDICTED: LOW QUALITY PROTEIN: dnaJ homolog subfamily C member 17-like [Cucumis sativus]

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 197/289 (68%), Positives = 238/289 (82%), Gaps = 6/289 (2%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           VDHY +LGLPSGE+GAKLTEKEISKAY+ KALELHPDKRPDDP+AH NFQ LKSSYEILK
Sbjct: 3   VDHYAILGLPSGEQGAKLTEKEISKAYRAKALELHPDKRPDDPNAHANFQTLKSSYEILK 62

Query: 66  DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           DEKARKLFDDLL++KRE+ +RQS++D KR+KMM+DLE RER+AFAPDPA K  +EEE IA
Sbjct: 63  DEKARKLFDDLLRVKREQHRRQSERDSKRQKMMTDLEARERSAFAPDPAAKELEEEEXIA 122

Query: 126 RQLKEEIERIRAMHENKRTPAAFASVKET-----KQSGSGGVGLDKEKVLKVSWEKFGED 180
           R+LKEEI RIRAMH  K  P  F   KET     K  G  G  +DKE++LKVSWEK GED
Sbjct: 123 RKLKEEIARIRAMHAKKGAPTTFPPKKETGGVGKKSDGDAGPTMDKERMLKVSWEKIGED 182

Query: 181 YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPL 240
           YTAE+LRE+FS+FG+VEDVVI+ +KKKGSA++VM++K AA A+T +V G+LSNPLLVLPL
Sbjct: 183 YTAEKLREMFSKFGEVEDVVIRHNKKKGSAVIVMSSKDAAVASTRAVLGDLSNPLLVLPL 242

Query: 241 QPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNKK 289
           QP  + ++PSA +  E   ++NLVGAGYQA ED+IL+KL +KA EK K+
Sbjct: 243 QPVSSVEMPSAERSPEHNRLDNLVGAGYQAFEDSILKKL-QKAGEKQKQ 290

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575456|ref|XP_003555857.1| PREDICTED: dnaJ homolog subfamily C member 17-like [Glycine max]

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 196/283 (69%), Positives = 232/283 (81%), Gaps = 3/283 (1%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           +DHY VLGLPSGEEGAKLTEKEI+KAY+WKALELHPDKRPDDP+A  NFQ+L++SY+IL+
Sbjct: 5   MDHYAVLGLPSGEEGAKLTEKEINKAYRWKALELHPDKRPDDPNAAANFQQLRTSYDILR 64

Query: 66  DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           D+KARKLFDDLL++KRE++ R  Q+DGKRRKM+SDLE RER A APDPA K R+EE +IA
Sbjct: 65  DDKARKLFDDLLRVKRERELRNLQRDGKRRKMVSDLERRERDANAPDPAAKEREEEARIA 124

Query: 126 RQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTAER 185
           RQLKEEI RIRAMH  K    A A  KE    GS GV  D+EKVLKVSWEK GEDY+A++
Sbjct: 125 RQLKEEIARIRAMHGKKEEAPAAAPAKEKDSGGSSGV--DQEKVLKVSWEKVGEDYSADK 182

Query: 186 LREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQPAVA 245
           LRE+FS+FG+VEDVVIK SKKKGSALVVMA K  A AATGSV G+L+NPLLV+PL+PA  
Sbjct: 183 LRELFSKFGEVEDVVIKGSKKKGSALVVMAIKEGAVAATGSVIGHLANPLLVVPLKPASV 242

Query: 246 TQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNK 288
               S PK  ET  ++NLVGAGYQA ED++L+KL +KA EK +
Sbjct: 243 ADSSSVPKSAETTRMSNLVGAGYQAFEDSVLKKL-QKAAEKQR 284

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30689058|ref|NP_197749.2| DNAJ heat shock N-terminal domain-containing protein [Arabidopsis thaliana] gi|79328547|ref|NP_001031930.1| DNAJ heat shock N-terminal domain-containing protein [Arabidopsis thaliana] gi|22135988|gb|AAM91576.1| putative protein [Arabidopsis thaliana] gi|30023808|gb|AAP13437.1| At5g23590 [Arabidopsis thaliana] gi|332005804|gb|AED93187.1| DNAJ heat shock N-terminal domain-containing protein [Arabidopsis thaliana] gi|332005805|gb|AED93188.1| DNAJ heat shock N-terminal domain-containing protein [Arabidopsis thaliana]

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 190/290 (65%), Positives = 235/290 (81%), Gaps = 6/290 (2%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           VDHY VLGL SGEE  KLTEKEI+KAYK KAL+LHPDKRPDDPDAH+ FQ+LK+SYE+LK
Sbjct: 5   VDHYIVLGLASGEEALKLTEKEIAKAYKLKALDLHPDKRPDDPDAHEKFQRLKTSYEVLK 64

Query: 66  DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           DEKARKLFDDLL+I+REKQ ++SQ D KRRKMMSDLEERER+AF+P+P+ +A  EEE+IA
Sbjct: 65  DEKARKLFDDLLRIQREKQHKKSQVDSKRRKMMSDLEERERSAFSPNPSARAYDEEERIA 124

Query: 126 RQLKEEIERIRAMHENKR----TPAAFASVKETKQ-SGSGG-VGLDKEKVLKVSWEKFGE 179
           R+LKEEI+RIRA H  K+    TP +    K  ++ SG+G  V LDKE++LKVSWEK GE
Sbjct: 125 RKLKEEIDRIRARHAKKKSGFQTPESNVDEKRKEERSGAGASVQLDKERMLKVSWEKSGE 184

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLP 239
            YTA RLRE+FSEFG+VEDVVI+S+KKK SAL+VMATK  A AAT ++CGNLSNPLLV+P
Sbjct: 185 GYTAGRLREVFSEFGEVEDVVIRSTKKKCSALIVMATKDGAVAATRTLCGNLSNPLLVVP 244

Query: 240 LQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNKK 289
           LQ A  T   +A K  E E  +N+VGAG QA+EDA++++L + A ++ K+
Sbjct: 245 LQKAAQTDFLTAKKSAEAEPQSNIVGAGLQAYEDAVMQRLLQAAMDQKKR 294

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536396|ref|XP_003536724.1| PREDICTED: dnaJ homolog subfamily C member 17-like [Glycine max]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 193/284 (67%), Positives = 233/284 (82%), Gaps = 2/284 (0%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           +DHY VLGLPSGEEGAKLT+KEI+KAY+WKALELHPDKRPDD +A  NFQ+L++SY+IL+
Sbjct: 5   IDHYAVLGLPSGEEGAKLTDKEINKAYRWKALELHPDKRPDDANAAANFQQLRTSYDILR 64

Query: 66  DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           D+KARKLFDDLL++KR+++ R SQ+DGKRRKM+SDLE RER A APDPA K R+EE +IA
Sbjct: 65  DDKARKLFDDLLRVKRDRELRNSQRDGKRRKMVSDLERRERDANAPDPAAKEREEEARIA 124

Query: 126 RQLKEEIERIRAMHENKRTPAAFASVKETKQ-SGSGGVGLDKEKVLKVSWEKFGEDYTAE 184
           RQLKEEI RIRAMH  K   A   + K+ +   G GG G+D+EKVLKVSWEK GEDY A+
Sbjct: 125 RQLKEEIARIRAMHGKKEEAAVKPAAKKKESGGGGGGGGVDQEKVLKVSWEKVGEDYAAD 184

Query: 185 RLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQPAV 244
           +LRE+FS+FG VEDVVIK SKKKGSALVVMATK  A +ATGSV G+L+NPLLVLPL+PA 
Sbjct: 185 KLRELFSKFGAVEDVVIKGSKKKGSALVVMATKEGAVSATGSVIGHLANPLLVLPLKPAT 244

Query: 245 ATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNK 288
                S PK  ET  ++NLVGAGYQA ED++L+KL +KA EK +
Sbjct: 245 VADSSSVPKSAETTRMSNLVGAGYQAFEDSVLKKL-QKAAEKQR 287

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8809700|dbj|BAA97241.1| unnamed protein product [Arabidopsis thaliana]

 Score =  369 bits (948), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 188/280 (67%), Positives = 229/280 (81%), Gaps = 6/280 (2%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           VDHY VLGL SGEE  KLTEKEI+KAYK KAL+LHPDKRPDDPDAH+ FQ+LK+SYE+LK
Sbjct: 5   VDHYIVLGLASGEEALKLTEKEIAKAYKLKALDLHPDKRPDDPDAHEKFQRLKTSYEVLK 64

Query: 66  DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           DEKARKLFDDLL+I+REKQ ++SQ D KRRKMMSDLEERER+AF+P+P+ +A  EEE+IA
Sbjct: 65  DEKARKLFDDLLRIQREKQHKKSQVDSKRRKMMSDLEERERSAFSPNPSARAYDEEERIA 124

Query: 126 RQLKEEIERIRAMHENKR----TPAAFASVKETKQ-SGSGG-VGLDKEKVLKVSWEKFGE 179
           R+LKEEI+RIRA H  K+    TP +    K  ++ SG+G  V LDKE++LKVSWEK GE
Sbjct: 125 RKLKEEIDRIRARHAKKKSGFQTPESNVDEKRKEERSGAGASVQLDKERMLKVSWEKSGE 184

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLP 239
            YTA RLRE+FSEFG+VEDVVI+S+KKK SAL+VMATK  A AAT ++CGNLSNPLLV+P
Sbjct: 185 GYTAGRLREVFSEFGEVEDVVIRSTKKKCSALIVMATKDGAVAATRTLCGNLSNPLLVVP 244

Query: 240 LQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKL 279
           LQ A  T   +A K  E E  +N+VGAG QA+EDA++++L
Sbjct: 245 LQKAAQTDFLTAKKSAEAEPQSNIVGAGLQAYEDAVMQRL 284

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297812513|ref|XP_002874140.1| DNAJ heat shock N-terminal domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297319977|gb|EFH50399.1| DNAJ heat shock N-terminal domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  366 bits (939), Expect = 8e-99,   Method: Compositional matrix adjust.
 Identities = 186/290 (64%), Positives = 233/290 (80%), Gaps = 6/290 (2%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           VDHY VLGLPSGEE  KLT+KEI+KAYK KAL+LHPDKRPDDP AHD FQ+LK+SYE+LK
Sbjct: 5   VDHYIVLGLPSGEEALKLTDKEIAKAYKLKALDLHPDKRPDDPHAHDKFQRLKTSYEVLK 64

Query: 66  DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           DEKARKLFDDLL+I+REKQ ++SQ D KRRKMMSDLE+RER+AF+P PA +A  EEE+IA
Sbjct: 65  DEKARKLFDDLLRIQREKQHKKSQVDSKRRKMMSDLEQRERSAFSPHPAARAYDEEERIA 124

Query: 126 RQLKEEIERIRAMHENKR----TPAAFASVKETK-QSGSGG-VGLDKEKVLKVSWEKFGE 179
           R+LKEEIERIRA H  K+    TP +    K  + +SG+G  V LDK+++LKVSWEK GE
Sbjct: 125 RKLKEEIERIRARHAKKKSGFETPESGVDEKRKEDRSGTGASVQLDKDRMLKVSWEKIGE 184

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLP 239
            YTA RLR++FSEFG+VEDVVI+S+KKK SAL+VMATK  A AAT ++CG+LSNPLLV+P
Sbjct: 185 GYTAGRLRQVFSEFGEVEDVVIRSTKKKCSALIVMATKDGAVAATRTLCGDLSNPLLVVP 244

Query: 240 LQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLREKAKEKNKK 289
           LQ A      +A K  E E  +++VGAG QA+EDA++++LR+ A ++  +
Sbjct: 245 LQKAAQNDFLTAKKSAEAEPRSDIVGAGLQAYEDAVMQRLRKAAMDQKNR 294

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	292
TAIR|locus:2171736	296	AT5G23590 [Arabidopsis thalian	0.928	0.915	0.620	1.7e-84
UNIPROTKB|E1C0R0	304	DNAJC17 "Uncharacterized prote	0.684	0.657	0.364	2.2e-25
FB|FBgn0037882	299	CG17187 [Drosophila melanogast	0.640	0.625	0.368	2.9e-25
UNIPROTKB|Q2KI83	304	DNAJC17 "DnaJ homolog subfamil	0.674	0.648	0.363	4.6e-25
ZFIN|ZDB-GENE-040426-894	307	dnajc17 "DnaJ (Hsp40) homolog,	0.667	0.635	0.369	9.7e-25
UNIPROTKB|E2RGH7	304	DNAJC17 "Uncharacterized prote	0.678	0.651	0.351	1.2e-24
UNIPROTKB|Q9NVM6	304	DNAJC17 "DnaJ homolog subfamil	0.667	0.641	0.351	2e-24
UNIPROTKB|F1SST1	304	DNAJC17 "Uncharacterized prote	0.671	0.644	0.325	4.8e-23
MGI|MGI:1916658	303	Dnajc17 "DnaJ (Hsp40) homolog,	0.667	0.643	0.342	2.1e-22
RGD|1308015	303	Dnajc17 "DnaJ (Hsp40) homolog,	0.667	0.643	0.337	2.6e-22

TAIR|locus:2171736 AT5G23590 [Arabidopsis thaliana (taxid:3702)]

 Score = 846 (302.9 bits), Expect = 1.7e-84, P = 1.7e-84
 Identities = 172/277 (62%), Positives = 209/277 (75%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             VDHY VLGL SGEE  KLTEKEI+KAYK KAL+LHPDKRPDDPDAH+ FQ+LK+SYE+LK
Sbjct:     5 VDHYIVLGLASGEEALKLTEKEIAKAYKLKALDLHPDKRPDDPDAHEKFQRLKTSYEVLK 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
             DEKARKLFDDLL+I+REKQ ++SQ D KRRKMMSDLEERER+AF+P+P+ +A  EEE+IA
Sbjct:    65 DEKARKLFDDLLRIQREKQHKKSQVDSKRRKMMSDLEERERSAFSPNPSARAYDEEERIA 124

Query:   126 RQLKEEIERIRAMHENKR----TPAAFASVKETKQ-SGSGG-VGLDKEKVLKVSWEKFGE 179
             R+LKEEI+RIRA H  K+    TP +    K  ++ SG+G  V LDKE++LKVSWEK GE
Sbjct:   125 RKLKEEIDRIRARHAKKKSGFQTPESNVDEKRKEERSGAGASVQLDKERMLKVSWEKSGE 184

Query:   180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMXXXXXXXXXXXXVCGNLSNXXXXXX 239
              YTA RLRE+FSEFG+VEDVVI+S+KKK SAL+VM            +CGNLSN      
Sbjct:   185 GYTAGRLREVFSEFGEVEDVVIRSTKKKCSALIVMATKDGAVAATRTLCGNLSNPLLVVP 244

Query:   240 XXXXXXTQIPSAPKPVETESINNLVGAGYQAHEDAIL 276
                   T   +A K  E E  +N+VGAG QA+EDA++
Sbjct:   245 LQKAAQTDFLTAKKSAEAEPQSNIVGAGLQAYEDAVM 281

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0006457 "protein folding" evidence=IEA;ISS

GO:0031072 "heat shock protein binding" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

UNIPROTKB|E1C0R0 DNAJC17 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 82/225 (36%), Positives = 123/225 (54%)

Query:     2 DVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSY 61
             D+  +D Y +LG+     G K +EKE+ KAY+ KAL  HPDK PD+P A + F +L  + 
Sbjct:     6 DLLQLDLYGLLGV-----GEKASEKEVKKAYRQKALTCHPDKNPDNPQAAEVFHQLSQAL 60

Query:    62 EILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEE 121
              +L D  AR  +D + K K++  +R  + D KR+K+  DLE RER A A D      +EE
Sbjct:    61 AVLTDAAARAAYDKVRKAKKQAAERTQKLDEKRKKVKLDLEAREREAQARDN----EEEE 116

Query:   122 EKIARQLKEEIERIRA-----MHENKRTPAAFASVKETK----QSGSGGVGLDKEKVLKV 172
              +I R L++EI R+R      + E +R       ++  +    + GSG  G    K LK+
Sbjct:   117 IRITRTLEQEIIRLREEGSRQLEEQQRLIREQIQLERQQRIQGEIGSGAEGRVTPK-LKL 175

Query:   173 SWEKFGED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
              W+   ED     Y+ E L  I  ++G V +++I SS+K GSA+V
Sbjct:   176 KWKCRKEDETGGGYSKEVLLRILQKYGDVLNLLI-SSRKAGSAVV 219

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0037882 CG17187 [Drosophila melanogaster (taxid:7227)]

 Score = 287 (106.1 bits), Expect = 2.9e-25, P = 2.9e-25
 Identities = 73/198 (36%), Positives = 113/198 (57%)

Query:    25 EKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREKQ 84
             + EI KAY+ KALE HPDK PD+P A + F +L  + EIL DE AR  +D +LK K+  +
Sbjct:    23 QNEIRKAYRKKALECHPDKNPDNPKAVERFHELSKALEILTDESARAAYDKVLKAKKAAE 82

Query:    85 QRQSQQDGKRRKMMSDLEERERAAF----APDP-AVKARQEEEKIARQLKE-EIERIRAM 138
              R  Q DGKR+K+  +LEERERAA        P +  A+ +EE +  Q++    E  R +
Sbjct:    83 LRSRQLDGKRQKLKLELEERERAALHKLAKSQPYSTVAKSDEEVLHEQIERLRREGSRLL 142

Query:   139 HENKRT-PAAFA-SVKETKQSGSGGVGLDK-EKVLKVSWE-KFGEDYTAERLREIFSEFG 194
              E +R     F  +  E ++     V  D  +  +K+ W+ + G+DYT + L +   ++G
Sbjct:   143 EEEQRAMQEQFRRNHAEQQKLQQQPVQFDSAQHRIKMKWKAEPGQDYTQQELLKYLKKYG 202

Query:   195 KVEDVVIKSSKKKGSALV 212
              V  +V+ +SK++G A+V
Sbjct:   203 DVVALVV-NSKRRGRAMV 219

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

UNIPROTKB|Q2KI83 DNAJC17 "DnaJ homolog subfamily C member 17" [Bos taurus (taxid:9913)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 80/220 (36%), Positives = 127/220 (57%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             +D Y +LG+   EE A+  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L 
Sbjct:    10 MDLYALLGI---EEKAE--DKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLT 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEK-I 124
             D  AR  +D + K K++  +R  + D +R+K+  DLE RER A     A+ + +EEE   
Sbjct:    65 DAAARAAYDKVRKAKKQAAERTQKLDERRKKVKLDLEARERQA----QALGSEEEEESGS 120

Query:   125 ARQLKEEIERIRA-----MHENKRT-PAAFASVKETKQSGSGGVGLDKEKV-LKVSWE-- 175
             AR L++EIER+R      + E +R         +E + +G      +KE   LK+ W+  
Sbjct:   121 ARTLEQEIERLREEGSRQLEEQQRLIREQIRQEQEQRLTGMAKNPENKETPKLKLKWKSK 180

Query:   176 KFGED---YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
             K  E    Y+ + L ++F ++G+V ++V+ SSKK G+A+V
Sbjct:   181 KEAESQGGYSRDVLLQLFQKYGEVLNLVL-SSKKAGTAVV 219

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-894 dnajc17 "DnaJ (Hsp40) homolog, subfamily C, member 17" [Danio rerio (taxid:7955)]

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 82/222 (36%), Positives = 120/222 (54%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             +D Y +LG+ S       TEK+I KAY+ +AL  HPDK PD+P A + F +L  + E+L 
Sbjct:    10 MDLYALLGVESTS-----TEKQIKKAYRQRALSCHPDKNPDNPKAAELFHQLSQALEVLT 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
             D  A+  +D +   K++ ++R  + D KR+K+  DLE RER A      VKA  EE KI 
Sbjct:    65 DAAAKAAYDKVRAAKKQAEERNRKLDDKRKKIKLDLEARERRA----ENVKA--EEVKIT 118

Query:   126 RQLKEEIERIRA-----MHENKRTPAAFASVKETKQSG--SGGVGLDKEKV---LKVSWE 175
             R L+EEI R+R      + E +R        +    +   S  V      V   LK+ W+
Sbjct:   119 RTLEEEIARLREEGSRELQEQQRLIREQIERERDAHTNTDSSAVQQGSNNVTPKLKLKWK 178

Query:   176 KFGED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
                ED     Y+ E L+ +F ++G V +++I SSKKKGSA+V
Sbjct:   179 CKKEDESNAGYSHECLQNLFQKYGDVLNILI-SSKKKGSAVV 219

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RGH7 DNAJC17 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 281 (104.0 bits), Expect = 1.2e-24, P = 1.2e-24
 Identities = 77/219 (35%), Positives = 121/219 (55%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             +D Y +LG+   EE  K  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L 
Sbjct:    10 MDLYALLGI---EE--KAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLT 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
             D  AR  +D + K K++  +R  + D +R+K+  DLE RER A A        +EE +  
Sbjct:    65 DTAARAAYDKVRKAKKQAAERTQKLDERRKKVKLDLEARERQAQAHG---SDDEEESRST 121

Query:   126 RQLKEEIERIRA-----MHENKRT-PAAFASVKETKQSGSGGVGLDK-EKVLKVSWEKFG 178
             R L++EIER+R      + E +R         +E +  G      D+    LK+ W+   
Sbjct:   122 RTLEQEIERLREEGSRQLEEQQRLIQEQIRQEREQRLRGKAENPEDRGTPKLKLKWKCKK 181

Query:   179 ED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
             ED     Y+ + L ++F ++G+V ++V+ SSKK G+A+V
Sbjct:   182 EDESKGGYSRDVLLQLFQKYGEVLNLVL-SSKKAGTAVV 219

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9NVM6 DNAJC17 "DnaJ homolog subfamily C member 17" [Homo sapiens (taxid:9606)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 78/222 (35%), Positives = 121/222 (54%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             +D Y +LG+   EE  K  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L 
Sbjct:    10 MDLYALLGI---EE--KAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLT 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
             D  AR  +D + K K++  +R  + D KR+K+  DLE RER A A +      +EE +  
Sbjct:    65 DAAARAAYDKVRKAKKQAAERTQKLDEKRKKVKLDLEARERQAQAQE---SEEEEESRST 121

Query:   126 RQLKEEIERIRA-----MHENKRT-PAAFASVKETKQSGSG----GVGLDKEKVLKVSWE 175
             R L++EIER+R      + E +R         ++ +  G      G G  K   LK+ W+
Sbjct:   122 RTLEQEIERLREEGSRQLEEQQRLIREQIRQERDQRLRGKAENTEGQGTPK---LKLKWK 178

Query:   176 KFGED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
                ED     Y+ + L  +  ++G+V ++V+ SSKK G+A+V
Sbjct:   179 CKKEDESKGGYSKDVLLRLLQKYGEVLNLVL-SSKKPGTAVV 219

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1SST1 DNAJC17 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 72/221 (32%), Positives = 120/221 (54%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             +D Y +LG+     G K  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L 
Sbjct:    10 MDLYALLGI-----GEKAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLT 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
             D  AR  +D + K K++  +R  + D +R+K+  DLE RE  A          +EE + A
Sbjct:    65 DAAARAAYDKVRKAKKQAAERTQKLDERRKKVKLDLEARELQAQTHG---SEEEEESRSA 121

Query:   126 RQLKEEIERIRA-----MHENKRTPAAFASVKETKQSGSGGV--GLDKEKV--LKVSWEK 176
             R L++EIER+R      + E +R       +++ ++    G+   L+ +    LK+ W+ 
Sbjct:   122 RTLEQEIERLREEGSRQLEEQQRLIQE--QIRQEREQRLRGMTENLESKGTPKLKLKWKS 179

Query:   177 FGED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
               E      Y+ + L  +  ++G+V ++V+ SSKK G+A+V
Sbjct:   180 TKESESQGGYSKDVLLRLLQKYGEVLNLVL-SSKKAGTAVV 219

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1916658 Dnajc17 "DnaJ (Hsp40) homolog, subfamily C, member 17" [Mus musculus (taxid:10090)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 76/222 (34%), Positives = 118/222 (53%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             +D Y +LG+   EE  K  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L 
Sbjct:    10 MDLYALLGI---EE--KAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLT 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
             D  AR  +D + K K++  +R  + D  R+K+  DLE RER A A        +EE + A
Sbjct:    65 DAAARAAYDKVRKAKKQAAERTQRLDENRKKVKLDLEARERQAQAHG---SEEEEESRSA 121

Query:   126 RQLKEEIERIRA-----MHENKRT-PAAFASVKETKQSG----SGGVGLDKEKVLKVSWE 175
               L++EI R+R      + E +R         +E +  G    + G G  K   LK+ W+
Sbjct:   122 TTLEQEIARLREEGSRQLEEQQRLIQEQIRQDREQRLRGRTENTEGKGTPK---LKLKWK 178

Query:   176 KFGED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
                ED     Y+ + L  +  ++G+V ++V+ S KK G+A+V
Sbjct:   179 CKKEDESQGGYSRDVLLRLLQKYGEVLNLVL-SRKKAGNAIV 219

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

RGD|1308015 Dnajc17 "DnaJ (Hsp40) homolog, subfamily C, member 17" [Rattus norvegicus (taxid:10116)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 75/222 (33%), Positives = 118/222 (53%)

Query:     6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
             +D Y +LG+   EE  K  +KE+ KAY+ KAL  HPDK PD+P A + F +L  + E+L 
Sbjct:    10 MDLYALLGI---EE--KAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLT 64

Query:    66 DEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
             D  AR  +D + K +++  +R  + D KR+K+  DLE RER A A        +EE +  
Sbjct:    65 DAAARAAYDKVRKARKQAAERTQRLDEKRKKVKLDLEARERQAQAQGTE---EEEESRST 121

Query:   126 RQLKEEIERIRA-----MHENKRT-PAAFASVKETKQSG----SGGVGLDKEKVLKVSWE 175
               L++EI R+R      + E +R         +E +  G    + G G  K   LK+ W+
Sbjct:   122 TTLEQEIARLREEGSRQLEEQQRLIQEQIRQDREQRLRGRTENTEGKGTPK---LKLKWK 178

Query:   176 KFGED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
                ED     Y+ + L  +  ++G+V ++V+ S KK G+A+V
Sbjct:   179 CKKEDESQGGYSRDILLRLLQKYGEVLNLVL-SKKKAGNAIV 219

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00038614001 SubName- Full=Chromosome chr3 scaffold_95, whole genome shotgun sequence; (338 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	292
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	3e-24
pfam00226	63	pfam00226, DnaJ, DnaJ domain	3e-16
COG0484	371	COG0484, DnaJ, DnaJ-class molecular chaperone with	7e-14
cd06257	55	cd06257, DnaJ, DnaJ domain or J-domain	8e-14
PRK10767	371	PRK10767, PRK10767, chaperone protein DnaJ; Provis	3e-12
smart00271	60	smart00271, DnaJ, DnaJ molecular chaperone homolog	7e-12
PRK14279	392	PRK14279, PRK14279, chaperone protein DnaJ; Provis	3e-11
TIGR02349	354	TIGR02349, DnaJ_bact, chaperone protein DnaJ	4e-11
PRK14301	373	PRK14301, PRK14301, chaperone protein DnaJ; Provis	5e-11
PRK14295	389	PRK14295, PRK14295, chaperone protein DnaJ; Provis	1e-10
PRK14284	391	PRK14284, PRK14284, chaperone protein DnaJ; Provis	4e-10
PRK14281	397	PRK14281, PRK14281, chaperone protein DnaJ; Provis	7e-10
COG2214	237	COG2214, CbpA, DnaJ-class molecular chaperone [Pos	7e-09
PRK14289	386	PRK14289, PRK14289, chaperone protein DnaJ; Provis	7e-09
PRK14277	386	PRK14277, PRK14277, chaperone protein DnaJ; Provis	2e-08
PRK14294	366	PRK14294, PRK14294, chaperone protein DnaJ; Provis	2e-08
PRK14278	378	PRK14278, PRK14278, chaperone protein DnaJ; Provis	3e-08
PRK14297	380	PRK14297, PRK14297, chaperone protein DnaJ; Provis	1e-07
PRK14291	382	PRK14291, PRK14291, chaperone protein DnaJ; Provis	2e-07
PRK14298	377	PRK14298, PRK14298, chaperone protein DnaJ; Provis	4e-07
PRK14283	378	PRK14283, PRK14283, chaperone protein DnaJ; Provis	7e-07
PRK14285	365	PRK14285, PRK14285, chaperone protein DnaJ; Provis	1e-06
PRK14290	365	PRK14290, PRK14290, chaperone protein DnaJ; Provis	3e-06
PRK14286	372	PRK14286, PRK14286, chaperone protein DnaJ; Provis	3e-06
PTZ00037	421	PTZ00037, PTZ00037, DnaJ_C chaperone protein; Prov	5e-06
smart00360	73	smart00360, RRM, RNA recognition motif	6e-06
PRK14282	369	PRK14282, PRK14282, chaperone protein DnaJ; Provis	6e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-06
PRK14299	291	PRK14299, PRK14299, chaperone protein DnaJ; Provis	8e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-05
PRK14280	376	PRK14280, PRK14280, chaperone protein DnaJ; Provis	3e-05
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-05
PRK14300	372	PRK14300, PRK14300, chaperone protein DnaJ; Provis	6e-05
PRK14292	371	PRK14292, PRK14292, chaperone protein DnaJ; Provis	8e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	8e-05
PRK14276	380	PRK14276, PRK14276, chaperone protein DnaJ; Provis	1e-04
PRK10266	306	PRK10266, PRK10266, curved DNA-binding protein Cbp	1e-04
PRK14288	369	PRK14288, PRK14288, chaperone protein DnaJ; Provis	2e-04
PRK14296	372	PRK14296, PRK14296, chaperone protein DnaJ; Provis	2e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.001
PRK14287	371	PRK14287, PRK14287, chaperone protein DnaJ; Provis	0.001
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.002
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.003
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	0.004
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.004

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 92.7 bits (231), Expect = 3e-24
 Identities = 41/75 (54%), Positives = 52/75 (69%), Gaps = 3/75 (4%)

Query: 168 KVLKVSW--EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG 225
           + LKV W  +K   DY+ + LR+IFS++G V DVV+ SSKKKGSA+V  A+K AA AA  
Sbjct: 1   RRLKVKWKRKKGNGDYSEDELRKIFSKYGDVSDVVV-SSKKKGSAIVEFASKKAAEAAVE 59

Query: 226 SVCGNLSNPLLVLPL 240
           + CG  SNPLLV  L
Sbjct: 60  NECGLPSNPLLVSWL 74

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|215804 pfam00226, DnaJ, DnaJ domain

 Score = 71.0 bits (175), Expect = 3e-16
 Identities = 27/68 (39%), Positives = 44/68 (64%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+P        +++EI KAY+  AL+ HPDK P DP A + F+++  +YE+L D
Sbjct: 1  DYYEILGVPRD-----ASDEEIKKAYRKLALKYHPDKNPGDPAAEEKFKEINEAYEVLSD 55

Query: 67 EKARKLFD 74
           + R ++D
Sbjct: 56 PEKRAIYD 63

DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature. Length = 63

>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]

 Score = 70.7 bits (174), Expect = 7e-14
 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           D+Y +LG+         +E+EI KAY+  A + HPD+ P D +A + F+++  +YE+L 
Sbjct: 4  RDYYEILGVSKDA-----SEEEIKKAYRKLAKKYHPDRNPGDKEAEEKFKEINEAYEVLS 58

Query: 66 DEKARKLFD 74
          D + R  +D
Sbjct: 59 DPEKRAAYD 67

Length = 371

>gnl|CDD|99751 cd06257, DnaJ, DnaJ domain or J-domain

 Score = 64.5 bits (158), Expect = 8e-14
 Identities = 26/60 (43%), Positives = 41/60 (68%), Gaps = 5/60 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+P        +++EI KAY+  AL+ HPDK PDDP+A + F+++  +YE+L D
Sbjct: 1  DYYDILGVPPD-----ASDEEIKKAYRKLALKYHPDKNPDDPEAEEKFKEINEAYEVLSD 55

DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification. Length = 55

>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional

 Score = 65.9 bits (162), Expect = 3e-12
 Identities = 27/68 (39%), Positives = 43/68 (63%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLG+      A  +E EI KAY+  A++ HPD+ P D +A + F+++K +YE+L D
Sbjct: 5  DYYEVLGV---SRNA--SEDEIKKAYRKLAMKYHPDRNPGDKEAEEKFKEIKEAYEVLSD 59

Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 60 PQKRAAYD 67

Length = 371

>gnl|CDD|197617 smart00271, DnaJ, DnaJ molecular chaperone homology domain

 Score = 59.2 bits (144), Expect = 7e-12
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 6/64 (9%)

Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEIL 64
           D+Y +LG+P        +  EI KAY+  AL+ HPDK P D  +A + F+++  +YE+L
Sbjct: 1  TDYYEILGVPRD-----ASLDEIKKAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVL 55

Query: 65 KDEK 68
           D +
Sbjct: 56 SDPE 59

Length = 60

>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional

 Score = 63.2 bits (154), Expect = 3e-11
 Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D Y+ LG+ S       + +EI KAY+  A ELHPD  P DP A + F+ +  ++++L D
Sbjct: 10 DFYKELGVSS-----DASAEEIKKAYRKLARELHPDANPGDPAAEERFKAVSEAHDVLSD 64

Query: 67 EKARKLFDDL 76
             RK +D+ 
Sbjct: 65 PAKRKEYDET 74

Length = 392

>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ

 Score = 62.2 bits (152), Expect = 4e-11
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+         +E+EI KAY+  A + HPD+   D +A + F+++  +YE+L D
Sbjct: 1  DYYEILGVSKDA-----SEEEIKKAYRKLAKKYHPDRNK-DKEAEEKFKEINEAYEVLSD 54

Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 55 PEKRAQYD 62

This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family. Length = 354

>gnl|CDD|237668 PRK14301, PRK14301, chaperone protein DnaJ; Provisional

 Score = 62.5 bits (152), Expect = 5e-11
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 5/71 (7%)

Query: 4  DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEI 63
             D+Y VLG+         +E EI KAY+  AL+ HPD+ PD+P+A   F++   +YE+
Sbjct: 2  SQRDYYEVLGV-----SRDASEDEIKKAYRKLALQYHPDRNPDNPEAEQKFKEAAEAYEV 56

Query: 64 LKDEKARKLFD 74
          L+D + R  +D
Sbjct: 57 LRDAEKRARYD 67

Length = 373

>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional

 Score = 61.0 bits (148), Expect = 1e-10
 Identities = 29/69 (42%), Positives = 42/69 (60%), Gaps = 5/69 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y+VLG+P        TE EI KAY+  A E HPD    D  A + F+++  +Y++L D
Sbjct: 10 DYYKVLGVPK-----DATEAEIKKAYRKLAREYHPDANKGDAKAEERFKEISEAYDVLSD 64

Query: 67 EKARKLFDD 75
          EK RK +D+
Sbjct: 65 EKKRKEYDE 73

Length = 389

>gnl|CDD|237658 PRK14284, PRK14284, chaperone protein DnaJ; Provisional

 Score = 59.5 bits (144), Expect = 4e-10
 Identities = 24/68 (35%), Positives = 41/68 (60%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+         + +EI KAY+  A++ HPDK P D +A   F+++  +YE+L D
Sbjct: 2  DYYTILGVSKTA-----SPEEIKKAYRKLAVKYHPDKNPGDAEAEKRFKEVSEAYEVLSD 56

Query: 67 EKARKLFD 74
           + R+ +D
Sbjct: 57 AQKRESYD 64

Length = 391

>gnl|CDD|237657 PRK14281, PRK14281, chaperone protein DnaJ; Provisional

 Score = 59.1 bits (143), Expect = 7e-10
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLG+          + EI KAY+  AL+ HPDK PD+ +A ++F+++  +YE+L +
Sbjct: 4  DYYEVLGV-----SRSADKDEIKKAYRKLALKYHPDKNPDNKEAEEHFKEVNEAYEVLSN 58

Query: 67 EKARKLFD 74
          +  R+ +D
Sbjct: 59 DDKRRRYD 66

Length = 397

>gnl|CDD|225124 COG2214, CbpA, DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones]

 Score = 54.8 bits (131), Expect = 7e-09
 Identities = 40/214 (18%), Positives = 78/214 (36%), Gaps = 11/214 (5%)

Query: 1   MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDN-FQKLKS 59
           M  D +D+Y +LG+P        + +EI KAY+  AL+ HPD+ P DP   +  F+++  
Sbjct: 1   MMSDLLDYYEILGVPPNA-----SLEEIKKAYRKLALKYHPDRNPGDPKVAEEKFKEINE 55

Query: 60  SYEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQ 119
           +YEIL D + R  +D +        +   +      +    L                 +
Sbjct: 56  AYEILSDPERRAEYDKIGADNYFPGKSYRESAAFPIEGSLQLTGLYEEWRG---KRNKTE 112

Query: 120 EEEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGE 179
            +  +A  L   +  + A        AA  S    ++  +  +  + E+ L    +    
Sbjct: 113 RKASLADLLSRGLSGLAAALSLFADEAALRSGSLRRRDLAANLADNFEEALAGVKKAVAR 172

Query: 180 D--YTAERLREIFSEFGKVEDVVIKSSKKKGSAL 211
                 +   +  +  GK   +       +G+  
Sbjct: 173 LLGKALKSTIKAGALEGKALRLKGLLKSARGALG 206

Length = 237

>gnl|CDD|237660 PRK14289, PRK14289, chaperone protein DnaJ; Provisional

 Score = 55.6 bits (134), Expect = 7e-09
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLG+         T  EI KAY+ KA++ HPDK P D +A + F++   +Y++L D
Sbjct: 6  DYYEVLGVSK-----TATVDEIKKAYRKKAIQYHPDKNPGDKEAEEKFKEAAEAYDVLSD 60

Query: 67 EKARKLFDDL 76
             R  +D  
Sbjct: 61 PDKRSRYDQF 70

Length = 386

>gnl|CDD|184599 PRK14277, PRK14277, chaperone protein DnaJ; Provisional

 Score = 54.4 bits (131), Expect = 2e-08
 Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+         TE+EI KAY+  A + HPD  P D +A   F+++  +YEIL D
Sbjct: 6  DYYEILGVDRNA-----TEEEIKKAYRRLAKKYHPDLNPGDKEAEQKFKEINEAYEILSD 60

Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 61 PQKRAQYD 68

Length = 386

>gnl|CDD|237664 PRK14294, PRK14294, chaperone protein DnaJ; Provisional

 Score = 54.4 bits (131), Expect = 2e-08
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+      A  +E+EI K+Y+  A++ HPD+ P D +A + F++   +YE+L D
Sbjct: 5  DYYEILGV---TRDA--SEEEIKKSYRKLAMKYHPDRNPGDKEAEELFKEAAEAYEVLSD 59

Query: 67 EKARKLFD 74
           K R ++D
Sbjct: 60 PKKRGIYD 67

Length = 366

>gnl|CDD|237654 PRK14278, PRK14278, chaperone protein DnaJ; Provisional

 Score = 53.9 bits (130), Expect = 3e-08
 Identities = 25/68 (36%), Positives = 42/68 (61%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+      A  ++ EI +AY+  A ELHPD  P D +A + F+++  +YE+L D
Sbjct: 4  DYYGLLGV---SRNA--SDAEIKRAYRKLARELHPDVNP-DEEAQEKFKEISVAYEVLSD 57

Query: 67 EKARKLFD 74
           + R++ D
Sbjct: 58 PEKRRIVD 65

Length = 378

>gnl|CDD|184611 PRK14297, PRK14297, chaperone protein DnaJ; Provisional

 Score = 52.1 bits (125), Expect = 1e-07
 Identities = 24/68 (35%), Positives = 44/68 (64%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLGL   E+GA  ++ EI KA++  A++ HPDK   + +A + F+++  +Y++L D
Sbjct: 5  DYYEVLGL---EKGA--SDDEIKKAFRKLAIKYHPDKNKGNKEAEEKFKEINEAYQVLSD 59

Query: 67 EKARKLFD 74
           + +  +D
Sbjct: 60 PQKKAQYD 67

Length = 380

>gnl|CDD|237661 PRK14291, PRK14291, chaperone protein DnaJ; Provisional

 Score = 51.7 bits (124), Expect = 2e-07
 Identities = 24/68 (35%), Positives = 42/68 (61%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+         T++EI KAY+  A + HPD   + P+A + F+++  +Y++L D
Sbjct: 4  DYYEILGVSRNA-----TQEEIKKAYRRLARKYHPDFNKN-PEAEEKFKEINEAYQVLSD 57

Query: 67 EKARKLFD 74
           + RKL+D
Sbjct: 58 PEKRKLYD 65

Length = 382

>gnl|CDD|184612 PRK14298, PRK14298, chaperone protein DnaJ; Provisional

 Score = 50.6 bits (121), Expect = 4e-07
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LGL         + ++I KAY+  A++ HPDK   +PDA + F+++  +Y +L D
Sbjct: 6  DYYEILGLSKDA-----SVEDIKKAYRKLAMKYHPDKN-KEPDAEEKFKEISEAYAVLSD 59

Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 60 AEKRAQYD 67

Length = 377

>gnl|CDD|184604 PRK14283, PRK14283, chaperone protein DnaJ; Provisional

 Score = 49.4 bits (118), Expect = 7e-07
 Identities = 22/68 (32%), Positives = 40/68 (58%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLG+    +     +KEI KAY+  A + HPD   ++  A + F+++  +Y +L D
Sbjct: 6  DYYEVLGVDRNAD-----KKEIKKAYRKLARKYHPDVS-EEEGAEEKFKEISEAYAVLSD 59

Query: 67 EKARKLFD 74
          ++ R+ +D
Sbjct: 60 DEKRQRYD 67

Length = 378

>gnl|CDD|172773 PRK14285, PRK14285, chaperone protein DnaJ; Provisional

 Score = 48.8 bits (116), Expect = 1e-06
 Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LGL  G      ++ EI KAY+  A++ HPDK   + +A   F++   +YE+L D
Sbjct: 4  DYYEILGLSKGA-----SKDEIKKAYRKIAIKYHPDKNKGNKEAESIFKEATEAYEVLID 58

Query: 67 EKARKLFD 74
          +  R  +D
Sbjct: 59 DNKRAQYD 66

Length = 365

>gnl|CDD|172778 PRK14290, PRK14290, chaperone protein DnaJ; Provisional

 Score = 47.6 bits (113), Expect = 3e-06
 Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 6/70 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD-PDAHDNFQKLKSSYEILK 65
          D+Y++LG+         ++++I KA++  A + HPD  P +  +A + F+++  +YE+L 
Sbjct: 4  DYYKILGVDRNA-----SQEDIKKAFRELAKKWHPDLHPGNKAEAEEKFKEISEAYEVLS 58

Query: 66 DEKARKLFDD 75
          D + R+ +D 
Sbjct: 59 DPQKRRQYDQ 68

Length = 365

>gnl|CDD|172774 PRK14286, PRK14286, chaperone protein DnaJ; Provisional

 Score = 47.7 bits (113), Expect = 3e-06
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 8  HYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDE 67
          +Y +LG+          ++EI  AY+  A++ HPDK   + ++ + F++   +YEIL+D 
Sbjct: 6  YYDILGVSKSA-----NDEEIKSAYRKLAIKYHPDKNKGNKESEEKFKEATEAYEILRDP 60

Query: 68 KARKLFDDLLK 78
          K R+ +D   K
Sbjct: 61 KKRQAYDQFGK 71

Length = 372

>gnl|CDD|240236 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional

 Score = 47.1 bits (112), Expect = 5e-06
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 9/74 (12%)

Query: 2  DVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSY 61
          +VD+   Y VL L         T  EI KAY+  A++ HPDK  D     + F+++  +Y
Sbjct: 24 EVDNEKLYEVLNLSK-----DCTTSEIKKAYRKLAIKHHPDKGGDP----EKFKEISRAY 74

Query: 62 EILKDEKARKLFDD 75
          E+L D + RK++D+
Sbjct: 75 EVLSDPEKRKIYDE 88

Length = 421

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
            D T E LRE+FS+FGKVE V +    ++ K KG A V   ++  A  A
Sbjct: 9   PDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKA 57

Length = 73

>gnl|CDD|184603 PRK14282, PRK14282, chaperone protein DnaJ; Provisional

 Score = 46.7 bits (111), Expect = 6e-06
 Identities = 23/69 (33%), Positives = 42/69 (60%), Gaps = 6/69 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD-PDAHDNFQKLKSSYEILK 65
          D+Y +LG+         T++EI +AYK    E HPD+ P++  +A   F++++ +YE+L 
Sbjct: 5  DYYEILGVSRNA-----TQEEIKRAYKRLVKEWHPDRHPENRKEAEQKFKEIQEAYEVLS 59

Query: 66 DEKARKLFD 74
          D + R ++D
Sbjct: 60 DPQKRAMYD 68

Length = 369

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 43.1 bits (102), Expect = 7e-06
 Identities = 21/48 (43%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
            D T E LRE+FS+FG++E V I   K  K KG A V   +   A  A
Sbjct: 8   PDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKA 55

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|237667 PRK14299, PRK14299, chaperone protein DnaJ; Provisional

 Score = 46.1 bits (109), Expect = 8e-06
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+P        ++ EI KA+K  A + HPD     P A + F+++  +Y +L D
Sbjct: 5  DYYAILGVPKNA-----SQDEIKKAFKKLARKYHPDVN-KSPGAEEKFKEINEAYTVLSD 58

Query: 67 EKARKLFD 74
           + R+++D
Sbjct: 59 PEKRRIYD 66

Length = 291

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 42.5 bits (101), Expect = 9e-06
 Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 176 KFGEDYTAERLREIFSEFGKVEDVVIKSSKK--KGSALVVMATKSAAGAA 223
                 T E LRE FS +GKVE V +  +K   +G A V  A+   A AA
Sbjct: 5   NLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAA 54

k.a. RRM, RBD, or RNP domain). Length = 69

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 4/48 (8%)

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKK----KGSALVVMATKSAAGAA 223
             T + LR+ FS+FG++E+ V+ + ++    +G   V    K +A  A
Sbjct: 11  HTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|237656 PRK14280, PRK14280, chaperone protein DnaJ; Provisional

 Score = 44.7 bits (106), Expect = 3e-05
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLG+         ++ EI KAY+  + + HPD    +  A + F+++  +YE+L D
Sbjct: 5  DYYEVLGVSKSA-----SKDEIKKAYRKLSKKYHPDIN-KEEGADEKFKEISEAYEVLSD 58

Query: 67 EKARKLFD 74
          ++ R  +D
Sbjct: 59 DQKRAQYD 66

Length = 376

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 177 FGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAA 223
              D T E L+++FS+FG +E + I      + KG A V    +  A  A
Sbjct: 6   LPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKA 55

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|172788 PRK14300, PRK14300, chaperone protein DnaJ; Provisional

 Score = 43.5 bits (102), Expect = 6e-05
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 6/79 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y++LG+      A     ++ KAY   A + HPD   D  DA   F+++ ++Y++LKD
Sbjct: 4  DYYQILGVSKTASQA-----DLKKAYLKLAKQYHPDT-TDAKDAEKKFKEINAAYDVLKD 57

Query: 67 EKARKLFDDLLKIKREKQQ 85
          E+ R  +D       + QQ
Sbjct: 58 EQKRAAYDRFGHDAFQNQQ 76

Length = 372

>gnl|CDD|237662 PRK14292, PRK14292, chaperone protein DnaJ; Provisional

 Score = 43.3 bits (102), Expect = 8e-05
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
          +D+Y +LG+            EI  AY+  AL+ HPD+   +  A + F ++  +Y +L 
Sbjct: 2  MDYYELLGVSRTASAD-----EIKSAYRKLALKYHPDRNK-EKGAAEKFAQINEAYAVLS 55

Query: 66 DEKARKLFD 74
          D + R  +D
Sbjct: 56 DAEKRAHYD 64

Length = 371

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 39.8 bits (94), Expect = 8e-05
 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 186 LREIFSEFGKVEDVVI-KSSKKKGSALVVMATKSAAGAA 223
           L  +FS+FG V D+V  K+ K +G A VV     +A  A
Sbjct: 20  LYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNA 58

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional

 Score = 42.8 bits (101), Expect = 1e-04
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          ++Y  LG+         ++ EI KAY+  + + HPD    +P A + +++++ +YE L D
Sbjct: 5  EYYDRLGV-----SKDASQDEIKKAYRKLSKKYHPDIN-KEPGAEEKYKEVQEAYETLSD 58

Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 59 PQKRAAYD 66

Length = 380

>gnl|CDD|182347 PRK10266, PRK10266, curved DNA-binding protein CbpA; Provisional

 Score = 42.5 bits (100), Expect = 1e-04
 Identities = 27/87 (31%), Positives = 46/87 (52%), Gaps = 7/87 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y ++G+   +    L  K I  AY+  A + HPD    +PDA   F+++  ++E+L D
Sbjct: 5  DYYAIMGV---KPTDDL--KTIKTAYRRLARKYHPDVS-KEPDAEARFKEVAEAWEVLSD 58

Query: 67 EKARKLFDDLLKIKREKQ-QRQSQQDG 92
          E+ R  +D L + + + Q  RQ Q   
Sbjct: 59 EQRRAEYDQLWQHRNDPQFNRQFQHGD 85

Length = 306

>gnl|CDD|172776 PRK14288, PRK14288, chaperone protein DnaJ; Provisional

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 25 EKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREKQ 84
          ++ I K+Y+  AL+ HPD+   D +A + F+ +  +Y +L DEK R L+D   K K   Q
Sbjct: 17 QETIKKSYRKLALKYHPDRNAGDKEAEEKFKLINEAYGVLSDEKKRALYDRYGK-KGLNQ 75

Query: 85 QRQSQQD 91
             SQ D
Sbjct: 76 AGASQSD 82

Length = 369

>gnl|CDD|237666 PRK14296, PRK14296, chaperone protein DnaJ; Provisional

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLG+         +E+EI +AY+  A + HPD     PDAHD   ++  + ++L D
Sbjct: 5  DYYEVLGVSKTA-----SEQEIRQAYRKLAKQYHPDLN-KSPDAHDKMVEINEAADVLLD 58

Query: 67 EKARKLFD 74
          +  RK +D
Sbjct: 59 KDKRKQYD 66

Length = 372

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 9/66 (13%)

Query: 181 YTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAAT----GSV-CGNL 231
            T E +R +F E+G +E+V I     + + KG A V  +++  A  A     G V     
Sbjct: 11  ATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGA 70

Query: 232 SNPLLV 237
           S PL V
Sbjct: 71  SRPLQV 76

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)

Query: 186 LREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           L ++FS FG VE + +   KK G A V  +T+ AA  A
Sbjct: 1   LYKLFSPFGNVEKIKL-LKKKPGFAFVEFSTEEAAEKA 37

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)

Query: 182 TAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
           T   L+++FS FG V +V I      KKKG A V   +K+ A  A
Sbjct: 12  TEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKA 56

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 7/49 (14%)

Query: 182 TAERLREIFSEFGKVEDVVI-------KSSKKKGSALVVMATKSAAGAA 223
             + LR IFS+FG+VE + I       +     G A V     S+A  A
Sbjct: 13  DEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|237659 PRK14287, PRK14287, chaperone protein DnaJ; Provisional

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y VLG+         +  E+ KAY+  A + HPD     PDA D F+++K +Y+ L D
Sbjct: 5  DYYEVLGVDRNA-----SVDEVKKAYRKLARKYHPDVN-KAPDAEDKFKEVKEAYDTLSD 58

Query: 67 EKARKLFD 74
           + +  +D
Sbjct: 59 PQKKAHYD 66

Length = 371

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 5/48 (10%)

Query: 181 YTAER-LREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           YT ER LRE+FS +G +E V +    K+ + +G   V   +   A  A
Sbjct: 10  YTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEA 57

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 5/55 (9%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS---VCGN 230
           E     +L E FS+FG + ++ +  + +  SALV  +T   A  A  S   V  N
Sbjct: 12  ELNNITKLNEHFSKFGTIVNIQVNYNPE--SALVQFSTSEEAKKAYRSPEAVFNN 64

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 177 FGEDYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
            GED   E+L+E+F ++GK+    +      K KG   V      AA  A
Sbjct: 9   LGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKA 58

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           T E L+++F +FG+V    +    ++ + +G   V M T   A AA
Sbjct: 12  TEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	292
KOG0691	296	consensus Molecular chaperone (DnaJ superfamily) [	99.95
COG0484	371	DnaJ DnaJ-class molecular chaperone with C-termina	99.87
KOG0713	336	consensus Molecular chaperone (DnaJ superfamily) [	99.87
PRK14288	369	chaperone protein DnaJ; Provisional	99.77
PRK14279	392	chaperone protein DnaJ; Provisional	99.75
KOG0716	279	consensus Molecular chaperone (DnaJ superfamily) [	99.74
PRK14296	372	chaperone protein DnaJ; Provisional	99.74
KOG0712	337	consensus Molecular chaperone (DnaJ superfamily) [	99.73
PRK14286	372	chaperone protein DnaJ; Provisional	99.73
PRK14277	386	chaperone protein DnaJ; Provisional	99.7
PRK14285	365	chaperone protein DnaJ; Provisional	99.7
PF00226	64	DnaJ: DnaJ domain; InterPro: IPR001623 The prokary	99.7
PRK14295	389	chaperone protein DnaJ; Provisional	99.69
PRK14282	369	chaperone protein DnaJ; Provisional	99.69
PRK14294	366	chaperone protein DnaJ; Provisional	99.69
PRK14301	373	chaperone protein DnaJ; Provisional	99.69
PRK14297	380	chaperone protein DnaJ; Provisional	99.69
PRK14287	371	chaperone protein DnaJ; Provisional	99.68
PRK14283	378	chaperone protein DnaJ; Provisional	99.68
PRK14284	391	chaperone protein DnaJ; Provisional	99.68
PRK14276	380	chaperone protein DnaJ; Provisional	99.68
PRK10767	371	chaperone protein DnaJ; Provisional	99.68
PRK14299	291	chaperone protein DnaJ; Provisional	99.68
PTZ00037	421	DnaJ_C chaperone protein; Provisional	99.68
PRK14278	378	chaperone protein DnaJ; Provisional	99.67
KOG0718	546	consensus Molecular chaperone (DnaJ superfamily) [	99.67
PRK14291	382	chaperone protein DnaJ; Provisional	99.67
KOG0717	508	consensus Molecular chaperone (DnaJ superfamily) [	99.67
PRK14281	397	chaperone protein DnaJ; Provisional	99.67
PRK14298	377	chaperone protein DnaJ; Provisional	99.66
PRK14280	376	chaperone protein DnaJ; Provisional	99.66
PRK14289	386	chaperone protein DnaJ; Provisional	99.65
PRK14290	365	chaperone protein DnaJ; Provisional	99.63
TIGR02349	354	DnaJ_bact chaperone protein DnaJ. This model repre	99.61
KOG0715	288	consensus Molecular chaperone (DnaJ superfamily) [	99.61
PRK14300	372	chaperone protein DnaJ; Provisional	99.61
PTZ00341	1136	Ring-infected erythrocyte surface antigen; Provisi	99.6
smart00271	60	DnaJ DnaJ molecular chaperone homology domain.	99.6
PRK10266	306	curved DNA-binding protein CbpA; Provisional	99.6
KOG0719	264	consensus Molecular chaperone (DnaJ superfamily) [	99.6
PRK14292	371	chaperone protein DnaJ; Provisional	99.6
PRK14293	374	chaperone protein DnaJ; Provisional	99.59
cd06257	55	DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat sho	99.58
COG2214	237	CbpA DnaJ-class molecular chaperone [Posttranslati	99.56
PRK05014	171	hscB co-chaperone HscB; Provisional	99.55
KOG0721	230	consensus Molecular chaperone (DnaJ superfamily) [	99.53
PRK00294	173	hscB co-chaperone HscB; Provisional	99.5
PRK03578	176	hscB co-chaperone HscB; Provisional	99.49
KOG1150	250	consensus Predicted molecular chaperone (DnaJ supe	99.49
PRK01356	166	hscB co-chaperone HscB; Provisional	99.47
TIGR03835	871	termin_org_DnaJ terminal organelle assembly protei	99.44
PHA03102	153	Small T antigen; Reviewed	99.4
KOG0720	490	consensus Molecular chaperone (DnaJ superfamily) [	99.4
KOG0722	329	consensus Molecular chaperone (DnaJ superfamily) [	99.32
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.24
KOG0714	306	consensus Molecular chaperone (DnaJ superfamily) [	99.14
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	99.13
PRK09430	267	djlA Dna-J like membrane chaperone protein; Provis	99.12
PTZ00100	116	DnaJ chaperone protein; Provisional	99.1
PRK01773	173	hscB co-chaperone HscB; Provisional	99.08
PHA02624	647	large T antigen; Provisional	99.0
TIGR00714	157	hscB Fe-S protein assembly co-chaperone HscB. This	98.99
COG5407	610	SEC63 Preprotein translocase subunit Sec63 [Intrac	98.93
COG5269	379	ZUO1 Ribosome-associated chaperone zuotin [Transla	98.91
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.9
KOG0122	270	consensus Translation initiation factor 3, subunit	98.74
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.57
PLN03120	260	nucleic acid binding protein; Provisional	98.55
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.52
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	98.49
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	98.47
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.46
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.42
smart00360	71	RRM RNA recognition motif.	98.36
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.35
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.33
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.3
PLN03121	243	nucleic acid binding protein; Provisional	98.29
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.23
KOG1789	2235	consensus Endocytosis protein RME-8, contains DnaJ	98.23
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.23
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.21
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.21
smart00361	70	RRM_1 RNA recognition motif.	98.21
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.18
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.17
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	98.17
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.17
smart00362	72	RRM_2 RNA recognition motif.	98.16
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.15
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.14
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.09
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.09
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.03
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.03
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.01
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.0
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	97.98
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.96
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.93
KOG0568	342	consensus Molecular chaperone (DnaJ superfamily) [	97.92
COG0724	306	RNA-binding proteins (RRM domain) [General functio	97.87
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	97.82
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	97.78
PLN03213	759	repressor of silencing 3; Provisional	97.78
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	97.77
KOG3192	168	consensus Mitochondrial J-type chaperone [Posttran	97.77
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	97.76
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	97.69
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.67
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	97.67
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	97.66
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	97.53
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	97.47
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.45
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	97.42
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	97.42
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	97.38
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	97.36
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	97.27
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	97.24
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	97.23
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.19
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	97.17
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	97.13
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	97.07
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	97.0
KOG0723	112	consensus Molecular chaperone (DnaJ superfamily) [	96.99
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	96.79
KOG0533	243	consensus RRM motif-containing protein [RNA proces	96.67
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	96.62
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	96.55
KOG0431	453	consensus Auxilin-like protein and related protein	96.48
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.35
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	96.24
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	96.23
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	96.17
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.07
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.06
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.97
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	95.95
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	95.87
KOG2314	698	consensus Translation initiation factor 3, subunit	95.71
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	95.67
KOG4660	549	consensus Protein Mei2, essential for commitment t	95.52
COG1076	174	DjlA DnaJ-domain-containing proteins 1 [Posttransl	95.4
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	95.39
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	95.36
KOG0151	877	consensus Predicted splicing regulator, contains R	95.33
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.23
COG1076	174	DjlA DnaJ-domain-containing proteins 1 [Posttransl	95.21
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	94.83
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	94.81
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	94.56
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	94.34
KOG2135	526	consensus Proteins containing the RNA recognition	94.3
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	94.27
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	94.19
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	93.07
KOG1548	382	consensus Transcription elongation factor TAT-SF1	92.38
KOG1457	284	consensus RNA binding protein (contains RRM repeat	91.63
KOG1855	484	consensus Predicted RNA-binding protein [General f	91.61
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	90.81
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	90.19
KOG0226	290	consensus RNA-binding proteins [General function p	90.11
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	89.54
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	89.38
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	88.99
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	88.4
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	87.44
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	83.22
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	82.69
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	81.39
PF03656	127	Pam16: Pam16; InterPro: IPR005341 The Pam16 protei	80.55
COG5175	480	MOT2 Transcriptional repressor [Transcription]	80.49

>KOG0691 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.95  E-value=1.6e-28  Score=227.32  Aligned_cols=265  Identities=27%  Similarity=0.336  Sum_probs=169.2

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREK   83 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~~~~   83 (292)
                      .+.|||+||||+.+     ++..+|++|||.+|++|||||||+||.|.+.|+.|.+||+||+|+.+|..||.+++.....
T Consensus         3 ~~~dyY~lLgi~~~-----at~~eIkKaYr~kaL~~HPDKNp~dP~A~ekFq~L~eAy~VL~D~~~R~~YDk~~k~~~~~   77 (296)
T KOG0691|consen    3 KDTDYYDLLGISED-----ATDAEIKKAYRKKALQYHPDKNPGDPQAAEKFQELSEAYEVLSDEESRAAYDKLRKSGSSA   77 (296)
T ss_pred             ccchHHHHhCCCCC-----CCHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhcccc
Confidence            47899999999998     9999999999999999999999999999999999999999999999999999999999888


Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCh-----hhhhhhhhhhcCC
Q 022800           84 QQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIARQLKEEIERIRAMHENKRTP-----AAFASVKETKQSG  158 (292)
Q Consensus        84 ~~r~~~~~~kr~~~~~dLe~RE~~~~~~~~~~~~~~~~~~~~~~l~eE~~r~r~~~~~~~~~-----~~~~~~~~~~~~~  158 (292)
                      ..+..+.+..|..+..|+++++..+.+..........+ .  ..+.+++...+++...++..     ........  .  
T Consensus        78 ~~~~d~~~~~r~~f~~dl~~~~~~~~a~~~~~~e~~~e-~--~~~~~k~~~~~~er~~~l~~~~~~~l~~~~~~~--~--  150 (296)
T KOG0691|consen   78 QGREDQADGFRKKFGSDLFERERGALALLKESEESELE-R--ERLQEKFRAVQRERVDKLVEILREKLSEVVESV--E--  150 (296)
T ss_pred             hhhhhHHHHHHHHhhhhhhhhHHHHHhHHhhhhhhhhh-H--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh--h--
Confidence            89999999999999999999999866644331000000 0  01111221221111111000     00000000  0  


Q ss_pred             CCCCCCC----ccceEEEEeee-cCCCCCHHHHHHHhcccCCeeEEEEec--CCCcce---EEEEecCHHHHHHHHHhhc
Q 022800          159 SGGVGLD----KEKVLKVSWEK-FGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGS---ALVVMATKSAAGAATGSVC  228 (292)
Q Consensus       159 ~~~~~~~----~~~~lkvKWk~-~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~---A~V~F~~~~~A~~Av~~~~  228 (292)
                      ...-.+.    ....+...|-. .+..|+. .....|++|+.+..|....  .+.+|-   +.+.+++...+.....++.
T Consensus       151 ~~~~~~e~~~l~~e~~~~e~~~~~g~~y~~-~~~~~~~~~~~~~~v~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~e~  229 (296)
T KOG0691|consen  151 ERKLATEALQLQRERFGEELLHTIGRTYSR-TKALKPIKFRTSPGVSKLSEGSRAKGGALRAMWNLAAGAVALYGGQDEM  229 (296)
T ss_pred             hhhhhHHHHHHHHhhhhHHHHHhhcccchh-hHhhhccccccccCcchhhhcccccchhHHHHHhhhHHHHHHHHHHHHH
Confidence            0000000    00112222222 4445665 6777777777655555432  333332   3456666666666667788


Q ss_pred             CCCCCCeEEEecCCCccCCCCCCCCCCCccccCcCCCcChHhHHHHHHHHHH--hHHHHHh
Q 022800          229 GNLSNPLLVLPLQPAVATQIPSAPKPVETESINNLVGAGYQAHEDAILEKLR--EKAKEKN  287 (292)
Q Consensus       229 g~~~~pl~v~~~~~~~~~~~p~~~~~~~~~~~s~~~~~s~~d~E~~vl~rlr--~a~erk~  287 (292)
                      +.+.+|+.+.|..++   ..+.  ..+ ....+++.+++..|+|+.+++.++  ++.+..+
T Consensus       230 ~~~~~~~~~~~e~~~---~~~~--~~~-~~~~~~~~~~s~~dies~l~~~~~~~~d~~v~~  284 (296)
T KOG0691|consen  230 EKLLEALGEALEKRA---EYAS--AKT-GKSLDTLWHGSSFDIESTLIRVCQKIKDPSVPL  284 (296)
T ss_pred             HhhhcchHHHhhhch---HHHH--Hhh-cchhhhhhHhHHHHHHHHHHHHHHHhcChHHHH
Confidence            899999888887631   0100  001 111233456789999999999999  6555544

>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.87  E-value=1.7e-22  Score=191.71  Aligned_cols=74  Identities=32%  Similarity=0.625  Sum_probs=69.6

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKR   81 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~~   81 (292)
                      +...|||+||||+++     ||.+|||+|||+||++||||+||++++|.++|++|++||+||+||.+|+.||.+..+..
T Consensus         1 ~~~~dyYeiLGV~k~-----As~~EIKkAYRkLA~kyHPD~n~g~~~AeeKFKEI~eAYEVLsD~eKRa~YD~fG~~~~   74 (371)
T COG0484           1 MAKRDYYEILGVSKD-----ASEEEIKKAYRKLAKKYHPDRNPGDKEAEEKFKEINEAYEVLSDPEKRAAYDQFGHAGF   74 (371)
T ss_pred             CCccchhhhcCCCCC-----CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHhCCHHHHHHhhccCcccc
Confidence            357899999999998     99999999999999999999999999999999999999999999999999999886544

>KOG0713 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.87  E-value=1.8e-22  Score=187.51  Aligned_cols=70  Identities=41%  Similarity=0.805  Sum_probs=67.5

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     |++.+||+|||+||++|||||||+||.|.+.|+.|+.||+||+||.+|+.||....
T Consensus        14 ~~rDfYelLgV~k~-----Asd~eIKkAYRKLALk~HPDkNpddp~A~e~F~~in~AYEVLsDpekRk~YD~~GE   83 (336)
T KOG0713|consen   14 AGRDFYELLGVPKN-----ASDQEIKKAYRKLALKYHPDKNPDDPNANEKFKEINAAYEVLSDPEKRKHYDTYGE   83 (336)
T ss_pred             cCCCHHHHhCCCCC-----CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHhhhH
Confidence            46899999999998     99999999999999999999999999999999999999999999999999999983

>PRK14288 chaperone protein DnaJ; Provisional

Probab=99.77  E-value=2.9e-19  Score=171.72  Aligned_cols=69  Identities=32%  Similarity=0.605  Sum_probs=65.7

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     ||.++||+|||+||++||||+|++++.|.+.|+.|++||+||+||.+|..||.+..
T Consensus         2 ~~dyY~vLgv~~~-----As~~eIkkayrkla~k~HPD~~~~~~~a~~~f~~i~~AYevLsd~~kR~~YD~~G~   70 (369)
T PRK14288          2 ELSYYEILEVEKH-----SNQETIKKSYRKLALKYHPDRNAGDKEAEEKFKLINEAYGVLSDEKKRALYDRYGK   70 (369)
T ss_pred             CCChHHHcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCCCccHHHHHHHHHHHHHHHhccHHHHHHHHHhcc
Confidence            5799999999998     99999999999999999999999888899999999999999999999999999764

>PRK14279 chaperone protein DnaJ; Provisional

Probab=99.75  E-value=1.4e-18  Score=168.26  Aligned_cols=71  Identities=37%  Similarity=0.620  Sum_probs=66.7

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +...|||+||||+++     |+.++||+|||++|++||||+|++++.|.+.|+.|++||+||+||.+|+.||.+..
T Consensus         6 ~~~~Dyy~~Lgv~~~-----a~~~eik~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vLsD~~KR~~YD~~G~   76 (392)
T PRK14279          6 WVEKDFYKELGVSSD-----ASAEEIKKAYRKLARELHPDANPGDPAAEERFKAVSEAHDVLSDPAKRKEYDETRR   76 (392)
T ss_pred             hcccCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCChHHHHHHHHHHHHHHHhcchhhhhHHHHhhh
Confidence            345799999999998     89999999999999999999999888999999999999999999999999999863

>KOG0716 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.74  E-value=1.8e-18  Score=156.57  Aligned_cols=70  Identities=43%  Similarity=0.760  Sum_probs=66.8

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|+|+||||+++     ++.++|||+||+++++||||+++++|++..+|+.|+.||.||+||.+|..||.++.
T Consensus        29 ~~~~LYdVLgl~k~-----at~d~IKKaYR~L~~k~HPD~~gd~P~~~dkf~eIN~Ay~ILsD~~kR~~YD~~g~   98 (279)
T KOG0716|consen   29 IRLDLYDVLGLPKT-----ATKDEIKKAYRKLALKYHPDKNGDNPEATDKFKEINTAYAILSDPTKRNVYDEYGE   98 (279)
T ss_pred             chhHHHHHhCCCcc-----cchHHHHHHHHHHHHHhCCCcCCCCchhHHHHHHHHHHHHHhcChhhhhhHHHhhh
Confidence            46789999999998     89999999999999999999999999999999999999999999999999999864

>PRK14296 chaperone protein DnaJ; Provisional

Probab=99.74  E-value=2.3e-18  Score=165.62  Aligned_cols=68  Identities=35%  Similarity=0.608  Sum_probs=64.2

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++||+|||++|++||||+|+ ++.|.+.|+.|++||+||+||.+|+.||.+..
T Consensus         3 ~~dyY~~Lgv~~~-----a~~~eik~ayrkla~~~HPD~n~-~~~a~~~F~~i~~AyevLsD~~KR~~YD~~G~   70 (372)
T PRK14296          3 KKDYYEVLGVSKT-----ASEQEIRQAYRKLAKQYHPDLNK-SPDAHDKMVEINEAADVLLDKDKRKQYDQFGH   70 (372)
T ss_pred             CCCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CchHHHHHHHHHHHHHHhcCHHHhhhhhhccc
Confidence            5799999999998     89999999999999999999998 57899999999999999999999999999754

>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.73  E-value=3.1e-18  Score=160.74  Aligned_cols=67  Identities=37%  Similarity=0.733  Sum_probs=63.2

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .+..||+||||+++     ||+.|||+|||++|++|||||||+   +.++|++|+.||+||+||.+|..||.+..
T Consensus         2 ~~~~~y~il~v~~~-----As~~eikkayrkla~k~HpDkn~~---~~ekfkei~~AyevLsd~ekr~~yD~~g~   68 (337)
T KOG0712|consen    2 KNTKLYDILGVSPD-----ASEEEIKKAYRKLALKYHPDKNPD---AGEKFKEISQAYEVLSDPEKREIYDQYGE   68 (337)
T ss_pred             cccccceeeccCCC-----cCHHHHHHHHHHHHHHhCCCCCcc---HHHHHHHHHHHHHHhcCHHHHHHHHhhhh
Confidence            46789999999998     999999999999999999999985   78999999999999999999999999874

>PRK14286 chaperone protein DnaJ; Provisional

Probab=99.73  E-value=4e-18  Score=164.07  Aligned_cols=69  Identities=32%  Similarity=0.635  Sum_probs=65.6

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +.|||+||||+++     ||.++|++|||++|++||||+|++++.|.+.|+.|++||+||+||.+|..||.+..
T Consensus         3 ~~d~y~~Lgv~~~-----a~~~eik~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~kR~~YD~~G~   71 (372)
T PRK14286          3 ERSYYDILGVSKS-----ANDEEIKSAYRKLAIKYHPDKNKGNKESEEKFKEATEAYEILRDPKKRQAYDQFGK   71 (372)
T ss_pred             CCCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHhccHHHHHHHHHhCc
Confidence            5799999999998     89999999999999999999999888899999999999999999999999998754

>PRK14277 chaperone protein DnaJ; Provisional

Probab=99.70  E-value=1.6e-17  Score=160.52  Aligned_cols=70  Identities=37%  Similarity=0.660  Sum_probs=66.1

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     ||.++|++|||++|++||||+|++++.|.+.|+.|++||++|+||.+|..||.+..
T Consensus         3 ~~~d~y~~Lgv~~~-----a~~~eik~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~kr~~yD~~G~   72 (386)
T PRK14277          3 AKKDYYEILGVDRN-----ATEEEIKKAYRRLAKKYHPDLNPGDKEAEQKFKEINEAYEILSDPQKRAQYDQFGH   72 (386)
T ss_pred             CCCCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCCCcCCCchHHHHHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence            45799999999998     99999999999999999999999888899999999999999999999999999753

>PRK14285 chaperone protein DnaJ; Provisional

Probab=99.70  E-value=1.5e-17  Score=159.71  Aligned_cols=69  Identities=35%  Similarity=0.635  Sum_probs=65.4

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     ||.++||+|||+++++||||+|++++.|.+.|+.|++||+||+||.+|..||.+..
T Consensus         2 ~~d~y~iLgv~~~-----a~~~eIk~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~kr~~yd~~g~   70 (365)
T PRK14285          2 KRDYYEILGLSKG-----ASKDEIKKAYRKIAIKYHPDKNKGNKEAESIFKEATEAYEVLIDDNKRAQYDRFGH   70 (365)
T ss_pred             CCCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHcCcchhHHHHhcCc
Confidence            4699999999998     99999999999999999999999888899999999999999999999999999754

>PF00226 DnaJ: DnaJ domain; InterPro: IPR001623 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []

Probab=99.70  E-value=2e-17  Score=120.03  Aligned_cols=63  Identities=38%  Similarity=0.790  Sum_probs=59.7

Q ss_pred             ccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchhhhhHH
Q 022800            7 DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKARKLFD   74 (292)
Q Consensus         7 d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~R~~YD   74 (292)
                      |||+||||+++     ++.++|+++|+++++.+|||++++++ .+...|..|+.||++|+||..|..||
T Consensus         1 ~~y~iLgl~~~-----~~~~eik~~y~~l~~~~HPD~~~~~~~~~~~~~~~i~~Ay~~L~~~~~R~~YD   64 (64)
T PF00226_consen    1 NPYEILGLPPD-----ASDEEIKKAYRRLSKQYHPDKNSGDEAEAEEKFARINEAYEILSDPERRRRYD   64 (64)
T ss_dssp             HHHHHCTSTTT-----SSHHHHHHHHHHHHHHTSTTTGTSTHHHHHHHHHHHHHHHHHHHSHHHHHHHH
T ss_pred             ChHHHCCCCCC-----CCHHHHHHHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHhCCHHHHHhcC
Confidence            69999999998     89999999999999999999998766 68899999999999999999999998

Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Such a structure is shown in the following schematic representation: +------------+-+-------+-----+-----------+--------------------------------+ | N-terminal | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+ It is thought that the 'J' domain of DnaJ mediates the interaction with the dnaK protein and consists of four helices, the second of which has a charged surface that includes at least one pair of basic residues that are essential for interaction with the ATPase domain of Hsp70. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins [], either together or separately. In yeast, J-domains have been classified into 3 groups; the class III proteins are functionally distinct and do not appear to act as molecular chaperones []. ; GO: 0031072 heat shock protein binding; PDB: 2GUZ_C 2L6L_A 1HDJ_A 2EJ7_A 1FPO_C 2CUG_A 2QSA_A 2OCH_A 3BVO_B 3APQ_A ....

>PRK14295 chaperone protein DnaJ; Provisional

Probab=99.69  E-value=2.4e-17  Score=159.52  Aligned_cols=68  Identities=43%  Similarity=0.716  Sum_probs=64.3

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDL   76 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~   76 (292)
                      +..|||+||||+++     |+.++|++|||++|++||||+|++++.|.+.|+.|++||+||+||.+|+.||..
T Consensus         7 ~~~d~y~~Lgv~~~-----a~~~eik~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~~r~~yD~~   74 (389)
T PRK14295          7 IEKDYYKVLGVPKD-----ATEAEIKKAYRKLAREYHPDANKGDAKAEERFKEISEAYDVLSDEKKRKEYDEA   74 (389)
T ss_pred             cccCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCCCcCCCchhHHHHHHHHHHHHHHHCchhhHHHHHHH
Confidence            35699999999998     899999999999999999999998888999999999999999999999999983

>PRK14282 chaperone protein DnaJ; Provisional

Probab=99.69  E-value=2.3e-17  Score=158.57  Aligned_cols=69  Identities=33%  Similarity=0.691  Sum_probs=64.4

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC-hhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD-PDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~-~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     ||.++|++|||++|++||||+|+++ +.|.+.|+.|++||++|+||.+|+.||.+..
T Consensus         3 ~~d~y~~lgv~~~-----a~~~eik~ayr~la~~~HPD~~~~~~~~a~~~f~~i~~Ay~vL~d~~kR~~YD~~g~   72 (369)
T PRK14282          3 KKDYYEILGVSRN-----ATQEEIKRAYKRLVKEWHPDRHPENRKEAEQKFKEIQEAYEVLSDPQKRAMYDRFGY   72 (369)
T ss_pred             CCChHHhcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHhcChhhHHHHhhcCc
Confidence            5799999999998     9999999999999999999999865 6788999999999999999999999998753

>PRK14294 chaperone protein DnaJ; Provisional

Probab=99.69  E-value=2.8e-17  Score=157.91  Aligned_cols=70  Identities=34%  Similarity=0.652  Sum_probs=65.9

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     |+..+|++|||++|++||||++++++.+.+.|+.|++||+||+||.+|..||.+..
T Consensus         2 ~~~d~y~~lgv~~~-----a~~~eik~ayr~la~~~HPD~~~~~~~~~~~f~~~~~Ay~vL~d~~~r~~yD~~G~   71 (366)
T PRK14294          2 VKRDYYEILGVTRD-----ASEEEIKKSYRKLAMKYHPDRNPGDKEAEELFKEAAEAYEVLSDPKKRGIYDQYGH   71 (366)
T ss_pred             CCCChHHHhCCCCC-----CCHHHHHHHHHHHHHHHCCCCCCCchHHHHHHHHHHHHHHHhccHHHHHHHHhhcc
Confidence            35799999999998     89999999999999999999999888899999999999999999999999998763

>PRK14301 chaperone protein DnaJ; Provisional

Probab=99.69  E-value=2.4e-17  Score=158.64  Aligned_cols=69  Identities=39%  Similarity=0.740  Sum_probs=65.5

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     ||.++|++|||++|++||||+|++++.|.+.|+.|++||+||+||.+|..||.+..
T Consensus         3 ~~~~y~~Lgv~~~-----a~~~~ik~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~kr~~yD~~g~   71 (373)
T PRK14301          3 QRDYYEVLGVSRD-----ASEDEIKKAYRKLALQYHPDRNPDNPEAEQKFKEAAEAYEVLRDAEKRARYDRFGH   71 (373)
T ss_pred             CCChHHhcCCCCC-----CCHHHHHHHHHHHHHHhCCCcCCCChHHHHHHHHHHHHHHHhcchhhhhhhhhccc
Confidence            5799999999998     89999999999999999999999888899999999999999999999999998754

>PRK14297 chaperone protein DnaJ; Provisional

Probab=99.69  E-value=2.7e-17  Score=158.69  Aligned_cols=69  Identities=32%  Similarity=0.657  Sum_probs=65.4

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++|++|||++|++||||+|++++.|.+.|+.|++||++|+||.+|+.||.+..
T Consensus         3 ~~d~y~~Lgv~~~-----a~~~~ik~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~~r~~yD~~G~   71 (380)
T PRK14297          3 SKDYYEVLGLEKG-----ASDDEIKKAFRKLAIKYHPDKNKGNKEAEEKFKEINEAYQVLSDPQKKAQYDQFGT   71 (380)
T ss_pred             CCChHHhhCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHhcCHhhhCchhhcCc
Confidence            4799999999998     89999999999999999999999888899999999999999999999999998753

>PRK14287 chaperone protein DnaJ; Provisional

Probab=99.68  E-value=4.3e-17  Score=156.85  Aligned_cols=68  Identities=34%  Similarity=0.605  Sum_probs=63.9

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++|++|||++|++||||+|+ ++.|.+.|+.|++||++|+||.+|+.||.+..
T Consensus         3 ~~d~y~~Lgv~~~-----a~~~eik~ayr~la~~~HpD~~~-~~~~~~~f~~i~~Ay~~L~d~~kR~~YD~~G~   70 (371)
T PRK14287          3 KRDYYEVLGVDRN-----ASVDEVKKAYRKLARKYHPDVNK-APDAEDKFKEVKEAYDTLSDPQKKAHYDQFGH   70 (371)
T ss_pred             CCCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-ChhHHHHHHHHHHHHHHhCcHhHHHHHHhhCC
Confidence            4699999999998     89999999999999999999997 57889999999999999999999999999753

>PRK14283 chaperone protein DnaJ; Provisional

Probab=99.68  E-value=4.2e-17  Score=157.27  Aligned_cols=69  Identities=32%  Similarity=0.602  Sum_probs=64.8

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     |+.++||+|||++|++||||+|+ ++.|.+.|+.|++||++|+||.+|..||.+..
T Consensus         3 ~~~d~y~~Lgv~~~-----a~~~eik~ayr~la~~~HPD~~~-~~~a~~~f~~i~~Ay~~Lsd~~kR~~YD~~G~   71 (378)
T PRK14283          3 EKRDYYEVLGVDRN-----ADKKEIKKAYRKLARKYHPDVSE-EEGAEEKFKEISEAYAVLSDDEKRQRYDQFGH   71 (378)
T ss_pred             CcCChHHhhCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CccHHHHHHHHHHHHHHhchhHHHHHHhhhcc
Confidence            46899999999998     99999999999999999999998 47899999999999999999999999999753

>PRK14284 chaperone protein DnaJ; Provisional

Probab=99.68  E-value=4.2e-17  Score=157.92  Aligned_cols=68  Identities=37%  Similarity=0.693  Sum_probs=64.8

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .|||+||||+++     ||.++||+|||++|++||||+|++++.|.+.|+.|++||++|+||.+|+.||.+..
T Consensus         1 ~d~y~iLgv~~~-----a~~~eikkayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~kR~~YD~~G~   68 (391)
T PRK14284          1 MDYYTILGVSKT-----ASPEEIKKAYRKLAVKYHPDKNPGDAEAEKRFKEVSEAYEVLSDAQKRESYDRYGK   68 (391)
T ss_pred             CCHHHhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHhcCHHHHHHHHhccc
Confidence            489999999998     99999999999999999999999888899999999999999999999999999764

>PRK14276 chaperone protein DnaJ; Provisional

Probab=99.68  E-value=4.3e-17  Score=157.31  Aligned_cols=68  Identities=28%  Similarity=0.566  Sum_probs=64.0

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +.|||+||||+++     ||.++|++|||++|++||||+|+ ++.|.+.|+.|++||++|+||.+|..||.+..
T Consensus         3 ~~d~y~~Lgv~~~-----a~~~eik~ayr~la~~~HpD~~~-~~~a~~~f~~i~~Ay~vL~d~~kR~~YD~~G~   70 (380)
T PRK14276          3 NTEYYDRLGVSKD-----ASQDEIKKAYRKLSKKYHPDINK-EPGAEEKYKEVQEAYETLSDPQKRAAYDQYGA   70 (380)
T ss_pred             CCCHHHhhCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CcCHHHHHHHHHHHHHHhcCHhhhhhHhhcCC
Confidence            5799999999998     89999999999999999999998 57889999999999999999999999998753

>PRK10767 chaperone protein DnaJ; Provisional

Probab=99.68  E-value=5.2e-17  Score=156.26  Aligned_cols=70  Identities=37%  Similarity=0.702  Sum_probs=65.7

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     |+.++|++|||++|++||||+|++++.|.+.|+.|++||++|+||.+|..||.+..
T Consensus         2 ~~~d~y~iLgv~~~-----as~~eik~ayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~~L~d~~~r~~yd~~g~   71 (371)
T PRK10767          2 AKRDYYEVLGVSRN-----ASEDEIKKAYRKLAMKYHPDRNPGDKEAEEKFKEIKEAYEVLSDPQKRAAYDQYGH   71 (371)
T ss_pred             CCCChHHhcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCCCcHHHHHHHHHHHHHHHHhcchhhhhHhhhccc
Confidence            35799999999998     89999999999999999999999888899999999999999999999999998753

>PRK14299 chaperone protein DnaJ; Provisional

Probab=99.68  E-value=5.6e-17  Score=151.32  Aligned_cols=68  Identities=32%  Similarity=0.639  Sum_probs=64.2

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     ||.++||+|||++|++||||+|+ ++.+.+.|+.|++||++|+||.+|..||.+..
T Consensus         3 ~~d~y~vLgv~~~-----a~~~eik~ayr~la~~~HPD~~~-~~~~~~~f~~i~~Ay~~L~d~~kr~~yD~~g~   70 (291)
T PRK14299          3 YKDYYAILGVPKN-----ASQDEIKKAFKKLARKYHPDVNK-SPGAEEKFKEINEAYTVLSDPEKRRIYDTYGT   70 (291)
T ss_pred             CCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-ChhHHHHHHHHHHHHHHhcCHHHHHHHHhcCC
Confidence            5799999999998     89999999999999999999997 68899999999999999999999999999764

>PTZ00037 DnaJ_C chaperone protein; Provisional

Probab=99.68  E-value=4.1e-17  Score=159.07  Aligned_cols=66  Identities=38%  Similarity=0.657  Sum_probs=61.0

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     ||.++||+|||++|++||||+|++    .+.|+.|++||+||+||.+|+.||.+..
T Consensus        26 ~~~d~Y~vLGV~~~-----As~~eIKkAYrkla~k~HPDk~~~----~e~F~~i~~AYevLsD~~kR~~YD~~G~   91 (421)
T PTZ00037         26 DNEKLYEVLNLSKD-----CTTSEIKKAYRKLAIKHHPDKGGD----PEKFKEISRAYEVLSDPEKRKIYDEYGE   91 (421)
T ss_pred             cchhHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCch----HHHHHHHHHHHHHhccHHHHHHHhhhcc
Confidence            35799999999998     899999999999999999999863    4799999999999999999999999764

>PRK14278 chaperone protein DnaJ; Provisional

Probab=99.67  E-value=5.4e-17  Score=156.50  Aligned_cols=68  Identities=35%  Similarity=0.623  Sum_probs=63.8

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++|++|||++|++||||+|+ ++.|.+.|+.|++||+||+||.+|..||.+..
T Consensus         2 ~~d~y~iLgv~~~-----a~~~eik~ayr~la~~~hpD~~~-~~~a~~~f~~i~~Ay~vL~d~~~r~~YD~~G~   69 (378)
T PRK14278          2 ARDYYGLLGVSRN-----ASDAEIKRAYRKLARELHPDVNP-DEEAQEKFKEISVAYEVLSDPEKRRIVDLGGD   69 (378)
T ss_pred             CCCcceecCCCCC-----CCHHHHHHHHHHHHHHHCCCCCC-cHHHHHHHHHHHHHHHHhchhhhhhhhhccCC
Confidence            3699999999998     89999999999999999999998 68899999999999999999999999998753

>KOG0718 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.67  E-value=2.5e-17  Score=158.13  Aligned_cols=72  Identities=35%  Similarity=0.700  Sum_probs=65.3

Q ss_pred             CCCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC---hhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            2 DVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD---PDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         2 ~~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~---~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +++++|||.+|||+++     ||++||++|||++|+.|||||..|.   ..|.+.|+.|..||+||+||.+|+.||.+..
T Consensus         5 e~~e~e~Ya~LNlpkd-----At~eeI~~AYrr~~~lfHPDkh~dpd~K~~AE~~F~~i~~AyEVLsDp~kRaIYD~~G~   79 (546)
T KOG0718|consen    5 ELDEIELYALLNLPKD-----ATDEEIKKAYRRLSRLFHPDKHTDPDQKKAAEEKFQRIQRAYEVLSDPQKRAIYDNYGE   79 (546)
T ss_pred             ccchhhHHHHhCCCcc-----cCHHHHHHHHHHHHHhcCCcccCChhHHHHHHHHHHHHHHHHHHhcChHHHHHHHHhhh
Confidence            3567899999999998     9999999999999999999998642   2488999999999999999999999999974

>PRK14291 chaperone protein DnaJ; Provisional

Probab=99.67  E-value=5.8e-17  Score=156.53  Aligned_cols=68  Identities=35%  Similarity=0.696  Sum_probs=64.0

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++||+|||++|++||||+|+ ++.+.+.|+.|++||++|+||.+|..||.+..
T Consensus         2 ~~d~Y~~Lgv~~~-----a~~~~ik~ayr~la~~~HPD~~~-~~~~~~~f~~i~~Ay~vLsd~~kR~~YD~~g~   69 (382)
T PRK14291          2 KKDYYEILGVSRN-----ATQEEIKKAYRRLARKYHPDFNK-NPEAEEKFKEINEAYQVLSDPEKRKLYDQFGH   69 (382)
T ss_pred             CCCHHHhhCCCCC-----CCHHHHHHHHHHHHHHHCCCCCC-CccHHHHHHHHHHHHHHhcCHHHHHHHhhhcc
Confidence            4699999999998     89999999999999999999998 47889999999999999999999999999764

>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.67  E-value=6.2e-17  Score=155.27  Aligned_cols=71  Identities=35%  Similarity=0.610  Sum_probs=65.1

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .+..+||+||||..+     +++.+|+++||++||+|||||||+.- +|++.|+.|+.||+|||||..|+.||....
T Consensus         5 ~~~~c~YE~L~v~~~-----a~d~eik~~YRklALq~HPDknpd~ieeat~~F~~i~aAYeVLSdp~eR~wyd~hre   76 (508)
T KOG0717|consen    5 FKKRCYYEVLGVERD-----ADDDEIKKNYRKLALQYHPDKNPDRIEEATQQFQLIQAAYEVLSDPQERAWYDSHRE   76 (508)
T ss_pred             hhhhHHHHHhccccc-----CCHHHHHHHHHHHHHhhCCCCCCccHHHHHHHHHHHHHHHHHhcChHhhhhHHHHHH
Confidence            356789999999998     89999999999999999999998764 699999999999999999999999998654

>PRK14281 chaperone protein DnaJ; Provisional

Probab=99.67  E-value=7.2e-17  Score=156.57  Aligned_cols=69  Identities=36%  Similarity=0.717  Sum_probs=65.3

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+..+|++|||++|++||||++++++.|.+.|+.|++||++|+||.+|..||.+..
T Consensus         2 ~~d~y~iLgv~~~-----a~~~eikkayr~la~~~HPD~~~~~~~a~~~f~~i~~Ay~vL~d~~~r~~yD~~g~   70 (397)
T PRK14281          2 KRDYYEVLGVSRS-----ADKDEIKKAYRKLALKYHPDKNPDNKEAEEHFKEVNEAYEVLSNDDKRRRYDQFGH   70 (397)
T ss_pred             CCChhhhcCCCCC-----CCHHHHHHHHHHHHHHHCCCcCCCchHHHHHHHHHHHHHHHhhhhhhhhhhhhccc
Confidence            4699999999998     89999999999999999999999888899999999999999999999999998764

>PRK14298 chaperone protein DnaJ; Provisional

Probab=99.66  E-value=9.3e-17  Score=154.81  Aligned_cols=68  Identities=34%  Similarity=0.673  Sum_probs=63.8

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++|++|||++|++||||+|+ ++.+.+.|+.|++||++|+||.+|+.||.+..
T Consensus         4 ~~d~y~iLgv~~~-----a~~~eik~ayr~la~~~HPD~~~-~~~~~~~f~~i~~Ay~vL~d~~kR~~YD~~G~   71 (377)
T PRK14298          4 TRDYYEILGLSKD-----ASVEDIKKAYRKLAMKYHPDKNK-EPDAEEKFKEISEAYAVLSDAEKRAQYDRFGH   71 (377)
T ss_pred             CCCHHHhhCCCCC-----CCHHHHHHHHHHHHHHhCccccC-ChhHHHHHHHHHHHHHHhcchHhhhhhhhcCc
Confidence            4699999999998     89999999999999999999997 57888999999999999999999999998753

>PRK14280 chaperone protein DnaJ; Provisional

Probab=99.66  E-value=1.1e-16  Score=154.22  Aligned_cols=68  Identities=31%  Similarity=0.606  Sum_probs=63.8

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++||+|||++|++||||+|+ ++.|.+.|++|++||++|+||.+|+.||.+..
T Consensus         3 ~~~~y~iLgv~~~-----a~~~eik~ayr~la~~~HpD~~~-~~~a~~~f~~i~~Ay~vL~d~~kr~~yD~~G~   70 (376)
T PRK14280          3 KRDYYEVLGVSKS-----ASKDEIKKAYRKLSKKYHPDINK-EEGADEKFKEISEAYEVLSDDQKRAQYDQFGH   70 (376)
T ss_pred             CCChHHhhCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CccHHHHHHHHHHHHHHhccHhHHHHHHhcCc
Confidence            4799999999998     89999999999999999999998 57789999999999999999999999999753

>PRK14289 chaperone protein DnaJ; Provisional

Probab=99.65  E-value=1.7e-16  Score=153.48  Aligned_cols=70  Identities=37%  Similarity=0.681  Sum_probs=66.2

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     |+.++|++|||++|++||||+|++++.|.+.|+.|++||++|+||.+|..||.+..
T Consensus         3 ~~~~~y~~Lgv~~~-----a~~~eik~ayr~la~~~HpD~~~~~~~a~~~f~~i~~Ay~~L~d~~~R~~yD~~G~   72 (386)
T PRK14289          3 EKRDYYEVLGVSKT-----ATVDEIKKAYRKKAIQYHPDKNPGDKEAEEKFKEAAEAYDVLSDPDKRSRYDQFGH   72 (386)
T ss_pred             ccCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCCCChHHHHHHHHHHHHHHHhcCHHHHHHHHHhcc
Confidence            46899999999998     89999999999999999999999888999999999999999999999999999754

>PRK14290 chaperone protein DnaJ; Provisional

Probab=99.63  E-value=3.4e-16  Score=150.30  Aligned_cols=68  Identities=29%  Similarity=0.627  Sum_probs=63.9

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .|||+||||+++     |+..+|++|||+++++||||++++++ .|.+.|+.|++||++|+|+.+|..||.+..
T Consensus         3 ~d~y~vLgv~~~-----a~~~eik~ayr~la~~~HPD~~~~~~~~a~~~f~~i~~Ay~~L~d~~~r~~yd~~G~   71 (365)
T PRK14290          3 KDYYKILGVDRN-----ASQEDIKKAFRELAKKWHPDLHPGNKAEAEEKFKEISEAYEVLSDPQKRRQYDQTGT   71 (365)
T ss_pred             CChhhhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCchhHHHHHHHHHHHHHHHhcChhhhhhhcccCC
Confidence            699999999998     99999999999999999999998765 788999999999999999999999998653

>TIGR02349 DnaJ_bact chaperone protein DnaJ

Probab=99.61  E-value=5.7e-16  Score=148.17  Aligned_cols=66  Identities=35%  Similarity=0.683  Sum_probs=62.4

Q ss_pred             ccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            7 DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         7 d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      |||+||||+++     |+.++||+|||++|++||||+++ ++.+.+.|+.|++||++|+|+.+|..||.+..
T Consensus         1 d~y~~Lgv~~~-----a~~~~ik~ayr~la~~~HPD~~~-~~~~~~~f~~i~~Ay~vL~d~~~R~~yd~~g~   66 (354)
T TIGR02349         1 DYYEILGVSKD-----ASEEEIKKAYRKLAKKYHPDRNK-DKEAEEKFKEINEAYEVLSDPEKRAQYDQFGH   66 (354)
T ss_pred             ChHHhCCCCCC-----CCHHHHHHHHHHHHHHHCCCCCC-CccHHHHHHHHHHHHHHhhChHHHHhhhhccc
Confidence            79999999998     89999999999999999999998 67788999999999999999999999998754

This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.

>KOG0715 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.61  E-value=7.8e-16  Score=143.34  Aligned_cols=70  Identities=34%  Similarity=0.536  Sum_probs=65.5

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIK   80 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~   80 (292)
                      ..|||+||||+++     |+..|||+||++||++||||.|.+ +.|.+.|+.|.+||++|+|+.+|..||..+...
T Consensus        42 ~~d~Y~vLgv~~~-----At~~EIK~Af~~LaKkyHPD~n~~-~~a~~kF~eI~~AYEiLsd~eKR~~YD~~~~~~  111 (288)
T KOG0715|consen   42 KEDYYKVLGVSRN-----ATLSEIKSAFRKLAKKYHPDVNKD-KEASKKFKEISEAYEILSDEEKRQEYDVYGLEQ  111 (288)
T ss_pred             CcchhhhhCcCCC-----CCHHHHHHHHHHHHHhhCCCCCCC-cchhhHHHHHHHHHHHhcCHHHHHHHHHhhhhc
Confidence            3499999999998     999999999999999999999985 589999999999999999999999999998754

>PRK14300 chaperone protein DnaJ; Provisional

Probab=99.61  E-value=7.2e-16  Score=148.43  Aligned_cols=67  Identities=31%  Similarity=0.607  Sum_probs=63.1

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .|||+||||+++     ||..+|++|||+++++||||+++ ++.+.+.|+.|++||++|+|+.+|..||.+..
T Consensus         3 ~~~y~iLgv~~~-----as~~eik~ayr~la~~~HPD~~~-~~~~~~~f~~i~~Ay~~L~d~~~r~~yD~~G~   69 (372)
T PRK14300          3 QDYYQILGVSKT-----ASQADLKKAYLKLAKQYHPDTTD-AKDAEKKFKEINAAYDVLKDEQKRAAYDRFGH   69 (372)
T ss_pred             CChHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CcCHHHHHHHHHHHHHHhhhHhHhhHHHhccc
Confidence            699999999998     89999999999999999999997 57788999999999999999999999999753

>PTZ00341 Ring-infected erythrocyte surface antigen; Provisional

Probab=99.60  E-value=8.2e-16  Score=158.83  Aligned_cols=70  Identities=27%  Similarity=0.458  Sum_probs=65.0

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +.+.+||+||||+++     ||..+||+|||++|++||||++|++ .|...|+.|++||+||+||.+|..||.+..
T Consensus       570 ~~d~dYYdILGVs~d-----AS~~EIKKAYRKLAlkyHPDKN~~~-~A~ekFq~I~EAYeVLSDp~kRk~YD~~G~  639 (1136)
T PTZ00341        570 IPDTLFYDILGVGVN-----ADMKEISERYFKLAENYYPPKRSGN-EGFHKFKKINEAYQILGDIDKKKMYNKFGY  639 (1136)
T ss_pred             CCCCChHHHcCCCCC-----CCHHHHHHHHHHHHHHhCCCCCCCc-hHHHHHHHHHHHHHHhCCHHHHHHHhhccc
Confidence            356899999999998     9999999999999999999999965 688899999999999999999999999764

>smart00271 DnaJ DnaJ molecular chaperone homology domain

Probab=99.60  E-value=1.4e-15  Score=108.61  Aligned_cols=58  Identities=40%  Similarity=0.774  Sum_probs=54.1

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCC-ChhHHHHHHHHHHHHHHccCch
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPD-DPDAHDNFQKLKSSYEILKDEK   68 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~-~~~a~~~f~~i~~Ay~vL~d~~   68 (292)
                      .|||+||||+++     ++..+|+++|+++++.||||++++ .+.+.+.|..|++||++|+||.
T Consensus         1 ~~~y~vLgl~~~-----~~~~~ik~ay~~l~~~~HPD~~~~~~~~~~~~~~~l~~Ay~~L~~~~   59 (60)
T smart00271        1 TDYYEILGVPRD-----ASLDEIKKAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVLSDPE   59 (60)
T ss_pred             CCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHHHcCCC
Confidence            489999999997     899999999999999999999986 5778899999999999999985

>PRK10266 curved DNA-binding protein CbpA; Provisional

Probab=99.60  E-value=9.9e-16  Score=143.87  Aligned_cols=67  Identities=33%  Similarity=0.577  Sum_probs=63.0

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ..|||+||||+++     ++.++|++|||++|++||||+++ ++.+.+.|+.|++||++|+||.+|..||.+.
T Consensus         3 ~~d~y~~Lgv~~~-----a~~~eik~ayr~la~k~HPD~~~-~~~~~~~f~~i~~Ay~~L~~~~kr~~yD~~g   69 (306)
T PRK10266          3 LKDYYAIMGVKPT-----DDLKTIKTAYRRLARKYHPDVSK-EPDAEARFKEVAEAWEVLSDEQRRAEYDQLW   69 (306)
T ss_pred             cCChHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CccHHHHHHHHHHHHHHhhhHHHHHHHHHhh
Confidence            3699999999998     89999999999999999999987 5678999999999999999999999999875

>KOG0719 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.60  E-value=7.5e-16  Score=136.79  Aligned_cols=70  Identities=44%  Similarity=0.720  Sum_probs=64.1

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCC--CChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRP--DDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~--~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|+|+||||..+     |++.+|++|||++++.||||+++  +..+|.+.|+.|+.||.||+|..+|+.||....
T Consensus        12 ~~~d~YevLGVer~-----a~~~eIrkAY~klal~~HPDk~~eed~~ea~~kFq~l~k~y~iLsDeekR~~YDetG~   83 (264)
T KOG0719|consen   12 NKKDLYEVLGVERD-----ATDKEIRKAYHKLALRLHPDKNHEEDKVEATEKFQQLQKAYQILSDEEKRAVYDETGS   83 (264)
T ss_pred             cccCHHHHhhhccc-----CCHHHHHHHHHHHHHHhCCCcchhhhHHHHHHHHHHHHHHHHHhhHHHHHHHHhccCC
Confidence            45699999999998     99999999999999999999994  455799999999999999999999999998754

>PRK14292 chaperone protein DnaJ; Provisional

Probab=99.60  E-value=1.1e-15  Score=147.22  Aligned_cols=67  Identities=30%  Similarity=0.600  Sum_probs=63.2

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +|||+||||+++     |+.++|++|||+++++||||+++ ++.+.+.|+.|++||++|+||.+|+.||.+..
T Consensus         2 ~d~y~~Lgv~~~-----a~~~~ik~ayr~l~~~~hpD~~~-~~~a~~~~~~i~~Ay~vL~d~~~r~~yd~~G~   68 (371)
T PRK14292          2 MDYYELLGVSRT-----ASADEIKSAYRKLALKYHPDRNK-EKGAAEKFAQINEAYAVLSDAEKRAHYDRFGT   68 (371)
T ss_pred             CChHHHcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCC-ChhHHHHHHHHHHHHHHhcchhhhhhHhhcCC
Confidence            599999999998     89999999999999999999997 67889999999999999999999999999753

>PRK14293 chaperone protein DnaJ; Provisional

Probab=99.59  E-value=1.3e-15  Score=146.72  Aligned_cols=68  Identities=31%  Similarity=0.643  Sum_probs=63.6

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+..+|++|||+++++||||+|+ ++.+.+.|+.|++||++|+||.+|+.||.+..
T Consensus         2 ~~d~y~vLgv~~~-----a~~~eik~ayr~la~~~HPD~~~-~~~a~~~f~~i~~Ay~vL~~~~~R~~yd~~g~   69 (374)
T PRK14293          2 AADYYEILGVSRD-----ADKDELKRAYRRLARKYHPDVNK-EPGAEDRFKEINRAYEVLSDPETRARYDQFGE   69 (374)
T ss_pred             CCChhhhcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCC-CcCHHHHHHHHHHHHHHHhchHHHHHHhhccc
Confidence            4699999999998     89999999999999999999998 57789999999999999999999999998753

>cd06257 DnaJ DnaJ domain or J-domain

Probab=99.58  E-value=3.1e-15  Score=104.84  Aligned_cols=55  Identities=47%  Similarity=0.950  Sum_probs=51.4

Q ss_pred             ccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccC
Q 022800            7 DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD   66 (292)
Q Consensus         7 d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d   66 (292)
                      |||+||||+++     ++.++|+++|+++++.||||++++.+.+.+.|..|+.||++|+|
T Consensus         1 ~~y~vLgl~~~-----~~~~~ik~~y~~l~~~~HPD~~~~~~~~~~~~~~l~~Ay~~L~d   55 (55)
T cd06257           1 DYYDILGVPPD-----ASDEEIKKAYRKLALKYHPDKNPDDPEAEEKFKEINEAYEVLSD   55 (55)
T ss_pred             ChHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHhcC
Confidence            79999999987     89999999999999999999997556788999999999999987

DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.

>COG2214 CbpA DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones]

Probab=99.56  E-value=5.1e-15  Score=128.86  Aligned_cols=72  Identities=40%  Similarity=0.746  Sum_probs=66.8

Q ss_pred             CCCCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh-HHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            1 MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-AHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         1 ~~~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~-a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      |.....|||+||||+++     ++..+|+++||+++++||||++++++. +.+.|..|++||++|+|+..|..||...
T Consensus         1 ~~~~~~~~y~iLgv~~~-----as~~eik~ayrkla~~~HPD~~~~~~~~a~~~f~~i~~Ay~vLsd~~~r~~yd~~~   73 (237)
T COG2214           1 MMSDLLDYYEILGVPPN-----ASLEEIKKAYRKLALKYHPDRNPGDPKVAEEKFKEINEAYEILSDPERRAEYDKIG   73 (237)
T ss_pred             CchhhhhHHHHhCCCCC-----CCHHHHHHHHHHHHHHhCCCCCCCchhHHHHHHHHHHHHHHHhhCHHHHHHhhhhc
Confidence            34567899999999987     999999999999999999999998885 9999999999999999999999999864

>PRK05014 hscB co-chaperone HscB; Provisional

Probab=99.55  E-value=2.7e-14  Score=123.67  Aligned_cols=96  Identities=20%  Similarity=0.303  Sum_probs=73.7

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh-----HHHHHHHHHHHHHHccCchhhhhHHHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSSYEILKDEKARKLFDDLLKIK   80 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~-----a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~   80 (292)
                      +|||+||||++.+   +++..+|+++||++++++|||+.++.+.     +.+.|..|++||++|+||..|+.|+..+...
T Consensus         1 ~~yf~llgl~~~~---~~d~~~L~~~yr~l~~~~HPDk~~~~~~~~~~~a~~~s~~iN~AY~~L~dp~~Ra~Yll~l~g~   77 (171)
T PRK05014          1 MDYFTLFGLPARY---DIDTQLLASRYQELQRQFHPDKFANASERERLLAVQQAATINDAYQTLKHPLKRAEYLLSLHGF   77 (171)
T ss_pred             CCHHHHCCCCCCC---CCCHHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHHHHHHHHHHHHCChhHHHHHHHHhcCC
Confidence            4899999999963   4789999999999999999999876543     5678999999999999999999999766532


Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHH
Q 022800           81 REKQQRQSQQDGKRRKMMSDLEERER  106 (292)
Q Consensus        81 ~~~~~r~~~~~~kr~~~~~dLe~RE~  106 (292)
                      .....  ......-.-+++.++.||.
T Consensus        78 ~~~~~--~~~~~d~efLme~me~rE~  101 (171)
T PRK05014         78 DLAHE--QHTVRDTAFLMEQMELREE  101 (171)
T ss_pred             ccccc--cCCcCCHHHHHHHHHHHHH
Confidence            21111  0011123467788888886

>KOG0721 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=1.4e-14  Score=127.64  Aligned_cols=69  Identities=35%  Similarity=0.685  Sum_probs=63.1

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .-|||+||||+++     +++.|||+|||+|+++|||||+|+-.+..+.|..|.+||..|+|+..|..|..+..
T Consensus        98 ~fDPyEILGl~pg-----as~~eIKkaYR~LSik~HPDK~~~~~~~e~~~~~I~KAY~aLTD~~sreN~ekYG~  166 (230)
T KOG0721|consen   98 KFDPYEILGLDPG-----ASEKEIKKAYRRLSIKYHPDKQPPEEGDEEFFEAIAKAYQALTDKKSRENWEKYGN  166 (230)
T ss_pred             cCCcHHhhCCCCC-----CCHHHHHHHHHHhhhhhCCCcCCCcchhHHHHHHHHHHHHHhcchhhHHHHHHhCC
Confidence            4699999999998     89999999999999999999998545667889999999999999999999998754

>PRK00294 hscB co-chaperone HscB; Provisional

Probab=99.50  E-value=1.4e-13  Score=119.31  Aligned_cols=97  Identities=21%  Similarity=0.298  Sum_probs=77.5

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh-----HHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~-----a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||++|||++..   .++..+|+++||+++++||||++++.+.     +.+.|..|+.||.+|+||..|+.|+..+.
T Consensus         2 ~~~~~F~l~~l~~~f---~id~~~L~~~Yr~Lq~~~HPDk~~~~~~~e~~~a~~~s~~IN~AY~~L~~p~~Ra~YlL~l~   78 (173)
T PRK00294          2 GTPCHFALFDLQPSF---RLDLDQLATRYRELAREVHPDRFADAPEREQRLALERSASLNEAYQTLKSPPRRARYLLALS   78 (173)
T ss_pred             CCCChhhhcCcCCCC---CCCHHHHHHHHHHHHHHHCcCCCCCCcHHHHHHHHHHHHHHHHHHHHhCChhhhHHHHHHhc
Confidence            578999999999974   6889999999999999999999877653     56789999999999999999999998776


Q ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 022800           79 IKREKQQRQSQQDGKRRKMMSDLEERER  106 (292)
Q Consensus        79 ~~~~~~~r~~~~~~kr~~~~~dLe~RE~  106 (292)
                      ......   ......-.-+++.|+.||.
T Consensus        79 g~~~~~---~~~~~d~~fLme~me~rE~  103 (173)
T PRK00294         79 GHEVPL---EVTVHDPEFLLQQMQLREE  103 (173)
T ss_pred             CCCCCc---ccCCCCHHHHHHHHHHHHH
Confidence            322111   1111133467888999987

>PRK03578 hscB co-chaperone HscB; Provisional

Probab=99.49  E-value=5.4e-14  Score=122.24  Aligned_cols=100  Identities=23%  Similarity=0.301  Sum_probs=75.7

Q ss_pred             CCCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhH-----HHHHHHHHHHHHHccCchhhhhHHHH
Q 022800            2 DVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDA-----HDNFQKLKSSYEILKDEKARKLFDDL   76 (292)
Q Consensus         2 ~~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a-----~~~f~~i~~Ay~vL~d~~~R~~YD~~   76 (292)
                      .....|||+||||++.+   +++..+|+++||+++++||||++++.+.+     .+.+..|+.||.+|+||..|+.|...
T Consensus         2 ~~~~~dyf~llglp~~f---~~d~~~L~~~yr~lq~~~HPD~~~~~~~~e~~~a~~~s~~iN~AY~tL~~p~~Ra~Yll~   78 (176)
T PRK03578          2 VSLKDDHFSLFGLPARF---ALDEAALDAAYRTVQAQVHPDRFAAAGDAEKRVAMQWATRANEAYQTLRDPLKRARYLLH   78 (176)
T ss_pred             CCCCCCHHHHcCCCCCC---CCCHHHHHHHHHHHHHHHCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHH
Confidence            34568999999999963   57899999999999999999998866654     34468999999999999999999987


Q ss_pred             HHHHHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 022800           77 LKIKREKQQRQSQQDGKRRKMMSDLEERER  106 (292)
Q Consensus        77 ~~~~~~~~~r~~~~~~kr~~~~~dLe~RE~  106 (292)
                      +........  ......-.-|++-++.||.
T Consensus        79 l~G~~~~~e--~~~~~d~~fLme~mE~rE~  106 (176)
T PRK03578         79 LRGVDVQAE--NNTAMPPAFLMQQMEWREA  106 (176)
T ss_pred             hcCCCCccc--cCCCCCHHHHHHHHHHHHH
Confidence            653211100  0111233467788888887

>KOG1150 consensus Predicted molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.49  E-value=3.6e-13  Score=117.30  Aligned_cols=71  Identities=31%  Similarity=0.580  Sum_probs=63.7

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC-hhHHHHHHHHHHHHHHccCchhhhhHHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD-PDAHDNFQKLKSSYEILKDEKARKLFDDLLKI   79 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~-~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~   79 (292)
                      -++|+|+||.|.++     .+.++|++.||++++..|||||||| +.|...|..+..||.+|-|+..|..-+....+
T Consensus        51 fnLNpfeVLqIdpe-----v~~edikkryRklSilVHPDKN~Dd~~rAqkAFdivkKA~k~l~n~~~rkr~~~~y~~  122 (250)
T KOG1150|consen   51 FNLNPFEVLQIDPE-----VTDEDIKKRYRKLSILVHPDKNPDDAERAQKAFDIVKKAYKLLENDKIRKRCLDVYTA  122 (250)
T ss_pred             cccChHHHHhcCCC-----CCHHHHHHHHHhhheeecCCCCcccHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence            47899999999998     8999999999999999999999998 67999999999999999999977765554443

>PRK01356 hscB co-chaperone HscB; Provisional

Probab=99.47  E-value=3e-13  Score=116.60  Aligned_cols=97  Identities=23%  Similarity=0.258  Sum_probs=71.4

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh---HHHHHHHHHHHHHHccCchhhhhHHHHHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD---AHDNFQKLKSSYEILKDEKARKLFDDLLKIKRE   82 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~---a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~~~   82 (292)
                      .|||+||||++..   +++..+|+++||+++++||||++++.++   +...|..|++||++|+||.+|+.|+..+..-..
T Consensus         2 ~~yf~llgl~~~f---~id~~~L~~aYr~lq~~~HPDk~~~~~~k~~~~~~s~~in~AY~~L~dp~~Ra~YlL~l~g~~~   78 (166)
T PRK01356          2 QNYFQLLGLPQEY---NIDLKILEKQYFAMQVKYHPDKAKTLQEKEQNLIIASELNNAYSTLKDALKRAEYMLLLQNINL   78 (166)
T ss_pred             CCHHHHcCCCCCC---CCCHHHHHHHHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHccCCCC
Confidence            5899999999973   4899999999999999999999874332   345688999999999999999999877642211


Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHH
Q 022800           83 KQQRQSQQDGKRRKMMSDLEERER  106 (292)
Q Consensus        83 ~~~r~~~~~~kr~~~~~dLe~RE~  106 (292)
                      ..... .....-.-+++.++.||.
T Consensus        79 ~~~~~-~~~~d~~fLme~me~rE~  101 (166)
T PRK01356         79 NDEKT-RSLLSPLELSIFWDEMER  101 (166)
T ss_pred             CCccc-cccCCHHHHHHHHHHHHH
Confidence            00000 000123356778888876

>TIGR03835 termin_org_DnaJ terminal organelle assembly protein TopJ

Probab=99.44  E-value=1.1e-13  Score=140.37  Aligned_cols=67  Identities=33%  Similarity=0.554  Sum_probs=63.1

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .|||+||||+++     |+..+||++||+++++||||++++ +.+...|+.|+.||++|+||.+|..||.+..
T Consensus         2 ~DYYeVLGVs~d-----AS~eEIKKAYRKLAKKyHPDKn~~-~eAeekFqeINEAYEVLSDP~KRa~YD~fG~   68 (871)
T TIGR03835         2 RDYYEVLGIDRD-----ADEQEIKKAFRKLAKKYHPDRNKA-PDAASIFAEINEANDVLSNPKKRANYDKYGH   68 (871)
T ss_pred             CChhHhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCC-hhHHHHHHHHHHHHHHhCCHHHHHHHhhhcc
Confidence            589999999998     899999999999999999999975 7888999999999999999999999999764

This model describes TopJ (MG_200, CbpA), a DnaJ homolog and probable assembly protein of the Mycoplasma terminal organelle. The terminal organelle is involved in both cytadherence and gliding motility.

>PHA03102 Small T antigen; Reviewed

Probab=99.40  E-value=1.7e-13  Score=116.23  Aligned_cols=64  Identities=28%  Similarity=0.393  Sum_probs=58.1

Q ss_pred             cccccccccccCCCCCCC--CHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKL--TEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a--~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..+|+||||+++     |  |..+||+|||++++++||||+++    .+.|+.|++||++|+|+..|..||....
T Consensus         5 ~~l~~vLGl~~~-----A~~s~~eIKkAYr~la~~~HPDkgg~----~e~~k~in~Ay~~L~d~~~r~~yd~~g~   70 (153)
T PHA03102          5 KELMDLLGLPRS-----AWGNLPLMRKAYLRKCLEFHPDKGGD----EEKMKELNTLYKKFRESVKSLRDLDGEE   70 (153)
T ss_pred             HHHHHHcCCCCC-----CCCCHHHHHHHHHHHHHHHCcCCCch----hHHHHHHHHHHHHHhhHHHhccccccCC
Confidence            357999999998     8  99999999999999999999753    3699999999999999999999998763

>KOG0720 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.40  E-value=9.6e-13  Score=126.71  Aligned_cols=70  Identities=39%  Similarity=0.657  Sum_probs=65.8

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKI   79 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~   79 (292)
                      +..|+|.+|||+++     +++.+||+.||++|...|||||- .|.|.+.|..|+.||++|+|+.+|..||..+..
T Consensus       233 ~~~daYsvlGl~~d-----~sd~~lKk~Yrk~A~LVhPDKn~-~~~A~Eafk~Lq~Afevig~~~kR~eYd~e~~k  302 (490)
T KOG0720|consen  233 NILDAYSALGLPSD-----CSDADLKKNYRKKAMLVHPDKNM-IPRAEEAFKKLQVAFEVIGDSVKRKEYDLELKK  302 (490)
T ss_pred             cCCCchhhcCCCCC-----CCHHHHHHHHHhhceEeCCCccC-ChhHHHHHHHHHHHHHHhcchhhhhHHHHHHHH
Confidence            35799999999987     99999999999999999999997 899999999999999999999999999998753

>KOG0722 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.32  E-value=8.5e-13  Score=118.81  Aligned_cols=71  Identities=37%  Similarity=0.605  Sum_probs=64.7

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKIKR   81 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~~   81 (292)
                      ..|+|+||||.++     ++..+|.+|||+||++||||+++ ++++...|..|..||++|.|...|..||-.+..-.
T Consensus        32 ~enCYdVLgV~Re-----a~KseIakAYRqLARrhHPDr~r-~~e~k~~F~~iAtayeilkd~e~rt~ydyaldhpd  102 (329)
T KOG0722|consen   32 AENCYDVLGVARE-----ANKSEIAKAYRQLARRHHPDRNR-DPESKKLFVKIATAYEILKDNETRTQYDYALDHPD  102 (329)
T ss_pred             chhHHHHhhhhhh-----ccHHHHHHHHHHHHHHhCCcccC-CchhhhhhhhhhcccccccchhhHHhHHHHhcCch
Confidence            4689999999998     89999999999999999999998 56677999999999999999999999998876433

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.24  E-value=4.9e-12  Score=118.84  Aligned_cols=69  Identities=32%  Similarity=0.553  Sum_probs=62.7

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh---hHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP---DAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~---~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ...|||.||||.++     |+..+|-||||++|.+||||-..+..   .|..+|.-|..|-+||+||.+|+.||+..
T Consensus       392 ~kRDYYKILGVkRn-----AsKqEI~KAYRKlAqkWHPDNFqdEeEKKkAEKKFIDIAAAKEVLsd~EkRrqFDnGe  463 (504)
T KOG0624|consen  392 GKRDYYKILGVKRN-----ASKQEITKAYRKLAQKWHPDNFQDEEEKKKAEKKFIDIAAAKEVLSDPEKRRQFDNGE  463 (504)
T ss_pred             ccchHHHHhhhccc-----ccHHHHHHHHHHHHHhcCCccccCHHHHHHHHHhhhhHHHHHHhhcCHHHHhhccCCC
Confidence            35799999999998     89999999999999999999987543   48889999999999999999999999864

>KOG0714 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.14  E-value=2.4e-11  Score=110.68  Aligned_cols=69  Identities=38%  Similarity=0.692  Sum_probs=61.5

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC-hhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD-PDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~-~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||.||||.++     ++..+|++||++++++||||+|+.+ ..+...|.+|.+||++|+|+.+|..||....
T Consensus         2 ~~d~~~~l~i~~~-----as~~~i~ka~~~~a~~~hpdk~~~~~~~~~~~~~~~~ea~~~ls~~~kr~~~d~~~~   71 (306)
T KOG0714|consen    2 GKDYYKILGIARS-----ASEEDIKKAYRKLALKYHPDKNPSPKEVAEAKFKEIAEAYEVLSDPKKRKIYDQYGE   71 (306)
T ss_pred             cccHHHHhCcccc-----ccHHHHHHHHHHHHHhhCCCCCCCchhhHHHHHhhhhccccccCCHHHhhhccccCc
Confidence            5799999999987     7888999999999999999998865 2455589999999999999999999999875

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.13  E-value=3.2e-11  Score=115.40  Aligned_cols=68  Identities=35%  Similarity=0.587  Sum_probs=64.0

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC-hhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD-PDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~-~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      -.|||.||||+.+     ++..+|++|||++++.||||++.++ .++...|..+..||.+|+||.+|..||...
T Consensus       372 Rkd~ykilGi~~~-----as~~eikkayrk~AL~~Hpd~~agsq~eaE~kFkevgeAy~il~d~~kr~r~dsg~  440 (486)
T KOG0550|consen  372 RKDWYKILGISRN-----ASDDEIKKAYRKLALVHHPDKNAGSQKEAEAKFKEVGEAYTILSDPMKRVRFDSGQ  440 (486)
T ss_pred             hhhHHHHhhhhhh-----cccchhhhHHHHHHHHhCCCcCcchhHHHHHHHHHHHHHHHHhcCHHHHhhccccc
Confidence            5799999999998     8999999999999999999999988 688999999999999999999999999764

>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional

Probab=99.12  E-value=5.9e-11  Score=109.65  Aligned_cols=56  Identities=34%  Similarity=0.543  Sum_probs=50.2

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCC--C-----hhHHHHHHHHHHHHHHccC
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPD--D-----PDAHDNFQKLKSSYEILKD   66 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~--~-----~~a~~~f~~i~~Ay~vL~d   66 (292)
                      .|+|+||||+++     +|.++||++||+++++||||++.+  .     +.+.+.|+.|++||++|+.
T Consensus       200 ~~ay~vLgv~~~-----as~~eIk~aYr~L~~~~HPDk~~~~g~~~~~~~~a~ek~~~I~~AYe~L~~  262 (267)
T PRK09430        200 EDAYKVLGVSES-----DDDQEIKRAYRKLMSEHHPDKLVAKGLPPEMMEMAKEKAQEIQAAYELIKK  262 (267)
T ss_pred             HhHHHHcCCCCC-----CCHHHHHHHHHHHHHHhCcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHH
Confidence            689999999998     899999999999999999999743  2     2478999999999999974

>PTZ00100 DnaJ chaperone protein; Provisional

Probab=99.10  E-value=7.4e-11  Score=95.54  Aligned_cols=52  Identities=21%  Similarity=0.338  Sum_probs=46.5

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHcc
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK   65 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~   65 (292)
                      ..++|+||||+++     +|.++|+++||++++++|||+. ++   ...|.+|++||++|.
T Consensus        64 ~~eAy~ILGv~~~-----As~~eIkkaYRrLa~~~HPDkg-Gs---~~~~~kIneAyevL~  115 (116)
T PTZ00100         64 KSEAYKILNISPT-----ASKERIREAHKQLMLRNHPDNG-GS---TYIASKVNEAKDLLL  115 (116)
T ss_pred             HHHHHHHcCCCCC-----CCHHHHHHHHHHHHHHhCCCCC-CC---HHHHHHHHHHHHHHh
Confidence            3689999999998     8999999999999999999985 33   468999999999985

>PRK01773 hscB co-chaperone HscB; Provisional

Probab=99.08  E-value=1.3e-09  Score=94.56  Aligned_cols=97  Identities=21%  Similarity=0.265  Sum_probs=73.9

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh-----HHHHHHHHHHHHHHccCchhhhhHHHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSSYEILKDEKARKLFDDLLKIK   80 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~-----a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~   80 (292)
                      .|||++|||++..   .++...+++.|+.+...+|||+..+.+.     +.+.-..||+||.+|.||..|+.|--.+...
T Consensus         2 ~nyF~lf~lp~~F---~iD~~~L~~~y~~Lq~~~HPD~f~~~~~~eq~~a~~~ss~iN~AY~tLkdPl~RA~YLL~L~~g   78 (173)
T PRK01773          2 NNPFALFDLPVDF---QLDNALLSERYLALQKSLHPDNFANSSAQEQRLAMQKSAEVNDALQILKDPILRAEAIIALNTG   78 (173)
T ss_pred             CChHHhcCCCCCC---CCCHHHHHHHHHHHHHHhCcCcccCCCHHHHHHHHHHHHHHHHHHHHHCChHHHHHHHHHhccC
Confidence            5899999999975   6999999999999999999999876542     4556789999999999999999998877621


Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHH
Q 022800           81 REKQQRQSQQDGKRRKMMSDLEERER  106 (292)
Q Consensus        81 ~~~~~r~~~~~~kr~~~~~dLe~RE~  106 (292)
                      ..... .......-.-+++-++.||.
T Consensus        79 ~~~~~-e~~~~~d~~fLme~ME~rE~  103 (173)
T PRK01773         79 EQQNL-EEKSTQDMAFLMQQMEWREQ  103 (173)
T ss_pred             CCCCc-ccccCCCHHHHHHHHHHHHH
Confidence            10000 01112233467888888886

>PHA02624 large T antigen; Provisional

Probab=99.00  E-value=3.6e-10  Score=113.78  Aligned_cols=59  Identities=31%  Similarity=0.436  Sum_probs=54.6

Q ss_pred             cccccccccccCCCCCCC--CHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhH
Q 022800            6 VDHYRVLGLPSGEEGAKL--TEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLF   73 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a--~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~Y   73 (292)
                      .++|+||||+++     +  +..+||+|||++|++||||++. +   .+.|+.|+.||++|+|+.++..|
T Consensus        11 ~elyelLGL~~~-----A~gs~~eIKkAYRkLAkkyHPDKgG-d---eekfk~Ln~AYevL~d~~k~~r~   71 (647)
T PHA02624         11 KELMDLLGLPMA-----AWGNLPLMRKAYLRKCKEYHPDKGG-D---EEKMKRLNSLYKKLQEGVKSARQ   71 (647)
T ss_pred             HHHHHHcCCCCC-----CCCCHHHHHHHHHHHHHHHCcCCCC-c---HHHHHHHHHHHHHHhcHHHhhhc
Confidence            479999999998     8  9999999999999999999964 3   57999999999999999999888

>TIGR00714 hscB Fe-S protein assembly co-chaperone HscB

Probab=98.99  E-value=4.2e-09  Score=90.08  Aligned_cols=83  Identities=25%  Similarity=0.266  Sum_probs=60.9

Q ss_pred             CCCHHHHHHHHHHHHHHhCCCCCCCCh-----hHHHHHHHHHHHHHHccCchhhhhHHHHHHHHHHHHHHHhhhhhHHHH
Q 022800           22 KLTEKEISKAYKWKALELHPDKRPDDP-----DAHDNFQKLKSSYEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRK   96 (292)
Q Consensus        22 ~a~~~eIkkaYrk~al~~HPDk~~~~~-----~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~~~~~~r~~~~~~kr~~   96 (292)
                      ..+..+|+++||+++.+||||+.++.+     .+...|..|++||++|+||.+|+.|...+...........  ...-.-
T Consensus         2 ~iD~~~L~~~yr~lq~~~HPD~~~~~~~~~~~~a~~~s~~iN~AY~~L~~p~~Ra~ylL~l~g~~~~~e~~~--~~d~~f   79 (157)
T TIGR00714         2 QLDTQALSLRYQDLQRQYHPDKFASGSAQEQLAAVQQSTTLNQAYQTLKDPLMRAEYMLSLHGIDLASEQHS--VRDTAF   79 (157)
T ss_pred             CCCHHHHHHHHHHHHHHHCcCCCCCCChhhhHHHHHHHHHHHHHHHHhCChhhhHHHHHHhcCCCCCcccCC--CCCHHH
Confidence            368899999999999999999976543     2668899999999999999999999998863221111001  112235


Q ss_pred             HHHHHHHHHH
Q 022800           97 MMSDLEERER  106 (292)
Q Consensus        97 ~~~dLe~RE~  106 (292)
                      +++-++.||.
T Consensus        80 Lme~Me~rE~   89 (157)
T TIGR00714        80 LMEQLELREE   89 (157)
T ss_pred             HHHHHHHHHH
Confidence            6677777775

This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.

>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]

Probab=98.93  E-value=6.5e-10  Score=107.15  Aligned_cols=67  Identities=27%  Similarity=0.641  Sum_probs=60.9

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCC-----ChhHHHHHHHHHHHHHHccCchhhhhHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPD-----DPDAHDNFQKLKSSYEILKDEKARKLFDDL   76 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~-----~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~   76 (292)
                      .-|||+||||+.+     +++.+||++||+|+.++||||.|.     ..+-.+.+..|++||..|+|...|..|-.+
T Consensus        97 ~fDPyEILGI~~~-----ts~rdik~~yr~Ls~KfhpdK~~~mvn~~rse~Ee~y~~ItkAY~~lTd~k~renyl~y  168 (610)
T COG5407          97 GFDPYEILGIDQD-----TSERDIKKRYRMLSMKFHPDKAPPMVNELRSEYEEKYKTITKAYGLLTDKKRRENYLNY  168 (610)
T ss_pred             CCChHHhhcccCC-----CcHHHHHHHHHhheeecChhhcCCCChhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhc
Confidence            4699999999998     899999999999999999999875     125688999999999999999999999877

>COG5269 ZUO1 Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]

Probab=98.91  E-value=8.2e-10  Score=100.52  Aligned_cols=73  Identities=32%  Similarity=0.436  Sum_probs=64.3

Q ss_pred             CCCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCC--CCChhHHHHHHHHHHHHHHccCchhhhhHHHH
Q 022800            2 DVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKR--PDDPDAHDNFQKLKSSYEILKDEKARKLFDDL   76 (292)
Q Consensus         2 ~~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~--~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~   76 (292)
                      +|...|+|.+|||+.-  ...++..+|.++.++...+||||+.  .++......|..|+.||+||+|+..|..||..
T Consensus        39 ~Wk~~DlYa~lgLsky--R~ka~~~qi~kah~kkv~kyHPDk~aa~g~~~~d~fFk~iqkA~evL~D~~~R~qyDS~  113 (379)
T COG5269          39 NWKKVDLYALLGLSKY--RTKAIPPQILKAHKKKVYKYHPDKTAAGGNKGCDEFFKLIQKAREVLGDRKLRLQYDSN  113 (379)
T ss_pred             hhhhhhHHHHhchHhh--hcCCCcHHHHHHHHHHHHHhCccchhccCCCCcHHHHHHHHHHHHHhccHHHHhhcccc
Confidence            4678999999999874  3368999999999999999999996  34556788999999999999999999999974

>PF13893 RRM_5: RNA recognition motif

Probab=98.90  E-value=3.2e-09  Score=74.58  Aligned_cols=54  Identities=33%  Similarity=0.364  Sum_probs=45.3

Q ss_pred             HHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEec
Q 022800          186 LREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPL  240 (292)
Q Consensus       186 L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~  240 (292)
                      |.++|++||+|..|.+.. +++|+|+|+|.+.++|..|+.  ++.-..++||.|.|.
T Consensus         1 L~~~f~~fG~V~~i~~~~-~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFK-KKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEET-TSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            789999999999999943 336999999999999999998  466678889999873

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=98.74  E-value=2.7e-08  Score=89.41  Aligned_cols=72  Identities=26%  Similarity=0.381  Sum_probs=63.1

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      +|+|  .+.+.+++++.|++||.+||.|..|.|.    ++..+|||||.|.+.++|..||.  +++|+....|.|.|..|
T Consensus       191 tvRv--tNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP  268 (270)
T KOG0122|consen  191 TVRV--TNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKP  268 (270)
T ss_pred             eeEE--ecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCC
Confidence            4444  4566789999999999999999999884    37789999999999999999997  58999999999999986

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=98.71  E-value=6.4e-08  Score=81.57  Aligned_cols=67  Identities=22%  Similarity=0.270  Sum_probs=57.8

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|+++|+++|++||.|.+|.|.    +++.+|+|||+|.+.++|..|+..  ...+.+.+|+|.|..+
T Consensus        41 nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~  113 (144)
T PLN03134         41 GLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAND  113 (144)
T ss_pred             CCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCc
Confidence            556679999999999999999999885    256799999999999999999975  4556789999999764

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.57  E-value=2e-07  Score=88.17  Aligned_cols=69  Identities=25%  Similarity=0.193  Sum_probs=59.3

Q ss_pred             eeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          174 WEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       174 Wk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .......++++.|.++|++||.|..|.|.    ++..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus       274 V~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       274 VYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             EeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            34455679999999999999999999885    356799999999999999999974  6667889999999853

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.55  E-value=1.2e-06  Score=80.26  Aligned_cols=68  Identities=21%  Similarity=0.235  Sum_probs=58.3

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec-CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS-SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~-~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ...+...|+++|+++|+.||.|.+|.|.. ...+|+|||+|.+.++|..|+. ++..+.+.+|.|.+..+
T Consensus        10 gNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         10 SNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAED   79 (260)
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccC
Confidence            34556799999999999999999999964 3468999999999999999996 47778899999999753

>PF00076 RRM_1: RNA recognition motif

Probab=98.52  E-value=3.1e-07  Score=65.95  Aligned_cols=53  Identities=36%  Similarity=0.568  Sum_probs=46.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCG  229 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g  229 (292)
                      .+.++|++.|+++|+.||.|..+.+..   +..+|+|||+|.+.++|..|+....|
T Consensus         6 lp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g   61 (70)
T PF00076_consen    6 LPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNG   61 (70)
T ss_dssp             ETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCC
Confidence            356799999999999999999988853   56799999999999999999986444

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=98.49  E-value=5.4e-07  Score=86.28  Aligned_cols=68  Identities=22%  Similarity=0.322  Sum_probs=56.1

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcCC----CCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCGN----LSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g~----~~~pl~v~~~~~  242 (292)
                      ......+|+++|+++|++||.|..|.|..    ++.+|+|||+|.+.++|+.||....+.    ...||.|.|..+
T Consensus       199 ~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       199 TNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEE  274 (346)
T ss_pred             eCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCc
Confidence            34556799999999999999999988852    456899999999999999999864443    347999999764

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=98.47  E-value=7.9e-07  Score=85.16  Aligned_cols=66  Identities=20%  Similarity=0.227  Sum_probs=56.8

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ....+|++.|+++|+.||+|.+|.|.    +.+++|+|||+|.+.++|..|+..  ...+...||+|.|..+
T Consensus       115 Lp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p  186 (346)
T TIGR01659       115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP  186 (346)
T ss_pred             CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccc
Confidence            45679999999999999999999874    256789999999999999999964  6667789999999764

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.46  E-value=5.1e-07  Score=71.66  Aligned_cols=65  Identities=25%  Similarity=0.390  Sum_probs=54.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec-CCCcceEEEEecCHHHHHHHHHhhcCCC--CCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS-SKKKGSALVVMATKSAAGAATGSVCGNL--SNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~-~k~~g~A~V~F~~~~~A~~Av~~~~g~~--~~pl~v~~~~  241 (292)
                      ....+|.+...+||.+||+|..|.|.+ ...+|+|||+|++..+|.+|+.+..|.-  +.+|.|.+-.
T Consensus        26 Lp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   26 LPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             CCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            566799999999999999999999964 5579999999999999999999866654  4455555543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.42  E-value=7.8e-07  Score=84.09  Aligned_cols=67  Identities=18%  Similarity=0.255  Sum_probs=57.8

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|+.||+|.+|.|..    ++.+|||||+|.+.++|..|+.  ++..+.+.+|.|.|..+
T Consensus        10 nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661        10 YLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            3556799999999999999999998842    5678999999999999999996  46677789999999765

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>smart00360 RRM RNA recognition motif

Probab=98.36  E-value=1.7e-06  Score=60.65  Aligned_cols=50  Identities=40%  Similarity=0.566  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhc
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVC  228 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~  228 (292)
                      ..++.+.|+++|+.||.|..|.+..    +..+|+|||+|.+.++|..|+....
T Consensus         6 ~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~   59 (71)
T smart00360        6 PDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALN   59 (71)
T ss_pred             cccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcC
Confidence            4589999999999999999998853    3348999999999999999997543

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

Probab=98.35  E-value=8.9e-07  Score=78.85  Aligned_cols=66  Identities=27%  Similarity=0.423  Sum_probs=57.1

Q ss_pred             cCCCCCHHHHHH----HhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLRE----IFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~----~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+..+.|++    |||.||.|.+|++. ..+.+|.|+|+|.+.++|-.|+..  ++-++++||++.+...
T Consensus        17 LnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s   89 (221)
T KOG4206|consen   17 LNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKS   89 (221)
T ss_pred             ccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccC
Confidence            456677777776    99999999999985 578899999999999999999987  6667899999999864

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=98.33  E-value=2.2e-06  Score=85.36  Aligned_cols=73  Identities=26%  Similarity=0.248  Sum_probs=56.8

Q ss_pred             EEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCCC----CCCeEEEecCC
Q 022800          170 LKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNL----SNPLLVLPLQP  242 (292)
Q Consensus       170 lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~~----~~pl~v~~~~~  242 (292)
                      +.|--......+|++.|.++|++||.|..|.|...+..|+|||+|.+.++|..|+....|..    .++|+|.|..+
T Consensus        97 ~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~  173 (481)
T TIGR01649        97 LRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKP  173 (481)
T ss_pred             EEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecC
Confidence            34433334557999999999999999999988544445899999999999999998644432    36899998764

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=98.30  E-value=8.3e-07  Score=85.40  Aligned_cols=66  Identities=36%  Similarity=0.505  Sum_probs=56.2

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcCC-----CCCCeEEEecCCC
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCGN-----LSNPLLVLPLQPA  243 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g~-----~~~pl~v~~~~~~  243 (292)
                      +-..|+.++++||++||.|++|.|..   +.++|+|||.|.+.+-|..||....|.     -+.||.|.|..+.
T Consensus       133 sK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtq  206 (510)
T KOG0144|consen  133 SKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQ  206 (510)
T ss_pred             cccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccC
Confidence            34589999999999999999999853   678999999999999999999874443     4689999998753

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.29  E-value=3.2e-06  Score=76.54  Aligned_cols=65  Identities=20%  Similarity=0.178  Sum_probs=56.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      .....|++.|+++|+.||+|.+|.|. ++...|+|||+|.+.++|..|+. ++.-+.+.|+.|.+..
T Consensus        13 LS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121         13 LSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            45569999999999999999999996 35567899999999999999996 5777888999998754

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=98.23  E-value=5.8e-06  Score=84.27  Aligned_cols=64  Identities=16%  Similarity=0.214  Sum_probs=55.5

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ...++++.|+++|+.||.|.+|.|..    ++.+|||||+|.+.++|..|+..  .+.+.+.+|.|.|.-
T Consensus       213 p~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       213 HPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             CCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            44689999999999999999998852    46799999999999999999975  666678999999854

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG1789 consensus Endocytosis protein RME-8, contains DnaJ domain [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]

Probab=98.23  E-value=1.3e-06  Score=91.53  Aligned_cols=61  Identities=21%  Similarity=0.377  Sum_probs=49.9

Q ss_pred             CCCCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHcc
Q 022800            1 MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK   65 (292)
Q Consensus         1 ~~~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~   65 (292)
                      |++..-+-|+||.|+-+- ++.-....||++|+++|.+|||||||   +..++|..+++||+.|+
T Consensus      1276 ~~mS~d~A~eiL~i~l~n-~~hD~~~KirrqY~kLA~kYHPDKNP---EGRemFe~VnKAYE~L~ 1336 (2235)
T KOG1789|consen 1276 ATMSVDLAREILSVDLTN-EEHDKPAKIRRQYYKLAAKYHPDKNP---EGREMFERVNKAYELLS 1336 (2235)
T ss_pred             CccchHHHHHHhccccCC-CCcccHHHHHHHHHHHHHHhCCCCCc---hHHHHHHHHHHHHHHHH
Confidence            455666789999998762 22234478999999999999999986   56789999999999998

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.23  E-value=3.4e-06  Score=61.18  Aligned_cols=51  Identities=31%  Similarity=0.421  Sum_probs=42.3

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEecC---CCcceEEEEecCHHHHHHHHHhhc
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKSS---KKKGSALVVMATKSAAGAATGSVC  228 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~~---k~~g~A~V~F~~~~~A~~Av~~~~  228 (292)
                      +...|++.|+++|+.||.|..|.+...   ..+|+|||+|.|.++|..|+....
T Consensus         7 p~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~   60 (70)
T PF14259_consen    7 PPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN   60 (70)
T ss_dssp             TTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC
Confidence            456899999999999999999998633   358999999999999999998643

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.21  E-value=1.7e-06  Score=77.64  Aligned_cols=48  Identities=27%  Similarity=0.441  Sum_probs=42.8

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      .....+.|++.|.+||+|+..+|++    ++++|++||+|.+.++|.+|+.+
T Consensus        22 w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d   73 (247)
T KOG0149|consen   22 WETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD   73 (247)
T ss_pred             cccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC
Confidence            3478899999999999999987764    77899999999999999999975

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

Probab=98.21  E-value=2.3e-06  Score=75.51  Aligned_cols=72  Identities=24%  Similarity=0.326  Sum_probs=57.7

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcC--CCCCCeEEEec
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCG--NLSNPLLVLPL  240 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~pl~v~~~  240 (292)
                      .+-||-.+...-.|.++|+.+|.+||.|.+|.|+-    ...+|||||-|....+|+.|+.+..|  +.+.-|.|...
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            44555555555689999999999999999999962    56799999999999999999987544  45667777654

>smart00361 RRM_1 RNA recognition motif

Probab=98.21  E-value=3.2e-06  Score=62.15  Aligned_cols=48  Identities=23%  Similarity=0.375  Sum_probs=39.8

Q ss_pred             HHHHHHHhc----ccCCeeEEE--Eec-----CCCcceEEEEecCHHHHHHHHHhhcCC
Q 022800          183 AERLREIFS----EFGKVEDVV--IKS-----SKKKGSALVVMATKSAAGAATGSVCGN  230 (292)
Q Consensus       183 ~~~L~~~fs----~yG~V~~v~--i~~-----~k~~g~A~V~F~~~~~A~~Av~~~~g~  230 (292)
                      +++|+++|+    +||.|.+|.  +..     +..+|+|||+|.+.++|..|+....|.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~   60 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGR   60 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            467888888    999999984  322     557999999999999999999976654

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=98.18  E-value=4.9e-06  Score=82.91  Aligned_cols=64  Identities=22%  Similarity=0.176  Sum_probs=54.8

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh----hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS----VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~----~~g~~~~pl~v~~~~~  242 (292)
                      ....+|++.|+++|+.||.|.+|.|.  +.+|+|||+|.+.++|..|+..    ..-+.+.||.|.|...
T Consensus        10 Lp~~~te~~L~~~f~~fG~V~~v~i~--~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~   77 (481)
T TIGR01649        10 LPQDVVEADLVEALIPFGPVSYVMML--PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTS   77 (481)
T ss_pred             CCCCCCHHHHHHHHHhcCCeeEEEEE--CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCC
Confidence            45569999999999999999999885  3569999999999999999974    3446789999999754

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=98.17  E-value=6.5e-06  Score=83.20  Aligned_cols=67  Identities=25%  Similarity=0.331  Sum_probs=57.2

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|+.||.|.+|.|.   .+..+|+|||+|.+.++|..|+..  ...+.+.||.|.|...
T Consensus       292 nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~  363 (562)
T TIGR01628       292 NLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR  363 (562)
T ss_pred             CCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccC
Confidence            345569999999999999999999875   256799999999999999999975  5566789999998754

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=98.17  E-value=4.6e-06  Score=71.92  Aligned_cols=66  Identities=21%  Similarity=0.257  Sum_probs=55.8

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCCC--CCCeEEEecC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNL--SNPLLVLPLQ  241 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~~--~~pl~v~~~~  241 (292)
                      -..+...++.+|..+|+.||+|-+|+|- -...|||||||++.-+|..|+.+..|.-  +.-+.|+...
T Consensus        16 GnL~~~a~k~eLE~~F~~yG~lrsvWvA-rnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen   16 GNLGSRATKRELERAFSKYGPLRSVWVA-RNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             ccCCCCcchHHHHHHHHhcCcceeEEEe-ecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3355678999999999999999999994 4679999999999999999999877776  5557887654

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=98.17  E-value=4.5e-06  Score=84.34  Aligned_cols=65  Identities=22%  Similarity=0.276  Sum_probs=55.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ....+|+++|+++|++||.|.+|.|.    +++++|+|||+|.+.++|.+|+..  .....++|+.|.|..
T Consensus         8 Lp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628         8 LDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence            45579999999999999999999884    256789999999999999999975  344678999999975

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>smart00362 RRM_2 RNA recognition motif

Probab=98.16  E-value=7.2e-06  Score=57.73  Aligned_cols=51  Identities=37%  Similarity=0.526  Sum_probs=43.4

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHhhc
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGSVC  228 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~~~  228 (292)
                      +..++.+.|+++|..||+|..+.+..  +..+|+|+|+|.+.++|..|+....
T Consensus         8 ~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~   60 (72)
T smart00362        8 PPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALN   60 (72)
T ss_pred             CCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhC
Confidence            44689999999999999999998853  3357999999999999999997644

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=98.15  E-value=1.1e-05  Score=82.25  Aligned_cols=64  Identities=20%  Similarity=0.203  Sum_probs=54.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      ....++++.|+++|++||+|.+|.|.    +++++|||||+|.+.++|..|+..  +.-+.+.+|.|.+.
T Consensus       115 Lp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       115 ISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             CCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            55679999999999999999999884    367899999999999999999975  44456778888753

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=98.14  E-value=1.4e-05  Score=56.52  Aligned_cols=61  Identities=43%  Similarity=0.527  Sum_probs=48.7

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEecC---CCcceEEEEecCHHHHHHHHHhhcCC--CCCCeEEE
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKSS---KKKGSALVVMATKSAAGAATGSVCGN--LSNPLLVL  238 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~~---k~~g~A~V~F~~~~~A~~Av~~~~g~--~~~pl~v~  238 (292)
                      ...++.+.|.++|..||.|..+.+...   ...|+|+|+|.+.++|..|+....|.  .+.++.|.
T Consensus         8 ~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~   73 (74)
T cd00590           8 PPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE   73 (74)
T ss_pred             CCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence            345899999999999999999998532   34899999999999999999875554  44455544

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=98.09  E-value=6.8e-06  Score=76.87  Aligned_cols=77  Identities=30%  Similarity=0.364  Sum_probs=56.4

Q ss_pred             CCccceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHHhhcCC--CCCCeEEEe
Q 022800          164 LDKEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATGSVCGN--LSNPLLVLP  239 (292)
Q Consensus       164 ~~~~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~~~~g~--~~~pl~v~~  239 (292)
                      ++..++|-|.  +....|-+-+|+.||.+||.|.+|.|+  ...+|||+||+|++.++|++|-....|.  -+.-+.|--
T Consensus        93 ~~~pkRLhVS--NIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVS--NIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCceeEee--cCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            3445566654  345568888999999999999999997  3678999999999999999997654433  333444444


Q ss_pred             cCC
Q 022800          240 LQP  242 (292)
Q Consensus       240 ~~~  242 (292)
                      ...
T Consensus       171 ATa  173 (376)
T KOG0125|consen  171 ATA  173 (376)
T ss_pred             cch
Confidence            433

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

Probab=98.09  E-value=5.1e-06  Score=68.96  Aligned_cols=64  Identities=25%  Similarity=0.289  Sum_probs=55.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      .....+++.+.+.|..||+|.+|.+.-    +=-+|||+|+|++.+.|..|+..  +..+++.++.|.|.
T Consensus        80 vHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   80 VHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             cCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            334589999999999999999999832    34589999999999999999975  56789999999993

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=98.03  E-value=1.4e-05  Score=78.33  Aligned_cols=66  Identities=26%  Similarity=0.345  Sum_probs=56.1

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .....+|++.|.++|+.||.|..|.|..    ++.+|+|||+|.+.++|..|+..  +..+.+.||.|.|..
T Consensus       193 nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       193 NLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            3456799999999999999999998852    46789999999999999999975  455678999999954

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=98.03  E-value=1.6e-05  Score=78.11  Aligned_cols=66  Identities=27%  Similarity=0.279  Sum_probs=56.2

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      ..+..++++.|.++|++||.|.+|.|..    ++.+|+|||+|.+.++|..|+. ++..+.++||.|.+..
T Consensus        96 nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        96 QLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecc
Confidence            3556799999999999999999999852    5679999999999999999996 3666778899988754

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=98.01  E-value=9.6e-06  Score=70.61  Aligned_cols=72  Identities=14%  Similarity=0.159  Sum_probs=63.1

Q ss_pred             EEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec-CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecC
Q 022800          170 LKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS-SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       170 lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~-~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~  241 (292)
                      -.|-|.+..+++-+..|.+||.+||.|..|.+++ ....+||||+|++.-+|+.||.  +.+.+-.+-|.|++..
T Consensus         7 ~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    7 RRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            3677888888899999999999999999999974 3447899999999999999996  4888899999999864

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

Probab=98.00  E-value=1e-05  Score=74.05  Aligned_cols=63  Identities=25%  Similarity=0.250  Sum_probs=55.0

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ....|++.|+..|+.||+|..|.|  -|.+|||||-|.+.++|..||-.  +....+++.+-.|-+.
T Consensus       173 ~~~lte~~mr~~Fs~fG~I~EVRv--Fk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  173 ASGLTEDLMRQTFSPFGPIQEVRV--FKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             CccccHHHHHHhcccCCcceEEEE--ecccceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            346999999999999999999998  47789999999999999999974  6667788988888654

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

Probab=98.00  E-value=1.2e-05  Score=74.50  Aligned_cols=63  Identities=22%  Similarity=0.339  Sum_probs=51.7

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcCC--CCCCeEEE
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCGN--LSNPLLVL  238 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g~--~~~pl~v~  238 (292)
                      ..+...+++.|+..|++||+|..|.|+    +++.+|||||||.+.-+...|..+-.|.  -+.-+.|.
T Consensus       108 RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen  108 RLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             eccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            467789999999999999999999885    4889999999999999999999864333  34444554

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=97.98  E-value=2e-05  Score=79.99  Aligned_cols=63  Identities=27%  Similarity=0.236  Sum_probs=54.5

Q ss_pred             cCCCCCHHHHHHHhccc--CCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCCC
Q 022800          177 FGEDYTAERLREIFSEF--GKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~y--G~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~~  243 (292)
                      ....+|++.|+++|+.|  |.|..|.+.    +++|||+|.+.++|..|+..  ...+.+.+|.|.|..|.
T Consensus       241 L~~~~tee~L~~~F~~f~~G~I~rV~~~----rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       241 LMTTTTEEIIEKSFSEFKPGKVERVKKI----RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPV  307 (578)
T ss_pred             CCCCCCHHHHHHHHHhcCCCceEEEEee----cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence            34568999999999999  999999773    57999999999999999974  56678899999999763

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=97.96  E-value=2.5e-05  Score=77.62  Aligned_cols=65  Identities=17%  Similarity=0.189  Sum_probs=55.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ....+|++.|.++|+.||.|..|.|.    +++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.+..
T Consensus       303 lp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       303 LPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45679999999999999999998874    256799999999999999999974  566678889999864

Members of this subfamily are found in plants, metazoa and fungi.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.93  E-value=4.2e-05  Score=64.09  Aligned_cols=77  Identities=18%  Similarity=0.179  Sum_probs=61.0

Q ss_pred             CccceEEEEeeec--CCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          165 DKEKVLKVSWEKF--GEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       165 ~~~~~lkvKWk~~--~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      +.+.+|.|+|-+.  ...++-..+..-++.||+|.+|.+ ++  +-+|+|+|.+..+|=+||.+ ..+-+++-+.-+|..
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-cG--rqsavVvF~d~~SAC~Av~Af~s~~pgtm~qCsWqq  160 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-CG--RQSAVVVFKDITSACKAVSAFQSRAPGTMFQCSWQQ  160 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-cC--CceEEEEehhhHHHHHHHHhhcCCCCCceEEeeccc
Confidence            3456899999663  334555667788899999999998 44  56999999999999999987 667777888888877


Q ss_pred             CCc
Q 022800          242 PAV  244 (292)
Q Consensus       242 ~~~  244 (292)
                      +.+
T Consensus       161 rFM  163 (166)
T PF15023_consen  161 RFM  163 (166)
T ss_pred             ccc
Confidence            543

>KOG0568 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.92  E-value=7.6e-06  Score=73.43  Aligned_cols=56  Identities=21%  Similarity=0.560  Sum_probs=48.4

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHH-HccCc
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYE-ILKDE   67 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~-vL~d~   67 (292)
                      +.||.||||..+     |+..+++.+|..++..+|||... +....+.|.+|.+||. ||+..
T Consensus        47 ~e~fril~v~e~-----~~adevr~af~~lakq~hpdsgs-~~adaa~f~qideafrkvlq~~  103 (342)
T KOG0568|consen   47 MECFRILGVEEG-----ADADEVREAFHDLAKQVHPDSGS-EEADAARFIQIDEAFRKVLQEK  103 (342)
T ss_pred             HHHHHHhccccc-----CchhHHHHHHHHHHHHcCCCCCC-ccccHHHHHHHHHHHHHHHHHH
Confidence            468999999998     89999999999999999999875 4556789999999998 76543

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

Probab=97.87  E-value=3.9e-05  Score=67.21  Aligned_cols=65  Identities=32%  Similarity=0.382  Sum_probs=57.0

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .+..+|++.|.++|..||.|..|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.+..
T Consensus       123 L~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         123 LPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            456799999999999999998888842    57899999999999999999986  567788999999964

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

Probab=97.82  E-value=4.5e-05  Score=62.85  Aligned_cols=64  Identities=17%  Similarity=0.124  Sum_probs=55.3

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .-.+++.|.+||++-|+|..|+|.-    ...=|++||+|-+.++|+.|+.+  .+-+-+.|+.+.|-..
T Consensus        46 fyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~G  115 (153)
T KOG0121|consen   46 FYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAG  115 (153)
T ss_pred             eeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecccc
Confidence            3478999999999999999999942    23469999999999999999996  7778899999999654

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.78  E-value=1.8e-05  Score=70.52  Aligned_cols=65  Identities=25%  Similarity=0.372  Sum_probs=57.6

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~~  243 (292)
                      ..+|+..|..-|-.||+|.+|.|+    +.+.+|+|||+|.-.++|.+||.+  +..+++..|+|-+..|.
T Consensus        20 deVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~   90 (298)
T KOG0111|consen   20 DEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPE   90 (298)
T ss_pred             HHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCc
Confidence            358888999999999999999995    378899999999999999999986  77888999999887764

>PLN03213 repressor of silencing 3; Provisional

Probab=97.78  E-value=9.2e-05  Score=72.72  Aligned_cols=73  Identities=18%  Similarity=0.233  Sum_probs=59.6

Q ss_pred             EEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCH--HHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          170 LKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATK--SAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       170 lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~--~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|=-......+++++|..+|+.||.|.+|.|+..+.+|||||+|.+.  .++..||..  ++...+..|+|.-..|
T Consensus        11 MRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         11 VRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            455555566789999999999999999999997544499999999987  678888874  6667888999986654

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

Probab=97.77  E-value=6.6e-05  Score=72.83  Aligned_cols=74  Identities=30%  Similarity=0.337  Sum_probs=61.8

Q ss_pred             ccceEEEEeee-cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          166 KEKVLKVSWEK-FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       166 ~~~~lkvKWk~-~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+.+|||=+-+ ....+|++.|..+|+.||.|+.|+.+    +-||||.|.+.++|..|+.+  .+.+-+.||-|...+|
T Consensus       255 ~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~----rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  255 TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP----RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecc----cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            34456666665 44569999999999999999999864    45999999999999999986  6777889999999887


Q ss_pred             C
Q 022800          243 A  243 (292)
Q Consensus       243 ~  243 (292)
                      .
T Consensus       331 ~  331 (506)
T KOG0117|consen  331 V  331 (506)
T ss_pred             h
Confidence            4

>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]

Probab=97.77  E-value=0.0002  Score=60.65  Aligned_cols=132  Identities=20%  Similarity=0.271  Sum_probs=87.1

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCC----CCh-hHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRP----DDP-DAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~----~~~-~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...+||.+||.....   .....-+.--|--...+.|||+..    +++ .|.+....|++||.+|.||-+|+.|-..+.
T Consensus         6 ~~~~ff~~Fg~e~~~---~~~p~~l~~~~~~~skkL~~d~~~~~~~~~~d~a~eqSa~lnkAY~TLk~pL~RA~Yilkl~   82 (168)
T KOG3192|consen    6 SPSRFFDIFGMELSF---KIDPDKLKEKYTDISKKLHPDRPGLSFAGDTDQASEQSAELNKAYDTLKDPLARARYLLKLK   82 (168)
T ss_pred             hHHHHHHHhccccCC---CCCcchhhHHHHHHHHhhCcccccccccccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence            356899999876652   355555665788999999999832    112 478889999999999999999999987765


Q ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 022800           79 IKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIARQLKEEIERIRAMHENK  142 (292)
Q Consensus        79 ~~~~~~~r~~~~~~kr~~~~~dLe~RE~~~~~~~~~~~~~~~~~~~~~~l~eE~~r~r~~~~~~  142 (292)
                      ....   -..+....-.-+++-|+.+|. ....+-.....+...+..+++...++.+++..+.+
T Consensus        83 g~e~---~sne~stDpe~Lmevle~~E~-IS~~~De~~l~~lk~q~q~ri~q~~~qlge~~esk  142 (168)
T KOG3192|consen   83 GQEQ---TSNELSTDPEFLMEVLEYHEA-ISEMDDEEDLKQLKSQNQERIAQCKQQLGEAFESK  142 (168)
T ss_pred             CCCC---chhhhccCHHHHHHHHHHHHH-HHhccCcHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            4222   123344444566777777776 33222222233444455666666777777665544

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=97.76  E-value=7.1e-05  Score=76.10  Aligned_cols=64  Identities=22%  Similarity=0.252  Sum_probs=51.4

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHhhcCCC---CCCeEEEe
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGSVCGNL---SNPLLVLP  239 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~~~g~~---~~pl~v~~  239 (292)
                      .....++++.|.++|++||.|.+|.|.   +++++|+|||+|.+.++|..||....|..   ...|.|.+
T Consensus        65 nLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        65 KIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            456679999999999999999999874   36789999999999999999998754432   34444443

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

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

Probab=97.69  E-value=7.5e-05  Score=74.03  Aligned_cols=63  Identities=29%  Similarity=0.260  Sum_probs=54.0

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...+++|..+||.||.|..|+|+.   ++..|||||.|....+|..|+..  .....+.|+-|.|.-+
T Consensus       128 ~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  128 KCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             ccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            355669999999999999999963   66789999999999999999985  5556789999999643

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=97.67  E-value=7.6e-05  Score=74.19  Aligned_cols=58  Identities=17%  Similarity=0.188  Sum_probs=48.4

Q ss_pred             HHHHHHhcccCCeeEEEEec-------CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          184 ERLREIFSEFGKVEDVVIKS-------SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       184 ~~L~~~fs~yG~V~~v~i~~-------~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      +.|+++|++||.|.+|+|..       +...|+|||+|.+.++|..|+..  +..+.+.+|.+.|..
T Consensus       434 edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~  500 (509)
T TIGR01642       434 EDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYG  500 (509)
T ss_pred             HHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeC
Confidence            56899999999999999852       23469999999999999999985  455678899988874

Members of this subfamily are found in plants, metazoa and fungi.

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

Probab=97.67  E-value=0.00016  Score=66.13  Aligned_cols=66  Identities=20%  Similarity=0.338  Sum_probs=57.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcC--CCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCG--NLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~pl~v~~~~~  242 (292)
                      ...++|+|.|+.||+.-|+|+++.+..    +.+-||+||.|-+.++|+.||....|  +-...++|++..|
T Consensus        49 LPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARP  120 (360)
T KOG0145|consen   49 LPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARP  120 (360)
T ss_pred             cccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccC
Confidence            556799999999999999999998853    56789999999999999999986554  5678899999876

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

Probab=97.66  E-value=0.00012  Score=67.24  Aligned_cols=64  Identities=27%  Similarity=0.345  Sum_probs=54.4

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcC--CCCCCeEEEecC
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCG--NLSNPLLVLPLQ  241 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~pl~v~~~~  241 (292)
                      ...++-+.|++-|.+||+|.+..|+    +.|++||+||.|-+..+|++||..+.|  +.+..++.-|..
T Consensus        71 s~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   71 SPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             chhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            3458889999999999999998774    388999999999999999999997555  566777888864

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

Probab=97.53  E-value=0.00021  Score=69.21  Aligned_cols=72  Identities=21%  Similarity=0.336  Sum_probs=57.9

Q ss_pred             ceEEEEeee----------cCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCC
Q 022800          168 KVLKVSWEK----------FGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSN  233 (292)
Q Consensus       168 ~~lkvKWk~----------~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~  233 (292)
                      +.++|-|..          .+..+|...|.++|+.||.|.++.+..  ...+|+ ||+|++.++|.+|+..  +--+.++
T Consensus        65 ~~~rim~s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~k  143 (369)
T KOG0123|consen   65 KPIRIMWSQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGK  143 (369)
T ss_pred             cEEEeehhccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCC
Confidence            457778876          345689999999999999999998853  448999 9999999999999986  4445677


Q ss_pred             CeEEEec
Q 022800          234 PLLVLPL  240 (292)
Q Consensus       234 pl~v~~~  240 (292)
                      ++.|...
T Consensus       144 ki~vg~~  150 (369)
T KOG0123|consen  144 KIYVGLF  150 (369)
T ss_pred             eeEEeec
Confidence            8877543

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

Probab=97.47  E-value=0.00021  Score=69.13  Aligned_cols=73  Identities=21%  Similarity=0.352  Sum_probs=57.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhc-----CCCCCCeEEEe
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVC-----GNLSNPLLVLP  239 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~-----g~~~~pl~v~~  239 (292)
                      .||+--....-.+||.+|+++|.+||.|..|.|+.    +-++|++||.|.+.++|..|+++..     --.-.|+.|.+
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            46666555666799999999999999999999863    4479999999999999999987622     22346777777


Q ss_pred             cC
Q 022800          240 LQ  241 (292)
Q Consensus       240 ~~  241 (292)
                      ..
T Consensus       114 Ad  115 (510)
T KOG0144|consen  114 AD  115 (510)
T ss_pred             cc
Confidence            64

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.45  E-value=0.00043  Score=68.74  Aligned_cols=66  Identities=24%  Similarity=0.337  Sum_probs=57.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      ...+++++.|+.||..||.|..|.+.    .+..+||+||+|.+.+.|.+|+.  +++.+.+-+|+|.-+..
T Consensus       286 LHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  286 LHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             cccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            34579999999999999999999884    26789999999999999999975  57778899999988764

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

Probab=97.42  E-value=0.00037  Score=68.65  Aligned_cols=72  Identities=21%  Similarity=0.129  Sum_probs=61.6

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .|-.......++++.|..+|+..|.|.++.+.    +++.+||||++|.+.+.|..||..  .....+.+|+|.|...
T Consensus        20 ~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   20 SVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             ceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            34444566789999999999999999999985    378899999999999999999986  6777889999999643

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

Probab=97.42  E-value=0.00028  Score=64.72  Aligned_cols=53  Identities=25%  Similarity=0.517  Sum_probs=46.5

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcCCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCGNL  231 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g~~  231 (292)
                      ..-++|+++.+|+.||.|+.+.+..   +.++|+|||-|.+.-+|..||....|.-
T Consensus        29 kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSq   84 (371)
T KOG0146|consen   29 KQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQ   84 (371)
T ss_pred             ccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccc
Confidence            3468999999999999999998852   6789999999999999999999866654

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

Probab=97.38  E-value=0.0006  Score=62.38  Aligned_cols=62  Identities=27%  Similarity=0.239  Sum_probs=53.4

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      .+.++..|-.||+.||.|.+|.|..    .+=+||+||.+.+.++|.+|+..  ++-+.+.-|.|+|-
T Consensus       288 pd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  288 PDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            4577888999999999999998852    56699999999999999999975  77778888999874

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

Probab=97.36  E-value=0.00042  Score=67.38  Aligned_cols=63  Identities=24%  Similarity=0.302  Sum_probs=54.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcCC---CCCCeEEEe
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCGN---LSNPLLVLP  239 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g~---~~~pl~v~~  239 (292)
                      ..-++.+|.|.-+|.+-|.|-.|.|.    ++.++|||||.|.+++.|..||....+.   .+.+|.|+-
T Consensus        91 IPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   91 IPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            34579999999999999999998873    4789999999999999999999865555   778888864

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.27  E-value=0.00089  Score=63.33  Aligned_cols=62  Identities=23%  Similarity=0.347  Sum_probs=49.7

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC---CCCCCeEEEecCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG---NLSNPLLVLPLQP  242 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g---~~~~pl~v~~~~~  242 (292)
                      ..+++..|++.|-+||+|..|++.  -.+|+|||+|.|..+|+.|....+.   .-+.-|.|.|-.+
T Consensus       238 d~v~e~dIrdhFyqyGeirsi~~~--~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  238 DEVLEQDIRDHFYQYGEIRSIRIL--PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cchhHHHHHHHHhhcCCeeeEEee--cccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            369999999999999999999984  4567999999999999999875322   1234467788765

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

Probab=97.24  E-value=0.00065  Score=69.90  Aligned_cols=63  Identities=17%  Similarity=0.331  Sum_probs=54.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ....+++.+|..+|..||.|++|.++  ..+|+|||++-...+|++|+.+  +++..+.-++|.|.-
T Consensus       429 i~k~v~e~dL~~~feefGeiqSi~li--~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  429 IPKNVTEQDLANLFEEFGEIQSIILI--PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             ccchhhHHHHHHHHHhcccceeEeec--cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            34469999999999999999999984  5689999999999999999986  677777778889953

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.23  E-value=3.3e-05  Score=67.15  Aligned_cols=64  Identities=19%  Similarity=0.252  Sum_probs=54.0

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      +...|+.+|.-.||.||.|++|.+.    +++++||||..|++.-+-..||.+  +.-..+..++|..+.
T Consensus        44 ~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   44 PYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            3468999999999999999999985    388999999999999999999987  444567778887653

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=97.19  E-value=0.00083  Score=59.43  Aligned_cols=67  Identities=18%  Similarity=0.272  Sum_probs=54.0

Q ss_pred             cCCCCCHHHHHHHhccc-CCeeEEEEe----cCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCCC
Q 022800          177 FGEDYTAERLREIFSEF-GKVEDVVIK----SSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~y-G~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~~  243 (292)
                      .+.++.+..+..+|..| |.|..+++.    +++++|||||+|.+.+-|.-|-.  |++=+++.-|.+.++.|.
T Consensus        57 ~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   57 IPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             cccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            44568888899999999 777777772    37889999999999999998876  466677888888887653

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

Probab=97.17  E-value=0.00046  Score=65.71  Aligned_cols=50  Identities=26%  Similarity=0.454  Sum_probs=44.2

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcC
Q 022800          180 DYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCG  229 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g  229 (292)
                      .+.+|.|+.-|..||+|.+|-|.    +.+.+|||||+|+-.++|..|+....|
T Consensus       124 El~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg  177 (544)
T KOG0124|consen  124 ELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNG  177 (544)
T ss_pred             EechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhcc
Confidence            47789999999999999999993    378999999999999999999986443

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

Probab=97.13  E-value=0.00067  Score=59.04  Aligned_cols=65  Identities=23%  Similarity=0.293  Sum_probs=56.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~  241 (292)
                      .....|++.|.+||-+-|+|.+|.|+.    .+..|||||+|.+.++|+=|++  +...+.+.||+|.-++
T Consensus        17 ld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   17 LDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            344588999999999999999999953    5679999999999999999997  5888999999998765

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

Probab=97.07  E-value=0.0012  Score=64.04  Aligned_cols=64  Identities=22%  Similarity=0.169  Sum_probs=55.3

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...|+..|.++|+.+|+|.+|.|- +..+-|+|+|.|.+..+|+.|+..  ..-+.+.|+.+.|...
T Consensus         8 ~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~r   74 (369)
T KOG0123|consen    8 PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQR   74 (369)
T ss_pred             CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhcc
Confidence            568999999999999999999882 113889999999999999999974  6667789999999764

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.00  E-value=0.0016  Score=61.86  Aligned_cols=49  Identities=24%  Similarity=0.262  Sum_probs=42.0

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG  225 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~  225 (292)
                      .|.-.+.++|.-|||.||.|.++.|+.    +.+--+|||+|.+.++|+.|.-
T Consensus       247 LNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyF  299 (479)
T KOG0415|consen  247 LNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYF  299 (479)
T ss_pred             cCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHh
Confidence            556588899999999999999988753    4556799999999999999974

>KOG0723 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.99  E-value=0.0015  Score=52.08  Aligned_cols=48  Identities=25%  Similarity=0.441  Sum_probs=41.2

Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCc
Q 022800           11 VLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDE   67 (292)
Q Consensus        11 iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~   67 (292)
                      ||||.++     ++.+.||.|+|++-+..|||+.. .|-   .-..|++|+++|...
T Consensus        61 IL~v~~s-----~~k~KikeaHrriM~~NHPD~GG-SPY---lAsKINEAKdlLe~~  108 (112)
T KOG0723|consen   61 ILGVTPS-----LDKDKIKEAHRRIMLANHPDRGG-SPY---LASKINEAKDLLEGT  108 (112)
T ss_pred             HhCCCcc-----ccHHHHHHHHHHHHHcCCCcCCC-CHH---HHHHHHHHHHHHhcc
Confidence            9999987     89999999999999999999874 553   345799999999754

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=96.79  E-value=0.0043  Score=60.00  Aligned_cols=66  Identities=26%  Similarity=0.221  Sum_probs=56.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~~  243 (292)
                      ....+|.|.|..+|+-||+|..|.|. .+++-.|+|.|++...|..|+.+  +..+.+++|+|.+.+.+
T Consensus       306 n~~~VT~d~LftlFgvYGdVqRVkil-~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  306 NEEAVTPDVLFTLFGVYGDVQRVKIL-YNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             chhccchhHHHHHHhhhcceEEEEee-ecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            44569999999999999999999995 44568999999999999999987  44567899999987643

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=96.67  E-value=0.0084  Score=54.80  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=63.3

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~~  243 (292)
                      ..+|--.....+++.++|+++|..||.+..|.|.   .+.+.|+|-|.|...++|..||.-  ++-+-+.||.+.-+.++
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            3566666677789999999999999999888883   377899999999999999999973  67777888999887664

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.62  E-value=0.0048  Score=63.09  Aligned_cols=65  Identities=26%  Similarity=0.213  Sum_probs=53.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCC-------CcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSK-------KKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k-------~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .+...|.+.|...|+++|.|.++.|...+       +.|+|||+|.+.++|..|+..  +.-+-+.+|.|....
T Consensus       523 lnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  523 LNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             CCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            34567889999999999999999984211       239999999999999999987  566778888888754

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

Probab=96.55  E-value=0.004  Score=54.28  Aligned_cols=66  Identities=23%  Similarity=0.278  Sum_probs=52.6

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeE--EEEe---cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          176 KFGEDYTAERLREIFSEFGKVED--VVIK---SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~--v~i~---~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .....+++..|.++||.||.|..  =++.   +++.+|+|+|.|++.+++..|+..  +.-+.+.|++|++..
T Consensus       103 NLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~  175 (203)
T KOG0131|consen  103 NLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAF  175 (203)
T ss_pred             ccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEE
Confidence            33446999999999999999877  2332   267899999999999999999986  444567888888864

>KOG0431 consensus Auxilin-like protein and related proteins containing DnaJ domain [General function prediction only]

Probab=96.48  E-value=0.003  Score=62.69  Aligned_cols=42  Identities=29%  Similarity=0.457  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHHHHhCCCCCCCCh-------hHHHHHHHHHHHHHHc
Q 022800           23 LTEKEISKAYKWKALELHPDKRPDDP-------DAHDNFQKLKSSYEIL   64 (292)
Q Consensus        23 a~~~eIkkaYrk~al~~HPDk~~~~~-------~a~~~f~~i~~Ay~vL   64 (292)
                      ++.++|||+||+.+|..||||.++.+       -|.+.|..|++|+...
T Consensus       400 Vtp~~VKKaYrKA~L~VHPDKlqq~gas~~qK~Iaekvfd~l~eawn~f  448 (453)
T KOG0431|consen  400 VTPAQVKKAYRKAVLCVHPDKLQQKGASLEQKYIAEKVFDALSEAWNKF  448 (453)
T ss_pred             cCHHHHHHHHHhhhheeCcccccCCcccHHHHHHHHHHHHHHHHHHHhh
Confidence            78999999999999999999987654       2566677777777643

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.35  E-value=0.0074  Score=42.21  Aligned_cols=39  Identities=21%  Similarity=0.370  Sum_probs=33.7

Q ss_pred             HHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHH
Q 022800          184 ERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAAT  224 (292)
Q Consensus       184 ~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av  224 (292)
                      +.+...|..||+|.++.+  ......++|.|.+..+|+.|+
T Consensus        15 ~~vl~~F~~fGeI~~~~~--~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   15 EEVLEHFASFGEIVDIYV--PESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             HHHHHHHHhcCCEEEEEc--CCCCcEEEEEECCHHHHHhhC
Confidence            456779999999999998  356779999999999999985

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

Probab=96.24  E-value=0.0064  Score=60.72  Aligned_cols=66  Identities=26%  Similarity=0.282  Sum_probs=56.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcC--CCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCG--NLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~pl~v~~~~~  242 (292)
                      .+...+.+.|.+.||.+|+|.+.++..    +.++||+||.|+=.+++..|+..-.+  +-++.|.|.++.+
T Consensus        13 lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen   13 LPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            456688899999999999999988753    46799999999999999999987555  7888999998865

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

Probab=96.23  E-value=0.011  Score=56.59  Aligned_cols=63  Identities=14%  Similarity=0.234  Sum_probs=53.1

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEE
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVL  238 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~  238 (292)
                      ....+.++++|...|..||+|..+.+-    ..+.+||+||+|.+..+-..||.  +.+.+.+.=|+|-
T Consensus       217 SvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVG  285 (544)
T KOG0124|consen  217 SVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVG  285 (544)
T ss_pred             ecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecc
Confidence            345679999999999999999999884    16689999999999999999986  5777777777764

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.17  E-value=0.0045  Score=63.27  Aligned_cols=65  Identities=18%  Similarity=0.249  Sum_probs=52.8

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...-+...++.||+.||.|.+|.|+.    +-.+|+|||+|-+...|.+|+.+  .+-+.+.-|.+.|...
T Consensus       622 pFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  622 PFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             chHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            34467788999999999999999952    22499999999999999999965  5556667789999864

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

Probab=96.07  E-value=0.026  Score=54.19  Aligned_cols=75  Identities=25%  Similarity=0.193  Sum_probs=60.6

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC----CCCCCeEEEecCCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG----NLSNPLLVLPLQPA  243 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g----~~~~pl~v~~~~~~  243 (292)
                      +.|.+.--.....+|.|.|.+|...-|.|..|+|- .|.--+|+|||++.+.|.+|-.+..|    ..=|.|+|.+.+|+
T Consensus       121 ~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIf-kkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  121 KVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIF-KKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             eEEEEEeecCccccchhhhhhhcCCCCceEEEEEE-eccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcc
Confidence            35666555556679999999999999999999983 45677999999999999999876433    34588999998875

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

Probab=96.06  E-value=0.022  Score=45.52  Aligned_cols=54  Identities=28%  Similarity=0.388  Sum_probs=34.1

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      .|+-...+...+-+.|.+.|+.||+|.-|-+.  +.-..|+|-|.+.++|..|+..
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~--~G~~~g~VRf~~~~~A~~a~~~   56 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS--RGDTEGYVRFKTPEAAQKALEK   56 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE----TT-SEEEEEESS---HHHHHHH
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEec--CCCCEEEEEECCcchHHHHHHH
Confidence            35555555668899999999999999998884  3345899999999999999986

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=95.97  E-value=0.014  Score=54.42  Aligned_cols=61  Identities=25%  Similarity=0.302  Sum_probs=48.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh--cCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV--CGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~--~g~~~~pl~v~~~~  241 (292)
                      .....++..|+.+|.+||.|..+-|+    |.||||..++..+|..||.+.  +-+-+.-+.|...+
T Consensus        10 Lp~~~~~~elr~lFe~ygkVlECDIv----KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSk   72 (346)
T KOG0109|consen   10 LPREATEQELRSLFEQYGKVLECDIV----KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASK   72 (346)
T ss_pred             CCcccchHHHHHHHHhhCceEeeeee----cccceEEeecccccHHHHhhcccceecceEEEEEecc
Confidence            34457889999999999999998884    569999999999999999974  44445555666543

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

Probab=95.95  E-value=0.014  Score=58.64  Aligned_cols=60  Identities=20%  Similarity=0.227  Sum_probs=46.3

Q ss_pred             CCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          181 YTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       181 ~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      .-..+|..|||+||.|+...|.+    ...+.|+||++.+...|...|.+  -..+-+.-+.|.-.
T Consensus       417 TRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  417 TRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             hhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            44567999999999998865542    55789999999999999999986  45555555666543

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

Probab=95.87  E-value=0.012  Score=54.21  Aligned_cols=59  Identities=20%  Similarity=0.276  Sum_probs=46.4

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcCC--CCCCeEEE
Q 022800          180 DYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCGN--LSNPLLVL  238 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g~--~~~pl~v~  238 (292)
                      .+.+..|..+|-.||.|.+-.|-    +..++.|+||.|+|..+|..||....|+  .=+-|+|.
T Consensus       296 EFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  296 EFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             hhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            47889999999999999885541    3668999999999999999999975554  22344444

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

Probab=95.71  E-value=0.015  Score=58.43  Aligned_cols=50  Identities=26%  Similarity=0.319  Sum_probs=42.4

Q ss_pred             CCHHHHHHHhcccCCeeEEEEe-c--CCCcceEEEEecCHHHHHHHHHhhcCC
Q 022800          181 YTAERLREIFSEFGKVEDVVIK-S--SKKKGSALVVMATKSAAGAATGSVCGN  230 (292)
Q Consensus       181 ~t~~~L~~~fs~yG~V~~v~i~-~--~k~~g~A~V~F~~~~~A~~Av~~~~g~  230 (292)
                      .-...|..+|++||+|.++.++ +  ++.+|+.|++|++..+|..||+...|.
T Consensus        76 klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~  128 (698)
T KOG2314|consen   76 KLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGK  128 (698)
T ss_pred             HHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccc
Confidence            3345577999999999999996 2  778999999999999999999975554

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

Probab=95.67  E-value=0.006  Score=57.73  Aligned_cols=46  Identities=37%  Similarity=0.575  Sum_probs=40.5

Q ss_pred             CCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh
Q 022800          181 YTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       181 ~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      .|++.|+..|++||.|.++++..    +.++|++||+|++.+....++..
T Consensus        18 ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~   67 (311)
T KOG4205|consen   18 TTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA   67 (311)
T ss_pred             ccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc
Confidence            78999999999999999988852    67899999999999888777765

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

Probab=95.52  E-value=0.012  Score=58.83  Aligned_cols=49  Identities=18%  Similarity=0.350  Sum_probs=43.9

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      ....++.+.|+.||+.||+|..|.. +..++|..||+|=++-+|+.|++.
T Consensus        83 l~~~Vsn~~L~~~f~~yGeir~ir~-t~~~~~~~~v~FyDvR~A~~Alk~  131 (549)
T KOG4660|consen   83 LPRSVSNDTLLRIFGAYGEIREIRE-TPNKRGIVFVEFYDVRDAERALKA  131 (549)
T ss_pred             cCCcCCHHHHHHHHHhhcchhhhhc-ccccCceEEEEEeehHhHHHHHHH
Confidence            4456999999999999999999776 677899999999999999999975

>COG1076 DjlA DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.40  E-value=0.0089  Score=51.85  Aligned_cols=69  Identities=22%  Similarity=0.344  Sum_probs=55.3

Q ss_pred             ccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh-----HHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            7 DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         7 d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~-----a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      |++.++|.+..+   ....+.+...|+.+...+|||.....+.     +...+..++.||.+|.||-.|..|-..+.
T Consensus         2 ~~~~~~~~~~~f---~~~~~~l~~~~~~~~~~~~~dr~~~~~~~~~~~~l~~~~~~~~a~~tLk~~l~ra~~~lal~   75 (174)
T COG1076           2 DGFVLFGLPRAF---QIDLDALKLQYRELQRAYHPDRFGKASEAEQRKALQQSAEVNPAYQTLKDPLLRAEYLLALA   75 (174)
T ss_pred             CcccccccHHHH---HHHHhHhhhhHHHHHHhhCcccccccchHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhc
Confidence            567777777653   3456778889999999999999765443     44579999999999999999999987665

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

Probab=95.39  E-value=0.023  Score=55.83  Aligned_cols=52  Identities=25%  Similarity=0.357  Sum_probs=43.9

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe--c--CCCcceEEEEecCHHHHHHHHHhh
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK--S--SKKKGSALVVMATKSAAGAATGSV  227 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~--~--~k~~g~A~V~F~~~~~A~~Av~~~  227 (292)
                      ....+.+.+.|.+.|..||+|...-|.  +  ++..+||||+|.+.+++..|+.+.
T Consensus       295 nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As  350 (419)
T KOG0116|consen  295 NLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS  350 (419)
T ss_pred             cCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC
Confidence            345678999999999999999997663  3  555699999999999999999874

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

Probab=95.36  E-value=0.029  Score=50.96  Aligned_cols=70  Identities=16%  Similarity=0.069  Sum_probs=55.6

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      |.|.....+.+.+.+...|+.+|.|..|.|+.    +..+|+|+|+|.+.+..++|+. ++..+.+.++.|+|..
T Consensus       104 v~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  104 VWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             EEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeee
Confidence            34444555666666999999999999888753    3468999999999999999998 6777778888888753

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

Probab=95.33  E-value=0.11  Score=53.69  Aligned_cols=65  Identities=15%  Similarity=0.225  Sum_probs=53.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe---c----CCCcceEEEEecCHHHHHHHHHhhcC--CCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK---S----SKKKGSALVVMATKSAAGAATGSVCG--NLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~---~----~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~pl~v~~~~  241 (292)
                      .+..++++.|...|..||+|.+|.|.   +    ..-+.++||-|.+..+|+.|+.+..|  ..+-+|++-|.+
T Consensus       182 lnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk  255 (877)
T KOG0151|consen  182 LNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGK  255 (877)
T ss_pred             CCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeecccc
Confidence            56679999999999999999999884   1    34588999999999999999987444  456677888853

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

Probab=95.23  E-value=0.031  Score=52.13  Aligned_cols=58  Identities=22%  Similarity=0.182  Sum_probs=50.3

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecC
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~  241 (292)
                      .-+.+.|+..|.+||+|...-|.    ++++||.|.-.++|..|+.  ++...-+.||+|....
T Consensus        89 tctn~ElRa~fe~ygpviecdiv----kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen   89 TCTNQELRAKFEKYGPVIECDIV----KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLST  148 (346)
T ss_pred             cccCHHHhhhhcccCCceeeeee----cceeEEEEeeccchHHHHhcccccccccceeeeeeec
Confidence            46778899999999999998873    6799999999999999995  5777889999998654

>COG1076 DjlA DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.21  E-value=0.014  Score=50.56  Aligned_cols=54  Identities=30%  Similarity=0.452  Sum_probs=45.5

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCC--Ch-----hHHHHHHHHHHHHHHc
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPD--DP-----DAHDNFQKLKSSYEIL   64 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~--~~-----~a~~~f~~i~~Ay~vL   64 (292)
                      .|.|.+||+...     ....+|+++|+++...+|||+-.+  .|     .+.+.++.|+.||+.+
T Consensus       113 ~~~l~~l~~~~~-----~~~~~i~~~~r~l~~e~~~d~a~~~~~~~e~~~~~~~~~~~i~~a~~~~  173 (174)
T COG1076         113 EDALKVLGVEIK-----ADQDAIKKAYRKLLSEQHPDKAAAKGLKLEFIEKLKEKLQEIQEAYEDI  173 (174)
T ss_pred             hhHHHHhcCchh-----hhHHHHHHHHHHHHHhcCHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhc
Confidence            689999999997     899999999999999999998432  23     3677888999998754

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

Probab=94.83  E-value=0.11  Score=49.93  Aligned_cols=71  Identities=23%  Similarity=0.239  Sum_probs=56.5

Q ss_pred             EEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          170 LKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       170 lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      |..-+.-+.+.++-|.|.+||--||.|..|.+. ..+.|.|+|++.+..+.++||.+  +.-+|+.-|.|.+.+
T Consensus       289 VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFm-kTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  289 VMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFM-KTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             EEEEEeccccccchhhhhhhhhhcCceeeEEEe-ecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            444444455668889999999999999999874 45789999999999999999986  555667777776543

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=94.81  E-value=0.033  Score=50.05  Aligned_cols=62  Identities=19%  Similarity=0.103  Sum_probs=51.3

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEec
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPL  240 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~  240 (292)
                      .++|++.|.++|-.=|+|..|.|.+  +.+..||+|.|.+..+..-|++  ++..+++.|+.+.+-
T Consensus        19 ~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen   19 SGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            3589999999999999999999964  2233399999999999999986  566778888888764

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=94.56  E-value=0.09  Score=51.56  Aligned_cols=65  Identities=23%  Similarity=0.260  Sum_probs=53.8

Q ss_pred             cCCCCCHHHHHHHhc-ccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFS-EFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs-~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ...+|-=.+|.+||. +-|.|.-|.+.   ++|.+|+|+|||++.+.+++|+..  -+.....||.|....
T Consensus        52 Ipyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   52 IPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             CcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            455666678888884 68999999885   489999999999999999999974  677788999997654

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

Probab=94.34  E-value=0.025  Score=50.82  Aligned_cols=59  Identities=20%  Similarity=0.280  Sum_probs=46.0

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC--CCCCCeEEEecC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG--NLSNPLLVLPLQ  241 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~pl~v~~~~  241 (292)
                      ....+..|..+|..||.|-+|.|    +.|++||+|.+.-+|..||....|  +...-+.|.|..
T Consensus        11 ~~~~~~d~E~~f~~yg~~~d~~m----k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen   11 YRARERDVERFFKGYGKIPDADM----KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             CccchhHHHHHHhhcccccccee----ecccceeccCchhhhhcccchhcCceecceeeeeeccc
Confidence            44678889999999999999999    478999999999999999975222  122226677765

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.30  E-value=0.078  Score=52.33  Aligned_cols=77  Identities=23%  Similarity=0.306  Sum_probs=56.2

Q ss_pred             EEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHH-HHhhcCCCCCCeEEEecCCCccCCC
Q 022800          170 LKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA-TGSVCGNLSNPLLVLPLQPAVATQI  248 (292)
Q Consensus       170 lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~A-v~~~~g~~~~pl~v~~~~~~~~~~~  248 (292)
                      |.+.-.+. ++-|-.+|..-|.+||.|.+|-|.  -..-.|+|+|.+..+|-.| .-++--+-+.+++|-|..|..-+..
T Consensus       375 l~lek~~~-glnt~a~ln~hfA~fG~i~n~qv~--~~~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps~~tn~  451 (526)
T KOG2135|consen  375 LALEKSPF-GLNTIADLNPHFAQFGEIENIQVD--YSSLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPSPVTNI  451 (526)
T ss_pred             hhhhccCC-CCchHhhhhhhhhhcCcccccccc--CchhhheeeeeccccccchhccccceecCceeEEEEecCCcccCc
Confidence            44444433 347788899999999999999983  2255899999999999444 4457777788999999877433333


Q ss_pred             C
Q 022800          249 P  249 (292)
Q Consensus       249 p  249 (292)
                      |
T Consensus       452 p  452 (526)
T KOG2135|consen  452 P  452 (526)
T ss_pred             c
Confidence            3

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

Probab=94.27  E-value=0.048  Score=51.71  Aligned_cols=73  Identities=25%  Similarity=0.307  Sum_probs=54.9

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      +.||.-.....++++.+|++.|.+||.|..+++.    ..+.+|+++|.|.+.++...++.. -..+-..++.|.-..
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeecc
Confidence            4566555677789999999999999999998874    267899999999999999998864 333333444444333

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=94.19  E-value=0.054  Score=54.16  Aligned_cols=61  Identities=31%  Similarity=0.326  Sum_probs=51.5

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEec
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPL  240 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~  240 (292)
                      ..+.-+|.++|+.+|.|.+|.|+.    ..++|.|+|+|-+..+.-.||. .+.-+.+.|+.|...
T Consensus       190 r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  190 RNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLS  255 (549)
T ss_pred             cCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEeccc
Confidence            356778999999999999999863    5679999999999999999885 477788889888753

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

Probab=93.07  E-value=0.056  Score=48.59  Aligned_cols=56  Identities=18%  Similarity=0.101  Sum_probs=47.8

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEE
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVL  238 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~  238 (292)
                      ..++...|.+.|.+||.+..+++    .+++|||+|.+.++|..|+.  ++.++++++|.+.
T Consensus       109 ~r~~~qdl~d~~~~~g~~~~~~~----~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen  109 LRVSWQDLKDHFRPAGEVTYVDA----RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             hhhhHHHHhhhhcccCCCchhhh----hccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence            34777889999999999955544    68899999999999999997  4888899999984

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=92.38  E-value=0.28  Score=46.78  Aligned_cols=64  Identities=20%  Similarity=0.275  Sum_probs=47.9

Q ss_pred             cceEEEEeeecCC--CCC-------HHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCC
Q 022800          167 EKVLKVSWEKFGE--DYT-------AERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGN  230 (292)
Q Consensus       167 ~~~lkvKWk~~~~--~~t-------~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~  230 (292)
                      +++|.|+.--...  .-+       +++|++=.++||.|..|+|-.....|-+.|.|.|.+.|..+|+...|.
T Consensus       265 ~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  265 DRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             CcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCe
Confidence            4577777665222  122       244556689999999999954556899999999999999999986664

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=91.63  E-value=0.33  Score=43.92  Aligned_cols=54  Identities=19%  Similarity=0.283  Sum_probs=44.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGN  230 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~  230 (292)
                      .+...|+|.|+.+|+.|--..-+.|........|||+|.+.+-|..|+.+..|.
T Consensus       218 l~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~  271 (284)
T KOG1457|consen  218 LGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGN  271 (284)
T ss_pred             cCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcc
Confidence            345699999999999998777676644445668999999999999999887776

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=91.61  E-value=0.12  Score=50.52  Aligned_cols=47  Identities=32%  Similarity=0.358  Sum_probs=38.2

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEec-----------CC------CcceEEEEecCHHHHHHHHH
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKS-----------SK------KKGSALVVMATKSAAGAATG  225 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~-----------~k------~~g~A~V~F~~~~~A~~Av~  225 (292)
                      .+..-+.|.+||+.+|.|.+|.|..           .+      .+-+|+|+|.+.++|..|..
T Consensus       241 ~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  241 LDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            3445599999999999999999821           11      26789999999999999986

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

Probab=90.81  E-value=0.58  Score=37.09  Aligned_cols=45  Identities=13%  Similarity=0.165  Sum_probs=34.5

Q ss_pred             CHHHHHHHhcccCCeeEEE-E----------ecCCCcceEEEEecCHHHHHHHHHh
Q 022800          182 TAERLREIFSEFGKVEDVV-I----------KSSKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       182 t~~~L~~~fs~yG~V~~v~-i----------~~~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      ..+.+.+.|++||+|.... +          +.....+.--|.|++..+|..|+..
T Consensus        18 ~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~   73 (100)
T PF05172_consen   18 ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK   73 (100)
T ss_dssp             GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh
Confidence            4566889999999998886 0          0123567899999999999999975

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=90.19  E-value=0.28  Score=47.77  Aligned_cols=72  Identities=22%  Similarity=0.147  Sum_probs=52.8

Q ss_pred             EEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhc----CCCCCCeEEEecC
Q 022800          170 LKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVC----GNLSNPLLVLPLQ  241 (292)
Q Consensus       170 lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~----g~~~~pl~v~~~~  241 (292)
                      |++--...-..+|-|.|..+||+||.|..|+--.....=+|+|.|.+...|..|-....    -..-|.|++.+..
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            44433334456899999999999999999876333334469999999999988876533    3456888888754

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=90.11  E-value=0.39  Score=44.13  Aligned_cols=51  Identities=18%  Similarity=0.261  Sum_probs=42.3

Q ss_pred             CCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcCCC
Q 022800          181 YTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCGNL  231 (292)
Q Consensus       181 ~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g~~  231 (292)
                      .|.++|-..|.+|-.-..-.+.    .++++||+||.|.+..++..|+....|..
T Consensus       202 vnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gky  256 (290)
T KOG0226|consen  202 VNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKY  256 (290)
T ss_pred             ccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccc
Confidence            8899999999999866554332    37899999999999999999998876653

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

Probab=89.54  E-value=0.66  Score=42.67  Aligned_cols=62  Identities=26%  Similarity=0.382  Sum_probs=48.7

Q ss_pred             CccceEEEEeee--------cCCCCCHHHHHHHhcccCCeeEEEEe-c--CCCcceEEEEecCHHHHHHHHHh
Q 022800          165 DKEKVLKVSWEK--------FGEDYTAERLREIFSEFGKVEDVVIK-S--SKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       165 ~~~~~lkvKWk~--------~~~~~t~~~L~~~fs~yG~V~~v~i~-~--~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      .+.+.|.|.+-.        .....+-|.|..-|+.||+|+.-|+. .  .+..|-++|+|...-.|..|...
T Consensus        19 ~~~~~lr~rfa~~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr   91 (275)
T KOG0115|consen   19 PKGRSLRVRFAMHAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARR   91 (275)
T ss_pred             CCCCceEEEeeccceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHH
Confidence            344567777665        23458889999999999999996653 2  56788899999999999999875

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

Probab=89.38  E-value=1.1  Score=34.55  Aligned_cols=45  Identities=20%  Similarity=0.389  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhc
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVC  228 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~  228 (292)
                      .+-..+|.+||+.||.|.--.| +   -.+|||...+.+.|..|+....
T Consensus        19 eWK~~DI~qlFspfG~I~VsWi-~---dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   19 EWKTSDIYQLFSPFGQIYVSWI-N---DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             T--HHHHHHHCCCCCCEEEEEE-C---TTEEEEEECCCHHHHHHHHHHT
T ss_pred             HhhhhhHHHHhccCCcEEEEEE-c---CCcEEEEeecHHHHHHHHHHhc
Confidence            3667889999999999976666 3   3499999999999998887643

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

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

Probab=88.99  E-value=1.3  Score=34.24  Aligned_cols=51  Identities=25%  Similarity=0.257  Sum_probs=35.8

Q ss_pred             HHHHHHhcccC-CeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          184 ERLREIFSEFG-KVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       184 ~~L~~~fs~yG-~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      ..|+.|+...| .|..|.      .|+|+|-|.+.+.|..|..-  +-.-|++-+.|.+.
T Consensus        21 ~RL~qLsdNCGGkVl~v~------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~   74 (90)
T PF11608_consen   21 NRLRQLSDNCGGKVLSVS------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFS   74 (90)
T ss_dssp             HHHHHHHHTTT--EEE--------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS
T ss_pred             HHHHHHhhccCCEEEEEe------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEc
Confidence            44888998887 676663      47999999999999999975  44567888889886

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=88.40  E-value=0.82  Score=45.99  Aligned_cols=57  Identities=21%  Similarity=0.293  Sum_probs=41.6

Q ss_pred             HHHHHHhcccCCeeEEEEec-------CCCcceEEEEecCHHHHHHHHHhhcCC--CCCCeEEEec
Q 022800          184 ERLREIFSEFGKVEDVVIKS-------SKKKGSALVVMATKSAAGAATGSVCGN--LSNPLLVLPL  240 (292)
Q Consensus       184 ~~L~~~fs~yG~V~~v~i~~-------~k~~g~A~V~F~~~~~A~~Av~~~~g~--~~~pl~v~~~  240 (292)
                      ++++.=+++||.|.+|.|+-       .-.-|.-||+|++.++|+.|.....|.  .+.....++.
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYy  489 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYY  489 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEec
Confidence            34566678999999999952       234788999999999999999885553  3344444444

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

Probab=87.44  E-value=1.5  Score=43.78  Aligned_cols=60  Identities=15%  Similarity=0.227  Sum_probs=48.5

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEE
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLV  237 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v  237 (292)
                      ....-|+++|.+.|+.- .|.++++.  +++..|=|+|||.+.+++.+|++......+++-.-
T Consensus        18 LPwsat~~ei~~Ff~~~-~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIE   79 (510)
T KOG4211|consen   18 LPWSATEKEILDFFSNC-GIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIE   79 (510)
T ss_pred             CCccccHHHHHHHHhcC-ceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEE
Confidence            34447889999999976 67888875  37889999999999999999999877666666443

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=83.22  E-value=1.6  Score=46.44  Aligned_cols=68  Identities=22%  Similarity=0.138  Sum_probs=54.5

Q ss_pred             EeeecCCC-CCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh----hcCCCCCCeEEEecCC
Q 022800          173 SWEKFGED-YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS----VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       173 KWk~~~~~-~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~----~~g~~~~pl~v~~~~~  242 (292)
                      .|....+. .....|...|..||+|..|.+  .+.--||.|.|.+..+|++|+..    -.|.+..+|.|.++.+
T Consensus       458 ~~sgglg~w~p~~~l~r~fd~fGpir~Idy--~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  458 LQSGGLGPWSPVSRLNREFDRFGPIRIIDY--RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             eccCCCCCCChHHHHHHHhhccCcceeeec--ccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            45543333 445668899999999999988  45566999999999999999986    6778889999998765

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=82.69  E-value=9.3  Score=30.09  Aligned_cols=53  Identities=25%  Similarity=0.229  Sum_probs=38.7

Q ss_pred             ecCCCCCHHHHHHHhcc--cCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhc
Q 022800          176 KFGEDYTAERLREIFSE--FGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVC  228 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~--yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~  228 (292)
                      ..+-.||.+.|.+++..  .|...=+.++    +..+.|||||-|.+..+|..-...-.
T Consensus         8 NIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~   66 (97)
T PF04059_consen    8 NIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFN   66 (97)
T ss_pred             cCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHc
Confidence            34445999998887755  3555556664    25679999999999999987766533

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=81.39  E-value=2.8  Score=41.47  Aligned_cols=60  Identities=27%  Similarity=0.294  Sum_probs=46.6

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHhhcCC
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGSVCGN  230 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~~~g~  230 (292)
                      ..+|.|+-  .+.+||=..|++-|..||.|.-+.|. .++.+|  +|-|.+.+.|+.|+....|.
T Consensus       536 a~qIiirN--lP~dfTWqmlrDKfre~G~v~yadime~GkskG--VVrF~s~edAEra~a~Mngs  596 (608)
T KOG4212|consen  536 ACQIIIRN--LPFDFTWQMLRDKFREIGHVLYADIMENGKSKG--VVRFFSPEDAERACALMNGS  596 (608)
T ss_pred             ccEEEEec--CCccccHHHHHHHHHhccceehhhhhccCCccc--eEEecCHHHHHHHHHHhccC
Confidence            33555543  45679999999999999999887763 466666  99999999999999865543

>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []

Probab=80.55  E-value=3.5  Score=34.12  Aligned_cols=32  Identities=28%  Similarity=0.367  Sum_probs=24.6

Q ss_pred             ccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCC
Q 022800            9 YRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRP   45 (292)
Q Consensus         9 Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~   45 (292)
                      ..||||++.     ++.++|.+.|..|-...+|++..
T Consensus        61 ~~ILnv~~~-----~~~eeI~k~y~~Lf~~Nd~~kGG   92 (127)
T PF03656_consen   61 RQILNVKEE-----LSREEIQKRYKHLFKANDPSKGG   92 (127)
T ss_dssp             HHHHT--G-------SHHHHHHHHHHHHHHT-CCCTS
T ss_pred             HHHcCCCCc-----cCHHHHHHHHHHHHhccCCCcCC
Confidence            469999996     89999999999999999999864

In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=80.49  E-value=2.4  Score=40.63  Aligned_cols=52  Identities=23%  Similarity=0.373  Sum_probs=35.7

Q ss_pred             HHHhcccCCeeEEEEec-----CCCcceE--EEEecCHHHHHHHHHhhcC--CCCCCeEEE
Q 022800          187 REIFSEFGKVEDVVIKS-----SKKKGSA--LVVMATKSAAGAATGSVCG--NLSNPLLVL  238 (292)
Q Consensus       187 ~~~fs~yG~V~~v~i~~-----~k~~g~A--~V~F~~~~~A~~Av~~~~g--~~~~pl~v~  238 (292)
                      .++|.+||.|..|+|..     ....+-+  +|+|.+.++|..+|..-.|  +.+.-|+.+
T Consensus       138 ~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkat  198 (480)
T COG5175         138 HEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKAT  198 (480)
T ss_pred             hhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceEeee
Confidence            48999999999999931     0112223  8999999999999986333  333344444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	292
3apo_A	780	Crystal Structure Of Full-Length Erdj5 Length = 780		1e-09
3apq_A	210	Crystal Structure Of J-Trx1 Fragment Of Erdj5 Lengt		1e-09
2dn9_A	79	Solution Structure Of J-Domain From The Dnaj Homolo		9e-09
2ctw_A	109	Solution Structure Of J-Domain From Mouse Dnaj Subf		1e-07
1bqz_A	77	J-Domain (Residues 1-77) Of The Escherichia Coli N-		2e-07
1xbl_A	107	Nmr Structure Of The J-Domain (Residues 2-76) In Th		3e-07
1bq0_A	103	J-Domain (Residues 1-77) Of The Escherichia Coli N-		4e-07
1hdj_A	77	Human Hsp40 (Hdj-1), Nmr Length = 77		6e-07
2och_A	73	J-domain Of Dnj-12 From Caenorhabditis Elegans Leng		9e-07
2ctq_A	112	Solution Structure Of J-Domain From Human Dnaj Subf		1e-06
2lo1_A	71	Nmr Structure Of The Protein Bc008182, A Dnaj-Like		5e-06
2dmx_A	92	Solution Structure Of The J Domain Of Dnaj Homolog		5e-06
2ej7_A	82	Solution Structure Of The Dnaj Domain Of The Human		7e-06
2cug_A	88	Solution Structure Of The J Domain Of The Pseudo Dn		8e-06
2lgw_A	99	Solution Structure Of The J Domain Of Hsj1a Length		1e-05
2ctr_A	88	Solution Structure Of J-Domain From Human Dnaj Subf		3e-05
2ctp_A	78	Solution Structure Of J-Domain From Human Dnaj Subf		1e-04

>pdb|3APO|A Chain A, Crystal Structure Of Full-Length Erdj5 Length = 780

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          + Y +LG+         + +EI +A+K  AL+LHPDK P++P+AH +F K+  +YE+LKD
Sbjct: 22 NFYSLLGV-----SKTASSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKD 76
Query: 67 EKARKLFD 74
          E  RK +D
Sbjct: 77 EDLRKKYD 84

>pdb|3APQ|A Chain A, Crystal Structure Of J-Trx1 Fragment Of Erdj5 Length = 210

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          + Y +LG+         + +EI +A+K  AL+LHPDK P++P+AH +F K+  +YE+LKD
Sbjct: 3  NFYSLLGVSK-----TASSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKD 57
Query: 67 EKARKLFD 74
          E  RK +D
Sbjct: 58 EDLRKKYD 65

>pdb|2DN9|A Chain A, Solution Structure Of J-Domain From The Dnaj Homolog, Human Tid1 Protein Length = 79

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 5/68 (7%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y++LG+P        ++KEI KAY   A + HPD   DDP A + F +L  +YE+L D
Sbjct: 8  DYYQILGVPR-----NASQKEIKKAYYQLAKKYHPDTNKDDPKAKEKFSQLAEAYEVLSD 62
Query: 67 EKARKLFD 74
          E  RK +D
Sbjct: 63 EVKRKQYD 70

>pdb|2CTW|A Chain A, Solution Structure Of J-Domain From Mouse Dnaj Subfamily C Menber 5 Length = 109

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 9  YRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEK 68
          Y VLGL         T  +I K+Y+  AL+ HPDK PD+P+A D F+++ +++ IL D  
Sbjct: 20 YHVLGLDKNA-----TSDDIKKSYRKLALKYHPDKNPDNPEAADKFKEINNAHAILTDAT 74
Query: 69 ARKLFD 74
           R ++D
Sbjct: 75 KRNIYD 80

>pdb|1BQZ|A Chain A, J-Domain (Residues 1-77) Of The Escherichia Coli N-Terminal Fragment (Residues 1-78) Of The Molecular Chaperone Dnaj, Nmr, 20 Structures Length = 77

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 5/68 (7%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+    E     E+EI KAYK  A++ HPD+   D +A   F+++K +YE+L D
Sbjct: 4  DYYEILGVSKTAE-----EREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTD 58
Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 59 SQKRAAYD 66

>pdb|1XBL|A Chain A, Nmr Structure Of The J-Domain (Residues 2-76) In The Escherichia Coli N-Terminal Fragment (Residues 2-108) Of The Molecular Chaperone Dnaj, 20 Structures Length = 107

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 5/68 (7%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+    E     E+EI KAYK  A++ HPD+   D +A   F+++K +YE+L D
Sbjct: 4  DYYEILGVSKTAE-----EREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTD 58
Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 59 SQKRAAYD 66

>pdb|1BQ0|A Chain A, J-Domain (Residues 1-77) Of The Escherichia Coli N-Terminal Fragment (Residues 1-104) Of The Molecular Chaperone Dnaj, Nmr, 20 Structures Length = 103

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 5/68 (7%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+    E     E+EI KAYK  A++ HPD+   D +A   F+++K +YE+L D
Sbjct: 4  DYYEILGVSKTAE-----EREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTD 58
Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 59 SQKRAAYD 66

>pdb|1HDJ|A Chain A, Human Hsp40 (Hdj-1), Nmr Length = 77

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 44/68 (64%), Gaps = 6/68 (8%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y+ LGL  G      +++EI +AY+ +AL  HPDK  + P A + F+++  +Y++L D
Sbjct: 4  DYYQTLGLARG-----ASDEEIKRAYRRQALRYHPDKNKE-PGAEEKFKEIAEAYDVLSD 57
Query: 67 EKARKLFD 74
           + R++FD
Sbjct: 58 PRKREIFD 65

>pdb|2OCH|A Chain A, J-domain Of Dnj-12 From Caenorhabditis Elegans Length = 73

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 8/72 (11%)
Query: 3  VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYE 62
          V    +Y VLG+         ++ E+ KAY+  AL+ HPDK   +PD  + F+++  +YE
Sbjct: 5  VKETGYYDVLGVKP-----DASDNELKKAYRKMALKFHPDK---NPDGAEQFKQISQAYE 56
Query: 63 ILKDEKARKLFD 74
          +L DEK R+++D
Sbjct: 57 VLSDEKKRQIYD 68

>pdb|2CTQ|A Chain A, Solution Structure Of J-Domain From Human Dnaj Subfamily C Menber 12 Length = 112

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 46/71 (64%), Gaps = 5/71 (7%)
Query: 4  DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEI 63
          D  D+Y +LG    +E + +  ++I   +K +ALE HPDK P++P A + FQKL+ + EI
Sbjct: 18 DTEDYYTLLGC---DELSSV--EQILAEFKVRALECHPDKHPENPKAVETFQKLQKAKEI 72
Query: 64 LKDEKARKLFD 74
          L +E++R  +D
Sbjct: 73 LTNEESRARYD 83

>pdb|2LO1|A Chain A, Nmr Structure Of The Protein Bc008182, A Dnaj-Like Domain From Homo Sapiens Length = 71

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 10/73 (13%)
Query: 3  VDHVDHYRVLGL-PSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSY 61
          V    +Y VLG+ P+       T++E+ KAY+  AL+ HPDK P++    + F+++  +Y
Sbjct: 3  VKETTYYDVLGVKPNA------TQEELKKAYRKLALKYHPDKNPNE---GEKFKQISQAY 53
Query: 62 EILKDEKARKLFD 74
          E+L D K R+L+D
Sbjct: 54 EVLSDAKKRELYD 66

>pdb|2DMX|A Chain A, Solution Structure Of The J Domain Of Dnaj Homolog Subfamily B Member 8 Length = 92

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 6/70 (8%)
Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEIL 64
           ++Y VLG+      A  + ++I KAY+  AL  HPDK PD+  +A   F+ +  +YE+L
Sbjct: 9  ANYYEVLGVQ-----ASASPEDIKKAYRKLALRWHPDKNPDNKEEAEKKFKLVSEAYEVL 63
Query: 65 KDEKARKLFD 74
           D K R L+D
Sbjct: 64 SDSKKRSLYD 73

>pdb|2EJ7|A Chain A, Solution Structure Of The Dnaj Domain Of The Human Protein Hcg3, A Hypothetical Protein Tmp_locus_21 Length = 82

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 43/70 (61%), Gaps = 6/70 (8%)
Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEIL 64
          VD+Y VL +P      + + + I KAY+  AL+ HPDK P++  +A   F+++  +YE+L
Sbjct: 9  VDYYEVLDVPR-----QASSEAIKKAYRKLALKWHPDKNPENKEEAERRFKQVAEAYEVL 63
Query: 65 KDEKARKLFD 74
           D K R ++D
Sbjct: 64 SDAKKRDIYD 73

>pdb|2CUG|A Chain A, Solution Structure Of The J Domain Of The Pseudo Dnaj Protein, Mouse Hypothetical Mkiaa0962 Length = 88

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK 65
           D YRVLG+         ++ +I KAYK  A E HPDK   DP A D F ++  +YEIL 
Sbjct: 17 FDPYRVLGVSR-----TASQADIKKAYKKLAREWHPDKN-KDPGAEDRFIQISKAYEILS 70
Query: 66 DEKARKLFD 74
          +E+ R  +D
Sbjct: 71 NEEKRTNYD 79

>pdb|2LGW|A Chain A, Solution Structure Of The J Domain Of Hsj1a Length = 99

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 42/68 (61%), Gaps = 6/68 (8%)
Query: 8  HYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-AHDNFQKLKSSYEILKD 66
          +Y +L +P        +  +I KAY+ KAL+ HPDK PD+ + A   F+++  +YE+L D
Sbjct: 4  YYEILDVPR-----SASADDIKKAYRRKALQWHPDKNPDNKEFAEKKFKEVAEAYEVLSD 58
Query: 67 EKARKLFD 74
          +  R+++D
Sbjct: 59 KHKREIYD 66

>pdb|2CTR|A Chain A, Solution Structure Of J-Domain From Human Dnaj Subfamily B Menber 9 Length = 88

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 8  HYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDE 67
          +Y +LG+P        +E++I KA+   A++ HPDK    PDA   F+++  +YE L D 
Sbjct: 9  YYDILGVPK-----SASERQIKKAFHKLAMKYHPDKN-KSPDAEAKFREIAEAYETLSDA 62
Query: 68 KARKLFDDL 76
            RK +D L
Sbjct: 63 NRRKEYDTL 71

>pdb|2CTP|A Chain A, Solution Structure Of J-Domain From Human Dnaj Subfamily B Menber 12 Length = 78

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 6/70 (8%)
Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+  G      +++++ KAY+  AL+ HPDK    P A + F+ + ++Y +L +
Sbjct: 8  DYYEILGVSRGA-----SDEDLKKAYRRLALKFHPDKN-HAPGATEAFKAIGTAYAVLSN 61
Query: 67 EKARKLFDDL 76
           + RK +D  
Sbjct: 62 PEKRKQYDQF 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	292
3apq_A	210	DNAJ homolog subfamily C member 10; thioredoxin fo	2e-17
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	6e-16
2ctq_A	112	DNAJ homolog subfamily C member 12; J-domain, chap	4e-14
1bq0_A	103	DNAJ, HSP40; chaperone, heat shock, protein foldin	1e-13
2ctw_A	109	DNAJ homolog subfamily C member 5; J-domain, chape	3e-13
2yua_A	99	Williams-beuren syndrome chromosome region 18 prot	4e-13
2dn9_A	79	DNAJ homolog subfamily A member 3; J-domain, TID1,	1e-12
3apo_A	780	DNAJ homolog subfamily C member 10; PDI family, th	1e-12
2qsa_A	109	DNAJ homolog DNJ-2; J-domain, HSP40, APC90001.8, s	2e-12
2pf4_E	174	Small T antigen; PP2A, SV40, DNAJ, aalpha subunit,	3e-12
2lgw_A	99	DNAJ homolog subfamily B member 2; J domain, HSJ1A	1e-11
1gh6_A	114	Large T antigen; tumor suppressor, oncoprotein, an	2e-11
1fpo_A	171	HSC20, chaperone protein HSCB; molecular chaperone	3e-11
2l6l_A	155	DNAJ homolog subfamily C member 24; DPH4, Zn-CSL,	4e-11
3lz8_A	329	Putative chaperone DNAJ; structure genomics, struc	4e-11
3hho_A	174	CO-chaperone protein HSCB homolog; structural geno	5e-11
2ctr_A	88	DNAJ homolog subfamily B member 9; J-domain, chape	1e-10
1hdj_A	77	Human HSP40, HDJ-1; molecular chaperone; NMR {Homo	2e-10
2dmx_A	92	DNAJ homolog subfamily B member 8; DNAJ J domain,	3e-10
2cug_A	88	Mkiaa0962 protein; DNAJ-like domain, structural ge	3e-10
2o37_A	92	Protein SIS1; HSP40, J-domain, cochaperone, APC900	4e-10
2ej7_A	82	HCG3 gene; HCG3 protein, DNAJ domain, NPPSFA, nati	4e-10
2ctp_A	78	DNAJ homolog subfamily B member 12; J-domain, chap	6e-10
2och_A	73	Hypothetical protein DNJ-12; HSP40, J-domain, chap	8e-10
2ys8_A	90	RAB-related GTP-binding protein RABJ; DNAJ domain,	4e-09
1wjz_A	94	1700030A21RIK protein; J-domain, DNAJ like protein	8e-09
1iur_A	88	KIAA0730 protein; DNAJ like domain, riken structur	6e-07
3uo3_A	181	J-type CO-chaperone JAC1, mitochondrial; structura	6e-07
3bvo_A	207	CO-chaperone protein HSCB, mitochondrial precurso;	7e-07
1faf_A	79	Large T antigen; J domain, HPD motif, anti-paralle	1e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-06
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	7e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-06
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-04
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-05
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-05
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-05
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-05
1n4c_A	182	Auxilin; four helix bundle, protein binding; NMR {	4e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-05
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	5e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-05
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-05
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-05
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	9e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-04
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-04
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-04
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	1e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-04
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-04
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-04
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-04
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-04
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-04
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-04
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-04
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-04
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-04
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-04
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-04
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-04
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-04
2qwo_B	92	Putative tyrosine-protein phosphatase auxilin; cha	4e-04
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-04
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-04
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-04
2guz_A	71	Mitochondrial import inner membrane translocase su	5e-04
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-04
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-04
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	6e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-04
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-04
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-04
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	7e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-04
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-04
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	9e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-04
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	9e-04

>3apq_A DNAJ homolog subfamily C member 10; thioredoxin fold, DNAJ domain, endoplasmic reticulum, oxidor; 1.84A {Mus musculus} Length = 210

 Score = 78.4 bits (193), Expect = 2e-17
 Identities = 29/68 (42%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          + Y +LG+         + +EI +A+K  AL+LHPDK P++P+AH +F K+  +YE+LKD
Sbjct: 3  NFYSLLGVSKTA-----SSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKD 57

Query: 67 EKARKLFD 74
          E  RK +D
Sbjct: 58 EDLRKKYD 65

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 71.0 bits (173), Expect = 6e-16
 Identities = 31/89 (34%), Positives = 48/89 (53%), Gaps = 8/89 (8%)

Query: 170 LKVSWEKFGED-----YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAAT 224
           LK+ W+   ED     Y+ + L  +  ++G+V ++V+ SSKK G+A+V  AT  AA  A 
Sbjct: 13  LKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVL-SSKKPGTAVVEFATVKAAELAV 71

Query: 225 GSVCGNLSNPLLV--LPLQPAVATQIPSA 251
            +  G + NPL +  L  QP  A+   S 
Sbjct: 72  QNEVGLVDNPLKISWLEGQPQDASGPSSG 100

>2ctq_A DNAJ homolog subfamily C member 12; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 112

 Score = 66.3 bits (162), Expect = 4e-14
 Identities = 27/68 (39%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG    +E +  + ++I   +K +ALE HPDK P++P A + FQKL+ + EIL +
Sbjct: 21 DYYTLLGC---DELS--SVEQILAEFKVRALECHPDKHPENPKAVETFQKLQKAKEILTN 75

Query: 67 EKARKLFD 74
          E++R  +D
Sbjct: 76 EESRARYD 83

>1bq0_A DNAJ, HSP40; chaperone, heat shock, protein folding, DNAK; NMR {Escherichia coli} SCOP: a.2.3.1 PDB: 1xbl_A 1bqz_A Length = 103

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 25/68 (36%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+          E+EI KAYK  A++ HPD+   D +A   F+++K +YE+L D
Sbjct: 4  DYYEILGVSKTA-----EEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTD 58

Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 59 SQKRAAYD 66

>2ctw_A DNAJ homolog subfamily C member 5; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Mus musculus} Length = 109

 Score = 64.0 bits (156), Expect = 3e-13
 Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
            Y VLGL         T  +I K+Y+  AL+ HPDK PD+P+A D F+++ +++ IL D
Sbjct: 18 SLYHVLGLDKNA-----TSDDIKKSYRKLALKYHPDKNPDNPEAADKFKEINNAHAILTD 72

Query: 67 EKARKLFD 74
             R ++D
Sbjct: 73 ATKRNIYD 80

>2yua_A Williams-beuren syndrome chromosome region 18 protein; J domain, all helix protein, chaperone, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 99

 Score = 63.2 bits (154), Expect = 4e-13
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
            Y +LG+PS       T+ +I  AY  +    HPD+     +A + F ++  +Y +L  
Sbjct: 18 ALYDLLGVPSTA-----TQAQIKAAYYRQCFLYHPDRNSGSAEAAERFTRISQAYVVLGS 72

Query: 67 EKARKLFD 74
             R+ +D
Sbjct: 73 ATLRRKYD 80

>2dn9_A DNAJ homolog subfamily A member 3; J-domain, TID1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 79

 Score = 61.1 bits (149), Expect = 1e-12
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y++LG+P        ++KEI KAY   A + HPD   DDP A + F +L  +YE+L D
Sbjct: 8  DYYQILGVPRNA-----SQKEIKKAYYQLAKKYHPDTNKDDPKAKEKFSQLAEAYEVLSD 62

Query: 67 EKARKLFD 74
          E  RK +D
Sbjct: 63 EVKRKQYD 70

>3apo_A DNAJ homolog subfamily C member 10; PDI family, thioredoxin, endoplasmic reticulum, oxidoreducta; 2.40A {Mus musculus} Length = 780

 Score = 67.1 bits (163), Expect = 1e-12
 Identities = 29/68 (42%), Positives = 45/68 (66%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          + Y +LG+         + +EI +A+K  AL+LHPDK P++P+AH +F K+  +YE+LKD
Sbjct: 22 NFYSLLGVSKTA-----SSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKD 76

Query: 67 EKARKLFD 74
          E  RK +D
Sbjct: 77 EDLRKKYD 84

>2qsa_A DNAJ homolog DNJ-2; J-domain, HSP40, APC90001.8, structural genomics, PSI-2, Pro structure initiative; 1.68A {Caenorhabditis elegans} Length = 109

 Score = 61.7 bits (150), Expect = 2e-12
 Identities = 23/99 (23%), Positives = 49/99 (49%), Gaps = 9/99 (9%)

Query: 7   DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD---AHDNFQKLKSSYEI 63
           + Y VL +   E      +++++KAY+  A + HPD+  +  +   A + F+ + ++YE 
Sbjct: 16  NCYDVLEVNREEF----DKQKLAKAYRALARKHHPDRVKNKEEKLLAEERFRVIATAYET 71

Query: 64  LKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLE 102
           LKD++A+  +D  L      Q+  +     R +    ++
Sbjct: 72  LKDDEAKTNYDYYL--DHPDQRFYNYYQYYRLRAAPKVD 108

>2pf4_E Small T antigen; PP2A, SV40, DNAJ, aalpha subunit, hydrolase regulat protein complex; 3.10A {Simian virus 40} PDB: 2pkg_C Length = 174

 Score = 63.0 bits (153), Expect = 3e-12
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 7/69 (10%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
              +LGL      A      + KAY  K  E HPDK  D+    +  +K+ + Y+ ++D
Sbjct: 12 QLMDLLGLE---RSAWGNIPLMRKAYLKKCKEFHPDKGGDE----EKMKKMNTLYKKMED 64

Query: 67 EKARKLFDD 75
                  D
Sbjct: 65 GVKYAHQPD 73

>2lgw_A DNAJ homolog subfamily B member 2; J domain, HSJ1A, CO-chaperon, chaperone; NMR {Homo sapiens} Length = 99

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 6/70 (8%)

Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-AHDNFQKLKSSYEIL 64
            +Y +L +P        +  +I KAY+ KAL+ HPDK PD+ + A   F+++  +YE+L
Sbjct: 2  ASYYEILDVPRSA-----SADDIKKAYRRKALQWHPDKNPDNKEFAEKKFKEVAEAYEVL 56

Query: 65 KDEKARKLFD 74
           D+  R+++D
Sbjct: 57 SDKHKREIYD 66

>1gh6_A Large T antigen; tumor suppressor, oncoprotein, antitumor protein; 3.20A {Simian virus 40} SCOP: a.2.3.1 Length = 114

 Score = 59.1 bits (143), Expect = 2e-11
 Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 7/92 (7%)

Query: 1  MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSS 60
          M  + +    +LGL      A      + KAY  K  E HPDK  D+    +  +K+ + 
Sbjct: 3  MREESLQLMDLLGLE---RSAWGNIPLMRKAYLKKCKEFHPDKGGDE----EKMKKMNTL 55

Query: 61 YEILKDEKARKLFDDLLKIKREKQQRQSQQDG 92
          Y+ ++D        D        +      D 
Sbjct: 56 YKKMEDGVKYAHQPDFGGFWDATEIPTYGTDE 87

>1fpo_A HSC20, chaperone protein HSCB; molecular chaperone; 1.80A {Escherichia coli} SCOP: a.2.3.1 a.23.1.1 Length = 171

 Score = 60.0 bits (145), Expect = 3e-11
 Identities = 20/153 (13%), Positives = 53/153 (34%), Gaps = 8/153 (5%)

Query: 6   VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSS 60
           +D++ + GLP      +L  + +S  ++    + HPDK           A      +  +
Sbjct: 1   MDYFTLFGLP---ARYQLDTQALSLRFQDLQRQYHPDKFASGSQAEQLAAVQQSATINQA 57

Query: 61  YEILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQE 120
           ++ L+    R  +   L       ++ + +D        +L E            +    
Sbjct: 58  WQTLRHPLMRAEYLLSLHGFDLASEQHTVRDTAFLMEQLELREELDEIEQAKDEARLESF 117

Query: 121 EEKIARQLKEEIERIRAMHENKRTPAAFASVKE 153
            +++ +      + +    +N+   AA  + ++
Sbjct: 118 IKRVKKMFDTRHQLMVEQLDNETWDAAADTCRK 150

>2l6l_A DNAJ homolog subfamily C member 24; DPH4, Zn-CSL, J-domain, chaperone; NMR {Homo sapiens} Length = 155

 Score = 59.1 bits (143), Expect = 4e-11
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 11/74 (14%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP------DAHDNFQKLKSS 60
          D Y +LG             ++ + Y+   L  HPDK+  D       +    F ++  +
Sbjct: 11 DWYSILGADPSA-----NISDLKQKYQKLILMYHPDKQSTDVPAGTVEECVQKFIEIDQA 65

Query: 61 YEILKDEKARKLFD 74
          ++IL +E+ ++ +D
Sbjct: 66 WKILGNEETKREYD 79

>3lz8_A Putative chaperone DNAJ; structure genomics, structural genomics, PSI-2, protein STRU initiative; 2.90A {Klebsiella pneumoniae subsp} PDB: 2kqx_A Length = 329

 Score = 61.5 bits (150), Expect = 4e-11
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+           K I  AY+  A + HPD    + DA   F+ L  ++E+LKD
Sbjct: 29 DYYAILGVQ---PTD--DLKTIKTAYRRLARKYHPDVSK-ENDAEAKFKDLAEAWEVLKD 82

Query: 67 EKARKLFD 74
          E+ R  +D
Sbjct: 83 EQRRAEYD 90

>2ctr_A DNAJ homolog subfamily B member 9; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 55.8 bits (135), Expect = 1e-10
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
           +Y +LG+P        +E++I KA+   A++ HPDK    PDA   F+++  +YE L D
Sbjct: 8  SYYDILGVPKSA-----SERQIKKAFHKLAMKYHPDKNK-SPDAEAKFREIAEAYETLSD 61

Query: 67 EKARKLFD 74
             RK +D
Sbjct: 62 ANRRKEYD 69

>1hdj_A Human HSP40, HDJ-1; molecular chaperone; NMR {Homo sapiens} SCOP: a.2.3.1 Length = 77

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 25/68 (36%), Positives = 44/68 (64%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y+ LGL  G      +++EI +AY+ +AL  HPDK   +P A + F+++  +Y++L D
Sbjct: 4  DYYQTLGLARGA-----SDEEIKRAYRRQALRYHPDKNK-EPGAEEKFKEIAEAYDVLSD 57

Query: 67 EKARKLFD 74
           + R++FD
Sbjct: 58 PRKREIFD 65

>2dmx_A DNAJ homolog subfamily B member 8; DNAJ J domain, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 6/70 (8%)

Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEIL 64
           ++Y VLG+ +       + ++I KAY+  AL  HPDK PD+  +A   F+ +  +YE+L
Sbjct: 9  ANYYEVLGVQASA-----SPEDIKKAYRKLALRWHPDKNPDNKEEAEKKFKLVSEAYEVL 63

Query: 65 KDEKARKLFD 74
           D K R L+D
Sbjct: 64 SDSKKRSLYD 73

>2cug_A Mkiaa0962 protein; DNAJ-like domain, structural genomics, molecular chaperone, NPPSFA; NMR {Mus musculus} Length = 88

 Score = 55.1 bits (133), Expect = 3e-10
 Identities = 29/68 (42%), Positives = 39/68 (57%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D YRVLG+         ++ +I KAYK  A E HPDK  D P A D F ++  +YEIL +
Sbjct: 18 DPYRVLGVSRTA-----SQADIKKAYKKLAREWHPDKNKD-PGAEDRFIQISKAYEILSN 71

Query: 67 EKARKLFD 74
          E+ R  +D
Sbjct: 72 EEKRTNYD 79

>2o37_A Protein SIS1; HSP40, J-domain, cochaperone, APC90055.5, structural genomics, PSI-2, protein structure initiative; 1.25A {Saccharomyces cerevisiae} Length = 92

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 8/68 (11%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
            Y +LG+          E+E+ K Y+  AL+ HPDK   D    + F+++  ++EIL D
Sbjct: 9  KLYDLLGVSPSA-----NEQELKKGYRKAALKYHPDKPTGDT---EKFKEISEAFEILND 60

Query: 67 EKARKLFD 74
           + R+++D
Sbjct: 61 PQKREIYD 68

>2ej7_A HCG3 gene; HCG3 protein, DNAJ domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 82

 Score = 54.6 bits (132), Expect = 4e-10
 Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 6/70 (8%)

Query: 6  VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEIL 64
          VD+Y VL +P        + + I KAY+  AL+ HPDK P++  +A   F+++  +YE+L
Sbjct: 9  VDYYEVLDVPRQA-----SSEAIKKAYRKLALKWHPDKNPENKEEAERRFKQVAEAYEVL 63

Query: 65 KDEKARKLFD 74
           D K R ++D
Sbjct: 64 SDAKKRDIYD 73

>2ctp_A DNAJ homolog subfamily B member 12; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 78

 Score = 53.8 bits (130), Expect = 6e-10
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+  G      +++++ KAY+  AL+ HPDK    P A + F+ + ++Y +L +
Sbjct: 8  DYYEILGVSRGA-----SDEDLKKAYRRLALKFHPDKNH-APGATEAFKAIGTAYAVLSN 61

Query: 67 EKARKLFD 74
           + RK +D
Sbjct: 62 PEKRKQYD 69

>2och_A Hypothetical protein DNJ-12; HSP40, J-domain, chaperone, APC90013.2, structural genomics, protein structure initiative; 1.86A {Caenorhabditis elegans} PDB: 2lo1_A Length = 73

 Score = 53.4 bits (129), Expect = 8e-10
 Identities = 25/68 (36%), Positives = 42/68 (61%), Gaps = 8/68 (11%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
           +Y VLG+         ++ E+ KAY+  AL+ HPDK   +PD  + F+++  +YE+L D
Sbjct: 9  GYYDVLGVKPDA-----SDNELKKAYRKMALKFHPDK---NPDGAEQFKQISQAYEVLSD 60

Query: 67 EKARKLFD 74
          EK R+++D
Sbjct: 61 EKKRQIYD 68

>2ys8_A RAB-related GTP-binding protein RABJ; DNAJ domain, RAS-associated protein RAP1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 90

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 6/65 (9%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D + +LG+  G      +  E++KAY+  A+ LHPDK    P + D F+ + ++   L  
Sbjct: 28 DSWDMLGVKPGA-----SRDEVNKAYRKLAVLLHPDKCV-APGSEDAFKAVVNARTALLK 81

Query: 67 EKARK 71
               
Sbjct: 82 NIKSG 86

>1wjz_A 1700030A21RIK protein; J-domain, DNAJ like protein, structural genomics, riken structural genomics/proteomics initiative, RSGI, chaperone; NMR {Mus musculus} SCOP: a.2.3.1 Length = 94

 Score = 51.3 bits (123), Expect = 8e-09
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 11/74 (14%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP------DAHDNFQKLKSS 60
          D Y +LG             ++ + Y+   L  HPDK+  D       +    F ++  +
Sbjct: 17 DWYSILGADPSA-----NMSDLKQKYQKLILLYHPDKQSADVPAGTMEECMQKFIEIDQA 71

Query: 61 YEILKDEKARKLFD 74
          ++IL +E+ +K +D
Sbjct: 72 WKILGNEETKKKYD 85

>1iur_A KIAA0730 protein; DNAJ like domain, riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Homo sapiens} SCOP: a.2.3.1 Length = 88

 Score = 45.9 bits (109), Expect = 6e-07
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 6/60 (10%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-AHDNFQKLKSSYEILK 65
          +   V+          L E E  K  +   L+ HPDK P++ D A++ F+ L++    L+
Sbjct: 17 EVTSVVEQAWK-----LPESERKKIIRRLYLKWHPDKNPENHDIANEVFKHLQNEINRLE 71

>3uo3_A J-type CO-chaperone JAC1, mitochondrial; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, J-protein; 1.85A {Saccharomyces cerevisiae} PDB: 3uo2_A Length = 181

 Score = 48.1 bits (114), Expect = 6e-07
 Identities = 24/152 (15%), Positives = 50/152 (32%), Gaps = 9/152 (5%)

Query: 7   DHYRVLGL--PSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEIL 64
             Y +     P       + +  + K Y+    + HPD         +    L  +Y  L
Sbjct: 12  TFYELFPKTFPKKLPIWTIDQSRLRKEYRQLQAQHHPDM---AQQGSEQSSTLNQAYHTL 68

Query: 65  KDEKARKLFDDLLKIKREKQQRQSQQDGKRRKM---MSDLEERERAAFAPDPAVKARQEE 121
           KD   R  +   L    +  Q Q+  +         +  L+  +  +   D A     E+
Sbjct: 69  KDPLRRSQYMLKLLRNIDLTQEQTSNEVTTSDPQLLLKVLDIHDELSQMDDEAGVKLLEK 128

Query: 122 EKIARQLKEEIERIRAMHENKRTPAAFASVKE 153
           +    ++++   ++   + +K   AA     E
Sbjct: 129 Q-NKERIQDIEAQLGQCYNDKDYAAAVKLTVE 159

>3bvo_A CO-chaperone protein HSCB, mitochondrial precurso; structural genomics medical relev protein structure initiative, PSI-2; 3.00A {Homo sapiens} Length = 207

 Score = 48.2 bits (114), Expect = 7e-07
 Identities = 22/152 (14%), Positives = 56/152 (36%), Gaps = 11/152 (7%)

Query: 7   DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSSY 61
           D++ ++         ++   ++   Y+     +HPD            +  +   +  +Y
Sbjct: 44  DYFSLMDCN---RSFRVDTAKLQHRYQQLQRLVHPDFFSQRSQTEKDFSEKHSTLVNDAY 100

Query: 62  EILKDEKARKLFDDLLKIKREKQQRQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEE 121
           + L    +R L+   LK+   +   ++  +  R+ ++  +E  E+ A A   A     E 
Sbjct: 101 KTLLAPLSRGLYL--LKLHGIEIPERTDYEMDRQFLIEIMEINEKLAEAESEAAMKEIES 158

Query: 122 EKIARQLKEEIERIRAMHENKRTPAAFASVKE 153
             +  + KE  + + +  E      A   + +
Sbjct: 159 I-VKAKQKEFTDNVSSAFEQDDFEEAKEILTK 189

>1faf_A Large T antigen; J domain, HPD motif, anti-parallel hairpin of helices, viral protein; NMR {Murine polyomavirus} SCOP: a.2.3.1 Length = 79

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 19/71 (26%), Positives = 27/71 (38%), Gaps = 7/71 (9%)

Query: 4  DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEI 63
          D      +L LP            + +AYK ++L LHPDK       H   Q+L S +  
Sbjct: 9  DKERLLELLKLP---RQLWGDFGRMQQAYKQQSLLLHPDKGGS----HALMQELNSLWGT 61

Query: 64 LKDEKARKLFD 74
           K E      +
Sbjct: 62 FKTEVYNLRMN 72

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 46.6 bits (110), Expect = 1e-06
 Identities = 22/102 (21%), Positives = 45/102 (44%), Gaps = 5/102 (4%)

Query: 128 LKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTAERLR 187
            +  ++ + ++       AA A+  +   + +G     +  VL++  E      T + L 
Sbjct: 10  AQAALQAVNSVQSGNLALAASAAAVDAGMAMAG-----QSPVLRIIVENLFYPVTLDVLH 64

Query: 188 EIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG 229
           +IFS+FG V  ++  +   +  AL+  A   +A  A  S+ G
Sbjct: 65  QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDG 106

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

 Score = 48.7 bits (115), Expect = 1e-06
 Identities = 31/182 (17%), Positives = 57/182 (31%), Gaps = 58/182 (31%)

Query: 3   VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRP----------------- 45
            D +       +        LT  E  K+   K L+  P   P                 
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDE-VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES 336

Query: 46  --DDPDAHDNFQK---------LKSSYEILKDEKARKLFDDL------LKIKREKQQRQS 88
             D     DN++          ++SS  +L+  + RK+FD L        I        +
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP-------T 389

Query: 89  Q------QDGKRRKMMSDLEERERAAFAPDPAVKARQEEEK-----IARQLKEEIERIRA 137
                   D  +  +M  + +  + +      V+ + +E       I  +LK ++E   A
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYS-----LVEKQPKESTISIPSIYLELKVKLENEYA 444

Query: 138 MH 139
           +H
Sbjct: 445 LH 446

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

 Score = 47.9 bits (113), Expect = 2e-06
 Identities = 36/206 (17%), Positives = 60/206 (29%), Gaps = 60/206 (29%)

Query: 27  EISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSY------EILK----DEKARKLFDDL 76
           E    YK   L +  D   D+ D  D     KS         I+          +LF  L
Sbjct: 13  EHQYQYK-DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL 71

Query: 77  LKIKREKQQR-----------------QSQQDGKRRKMMSDLEERERAAFAPDPAVK--- 116
           L  + E  Q+                 +++Q          +E+R+R         K   
Sbjct: 72  LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 117 ARQEEEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQSGSGGVG--------LDKEK 168
           +R +      +L++ +  +R        PA    +      G  G G            K
Sbjct: 132 SRLQPYL---KLRQALLELR--------PAKNVLID-----GVLGSGKTWVALDVCLSYK 175

Query: 169 VL-----KVSWEKFGEDYTAERLREI 189
           V      K+ W       + E + E+
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEM 201

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

 Score = 43.7 bits (102), Expect = 6e-05
 Identities = 37/286 (12%), Positives = 82/286 (28%), Gaps = 79/286 (27%)

Query: 2   DVDHV--------DHYRVLG--LPSGEEGAK-LTEKEISKAYKWKALELHPDKRPDDP-- 48
           ++DH+           R+    L   EE  +   E+ +   YK+    +        P  
Sbjct: 50  EIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIK--TEQRQPSM 107

Query: 49  ------DAHDNFQ---KLKSSYEILKDEKARKLFDDLLKIKRE------------KQ--- 84
                 +  D      ++ + Y + + +   KL   LL+++              K    
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVA 167

Query: 85  -------QRQSQQD--------GKRRKMMSDLEERERAAFAPDPAVKARQEEEKIARQLK 129
                  + Q + D               + LE  ++  +  DP   +R +     +   
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI 227

Query: 130 EEI-ERIR-----AMHEN----------KRTPAAFA-SVK---ETKQSGSGGVGLDKEKV 169
             I   +R       +EN           +   AF  S K    T+        L     
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDF-LSAATT 286

Query: 170 LKVSWEKFGEDYTAERLREIFSEF--GKVEDVVIKSSKKKGSALVV 213
             +S +      T + ++ +  ++   + +D  +       +   +
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQD--LPREVLTTNPRRL 330

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 137 AMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTAERLREIFSEFGKV 196
           ++       AA A+  +   + +G     +  VL++  E      T + L +IFS+FG V
Sbjct: 1   SVQSGNLALAASAAAVDAGMAMAG-----QSPVLRIIVENLFYPVTLDVLHQIFSKFGTV 55

Query: 197 EDVVIKSSKKKGSALVVMATKSAAGAATGSVCGN 230
             ++  +   +  AL+  A   +A  A  S+ G 
Sbjct: 56  LKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 89

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 180 DYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAATGSVCGNLSNPL 235
           +   + L+ +F EFGK+ ++ +     +   KG A +    + +A  A  ++    + P 
Sbjct: 24  NLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPG 83

Query: 236 LVLPLQPAVAT---QIPSAPK 253
           +  P+Q   A    +  S P 
Sbjct: 84  MNRPIQVKPADSESRGGSGPS 104

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A Length = 450

 Score = 46.2 bits (110), Expect = 7e-06
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 8/71 (11%)

Query: 7   DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP---DAHDNFQKLKSSYEI 63
           D+Y++LG+          ++EI KAY+  AL+ HPD   ++     A   F  + ++ E+
Sbjct: 383 DYYKILGVKRNA-----KKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKFIDIAAAKEV 437

Query: 64  LKDEKARKLFD 74
           L D + RK FD
Sbjct: 438 LSDPEMRKKFD 448

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 43.2 bits (102), Expect = 7e-06
 Identities = 17/70 (24%), Positives = 23/70 (32%), Gaps = 6/70 (8%)

Query: 156 QSGSGGVGLDKE--KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVV 213
            SGS G         V+ V      E      L E   +FG +  V++     K  ALV 
Sbjct: 2   SSGSSGSHHKVSVSPVVHVR--GLCESVVEADLVEALEKFGTICYVMMM--PFKRQALVE 57

Query: 214 MATKSAAGAA 223
                +A   
Sbjct: 58  FENIDSAKEC 67

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 44.5 bits (105), Expect = 9e-06
 Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           E  T + L  +F  +G V+ V I    KK +ALV MA  + A  A
Sbjct: 14  ERVTPQSLFILFGVYGDVQRVKI-LFNKKENALVQMADGNQAQLA 57

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 12/45 (26%), Positives = 18/45 (40%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
              + E L+ +FS  G V        K +  AL+ M +   A  A
Sbjct: 130 PSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQA 174

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 180 DYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
             T E L EI    G V+D+ +   ++ K KG A V    +S A  A
Sbjct: 28  SCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQA 74

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 44.6 bits (105), Expect = 1e-05
 Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           E  T + L  +F  +G V+ V I    KK +ALV MA  + A  A
Sbjct: 45  ERVTPQSLFILFGVYGDVQRVKI-LFNKKENALVQMADGNQAQLA 88

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 12/45 (26%), Positives = 18/45 (40%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
              + E L+ +FS  G V        K +  AL+ M +   A  A
Sbjct: 161 PSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQA 205

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 10/48 (20%), Positives = 24/48 (50%), Gaps = 3/48 (6%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
            +   + L+ +F + G + +V++   ++SK +G A +     + A  A
Sbjct: 17  RETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNA 64

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 6/92 (6%)

Query: 135 IRAMHENKRTPAAFASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTAERLREIFSEFG 194
             A+H N +         + K + S      +++ L +      +  T   +R +FS FG
Sbjct: 64  QNALH-NMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIG--MISKKCTENDIRVMFSSFG 120

Query: 195 KVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
           ++E+  I        +G A V   T++ A  A
Sbjct: 121 QIEECRILRGPDGLSRGCAFVTFTTRAMAQTA 152

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 180 DYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
             +   ++E+F+EFG ++   +   +S +  G+A V    K+ A  A
Sbjct: 40  GVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKA 86

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 157 SGSGGVGLDKEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDV-VIKSSKKKGSALVVMA 215
           SGS G    ++++ K+           E L  +  ++G VE    + +  +     V  +
Sbjct: 3   SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYS 62

Query: 216 TKSAAGAA 223
           +K  A  A
Sbjct: 63  SKDQARQA 70

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 3/50 (6%)

Query: 177 FGEDYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
                    +R  F+ +G V++V I   ++   KG   V           
Sbjct: 17  IDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKI 66

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           +  T   LR  F +FG++  + +   +++  A +  AT+ AA  A
Sbjct: 22  DTITETDLRNHFYQFGEIRTITV--VQRQQCAFIQFATRQAAEVA 64

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 2/46 (4%)

Query: 178 GEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           GED T   LR  FS FG + D+ +     +  A V      +A  A
Sbjct: 22  GEDMTPTLLRGAFSPFGNIIDLSMD--PPRNCAFVTYEKMESADQA 65

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 180 DYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
             + E +  +F  FG +++  +        KG A V  ++ + A AA
Sbjct: 26  QQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAA 72

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 2/48 (4%)

Query: 176 KFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
             G + +   L   F  FG +  +     K    A +   +  AA AA
Sbjct: 24  GLGPNTSLAALAREFDRFGSIRTIDHV--KGDSFAYIQYESLDAAQAA 69

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 4/48 (8%)

Query: 180 DYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
             T   L  IFS++GKV  V I     + K KG A ++   K +A   
Sbjct: 27  SLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 180 DYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
             +   ++E+F+EFG ++   +   +S +  G+A V    ++ A  A
Sbjct: 46  GVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKA 92

>1n4c_A Auxilin; four helix bundle, protein binding; NMR {Bos taurus} SCOP: a.2.3.1 PDB: 1xi5_J Length = 182

 Score = 42.5 bits (99), Expect = 4e-05
 Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 23  LTEKEISKAYKWKALELHPDKRPDDPD---AHDNFQKLKSSYEILKDEKARKLF 73
           +T +++ K Y+   L +HPDK    P    A   F +L  ++   +++  + L+
Sbjct: 129 VTPEQVKKVYRKAVLVVHPDKATGQPYEQYAKMIFMELNDAWSEFENQGQKPLY 182

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           D T E +R++F ++GK  +V I   K KG   + + T++ A  A
Sbjct: 26  DITEEEMRKLFEKYGKAGEVFIH--KDKGFGFIRLETRTLAEIA 67

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 12/74 (16%)

Query: 157 SGSGGVGLDKEKVLKV---SWEKFGEDYTAERLREIFSEFGKVEDVVI----KSSKKKGS 209
           SGS G  +D    LKV   ++       + + LR +F ++G+V DV I     +   +G 
Sbjct: 3   SGSSGPDVDGMITLKVDNLTY-----RTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGF 57

Query: 210 ALVVMATKSAAGAA 223
           A V    +  A  A
Sbjct: 58  AFVRFHDRRDAQDA 71

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 3/48 (6%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
                E L E+F + G +  V I   +  K K    V      +   A
Sbjct: 26  ARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYA 73

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 15/56 (26%), Positives = 20/56 (35%), Gaps = 4/56 (7%)

Query: 168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
            V+ +      +      L E   EFG +  VV+    KK  ALV       A  A
Sbjct: 22  PVVHIR--GLIDGVVEADLVEALQEFGPISYVVV--MPKKRQALVEFEDVLGACNA 73

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 3/45 (6%)

Query: 182 TAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
             ++L+E+FS  G V    I   K  K +G   V       A  A
Sbjct: 28  GWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQA 72

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           ED     L+E+F  FG +  + +     + + KG A +    +  A  A
Sbjct: 25  EDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 40.2 bits (95), Expect = 5e-05
 Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           TAE L   F   G V  V I     S   KG A +  + K +   +
Sbjct: 19  TAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           T   LRE+FS++G + DV I    +S + +G A V       A  A
Sbjct: 28  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
              T   L  +F+ F + +   I     + + +G A +    K  A  A
Sbjct: 35  PRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 83

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 177 FGEDYTAERLREIFSEFGKVEDVVIKSSKK-KGSALVVMATKSAAGAA 223
                TAE + +IF ++G +  + + ++ + +G+A VV      A  A
Sbjct: 16  LPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 63

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 175 EKFGEDYTAERLREIFSEFGKVEDVVI-KSSKKKGSALVVMATKSAAGAA 223
           EK  +D   + L  IFS FG++ D+++ +S K +G A V+    S+A  A
Sbjct: 18  EKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 41.7 bits (99), Expect = 6e-05
 Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
            D   +   E FS++G + D  +     + + +G   V   +  A    
Sbjct: 97  PDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           ++     L+++  ++G+VE+V I    ++ K  G A V+  +   A   
Sbjct: 16  DNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           + E L ++FS +G + ++       + K KG A V       A  A
Sbjct: 21  SEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 42.2 bits (98), Expect = 9e-05
 Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKK-KGSALVVMATKSAAGAA 223
           EK  +D   + L  IFS+FG++ D+++  S K +G A V+    S+A  A
Sbjct: 19  EKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 41.6 bits (97), Expect = 9e-05
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAA 223
            + T E   EI  E G      +K     S++  S L+   +KS A   
Sbjct: 133 LEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 182 TAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
             +R+  +F  +G VE V      K G+A+V MA   A   A
Sbjct: 18  NCDRVFNVFCLYGNVEKVKF-MKSKPGAAMVEMADGYAVDRA 58

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 10/42 (23%), Positives = 14/42 (33%), Gaps = 2/42 (4%)

Query: 182 TAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           T   L  +F  FG + D       +KG   +   T   A   
Sbjct: 40  TEADLIPLFQNFGFILDFKH--YPEKGCCFIKYDTHEQAAVC 79

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 177 FGEDYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
           F  D T + ++E   + G+V ++ +        KGS  VV  +  +A   
Sbjct: 19  FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 68

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 39.4 bits (93), Expect = 1e-04
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 182 TAERLREIFSEFGKVEDVVI-----KSSKKKGSALVVMATKSAAGAA 223
           T + + EIFS +GK++ + +          KG A V       A  A
Sbjct: 17  TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           ED     LR+ F ++GK+E + I     S KK+G A V      +    
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 41.3 bits (96), Expect = 1e-04
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 23/83 (27%)

Query: 67  EKARKLFDDLLKIKREKQQ-RQSQQDGKRRKMMSDLEERERAAFAPDPAVKARQEEEKIA 125
           E  RK         RE+Q+ R  + D   + M  +  E            KA+++ E+  
Sbjct: 85  ESIRKW--------REEQRKRLQELDAASKVMEQEWRE------------KAKKDLEEWN 124

Query: 126 RQLKEEIERIRAMHENKRTPAAF 148
           ++  E++E+ +    N+    AF
Sbjct: 125 QRQSEQVEKNKI--NNRIADKAF 145

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 9/71 (12%)

Query: 158 GSGGVGLDKE-----KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALV 212
           GS G   DK      +VL +   K   + T   +  +   FGKV ++++   K K  A +
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIR--KLPGEVTETEVIALGLPFGKVTNILM--LKGKNQAFL 56

Query: 213 VMATKSAAGAA 223
            +AT+ AA   
Sbjct: 57  ELATEEAAITM 67

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           E+ T E + + F+E+G+++++ +    ++   KG  LV   T   A AA
Sbjct: 33  EEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 2/45 (4%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
            D T   +  +   FGKV ++++   K K  A + M T+ AA   
Sbjct: 26  IDVTEGEVISLGLPFGKVTNLLML--KGKNQAFIEMNTEEAANTM 68

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 180 DYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
             +   ++E+F+EFG ++   +   +S +  G+A V    ++ A  A
Sbjct: 99  GVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKA 145

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 13/71 (18%)

Query: 166 KEKVLKVSWEK---------FGEDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALV 212
           +E+ L V  +               T ++  E+   FG +E   +    ++ + KG    
Sbjct: 83  RERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFA 142

Query: 213 VMATKSAAGAA 223
               K +A  A
Sbjct: 143 EYMKKDSAARA 153

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 40.0 bits (94), Expect = 4e-04
 Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 3/44 (6%)

Query: 183 AERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
            + L    S         +   +  + KG A++   T   A  A
Sbjct: 199 VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 242

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 4/48 (8%)

Query: 180 DYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           D   E L E+  +FG ++ V +     +   KG A     T+ AA   
Sbjct: 26  DSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           T + LR IF  FGK++++V+     + + KG   +  +    A  A
Sbjct: 18  TEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
             + L   F  FG + D+ I    ++ K +G A V       A AA
Sbjct: 20  DDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 2/45 (4%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
               A  ++E FS FG +  V++       +A+V       A  A
Sbjct: 20  AGTLAAEIQETFSRFGSLGRVLLPEG--GITAIVEFLEPLEARKA 62

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
            D T + LRE FS++G V DV I     +  A V  A    A + 
Sbjct: 15  GDMTEDELREFFSQYGDVMDVFIP-KPFRAFAFVTFADDQIAQSL 58

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
             + L ++FS++G++ +VV+    ++ + +G   V       A  A
Sbjct: 25  NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 2/45 (4%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
            D T   +  +   FGKV ++++   K K  A + M T+ AA   
Sbjct: 41  IDVTEGEVISLGLPFGKVTNLLML--KGKNQAFIEMNTEEAANTM 83

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 180 DYTAERLREIFSEFGKVE--DVVIKSSKKKGSALVVMATKSAAGAA 223
           D+T + L++ F+E G V   D+ +++ K KG  +V   +   A  A
Sbjct: 19  DFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 64

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 17/75 (22%), Positives = 28/75 (37%), Gaps = 19/75 (25%)

Query: 168 KVLKVSW-----EKFGE----------DYTAERLREIFSEFGKVEDVVI----KSSKKKG 208
           K LKVS+     E   +            T ++L  IF ++G +    I     + + +G
Sbjct: 73  KRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG 132

Query: 209 SALVVMATKSAAGAA 223
            A V    +  A  A
Sbjct: 133 VAFVRYNKREEAQEA 147

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           T   LRE+FS++G + DV I    +S + +G A V       A  A
Sbjct: 59  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 9/56 (16%), Positives = 22/56 (39%), Gaps = 2/56 (3%)

Query: 168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           + L V+    G   +  +L  +  + G V+ +++  +  K  +     T   +  A
Sbjct: 26  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN--KPYSFARYRTTEESKRA 79

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 4/44 (9%)

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
             T++ LR +F   G+V +  +     K  A V M  ++ A AA
Sbjct: 20  ACTSQELRSLFERRGRVIECDV----VKDYAFVHMEKEADAKAA 59

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 4/48 (8%)

Query: 180 DYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           + T E+L++IFSE G V    +    ++ K KG        +  A +A
Sbjct: 19  EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 20/76 (26%), Positives = 27/76 (35%), Gaps = 14/76 (18%)

Query: 157 SGSGGVGLDKEKVLKV-----SWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKK 207
           SGS GV    +K   +      W       T + L+E FS FG+V  V +K    +   K
Sbjct: 3   SGSSGVKRAVQKTSDLIVLGLPW-----KTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSK 57

Query: 208 GSALVVMATKSAAGAA 223
           G   V           
Sbjct: 58  GFGFVRFTEYETQVKV 73

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 37.4 bits (88), Expect = 4e-04
 Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAA 223
            + T E ++  F +FGKV+D ++     +++ +G   V   ++      
Sbjct: 9   VNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 17/104 (16%)

Query: 125 ARQLKEEIERIRAMHENKRTPAAF-ASVKETKQSGSGGVGLDKEKVLKVSWEKFGEDYTA 183
           A  ++    ++ A    +  P    A  K+     S  VG        V +       TA
Sbjct: 3   APCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVG-------NVDYGS-----TA 50

Query: 184 ERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           + L   FS  G +  + I     S   KG A +  A +++  AA
Sbjct: 51  QDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 5/47 (10%)

Query: 182 TAERLREIFSEFGKVEDVVI-----KSSKKKGSALVVMATKSAAGAA 223
               +RE+FS FG+++ V +      +   +G   V   TK  A  A
Sbjct: 28  NQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
            D   E++RE F  FG+VE + +    K++K++G   +    +      
Sbjct: 9   PDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 159 SGGVGLDKEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKS 218
           SG  G+ K KVL V         T E L + FS+FGK+E V       K  A +    + 
Sbjct: 3   SGSSGMAKVKVLFVR--NLANTVTEEILEKAFSQFGKLERVKK----LKDYAFIHFDERD 56

Query: 219 AAGAA 223
            A  A
Sbjct: 57  GAVKA 61

>2qwo_B Putative tyrosine-protein phosphatase auxilin; chaperone-cochaperone complex, ATP-binding, nucleotide-bindi nucleus, phosphorylation, stress response; HET: ADP; 1.70A {Bos taurus} PDB: 2qwp_B* 2qwq_B* 2qwr_B* 2qwn_B* 1nz6_A Length = 92

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 23 LTEKEISKAYKWKALELHPDKRPDDPD---AHDNFQKLKSSYEILKDE 67
          +T +++ K Y+   L +HP K    P    A   F +L  ++   +++
Sbjct: 45 VTPEQVKKVYRKAVLVVHPCKATGQPYEQYAKMIFMELNDAWSEFENQ 92

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           E+   + ++E F ++G+++++ +    ++   KG ALV   T   A AA
Sbjct: 36  EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           E+ T E + + F+E+G+++++ +    ++   KG  LV   T   A AA
Sbjct: 32  EEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 4/44 (9%)

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
             T + LR  F E+G V +  I     K  A V M     A  A
Sbjct: 21  TCTNQELRAKFEEYGPVIECDI----VKDYAFVHMERAEDAVEA 60

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 37.9 bits (89), Expect = 4e-04
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 179 EDYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
            +     LRE F +FG V +VV+    +  + +G   +    + +   A
Sbjct: 20  HNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA 68

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 7/49 (14%)

Query: 182 TAERLREIFSEFGKVEDVVIKSSKK-------KGSALVVMATKSAAGAA 223
           T E L+ +FS+ G ++   I   K         G   V       A  A
Sbjct: 18  TEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

>2guz_A Mitochondrial import inner membrane translocase subunit TIM14; DNAJ-fold, chaperone, protein transport; HET: FLC; 2.00A {Saccharomyces cerevisiae} Length = 71

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 8/63 (12%)

Query: 9  YRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEK 68
           ++L L        LT+K++ + ++   L  HPDK            K+  + + L+   
Sbjct: 17 LQILNLTEN----TLTKKKLKEVHRKIMLANHPDKGGSP----FLATKINEAKDFLEKRG 68

Query: 69 ARK 71
            K
Sbjct: 69 ISK 71

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
             + L   F  FG + D+ I    ++ K +G A V       A AA
Sbjct: 76  DDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
             + L   F  FG + D+ I    ++ K +G A V       A AA
Sbjct: 25  DDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 2/42 (4%)

Query: 182 TAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           TA+ LR++F +        +    K G A V    ++ A  A
Sbjct: 21  TADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRA 60

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 39.0 bits (90), Expect = 6e-04
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 174 WEKFGEDYTAERLREIFSEFGKVEDVVIKSSKK---KGSALVVMATKSAAGAA 223
            + F  D T + ++E   + G+V ++ ++ +     KGS  VV  +  +A   
Sbjct: 114 IKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 166

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 10/72 (13%)

Query: 160 GGVGLDK----EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVI----KSSKKKGSAL 211
           G +G D+         +   K       + L  +FS+ GKV ++       + K KG   
Sbjct: 1   GPLGSDQYIVVNGAPVIPSAKV--PVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLF 58

Query: 212 VVMATKSAAGAA 223
           V   + + A   
Sbjct: 59  VECGSMNDAKKI 70

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 4/44 (9%)

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAA 223
           + T + +R +F ++GKV +  I     K    V +  K+AA  A
Sbjct: 19  EATEQEIRSLFEQYGKVLECDI----IKNYGFVHIEDKTAAEDA 58

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 37.1 bits (87), Expect = 6e-04
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 4/48 (8%)

Query: 180 DYTAERLREIFSEFGKVEDV-VIK---SSKKKGSALVVMATKSAAGAA 223
             T + L ++   +GK+     I    ++K KG   V   + SAA  A
Sbjct: 16  GTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 180 DYTAERLREIFSEFGKVEDV-VIK-SSKKKGSALVVMATKSAAGAA 223
            +    LR++F +FGK+ DV +I      KG   V     + A  A
Sbjct: 26  RFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRA 71

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAA 223
           T   LR+ F  FG +E+ V+     + K +G   V MA ++AA  A
Sbjct: 30  TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 24/132 (18%), Positives = 45/132 (34%), Gaps = 15/132 (11%)

Query: 100 DLEERERAAFAPDPAVKARQEEEKIARQLKEEIERIRAMHENKRTPAAFASVKETKQSGS 159
           D++  E      D      Q   ++  + K    R      N R           +    
Sbjct: 6   DIDNAEEFEVDED----GDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDE 61

Query: 160 GGVGLDKEKVLKVSWEKF----GEDYTAERLREIFSEFGKVEDVVI----KSSKKKGSAL 211
              G  +       W  F     E+   + ++E F ++G+++++ +    ++   KG AL
Sbjct: 62  LEPGPQRSVE---GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118

Query: 212 VVMATKSAAGAA 223
           V   T   A AA
Sbjct: 119 VEYETHKQALAA 130

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 38.0 bits (88), Expect = 7e-04
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 175 EKFGEDYTAERLREIFSEFGKVEDVVI-KSSKKKGSALVVMATKSAAGAA 223
            +  ++     L  + S  G + D+V+  S    G A +V AT+ +A A 
Sbjct: 39  PEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAF 88

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 10/48 (20%), Positives = 24/48 (50%), Gaps = 4/48 (8%)

Query: 180 DYTAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           D T E++ ++ S  G V ++ +    ++ + KG A +      ++ +A
Sbjct: 13  DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGAA 223
           + + LR +F ++G+V DV I     + + +G A V    K  A  A
Sbjct: 60  SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 180 DYTAERLREIFSEFGKVEDVVIKSSKK--KGSALVVMATKSAAGAA 223
            +    LR++F +FGK+ DV I  +++  KG   V     + A  A
Sbjct: 40  RFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRA 85

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 36.9 bits (86), Expect = 9e-04
 Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGS-ALVVMATKSAAGAA 223
               + +L E F  FG V  VV+   K KG  A+V M    A  A 
Sbjct: 18  RGVDSAQLSEYFLAFGPVASVVMD--KDKGVFAIVEMGDVGAREAV 61

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 37.2 bits (87), Expect = 9e-04
 Identities = 6/47 (12%), Positives = 15/47 (31%), Gaps = 3/47 (6%)

Query: 180 DYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVVMATKSAAGAA 223
           + +   L+   SE     D+ +   ++   +    V   +      A
Sbjct: 28  NKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 74

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 38.9 bits (91), Expect = 9e-04
 Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 12/70 (17%)

Query: 166 KEKVLKVSWEKFG---------EDYTAERLREIFSEFGKVEDVVI---KSSKKKGSALVV 213
           K + L++ +   G            + E L + FS+FG VE  V+      +  G   V 
Sbjct: 84  KSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVE 143

Query: 214 MATKSAAGAA 223
            A K  A  A
Sbjct: 144 FAAKPPARKA 153

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 36.8 bits (86), Expect = 9e-04
 Identities = 17/45 (37%), Positives = 29/45 (64%), Gaps = 4/45 (8%)

Query: 182 TAERLREIFSEFGKVEDVVI----KSSKKKGSALVVMATKSAAGA 222
           T+E+++E+FS+FGKV +V +    ++ K KG   V M  +S + A
Sbjct: 14  TSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEA 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	292
2dn9_A	79	DNAJ homolog subfamily A member 3; J-domain, TID1,	99.8
2yua_A	99	Williams-beuren syndrome chromosome region 18 prot	99.79
2ctq_A	112	DNAJ homolog subfamily C member 12; J-domain, chap	99.79
1hdj_A	77	Human HSP40, HDJ-1; molecular chaperone; NMR {Homo	99.79
1wjz_A	94	1700030A21RIK protein; J-domain, DNAJ like protein	99.78
2ctw_A	109	DNAJ homolog subfamily C member 5; J-domain, chape	99.78
2cug_A	88	Mkiaa0962 protein; DNAJ-like domain, structural ge	99.77
2ej7_A	82	HCG3 gene; HCG3 protein, DNAJ domain, NPPSFA, nati	99.77
2ctp_A	78	DNAJ homolog subfamily B member 12; J-domain, chap	99.76
2ctr_A	88	DNAJ homolog subfamily B member 9; J-domain, chape	99.76
2och_A	73	Hypothetical protein DNJ-12; HSP40, J-domain, chap	99.76
1bq0_A	103	DNAJ, HSP40; chaperone, heat shock, protein foldin	99.75
2lgw_A	99	DNAJ homolog subfamily B member 2; J domain, HSJ1A	99.75
2dmx_A	92	DNAJ homolog subfamily B member 8; DNAJ J domain,	99.74
2o37_A	92	Protein SIS1; HSP40, J-domain, cochaperone, APC900	99.74
3hho_A	174	CO-chaperone protein HSCB homolog; structural geno	99.73
2qsa_A	109	DNAJ homolog DNJ-2; J-domain, HSP40, APC90001.8, s	99.72
1fpo_A	171	HSC20, chaperone protein HSCB; molecular chaperone	99.72
2l6l_A	155	DNAJ homolog subfamily C member 24; DPH4, Zn-CSL,	99.71
2ys8_A	90	RAB-related GTP-binding protein RABJ; DNAJ domain,	99.7
3apq_A	210	DNAJ homolog subfamily C member 10; thioredoxin fo	99.69
3bvo_A	207	CO-chaperone protein HSCB, mitochondrial precurso;	99.65
1iur_A	88	KIAA0730 protein; DNAJ like domain, riken structur	99.63
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.63
1n4c_A	182	Auxilin; four helix bundle, protein binding; NMR {	99.62
2qwo_B	92	Putative tyrosine-protein phosphatase auxilin; cha	99.62
3uo3_A	181	J-type CO-chaperone JAC1, mitochondrial; structura	99.62
3lz8_A	329	Putative chaperone DNAJ; structure genomics, struc	99.59
1gh6_A	114	Large T antigen; tumor suppressor, oncoprotein, an	99.59
3ag7_A	106	Putative uncharacterized protein F9E10.5; J-domain	99.58
2pf4_E	174	Small T antigen; PP2A, SV40, DNAJ, aalpha subunit,	99.54
1faf_A	79	Large T antigen; J domain, HPD motif, anti-paralle	99.54
2guz_A	71	Mitochondrial import inner membrane translocase su	99.51
3apo_A	780	DNAJ homolog subfamily C member 10; PDI family, th	99.44
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.03
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.02
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.02
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.01
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.0
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.0
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.99
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.98
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.98
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.98
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.98
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.98
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.98
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.97
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.97
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.96
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	98.96
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.96
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.95
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.95
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.95
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.95
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.95
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.94
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.93
1x5p_A	97	Negative elongation factor E; structure genomics,	98.93
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	98.93
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.93
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.93
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.93
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	98.93
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.93
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.92
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.92
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	98.92
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.92
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.91
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.91
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.91
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.9
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.9
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.9
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.9
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.9
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	98.9
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.89
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	98.89
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.89
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.89
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.89
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	98.88
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.88
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.88
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.87
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.87
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.87
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.87
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.87
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.87
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.87
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.87
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.87
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.86
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.86
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.86
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.86
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.86
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	98.86
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.86
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.85
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	98.85
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.85
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.84
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.84
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.83
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.83
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.83
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.83
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.83
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.83
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.82
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.82
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.82
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.82
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	98.81
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.81
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.8
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.8
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.8
2div_A	99	TRNA selenocysteine associated protein; structural	98.8
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.8
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.79
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.79
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.79
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.78
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.78
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.78
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.78
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	98.78
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.78
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.77
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.76
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.76
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.75
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.75
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.73
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.73
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.73
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	98.73
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.72
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.71
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.71
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.71
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.7
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.7
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.69
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.68
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.68
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.67
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.67
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.66
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.65
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.65
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.64
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.64
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.64
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.63
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.63
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.63
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.62
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.62
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.62
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.61
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.61
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.61
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.61
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.6
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.6
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.6
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.59
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.59
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.59
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.58
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.57
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.57
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.56
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	98.56
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.55
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.54
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.54
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.52
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.52
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.52
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.52
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.5
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.5
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.5
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.5
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.49
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.49
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.48
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.48
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	97.85
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.46
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.46
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.45
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.44
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.43
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.43
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.43
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.43
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.4
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.37
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.37
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.36
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.34
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.34
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.33
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.33
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.32
2guz_B	65	Mitochondrial import inner membrane translocase su	98.3
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.05
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	97.81
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.81
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	97.74
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.41
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.07
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	94.73
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	94.12
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	93.24
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	91.42
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	91.39
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	85.84
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	85.24

>2dn9_A DNAJ homolog subfamily A member 3; J-domain, TID1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=4.8e-20  Score=138.43  Aligned_cols=70  Identities=41%  Similarity=0.675  Sum_probs=65.9

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ....|||+||||+++     ++..+|+++||+++++||||++++++.+.+.|+.|++||++|+||.+|..||.++
T Consensus         4 ~~~~~~y~iLgv~~~-----a~~~~Ik~ayr~l~~~~HPD~~~~~~~a~~~f~~i~~Ay~~L~d~~~R~~YD~~g   73 (79)
T 2dn9_A            4 GSSGDYYQILGVPRN-----ASQKEIKKAYYQLAKKYHPDTNKDDPKAKEKFSQLAEAYEVLSDEVKRKQYDAYG   73 (79)
T ss_dssp             SCCSCHHHHHTCCTT-----CCHHHHHHHHHHHHHHTCTTTCSSCTTHHHHHHHHHHHHHHHHSHHHHHHHHHSC
T ss_pred             CCCCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhcc
Confidence            356799999999997     8999999999999999999999988899999999999999999999999999864

>2yua_A Williams-beuren syndrome chromosome region 18 protein; J domain, all helix protein, chaperone, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=6.3e-20  Score=143.90  Aligned_cols=71  Identities=27%  Similarity=0.523  Sum_probs=66.9

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +...|||+||||+++     ++..+|++|||+++++||||++++++.+.+.|+.|++||++|+||.+|..||..+.
T Consensus        14 ~~~~~~Y~vLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~~~~~a~~~f~~i~~Ay~~L~d~~~R~~YD~~l~   84 (99)
T 2yua_A           14 YSRTALYDLLGVPST-----ATQAQIKAAYYRQCFLYHPDRNSGSAEAAERFTRISQAYVVLGSATLRRKYDRGLL   84 (99)
T ss_dssp             SCSSHHHHHHTCCTT-----CCHHHHHHHHHHHHHHSCTTTCSSCSHHHHHHHHHHHHHHHTTSHHHHHHHHHTCC
T ss_pred             CCccCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHhcc
Confidence            456899999999998     89999999999999999999999889999999999999999999999999998764

>2ctq_A DNAJ homolog subfamily C member 12; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=1.3e-19  Score=145.25  Aligned_cols=70  Identities=39%  Similarity=0.634  Sum_probs=66.5

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     ++..+|++|||+++++||||++++++.+.+.|+.|++||++|+||.+|..||..+.
T Consensus        18 ~~~d~Y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   87 (112)
T 2ctq_A           18 DTEDYYTLLGCDEL-----SSVEQILAEFKVRALECHPDKHPENPKAVETFQKLQKAKEILTNEESRARYDHWRR   87 (112)
T ss_dssp             CCCCHHHHTTCCTT-----SCHHHHHHHHHHHHHTTCTTTCTTCSTHHHHHHHHHHHHHHHHSHHHHHHHHHHHH
T ss_pred             CCCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHHCCHHHHHHHHHhhh
Confidence            45799999999998     89999999999999999999999888999999999999999999999999999875

>1hdj_A Human HSP40, HDJ-1; molecular chaperone; NMR {Homo sapiens} SCOP: a.2.3.1

Probab=99.79  E-value=1.2e-19  Score=135.69  Aligned_cols=68  Identities=37%  Similarity=0.768  Sum_probs=63.5

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      +.|||+||||+++     ++..+|++|||+++++||||+++ ++.+.+.|+.|++||++|+||.+|..||..+.
T Consensus         2 ~~~~y~iLgv~~~-----as~~~Ik~ayr~l~~~~HPD~~~-~~~~~~~f~~i~~Ay~~L~d~~~R~~Yd~~~~   69 (77)
T 1hdj_A            2 GKDYYQTLGLARG-----ASDEEIKRAYRRQALRYHPDKNK-EPGAEEKFKEIAEAYDVLSDPRKREIFDRYGE   69 (77)
T ss_dssp             CCCSHHHHTCCTT-----CCHHHHHHHHHHHHHTTCTTTCC-CTTHHHHHHHHHHHHHHTTCHHHHHHHHHTCG
T ss_pred             CCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CccHHHHHHHHHHHHHHHCCHHHHHHHHHHcc
Confidence            5799999999998     89999999999999999999997 57789999999999999999999999998753

>1wjz_A 1700030A21RIK protein; J-domain, DNAJ like protein, structural genomics, riken structural genomics/proteomics initiative, RSGI, chaperone; NMR {Mus musculus} SCOP: a.2.3.1

Probab=99.78  E-value=9.8e-20  Score=141.04  Aligned_cols=71  Identities=24%  Similarity=0.446  Sum_probs=65.1

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC------hhHHHHHHHHHHHHHHccCchhhhhHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD------PDAHDNFQKLKSSYEILKDEKARKLFDDL   76 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~------~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~   76 (292)
                      +...|||+||||+++     ++..+|++|||+++++||||+++.+      +.+.+.|+.|++||++|+||.+|..||..
T Consensus        13 ~~~~~~y~iLgv~~~-----as~~eIk~aYr~l~~~~HPDk~~~~~~~~~~~~~~~~f~~i~~Ay~~L~d~~~R~~YD~~   87 (94)
T 1wjz_A           13 TLKKDWYSILGADPS-----ANMSDLKQKYQKLILLYHPDKQSADVPAGTMEECMQKFIEIDQAWKILGNEETKKKYDLQ   87 (94)
T ss_dssp             SSCSCHHHHTTCCTT-----CCHHHHHHHHHHTTSSSCSTTCCTTCCHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHHHH
T ss_pred             CCCCChHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCCCChhhhHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Confidence            456799999999998     8999999999999999999999854      46889999999999999999999999998


Q ss_pred             HH
Q 022800           77 LK   78 (292)
Q Consensus        77 ~~   78 (292)
                      +.
T Consensus        88 l~   89 (94)
T 1wjz_A           88 RS   89 (94)
T ss_dssp             SC
T ss_pred             cc
Confidence            74

>2ctw_A DNAJ homolog subfamily C member 5; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=4e-19  Score=141.73  Aligned_cols=72  Identities=36%  Similarity=0.667  Sum_probs=67.6

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKI   79 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~   79 (292)
                      ....|||+||||+++     ++..+|++|||+++++||||++++++.+.+.|+.|++||++|+||.+|..||.....
T Consensus        14 ~~~~~~Y~vLgv~~~-----as~~eIk~aYr~la~~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~g~~   85 (109)
T 2ctw_A           14 TSGESLYHVLGLDKN-----ATSDDIKKSYRKLALKYHPDKNPDNPEAADKFKEINNAHAILTDATKRNIYDKYGSL   85 (109)
T ss_dssp             SCSCCHHHHHTCCTT-----CCHHHHHHHHHHHHHHSCTTTSTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHTCHH
T ss_pred             CCCCCHHHHcCcCCC-----CCHHHHHHHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHHcCHHHHHHHHHhccc
Confidence            456899999999998     899999999999999999999998899999999999999999999999999987754

>2cug_A Mkiaa0962 protein; DNAJ-like domain, structural genomics, molecular chaperone, NPPSFA; NMR {Mus musculus}

Probab=99.77  E-value=3.6e-19  Score=136.62  Aligned_cols=69  Identities=42%  Similarity=0.657  Sum_probs=64.4

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ....|||+||||+++     ++..+|+++||+++++||||+++ ++.+.+.|+.|++||++|+||.+|..||.++
T Consensus        14 ~~~~d~y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~-~~~~~~~f~~i~~Ay~~L~d~~~R~~YD~~g   82 (88)
T 2cug_A           14 ALDFDPYRVLGVSRT-----ASQADIKKAYKKLAREWHPDKNK-DPGAEDRFIQISKAYEILSNEEKRTNYDHYG   82 (88)
T ss_dssp             SSSSCHHHHHTCCTT-----CCHHHHHHHHHHHHHHSCTTTCC-STTHHHHHHHHHHHHHHHHSHHHHHHHHHHT
T ss_pred             cCCCCHHHHcCcCCC-----CCHHHHHHHHHHHHHHHCcCCCC-ChhHHHHHHHHHHHHHHHCCHHHHHHHHHcC
Confidence            356899999999997     89999999999999999999998 4788999999999999999999999999875

>2ej7_A HCG3 gene; HCG3 protein, DNAJ domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.4e-19  Score=134.67  Aligned_cols=69  Identities=38%  Similarity=0.691  Sum_probs=63.7

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ...|||+||||+++     ++..+|++|||+++++||||++++++ .+.+.|+.|++||++|+||.+|..||.++
T Consensus         7 ~~~~~y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~~~~~~a~~~f~~i~~Ay~~L~d~~~R~~YD~~g   76 (82)
T 2ej7_A            7 GMVDYYEVLDVPRQ-----ASSEAIKKAYRKLALKWHPDKNPENKEEAERRFKQVAEAYEVLSDAKKRDIYDRYG   76 (82)
T ss_dssp             SSCCHHHHTTCCTT-----CCHHHHHHHHHHHHTTSCTTTCSTTHHHHHHHHHHHHHHHHHHSSTTHHHHHHHTC
T ss_pred             CCcCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHHHCCHHHHHHHHHcC
Confidence            45799999999998     89999999999999999999998764 67889999999999999999999999865

>2ctp_A DNAJ homolog subfamily B member 12; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=3.1e-19  Score=133.78  Aligned_cols=68  Identities=32%  Similarity=0.681  Sum_probs=63.8

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ...|||+||||+++     ++..+|++|||+++++||||+++ ++.+.+.|+.|++||++|+||.+|..||..+
T Consensus         5 ~~~~~y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~-~~~~~~~f~~i~~Ay~~L~d~~~R~~YD~~~   72 (78)
T 2ctp_A            5 SSGDYYEILGVSRG-----ASDEDLKKAYRRLALKFHPDKNH-APGATEAFKAIGTAYAVLSNPEKRKQYDQFG   72 (78)
T ss_dssp             CSCCHHHHHTCCTT-----CCHHHHHHHHHHHHTTSCTTTCS-SHHHHHHHHHHHHHHHHHTSHHHHHHHHHTC
T ss_pred             CCCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CccHHHHHHHHHHHHHHHCCHHHHHHHHHcC
Confidence            46799999999998     89999999999999999999997 5788999999999999999999999999865

>2ctr_A DNAJ homolog subfamily B member 9; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=5.2e-19  Score=135.68  Aligned_cols=70  Identities=36%  Similarity=0.635  Sum_probs=65.3

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ....|||+||||+++     ++.++|+++||+++++||||+++ ++.+.+.|+.|++||++|+||.+|..||..+.
T Consensus         4 ~~~~~~y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~-~~~a~~~f~~i~~Ay~~L~d~~~R~~Yd~~~~   73 (88)
T 2ctr_A            4 GSSGSYYDILGVPKS-----ASERQIKKAFHKLAMKYHPDKNK-SPDAEAKFREIAEAYETLSDANRRKEYDTLGH   73 (88)
T ss_dssp             CCCCSHHHHHTCCTT-----CCHHHHHHHHHHHHHHTCTTTCC-SHHHHHHHHHHHHHHHHHHSSHHHHHHHHTCH
T ss_pred             CCCCCHHHHcCcCCC-----CCHHHHHHHHHHHHHHHCcCCCC-ChHHHHHHHHHHHHHHHHCCHHHHHHHHHhCc
Confidence            356799999999997     89999999999999999999998 68899999999999999999999999998764

>2och_A Hypothetical protein DNJ-12; HSP40, J-domain, chaperone, APC90013.2, structural genomics, protein structure initiative; 1.86A {Caenorhabditis elegans} PDB: 2lo1_A

Probab=99.76  E-value=5.4e-19  Score=130.89  Aligned_cols=67  Identities=39%  Similarity=0.737  Sum_probs=61.3

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      +...|||+||||+++     ++..+|+++||+++++||||+++++   .+.|+.|+.||++|+||.+|..||..+
T Consensus         5 ~~~~~~y~iLgl~~~-----a~~~eIk~ayr~l~~~~HPD~~~~~---~~~f~~i~~Ay~~L~d~~~R~~YD~~g   71 (73)
T 2och_A            5 VKETGYYDVLGVKPD-----ASDNELKKAYRKMALKFHPDKNPDG---AEQFKQISQAYEVLSDEKKRQIYDQGG   71 (73)
T ss_dssp             -CCCCHHHHHTCCTT-----CCHHHHHHHHHHHHHHTCTTTCTTC---HHHHHHHHHHHHHHTSHHHHHHHHHTC
T ss_pred             cCCCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCcCH---HHHHHHHHHHHHHHCCHHHHHHHHhcC
Confidence            356899999999998     8999999999999999999999754   579999999999999999999999864

>1bq0_A DNAJ, HSP40; chaperone, heat shock, protein folding, DNAK; NMR {Escherichia coli} SCOP: a.2.3.1 PDB: 1xbl_A 1bqz_A

Probab=99.75  E-value=2.5e-19  Score=141.37  Aligned_cols=69  Identities=36%  Similarity=0.673  Sum_probs=65.3

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     ++.++|++|||+++++||||++++++.+.+.|+.|++||++|+||.+|..||..+.
T Consensus         2 ~~~~y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~~~~~a~~~f~~i~~Ay~~L~d~~~R~~YD~~~~   70 (103)
T 1bq0_A            2 KQDYYEILGVSKT-----AEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRAAYDQYGH   70 (103)
T ss_dssp             CCCSTTTTSSCSS-----CCHHHHHHHHHHHHTTTCTTTCTTTCTHHHHHHHHTTTTTSTTCSHHHHHTTTSTT
T ss_pred             CCCHHHHcCcCCC-----CCHHHHHHHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHHCCHHHHHHHHHHhh
Confidence            4799999999998     89999999999999999999999878899999999999999999999999998764

>2lgw_A DNAJ homolog subfamily B member 2; J domain, HSJ1A, CO-chaperon, chaperone; NMR {Homo sapiens}

Probab=99.75  E-value=1.7e-18  Score=135.82  Aligned_cols=68  Identities=35%  Similarity=0.711  Sum_probs=63.2

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .|||+||||+++     ++.++|++|||+++++||||+++++. .+.+.|+.|++||++|+||.+|..||..+.
T Consensus         2 ~d~Y~iLgv~~~-----as~~eIk~aYr~la~~~HPDk~~~~~~~a~~~f~~I~~AY~vL~d~~~R~~YD~~g~   70 (99)
T 2lgw_A            2 ASYYEILDVPRS-----ASADDIKKAYRRKALQWHPDKNPDNKEFAEKKFKEVAEAYEVLSDKHKREIYDRYGR   70 (99)
T ss_dssp             CCHHHHSSSCTT-----SCHHHHHHHHHHHHHHTSTTTCCSCCHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHH
T ss_pred             CCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCccHHHHHHHHHHHHHHHHHHCCHHHHHHHHHhCc
Confidence            589999999998     89999999999999999999998653 578999999999999999999999999864

>2dmx_A DNAJ homolog subfamily B member 8; DNAJ J domain, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-18  Score=134.80  Aligned_cols=69  Identities=38%  Similarity=0.675  Sum_probs=63.7

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ...|||+||||+++     ++..+|+++||+++++||||++++++ .+.+.|+.|++||++|+||.+|..||..+
T Consensus         7 ~~~~~y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~~~~~~a~~~f~~i~~Ay~~L~d~~~R~~Yd~~~   76 (92)
T 2dmx_A            7 GMANYYEVLGVQAS-----ASPEDIKKAYRKLALRWHPDKNPDNKEEAEKKFKLVSEAYEVLSDSKKRSLYDRAG   76 (92)
T ss_dssp             CCCCHHHHHTCCTT-----CCTTHHHHHHHHHHHHTCTTTCSSCSHHHHHHHHHHHHHHHHHHSHHHHHHHHHHC
T ss_pred             CCcCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCCCCCCccHHHHHHHHHHHHHHHHHHCCHHHHHHHHHhC
Confidence            45799999999998     89999999999999999999998654 68899999999999999999999999875

>2o37_A Protein SIS1; HSP40, J-domain, cochaperone, APC90055.5, structural genomics, PSI-2, protein structure initiative; 1.25A {Saccharomyces cerevisiae}

Probab=99.74  E-value=2.1e-18  Score=133.44  Aligned_cols=69  Identities=32%  Similarity=0.629  Sum_probs=63.1

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLKI   79 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~   79 (292)
                      +...|||+||||+++     ++..+|+++||+++++||||+++++   .+.|+.|++||++|+||.+|..||..+..
T Consensus         5 ~~~~~~y~iLgv~~~-----as~~eIk~ayr~l~~~~HPDk~~~~---~~~f~~i~~Ay~~L~d~~~R~~YD~~~~~   73 (92)
T 2o37_A            5 VKETKLYDLLGVSPS-----ANEQELKKGYRKAALKYHPDKPTGD---TEKFKEISEAFEILNDPQKREIYDQYGLE   73 (92)
T ss_dssp             CSCCHHHHHHTCCTT-----CCHHHHHHHHHHHHHHHCTTSTTCC---HHHHHHHHHHHHHHTSHHHHHHHHHHCHH
T ss_pred             ccCCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCh---HHHHHHHHHHHHHHCCHHHHHHHHHHCHH
Confidence            356899999999998     8999999999999999999999765   46999999999999999999999998753

>2qsa_A DNAJ homolog DNJ-2; J-domain, HSP40, APC90001.8, structural genomics, PSI-2, Pro structure initiative; 1.68A {Caenorhabditis elegans}

Probab=99.72  E-value=2.7e-18  Score=136.71  Aligned_cols=70  Identities=29%  Similarity=0.471  Sum_probs=64.7

Q ss_pred             CCcccccccccccCCCCCCC-CHHHHHHHHHHHHHHhCCCCCCC---ChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKL-TEKEISKAYKWKALELHPDKRPD---DPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a-~~~eIkkaYrk~al~~HPDk~~~---~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ...|||+||||+++     + +..+|++|||+++++||||++++   .+.+.+.|+.|++||++|+||.+|..||..+.
T Consensus        13 ~~~~~y~iLgv~~~-----a~s~~eIk~aYr~l~~~~HPDk~~~~~~~~~a~~~f~~i~~AY~~L~d~~~R~~YD~~~~   86 (109)
T 2qsa_A           13 GLENCYDVLEVNRE-----EFDKQKLAKAYRALARKHHPDRVKNKEEKLLAEERFRVIATAYETLKDDEAKTNYDYYLD   86 (109)
T ss_dssp             TTSCHHHHTTCCGG-----GCCHHHHHHHHHHHHHHTCGGGCCSHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHH
T ss_pred             CCCCHHHHcCCCCC-----CCCHHHHHHHHHHHHHHHCcCCCCCccccHHHHHHHHHHHHHHHHHCCHHHHHHHHHhcc
Confidence            46799999999998     7 99999999999999999999985   35688999999999999999999999999874

>1fpo_A HSC20, chaperone protein HSCB; molecular chaperone; 1.80A {Escherichia coli} SCOP: a.2.3.1 a.23.1.1

Probab=99.72  E-value=3.6e-18  Score=146.57  Aligned_cols=96  Identities=21%  Similarity=0.307  Sum_probs=74.9

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh-----HHHHHHHHHHHHHHccCchhhhhHHHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSSYEILKDEKARKLFDDLLKIK   80 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~-----a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~~   80 (292)
                      +|||+||||++++   .++..+|+++||+++++||||++++++.     |.+.|..|+.||++|+||.+|..||..+...
T Consensus         1 ~d~y~lLgl~~~a---~i~~~eIk~aYr~L~~~~HPDk~~~~~~~e~~~a~~~f~~In~AY~vL~dp~~R~~Yd~~l~g~   77 (171)
T 1fpo_A            1 MDYFTLFGLPARY---QLDTQALSLRFQDLQRQYHPDKFASGSQAEQLAAVQQSATINQAWQTLRHPLMRAEYLLSLHGF   77 (171)
T ss_dssp             CHHHHHTTCCSSS---CCCHHHHHHHHHHHHHHTCGGGGTTSCHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHTTTC
T ss_pred             CCHHHHCCCCCCC---CCCHHHHHHHHHHHHHHhCcCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHhcCC
Confidence            4899999999972   2399999999999999999999987653     5679999999999999999999999987532


Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHH
Q 022800           81 REKQQRQSQQDGKRRKMMSDLEERER  106 (292)
Q Consensus        81 ~~~~~r~~~~~~kr~~~~~dLe~RE~  106 (292)
                      .........++  -.-+++.|+.||.
T Consensus        78 ~~~~e~~~~~d--~~fLme~me~rE~  101 (171)
T 1fpo_A           78 DLASEQHTVRD--TAFLMEQLELREE  101 (171)
T ss_dssp             CTTCSSSCCSC--HHHHHHHHHHHHH
T ss_pred             CccccccccCC--HHHHHHHHHHHHH
Confidence            21111011122  2467888888885

>2l6l_A DNAJ homolog subfamily C member 24; DPH4, Zn-CSL, J-domain, chaperone; NMR {Homo sapiens}

Probab=99.71  E-value=1.4e-17  Score=140.33  Aligned_cols=72  Identities=22%  Similarity=0.423  Sum_probs=65.0

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh------hHHHHHHHHHHHHHHccCchhhhhHHHH
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP------DAHDNFQKLKSSYEILKDEKARKLFDDL   76 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~------~a~~~f~~i~~Ay~vL~d~~~R~~YD~~   76 (292)
                      +...|||+||||+++     ++.++|++|||+++++||||++++++      .+.+.|..|++||++|+||.+|+.||..
T Consensus         7 ~~~~~~y~iLgv~~~-----a~~~eIk~aYr~l~~~~HPDk~~~~~~~~~~~~a~~~f~~i~~Ay~~L~dp~~R~~Yd~~   81 (155)
T 2l6l_A            7 MPKKDWYSILGADPS-----ANISDLKQKYQKLILMYHPDKQSTDVPAGTVEECVQKFIEIDQAWKILGNEETKREYDLQ   81 (155)
T ss_dssp             CCCSHHHHHHTCCTT-----CCHHHHHHHHHHHHHHHSCCCCCCCCTTHHHHHHHHHHHHHHHHHHHSSSHHHHCHHHHH
T ss_pred             CCCCChhHhcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCCCchhHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            346799999999998     89999999999999999999998764      3678999999999999999999999988


Q ss_pred             HHH
Q 022800           77 LKI   79 (292)
Q Consensus        77 ~~~   79 (292)
                      +..
T Consensus        82 ~~~   84 (155)
T 2l6l_A           82 RCE   84 (155)
T ss_dssp             HHH
T ss_pred             cch
Confidence            753

>2ys8_A RAB-related GTP-binding protein RABJ; DNAJ domain, RAS-associated protein RAP1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=7.3e-18  Score=129.94  Aligned_cols=63  Identities=29%  Similarity=0.473  Sum_probs=58.0

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhh
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKL   72 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~   72 (292)
                      ...|||+||||+++     ++..+||+|||+++++||||+++ ++.+.+.|+.|++||++|+||.+|..
T Consensus        25 ~~~~~y~iLgv~~~-----as~~eIk~aYr~la~~~HPDk~~-~~~~~~~f~~i~~Ay~~L~d~~~R~~   87 (90)
T 2ys8_A           25 NSKDSWDMLGVKPG-----ASRDEVNKAYRKLAVLLHPDKCV-APGSEDAFKAVVNARTALLKNIKSGP   87 (90)
T ss_dssp             TCSSHHHHHTCCTT-----CCHHHHHHHHHHHHHHHCTTTCC-CTTHHHHHHHHHHHHHHHHHHHCCSC
T ss_pred             cCCCHHHHcCcCCC-----CCHHHHHHHHHHHHHHHCcCCCC-CccHHHHHHHHHHHHHHHCCcccccC
Confidence            35799999999997     89999999999999999999998 57788999999999999999988763

>3apq_A DNAJ homolog subfamily C member 10; thioredoxin fold, DNAJ domain, endoplasmic reticulum, oxidor; 1.84A {Mus musculus}

Probab=99.69  E-value=1.3e-17  Score=145.28  Aligned_cols=68  Identities=43%  Similarity=0.785  Sum_probs=64.9

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .|||+||||+++     ++..+||+|||+++++||||++++++.+.+.|+.|++||++|+||.+|..||....
T Consensus         2 ~~~y~~l~~~~~-----a~~~~ik~ay~~l~~~~HPD~~~~~~~~~~~f~~i~~Ay~~L~~~~~r~~yd~~~~   69 (210)
T 3apq_A            2 QNFYSLLGVSKT-----ASSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKDEDLRKKYDKYGE   69 (210)
T ss_dssp             CCHHHHHTCCTT-----CCHHHHHHHHHHHHHHHCGGGCTTCTTHHHHHHHHHHHHHHHTSHHHHHHHHHHTT
T ss_pred             CCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCChHHHHHHHHHHHHHHHhCCHHHHHHHHHhcc
Confidence            589999999998     89999999999999999999999889999999999999999999999999998763

>3bvo_A CO-chaperone protein HSCB, mitochondrial precurso; structural genomics medical relev protein structure initiative, PSI-2; 3.00A {Homo sapiens}

Probab=99.65  E-value=1.5e-16  Score=140.39  Aligned_cols=97  Identities=14%  Similarity=0.201  Sum_probs=73.5

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh-----HHHHHHHHHHHHHHccCchhhhhHHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD-----AHDNFQKLKSSYEILKDEKARKLFDDLLKI   79 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~-----a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~~   79 (292)
                      ..|||+||||++++   +++..+|+++||+++++||||++++++.     |.+.|..|++||++|+||.+|+.||..+..
T Consensus        42 ~~d~y~lLgv~~~~---~a~~~eIk~aYr~L~~~~HPDk~~~~~~~e~~~a~~~f~~In~AY~vLsdp~~R~~Yd~~l~G  118 (207)
T 3bvo_A           42 TRDYFSLMDCNRSF---RVDTAKLQHRYQQLQRLVHPDFFSQRSQTEKDFSEKHSTLVNDAYKTLLAPLSRGLYLLKLHG  118 (207)
T ss_dssp             TCCHHHHTTSCSCS---CCCHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHTT
T ss_pred             CCCHHHHcCCCCCC---CCCHHHHHHHHHHHHHHHCcCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHhcC
Confidence            57999999999863   4799999999999999999999987643     567899999999999999999999987642


Q ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 022800           80 KREKQQRQSQQDGKRRKMMSDLEERER  106 (292)
Q Consensus        80 ~~~~~~r~~~~~~kr~~~~~dLe~RE~  106 (292)
                      ..-.......++  -.-+++.++.||.
T Consensus       119 ~~~~~e~~~~~d--~~fLme~me~~E~  143 (207)
T 3bvo_A          119 IEIPERTDYEMD--RQFLIEIMEINEK  143 (207)
T ss_dssp             CCCCSSCSSSSC--HHHHHHHHHHHHH
T ss_pred             CCcccccccCCC--HHHHHHHHHHHHH
Confidence            210000000111  1256777888885

>1iur_A KIAA0730 protein; DNAJ like domain, riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Homo sapiens} SCOP: a.2.3.1

Probab=99.63  E-value=7.5e-17  Score=123.92  Aligned_cols=63  Identities=24%  Similarity=0.277  Sum_probs=56.7

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchhhh
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKARK   71 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~R~   71 (292)
                      ...++|+||||+++     ++.++|++|||+++++||||++++++ .+.+.|+.|++||++|+|...|.
T Consensus        14 ~~~~~y~vLgv~~~-----as~~eIKkaYrkla~~~HPDk~~~~~~~a~~~F~~I~~AYevL~~~~~r~   77 (88)
T 1iur_A           14 ILKEVTSVVEQAWK-----LPESERKKIIRRLYLKWHPDKNPENHDIANEVFKHLQNEINRLEKQAFLD   77 (88)
T ss_dssp             CHHHHHHHHHHTTS-----SCSHHHHHHHHHHHHHTCTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTCS
T ss_pred             cHHHHHHHhCCCCC-----CCHHHHHHHHHHHHHHHCCCCCCCchHHHHHHHHHHHHHHHHHHhhcccc
Confidence            34689999999998     89999999999999999999999774 58899999999999999976653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=3e-15  Score=117.47  Aligned_cols=76  Identities=32%  Similarity=0.458  Sum_probs=69.2

Q ss_pred             ccceEEEEeeec-----CCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEec
Q 022800          166 KEKVLKVSWEKF-----GEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPL  240 (292)
Q Consensus       166 ~~~~lkvKWk~~-----~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~  240 (292)
                      ..++|+|+|+..     +..+|++.|+++|++||.|.+|.|. .+.+|||||+|.+.++|..|+....|+.++||.|.|.
T Consensus         9 ~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a   87 (100)
T 2d9o_A            9 GTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-SKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWL   87 (100)
T ss_dssp             SSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-SSSSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECS
T ss_pred             ccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-cCCCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEc
Confidence            356899999983     3579999999999999999999995 6789999999999999999999999999999999998


Q ss_pred             CC
Q 022800          241 QP  242 (292)
Q Consensus       241 ~~  242 (292)
                      .+
T Consensus        88 ~~   89 (100)
T 2d9o_A           88 EG   89 (100)
T ss_dssp             SC
T ss_pred             cC
Confidence            75

>1n4c_A Auxilin; four helix bundle, protein binding; NMR {Bos taurus} SCOP: a.2.3.1 PDB: 1xi5_J

Probab=99.62  E-value=9.7e-17  Score=138.58  Aligned_cols=65  Identities=22%  Similarity=0.460  Sum_probs=59.9

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh---HHHHHHHHHHHHHHccCchhhhhH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD---AHDNFQKLKSSYEILKDEKARKLF   73 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~---a~~~f~~i~~Ay~vL~d~~~R~~Y   73 (292)
                      ...|||+||||+++     ++..+||+|||+++++|||||+++++.   |.+.|+.|++||++|+|+.+|..|
T Consensus       115 ~~~d~Y~vLgv~~~-----As~~eIKkAYRklal~~HPDK~~~~~~e~~A~~~F~~I~eAYevLsD~~kR~~Y  182 (182)
T 1n4c_A          115 AGETKWKPVGMADL-----VTPEQVKKVYRKAVLVVHPDKATGQPYEQYAKMIFMELNDAWSEFENQGQKPLY  182 (182)
T ss_dssp             TTCCCCCCCCGGGG-----SSHHHHHHHHHHHHHHTCGGGGSSCTTHHHHHHHHHHHHHHHHHHHHHHSSCCC
T ss_pred             CccchhhcCCCCCC-----CCHHHHHHHHHHHHHHHCcCcCCCcchHHHHHHHHHHHHHHHHHHCCHHhhhhC
Confidence            34699999999998     899999999999999999999987654   889999999999999999999877

>2qwo_B Putative tyrosine-protein phosphatase auxilin; chaperone-cochaperone complex, ATP-binding, nucleotide-bindi nucleus, phosphorylation, stress response; HET: ADP; 1.70A {Bos taurus} PDB: 2qwp_B* 2qwq_B* 2qwr_B* 2qwn_B* 1nz6_A

Probab=99.62  E-value=9.4e-17  Score=124.25  Aligned_cols=56  Identities=21%  Similarity=0.428  Sum_probs=51.7

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChh---HHHHHHHHHHHHHHccC
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD---AHDNFQKLKSSYEILKD   66 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~---a~~~f~~i~~Ay~vL~d   66 (292)
                      .++|.+|||+++     ++..+||+|||+++++|||||+|+++.   |.+.|+.|++||++|.+
T Consensus        33 ~~~y~~Lgv~~~-----as~~eIKkAYRklal~~HPDK~~~~~~~~~A~~~F~~i~eAyevL~~   91 (92)
T 2qwo_B           33 ETKWKPVGMADL-----VTPEQVKKVYRKAVLVVHPCKATGQPYEQYAKMIFMELNDAWSEFEN   91 (92)
T ss_dssp             CCSCCCCCGGGS-----SSHHHHHHHHHHHHHHTCHHHHTTSTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCeecCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCchhHhHHHHHHHHHHHHHHHHHh
Confidence            589999999998     899999999999999999999997763   78899999999999974

>3uo3_A J-type CO-chaperone JAC1, mitochondrial; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, J-protein; 1.85A {Saccharomyces cerevisiae} PDB: 3uo2_A

Probab=99.62  E-value=7.1e-16  Score=133.40  Aligned_cols=97  Identities=18%  Similarity=0.271  Sum_probs=73.3

Q ss_pred             CCccccccc------ccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            4 DHVDHYRVL------GLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         4 ~~~d~Y~iL------gv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ...|||+||      |+++-    +++..+|+++||+++++||||++++   +.+.|..|++||++|+||.+|..||..+
T Consensus         9 ~~~d~y~ll~~~~p~~~~~~----~a~~~eIk~aYr~la~~~HPDk~~~---a~~~f~~i~~AY~vL~dp~~R~~Yd~~l   81 (181)
T 3uo3_A            9 FTSTFYELFPKTFPKKLPIW----TIDQSRLRKEYRQLQAQHHPDMAQQ---GSEQSSTLNQAYHTLKDPLRRSQYMLKL   81 (181)
T ss_dssp             CSCCTGGGCTTTCTTCSCCS----CCCHHHHHHHHHHHHHTCCTTSCCS---CSSGGGSHHHHHHHHHSHHHHHHHHHHH
T ss_pred             CCCCHHHHhccccccCCCCC----CCCHHHHHHHHHHHHHHhCcCCCcc---HHHHHHHHHHHHHHHcChHHHHHHHHHH
Confidence            356999999      46552    3999999999999999999999975   6689999999999999999999999987


Q ss_pred             -HHHHHHHHH--HhhhhhHHHHHHHHHHHHHHH
Q 022800           78 -KIKREKQQR--QSQQDGKRRKMMSDLEERERA  107 (292)
Q Consensus        78 -~~~~~~~~r--~~~~~~kr~~~~~dLe~RE~~  107 (292)
                       .........  .......-.-+++.++.||.=
T Consensus        82 ~~g~~~~~e~~~~~~~~~d~~fLme~me~rE~l  114 (181)
T 3uo3_A           82 LRNIDLTQEQTSNEVTTSDPQLLLKVLDIHDEL  114 (181)
T ss_dssp             HHCCCTTSHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HhCCCccccccccccccCCHHHHHHHHHHHHHH
Confidence             321111110  001112235788889999873

>3lz8_A Putative chaperone DNAJ; structure genomics, structural genomics, PSI-2, protein STRU initiative; 2.90A {Klebsiella pneumoniae subsp} PDB: 2kqx_A

Probab=99.59  E-value=8.4e-17  Score=151.18  Aligned_cols=68  Identities=35%  Similarity=0.567  Sum_probs=0.0

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     |+.++||+|||+++++||||+++ ++.|.+.|+.|++||++|+||.+|..||.++.
T Consensus        27 ~~d~Y~vLgv~~~-----as~~eIk~aYr~la~~~HPDk~~-~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   94 (329)
T 3lz8_A           27 LKDYYAILGVQPT-----DDLKTIKTAYRRLARKYHPDVSK-ENDAEAKFKDLAEAWEVLKDEQRRAEYDQLWQ   94 (329)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             ccCHHHHcCcCCC-----CCHHHHHHHHHHHHHHHCCCCCC-ChHHHHHHHHHHHHHHHhhhhhhhcccchhhc
Confidence            4699999999998     89999999999999999999998 46789999999999999999999999999854

>1gh6_A Large T antigen; tumor suppressor, oncoprotein, antitumor protein; 3.20A {Simian virus 40} SCOP: a.2.3.1

Probab=99.59  E-value=5.8e-17  Score=130.29  Aligned_cols=62  Identities=27%  Similarity=0.385  Sum_probs=56.8

Q ss_pred             CcccccccccccCCCCCCCCH--HHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTE--KEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDD   75 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~--~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~   75 (292)
                      ..|||+||||+++     ++.  .+||+|||+++++||||++++    .+.|+.|++||++|+||.+|..||.
T Consensus         7 ~~~~Y~iLgv~~~-----as~~~~eIk~aYr~la~~~HPDk~~~----~e~f~~I~~AYevL~d~~~R~~~~~   70 (114)
T 1gh6_A            7 SLQLMDLLGLERS-----AWGNIPLMRKAYLKKCKEFHPDKGGD----EEKMKKMNTLYKKMEDGVKYAHQPD   70 (114)
T ss_dssp             HHHHHHHTTCCTT-----SCSCHHHHHHHHHHTTTTCCTTTCCT----TTTTHHHHHHHHHHHHHHHSCCSSC
T ss_pred             hhhHHHHcCCCCC-----CCcCHHHHHHHHHHHHHHHCCCCCcc----HHHHHHHHHHHHHHCCHHHHHHhhh
Confidence            3689999999998     677  999999999999999999875    3689999999999999999999984

>3ag7_A Putative uncharacterized protein F9E10.5; J-domain, AN auxilin-like J-domain containing protein, JAC1, chloroplast accumulation response; 1.80A {Arabidopsis thaliana}

Probab=99.58  E-value=4.4e-16  Score=123.59  Aligned_cols=60  Identities=20%  Similarity=0.259  Sum_probs=52.5

Q ss_pred             CCCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCC---Ch----hHHHHHHHHHHHHHHccCch
Q 022800            3 VDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPD---DP----DAHDNFQKLKSSYEILKDEK   68 (292)
Q Consensus         3 ~~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~---~~----~a~~~f~~i~~Ay~vL~d~~   68 (292)
                      +.+.|||.|||++.      ++..+||+|||+++++|||||+++   ++    .|.+.|+.|++||++|+|+.
T Consensus        38 ~~~~d~Y~vl~~~~------As~~eIKkAYRklal~~HPDK~~~~~~~~e~~~~A~~~F~~I~~AYevLsd~~  104 (106)
T 3ag7_A           38 WSGSGWKPVPLMDM------IEGNAVRKSYQRALLILHPDKLQQKGASANQKYMAEKVFELLQEAWDHFNTLG  104 (106)
T ss_dssp             CTTSCCCCCCGGGS------CSHHHHHHHHHHHHHHHCHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             cccCCHHHHcCCCC------CCHHHHHHHHHHHHHHHCcCcCCCcccchhhHHHHHHHHHHHHHHHHHHcCcc
Confidence            34679999999984      799999999999999999999874   12    36889999999999999985

>2pf4_E Small T antigen; PP2A, SV40, DNAJ, aalpha subunit, hydrolase regulat protein complex; 3.10A {Simian virus 40} PDB: 2pkg_C

Probab=99.54  E-value=3.1e-16  Score=134.55  Aligned_cols=64  Identities=27%  Similarity=0.346  Sum_probs=56.1

Q ss_pred             cccccccccccCCCCCCCC--HHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLT--EKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~--~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .|||+||||+++     ++  .++||+|||++++++|||++++    .+.|+.|++||++|+||.+|+.||....
T Consensus        11 ~d~Y~vLGl~~~-----as~~~~eIKkAYRkLa~~~HPDk~~~----~e~F~~I~~AYevLsdp~kR~~YD~~G~   76 (174)
T 2pf4_E           11 LQLMDLLGLERS-----AWGNIPLMRKAYLKKCKEFHPDKGGD----EEKMKKMNTLYKKMEDGVKYAHQPDFGG   76 (174)
T ss_dssp             HHHHHTTTCCGG-----GTTCHHHHHHHHHHHGGGCSCC---C----CTTTTHHHHHHHHHHHHHHHHTSCGGGG
T ss_pred             ccHHHHcCCCCC-----CCcCHHHHHHHHHHHHHHHCcCCCCC----HHHHHHHHHHHHHhCCHHHHHHHhccCC
Confidence            689999999998     56  7999999999999999999875    2689999999999999999999999774

>1faf_A Large T antigen; J domain, HPD motif, anti-parallel hairpin of helices, viral protein; NMR {Murine polyomavirus} SCOP: a.2.3.1

Probab=99.54  E-value=1.6e-15  Score=114.13  Aligned_cols=61  Identities=30%  Similarity=0.310  Sum_probs=53.6

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLF   73 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~Y   73 (292)
                      .++|+||||+++.   .++..+|++|||+++++||||++++    .+.|+.|++||++|+|+..|..+
T Consensus        11 ~~~y~iLgl~~~~---~a~~~eIk~aYr~la~~~HPDk~~~----~~~f~~i~~AYe~L~~~~~r~~~   71 (79)
T 1faf_A           11 ERLLELLKLPRQL---WGDFGRMQQAYKQQSLLLHPDKGGS----HALMQELNSLWGTFKTEVYNLRM   71 (79)
T ss_dssp             HHHHHHHTCCSSS---TTCHHHHHHHHHHHHHHSSGGGSCC----HHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHcCCCCCC---CCCHHHHHHHHHHHHHHHCcCCCCC----HHHHHHHHHHHHHHhhHHHHHHH
Confidence            4799999999862   2799999999999999999999853    47999999999999999888753

>2guz_A Mitochondrial import inner membrane translocase subunit TIM14; DNAJ-fold, chaperone, protein transport; HET: FLC; 2.00A {Saccharomyces cerevisiae}

Probab=99.51  E-value=4.1e-15  Score=109.60  Aligned_cols=57  Identities=21%  Similarity=0.270  Sum_probs=50.9

Q ss_pred             Cccccccccccc-CCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhh
Q 022800            5 HVDHYRVLGLPS-GEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKAR   70 (292)
Q Consensus         5 ~~d~Y~iLgv~~-~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R   70 (292)
                      ..++|+||||++ +     ++.++|+++||+++++||||++. +   .+.|+.|++||++|+|+..|
T Consensus        13 ~~~~y~iLgl~~~~-----a~~~eIk~ayr~l~~~~HPDk~g-~---~~~f~~i~~Aye~L~~~~~r   70 (71)
T 2guz_A           13 SKEALQILNLTENT-----LTKKKLKEVHRKIMLANHPDKGG-S---PFLATKINEAKDFLEKRGIS   70 (71)
T ss_dssp             HHHHHHHTTCCTTT-----CCHHHHHHHHHHHHHHHCGGGTC-C---HHHHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHcCCCCCC-----CCHHHHHHHHHHHHHHHCCCCCC-C---HHHHHHHHHHHHHHhhhhhc
Confidence            358999999998 6     89999999999999999999963 3   36999999999999998765

>3apo_A DNAJ homolog subfamily C member 10; PDI family, thioredoxin, endoplasmic reticulum, oxidoreducta; 2.40A {Mus musculus}

Probab=99.44  E-value=5.8e-15  Score=151.58  Aligned_cols=70  Identities=41%  Similarity=0.767  Sum_probs=40.2

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      .+.|||+||||+++     |+.++||+|||+++++||||++++++.+.+.|+.|++||++|+||.+|..||.++.
T Consensus        19 ~~~~~y~~lg~~~~-----a~~~~i~~ay~~l~~~~hpd~~~~~~~~~~~f~~i~~ay~~L~~~~~r~~yd~~~~   88 (780)
T 3apo_A           19 HDQNFYSLLGVSKT-----ASSREIRQAFKKLALKLHPDKNPNNPNAHGDFLKINRAYEVLKDEDLRKKYDKYGE   88 (780)
T ss_dssp             ----CHHHHTCCTT-----CCHHHHHHHHCC-----------------------CTHHHHHHSHHHHHHHTTC--
T ss_pred             CCCCHHHHcCCCCC-----CCHHHHHHHHHHHHHHHCcCCCCCChHHHHHHHHHHHHHHHHcChHHHHHHHhhcc
Confidence            46799999999998     89999999999999999999999888999999999999999999999999998764

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.08  E-value=1.5e-10  Score=89.70  Aligned_cols=67  Identities=24%  Similarity=0.286  Sum_probs=57.9

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|++||+|.+|.|..    +..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..|
T Consensus        26 nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           26 YLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             SCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            3556799999999999999999998852    56789999999999999999974  5666789999999875

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.08  E-value=6.2e-10  Score=94.61  Aligned_cols=76  Identities=24%  Similarity=0.176  Sum_probs=62.7

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCC--CCeEEEecCCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLS--NPLLVLPLQPA  243 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~--~pl~v~~~~~~  243 (292)
                      +.++|--......+|++.|+++|++||.|..|.|.....+|+|||+|.+.++|..|+..  +..+.+  ++|.|.|..+.
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            45666555666779999999999999999999986555689999999999999999986  444433  89999998764

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.07  E-value=1e-09  Score=85.71  Aligned_cols=71  Identities=21%  Similarity=0.275  Sum_probs=59.1

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh--cC--CCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV--CG--NLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~--~g--~~~~pl~v~~~~~  242 (292)
                      ++|-|.  ..+..+|++.|+++|++||.|.+|.|..  .+|+|||+|.+.++|..|+...  .+  +.+.||.|.|..+
T Consensus        16 ~~l~V~--nLp~~~te~~L~~~F~~fG~v~~v~i~~--~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   90 (101)
T 2cq1_A           16 RVLHIR--KLPGEVTETEVIALGLPFGKVTNILMLK--GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   90 (101)
T ss_dssp             SEEEEE--SCCTTCCHHHHHHTTTTTSCEEEEEEET--TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCEEEEEEEC--CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCc
Confidence            456664  3456799999999999999999998853  3899999999999999999853  34  6789999999864

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.07  E-value=3.7e-10  Score=88.45  Aligned_cols=71  Identities=24%  Similarity=0.250  Sum_probs=58.4

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC----CCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG----NLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g----~~~~pl~v~~~~~  242 (292)
                      ++|-|+  ..+..+|++.|+++|++||.|.+|.|.  +.+|+|||+|.+.++|..|+....|    ..+.||.|.|..+
T Consensus        22 ~~l~V~--NLp~~~te~~L~~lF~~fG~V~~v~i~--~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           22 PVVHIR--GLIDGVVEADLVEALQEFGPISYVVVM--PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             SEEEEE--SCCTTCCHHHHHHHHGGGSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             cEEEEe--CCCCCCCHHHHHHHHhccCCEEEEEEE--cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            344443  345679999999999999999999985  4689999999999999999987444    4489999999764

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.06  E-value=2.6e-10  Score=90.03  Aligned_cols=66  Identities=21%  Similarity=0.226  Sum_probs=56.3

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhc----CCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVC----GNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~----g~~~~pl~v~~~~~  242 (292)
                      ...+..+|++.|+++|++||.|.+|.|..  .+|+|||+|.+.++|..|+....    .+.+.||.|.|..+
T Consensus        22 ~nLp~~vte~dL~~lF~~fG~V~~v~i~~--~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           22 RKLPIDVTEGEVISLGLPFGKVTNLLMLK--GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH   91 (105)
T ss_dssp             CSCCTTSCHHHHHHHHHHHCCEEEEEEET--TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSS
T ss_pred             eCCCCCCCHHHHHHHHHhcCCEEEEEEEc--CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCC
Confidence            34556799999999999999999999864  37999999999999999998543    25689999999864

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.04  E-value=1.6e-09  Score=85.00  Aligned_cols=71  Identities=18%  Similarity=0.132  Sum_probs=59.4

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcC--CCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCG--NLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g--~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....++++.|+++|++||.|.+|.|..  .+|+|||+|.+.++|..|+..  ..+  +.+.||.|.|..+
T Consensus        16 ~~l~V~--nLp~~~te~~L~~~F~~fG~V~~v~i~~--~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~   90 (104)
T 1wex_A           16 PVVHVR--GLCESVVEADLVEALEKFGTICYVMMMP--FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             SEEEEE--SCCSSCCHHHHHHHHTTTSCEEEEEEET--TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhCCCEEEEEEEC--CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccC
Confidence            456664  3556799999999999999999999853  489999999999999999985  344  6789999999864

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.03  E-value=3e-09  Score=80.52  Aligned_cols=72  Identities=24%  Similarity=0.357  Sum_probs=60.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      +|-|.  .....+|++.|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+.  +..-+.+.+|.|.|..+
T Consensus         7 ~l~v~--nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   84 (95)
T 2dnz_A            7 GLYVG--SLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTE   84 (95)
T ss_dssp             EEEEE--SCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSC
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccc
Confidence            45443  4455799999999999999999999853    4568999999999999999997  46667899999999875

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.02  E-value=5.7e-10  Score=87.52  Aligned_cols=66  Identities=24%  Similarity=0.270  Sum_probs=56.3

Q ss_pred             eecCC-CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcC--CCCCCeEEEecCC
Q 022800          175 EKFGE-DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCG--NLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~-~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g--~~~~pl~v~~~~~  242 (292)
                      ...+. .+|+++|+++|++||.|.+|.|.  +.+|+|||+|.+.++|..|+.+  ..+  +.+.||.|.|..+
T Consensus        21 ~nLp~~~~te~dL~~lF~~fG~V~~v~i~--~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           21 MDFQRGKNLRYQLLQLVEPFGVISNHLIL--NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             ESCCCSSSHHHHHHTTTGGGSCEEEEEEC--SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             eCCCCCcCCHHHHHHHHHhcCCEEEEEEE--cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            34555 78999999999999999999985  3469999999999999999985  334  6789999999864

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.02  E-value=8.4e-10  Score=88.38  Aligned_cols=73  Identities=15%  Similarity=0.201  Sum_probs=59.9

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCC-------CCCCeEEEec
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGN-------LSNPLLVLPL  240 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~-------~~~pl~v~~~  240 (292)
                      ++|-|+-......+|++.|+++|++||.|.+|+|..  .+|||||+|.+.++|..|+....|.       .+.||+|.++
T Consensus        26 ~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~--~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a  103 (114)
T 2cq2_A           26 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV  103 (114)
T ss_dssp             SEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT--TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEE
T ss_pred             CEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEec
Confidence            457776333556799999999999999999999853  4799999999999999999976664       3678999998


Q ss_pred             CC
Q 022800          241 QP  242 (292)
Q Consensus       241 ~~  242 (292)
                      .+
T Consensus       104 ~~  105 (114)
T 2cq2_A          104 EK  105 (114)
T ss_dssp             SC
T ss_pred             cc
Confidence            64

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.01  E-value=5.8e-10  Score=91.33  Aligned_cols=74  Identities=27%  Similarity=0.237  Sum_probs=61.9

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcce-EEEEecCHHHHHHHHHhhcC--CCC--CCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGS-ALVVMATKSAAGAATGSVCG--NLS--NPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~-A~V~F~~~~~A~~Av~~~~g--~~~--~pl~v~~~~~  242 (292)
                      +.|+|--......+|++.|+++|++||.|..|+|.. +.+|+ |||+|.+.++|..|+....|  ..+  ++|+|.|..+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~-~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT-KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEE-ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEc-CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            467777777777899999999999999999999853 34677 99999999999999987444  444  8999999875

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=8.4e-10  Score=89.00  Aligned_cols=71  Identities=21%  Similarity=0.254  Sum_probs=59.0

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh----cCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV----CGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~----~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  ..+..+|++.|+++|++||.|.+|.|..  .+|+|||+|.+.++|..|+...    ..+.+.||.|.|..+
T Consensus        32 ~~LfVg--NLp~~vte~dL~~lF~~fG~V~~v~i~~--~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  106 (119)
T 2ad9_A           32 RVIHIR--KLPIDVTEGEVISLGLPFGKVTNLLMLK--GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH  106 (119)
T ss_dssp             SEEEEE--SCCTTCCHHHHHHHHTTTSCCCEEEEEG--GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSS
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccC
Confidence            355553  4556799999999999999999999864  3799999999999999999853    247789999999865

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.00  E-value=4.7e-09  Score=82.48  Aligned_cols=71  Identities=20%  Similarity=0.172  Sum_probs=59.0

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      |-.......+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (115)
T 2dgo_A           18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR   94 (115)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            33345566799999999999999999998852    45589999999999999999974  4446789999999875

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=2.1e-09  Score=82.90  Aligned_cols=73  Identities=21%  Similarity=0.078  Sum_probs=61.3

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|++.|+++|+.||.|..|.|..    ++.+|+|||+|.+.++|..|+.+...+.+.+|.|.|..+
T Consensus        16 ~~l~v--~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~~   92 (103)
T 2cqg_A           16 SDLIV--LGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS   92 (103)
T ss_dssp             CCEEE--ESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCT
T ss_pred             CEEEE--EcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecCC
Confidence            34554  34556799999999999999999998852    556899999999999999999976667789999999865

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.98  E-value=2.2e-09  Score=81.90  Aligned_cols=71  Identities=20%  Similarity=0.120  Sum_probs=58.5

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCC--CCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNL--SNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~--~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|++.|+++|++||.|.+|.+..  .+|+|||+|.+.++|..|+..  ...+.  +.+|.|.|..+
T Consensus        18 ~~l~V--~nlp~~~t~~~l~~~F~~~G~v~~v~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~   92 (97)
T 1why_A           18 TRLWV--GGLGPNTSLAALAREFDRFGSIRTIDHVK--GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             SCEEE--ECCCSSCCHHHHHHHHHTTSCEEEEEECS--SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhcCCeeEEEEeC--CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCC
Confidence            34555  34556799999999999999999999853  389999999999999999985  44455  78999999875

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.98  E-value=1.3e-09  Score=88.72  Aligned_cols=73  Identities=25%  Similarity=0.378  Sum_probs=59.3

Q ss_pred             ceEEEEeeecCCCCCHHHHH----HHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          168 KVLKVSWEKFGEDYTAERLR----EIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~----~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      ++|-|.  ..+..++++.|+    ++|++||.|.+|.+. +++.+|+|||+|.+.++|..|+..  +..+.+.||.|.|.
T Consensus        30 ~~LfV~--nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a  107 (127)
T 2a3j_A           30 QVVLIT--NINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS  107 (127)
T ss_dssp             SEEEEE--SCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEEC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEc
Confidence            345543  345568888765    799999999999885 467899999999999999999975  56678999999998


Q ss_pred             CC
Q 022800          241 QP  242 (292)
Q Consensus       241 ~~  242 (292)
                      .+
T Consensus       108 ~~  109 (127)
T 2a3j_A          108 ET  109 (127)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=3.6e-09  Score=81.55  Aligned_cols=72  Identities=26%  Similarity=0.340  Sum_probs=60.7

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|.  .....+|++.|+++|++||.|..|.|..  +..+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        17 ~l~V~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   92 (103)
T 2d9p_A           17 NLYVK--NLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQR   92 (103)
T ss_dssp             CEEEE--CCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSS
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecc
Confidence            45444  4455799999999999999999999863  46799999999999999999984  5567889999999875

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.98  E-value=4.2e-09  Score=80.84  Aligned_cols=66  Identities=20%  Similarity=0.132  Sum_probs=58.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~~  243 (292)
                      ....+|++.|+++|++||.|..|.|... .+|+|||+|.+.++|..|+.  ++....+.+|.|.|..+.
T Consensus         8 Lp~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            8 LGTGAGKGELERAFSYYGPLRTVWIARN-PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CCSSCSHHHHHHHHHHHCCCSEEEEESS-SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CCCCCCHHHHHHHHHhcCCeEEEEEeeC-CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            4557999999999999999999998644 79999999999999999998  467788999999998763

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.98  E-value=2.4e-09  Score=84.44  Aligned_cols=67  Identities=19%  Similarity=0.149  Sum_probs=57.6

Q ss_pred             eeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          174 WEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       174 Wk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .......+|++.|+++|++||.|..|.|.  +.+|+|||+|.+.++|..|+..  +..+.+.||.|.|...
T Consensus        15 V~nLp~~~te~~L~~~F~~~G~i~~v~i~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           15 AKNLPAGTLAAEIQETFSRFGSLGRVLLP--EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EESCCTTCCHHHHHHHHHTTSCEEEEECC--SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             EeCCCCCCCHHHHHHHHHhcCCEEEEEEe--CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            33455679999999999999999999984  5789999999999999999975  5557899999999764

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=5.7e-09  Score=79.80  Aligned_cols=73  Identities=19%  Similarity=0.336  Sum_probs=60.5

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|++.|+++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        11 ~~l~V~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a~~   88 (99)
T 2dgs_A           11 NKIFVG--GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEP   88 (99)
T ss_dssp             CEEEEE--SCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEECCC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            455553  4556799999999999999999999852    4578999999999999999997 45556789999999875

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.97  E-value=4e-09  Score=85.55  Aligned_cols=74  Identities=26%  Similarity=0.292  Sum_probs=60.8

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcce-EEEEecCHHHHHHHHHhhcCC--CC--CCeEEEecC
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGS-ALVVMATKSAAGAATGSVCGN--LS--NPLLVLPLQ  241 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~-A~V~F~~~~~A~~Av~~~~g~--~~--~pl~v~~~~  241 (292)
                      .++|+|--......+|++.|+++|++||.|..|+|.. + .|+ |||+|.+.++|..|+....|.  .+  ++|.|.|..
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            3467666666667899999999999999999999853 3 495 999999999999999875543  33  699999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus       101 ~  101 (124)
T 2e5i_A          101 P  101 (124)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.97  E-value=3.5e-09  Score=81.64  Aligned_cols=72  Identities=19%  Similarity=0.170  Sum_probs=59.9

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcc-cCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcC---CCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSE-FGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCG---NLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~-yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g---~~~~pl~v~~~~  241 (292)
                      +|-|  ......+|++.|+++|+. ||.|.+|.|..   +..+|+|||+|.+.++|..|+....|   +.+.+|.|.|..
T Consensus        11 ~l~V--~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~   88 (104)
T 2dhg_A           11 SLFV--GDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAI   88 (104)
T ss_dssp             CEEE--ECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEcc
Confidence            4444  345567999999999999 99999998852   55799999999999999999986444   678999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        89 ~   89 (104)
T 2dhg_A           89 P   89 (104)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.96  E-value=1.2e-09  Score=87.20  Aligned_cols=70  Identities=17%  Similarity=0.252  Sum_probs=58.2

Q ss_pred             eEEEEeeecCCC-CCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcC--CCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGED-YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCG--NLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~-~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g--~~~~pl~v~~~~~  242 (292)
                      +|-|.  ..+.. +|++.|+++|++||.|.+|.|.  +.+|+|||+|.+.++|..|+.+  ..+  +.+.+|.|.|..+
T Consensus        27 ~l~V~--NLp~~~~te~~L~~lF~~fG~V~~v~i~--~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           27 VIHLS--NLPHSGYSDSAVLKLAEPYGKIKNYILM--RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             EEEEE--SCCCSSCCSHHHHTTTTTTSCCSEEEEE--TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             EEEEe--CCCCccCCHHHHHHHHHhcCCEEEEEEe--cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            44443  34554 8999999999999999999985  4589999999999999999985  344  7889999999864

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=98.96  E-value=4.8e-10  Score=85.35  Aligned_cols=66  Identities=17%  Similarity=0.201  Sum_probs=55.9

Q ss_pred             cCCCCCHHHHHHHhcccC-CeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhc---CCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFG-KVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVC---GNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG-~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~---g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+++|++|| .|.+|.|.    +++.+|+|||+|.+.++|..|+....   -+.+.+|.|.|..|
T Consensus         9 Lp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~   82 (91)
T 2lxi_A            9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDP   82 (91)
T ss_dssp             CCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCS
T ss_pred             CCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCC
Confidence            456799999999999999 89999874    25679999999999999999997532   35689999999865

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.96  E-value=4.8e-09  Score=80.10  Aligned_cols=73  Identities=25%  Similarity=0.213  Sum_probs=60.3

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  .....+|++.|+++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..
T Consensus         9 ~~l~V~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   86 (99)
T 1whw_A            9 GRLFVR--NLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             EEEEEE--CCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            345543  4556799999999999999999999852    45789999999999999999964  455678999999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        87 ~   87 (99)
T 1whw_A           87 I   87 (99)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=98.95  E-value=8.7e-09  Score=79.62  Aligned_cols=72  Identities=21%  Similarity=0.426  Sum_probs=59.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcC--C---CCCCeEEEe
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCG--N---LSNPLLVLP  239 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g--~---~~~pl~v~~  239 (292)
                      +|-|  ......+|+++|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+....|  .   .+.+|.|.|
T Consensus        15 ~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~   92 (106)
T 2dgp_A           15 KLFI--GQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKP   92 (106)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEE
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEE
Confidence            4444  34566799999999999999999999853    45789999999999999999986444  3   679999999


Q ss_pred             cCC
Q 022800          240 LQP  242 (292)
Q Consensus       240 ~~~  242 (292)
                      ..+
T Consensus        93 a~~   95 (106)
T 2dgp_A           93 ADS   95 (106)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            865

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.95  E-value=7.5e-09  Score=79.70  Aligned_cols=72  Identities=24%  Similarity=0.257  Sum_probs=60.0

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|..|.|..  ...+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        17 ~l~V--~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   92 (103)
T 2cq3_A           17 RLHV--SNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   92 (103)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccc
Confidence            4444  45566799999999999999999999863  34689999999999999999974  4456789999999875

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=98.95  E-value=6e-09  Score=80.44  Aligned_cols=68  Identities=21%  Similarity=0.391  Sum_probs=57.1

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcC--CCC---CCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCG--NLS---NPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~---~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|..|.|..   ++.+|+|||+|.+.++|..|+....|  +.+   .+|.|.|..+
T Consensus        21 ~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~   96 (105)
T 2dnh_A           21 GMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADT   96 (105)
T ss_dssp             ESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCS
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECcc
Confidence            44566799999999999999999999853   45589999999999999999985333  455   8999999875

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.95  E-value=1.7e-09  Score=82.52  Aligned_cols=72  Identities=19%  Similarity=0.151  Sum_probs=59.0

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec--C-----CCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEe
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS--S-----KKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLP  239 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~--~-----k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~  239 (292)
                      +|-|.  .....+|++.|+++|++||.|..|.|..  .     ..+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|
T Consensus         7 ~l~V~--nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (98)
T 2cpf_A            7 GLFIK--NLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRI   84 (98)
T ss_dssp             CEEEE--SCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEEC
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            44443  3455699999999999999999999852  1     5689999999999999999984  5556789999999


Q ss_pred             cCC
Q 022800          240 LQP  242 (292)
Q Consensus       240 ~~~  242 (292)
                      ..+
T Consensus        85 a~~   87 (98)
T 2cpf_A           85 SER   87 (98)
T ss_dssp             SSC
T ss_pred             ccC
Confidence            875

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.95  E-value=3.8e-09  Score=81.41  Aligned_cols=68  Identities=16%  Similarity=0.148  Sum_probs=58.0

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|..|.|..  ...+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        21 ~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   92 (103)
T 2cqi_A           21 GNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   92 (103)
T ss_dssp             ESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             eCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCC
Confidence            34556799999999999999999999863  34689999999999999999974  4556789999999875

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.94  E-value=5.7e-09  Score=80.13  Aligned_cols=73  Identities=19%  Similarity=0.236  Sum_probs=60.8

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|  ......+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..
T Consensus        13 ~~l~v--~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   90 (102)
T 1x5s_A           13 GKLFV--GGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   90 (102)
T ss_dssp             SEEEE--ESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CEEEE--ECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            34554  44556799999999999999999999853    44689999999999999999964  556788999999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        91 ~   91 (102)
T 1x5s_A           91 K   91 (102)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.93  E-value=8.9e-09  Score=77.45  Aligned_cols=69  Identities=22%  Similarity=0.239  Sum_probs=58.5

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|++.|+++|++||.|..|.|.    +|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus         9 ~~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   79 (90)
T 2dnq_A            9 VKLFI--GNLPREATEQEIRSLFEQYGKVLECDII----KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN   79 (90)
T ss_dssp             EEEEE--ESCCSSCCHHHHHHHHHTSSCEEEEEEE----TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSC
T ss_pred             eEEEE--eCCCCCCCHHHHHHHHHhCCCEEEEEEE----CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCC
Confidence            34444  3556679999999999999999999994    78999999999999999975  4457899999999865

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.93  E-value=2.2e-09  Score=82.05  Aligned_cols=69  Identities=28%  Similarity=0.254  Sum_probs=58.8

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.-    ..+|++.|+++|++||.|.+|.|.  +.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        16 ~~l~V~n----~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~   86 (97)
T 1x5p_A           16 NTLYVYG----EDMTPTLLRGAFSPFGNIIDLSMD--PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   86 (97)
T ss_dssp             SEEEEEC----SSCCHHHHHHHHTTTSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSS
T ss_pred             CEEEEcC----CCCCHHHHHHHHhhCCCEEEEEec--CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCC
Confidence            4566653    379999999999999999999983  6789999999999999999974  4556789999999865

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=98.93  E-value=1.3e-09  Score=86.25  Aligned_cols=66  Identities=20%  Similarity=0.230  Sum_probs=56.5

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|++||.|.+|.|..  ...+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        13 Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A           13 LDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            456799999999999999999998853  44689999999999999999975  5556788999999865

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.93  E-value=3.7e-09  Score=82.55  Aligned_cols=67  Identities=22%  Similarity=0.278  Sum_probs=56.8

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      ...+..+|++.|+++|++||+|.+|.|..   +..+|+|||+|.+.++|..|+.. ...+.+.+|.|.|..
T Consensus        17 ~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           17 KGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   87 (103)
T ss_dssp             ECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHH
T ss_pred             ECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEch
Confidence            34556799999999999999999999863   55799999999999999999973 455678899999864

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.93  E-value=9.1e-09  Score=79.55  Aligned_cols=73  Identities=21%  Similarity=0.259  Sum_probs=60.2

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec-----CCCcceEEEEecCHHHHHHHHHh---hcCCCCCCeEEEe
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS-----SKKKGSALVVMATKSAAGAATGS---VCGNLSNPLLVLP  239 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~~---~~g~~~~pl~v~~  239 (292)
                      ++|-|  ......+|++.|+++|+.||.|..|.|..     +..+|+|||+|.+.++|..|+..   ..-+.+.+|.|.|
T Consensus        16 ~~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~   93 (107)
T 2cph_A           16 SKILV--RNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   93 (107)
T ss_dssp             CCEEE--ESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CEEEE--eCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEe
Confidence            34544  34556799999999999999999999842     34689999999999999999974   5566789999999


Q ss_pred             cCC
Q 022800          240 LQP  242 (292)
Q Consensus       240 ~~~  242 (292)
                      ..+
T Consensus        94 a~~   96 (107)
T 2cph_A           94 ADS   96 (107)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=98.93  E-value=1.3e-08  Score=80.79  Aligned_cols=73  Identities=16%  Similarity=0.263  Sum_probs=61.0

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~~  243 (292)
                      +|-|  ......+|++.|+++|++||.|.+|.|..   ++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+.
T Consensus         9 ~l~V--~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   86 (116)
T 2fy1_A            9 KLFI--GGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKP   86 (116)
T ss_dssp             EEEE--ECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCS
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4444  34556799999999999999999999863   55789999999999999999975  55578899999998753

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=98.93  E-value=1.6e-09  Score=81.73  Aligned_cols=66  Identities=18%  Similarity=0.150  Sum_probs=54.9

Q ss_pred             cCCCCCHHHHHHHhcccC--CeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFG--KVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG--~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ....+|+++|+++|+.||  .|.+|.|..    ++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.+..|
T Consensus         9 L~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~   82 (90)
T 3p5t_L            9 LTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNK   82 (90)
T ss_dssp             CCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC--
T ss_pred             CCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCC
Confidence            445689999999999999  999998742    56799999999999999999964  6668899999999875

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.93  E-value=6.3e-09  Score=80.13  Aligned_cols=72  Identities=25%  Similarity=0.326  Sum_probs=60.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        15 ~l~V--~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   92 (103)
T 2dnm_A           15 TLKV--DNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARY   92 (103)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSS
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCc
Confidence            4444  34556799999999999999999999852    45689999999999999999984  5667889999999875

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.92  E-value=4.5e-09  Score=82.00  Aligned_cols=70  Identities=19%  Similarity=0.201  Sum_probs=58.8

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+.+|+.||.|..|.|...  +|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        27 ~l~V--~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   98 (109)
T 1x4g_A           27 TVYC--GGIASGLTDQLMRQTFSPFGQIMEIRVFPE--KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   98 (109)
T ss_dssp             EEEE--ECCSSCCCHHHHHHHHHHHSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCeEEEEEeCC--CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCC
Confidence            4544  445667999999999999999999998533  89999999999999999975  4446789999999875

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.92  E-value=4.2e-09  Score=80.72  Aligned_cols=73  Identities=27%  Similarity=0.213  Sum_probs=60.7

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|++.|+++|+.||.|..|.|..   ++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        18 ~~l~v~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   95 (100)
T 2do4_A           18 HKLFIS--GLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNS   95 (100)
T ss_dssp             SCEEEE--SCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            355553  4556799999999999999999999853   45689999999999999999964  5557789999999875

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=98.92  E-value=2.9e-09  Score=79.19  Aligned_cols=69  Identities=17%  Similarity=0.140  Sum_probs=57.7

Q ss_pred             eeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          174 WEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       174 Wk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .......+|+++|+++|+.||.|.+|.|..    +..+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        11 v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   85 (87)
T 3bs9_A           11 VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR   85 (87)
T ss_dssp             EESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC-
T ss_pred             EeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCC
Confidence            344556799999999999999999999852    45689999999999999999985  4556789999999864

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.92  E-value=4.9e-09  Score=80.77  Aligned_cols=69  Identities=23%  Similarity=0.316  Sum_probs=58.6

Q ss_pred             eeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          174 WEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       174 Wk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .......+|++.|+++|++||.|..|.|..    +..+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        20 V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (103)
T 2cq0_A           20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP   94 (103)
T ss_dssp             EESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSC
T ss_pred             EeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCC
Confidence            345566799999999999999999999852    45689999999999999999985  4456789999999875

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.91  E-value=5.1e-09  Score=81.60  Aligned_cols=73  Identities=16%  Similarity=0.157  Sum_probs=60.2

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec-CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS-SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~-~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|+++|+++|++||.|..|.|.. ...+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        23 ~~l~V~--nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           23 CRIYVG--NLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             SEEEEE--SCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            345553  4556799999999999999999999863 45689999999999999999975  4446789999999865

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=98.91  E-value=2.5e-09  Score=79.66  Aligned_cols=66  Identities=20%  Similarity=0.244  Sum_probs=56.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecC----C-CcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSS----K-KKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~----k-~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|++||.|.+|.|...    . .+|+|||+|.+.++|..|+.  ++....+.+|.|.|..+
T Consensus        12 lp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   84 (88)
T 4a8x_A           12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLA   84 (88)
T ss_dssp             CCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             CCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCC
Confidence            4567999999999999999999988532    2 78999999999999999998  45667789999999865

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.91  E-value=1e-08  Score=79.63  Aligned_cols=67  Identities=22%  Similarity=0.211  Sum_probs=57.7

Q ss_pred             ecCCCCCHHHHHHHhcccCC-eeEEEEe-c----CCCcceEEEEecCHHHHHHHHHhh----cCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGK-VEDVVIK-S----SKKKGSALVVMATKSAAGAATGSV----CGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~-V~~v~i~-~----~k~~g~A~V~F~~~~~A~~Av~~~----~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|+.||. |.+|.|. .    ++.+|+|||+|.+.++|..|+...    ..+.+.+|.|.|..+
T Consensus        15 nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~   91 (109)
T 2dis_A           15 GIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEP   91 (109)
T ss_dssp             CCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCS
T ss_pred             CCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCC
Confidence            45567999999999999999 9999885 2    367999999999999999999853    456789999999876

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=98.90  E-value=1.3e-09  Score=84.16  Aligned_cols=73  Identities=10%  Similarity=0.121  Sum_probs=58.6

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCC--eeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcCC------CCCC
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGK--VEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCGN------LSNP  234 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~--V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g~------~~~p  234 (292)
                      +++|-|+  ..+...|++.|+++|++||.  |.+|.|..    ++.+|+|||+|.+.++|..|+....|.      .+.|
T Consensus         9 m~tlfV~--nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            9 MDTIILR--NIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCEEEEE--SCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             cCEEEEe--CCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            4455554  34567999999999999995  67887742    567999999999999999999876653      4789


Q ss_pred             eEEEecC
Q 022800          235 LLVLPLQ  241 (292)
Q Consensus       235 l~v~~~~  241 (292)
                      |.|.|..
T Consensus        87 i~V~~Ak   93 (95)
T 2lkz_A           87 IGVDFAK   93 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEEcc
Confidence            9999975

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=98.90  E-value=4.4e-09  Score=77.50  Aligned_cols=66  Identities=18%  Similarity=0.172  Sum_probs=56.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|+.||.|.+|.+..    +..+|+|||+|.+.++|..|+..  +.-..+.+|.|.|..+
T Consensus         9 lp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            9 LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            456699999999999999999998852    55699999999999999999974  5556789999999864

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.90  E-value=1.5e-09  Score=83.08  Aligned_cols=63  Identities=16%  Similarity=0.177  Sum_probs=55.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ....+|++.|+++|++||+|.++.+.  ..+|||||+|.|.++|..|+..  ++.+.+.||.|.+..
T Consensus        15 L~~~~te~~L~~lF~q~G~V~~~~l~--~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           15 LTAQIDGPTLRTLCMQHGPLVSFHPY--LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCTTCCCHHHHHHHHHHSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CCccCCHHHHHHHHHhhCCEEEEEEc--CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            45669999999999999999999984  3699999999999999999975  777888999998763

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.90  E-value=6.2e-09  Score=79.44  Aligned_cols=64  Identities=17%  Similarity=0.238  Sum_probs=55.9

Q ss_pred             eecCC-CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGE-DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~-~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..... .+|++.|+++|++||.|.+|.|.    +|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus        16 ~nlp~~~~t~~~l~~~F~~~G~v~~v~i~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   82 (96)
T 2kvi_A           16 GNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSS   82 (96)
T ss_dssp             ESSTTSCCCHHHHHHHHTTTCCCCEEEEE----TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEEC
T ss_pred             eCCCcccCCHHHHHHHHHhcCCEEEEEEe----CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCc
Confidence            45565 79999999999999999999993    79999999999999999985  4556689999999864

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.90  E-value=1.1e-08  Score=78.87  Aligned_cols=73  Identities=18%  Similarity=0.223  Sum_probs=61.1

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  .....+|++.|+++|++||.|..|.|..    +..+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..
T Consensus        16 ~~l~V~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   93 (105)
T 1x5u_A           16 ATVYVG--GLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   93 (105)
T ss_dssp             TEEEEE--CCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            455553  4556799999999999999999999852    45789999999999999999984  556788999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        94 ~   94 (105)
T 1x5u_A           94 A   94 (105)
T ss_dssp             T
T ss_pred             C
Confidence            5

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.90  E-value=4.5e-09  Score=79.71  Aligned_cols=72  Identities=21%  Similarity=0.213  Sum_probs=59.1

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEE-EEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDV-VIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v-~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      +|-|.  .....+|++.|+++|+.||.|..| .|..    +..+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..
T Consensus         7 ~l~V~--nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (96)
T 1x5t_A            7 GIFIG--NLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAF   84 (96)
T ss_dssp             EEEEE--CCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESC
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            45443  445669999999999999999998 7742    45689999999999999999984  445678999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        85 ~   85 (96)
T 1x5t_A           85 K   85 (96)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.89  E-value=6.9e-09  Score=78.05  Aligned_cols=72  Identities=24%  Similarity=0.188  Sum_probs=60.2

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|++||.|..|.|.  .++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        10 ~l~V--~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   85 (92)
T 2dgv_A           10 QIFV--RNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRN   85 (92)
T ss_dssp             EEEE--CSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            4444  3455679999999999999999999885  355789999999999999999984  5557789999999865

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=98.89  E-value=3.8e-09  Score=83.40  Aligned_cols=72  Identities=17%  Similarity=0.253  Sum_probs=59.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|.  ..+..+|++.|+++|++||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.+...
T Consensus         8 ~lfV~--nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~   85 (110)
T 3s8s_A            8 EVTFA--RLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK   85 (110)
T ss_dssp             EEEEE--SCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECST
T ss_pred             EEEEE--CCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            44443  3456799999999999999999998852    56799999999999999999975  5556889999999753

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=98.89  E-value=4e-09  Score=76.50  Aligned_cols=64  Identities=16%  Similarity=0.275  Sum_probs=53.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEec
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPL  240 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~  240 (292)
                      .+..+|++.|+++|++||+|.+|.+..    ++.+|+|||+|.+.++|..|+. +...+.+.+|.|.|.
T Consensus         7 lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            455799999999999999999998852    5568999999999999999986 355567788888763

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.89  E-value=7.3e-09  Score=80.63  Aligned_cols=72  Identities=21%  Similarity=0.197  Sum_probs=60.1

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--------hcCCCCCCeE
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--------VCGNLSNPLL  236 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--------~~g~~~~pl~  236 (292)
                      +|-|.  .....+|++.|+++|+.||.|.+|.|..    +..+|+|||+|.+.++|..|+..        ...+.+.+|.
T Consensus        17 ~l~V~--nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~   94 (111)
T 1x4h_A           17 TVFIR--NLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLK   94 (111)
T ss_dssp             CEEEE--SCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEE
T ss_pred             EEEEE--CCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEE
Confidence            45443  4556799999999999999999999852    45799999999999999999975        4557789999


Q ss_pred             EEecCC
Q 022800          237 VLPLQP  242 (292)
Q Consensus       237 v~~~~~  242 (292)
                      |.|..+
T Consensus        95 v~~a~~  100 (111)
T 1x4h_A           95 VDLAVT  100 (111)
T ss_dssp             EECCCC
T ss_pred             EEECCC
Confidence            999865

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=2.3e-09  Score=80.39  Aligned_cols=67  Identities=27%  Similarity=0.334  Sum_probs=56.5

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|++||.|.+|.|. .+.+|+|||+|.+.++|..|+.......+.+|.|.|..+
T Consensus        11 ~nLp~~~te~~l~~~F~~~G~i~~v~i~-~~~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A           11 GRCTGDMTEDELREFFSQYGDVMDVFIP-KPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEP   77 (88)
T ss_dssp             ESCCSSSCHHHHHHHSTTTSCCCEEECC-SSCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCC
T ss_pred             eCCCCCCCHHHHHHHHHHcCCeeEEEEe-cCCCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCC
Confidence            4456679999999999999999999985 347899999999999999887665555678899998765

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.88  E-value=3.9e-09  Score=81.09  Aligned_cols=73  Identities=26%  Similarity=0.360  Sum_probs=60.4

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  .....+|++.|+++|+.||.|..|.|..    ++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..
T Consensus        13 ~~l~V~--nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2cqb_A           13 RVLYVG--GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   90 (102)
T ss_dssp             SCEEEE--SCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCC
Confidence            345553  3455699999999999999999999842    45799999999999999999974  555678999999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        91 ~   91 (102)
T 2cqb_A           91 P   91 (102)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.88  E-value=9.2e-09  Score=78.74  Aligned_cols=70  Identities=27%  Similarity=0.315  Sum_probs=59.0

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|++||.|..|.|.  +.+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        17 ~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpj_A           17 RLFV--GNLPPDITEEEMRKLFEKYGKAGEVFIH--KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   88 (99)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHTSTTCCCSEEEEE--TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHhhcCCeEEEEEe--cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCC
Confidence            4444  4455679999999999999999999985  4589999999999999999975  4556789999999865

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.88  E-value=6.9e-09  Score=81.37  Aligned_cols=72  Identities=17%  Similarity=0.182  Sum_probs=59.5

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCe----eEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKV----EDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V----~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|    ..+.+.+++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        27 ~l~V--~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~  104 (115)
T 2cpx_A           27 VLYL--KNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN  104 (115)
T ss_dssp             EEEE--ECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccC
Confidence            4444  3456679999999999999999    455555677899999999999999999974  5567899999999875

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=8.4e-09  Score=79.71  Aligned_cols=72  Identities=25%  Similarity=0.280  Sum_probs=60.0

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|.+|.|..    +..+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        25 ~l~V--~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~  102 (106)
T 1p27_B           25 ILFV--TGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV  102 (106)
T ss_dssp             EEEE--ECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEE
T ss_pred             EEEE--eCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecC
Confidence            4444  34556799999999999999999999852    45689999999999999999974  5557789999999864

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=98.87  E-value=1.4e-08  Score=79.54  Aligned_cols=73  Identities=22%  Similarity=0.312  Sum_probs=60.7

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~  241 (292)
                      ++|-|  ......+|++.|+++|++||.|..|.|..    +..+|+|||+|.+.++|..|+.  ++.-+.+.+|.|.|..
T Consensus        27 ~~l~V--~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  104 (108)
T 2jrs_A           27 MRLYV--GSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVT  104 (108)
T ss_dssp             EEEEE--ECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcc
Confidence            34444  34556799999999999999999998852    4568999999999999999997  4666789999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus       105 ~  105 (108)
T 2jrs_A          105 E  105 (108)
T ss_dssp             S
T ss_pred             c
Confidence            5

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=98.87  E-value=8.1e-09  Score=81.09  Aligned_cols=72  Identities=22%  Similarity=0.336  Sum_probs=60.3

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|.  ..+..+|++.|+++|+.||.|.+|.|. .+..+|+|||+|.+.++|..|+..  +....+.+|.|.|..+
T Consensus        10 ~l~V~--nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A           10 ILYIR--NLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             EEEEE--SCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            45443  345679999999999999999999986 456799999999999999999984  5567789999999864

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.87  E-value=1.1e-08  Score=80.11  Aligned_cols=73  Identities=21%  Similarity=0.147  Sum_probs=59.9

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|+++|+++|+.||.|.+|.|..   ++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        16 ~~l~V--~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   93 (114)
T 2do0_A           16 STVFV--ANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER   93 (114)
T ss_dssp             SCEEE--ESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEccc
Confidence            34555  34556799999999999999999998853   44589999999999999999984  5556789999999864

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.87  E-value=9.3e-09  Score=78.53  Aligned_cols=72  Identities=17%  Similarity=0.141  Sum_probs=58.8

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|++.|+++|+.||.|. +.+..++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        20 ~~l~V--~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           20 ADVYV--GNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             CEEEE--ECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CEEEE--eCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            34444  44566799999999999999997 4444567899999999999999999964  5566889999999865

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=1.1e-08  Score=78.16  Aligned_cols=72  Identities=24%  Similarity=0.202  Sum_probs=59.0

Q ss_pred             EEEeeecCCCCCHHHHH----HHhcccCCeeEEEEec-CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLR----EIFSEFGKVEDVVIKS-SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~----~~fs~yG~V~~v~i~~-~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-.......++++.|+    ++|++||.|.+|.|.. ...+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        11 ~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   89 (96)
T 2dgx_A           11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   89 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            34444556679999999    9999999999999963 22289999999999999999985  4456789999999865

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.87  E-value=4e-09  Score=82.06  Aligned_cols=61  Identities=21%  Similarity=0.220  Sum_probs=53.5

Q ss_pred             CHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHHh--hcCCCCC-CeEEEecCC
Q 022800          182 TAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATGS--VCGNLSN-PLLVLPLQP  242 (292)
Q Consensus       182 t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~-pl~v~~~~~  242 (292)
                      |++.|+++|++||.|.+|.|.  +++.+|+|||+|.+.++|..|+..  +..+.+. +|.|.|..+
T Consensus        34 t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~   99 (105)
T 2nlw_A           34 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTD   99 (105)
T ss_dssp             HHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCC
T ss_pred             HHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcch
Confidence            789999999999999999985  356799999999999999999985  5556787 999999854

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=5.8e-09  Score=78.85  Aligned_cols=73  Identities=25%  Similarity=0.233  Sum_probs=59.8

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      .++|-|.  .....+|++.|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|.
T Consensus        15 ~~~l~v~--nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           15 NCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             GGCEEEE--SCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCEEEEE--CCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            3455553  4556799999999999999999999852    45689999999999999999984  45567899999987


Q ss_pred             C
Q 022800          241 Q  241 (292)
Q Consensus       241 ~  241 (292)
                      .
T Consensus        93 ~   93 (95)
T 2cqc_A           93 S   93 (95)
T ss_dssp             S
T ss_pred             C
Confidence            5

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=98.87  E-value=4.4e-09  Score=77.87  Aligned_cols=70  Identities=26%  Similarity=0.337  Sum_probs=56.8

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      +|-|.  ..+..+|++.|+++|++||.|.+|.|.    ++..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|.
T Consensus         9 ~l~V~--nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            9 VLYVG--GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             EEEEE--CCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             EEEEE--CCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            44443  344569999999999999999999884    245799999999999999999964  55567788999885

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.86  E-value=4.9e-09  Score=77.75  Aligned_cols=68  Identities=25%  Similarity=0.287  Sum_probs=56.2

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh---hcCCCCCCeEEEec
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS---VCGNLSNPLLVLPL  240 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~---~~g~~~~pl~v~~~  240 (292)
                      +|-|  ...+..+|++.|+++|++||.|..|.+..  .+|+|||+|.+.++|..|+..   .....+.+|.|.|.
T Consensus        14 ~l~V--~~l~~~~t~~~l~~~f~~~G~i~~~~~~~--~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           14 TLYV--GGLGDTITETDLRNHFYQFGEIRTITVVQ--RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             CEEE--ECCTTTSCHHHHHHHHHTTSCEEEEEEEG--GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             EEEE--cCCCCCCCHHHHHHHHHhCCCEeEEEEEC--CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            4544  34556799999999999999999999853  579999999999999999984   44566788998885

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.86  E-value=1.1e-08  Score=80.23  Aligned_cols=68  Identities=21%  Similarity=0.343  Sum_probs=56.9

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcCC----------CCCCeEEEecC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCGN----------LSNPLLVLPLQ  241 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g~----------~~~pl~v~~~~  241 (292)
                      ......+|++.|+++|+.||.|..|.|..   +..+|+|||+|.+.++|..|+....|.          .+.||.|.|..
T Consensus        31 ~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~  110 (114)
T 1x5o_A           31 SNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSG  110 (114)
T ss_dssp             ESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccC
Confidence            44556799999999999999999998853   456899999999999999999864443          47899999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      |
T Consensus       111 p  111 (114)
T 1x5o_A          111 P  111 (114)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.86  E-value=1.5e-08  Score=80.87  Aligned_cols=73  Identities=18%  Similarity=0.242  Sum_probs=60.6

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|++.|+++|+.||.|.+|.|..   ++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        36 ~~l~V--~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  113 (124)
T 2kt5_A           36 AKLLV--SNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS  113 (124)
T ss_dssp             EEEEE--ESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCC
Confidence            34444  34556799999999999999999999853   45789999999999999999984  5557789999999865

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=98.86  E-value=2.7e-09  Score=80.92  Aligned_cols=66  Identities=27%  Similarity=0.354  Sum_probs=53.5

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|++||.|.+|.|.. +.+|+|||+|.+.++|..+.+......+.++.|.|..|
T Consensus        18 ~Lp~~~te~~L~~~F~~~G~i~~v~i~~-~srGfaFV~F~~~~~A~~~~~~~~~~~g~~v~v~~a~~   83 (89)
T 3d2w_A           18 RCTEDMTAEELQQFFCQYGEVVDVFIPK-PFRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEP   83 (89)
T ss_dssp             SCCTTCCHHHHHHHHTTTSCEEEEECCS-SCCSEEEEEESCHHHHHHHTTCEEEETTEEEEEEECC-
T ss_pred             CCCCCCCHHHHHHHHhccCCEEEEEEee-CCCCEEEEEECCHHHHHHHcCCCcccCCEEEEEEEcCC
Confidence            3566799999999999999999999853 47999999999999999665544444577888888764

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=98.86  E-value=7.1e-09  Score=81.52  Aligned_cols=72  Identities=19%  Similarity=0.137  Sum_probs=59.4

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|..|.|..    ++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        27 ~l~V--~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~  104 (115)
T 2cpz_A           27 NLFI--YHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS  104 (115)
T ss_dssp             CEEE--ESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            4444  34556799999999999999999998852    45689999999999999999975  4456789999999875

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=98.86  E-value=1.2e-09  Score=101.45  Aligned_cols=65  Identities=37%  Similarity=0.625  Sum_probs=55.0

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC---hhHHHHHHHHHHHHHHccCchhhhhHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD---PDAHDNFQKLKSSYEILKDEKARKLFDD   75 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~---~~a~~~f~~i~~Ay~vL~d~~~R~~YD~   75 (292)
                      .++|.+||+...     ++..+|+++|+++++.+|||+.+++   +.+...|..|.+||++|+||.+|..||.
T Consensus       382 ~~~y~~lg~~~~-----~~~~~~~~~y~~~~l~~~pd~~~~~~~~~~a~~~~~~i~~ay~~L~d~~~r~~yd~  449 (450)
T 2y4t_A          382 RDYYKILGVKRN-----AKKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKFIDIAAAKEVLSDPEMRKKFDD  449 (450)
T ss_dssp             CCSGGGSCSSTT-----CCTTHHHHHHHHHHHHSCGGGCCSHHHHHHHHHHHHHHHHHHHHSSGGGGC-----
T ss_pred             hhHHHHhCCCcc-----CCHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHHHHHhCCHHHHHhccC
Confidence            489999999997     7889999999999999999999854   2478899999999999999999999996

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=98.86  E-value=5.8e-09  Score=78.96  Aligned_cols=72  Identities=19%  Similarity=0.185  Sum_probs=58.9

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  .....+|++.|+++|++||.|.+|.|..   +..+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..
T Consensus        17 ~~l~v~--nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           17 RTVFVG--NLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             GEEEEE--CCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CEEEEE--CCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            345553  4556799999999999999999999853   45689999999999999999984  555678899999864

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.85  E-value=2e-09  Score=83.18  Aligned_cols=63  Identities=21%  Similarity=0.178  Sum_probs=54.4

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCC-CCeEEEecCC
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLS-NPLLVLPLQP  242 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~-~pl~v~~~~~  242 (292)
                      ..+++.|+++|++||.|.+|.|+.    ++.+|+|||+|.+.++|..|+..  +.-+.+ .+|.|.|..|
T Consensus        23 ~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           23 PVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             HHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHH
T ss_pred             HHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECch
Confidence            688999999999999999999852    56799999999999999999974  555666 8999999854

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=98.85  E-value=7e-09  Score=78.96  Aligned_cols=67  Identities=18%  Similarity=0.118  Sum_probs=57.2

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|++||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  +....+.+|.|.|..+
T Consensus         9 nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             SCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            3456799999999999999999999852    45699999999999999999975  4456789999999865

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.85  E-value=3.6e-09  Score=80.00  Aligned_cols=69  Identities=22%  Similarity=0.192  Sum_probs=57.3

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCC-eeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC---CCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGK-VEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG---NLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~-V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g---~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|+++|+++|++||. |..+.+   .++|+|||+|.+.++|..|+....|   +.+.+|.|.|..+
T Consensus        10 ~l~V--~nLp~~~t~~~l~~~F~~~G~vv~~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~   82 (93)
T 2cqh_A           10 KLYI--GNLSPAVTADDLRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   82 (93)
T ss_dssp             CEEE--ECCCTTCCHHHHHHHHHHTTCCCSSCEE---EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHHcCCceEEEEE---cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccC
Confidence            4444  345667999999999999999 777766   3589999999999999999986555   7889999999875

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.84  E-value=8.6e-09  Score=79.28  Aligned_cols=66  Identities=24%  Similarity=0.201  Sum_probs=57.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ....+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        16 lp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A           16 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             CCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            445699999999999999999998852    45589999999999999999974  6667899999999865

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.84  E-value=2.4e-08  Score=75.38  Aligned_cols=64  Identities=23%  Similarity=0.199  Sum_probs=55.6

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|++||.|..|.|.    +++|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        16 ~nLp~~~t~~~l~~~F~~~G~v~~v~~~----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   81 (92)
T 2dgt_A           16 GNISPTCTNQELRAKFEEYGPVIECDIV----KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS   81 (92)
T ss_dssp             ESCCSSCCHHHHHHHHHTTSCCCEEEEC----SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEE----CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccC
Confidence            3456679999999999999999999994    56999999999999999974  5556789999999875

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.84  E-value=5.7e-09  Score=81.77  Aligned_cols=73  Identities=25%  Similarity=0.268  Sum_probs=60.1

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|++.|+++|++||.|.+|.|..  ++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        30 ~~l~V--~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  106 (109)
T 2err_A           30 KRLHV--SNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA  106 (109)
T ss_dssp             CEEEE--ESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEE--ECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            34444  45566799999999999999999999852  44689999999999999999985  4456789999999864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.83  E-value=1.2e-08  Score=80.28  Aligned_cols=68  Identities=18%  Similarity=0.248  Sum_probs=57.8

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|..|.|..    ++.+|+|||+|.+.++|..|+.. ...+.+.+|.|.|..+
T Consensus        33 ~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           33 GGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             ECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             eCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCC
Confidence            44566799999999999999999999853    45689999999999999999975 3446788999999865

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=98.83  E-value=6.3e-09  Score=78.09  Aligned_cols=65  Identities=29%  Similarity=0.386  Sum_probs=55.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ....+++++|+++|+.||.|.+|.|..    ++.+|+|||+|.+.+ |..|+..  +....+.+|.|.|..+
T Consensus         9 Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            9 LVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             ECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             CCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            455699999999999999999999852    556999999999999 9999985  5667899999999865

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=98.83  E-value=1.9e-08  Score=77.60  Aligned_cols=69  Identities=28%  Similarity=0.302  Sum_probs=57.9

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ......+|++.|+++|++||.|..|.|.    +|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        12 ~~l~V--~nl~~~~t~~~l~~~F~~~G~i~~v~~~----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   82 (103)
T 2dgu_A           12 KVLFV--RNLANTVTEEILEKAFSQFGKLERVKKL----KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP   82 (103)
T ss_dssp             CCEEE--ECCCTTCCHHHHHHHHHHHSCEEEEEEC----SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhcCCEEEEEEE----CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCC
Confidence            34554  3455679999999999999999999983    67999999999999999984  5556789999999875

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.83  E-value=6.7e-09  Score=75.42  Aligned_cols=64  Identities=19%  Similarity=0.265  Sum_probs=54.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEec
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPL  240 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~  240 (292)
                      .+..+|++.|+++|++||+|.+|.+..    ++.+|+|||+|.+.++|..|+.. ...+.+.+|.|.|.
T Consensus         8 lp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~a   76 (77)
T 1uaw_A            8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            455799999999999999999999853    45689999999999999999974 36667889998874

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=98.83  E-value=7.2e-09  Score=80.76  Aligned_cols=68  Identities=21%  Similarity=0.250  Sum_probs=57.7

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        32 ~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  105 (110)
T 1oo0_B           32 TSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV  105 (110)
T ss_dssp             ESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             eCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEccc
Confidence            34556799999999999999999999852    45689999999999999999984  4456789999999864

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.83  E-value=7.2e-09  Score=76.53  Aligned_cols=56  Identities=23%  Similarity=0.263  Sum_probs=46.9

Q ss_pred             CHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHHh--hcCCCCC-CeEE
Q 022800          182 TAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATGS--VCGNLSN-PLLV  237 (292)
Q Consensus       182 t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~-pl~v  237 (292)
                      |++.|+++|++||.|.+|.|.  +++.+|+|||+|.+.++|..|+..  +..+.+. ||.|
T Consensus        20 t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           20 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             HHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            789999999999999999985  356799999999999999999985  4444555 6654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.83  E-value=4.4e-09  Score=80.73  Aligned_cols=66  Identities=17%  Similarity=0.072  Sum_probs=56.0

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|.+|.|.  +.+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        33 ~nlp~~~~~~~l~~~f~~~G~i~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           33 GNIPHFATEADLIPLFQNFGFILDFKHY--PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             ESCCTTCCHHHHHHHHHTTSCCSEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             cCCCcccCHHHHHHHHHhCCCEEEEEEe--cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            4455679999999999999999999985  5689999999999999999975  4445688899988753

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=98.82  E-value=4e-09  Score=80.18  Aligned_cols=72  Identities=25%  Similarity=0.420  Sum_probs=59.4

Q ss_pred             eEEEEeeecCCCCCHHHHH----HHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLR----EIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~----~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      +|-|.  .....+|++.|+    ++|++||.|.+|.|. +++.+|+|||+|.+.++|..|+..  +....+.+|.|.|..
T Consensus        10 ~l~V~--nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   87 (97)
T 1nu4_A           10 TIYIN--NLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   87 (97)
T ss_dssp             EEEEE--SCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEcc
Confidence            45443  455679999999    999999999999985 345689999999999999999974  445678999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        88 ~   88 (97)
T 1nu4_A           88 T   88 (97)
T ss_dssp             S
T ss_pred             C
Confidence            5

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=98.82  E-value=1.2e-08  Score=76.06  Aligned_cols=66  Identities=23%  Similarity=0.252  Sum_probs=55.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|+.||.|.+|.+..    ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        14 lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A           14 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             CCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             CCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            455689999999999999999998852    4569999999999999999993 24446678999999864

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.82  E-value=1e-08  Score=77.36  Aligned_cols=72  Identities=26%  Similarity=0.301  Sum_probs=59.0

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      .++|-|.  .....+|++.|+++|++||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|.
T Consensus        16 ~~~l~V~--nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           16 KSTVYVS--NLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             TTSEEEE--SCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCEEEEE--CCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            3456664  4456799999999999999999999853    45689999999999999999974  44467889999885

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.82  E-value=2.7e-08  Score=75.42  Aligned_cols=68  Identities=16%  Similarity=0.147  Sum_probs=57.4

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEE-EEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDV-VIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v-~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|..| .|...+..|.|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        21 ~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           21 RNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             EEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             EcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            3455679999999999999999999 465555667799999999999999974  5666789999999875

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.82  E-value=1.7e-08  Score=77.28  Aligned_cols=66  Identities=26%  Similarity=0.324  Sum_probs=55.9

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeE--------EEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEec
Q 022800          175 EKFGEDYTAERLREIFSEFGKVED--------VVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPL  240 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~--------v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~  240 (292)
                      ......+|++.|+++|++||.|..        |.|..    ++.+|+|||+|.+.++|..|+.  ++..+.+.+|.|.|.
T Consensus        19 ~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           19 QGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             ECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             eCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEec
Confidence            345567999999999999999998        77742    4568999999999999999997  466678899999885

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.81  E-value=8.1e-09  Score=81.29  Aligned_cols=76  Identities=17%  Similarity=0.167  Sum_probs=60.7

Q ss_pred             cceEEEEeeecCCCC---------CHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhc--CCCCCCe
Q 022800          167 EKVLKVSWEKFGEDY---------TAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVC--GNLSNPL  235 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~---------t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~--g~~~~pl  235 (292)
                      .++|.|+.-.....+         +++.|+++|++||.|.+|.|.....+|+|||+|.+.++|..|+....  -+.+.+|
T Consensus        15 s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   94 (112)
T 2dit_A           15 ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI   94 (112)
T ss_dssp             CCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEEC
T ss_pred             ceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            457888766433221         36899999999999999988655579999999999999999998644  3578899


Q ss_pred             EEEecCC
Q 022800          236 LVLPLQP  242 (292)
Q Consensus       236 ~v~~~~~  242 (292)
                      .|.|..+
T Consensus        95 ~v~~a~~  101 (112)
T 2dit_A           95 TAQAWDG  101 (112)
T ss_dssp             EEEECCS
T ss_pred             EEEEeCC
Confidence            9999865

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=98.81  E-value=1.3e-08  Score=83.83  Aligned_cols=72  Identities=17%  Similarity=0.132  Sum_probs=59.9

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ...+..+|++.|+++|+.||.|.+|.|.. .++|+|||+|.+.++|..|+..  +..+.+.||.|.|..+
T Consensus        74 ~~l~V--~nl~~~~t~~~l~~~F~~~G~i~~v~i~~-~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  147 (150)
T 2i2y_A           74 CKVYV--GNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG  147 (150)
T ss_dssp             CEEEE--ESCCSCCSCHHHHHHHHHHSCEEEEEECS-SSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhhCCEEEEEEee-CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCC
Confidence            34444  34556789999999999999999999853 3689999999999999999974  5667899999999865

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=98.81  E-value=1.4e-08  Score=82.33  Aligned_cols=73  Identities=25%  Similarity=0.197  Sum_probs=60.8

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|  ......+|++.|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..
T Consensus        47 ~~l~V--~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~  124 (129)
T 2kxn_B           47 CCLGV--FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI  124 (129)
T ss_dssp             SCBCE--ETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCS
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            34444  34566799999999999999999999852    46799999999999999999984  556778999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus       125 ~  125 (129)
T 2kxn_B          125 T  125 (129)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.80  E-value=3.9e-08  Score=77.37  Aligned_cols=72  Identities=25%  Similarity=0.227  Sum_probs=59.2

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhc-CCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVC-GNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~-g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+.... -+.+.+|.|.|..+
T Consensus        19 ~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~   95 (116)
T 2cqd_A           19 KIFV--GGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYL   95 (116)
T ss_dssp             EEEE--ECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTT
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEccc
Confidence            4544  44556799999999999999999999852    4578999999999999999997633 35678999999864

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=98.80  E-value=1.5e-08  Score=77.77  Aligned_cols=70  Identities=17%  Similarity=0.233  Sum_probs=57.6

Q ss_pred             cceEEEEeeecCC-CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh--cCCCCCCeEEEecCC
Q 022800          167 EKVLKVSWEKFGE-DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV--CGNLSNPLLVLPLQP  242 (292)
Q Consensus       167 ~~~lkvKWk~~~~-~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~--~g~~~~pl~v~~~~~  242 (292)
                      .++|-|  ..... .+|++.|+++|+.||.|..|.|    .+|+|||+|.+.++|..|+...  ..+.+.+|.|.|..+
T Consensus        22 ~~~l~V--~nLp~~~~t~~~L~~~F~~~G~v~~v~i----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           22 KSRLFI--GNLPLKNVSKEDLFRIFSPYGHIMQINI----KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             TCEEEE--ESCCSSCCCHHHHHHHHGGGSCEEEEEE----CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCEEEE--eCCCcccCCHHHHHHHHHhcCCEEEEEE----eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            345555  34555 7999999999999999999998    3899999999999999999864  334689999999764

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.80  E-value=2.1e-08  Score=78.18  Aligned_cols=69  Identities=17%  Similarity=0.090  Sum_probs=56.4

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhc--CCCC-----CCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVC--GNLS-----NPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~--g~~~-----~pl~v~~~~~  242 (292)
                      +|-.......+|+++|+++|++||.|..|.|..+   |+|||+|.+.++|..|+....  .+.+     .+|.|.|..+
T Consensus        17 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~   92 (108)
T 1x4c_A           17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   92 (108)
T ss_dssp             EEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT---TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC---CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCC
Confidence            3333455677999999999999999999998533   999999999999999998533  3344     7899999875

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.80  E-value=1.1e-08  Score=78.05  Aligned_cols=68  Identities=12%  Similarity=0.022  Sum_probs=56.5

Q ss_pred             eecCCCCCHHHHHHHhcccCCee-EEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCC----eEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVE-DVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNP----LLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~-~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~p----l~v~~~~~  242 (292)
                      ......+|+++|+++|++||.|. +|.|..    +..+|+|||+|.+.++|..|+..  ..-+.+.+    |.|.|..+
T Consensus        15 ~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~   93 (99)
T 2div_A           15 GDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATY   93 (99)
T ss_dssp             CSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTC
T ss_pred             eCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCC
Confidence            44556799999999999999999 988852    45689999999999999999985  44456677    99999865

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.80  E-value=1e-08  Score=80.43  Aligned_cols=64  Identities=28%  Similarity=0.333  Sum_probs=56.2

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|++||.|..|.|.    +|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        37 ~nLp~~~t~~~L~~~F~~~G~i~~v~i~----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  102 (108)
T 2jvo_A           37 RPFPLDVQESELNEIFGPFGPMKEVKIL----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL  102 (108)
T ss_dssp             CSSCTTCCHHHHHHHHTTTSCCCEEEEE----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSC
T ss_pred             ECCCCCCCHHHHHHHHHhcCCEEEEEEE----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            4456679999999999999999999995    89999999999999999974  5556889999999865

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.80  E-value=1.7e-08  Score=75.88  Aligned_cols=69  Identities=22%  Similarity=0.175  Sum_probs=57.4

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|++.|+++|++||.|..|.|.    +|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        10 ~~l~V~--nlp~~~t~~~l~~~F~~~G~v~~~~~~----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   80 (90)
T 2dnp_A           10 WKIFVG--NVSAACTSQELRSLFERRGRVIECDVV----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTK   80 (90)
T ss_dssp             CCEEEE--SCCTTCCHHHHHHHHHHHSCEEEEEEC----SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHcCCCEEEEEEE----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCC
Confidence            345443  345569999999999999999999984    56999999999999999985  4556789999999875

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=98.80  E-value=1.4e-08  Score=81.01  Aligned_cols=72  Identities=25%  Similarity=0.306  Sum_probs=59.7

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      +|-|.  .....+|++.|.++|++||.|.+|.|.    +++.+|+|||+|.+.++|..|+.  +..-+.+.+|.|.|..+
T Consensus        24 ~l~V~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  101 (126)
T 3ex7_B           24 ILFVT--GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV  101 (126)
T ss_dssp             EEEEE--SCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEE
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Confidence            44443  345669999999999999999999985    24569999999999999999996  46667889999999865

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.79  E-value=1.4e-08  Score=79.61  Aligned_cols=75  Identities=13%  Similarity=-0.043  Sum_probs=58.4

Q ss_pred             ceEEEEeeecCC---CCCHHHHHHHhcccCCeeEEEEec-----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEE
Q 022800          168 KVLKVSWEKFGE---DYTAERLREIFSEFGKVEDVVIKS-----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLV  237 (292)
Q Consensus       168 ~~lkvKWk~~~~---~~t~~~L~~~fs~yG~V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v  237 (292)
                      ++|.|+--....   .-++++|+++|++||.|.+|.|..     +..+|+|||+|.+.++|..|+..  +..+.+.+|.|
T Consensus         9 ~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v   88 (105)
T 2pe8_A            9 KVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKA   88 (105)
T ss_dssp             SEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEE
Confidence            467776444322   236899999999999999999853     35699999999999999999985  44467889999


Q ss_pred             EecCC
Q 022800          238 LPLQP  242 (292)
Q Consensus       238 ~~~~~  242 (292)
                      .|..+
T Consensus        89 ~~a~~   93 (105)
T 2pe8_A           89 CFYNL   93 (105)
T ss_dssp             EECCH
T ss_pred             EEcCH
Confidence            98753

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.79  E-value=2.2e-08  Score=81.15  Aligned_cols=73  Identities=23%  Similarity=0.309  Sum_probs=61.1

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|  ......+|++.|+++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..
T Consensus        43 ~~l~V--~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  120 (139)
T 1u6f_A           43 RNLMV--NYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             SEEEE--ESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45555  45566799999999999999999998852    44699999999999999999984  555788999999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus       121 ~  121 (139)
T 1u6f_A          121 S  121 (139)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.79  E-value=1e-08  Score=81.40  Aligned_cols=71  Identities=8%  Similarity=0.053  Sum_probs=59.6

Q ss_pred             EEeeecCCCCCHHHHHHHhcccC-CeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFG-KVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG-~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      |--......+|+++|+++|+.|| .|..|.|...+.+|+|||+|.+.++|..|+..  +..+.+.+|.|.|...
T Consensus        31 l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             EEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            33345567799999999999999 99999985566899999999999999999974  5556788999999753

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=98.79  E-value=1.4e-08  Score=78.64  Aligned_cols=71  Identities=23%  Similarity=0.286  Sum_probs=58.7

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      +|-|.  .....+|++.|+++|+.||.|..|.|.   +++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|+.
T Consensus        31 ~l~V~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           31 KLLVS--NLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             EEEEE--SCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            45444  455679999999999999999999885   245689999999999999999984  555678899998863

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.78  E-value=1.2e-08  Score=77.78  Aligned_cols=72  Identities=15%  Similarity=0.152  Sum_probs=57.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|+++|+++|+.||.|..+.+.    +++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        17 ~l~v--~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   94 (98)
T 2cqp_A           17 IIKV--QNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG   94 (98)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCC
Confidence            4444  4456679999999999999999865543    245689999999999999999975  3456789999999764

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.78  E-value=1.3e-08  Score=79.76  Aligned_cols=73  Identities=18%  Similarity=0.244  Sum_probs=59.5

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|++.|+++|+.||.|.+|.|..    +..+|+|||+|.+.++|..|+.. +..+.+.+|.|.|..+
T Consensus        26 ~~lfV~--nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a~~  103 (109)
T 2rs2_A           26 CKMFIG--GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFP  103 (109)
T ss_dssp             CCEEEE--SCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEECCC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEccC
Confidence            345443  3456799999999999999999999853    55689999999999999999975 3555678999999864

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.78  E-value=1.8e-08  Score=78.78  Aligned_cols=73  Identities=23%  Similarity=0.219  Sum_probs=59.3

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCee--------EEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVE--------DVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSN  233 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~--------~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~  233 (292)
                      ++|-|.  .....+|++.|+++|+.||.|.        .|.|..    ++.+|+|||+|.+.++|..|+.  +...+.+.
T Consensus        16 ~~l~V~--nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   93 (113)
T 2cpe_A           16 SAIYVQ--GLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGS   93 (113)
T ss_dssp             CEEEEE--CCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTE
T ss_pred             CEEEEc--CCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCC
Confidence            345543  4556799999999999999999        577742    4568999999999999999997  45556789


Q ss_pred             CeEEEecCC
Q 022800          234 PLLVLPLQP  242 (292)
Q Consensus       234 pl~v~~~~~  242 (292)
                      +|.|.|..+
T Consensus        94 ~l~V~~a~~  102 (113)
T 2cpe_A           94 KLKVSLARK  102 (113)
T ss_dssp             ECEEECSSC
T ss_pred             EEEEEECCC
Confidence            999999875

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=98.78  E-value=6.8e-09  Score=75.14  Aligned_cols=63  Identities=17%  Similarity=0.293  Sum_probs=51.9

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEe
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLP  239 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~  239 (292)
                      .+..+|++.|+++|++||+|.+|.+..    ++.+|+|||+|.+.++|..|+.. .....+.+|.|.|
T Consensus         7 Lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~   74 (75)
T 1iqt_A            7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV   74 (75)
T ss_dssp             CCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEE
T ss_pred             CCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            345699999999999999999998852    55799999999999999999975 3445566777665

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=98.78  E-value=2.3e-08  Score=82.70  Aligned_cols=69  Identities=23%  Similarity=0.272  Sum_probs=59.2

Q ss_pred             eeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          174 WEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       174 Wk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .......+|+++|+++|+.||.|..|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.||.|.|..+
T Consensus        75 v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  149 (158)
T 2kn4_A           75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY  149 (158)
T ss_dssp             EESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECC
T ss_pred             EeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            344566799999999999999999999852    56799999999999999999974  5557789999999875

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.78  E-value=1.3e-08  Score=79.83  Aligned_cols=68  Identities=22%  Similarity=0.169  Sum_probs=57.1

Q ss_pred             eecCCCCCHHHHH---HHhcccCCeeEEEEecC-------CCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLR---EIFSEFGKVEDVVIKSS-------KKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~---~~fs~yG~V~~v~i~~~-------k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...+..+++++|.   ++|++||+|.+|.|...       +.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        21 ~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  100 (111)
T 2cpi_A           21 VGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTT  100 (111)
T ss_dssp             EEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCC
T ss_pred             ECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccc
Confidence            3355679999999   99999999999998532       3459999999999999999984  5556789999999875

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.77  E-value=2e-08  Score=81.96  Aligned_cols=73  Identities=26%  Similarity=0.301  Sum_probs=61.2

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  .....+|++.|+++|+.||.|..|.|..    ++.+|+|||+|.+.++|..|+.  +...+.+.+|.|.|..
T Consensus        48 ~~l~V~--nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  125 (135)
T 2lea_A           48 TSLKVD--NLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  125 (135)
T ss_dssp             CCEEEE--CCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            345554  4455699999999999999999999852    4679999999999999999997  4666788999999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus       126 ~  126 (135)
T 2lea_A          126 Y  126 (135)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=98.76  E-value=1.6e-08  Score=83.82  Aligned_cols=73  Identities=16%  Similarity=0.081  Sum_probs=60.5

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  .....+|+++|.++|++||.|..|.|..    +..+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..
T Consensus        40 ~~l~V~--nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  117 (156)
T 1h2v_Z           40 CTLYVG--NLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA  117 (156)
T ss_dssp             CEEEEE--SCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            345553  4556799999999999999999999852    45689999999999999999984  555678999999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus       118 ~  118 (156)
T 1h2v_Z          118 G  118 (156)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=9.5e-09  Score=79.39  Aligned_cols=68  Identities=25%  Similarity=0.324  Sum_probs=56.8

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+.. ..-+.+.+|.|.|..+
T Consensus        22 ~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a~~   94 (105)
T 2dh8_A           22 GGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTP   94 (105)
T ss_dssp             BSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCSCC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEccC
Confidence            34556799999999999999999998853    45689999999999999999984 4445678899998765

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.76  E-value=2.8e-08  Score=78.99  Aligned_cols=73  Identities=25%  Similarity=0.292  Sum_probs=59.2

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|..  ....+|++.|+++|++||.|.+|.|.    ++..+|+|||+|.+.++|..|+. ++..+.+.+|.|.|..+
T Consensus        37 ~~l~V~n--lp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           37 RSVYVGN--VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             TEEEEEE--ECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CEEEEeC--CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            3565543  44569999999999999999999884    25679999999999999999993 24446789999999864

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=98.75  E-value=2.2e-08  Score=74.56  Aligned_cols=69  Identities=16%  Similarity=0.231  Sum_probs=54.7

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEe
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLP  239 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~  239 (292)
                      +|-|  ...+..+|++.|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|.|
T Consensus        13 ~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A           13 KMFV--GGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             EEEE--ECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4544  34556799999999999999999999852    55699999999999999999964 2335566777765

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=98.75  E-value=2.4e-08  Score=78.72  Aligned_cols=69  Identities=19%  Similarity=0.122  Sum_probs=56.4

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      |-.......+|++.|+++|++||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|.
T Consensus        43 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             EEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            33344566799999999999999999999852    45699999999999999999985  44456788888875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.73  E-value=5.3e-08  Score=83.45  Aligned_cols=68  Identities=16%  Similarity=0.286  Sum_probs=58.3

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+.  ++.-+.+.+|.|.|..+
T Consensus       131 ~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~  204 (216)
T 2qfj_A          131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT  204 (216)
T ss_dssp             ECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSS
T ss_pred             eCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecC
Confidence            34455699999999999999999999852    4568999999999999999998  46667899999999865

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.73  E-value=1.6e-08  Score=76.75  Aligned_cols=72  Identities=15%  Similarity=0.175  Sum_probs=59.3

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|++.|+++|+.||.|..| ...++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        17 ~~l~V~--nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           17 RTLLAK--NLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             GEEEEE--SCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            345543  455679999999999999999888 33577899999999999999999984  5556789999999865

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=98.73  E-value=2.7e-08  Score=77.62  Aligned_cols=68  Identities=19%  Similarity=0.190  Sum_probs=56.9

Q ss_pred             eEEEEeeecCCC-CCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGED-YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~-~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ...... +|++.|+++|++||.|..|.|    .+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        29 ~l~V--~nl~~~~~t~~~l~~~F~~~G~v~~v~i----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           29 RVFI--GNLNTALVKKSDVETIFSKYGRVAGCSV----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             EEEE--CSCCCSSCCHHHHHHHHGGGSCCSEEEE----ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             EEEE--eCCCcccCCHHHHHHHHHhCCCeEEEEE----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            4444  345566 899999999999999999998    579999999999999999975  4445789999999864

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=98.73  E-value=3.4e-08  Score=79.67  Aligned_cols=71  Identities=25%  Similarity=0.322  Sum_probs=57.2

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      ++|-|  ......+|++.|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|.
T Consensus        64 ~~l~v--~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           64 RVLYV--GGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             CEEEE--ECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             cEEEE--EeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            34444  45566799999999999999999999852    55799999999999999999974  44466888888763

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.73  E-value=5e-08  Score=74.58  Aligned_cols=68  Identities=22%  Similarity=0.212  Sum_probs=56.8

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhccc--CCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEF--GKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~y--G~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|++|  |.|..|.+    .+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        17 ~l~V--~nLp~~~t~~~l~~~F~~~g~g~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpd_A           17 ILYV--RNLMLSTSEEMIEKEFNNIKPGAVERVKK----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   88 (99)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHHHTTSTTCEEEEEE----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCcceEEEEE----eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            4444  3455679999999999999  99999987    378999999999999999984  5556789999999875

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.73  E-value=1.7e-08  Score=77.34  Aligned_cols=73  Identities=23%  Similarity=0.199  Sum_probs=57.0

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|++.|+++|++||.|.-+....++.+|+|||+|.+.++|..|+..  ...+.+.+|.|.|..+
T Consensus        16 ~~l~V~--nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   90 (101)
T 2fc9_A           16 KTLVLS--NLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP   90 (101)
T ss_dssp             SEEEEE--SCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSS
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCC
Confidence            455553  455669999999999999998322212356799999999999999999984  4456789999999875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=1.8e-08  Score=74.70  Aligned_cols=65  Identities=20%  Similarity=0.170  Sum_probs=52.2

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEe
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLP  239 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~  239 (292)
                      ...+..++++.|+++|++||.|..|.|..    +..+|+|||+|.+.++|..|+..  +..+.+.++++.|
T Consensus        11 ~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A           11 RGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             ESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            34566799999999999999999998853    45689999999999999999985  4445555555544

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=8.5e-08  Score=73.93  Aligned_cols=70  Identities=16%  Similarity=0.106  Sum_probs=57.2

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeEEEEec-----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS-----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .|-.......+|+++|+++|+.|| |.+|.|..     ++.+|+|||+|.+.++|..|+ .  ..-+.+.+|.|.|..+
T Consensus        17 ~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~   93 (104)
T 1wi8_A           17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQ   93 (104)
T ss_dssp             EEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccC
Confidence            333345566799999999999999 99999852     456899999999999999999 5  3345688999999865

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.71  E-value=2.3e-08  Score=78.43  Aligned_cols=72  Identities=28%  Similarity=0.337  Sum_probs=58.7

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|.+|.|..    +..+|+|||+|.+.++|..|+. +...+.+.+|.|.|..+
T Consensus        27 ~l~V--~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           27 TVFC--MQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCC
Confidence            4444  34556799999999999999999999852    4578999999999999999993 24456789999999754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.71  E-value=9.3e-08  Score=73.56  Aligned_cols=67  Identities=15%  Similarity=0.068  Sum_probs=55.3

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.|| |.+|.|..    ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        21 ~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~   92 (103)
T 2dng_A           21 GNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEG   92 (103)
T ss_dssp             ESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEECCC
T ss_pred             eCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEecC
Confidence            34566799999999999998 99998852    4568999999999999999993 23345688999999865

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=98.71  E-value=2.8e-08  Score=83.37  Aligned_cols=67  Identities=21%  Similarity=0.254  Sum_probs=57.3

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|..+|++||.|..|.|..    +..+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        79 nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  151 (165)
T 1rk8_A           79 SIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV  151 (165)
T ss_dssp             SCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4556799999999999999999999852    44689999999999999999975  4446789999999864

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=7.8e-08  Score=74.50  Aligned_cols=72  Identities=15%  Similarity=0.140  Sum_probs=58.2

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeE-EEEe---cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVED-VVIK---SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~-v~i~---~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      +|-........|+++|+++|+.||.|.+ |.|.   +++.+|+|||+|.+.++|..|+.. ..-+.+.++.|.+..+
T Consensus        17 ~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~~~   93 (104)
T 1wg5_A           17 FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR   93 (104)
T ss_dssp             EEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECT
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEECCH
Confidence            4444556678999999999999999998 6664   356799999999999999999975 4455678899988653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.70  E-value=5.2e-08  Score=83.21  Aligned_cols=71  Identities=15%  Similarity=0.220  Sum_probs=59.9

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      |--......+|++.|.++|+.||.|..|.|..   +..+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|+.+
T Consensus        91 l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~  166 (177)
T 2f3j_A           91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS  166 (177)
T ss_dssp             EEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            33345566799999999999999999999853   55789999999999999999984  5667889999999864

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=98.70  E-value=2e-07  Score=83.53  Aligned_cols=75  Identities=25%  Similarity=0.451  Sum_probs=61.3

Q ss_pred             ceEEEEeee---------cCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHhh------cC
Q 022800          168 KVLKVSWEK---------FGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGSV------CG  229 (292)
Q Consensus       168 ~~lkvKWk~---------~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~~------~g  229 (292)
                      +.|+|.|..         .+..+|++.|+++|+.||.|..|.|.   +++.+|+|||+|.+.++|..|+...      .+
T Consensus        86 ~~l~v~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~  165 (261)
T 3sde_A           86 RPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLT  165 (261)
T ss_dssp             EECEEEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESS
T ss_pred             ceeEeeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEec
Confidence            356666664         34568999999999999999999885   2567999999999999999999863      33


Q ss_pred             CCCCCeEEEecCC
Q 022800          230 NLSNPLLVLPLQP  242 (292)
Q Consensus       230 ~~~~pl~v~~~~~  242 (292)
                      ..+.|+.|.|..+
T Consensus       166 ~~~r~i~v~~~~~  178 (261)
T 3sde_A          166 TTPRPVIVEPMEQ  178 (261)
T ss_dssp             SSCCBCEEEECCC
T ss_pred             CCCceEEEeeccc
Confidence            4488999999865

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.69  E-value=3.9e-08  Score=80.41  Aligned_cols=66  Identities=18%  Similarity=0.177  Sum_probs=56.3

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ..+..+|++.|+++|+.||.|..|.+..    +..+|+|||+|.+.++|..|+..  +.-..+.+|.|.|..
T Consensus        94 nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A           94 DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             SCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            3455799999999999999999998852    46689999999999999999974  555678999999975

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=98.68  E-value=2.4e-08  Score=76.77  Aligned_cols=72  Identities=14%  Similarity=0.090  Sum_probs=57.4

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec-----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS-----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      ++|-|  ......+|++.|+++|+.|| |.+|.|..     ++.+|+|||+|.+.++|..|+. ++..+.+.+|.|.|..
T Consensus        20 ~~l~V--~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~a~   96 (100)
T 2j76_E           20 YTAFL--GNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVAD   96 (100)
T ss_dssp             CEEEE--SCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEECC
T ss_pred             cEEEE--eCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEecc
Confidence            34444  34556699999999999999 99999852     4469999999999999999993 2555678899999876


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        97 ~   97 (100)
T 2j76_E           97 Q   97 (100)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=98.68  E-value=8.1e-08  Score=79.33  Aligned_cols=66  Identities=26%  Similarity=0.438  Sum_probs=54.9

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcC--CC---CCCeEEEec
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCG--NL---SNPLLVLPL  240 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g--~~---~~pl~v~~~  240 (292)
                      ...+..+|++.|+++|++||.|..|.+..   +..+|+|||+|.+.++|..|+....|  ..   +.||.|.|.
T Consensus       101 ~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          101 GMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             ESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             cCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            34556799999999999999999998852   45689999999999999999986444  33   389999986

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.67  E-value=1.5e-08  Score=77.84  Aligned_cols=68  Identities=18%  Similarity=0.221  Sum_probs=57.3

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||.|..|.|..   ++.+|+|||+|.+.++|..|+.+...+.+.+|.|.|..+
T Consensus        15 ~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A           15 GGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             ECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEEEE
T ss_pred             eCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEECCc
Confidence            34556799999999999999999998853   456899999999999999999965566778899988653

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=98.67  E-value=4.5e-08  Score=79.89  Aligned_cols=72  Identities=17%  Similarity=0.272  Sum_probs=58.5

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeE--------EEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEE
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVED--------VVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLV  237 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~--------v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v  237 (292)
                      +|-|.  .....+|++.|+.+|+.||.|..        |.+. +++.+|+|||+|.+.++|..|+..  +..+.+.+|.|
T Consensus        47 ~l~V~--nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V  124 (143)
T 3egn_A           47 RIYVK--NLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVV  124 (143)
T ss_dssp             EEEEE--EECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEE
T ss_pred             EEEEe--CCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            44443  34557999999999999999976        4333 478899999999999999999974  56677899999


Q ss_pred             EecCC
Q 022800          238 LPLQP  242 (292)
Q Consensus       238 ~~~~~  242 (292)
                      .|..+
T Consensus       125 ~~a~~  129 (143)
T 3egn_A          125 QFARS  129 (143)
T ss_dssp             EECCC
T ss_pred             EECCC
Confidence            99864

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=98.66  E-value=3e-08  Score=86.46  Aligned_cols=63  Identities=24%  Similarity=0.270  Sum_probs=55.3

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+|++.|+++|+.||.|.+|.|. ..++|+|||+|.+.++|..|+..  +..+.+.+|.|.|...
T Consensus        15 ~~~~~~~L~~~F~~~G~v~~v~i~-~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A           15 SKMNCDRVFNVFCLYGNVEKVKFM-KSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             TTCCHHHHHHHHTTTSCEEEEEEC-TTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             ccCCHHHHHHHHHhcCCeEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            569999999999999999999885 34689999999999999999974  6667889999999753

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=98.65  E-value=9.1e-08  Score=78.68  Aligned_cols=67  Identities=16%  Similarity=0.309  Sum_probs=57.4

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|++||.|..|.|..    +..+|+|||+|.+.++|..|+.. ..-+.+.+|.|.|..|
T Consensus        94 nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           94 GIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             EECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCC
T ss_pred             CCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCC
Confidence            3455799999999999999999999852    55789999999999999999973 5566789999999865

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.65  E-value=3.7e-08  Score=76.28  Aligned_cols=61  Identities=18%  Similarity=0.207  Sum_probs=51.7

Q ss_pred             ecCCCCCHHH----HHHHhccc-CCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAER----LREIFSEF-GKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~----L~~~fs~y-G~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+...+++.    |+++|++| |.|.+|+   +   |+|||+|.+.++|.+|+..  +..+++.||+|.+..+
T Consensus        16 NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt---g---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A           16 NLPANKDGKSVSNRLRRLSDNCGGKVLSIT---G---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             SCCTTSCHHHHHHHHHHHHHTTTCCEEECC---T---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             CCCCcCCHHHHHHHHHHHHHHcCCeeEEEe---c---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            3556678776    66999999 5999993   2   9999999999999999974  7778999999999864

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.64  E-value=2.8e-08  Score=78.29  Aligned_cols=71  Identities=11%  Similarity=-0.004  Sum_probs=58.0

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCe-eEEEEec---CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKV-EDVVIKS---SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V-~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      |-.......+|+++|+++|+.||.| .+|.|..   ++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|.|..+
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a~~   93 (114)
T 2cpy_A           18 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   93 (114)
T ss_dssp             EEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             EEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEECCH
Confidence            3334556679999999999999999 7888752   55799999999999999999975 4445778999999864

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.64  E-value=3e-08  Score=79.23  Aligned_cols=71  Identities=18%  Similarity=0.178  Sum_probs=57.1

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeE-EEEe---cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVED-VVIK---SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~-v~i~---~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      +|-.......+|+++|+++|+.||.|.+ ++|.   +++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..
T Consensus        27 ~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             EEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            4444456677999999999999999987 3442   25679999999999999999997 3555678899999875

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=98.64  E-value=5e-08  Score=77.13  Aligned_cols=65  Identities=15%  Similarity=0.023  Sum_probs=51.7

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEe
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLP  239 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~  239 (292)
                      |-.......+|+++|.++|++||.|..|.|...   |+|||+|.+.++|..|+..  ...+.+.+|.|.+
T Consensus        19 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~   85 (115)
T 3beg_B           19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   85 (115)
T ss_dssp             EEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT---SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC---CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEE
Confidence            333455677999999999999999999998532   9999999999999999985  4445677744443

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.64  E-value=7.1e-08  Score=77.82  Aligned_cols=66  Identities=11%  Similarity=0.096  Sum_probs=55.2

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeE--EEEe----cCCCcceEEEEecCHHHHHHHHHhhc------CCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVED--VVIK----SSKKKGSALVVMATKSAAGAATGSVC------GNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~--v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~------g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|++||.|..  |.|.    +++.+|||||+|.+. +|..|+....      .+.+.+|.|.|..+
T Consensus        30 nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~  107 (131)
T 2m2b_A           30 NLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKG  107 (131)
T ss_dssp             SCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCC
T ss_pred             CCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCC
Confidence            35567999999999999999966  7764    256799999999999 9999998644      45788999999876

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.63  E-value=3.4e-08  Score=78.85  Aligned_cols=75  Identities=13%  Similarity=0.043  Sum_probs=58.2

Q ss_pred             ceEEEEeeecCC--------CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEE
Q 022800          168 KVLKVSWEKFGE--------DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLV  237 (292)
Q Consensus       168 ~~lkvKWk~~~~--------~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v  237 (292)
                      ++|.|+--....        .--+++|++.|++||.|.+|.|.....+|+|||+|.+.++|..|+..  +..+.+.+|.|
T Consensus         8 ~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v   87 (114)
T 3s6e_A            8 QCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITA   87 (114)
T ss_dssp             SEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            456666555222        12346789999999999999995444689999999999999999985  45567899999


Q ss_pred             EecCC
Q 022800          238 LPLQP  242 (292)
Q Consensus       238 ~~~~~  242 (292)
                      .|..+
T Consensus        88 ~~~~~   92 (114)
T 3s6e_A           88 AYVPL   92 (114)
T ss_dssp             EEECH
T ss_pred             EEEcH
Confidence            99753

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.63  E-value=5.3e-08  Score=81.55  Aligned_cols=67  Identities=19%  Similarity=0.154  Sum_probs=57.3

Q ss_pred             ecCCCCCHHHHHHHhcccC--CeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFG--KVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG--~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|+.||  .|.+|.|.    +++.+|||||+|.+.++|..|+..  +..+.+.+|.|.|..+
T Consensus        62 nLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~  136 (156)
T 3n9u_C           62 SFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATR  136 (156)
T ss_dssp             CCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCH
T ss_pred             CCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCC
Confidence            3556799999999999999  99999885    256799999999999999999986  5556788999998753

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=98.63  E-value=2.9e-08  Score=75.05  Aligned_cols=71  Identities=17%  Similarity=0.158  Sum_probs=56.2

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      +|-|  ......+|+++|+++|+.||.|..+.+..    ++.+|+|||+|.+.++|..|+..  ..-+.+.+|.|.+..
T Consensus        17 ~l~V--~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           17 VIKV--QNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             EEEE--ECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            4444  44556799999999999999998766532    45689999999999999999974  555677888888753

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=98.62  E-value=1.2e-07  Score=80.03  Aligned_cols=73  Identities=21%  Similarity=0.229  Sum_probs=59.1

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ...+..+|++.|+++|+.||.|.+|.|..    +..+|+|||+|.+.++|..|+.. ..-+.+.+|.|.|..+
T Consensus        14 ~~l~V--~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~   91 (196)
T 1l3k_A           14 RKLFI--GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   91 (196)
T ss_dssp             GEEEE--ESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccC
Confidence            44555  35566799999999999999999998852    45689999999999999999975 3335678899998754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.62  E-value=4e-08  Score=75.31  Aligned_cols=72  Identities=10%  Similarity=0.073  Sum_probs=57.5

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      +|--......+|++.|+++|+.||.|..+++.   +++.+|+|||+|.+.++|..|+. +...+.+.+|.|.|..+
T Consensus        19 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~   94 (101)
T 1fj7_A           19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKG   94 (101)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCSC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcCC
Confidence            34444566679999999999999999883332   26679999999999999999996 34455689999999865

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.62  E-value=4.9e-08  Score=76.32  Aligned_cols=55  Identities=15%  Similarity=0.163  Sum_probs=44.6

Q ss_pred             HHHHh-cccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHhhcC--CCCCCeEEEec
Q 022800          186 LREIF-SEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGSVCG--NLSNPLLVLPL  240 (292)
Q Consensus       186 L~~~f-s~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~pl~v~~~  240 (292)
                      |++.| ++||.|.+|.|..   ++.+|+|||+|.+.++|..|+....|  +.+.+|.|.|.
T Consensus        43 l~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           43 VFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            44445 9999999999953   34699999999999999999986444  57788888875

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=98.61  E-value=1.6e-07  Score=76.84  Aligned_cols=64  Identities=17%  Similarity=0.264  Sum_probs=51.8

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCC--CCeEEEec
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLS--NPLLVLPL  240 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~--~pl~v~~~  240 (292)
                      .+..+|++.|+++|++||.|..|.+..    +..+|+|||+|.+.++|..|+..  +.-+.+  .||.|.|.
T Consensus        96 l~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A           96 LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            445689999999999999999998852    44589999999999999999985  333333  57888874

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.61  E-value=1.5e-07  Score=70.71  Aligned_cols=67  Identities=13%  Similarity=0.048  Sum_probs=55.5

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ......+|+++|+++|+.| .|..|.|..   ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        16 ~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~~   86 (91)
T 2dgw_A           16 RGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKS   86 (91)
T ss_dssp             ECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEESS
T ss_pred             ECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECCc
Confidence            4456679999999999999 899998852   5569999999999999999997 23335678999999865

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.61  E-value=1.4e-07  Score=76.98  Aligned_cols=66  Identities=17%  Similarity=0.085  Sum_probs=55.8

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|++||+|.+|.+..   ++.+|+|||+|.+.++|..|+..  +....+.+|.|.|..+
T Consensus         8 lp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~   78 (166)
T 3md3_A            8 LDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQ   78 (166)
T ss_dssp             EETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCC
Confidence            345689999999999999999999852   55789999999999999999964  5556788999999865

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=98.61  E-value=1.6e-07  Score=77.10  Aligned_cols=65  Identities=23%  Similarity=0.331  Sum_probs=53.3

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcC--C--CCCCeEEEec
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCG--N--LSNPLLVLPL  240 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g--~--~~~pl~v~~~  240 (292)
                      ..+..+|++.|+++|++||.|..|.+..    ++.+|+|||+|.+.++|..|+....|  +  .+.||.|.|.
T Consensus        96 nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A           96 NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             SCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            3455799999999999999999998852    44589999999999999999985333  3  3389999874

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=98.60  E-value=5e-08  Score=80.30  Aligned_cols=68  Identities=19%  Similarity=0.242  Sum_probs=57.0

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~~~  242 (292)
                      ...+..+|++.|+++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+.....+.+.+|.+.|..+
T Consensus         9 ~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            9 GGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             CSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCC
T ss_pred             eCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccc
Confidence            34556799999999999999999999852    567899999999999999999976666777888877643

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=98.60  E-value=4.8e-08  Score=76.54  Aligned_cols=74  Identities=16%  Similarity=0.119  Sum_probs=56.8

Q ss_pred             ceEEEEeeecCCCC--------CHHHHHHHhcccCCeeEEEEec------CCCcceEEEEecCHHHHHHHHHh--hcCCC
Q 022800          168 KVLKVSWEKFGEDY--------TAERLREIFSEFGKVEDVVIKS------SKKKGSALVVMATKSAAGAATGS--VCGNL  231 (292)
Q Consensus       168 ~~lkvKWk~~~~~~--------t~~~L~~~fs~yG~V~~v~i~~------~k~~g~A~V~F~~~~~A~~Av~~--~~g~~  231 (292)
                      ++|.|+--......        .+++|++.|++||.|.+|.|..      +..+|+|||+|.+.++|..|+..  +.-+.
T Consensus         6 ~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~   85 (105)
T 3v4m_A            6 EVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFA   85 (105)
T ss_dssp             SEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             eEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            45666655432222        3478999999999999999953      14689999999999999999986  44456


Q ss_pred             CCCeEEEecC
Q 022800          232 SNPLLVLPLQ  241 (292)
Q Consensus       232 ~~pl~v~~~~  241 (292)
                      +.+|.|.+..
T Consensus        86 GR~i~v~~~~   95 (105)
T 3v4m_A           86 NRVVVTKYCD   95 (105)
T ss_dssp             TEECEEEEEC
T ss_pred             CCEEEEEEeC
Confidence            8899999874

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=98.60  E-value=9.3e-08  Score=78.21  Aligned_cols=67  Identities=18%  Similarity=0.255  Sum_probs=57.1

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|+.||.|.+|.+..    ++.+|+|||+|.+.++|..|+..  +....+.+|.|.|..+
T Consensus         9 nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            9 YLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             SCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            4556799999999999999999998852    45679999999999999999974  5556789999999865

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.59  E-value=1.5e-07  Score=71.20  Aligned_cols=70  Identities=29%  Similarity=0.272  Sum_probs=53.0

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      |-.......+|++.|+++|+.||.|.+|++.....+ +|||+|.+.++|..|+. +...+.+.+|.|.|..+
T Consensus        11 l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~-~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A           11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             EEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCC-EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCc-EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCc
Confidence            333455667999999999999999999854222222 99999999999999998 22334578888887653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.59  E-value=5.7e-08  Score=76.53  Aligned_cols=68  Identities=18%  Similarity=0.221  Sum_probs=51.9

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec-------CCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEE
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS-------SKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVL  238 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~-------~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~  238 (292)
                      ++|-|  ......+|++.|+++|++||.|. +.+..       ++.+|+|||+|.+.++|..|+....++-+..+.+.
T Consensus         9 ~~lfV--gnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~   83 (114)
T 2dnl_A            9 RKVFV--GGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCV   83 (114)
T ss_dssp             CCEEE--ECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEE
T ss_pred             CEEEE--cCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEec
Confidence            34444  34556799999999999999999 65532       36699999999999999999987654445545444

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.59  E-value=9.1e-08  Score=83.11  Aligned_cols=66  Identities=20%  Similarity=0.231  Sum_probs=56.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ....+|++.|+++|+.||.|..|.|.  .+..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus       111 l~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          111 LDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45579999999999999999999885  245689999999999999999975  5556788999999865

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=98.58  E-value=8.4e-08  Score=78.85  Aligned_cols=68  Identities=19%  Similarity=0.192  Sum_probs=57.4

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...+..+|++.|+++|+.||+|.+|.+..    +..+|+|||+|.+.++|..|+..  +....+.+|.|.|..+
T Consensus         9 ~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            9 NYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             ECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            34556799999999999999999998842    44679999999999999999974  5555789999999865

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.57  E-value=1.6e-07  Score=72.85  Aligned_cols=72  Identities=18%  Similarity=0.156  Sum_probs=56.2

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      .+|-|  .......|+++|+++|+.||.| .|.|.   +++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|.+..+
T Consensus        16 ~~l~V--~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~~   91 (102)
T 1wez_A           16 HCVHM--RGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNST   91 (102)
T ss_dssp             CEEEE--ESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECC
T ss_pred             CEEEE--eCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCC
Confidence            34544  4556679999999999999955 87774   256799999999999999999953 4445678889988654

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=98.57  E-value=9.9e-08  Score=84.70  Aligned_cols=68  Identities=18%  Similarity=0.164  Sum_probs=58.2

Q ss_pred             eecCCCCCHHHHHHHhcccC--CeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFG--KVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG--~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|+.||  .|..|.|..    ++.+|||||+|.+.++|..||..  ...+.+.+|.|.|..+
T Consensus        74 gnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C           74 GNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             ESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCH
T ss_pred             eCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCC
Confidence            34556799999999999999  999998852    56799999999999999999974  5667889999999754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.56  E-value=7.8e-08  Score=86.35  Aligned_cols=59  Identities=20%  Similarity=0.251  Sum_probs=50.7

Q ss_pred             CHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhc--CC------------CCCCeEEEecCC
Q 022800          182 TAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVC--GN------------LSNPLLVLPLQP  242 (292)
Q Consensus       182 t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~--g~------------~~~pl~v~~~~~  242 (292)
                      +++.|+.+|++||+|.+|.|.  ..+|+|||+|.+.++|+.|+....  .+            .+.+|.|.|..+
T Consensus       156 tEe~L~~~F~~fG~I~~v~v~--~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~  228 (240)
T 3u1l_A          156 IESRIRFVFSRLGDIDRIRYV--ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANE  228 (240)
T ss_dssp             HHHHHHHHHHTTSCEEEEEEE--GGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-
T ss_pred             cHHHHHHHHHccCCEEEEEEE--CCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccC
Confidence            799999999999999999985  358999999999999999997633  33            467999999864

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=98.56  E-value=9.1e-08  Score=82.70  Aligned_cols=73  Identities=21%  Similarity=0.267  Sum_probs=58.4

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  ..+...|++.|+++|++||.|.+|.|..   +..+|+|||+|.+.++|..|+.. +..+.+.+|.|.|..+
T Consensus       110 ~~l~V~--nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          110 RSVYIK--GFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             TEEEEE--CCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             CEEEec--CCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            345553  2445699999999999999999998852   55789999999999999999975 3345678999998653

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=98.55  E-value=1.5e-07  Score=79.45  Aligned_cols=67  Identities=22%  Similarity=0.275  Sum_probs=55.7

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+.. ..-+.+.+|.|.|..+
T Consensus       111 nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~~  182 (196)
T 1l3k_A          111 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS  182 (196)
T ss_dssp             CCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC-
T ss_pred             CCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecCC
Confidence            3455799999999999999999998852    45699999999999999999964 3445678999999865

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=98.54  E-value=2.6e-07  Score=89.63  Aligned_cols=67  Identities=19%  Similarity=0.202  Sum_probs=57.6

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|..+|++||.|..|.|.    +++.+|||||+|.+.++|..||..  +.-+.+.+|.|.|..+
T Consensus       109 nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~  181 (437)
T 3pgw_S          109 RVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG  181 (437)
T ss_pred             CCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            355679999999999999999999885    255799999999999999999965  5556789999999865

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.54  E-value=2e-07  Score=71.40  Aligned_cols=73  Identities=26%  Similarity=0.215  Sum_probs=56.3

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|+++|+++|+.|+.|.-+.-. +++.+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        16 ~~l~V~--nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   91 (102)
T 2fc8_A           16 KTLFVK--GLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP   91 (102)
T ss_dssp             SSEEEE--CCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEe--CCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            345553  455679999999999999755443322 356689999999999999999974  5556789999999875

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=98.52  E-value=1.1e-07  Score=74.03  Aligned_cols=71  Identities=15%  Similarity=0.123  Sum_probs=56.2

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCC---eeEEEEec---CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGK---VEDVVIKS---SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~---V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      |-........|+++|+++|+.||.   |..|.|..   ++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|.+..+
T Consensus        14 l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINN   91 (107)
T ss_dssp             EEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCEECCH
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEEECCH
Confidence            333455667999999999999998   89998852   56799999999999999999973 3344567888887653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.52  E-value=4.4e-07  Score=77.65  Aligned_cols=72  Identities=19%  Similarity=0.158  Sum_probs=58.2

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        30 ~l~V--~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           30 RVYV--GSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             EEEE--ECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             EEEE--ECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            4554  34556799999999999999999999852    45799999999999999999974  5667789999988653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.52  E-value=3e-07  Score=78.14  Aligned_cols=67  Identities=21%  Similarity=0.131  Sum_probs=56.4

Q ss_pred             eecCCCCCHHHHHHHhcccC-CeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCC-CCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFG-KVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNL-SNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG-~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~-~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|++|| .|..|.|. .+.+|+|||+|.+.++|..|+..  +.-.. +.+|.|.|..+
T Consensus       126 ~nl~~~~~~~~l~~~f~~~G~~v~~v~i~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          126 SNIPPSVSEEDLKVLFSSNGGVVKGFKFF-QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             CCCCTTCCHHHHHHHHHHTTSCCCEEEES-STTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             eCCCCCCCHHHHHHHHHHcCCCceEEEEE-eCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            34556799999999999999 99999984 34589999999999999999985  44445 78999999865

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=98.52  E-value=2.3e-07  Score=69.47  Aligned_cols=65  Identities=12%  Similarity=0.236  Sum_probs=55.7

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...+..+|+++|+++|++| .|.+|.|.  +.+|+|||+|.+.++|..|+..  +....+.+|.|.|...
T Consensus        11 ~nLp~~~t~~~l~~~F~~~-~v~~~~i~--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A           11 KNLPQDSNCQEVHDLLKDY-DLKYCYVD--RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             ESCCSSCCHHHHHHHTCSS-CCCCEEEE--GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             eCCCCCCCHHHHHHHHhhC-CeEEEEEe--CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            3455679999999999999 99999883  7799999999999999999985  4456789999999743

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.50  E-value=2.9e-07  Score=78.20  Aligned_cols=66  Identities=26%  Similarity=0.257  Sum_probs=56.7

Q ss_pred             ecCC-CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGE-DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~-~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+. .+|++.|+++|+.||.|.+|.|.. .++|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus        10 nlp~~~~~~~~l~~~F~~~G~i~~v~i~~-~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~   78 (198)
T 1qm9_A           10 NLNPERVTPQSLFILFGVYGDVQRVKILF-NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   78 (198)
T ss_dssp             CCCSSSCCHHHHHHHHHTTCCCSEEECST-TCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCC
T ss_pred             CCCcccCCHHHHHHHHHhcCCEEEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecC
Confidence            3455 689999999999999999999853 4489999999999999999974  6667889999999764

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=98.50  E-value=1.5e-07  Score=77.30  Aligned_cols=71  Identities=13%  Similarity=0.097  Sum_probs=57.9

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCC---eeEEEEec---CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGK---VEDVVIKS---SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~---V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      +|-........|+++|+++|+.||.   |.+|.|..   ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.+..
T Consensus        46 ~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~~a~  123 (136)
T 2hgl_A           46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSH  123 (136)
T ss_dssp             EEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEEECC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEEECC
Confidence            4444556677999999999999999   78888752   5679999999999999999997 4455667889988764

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=98.50  E-value=3.4e-07  Score=75.49  Aligned_cols=67  Identities=22%  Similarity=0.461  Sum_probs=54.7

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec---C---CCcceEEEEecCHHHHHHHHHhhcCC-----CCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS---S---KKKGSALVVMATKSAAGAATGSVCGN-----LSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~---k~~g~A~V~F~~~~~A~~Av~~~~g~-----~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|++||+|.+|.|..   +   +.+|+|||+|.+.++|..|+....|.     ...|+.+.|..+
T Consensus        10 nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~   87 (175)
T 3nmr_A           10 QVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADS   87 (175)
T ss_dssp             SCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGG
T ss_pred             CCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccc
Confidence            3456799999999999999999998852   2   57899999999999999999764442     267888888654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.50  E-value=1.2e-07  Score=75.27  Aligned_cols=72  Identities=14%  Similarity=0.108  Sum_probs=57.7

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCC---eeEEEEe---cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGK---VEDVVIK---SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~---V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      +|-........|+++|+++|+.||.   |..|.|.   .++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.+..+
T Consensus        19 ~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~   97 (118)
T 2db1_A           19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHR   97 (118)
T ss_dssp             EEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEEEECH
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCH
Confidence            3444556677999999999999999   8888875   25669999999999999999997 33445678899988653

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=98.49  E-value=3.8e-07  Score=80.01  Aligned_cols=72  Identities=28%  Similarity=0.277  Sum_probs=59.7

Q ss_pred             ceEEEEeeecCC-CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGE-DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~-~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|  ..... .+|++.|+++|+.||.|.+|.|.. .++|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus        35 ~~l~V--~nLp~~~~te~~L~~~F~~~G~i~~v~i~~-~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           35 SVLLV--SNLNPERVTPQSLFILFGVYGDVQRVKILF-NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             SEEEE--ESCCTTTCCHHHHHHHHHHHTCEEEEEECC-TTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CEEEE--eCCCcccCCHHHHHHHHHhCCCeEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            34555  34555 799999999999999999999853 3489999999999999999974  5567889999999764

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.49  E-value=2.6e-07  Score=87.06  Aligned_cols=71  Identities=17%  Similarity=0.242  Sum_probs=55.3

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCC-----CCC--CeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGN-----LSN--PLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~-----~~~--pl~v~~~~  241 (292)
                      +|-|---....++|++.|+++|++||.|.+|+|.  ..+|||||+|.+.++|..|+....|.     .+.  ||++.++.
T Consensus        20 ~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~--~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           20 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP--PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             EEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC--TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             EEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe--CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            4555322223569999999999999999999884  36799999999999999999875553     223  88888874

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=98.48  E-value=1.3e-07  Score=78.10  Aligned_cols=70  Identities=16%  Similarity=0.194  Sum_probs=56.7

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      +|-|.  ..+..+|++.|+++|++||.|..|.+..    +..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|.
T Consensus        96 ~l~v~--nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           96 KLFIG--GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             CEEEE--CCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             EEEEE--cCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            44443  3345689999999999999999998852    44589999999999999999985  44456889999885

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=98.48  E-value=3.6e-07  Score=81.99  Aligned_cols=70  Identities=20%  Similarity=0.298  Sum_probs=56.8

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC--CC-CCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG--NL-SNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g--~~-~~pl~v~~~~  241 (292)
                      +|-|.  .....+|++.|+++|++||.|..|.|.. .++|+|||+|.+.++|..|+....|  +. +++|.|.|..
T Consensus       209 ~l~v~--nl~~~~~~~~l~~~F~~~G~i~~v~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          209 ILFLT--NLPEETNELMLSMLFNQFPGFKEVRLVP-GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEEe--CCCCcCCHHHHHHHHHhcCCeEEEEEec-CCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            44443  3445799999999999999999999853 3479999999999999999986444  44 7899999974

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=97.85  E-value=1.9e-08  Score=79.23  Aligned_cols=66  Identities=26%  Similarity=0.317  Sum_probs=55.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeE--------EEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVED--------VVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~--------v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      ....+|++.|+++|++||.|..        |.|..    +..+|+|||+|.+.++|..|+.  +...+.+.+|.|.|..+
T Consensus        15 Lp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (116)
T 2lcw_A           15 LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATR   94 (116)
Confidence            4456899999999999999998        66632    4568999999999999999997  46667789999999865

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=98.46  E-value=6.7e-07  Score=78.40  Aligned_cols=72  Identities=22%  Similarity=0.159  Sum_probs=58.6

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccC-CeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCC-CCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFG-KVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNL-SNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG-~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~-~~pl~v~~~~~  242 (292)
                      ++|-|.  .....+|++.|+++|+.|| .|..|.+. .+.+|+|||+|.+.++|..|+..  +.-+. +.+|.|.|..+
T Consensus       152 ~~l~V~--nlp~~~t~~~l~~~f~~~G~~i~~v~i~-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          152 ATLHLS--NIPPSVSEEDLKVLFSSNGGVVKGFKFF-QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             SEEEEE--CCCTTCCHHHHHHHHHTTSCCEEEEEEC-SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CEEEEe--CCCccCCHHHHHHHHHHcCCCeeEEEEE-ECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            345443  4556799999999999999 99999984 34589999999999999999985  44445 78999999865

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=98.46  E-value=4.9e-07  Score=81.15  Aligned_cols=73  Identities=25%  Similarity=0.423  Sum_probs=59.5

Q ss_pred             ceEEEEeeecCCCCCHHHHH----HHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          168 KVLKVSWEKFGEDYTAERLR----EIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~----~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      ++|-|.  .....+|++.|+    ++|+.||.|.+|.|. +++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|.
T Consensus        10 ~~l~V~--nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   87 (282)
T 3pgw_A           10 HTIYIN--NLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   87 (282)
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEe
Confidence            345443  345669999966    999999999999985 467899999999999999999975  44557899999997


Q ss_pred             CC
Q 022800          241 QP  242 (292)
Q Consensus       241 ~~  242 (292)
                      .+
T Consensus        88 ~~   89 (282)
T 3pgw_A           88 KT   89 (282)
T ss_pred             cc
Confidence            54

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=98.45  E-value=2.5e-07  Score=76.82  Aligned_cols=66  Identities=15%  Similarity=0.167  Sum_probs=56.1

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|+.||.|..| ...+..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..|
T Consensus       106 nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  173 (175)
T 1fje_B          106 NLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE  173 (175)
T ss_dssp             SCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSS
T ss_pred             CCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCC
Confidence            445679999999999999999887 33577899999999999999999984  5556789999999865

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.44  E-value=2.9e-07  Score=73.75  Aligned_cols=74  Identities=15%  Similarity=0.051  Sum_probs=56.5

Q ss_pred             ceEEEEeeecCCC---CCHHHHHHHhcccCCeeEEEEecC--------CCcceEEEEecCHHHHHHHHHh--hcCCCCCC
Q 022800          168 KVLKVSWEKFGED---YTAERLREIFSEFGKVEDVVIKSS--------KKKGSALVVMATKSAAGAATGS--VCGNLSNP  234 (292)
Q Consensus       168 ~~lkvKWk~~~~~---~t~~~L~~~fs~yG~V~~v~i~~~--------k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~p  234 (292)
                      ++|.|+--.....   --+++|++.|++||.|.+|.|...        ..+|+|||+|.+.++|..|+..  +.-+.+.+
T Consensus        21 ~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~  100 (118)
T 3ue2_A           21 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK  100 (118)
T ss_dssp             CEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4566665543322   236889999999999999998521        2469999999999999999986  44556889


Q ss_pred             eEEEecC
Q 022800          235 LLVLPLQ  241 (292)
Q Consensus       235 l~v~~~~  241 (292)
                      |.|.+..
T Consensus       101 i~v~~~~  107 (118)
T 3ue2_A          101 VVAEVYD  107 (118)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEcC
Confidence            9998864

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.43  E-value=3.8e-07  Score=77.00  Aligned_cols=73  Identities=15%  Similarity=0.181  Sum_probs=59.7

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  .....+|++.|+++|++||.|..|.+..    +..+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..
T Consensus       115 ~~l~v~--nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  192 (198)
T 2yh0_A          115 HKLFIG--GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  192 (198)
T ss_dssp             CEEEEE--CCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            345554  3445799999999999999999998852    44589999999999999999985  555678999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus       193 ~  193 (198)
T 2yh0_A          193 V  193 (198)
T ss_dssp             C
T ss_pred             C
Confidence            5

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.43  E-value=3e-07  Score=79.80  Aligned_cols=72  Identities=22%  Similarity=0.180  Sum_probs=57.9

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +|-|  ......+|++.|+++|++||+|.+|.|..    ++.+|+|||+|.+.++|..|+..  .....+.++.+.|..+
T Consensus        17 tlfV--gnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~   94 (213)
T 4f02_A           17 SLYV--GDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   94 (213)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             EEEE--eCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccc
Confidence            4544  33566799999999999999999998852    56789999999999999999975  3444577888888653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.43  E-value=5.2e-07  Score=71.16  Aligned_cols=71  Identities=18%  Similarity=0.188  Sum_probs=56.6

Q ss_pred             EEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          170 LKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       170 lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      .+|.........|+++|+++|+.| .|.+|.|..   ++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|.+..
T Consensus        17 ~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            355556667789999999999999 899998852   56799999999999999999953 444456788887654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.43  E-value=2e-07  Score=75.27  Aligned_cols=70  Identities=17%  Similarity=0.126  Sum_probs=53.4

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCe----eEEEEe---cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEec
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKV----EDVVIK---SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPL  240 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V----~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~  240 (292)
                      +|.........|+++|+++|+.||.|    .+|.|.   +++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|...
T Consensus        25 ~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~~a  102 (123)
T 2dha_A           25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRS  102 (123)
T ss_dssp             EEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCEEE
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEEEC
Confidence            45555667789999999999999986    577774   256799999999999999999974 33334455666544

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=98.40  E-value=2.2e-07  Score=76.51  Aligned_cols=70  Identities=20%  Similarity=0.126  Sum_probs=55.1

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      |-........|+++|+++|+.|| |.+|.|..   ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.+..+
T Consensus        49 lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~  122 (139)
T 2hgn_A           49 VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNST  122 (139)
T ss_dssp             EECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCC
Confidence            33345667799999999999999 66888752   5679999999999999999994 24445677888887654

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=98.37  E-value=6.1e-07  Score=80.31  Aligned_cols=71  Identities=21%  Similarity=0.313  Sum_probs=58.5

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  ..+..+|++.|+++|+.||.|.+|.|.  +.+|+|||+|.+.++|..|+..  +.-..+.+|.|.|..+
T Consensus        23 ~~l~V~--nLp~~~te~~l~~~F~~~G~i~~v~i~--~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           23 CRLFVG--NLPTDITEEDFKRLFERYGEPSEVFIN--RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             GEEEEE--SCCTTCCHHHHHHHTGGGCCCSEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEE--CCCCCCCHHHHHHHHHhcCCEEEEEEe--CCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            455553  455679999999999999999999984  5589999999999999999974  4556778999988754

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=98.37  E-value=6.8e-07  Score=80.25  Aligned_cols=75  Identities=19%  Similarity=0.228  Sum_probs=61.4

Q ss_pred             ceEEEEeee---------cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCC
Q 022800          168 KVLKVSWEK---------FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLS  232 (292)
Q Consensus       168 ~~lkvKWk~---------~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~  232 (292)
                      +.|.|.|..         .+..+|++.|+++|+.||.|..|.+.    ++..+|+|||+|.+.++|..|+..  +....+
T Consensus        85 ~~i~v~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g  164 (284)
T 3smz_A           85 RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP  164 (284)
T ss_dssp             EECEEEECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             eEEEEEecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            456777765         34568999999999999999999874    255689999999999999999964  455578


Q ss_pred             CCeEEEecCC
Q 022800          233 NPLLVLPLQP  242 (292)
Q Consensus       233 ~pl~v~~~~~  242 (292)
                      .+|.|.|..+
T Consensus       165 ~~i~v~~a~~  174 (284)
T 3smz_A          165 RTLYVHWTDA  174 (284)
T ss_dssp             EECEEEECCG
T ss_pred             cEEEEEECCC
Confidence            8999999865

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=98.36  E-value=8.9e-07  Score=65.49  Aligned_cols=66  Identities=21%  Similarity=0.226  Sum_probs=51.1

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhccc----C-------CeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC--CCCCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEF----G-------KVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG--NLSNP  234 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~y----G-------~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g--~~~~p  234 (292)
                      ++|-|.  .....+|++.|+++|+.|    |       .|.+|.+.  +.+|+|||+|.+.++|..|+ ...|  +.+.+
T Consensus         7 ~~l~V~--nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~--~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~   81 (87)
T 2hzc_A            7 RRLYVG--NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN--QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GEEEEE--SCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC--SSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec--CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            344443  345578999999999999    8       99999884  45899999999999999999 5433  45566


Q ss_pred             eEEE
Q 022800          235 LLVL  238 (292)
Q Consensus       235 l~v~  238 (292)
                      |.|.
T Consensus        82 l~V~   85 (87)
T 2hzc_A           82 LKIR   85 (87)
T ss_dssp             CEEE
T ss_pred             EEEe
Confidence            6654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=98.34  E-value=8.1e-07  Score=80.08  Aligned_cols=71  Identities=21%  Similarity=0.230  Sum_probs=57.7

Q ss_pred             eEEEEeeecCCC-CCHHHHHHHhcccCCeeEEEEec-----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          169 VLKVSWEKFGED-YTAERLREIFSEFGKVEDVVIKS-----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       169 ~lkvKWk~~~~~-~t~~~L~~~fs~yG~V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      +|-|.-  .+.. +|++.|+++|+.||.|..|.|..     +..+|+|||+|.+.++|..|+ .  +.-+.+.+|.|.|.
T Consensus       212 ~l~v~n--lp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a  288 (292)
T 2ghp_A          212 EIMIRN--LSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLA  288 (292)
T ss_dssp             EEEEEE--ECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEEC
T ss_pred             eEEEEC--CCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEe
Confidence            444443  3456 99999999999999999999853     456899999999999999999 5  44456899999998


Q ss_pred             CC
Q 022800          241 QP  242 (292)
Q Consensus       241 ~~  242 (292)
                      .+
T Consensus       289 ~~  290 (292)
T 2ghp_A          289 DK  290 (292)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=98.34  E-value=8.5e-07  Score=71.90  Aligned_cols=69  Identities=20%  Similarity=0.202  Sum_probs=53.6

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCee--EEEEec---CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVE--DVVIKS---SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~--~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      |--.......|+++|+++|+.| .|.  +|.|..   ++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|.+..
T Consensus        45 lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a~  119 (126)
T 2hgm_A           45 VRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSS  119 (126)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            4445667789999999999999 565  787742   56799999999999999999974 344456677776653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.33  E-value=2.9e-07  Score=75.26  Aligned_cols=62  Identities=16%  Similarity=0.158  Sum_probs=50.5

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecC----H-HH---HHHHHH----hhcCCCCCCeEEEe
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMAT----K-SA---AGAATG----SVCGNLSNPLLVLP  239 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~----~-~~---A~~Av~----~~~g~~~~pl~v~~  239 (292)
                      +..++++.|+++|+.||+|.++.+..    +..+|+|||+|.+    . ++   |..|+.    +++...+.+|.|..
T Consensus        15 ~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~l   92 (136)
T 2j8a_A           15 TTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVIL   92 (136)
T ss_dssp             CCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEE
T ss_pred             CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEE
Confidence            56799999999999999999999852    6779999999996    2 32   888887    56677888888885

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=98.33  E-value=8e-07  Score=79.81  Aligned_cols=66  Identities=17%  Similarity=0.080  Sum_probs=55.7

Q ss_pred             cCCCC-CHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDY-TAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~-t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+ |++.|+++|+.||.|..|.|..   ++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus       192 lp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  263 (284)
T 3smz_A          192 LPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP  263 (284)
T ss_dssp             CCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecC
Confidence            34454 8999999999999999998852   55699999999999999999985  5555788999999865

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=98.32  E-value=1.4e-06  Score=75.71  Aligned_cols=66  Identities=24%  Similarity=0.183  Sum_probs=51.7

Q ss_pred             eeecCCCCCHHHHHHHhcccCCe--eEEEEec--CCCcceEEEEecCHHHHHHHHHhhcCC------CCCCeEEEe
Q 022800          174 WEKFGEDYTAERLREIFSEFGKV--EDVVIKS--SKKKGSALVVMATKSAAGAATGSVCGN------LSNPLLVLP  239 (292)
Q Consensus       174 Wk~~~~~~t~~~L~~~fs~yG~V--~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~~~g~------~~~pl~v~~  239 (292)
                      .......+|++.|+++|+.||.|  ..|.+..  ++++|+|||+|.+.++|..|+....|.      ...|+.|.|
T Consensus       128 v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~  203 (205)
T 3tyt_A          128 FFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKL  203 (205)
T ss_dssp             EEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEE
T ss_pred             EeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEe
Confidence            34556679999999999999999  8888753  345699999999999999999864443      234676655

>2guz_B Mitochondrial import inner membrane translocase subunit TIM16; DNAJ-fold, chaperone, protein transport; HET: FLC; 2.00A {Saccharomyces cerevisiae}

Probab=98.30  E-value=6e-07  Score=64.69  Aligned_cols=53  Identities=15%  Similarity=0.189  Sum_probs=43.5

Q ss_pred             ccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHcc
Q 022800            7 DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILK   65 (292)
Q Consensus         7 d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~   65 (292)
                      .-|.||||+++.  ..++.++|+++||++...+|||+.. .   .-.+..|+.|+++|.
T Consensus         5 EA~~ILgv~~~~--~~a~~~~Ik~~yr~Lm~~nhPDkGG-S---~yl~~ki~~Ake~l~   57 (65)
T 2guz_B            5 ESCKILNIEESK--GDLNMDKINNRFNYLFEVNDKEKGG-S---FYLQSKVYRAAERLK   57 (65)
T ss_dssp             HHHHHTTCCGGG--TCCSHHHHHHHHHHHHHHTCGGGTC-C---HHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCc--CcCCHHHHHHHHHHHHHHhCCCCCC-C---HHHHHHHHHHHHHHH
Confidence            458899998751  0169999999999999999999963 3   467889999999885

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=98.28  E-value=1e-06  Score=79.35  Aligned_cols=76  Identities=16%  Similarity=0.185  Sum_probs=60.9

Q ss_pred             ceEEEEeee--------cCCCCCHHHHHHHhcccC-CeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCC
Q 022800          168 KVLKVSWEK--------FGEDYTAERLREIFSEFG-KVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSN  233 (292)
Q Consensus       168 ~~lkvKWk~--------~~~~~t~~~L~~~fs~yG-~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~  233 (292)
                      +.|.|.|..        .+..+|++.|+++|+.|| .|..|.|..   +..+|+|||+|.+.++|..|+..  +..+.+.
T Consensus       108 ~~i~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  187 (292)
T 2ghp_A          108 NEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGY  187 (292)
T ss_dssp             EECEEEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             cEEEEEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            457777765        345699999999999999 999999853   45799999999999999999984  5556779


Q ss_pred             CeEEEecCCC
Q 022800          234 PLLVLPLQPA  243 (292)
Q Consensus       234 pl~v~~~~~~  243 (292)
                      +|.|.|..+.
T Consensus       188 ~l~v~~a~~~  197 (292)
T 2ghp_A          188 TLVTKVSNPL  197 (292)
T ss_dssp             ECEEEECCCC
T ss_pred             EEEEEECCCC
Confidence            9999998753

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=98.13  E-value=9.4e-07  Score=73.32  Aligned_cols=69  Identities=10%  Similarity=0.077  Sum_probs=55.5

Q ss_pred             eeecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          174 WEKFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       174 Wk~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      -...+..+|++.|+++|+.||.|..+++.   .++.+|+|||+|.+.++|..|+. +..-..+.+|.|.|..+
T Consensus        18 V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~   90 (175)
T 1fje_B           18 IGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKG   90 (175)
T ss_dssp             EECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCC
T ss_pred             EeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCC
Confidence            34456679999999999999988773332   36789999999999999999995 34556689999999864

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=98.08  E-value=5.7e-06  Score=68.07  Aligned_cols=65  Identities=17%  Similarity=0.120  Sum_probs=52.5

Q ss_pred             ecCCCCCHHHHHHHhccc----C-------CeeEEEEecCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEF----G-------KVEDVVIKSSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~y----G-------~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|++|    |       .|.++.+  ...+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        11 nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~--~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~   87 (172)
T 2g4b_A           11 NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI--NQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHD   87 (172)
T ss_dssp             SCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE--ETTTTEEEEEESSHHHHHHHGGGTTCEETTEECEEECCSS
T ss_pred             CCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe--cCCCCEEEEEeCCHHHHHHHHHhCCcEecCceeeecCCcc
Confidence            345679999999999999    6       7777776  4568999999999999999993 24445788899988654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.05  E-value=5.6e-06  Score=69.70  Aligned_cols=65  Identities=17%  Similarity=0.120  Sum_probs=52.6

Q ss_pred             ecCCCCCHHHHHHHhccc----C-------CeeEEEEecCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEF----G-------KVEDVVIKSSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~y----G-------~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|+.|    |       .|.++.+  .+.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        11 nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~--~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v~~~~~   87 (198)
T 2yh0_A           11 NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI--NQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHD   87 (198)
T ss_dssp             SCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE--ETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEEECCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe--cCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEEeCCCC
Confidence            455679999999999999    5       5666665  4668999999999999999993 24445788999999764

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=97.81  E-value=3.9e-05  Score=66.73  Aligned_cols=62  Identities=16%  Similarity=0.094  Sum_probs=52.1

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEec---C-----CCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKS---S-----KKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~---~-----k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ...++.|.+.|++||.|.+|.|..   .     ..+|++||+|.+.++|..|+..  +.-+.+.+|.+.+..
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            356788999999999999999851   2     6789999999999999999986  555668899988863

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.81  E-value=6.3e-05  Score=57.54  Aligned_cols=72  Identities=17%  Similarity=0.173  Sum_probs=54.1

Q ss_pred             cceEEEEeeec--CCC-CCH---HHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEe
Q 022800          167 EKVLKVSWEKF--GED-YTA---ERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLP  239 (292)
Q Consensus       167 ~~~lkvKWk~~--~~~-~t~---~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~  239 (292)
                      +.+|.|.-...  ... +++   ..|.+.|+.||.|..|.+..    +.+||+|.+.++|.+|+. ++....+..|+|..
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~----d~~fVtF~d~~sAlaAi~mnG~~v~Gr~LkV~l   82 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE----DKMWVTFLEGSSALNVLSLNGKELLNRTITIAL   82 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS----SSEEEEESSHHHHHHGGGGTTCEETTEEEEEEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec----CCEEEEECChHHHHHHHhcCCeEeCCeEEEEEe
Confidence            44677777652  222 442   45889999999999999854    349999999999999997 45556788899987


Q ss_pred             cCC
Q 022800          240 LQP  242 (292)
Q Consensus       240 ~~~  242 (292)
                      ..|
T Consensus        83 kt~   85 (91)
T 2dnr_A           83 KSP   85 (91)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.74  E-value=0.00024  Score=57.14  Aligned_cols=55  Identities=13%  Similarity=0.165  Sum_probs=44.4

Q ss_pred             EEEEeeecCCC-CCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecC-HHHHHHHHHh
Q 022800          170 LKVSWEKFGED-YTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMAT-KSAAGAATGS  226 (292)
Q Consensus       170 lkvKWk~~~~~-~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~-~~~A~~Av~~  226 (292)
                      +.|+-...+.. .|.+.|+++|+.||+|..|.+..+.  .+|||.|.+ ..+|..|+..
T Consensus        19 ~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~--~tgfVrf~~~~~~A~~av~~   75 (121)
T 1owx_A           19 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA--KEGIILFKEKAKEALGKAKD   75 (121)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC--SEEEEEESSCHHHHHHHHHH
T ss_pred             eEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CEEEEEECCChHHHHHHHHH
Confidence            34455555555 8999999999999999999985333  379999999 7899999886

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.41  E-value=0.00014  Score=55.95  Aligned_cols=71  Identities=13%  Similarity=0.155  Sum_probs=52.3

Q ss_pred             cceEEEEeeecC----CCCCH---HHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEE
Q 022800          167 EKVLKVSWEKFG----EDYTA---ERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVL  238 (292)
Q Consensus       167 ~~~lkvKWk~~~----~~~t~---~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~  238 (292)
                      +.+|.|.-....    .-+++   ..|.+.|+.||.|..|.+..+    .+||+|.+.++|.+|+. +.....+..|+|.
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d----~~fVtF~d~~sAl~AI~ldG~~v~Gr~L~V~   90 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG----QMLVTFADSHSALSVLDVDGMKVKGRAVKIS   90 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT----EEEEECSCSHHHHHHHHGGGSEETTEEEEEE
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC----cEEEEEcChHHHHHHHhcCCeeeCCeEEEEe
Confidence            456777765421    12443   447899999999999998643    39999999999999997 4556677888887


Q ss_pred             ecC
Q 022800          239 PLQ  241 (292)
Q Consensus       239 ~~~  241 (292)
                      +-.
T Consensus        91 ~k~   93 (95)
T 1ufw_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            643

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.07  E-value=0.015  Score=56.61  Aligned_cols=53  Identities=15%  Similarity=0.235  Sum_probs=37.3

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG  225 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~  225 (292)
                      +|.|.  + ....++..|.++|+.||+|.++.+- ..+.-||+|||.+.+++..++.
T Consensus        55 sv~v~--~-~~~~~~~~l~~y~~~~g~i~~~~~~-~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           55 TVLIH--C-PEKISENKFLKYLSQFGPINNHFFY-ESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             EEEEE--E-CCC---CHHHHHHGGGSCCCCEEEE-CSSSEEEEEECC---CCHHHHS
T ss_pred             eEEEE--c-CCCCCHHHHHHHHHhcCCcceEEEE-ccCCeEEEEEeCCHHHHHHHHh
Confidence            57776  3 2348899999999999999999993 4456799999999998886643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=94.73  E-value=0.055  Score=42.65  Aligned_cols=61  Identities=7%  Similarity=0.059  Sum_probs=47.9

Q ss_pred             cCCCCCHHHHHHHhccc-----CCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEe
Q 022800          177 FGEDYTAERLREIFSEF-----GKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLP  239 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~y-----G~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~  239 (292)
                      ....++...++.+...|     |+|..|++.+  ..|-|+|+|.+...|-+|...  +..+-+..|.+..
T Consensus        29 ipDtvndarIr~lve~~~~i~~g~i~KI~L~p--DH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           29 LSDKVSPSLICQFLQEEIHINEKDIRKILLVS--DFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             CCTTCCHHHHHHHHHHHTCCCTTTCSEEEEET--TTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCCCCCHHHHHHHHhhhhccCccceeEEEEec--CCCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            45569999999999999     9999999953  478899999999999888765  3333355665543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.12  E-value=0.3  Score=37.87  Aligned_cols=67  Identities=13%  Similarity=0.030  Sum_probs=53.6

Q ss_pred             EEEeeecCCCCCHHHHHHHhcc-c----CCeeEEEEecCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          171 KVSWEKFGEDYTAERLREIFSE-F----GKVEDVVIKSSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~-y----G~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      +|.-.......+++.|.-+|.+ -    |+|.+|....    +.|+|+|.+...|.+.+.. ..-+...||.|.+--
T Consensus        10 ~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~----~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A           10 AVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG----CGGVLTFREPADAERVLAQADHELHGAQLSLRPAP   82 (104)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET----TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEEECC
T ss_pred             EEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC----CcEEEEEcChHHHHHHhcCCcceecCeEEEEEcCC
Confidence            3333445556889999999988 2    6999998732    8999999999999999987 777888999998753

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=93.24  E-value=0.17  Score=38.96  Aligned_cols=55  Identities=25%  Similarity=0.468  Sum_probs=41.6

Q ss_pred             ccceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh
Q 022800          166 KEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV  227 (292)
Q Consensus       166 ~~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~  227 (292)
                      .+..+-|   .-...+--.+|.++|+.||.|.-=.| ++   .+|+|+|.+.+.|..|+...
T Consensus        15 r~HVf~l---~FP~ewKt~DI~~lFs~fggv~I~Wi-dD---TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           15 RDHVLHV---TFPKEWKTSDLYQLFSAFGNIQISWI-DD---TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEE---ECCTTCCHHHHHHHHTTTCSCCCEEE-ET---TEEEEECSCHHHHHHHHHHH
T ss_pred             CCeEEEE---eCChhhhhHHHHHHhhccCCEEEEEE-cC---CeEEEEecCHHHHHHHHHhc
Confidence            4455666   33445888999999999996655555 33   38999999999999998864

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=91.42  E-value=0.45  Score=37.80  Aligned_cols=56  Identities=14%  Similarity=0.150  Sum_probs=42.6

Q ss_pred             CHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEe
Q 022800          182 TAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLP  239 (292)
Q Consensus       182 t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~  239 (292)
                      ..+.+...|++||.|.....  ......-.|.|.+..+|.+|+..+--.++.-+.|-+
T Consensus        36 ~~~~VL~~F~~~G~Iv~~~~--~~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV   91 (119)
T 1wwh_A           36 SASYILLQFAQYGNILKHVM--SNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGV   91 (119)
T ss_dssp             GHHHHHHHHHTTSCEEEEEE--CSSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEE
T ss_pred             HHHHHHHHHHhhCcEEEecc--CCCCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEE
Confidence            45668899999999999987  345679999999999999999864444443344433

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=91.39  E-value=0.15  Score=39.29  Aligned_cols=46  Identities=22%  Similarity=0.381  Sum_probs=35.3

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV  227 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~  227 (292)
                      +..+--.+|..+|+.||.|.-=.| ++   .+|+|+|.+.+.|..|+...
T Consensus        14 P~ewKt~Di~~lFs~fggv~I~Wi-dD---TsAlvvf~~~~~a~~al~~i   59 (101)
T 3ctr_A           14 PKEWKTSDLYQLFSAFGNIQISWI-DD---TSAFVSLSQPEQVKIAVNTS   59 (101)
T ss_dssp             CTTCCHHHHHHHTTTSEEEEEEEE-ET---TEEEEEEEEECHHHHHHHHH
T ss_pred             ChhhhhHHHHHHHhccCCEEEEEE-cC---CeEEEEecCHHHHHHHHHhc
Confidence            344788899999999994433333 33   48999999999999998763

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=85.84  E-value=0.8  Score=36.67  Aligned_cols=24  Identities=13%  Similarity=0.069  Sum_probs=21.1

Q ss_pred             cCCCcceEEEEecCHHHHHHHHHh
Q 022800          203 SSKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       203 ~~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      ..+.+|+|||+|.+.++|..|+..
T Consensus         9 ~~~~~G~~fV~f~~~~~A~~al~~   32 (158)
T 2kn4_A            9 GKTLKGETTTEAVDAATAEKVFKQ   32 (158)
T ss_dssp             CSSCEEEEEEECSSHHHHHHHHHH
T ss_pred             CccccchhHHHHHHHHhHHHHHHh
Confidence            356799999999999999999964

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=85.24  E-value=2.2  Score=32.94  Aligned_cols=58  Identities=12%  Similarity=0.074  Sum_probs=46.8

Q ss_pred             HHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          183 AERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       183 ~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      +..++.+|..|+++......  ++-+...|.|.+.++|..|-.  ++....+.+|++-+..+
T Consensus        24 k~~~e~Lf~~~~~~~tF~~l--kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A           24 RAKFESLFRTYDKDTTFQYF--KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             HHHHHHHHHTTCSSCEEEEE--TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             HHHHHHHHHhhCcCcceeec--CcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            35678999999999997763  455688999999999999875  46666778899888764

---

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	292
d1fpoa1	76	a.2.3.1 (A:1-76) HSC20 (HSCB), N-terminal (J) doma	7e-11
d1xbla_	75	a.2.3.1 (A:) DnaJ chaperone, N-terminal (J) domain	1e-09
d1nz6a_	98	a.2.3.1 (A:) Auxilin J-domain {Cow (Bos taurus) [T	2e-09
d1fafa_	79	a.2.3.1 (A:) Large T antigen, the N-terminal J dom	4e-09
d1wjza_	94	a.2.3.1 (A:) CSL-type zinc finger-containing prote	1e-08
d1gh6a_	114	a.2.3.1 (A:) Large T antigen, the N-terminal J dom	3e-08
d1hdja_	77	a.2.3.1 (A:) HSP40 {Human (Homo sapiens) [TaxId: 9	8e-08
d1iura_	88	a.2.3.1 (A:) Hypothetical protein KIAA0730 {Human	8e-06

>d1fpoa1 a.2.3.1 (A:1-76) HSC20 (HSCB), N-terminal (J) domain {Escherichia coli [TaxId: 562]} Length = 76

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: HSC20 (HSCB), N-terminal (J) domain
species: Escherichia coli [TaxId: 562]

 Score = 55.0 bits (132), Expect = 7e-11
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 8/73 (10%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDA-----HDNFQKLKSSY 61
          D++ + GLP      +L  + +S  ++    + HPDK      A           +  ++
Sbjct: 2  DYFTLFGLP---ARYQLDTQALSLRFQDLQRQYHPDKFASGSQAEQLAAVQQSATINQAW 58

Query: 62 EILKDEKARKLFD 74
          + L+    R  + 
Sbjct: 59 QTLRHPLMRAEYL 71

>d1xbla_ a.2.3.1 (A:) DnaJ chaperone, N-terminal (J) domain {Escherichia coli [TaxId: 562]} Length = 75

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: DnaJ chaperone, N-terminal (J) domain
species: Escherichia coli [TaxId: 562]

 Score = 51.6 bits (123), Expect = 1e-09
 Identities = 25/68 (36%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y +LG+          E+EI KAYK  A++ HPD+   D +A   F+++K +YE+L D
Sbjct: 4  DYYEILGVSKTA-----EEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTD 58

Query: 67 EKARKLFD 74
           + R  +D
Sbjct: 59 SQKRAAYD 66

>d1nz6a_ a.2.3.1 (A:) Auxilin J-domain {Cow (Bos taurus) [TaxId: 9913]} Length = 98

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Auxilin J-domain
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 51.5 bits (123), Expect = 2e-09
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 8/70 (11%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPD---AHDNFQKLKSSYEI 63
            ++ +G+        +T +++ K Y+   L +HPDK    P    A   F +L  ++  
Sbjct: 34 TKWKPVGM-----ADLVTPEQVKKVYRKAVLVVHPDKATGQPYEQYAKMIFMELNDAWSE 88

Query: 64 LKDEKARKLF 73
           +++  + L+
Sbjct: 89 FENQGQKPLY 98

>d1fafa_ a.2.3.1 (A:) Large T antigen, the N-terminal J domain {Murine polyomavirus [TaxId: 10634]} Length = 79

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Large T antigen, the N-terminal J domain
species: Murine polyomavirus [TaxId: 10634]

 Score = 50.4 bits (120), Expect = 4e-09
 Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 7/68 (10%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
              +L LP            + +AYK ++L LHPDK       H   Q+L S +   K 
Sbjct: 12 RLLELLKLP---RQLWGDFGRMQQAYKQQSLLLHPDKGGS----HALMQELNSLWGTFKT 64

Query: 67 EKARKLFD 74
          E      +
Sbjct: 65 EVYNLRMN 72

>d1wjza_ a.2.3.1 (A:) CSL-type zinc finger-containing protein 3 (J-domain protein DjC7, 1700030a21RIK) {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: CSL-type zinc finger-containing protein 3 (J-domain protein DjC7, 1700030a21RIK)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.3 bits (117), Expect = 1e-08
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 11/74 (14%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHD------NFQKLKSS 60
          D Y +LG             ++ + Y+   L  HPDK+  D  A         F ++  +
Sbjct: 17 DWYSILGADPSA-----NMSDLKQKYQKLILLYHPDKQSADVPAGTMEECMQKFIEIDQA 71

Query: 61 YEILKDEKARKLFD 74
          ++IL +E+ +K +D
Sbjct: 72 WKILGNEETKKKYD 85

>d1gh6a_ a.2.3.1 (A:) Large T antigen, the N-terminal J domain {Simian virus 40, Sv40 [TaxId: 10633]} Length = 114

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Large T antigen, the N-terminal J domain
species: Simian virus 40, Sv40 [TaxId: 10633]

 Score = 49.0 bits (116), Expect = 3e-08
 Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 7/92 (7%)

Query: 1  MDVDHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSS 60
          M  + +    +LGL      A      + KAY  K  E HPDK  D     +  +K+ + 
Sbjct: 3  MREESLQLMDLLGLE---RSAWGNIPLMRKAYLKKCKEFHPDKGGD----EEKMKKMNTL 55

Query: 61 YEILKDEKARKLFDDLLKIKREKQQRQSQQDG 92
          Y+ ++D        D        +      D 
Sbjct: 56 YKKMEDGVKYAHQPDFGGFWDATEIPTYGTDE 87

>d1hdja_ a.2.3.1 (A:) HSP40 {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: HSP40
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 8e-08
 Identities = 25/68 (36%), Positives = 44/68 (64%), Gaps = 6/68 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKD 66
          D+Y+ LGL  G      +++EI +AY+ +AL  HPDK   +P A + F+++  +Y++L D
Sbjct: 4  DYYQTLGLARGA-----SDEEIKRAYRRQALRYHPDKNK-EPGAEEKFKEIAEAYDVLSD 57

Query: 67 EKARKLFD 74
           + R++FD
Sbjct: 58 PRKREIFD 65

>d1iura_ a.2.3.1 (A:) Hypothetical protein KIAA0730 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Hypothetical protein KIAA0730
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 8e-06
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 7  DHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDK-RPDDPDAHDNFQKLKSSYEILK 65
          +   V+         KL E E  K  +   L+ HPDK   +   A++ F+ L++    L+
Sbjct: 17 EVTSVVEQAW-----KLPESERKKIIRRLYLKWHPDKNPENHDIANEVFKHLQNEINRLE 71

Query: 66 DEKARKLFDD 75
           +       D
Sbjct: 72 KQAFLDQNAD 81

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	292
d1xbla_	75	DnaJ chaperone, N-terminal (J) domain {Escherichia	99.85
d1hdja_	77	HSP40 {Human (Homo sapiens) [TaxId: 9606]}	99.79
d1wjza_	94	CSL-type zinc finger-containing protein 3 (J-domai	99.76
d1gh6a_	114	Large T antigen, the N-terminal J domain {Simian v	99.71
d1fpoa1	76	HSC20 (HSCB), N-terminal (J) domain {Escherichia c	99.69
d1nz6a_	98	Auxilin J-domain {Cow (Bos taurus) [TaxId: 9913]}	99.6
d1fafa_	79	Large T antigen, the N-terminal J domain {Murine p	99.6
d1iura_	88	Hypothetical protein KIAA0730 {Human (Homo sapiens	99.58
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.18
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.15
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.09
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.08
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.07
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.06
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.05
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.05
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.04
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.03
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.03
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.03
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.03
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.03
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.02
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.02
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.01
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.01
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.0
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.0
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.0
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.0
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.0
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	98.99
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.99
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.98
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.98
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.98
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.98
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.98
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.98
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.95
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.95
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.94
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	98.94
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	98.93
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.92
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.92
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.92
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.91
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.89
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	98.89
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.89
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.89
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.88
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.88
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.88
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.88
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.88
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.88
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.85
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.85
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	98.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.84
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.83
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.82
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	98.82
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.82
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.81
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.8
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.79
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.77
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.75
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.73
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.73
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.71
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.68
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.67
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	98.67
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.66
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.61
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.58
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.56
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.49
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.46
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.34
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.27
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.25
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.18
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.14
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	93.24
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	92.82
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	86.24

>d1xbla_ a.2.3.1 (A:) DnaJ chaperone, N-terminal (J) domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: DnaJ chaperone, N-terminal (J) domain
species: Escherichia coli [TaxId: 562]

Probab=99.85  E-value=8.4e-22  Score=145.47  Aligned_cols=68  Identities=37%  Similarity=0.680  Sum_probs=64.8

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ..|||+||||+++     +|..+|++|||+++++||||++++++.+...|..|++||+||+||.+|..||..+
T Consensus         2 k~dyY~vLgv~~~-----As~~eIk~aYr~l~~~~HPDk~~~~~~~~~~f~~i~~Ay~vL~d~~~R~~YD~~g   69 (75)
T d1xbla_           2 KQDYYEILGVSKT-----AEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRAAYDQYG   69 (75)
T ss_dssp             CCCTTTTTCCSSS-----CCHHHHHHHHHHHHHHTCCTTCTTTCHHHHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred             CCCHHHHcCCCCC-----cCHHHHHHHHHHHHhhhhhhccCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHhC
Confidence            3699999999998     8999999999999999999999988889999999999999999999999999875

>d1hdja_ a.2.3.1 (A:) HSP40 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: HSP40
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=5.2e-20  Score=136.33  Aligned_cols=68  Identities=37%  Similarity=0.768  Sum_probs=63.4

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLLK   78 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~~   78 (292)
                      ..|||+||||+++     +|.++|++||+++++++|||+++ ++.+.+.|..|++||+||+||.+|..||.++.
T Consensus         2 ~kdyY~iLgv~~~-----as~~eIk~ay~~l~~~~hPD~~~-~~~~~~~~~~i~~Ay~vLsdp~~R~~YD~~g~   69 (77)
T d1hdja_           2 GKDYYQTLGLARG-----ASDEEIKRAYRRQALRYHPDKNK-EPGAEEKFKEIAEAYDVLSDPRKREIFDRYGE   69 (77)
T ss_dssp             CCCSHHHHTCCTT-----CCHHHHHHHHHHHHHTTCTTTCC-CTTHHHHHHHHHHHHHHTTCHHHHHHHHHTCG
T ss_pred             CCChHHHcCCCCC-----cCHHHHHHHHHHHHHHhcccccc-chhHHHHHHHHHHHHHHhcCHHHHHHHHhhhh
Confidence            4699999999998     89999999999999999999997 67888999999999999999999999998653

>d1wjza_ a.2.3.1 (A:) CSL-type zinc finger-containing protein 3 (J-domain protein DjC7, 1700030a21RIK) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: CSL-type zinc finger-containing protein 3 (J-domain protein DjC7, 1700030a21RIK)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1.4e-19  Score=138.98  Aligned_cols=68  Identities=25%  Similarity=0.484  Sum_probs=62.3

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCC------hhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDD------PDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~------~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ..|||+||||+++     ++..+|++||+++++.||||+++.+      +.+.+.|+.|++||+||+||.+|..||..+
T Consensus        15 ~~d~Y~iLgv~~~-----as~~eIk~aY~~l~~~~HPDk~~~~~~~~~~~~a~~~f~~I~~Ay~vL~d~~~R~~YD~~~   88 (94)
T d1wjza_          15 KKDWYSILGADPS-----ANMSDLKQKYQKLILLYHPDKQSADVPAGTMEECMQKFIEIDQAWKILGNEETKKKYDLQR   88 (94)
T ss_dssp             CSCHHHHTTCCTT-----CCHHHHHHHHHHTTSSSCSTTCCTTCCHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHHHHS
T ss_pred             ccChHHHcCCCCC-----cCHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHcc
Confidence            4699999999998     8999999999999999999998764      347788999999999999999999999764

>d1gh6a_ a.2.3.1 (A:) Large T antigen, the N-terminal J domain {Simian virus 40, Sv40 [TaxId: 10633]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Large T antigen, the N-terminal J domain
species: Simian virus 40, Sv40 [TaxId: 10633]

Probab=99.71  E-value=2.5e-19  Score=142.12  Aligned_cols=66  Identities=26%  Similarity=0.322  Sum_probs=58.3

Q ss_pred             CcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            5 HVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         5 ~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      ..|||+||||++++   ..+..+||+|||++|++|||||+|+ +   +.|+.|+.||+||+||.+|..||...
T Consensus         7 ~~~ly~iLGv~~~a---~~~~~~IKkAYrkla~k~HPDk~~~-~---e~F~~I~~AY~vLsd~~kR~~YD~~~   72 (114)
T d1gh6a_           7 SLQLMDLLGLERSA---WGNIPLMRKAYLKKCKEFHPDKGGD-E---EKMKKMNTLYKKMEDGVKYAHQPDFG   72 (114)
T ss_dssp             HHHHHHHTTCCTTS---CSCHHHHHHHHHHTTTTCCTTTCCT-T---TTTHHHHHHHHHHHHHHHSCCSSCCS
T ss_pred             HHHHHHHcCCCCCC---CCCHHHHHHHHHHHHHHhcccchhh-H---HHHHHHHHHHHHhCCHHHHHHHhccC
Confidence            46899999999982   2378999999999999999999974 3   57999999999999999999999653

>d1fpoa1 a.2.3.1 (A:1-76) HSC20 (HSCB), N-terminal (J) domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: HSC20 (HSCB), N-terminal (J) domain
species: Escherichia coli [TaxId: 562]

Probab=99.69  E-value=7.1e-18  Score=124.26  Aligned_cols=69  Identities=20%  Similarity=0.335  Sum_probs=60.8

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-----hHHHHHHHHHHHHHHccCchhhhhHHHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-----DAHDNFQKLKSSYEILKDEKARKLFDDLL   77 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-----~a~~~f~~i~~Ay~vL~d~~~R~~YD~~~   77 (292)
                      +|||+||||++++   +++.++|+++||++++.||||++++.+     .+...|..|++||+||+||.+|..|+..+
T Consensus         1 lnyy~lLgl~~~~---~~d~~eIk~aYr~l~~~~HPDk~~~~~~~~~~~a~~~~~~i~~Ay~vL~dp~~R~~Yll~l   74 (76)
T d1fpoa1           1 MDYFTLFGLPARY---QLDTQALSLRFQDLQRQYHPDKFASGSQAEQLAAVQQSATINQAWQTLRHPLMRAEYLLSL   74 (76)
T ss_dssp             CHHHHHTTCCSSS---CCCHHHHHHHHHHHHHHTCGGGGTTSCHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHT
T ss_pred             CChHHHCCCCCCC---CCCHHHHHHHHHHHHHHhCccccccchHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHc
Confidence            5899999999863   477999999999999999999987654     26788999999999999999999998655

>d1nz6a_ a.2.3.1 (A:) Auxilin J-domain {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Auxilin J-domain
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.60  E-value=1.1e-16  Score=123.55  Aligned_cols=65  Identities=22%  Similarity=0.460  Sum_probs=58.7

Q ss_pred             CCcccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh---hHHHHHHHHHHHHHHccCchhhhhH
Q 022800            4 DHVDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP---DAHDNFQKLKSSYEILKDEKARKLF   73 (292)
Q Consensus         4 ~~~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~---~a~~~f~~i~~Ay~vL~d~~~R~~Y   73 (292)
                      .+.++|.+|||+..     +|.++|++|||++++.||||++++++   .|...|+.|++||++|+||.+|+.|
T Consensus        31 ~~~~~y~~Lgl~~~-----~t~~eIk~aYr~l~~~~HPDk~~~~~~~~~a~~~f~~I~~Ay~~L~d~~~R~~Y   98 (98)
T d1nz6a_          31 AGETKWKPVGMADL-----VTPEQVKKVYRKAVLVVHPDKATGQPYEQYAKMIFMELNDAWSEFENQGQKPLY   98 (98)
T ss_dssp             TTCCSCCCCCGGGC-----CSHHHHHHHHHHHHHHSCHHHHTTSTTHHHHHHHHHHHHHHHHHHHTTTCCCCC
T ss_pred             CcccCCeecCCCcc-----CCHHHHHHHHHHHHHHhccccCCChHHHHHHHHHHHHHHHHHHHHCCHHHHhcC
Confidence            34578999999997     99999999999999999999988654   3778999999999999999999987

>d1fafa_ a.2.3.1 (A:) Large T antigen, the N-terminal J domain {Murine polyomavirus [TaxId: 10634]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Large T antigen, the N-terminal J domain
species: Murine polyomavirus [TaxId: 10634]

Probab=99.60  E-value=1e-16  Score=118.85  Aligned_cols=63  Identities=29%  Similarity=0.291  Sum_probs=56.2

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCChhHHHHHHHHHHHHHHccCchhhhhHHH
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDPDAHDNFQKLKSSYEILKDEKARKLFDD   75 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~~a~~~f~~i~~Ay~vL~d~~~R~~YD~   75 (292)
                      .+||+||||++++   ..+.++|++|||+++++||||++. +   .+.|++|++||++|.|+.+|..||.
T Consensus        11 ~~~y~iLgl~~~~---~~~~~~IkkaYr~l~~~~HPDk~g-~---~e~~~~in~Ay~~L~d~~~r~~~~~   73 (79)
T d1fafa_          11 ERLLELLKLPRQL---WGDFGRMQQAYKQQSLLLHPDKGG-S---HALMQELNSLWGTFKTEVYNLRMNL   73 (79)
T ss_dssp             HHHHHHHTCCSSS---TTCHHHHHHHHHHHHHHSSGGGSC-C---HHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHhCCCCCC---CCCHHHHHHHHHHHHHHhCcccCC-C---HHHHHHHHHHHHHHCCHHHHHHHcc
Confidence            5899999999972   249999999999999999999985 4   3689999999999999999998875

>d1iura_ a.2.3.1 (A:) Hypothetical protein KIAA0730 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Chaperone J-domain
family: Chaperone J-domain
domain: Hypothetical protein KIAA0730
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.7e-16  Score=120.11  Aligned_cols=59  Identities=25%  Similarity=0.337  Sum_probs=53.6

Q ss_pred             cccccccccccCCCCCCCCHHHHHHHHHHHHHHhCCCCCCCCh-hHHHHHHHHHHHHHHccCchh
Q 022800            6 VDHYRVLGLPSGEEGAKLTEKEISKAYKWKALELHPDKRPDDP-DAHDNFQKLKSSYEILKDEKA   69 (292)
Q Consensus         6 ~d~Y~iLgv~~~~~~~~a~~~eIkkaYrk~al~~HPDk~~~~~-~a~~~f~~i~~Ay~vL~d~~~   69 (292)
                      .|+|+||||+.+     +|.++||+|||+++++||||++|+++ .|.+.|+.|+.||++|+++..
T Consensus        16 ~~~y~iL~v~~~-----as~~eIKkAYrrl~~~~HPDk~~~~~~~a~~~f~~i~~Ay~~L~~~~~   75 (88)
T d1iura_          16 KEVTSVVEQAWK-----LPESERKKIIRRLYLKWHPDKNPENHDIANEVFKHLQNEINRLEKQAF   75 (88)
T ss_dssp             HHHHHHHHHTTS-----SCSHHHHHHHHHHHHHTCTTTSSSCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhCCCCC-----CCHHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence            489999999998     99999999999999999999999876 488999999999999975433

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=5e-11  Score=87.06  Aligned_cols=69  Identities=28%  Similarity=0.254  Sum_probs=59.5

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ++|=|..    .++|+++|+++|++||.|.+|.+.  +.+|+|||+|.+.++|..|+..  +.-..+++|+|.|..+
T Consensus         6 ~ti~V~~----~~~te~~L~~~F~~~G~I~~v~~~--~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           6 NTLYVYG----EDMTPTLLRGAFSPFGNIIDLSMD--PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CEEEEEC----SSCCHHHHHHHHSTTCCCSCEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CEEEEEC----CCCCHHHHHHHHhccCccceeeec--cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4566653    359999999999999999999984  5689999999999999999975  6667899999999875

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=5.7e-11  Score=91.73  Aligned_cols=74  Identities=26%  Similarity=0.234  Sum_probs=61.8

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCC----CCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGN----LSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~----~~~pl~v~~~~~  242 (292)
                      ++.|--......+|++.|+++|++||.|..|.|...+++|+|||+|.+.++|..|+....|.    .+.+|.|.|..+
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~   84 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL   84 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCC
Confidence            45655555677899999999999999999998865677999999999999999999864443    468899999765

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=2.3e-10  Score=87.81  Aligned_cols=63  Identities=29%  Similarity=0.274  Sum_probs=55.0

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+|++.|+++|+.||.|..|.|. .+++|+|||+|.+.++|..|+..  ..-+.+.+|.|.|...
T Consensus        13 ~~~te~~L~~~F~~fG~I~~v~i~-~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1          13 ERVTPQSLFILFGVYGDVQRVKIL-FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             TTCCHHHHHHHHHHHTCEEEEEEC-CTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             ccCCHHHHHHHHhhccccceEEEE-ecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            358999999999999999999985 34689999999999999999986  4455889999999754

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.08  E-value=1.2e-10  Score=87.11  Aligned_cols=74  Identities=22%  Similarity=0.215  Sum_probs=60.7

Q ss_pred             ccceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcC--CCCCCeEEEecC
Q 022800          166 KEKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCG--NLSNPLLVLPLQ  241 (292)
Q Consensus       166 ~~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g--~~~~pl~v~~~~  241 (292)
                      .+++|-|.|=.. +.+|+++|.+||++||.|.+|.+.  +.+++|||+|++.++|..|+..  ..+  ..+.||+|.|..
T Consensus         7 ~sr~v~v~nl~~-~~~t~~eL~~lF~~fG~I~~i~i~--~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~   83 (89)
T d1x4da1           7 TRRVVHIMDFQR-GKNLRYQLLQLVEPFGVISNHLIL--NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   83 (89)
T ss_dssp             CCCEEEEESCCC-SSSHHHHHHTTTGGGSCEEEEEEC--SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCcEEEEECCCC-CcCCHHHHHHHHHhhCCeEEEEee--ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECC
Confidence            345777777643 338999999999999999999984  4578999999999999999984  333  678999999985


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        84 ~   84 (89)
T d1x4da1          84 K   84 (89)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=9.7e-11  Score=85.57  Aligned_cols=66  Identities=18%  Similarity=0.278  Sum_probs=57.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+++|++||+|.+|.|.    .++.+|+|||+|.+.++|..|+..  +.-..+++|.|.|..|
T Consensus        10 Lp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            45579999999999999999999885    256789999999999999999974  5666789999999875

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.06  E-value=2.1e-10  Score=86.38  Aligned_cols=68  Identities=21%  Similarity=0.266  Sum_probs=58.0

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec-----CCCcceEEEEecCHHHHHHHHHh---hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS-----SKKKGSALVVMATKSAAGAATGS---VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~~---~~g~~~~pl~v~~~~~  242 (292)
                      ...+..++++.|+++|+.||.|.+|.|..     +..+|+|||+|.+.++|..|+..   ..-+.+.||.|.|..+
T Consensus        14 ~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~   89 (94)
T d2cpha1          14 RNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS   89 (94)
T ss_dssp             ESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCC
T ss_pred             eCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCC
Confidence            33556799999999999999999998842     46799999999999999999975   3447889999999864

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.05  E-value=9e-11  Score=85.85  Aligned_cols=66  Identities=20%  Similarity=0.212  Sum_probs=56.9

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|++||+|.+|.|.    +++.+|+|||+|.+.++|..|+..  +.-..+.+|.|.|..|
T Consensus        10 Lp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          10 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45679999999999999999999874    256689999999999999999975  5556788999999865

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=6.7e-11  Score=88.10  Aligned_cols=66  Identities=27%  Similarity=0.348  Sum_probs=58.4

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~~~  242 (292)
                      .....+|+++|+++|++||.|.+|.+ ...++|+|||+|.+.++|..|+.+...+.+.+|.|.|..|
T Consensus        12 nLp~~~te~~L~~~F~~~G~v~~v~~-~~~~~gfafV~f~~~~~a~~a~~~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_          12 RCTGDMTEDELREFFSQYGDVMDVFI-PKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCSSSCHHHHHHHSTTTSCCCEEEC-CSSCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCC
T ss_pred             CCCCCCCHHHHHHHHHHcCCceEEEE-eeccCceEEEEECCHHHHHHHHhCCCEECCEEeEEEeCCC
Confidence            34567999999999999999999987 4567899999999999999999887778889999999865

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.04  E-value=1.5e-10  Score=89.85  Aligned_cols=72  Identities=22%  Similarity=0.348  Sum_probs=60.1

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  ..+..+|++.|+++|++||+|.+|.+. +++.+|+|||+|.+.++|..|+..  +..+.+.+|.|.|..
T Consensus         8 r~l~V~--nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           8 RILYIR--NLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             SEEEEE--SCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEE--CCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            345443  345679999999999999999999986 466799999999999999999974  555678999999975

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.03  E-value=3.1e-10  Score=87.30  Aligned_cols=64  Identities=20%  Similarity=0.170  Sum_probs=56.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ....++++.|+++|+.||+|..|.|  .+.+|+|||+|.+.++|..|+..  +.-+.+.||.|.|...
T Consensus        18 Lp~~~t~~~L~~~F~~fG~I~~v~l--~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          18 LPAGTLAAEIQETFSRFGSLGRVLL--PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             CCTTCCHHHHHHHHHTTSCEEEEEC--CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCCCCHHHHHhhhhccCCccEEEe--eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            4456999999999999999999998  45689999999999999999974  7778899999999754

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.03  E-value=4e-10  Score=82.78  Aligned_cols=64  Identities=17%  Similarity=0.254  Sum_probs=54.4

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC--C-CCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG--N-LSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g--~-~~~pl~v~~~~  241 (292)
                      .+..+|++.|.++|+.||+|.+|.+. .+++|+|||+|.+.++|..|+....|  . .+.||.|.|..
T Consensus        16 Lp~~~t~~~l~~~f~~~G~i~~v~~~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          16 LPEETNEMMLSMLFNQFPGFKEVRLV-PNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCTTCCHHHHHHHHTTSTTEEEEEEC-TTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCHHHHHhhhccCccEEEeeee-cccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            45679999999999999999999884 45689999999999999999986444  3 35799999974

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=3.2e-10  Score=83.82  Aligned_cols=66  Identities=15%  Similarity=0.190  Sum_probs=58.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|++||+|.+|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.||.|.|..+
T Consensus         9 lp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~   80 (85)
T d2u2fa_           9 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            456799999999999999999998852    56799999999999999999985  6677899999999864

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=2.3e-10  Score=85.37  Aligned_cols=66  Identities=17%  Similarity=0.153  Sum_probs=57.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|+.||+|.+|.|..  ...+|+|||+|.+.++|..|+..  +.-+.+.||+|.|..+
T Consensus        16 Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1          16 LSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            556799999999999999999998852  44689999999999999999974  5557889999999865

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=4.3e-10  Score=85.10  Aligned_cols=64  Identities=20%  Similarity=0.231  Sum_probs=55.9

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|++||.|.+|.|.  ..+|+|||+|.+.++|..|+..  +.-+.+++|+|.|..+
T Consensus        26 L~~~~te~~L~~~F~~fG~i~~v~i~--~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          26 IASGLTDQLMRQTFSPFGQIMEIRVF--PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CSSCCCHHHHHHHHHHHSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCCHHHHHHHHHHhCCceEEEEE--ecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45669999999999999999999985  3489999999999999999975  4445899999999864

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.02  E-value=2.3e-10  Score=85.75  Aligned_cols=67  Identities=19%  Similarity=0.093  Sum_probs=58.0

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|+.||.|.+|.|.    ++.++|+|||+|.+.++|..|+.....+-+.+|.|.|..+
T Consensus        15 nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~~   85 (90)
T d2cqga1          15 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS   85 (90)
T ss_dssp             SCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCT
T ss_pred             CCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCCC
Confidence            356679999999999999999999875    2677999999999999999999876666778999998754

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.02  E-value=4.1e-10  Score=82.99  Aligned_cols=65  Identities=23%  Similarity=0.339  Sum_probs=54.0

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcC--C--CCCCeEEEec
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCG--N--LSNPLLVLPL  240 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g--~--~~~pl~v~~~  240 (292)
                      ..+..+|++.|+++|++||+|.+|.|.    +++.+|+|||+|.+.++|..|+....|  .  ...||.|.|+
T Consensus        13 nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          13 NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             SCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            355679999999999999999999875    256789999999999999999986333  2  2389999984

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.01  E-value=1.7e-09  Score=82.65  Aligned_cols=72  Identities=18%  Similarity=0.127  Sum_probs=59.7

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh--cC--CCCCCeEEEecCC
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV--CG--NLSNPLLVLPLQP  242 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~--~g--~~~~pl~v~~~~~  242 (292)
                      .++|-|+.  ....+|+++|..+|++||.|..|.+.  +.+|+|||+|.+.++|..|+...  .+  ..+.||.|.|...
T Consensus        15 s~~l~v~n--lp~~~te~~l~~~F~~fG~I~~~~~~--~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          15 SPVVHVRG--LCESVVEADLVEALEKFGTICYVMMM--PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CSEEEEES--CCSSCCHHHHHHHHTTTSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             CCEEEEeC--CCCCCCHHHHHHhhhhcccceEEEEE--ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            45677765  34669999999999999999999984  56899999999999999999742  33  4589999999864

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=5.6e-10  Score=82.73  Aligned_cols=73  Identities=22%  Similarity=0.133  Sum_probs=59.7

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC--CC-CCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG--NL-SNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g--~~-~~pl~v~~~~~  242 (292)
                      ++|-|.  ..+..+|++.|+++|+.||.|..+++...+.+|+|||+|.+.++|..|+....|  +. +.||.|.|.++
T Consensus        11 ~tL~V~--NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          11 ATLHLS--NIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SEEEEE--CCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CEEEEE--CCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            345443  356679999999999999999988876677899999999999999999986444  33 68999999864

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.00  E-value=4.2e-10  Score=81.78  Aligned_cols=65  Identities=20%  Similarity=0.278  Sum_probs=56.4

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .+..+|+++|+++|++||+|..|.|.   +++.+|+|||+|.+.++|..|+..  ..-+.++||.|.++.
T Consensus         8 Lp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           8 LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45579999999999999999999985   366799999999999999999974  566778999999863

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=1.8e-10  Score=85.87  Aligned_cols=66  Identities=24%  Similarity=0.344  Sum_probs=57.4

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+++|++||+|.+|.|..    +..+|+|||+|.+.++|..|+..  +.-..++||.|.|..|
T Consensus        13 Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1          13 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            456799999999999999999998852    67799999999999999999975  5556789999999865

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=2.5e-10  Score=83.34  Aligned_cols=65  Identities=22%  Similarity=0.183  Sum_probs=56.0

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .+..+|++.|+++|++||+|.+|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.||+|.|..
T Consensus         8 L~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           8 LHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            345799999999999999999999852    55689999999999999999974  566678899999974

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=5.2e-10  Score=84.02  Aligned_cols=65  Identities=15%  Similarity=0.080  Sum_probs=55.9

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .+..+|++.|+++|++||+|.+|.|..    +..+|+|||+|.+.++|..|+..  +.-+.+.||.|.|..
T Consensus        15 lp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_          15 LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            455799999999999999999998842    55689999999999999999975  455578899999974

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=6.1e-10  Score=82.21  Aligned_cols=64  Identities=17%  Similarity=0.270  Sum_probs=53.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCC--CCCeEEEec
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNL--SNPLLVLPL  240 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~--~~pl~v~~~  240 (292)
                      .+..+|++.|+++|++||+|.+|.|..    +..+|+|||+|.+.++|..|+..  +.-+.  ..||.|.|.
T Consensus        14 Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          14 LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            456799999999999999999998852    56799999999999999999975  33333  478999884

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=4.4e-10  Score=83.82  Aligned_cols=68  Identities=24%  Similarity=0.334  Sum_probs=58.4

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ......+|++.|+++|++||+|..|.|..    +..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..|
T Consensus        14 ~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp   87 (90)
T d2cq0a1          14 TNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP   87 (90)
T ss_dssp             ESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSC
T ss_pred             ECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeC
Confidence            34566799999999999999999998852    56799999999999999999985  4556788999999875

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=8.1e-10  Score=82.94  Aligned_cols=73  Identities=18%  Similarity=0.224  Sum_probs=60.8

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .+|-|  ...+..+|++.|+++|++||+|.+|.|.    ++..+|+|||+|.+.++|..|+..  ..-+.+.+|+|.|..
T Consensus        10 ~tlfV--~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1          10 ATVYV--GGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TEEEE--ECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CEEEE--eCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34444  3456679999999999999999999874    256799999999999999999974  666778999999986


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        88 ~   88 (93)
T d1x5ua1          88 A   88 (93)
T ss_dssp             T
T ss_pred             C
Confidence            5

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=1.5e-09  Score=81.36  Aligned_cols=68  Identities=22%  Similarity=0.242  Sum_probs=58.3

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...+..+|++.|+++|++||+|..|.+..  ...+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        17 ~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1          17 SNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             ESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             ECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            34566799999999999999999998853  44689999999999999999964  6666789999999875

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.98  E-value=4.8e-10  Score=83.10  Aligned_cols=64  Identities=27%  Similarity=0.333  Sum_probs=56.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..++++.|+++|+.||+|.+|.+.  +.+|+|||+|.+.++|..|+..  +.-..+.+|.|.|..+
T Consensus        16 Lp~~~~~~~l~~~F~~~G~i~~i~~~--~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1          16 LPPDITEEEMRKLFEKYGKAGEVFIH--KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CCTTCCHHHHHHHTSTTCCCSEEEEE--TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCCCCHHHHHHHHHHhCCceEeeee--cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            45679999999999999999999985  4579999999999999999975  6667899999999854

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.98  E-value=9.2e-10  Score=83.19  Aligned_cols=71  Identities=23%  Similarity=0.224  Sum_probs=57.0

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh----cCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV----CGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~----~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.  ..+..+|++.|+++|++||.|..|.+.  +.+|+|||+|.+.++|..|+...    .+....+|+|.|..+
T Consensus        18 ~tl~V~--nLp~~~t~~~l~~~f~~~G~i~~~~~~--~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          18 TRLWVG--GLGPNTSLAALAREFDRFGSIRTIDHV--KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             SCEEEE--CCCSSCCHHHHHHHHHTTSCEEEEEEC--SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CEEEEc--CCCCCCCHHHHHHHHHhhcccceEeee--ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCC
Confidence            355544  345569999999999999999999983  56899999999999999999853    233346899999875

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.98  E-value=8.8e-10  Score=81.49  Aligned_cols=64  Identities=23%  Similarity=0.248  Sum_probs=53.0

Q ss_pred             CCC-CHHHHHHHhcccCCeeEEEEec-----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          179 EDY-TAERLREIFSEFGKVEDVVIKS-----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       179 ~~~-t~~~L~~~fs~yG~V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      ..+ +++.|+++|++||.|.+|.|..     ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        14 ~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a~~   84 (86)
T d2ghpa3          14 TELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADK   84 (86)
T ss_dssp             TTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECCC
T ss_pred             CCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEcCC
Confidence            344 5677999999999999998742     5679999999999999999996 45666789999999864

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=1.2e-09  Score=82.18  Aligned_cols=67  Identities=21%  Similarity=0.202  Sum_probs=55.7

Q ss_pred             ecCCCCCHHHHHHHhcccCC-eeEEEEec-----CCCcceEEEEecCHHHHHHHHHhh--cCC--CCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGK-VEDVVIKS-----SKKKGSALVVMATKSAAGAATGSV--CGN--LSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~-V~~v~i~~-----~k~~g~A~V~F~~~~~A~~Av~~~--~g~--~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|+.||+ |.+|.|..     ++++|+|||+|.+.++|..|+...  .+.  .++||.|.|..|
T Consensus         8 nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p   84 (96)
T d2disa1           8 GIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEP   84 (96)
T ss_dssp             CCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCS
T ss_pred             CCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCC
Confidence            34567999999999999996 88888842     467899999999999999999763  232  378999999976

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.98  E-value=3e-10  Score=84.43  Aligned_cols=66  Identities=21%  Similarity=0.258  Sum_probs=56.5

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|.++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+++|.|.|..+
T Consensus        15 L~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          15 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            556799999999999999999998742    55789999999999999999975  4556789999999753

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.95  E-value=6.5e-10  Score=81.01  Aligned_cols=66  Identities=15%  Similarity=0.164  Sum_probs=54.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+++|+.||.|..+++.    .++.+|+|||+|.+.++|..|+..  +.-..+.||.|.+..|
T Consensus         9 Lp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           9 FPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            45679999999999999999887663    267799999999999999999974  6667889999998864

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.95  E-value=2.4e-09  Score=81.00  Aligned_cols=71  Identities=23%  Similarity=0.200  Sum_probs=59.8

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      |=-...+..+|+++|+++|++||+|.+|.|..    ++.+|+|||+|.+.++|..|+..  ..-+.+++|+|.|..+
T Consensus        11 lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~   87 (99)
T d1whwa_          11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTI   87 (99)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCC
T ss_pred             EEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            33344566799999999999999999999852    56799999999999999999974  5667789999999865

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.94  E-value=5.1e-10  Score=82.33  Aligned_cols=65  Identities=20%  Similarity=0.145  Sum_probs=54.6

Q ss_pred             CCCCCHHHHHHHhcccCCeeEEEEec---C----CCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          178 GEDYTAERLREIFSEFGKVEDVVIKS---S----KKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v~i~~---~----k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +..+|++.|+++|++||.|.+|.|..   .    ..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus         7 p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           7 NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             CTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            45689999999999999999998852   1    2479999999999999999975  5556789999999753

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=1.6e-09  Score=80.36  Aligned_cols=67  Identities=18%  Similarity=0.254  Sum_probs=58.4

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|+++|.++|+.||.|..|.+..    +..+|+|||+|.+.++|..|+.  ++.-+.+.+|.|.|..+
T Consensus        12 nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1          12 GLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             SCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            3566799999999999999999998742    6679999999999999999996  47778899999999864

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=9.8e-10  Score=83.88  Aligned_cols=66  Identities=24%  Similarity=0.201  Sum_probs=57.4

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|.++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus        16 Lp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_          16 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             CCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            456799999999999999999998742    45689999999999999999974  6778899999999754

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.92  E-value=5.5e-10  Score=83.09  Aligned_cols=66  Identities=20%  Similarity=0.230  Sum_probs=57.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec--CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS--SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~--~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|++.|+++|+.||.|..+.|..  +..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus        16 Lp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2          16 LDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             CCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            566799999999999999999998853  44689999999999999999964  6667789999999864

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.92  E-value=6.2e-10  Score=81.51  Aligned_cols=65  Identities=23%  Similarity=0.231  Sum_probs=53.9

Q ss_pred             CCCCCHHHHHHHhcccCCeeEE-EEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          178 GEDYTAERLREIFSEFGKVEDV-VIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       178 ~~~~t~~~L~~~fs~yG~V~~v-~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      +..+|+++|+++|++||.|.++ .|.    +++.+|+|||+|.+.++|..|+..  +.-+.+.||.|.|..+
T Consensus         7 p~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~   78 (83)
T d1x5ta1           7 DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK   78 (83)
T ss_dssp             CTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCC
T ss_pred             CCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecC
Confidence            4569999999999999999775 332    256789999999999999999974  5556789999999865

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.92  E-value=2.6e-10  Score=83.40  Aligned_cols=64  Identities=20%  Similarity=0.111  Sum_probs=54.5

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcC---CCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCG---NLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g---~~~~pl~v~~~~~  242 (292)
                      .+.++|+++|+++|++||.|.++.+.  +++|+|||+|.+.++|..|+....|   ..+.||.|.|..|
T Consensus         9 Lp~~~te~~L~~~F~~~G~i~~~~~~--~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           9 LSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CCCCCCHHHHHHHHHHhCcEEEeEEe--cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            45679999999999999999887663  4689999999999999999987554   4589999999865

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.91  E-value=9.9e-10  Score=83.42  Aligned_cols=60  Identities=22%  Similarity=0.180  Sum_probs=53.0

Q ss_pred             CCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          179 EDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       179 ~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...+++.|+++|++||.|..|.|    .+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        26 ~~~~~~~L~~~F~~~G~i~~~~i----~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          26 LVVKKSDVEAIFSKYGKIVGCSV----HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             TTCCHHHHHHSSTTSSCEEEEEE----ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             ccCCHHHHHHHHhhcCCEEEEEE----eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            45788899999999999999998    479999999999999999975  4567789999999864

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=2.6e-09  Score=80.21  Aligned_cols=67  Identities=16%  Similarity=0.167  Sum_probs=58.4

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ..+..+|+++|+++|+.||.|..|.+. ....+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        21 nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          21 NLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             SCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            456679999999999999999999885 356789999999999999999974  6667889999999864

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=1.4e-09  Score=83.04  Aligned_cols=68  Identities=19%  Similarity=0.137  Sum_probs=57.4

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      ...+..+|++.|+++|+.||.|.+|.+..    +..+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus        24 ~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~   97 (102)
T d2cpza1          24 YHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS   97 (102)
T ss_dssp             ESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             eCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCC
Confidence            34566799999999999999999988742    56689999999999999999975  4445789999999865

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.89  E-value=2.9e-09  Score=81.73  Aligned_cols=73  Identities=14%  Similarity=0.039  Sum_probs=58.6

Q ss_pred             eEEEEeeec---CCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCCC
Q 022800          169 VLKVSWEKF---GEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQPA  243 (292)
Q Consensus       169 ~lkvKWk~~---~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~~  243 (292)
                      +|-|.--..   ..+.+++.|+.+|+.||.|.++.+.  +.+|+|||+|.+.++|..|+..  +.-+.+.||.|.|..+.
T Consensus         7 ~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~--k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   84 (104)
T d1weya_           7 GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF--KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             EEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE--TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             eEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe--cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccC
Confidence            455544432   2345567899999999999999984  5688999999999999999986  56677899999998764

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=2.4e-09  Score=81.77  Aligned_cols=71  Identities=24%  Similarity=0.228  Sum_probs=58.4

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhcC-CCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVCG-NLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~g-~~~~pl~v~~~~~  242 (292)
                      |=-...+..+|+++|+++|++||.|.+|.|..    ++.+|+|||+|.+.++|..|+....+ +.+.+|.|.|..+
T Consensus        13 lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          13 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYL   88 (103)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTT
T ss_pred             EEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcCC
Confidence            33344566799999999999999999999852    56799999999999999999986333 5578999999754

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=1.7e-09  Score=79.89  Aligned_cols=65  Identities=23%  Similarity=0.286  Sum_probs=54.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      .+..+|++.|+++|+.||+|.+|.|..   ++.+|+|||+|.+.++|..|+.. .....+.+|.|.|-.
T Consensus        14 lp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          14 FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             CCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            455699999999999999999999852   55689999999999999999964 444567889988853

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=2.4e-09  Score=77.12  Aligned_cols=62  Identities=19%  Similarity=0.278  Sum_probs=50.8

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEE
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVL  238 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~  238 (292)
                      .+..+|++.|+++|++||+|.+|.|..    ++.+|+|||+|.|.++|..|+.. ..-+.+.+|.|.
T Consensus         7 l~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~   73 (75)
T d1hd0a_           7 LSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPK   73 (75)
T ss_dssp             CCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEEC
T ss_pred             CCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEee
Confidence            456799999999999999999999852    56799999999999999999975 333456666653

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.88  E-value=9.4e-10  Score=83.65  Aligned_cols=61  Identities=16%  Similarity=0.195  Sum_probs=52.8

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hc--CCCCCCeEEEecCC
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VC--GNLSNPLLVLPLQP  242 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~--g~~~~pl~v~~~~~  242 (292)
                      .+|++.|.++|+.||.|.+|.+.  +.+|+|||+|.+.++|..|+.+  ..  ...+.+|.|.|...
T Consensus        30 ~~te~~l~~~F~~fG~V~~v~~~--~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          30 GYSDSAVLKLAEPYGKIKNYILM--RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             SCCSHHHHTTTTTTSCCSEEEEE--TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             ccCHHHHHhhhccccceeEEEEe--ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            48999999999999999999984  4579999999999999999973  33  46789999999753

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=2.5e-09  Score=81.90  Aligned_cols=72  Identities=18%  Similarity=0.244  Sum_probs=58.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      +|=|  ...+..+|+++|+++|++||.|.+|.|..    ...+|||||+|.+.++|..|+.. +.-+.+.+|.|.+..|
T Consensus        22 ~lfV--gnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          22 KLFI--GGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             EEEE--ECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             EEEE--eCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcc
Confidence            4444  34566799999999999999999999852    46799999999999999999963 3445678999998764

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=1.9e-09  Score=82.32  Aligned_cols=61  Identities=16%  Similarity=0.248  Sum_probs=51.2

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhhcCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSVCGN  230 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~~g~  230 (292)
                      ++|.|.-...+.++|++.|+++|++||.|.+|.+.  +.+|+|||+|.+.++|..|+....|.
T Consensus        19 ~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~--~~k~~aFV~f~~~e~A~~A~~~lng~   79 (101)
T d2cq2a1          19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP--PNKPYSFARYRTTEESKRAYVTLNGK   79 (101)
T ss_dssp             SEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC--TTCSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             ceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeec--cCccEEEEEECCHHHHHHHHHHhCCC
Confidence            35666554456779999999999999999999884  45789999999999999999876654

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=1.3e-09  Score=82.98  Aligned_cols=67  Identities=18%  Similarity=0.261  Sum_probs=55.2

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec---CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS---SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~---~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|+.||+|..+.+..   ++.+|+|||+|.+.++|..|+..  +.-+.+.|+.|.|..|
T Consensus        25 nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          25 NLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             SCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            4566799999999999999999988752   55689999999999999999974  5556677887776543

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=1.5e-09  Score=79.97  Aligned_cols=64  Identities=16%  Similarity=0.082  Sum_probs=56.1

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+++|+.||.|..+.+  .+.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..|
T Consensus        16 Lp~~~te~~l~~~F~~~g~i~~~~~--~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1          16 LMLSTSEEMIEKEFNNIKPGAVERV--KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCTTCCHHHHHHHHHTTSTTCEEEE--EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCCCCCHHHHHHhhcccceeeeEEE--ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            5667999999999999999998887  45689999999999999999975  5556789999999875

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=3.3e-09  Score=78.50  Aligned_cols=71  Identities=21%  Similarity=0.247  Sum_probs=58.6

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh----hcCCCCCCeEEEecCC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS----VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~----~~g~~~~pl~v~~~~~  242 (292)
                      ++|-|.+  .+..+|+++|.++|+.||.|.+|.+.  +.+|+|||+|.+.++|..|+..    .....+.||.|.|...
T Consensus         9 ~~l~V~n--Lp~~~t~~~L~~~f~~~G~i~~v~~~--~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           9 RVLHIRK--LPGEVTETEVIALGLPFGKVTNILML--KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SEEEEES--CCTTCCHHHHHHTTTTTSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CEEEEeC--CCCCCCHHHHHHHHhccccccccccc--ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            4677754  44569999999999999999999984  4579999999999999999974    2345788999999753

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=98.85  E-value=2.6e-09  Score=80.45  Aligned_cols=73  Identities=15%  Similarity=0.141  Sum_probs=60.9

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      .++|-|..  .+..+|+++|+++|+.||.|..+.. .++.+|+|||+|.+.++|..|+.  ++.-+.+.||.|.|..+
T Consensus        16 ~~~l~V~n--L~~~~te~~l~~~F~~~g~v~~~~~-~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          16 ARTLLAKN--LSFNITEDELKEVFEDALEIRLVSQ-DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             GGEEEEES--CCSSCCHHHHHHHHCSEEEECCEEE-TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCEEEEeC--CCCCCCHHHHHHHHHhcccceeeee-cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            34555544  4456999999999999999987765 67789999999999999999997  46677889999999875

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=98.84  E-value=6.7e-09  Score=83.05  Aligned_cols=67  Identities=22%  Similarity=0.300  Sum_probs=57.7

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .....+|++.|+++|++||.|..|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|..+
T Consensus        49 nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          49 YIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             SCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            3556799999999999999999988742    45689999999999999999974  6777889999999864

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.84  E-value=1.1e-09  Score=83.72  Aligned_cols=71  Identities=28%  Similarity=0.343  Sum_probs=58.3

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      +|-|.  .....+|++.|+++|+.||.|.+|.|..    ++.+|+|||+|.+.++|..|+. ++.-+.+.+|.|.+..
T Consensus        20 tifV~--nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          20 TVFCM--QLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             EEEEE--SCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             EEEEE--CCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            45443  3566799999999999999999999852    5689999999999999999995 3555677899998864

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.83  E-value=4e-09  Score=76.03  Aligned_cols=62  Identities=21%  Similarity=0.269  Sum_probs=52.8

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~  241 (292)
                      .+.++++++|+++|++|| |..+.+  ++.+|+|||+|.+.++|..|+.  ++.-+.+.||.|.|..
T Consensus         6 Lp~~~t~~~l~~~F~~~g-~~~~~~--~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           6 LPGDVTNQEVHDLLSDYE-LKYCFV--DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             CCTTCCHHHHHHHTTTSC-EEEEEE--ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CCCcCCHHHHHHHHhccc-ccceee--cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            345799999999999999 545544  5789999999999999999996  4677889999999984

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.83  E-value=2.1e-09  Score=78.61  Aligned_cols=61  Identities=26%  Similarity=0.308  Sum_probs=50.0

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEE
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLV  237 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v  237 (292)
                      .+..+|++.|+++|++||+|.+|.|..    ++.+|+|||+|.+.++|..|+..  +.-+.+++|+|
T Consensus        17 L~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          17 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            556799999999999999999998742    56689999999999999999975  44445566554

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.82  E-value=4.8e-09  Score=74.87  Aligned_cols=63  Identities=16%  Similarity=0.277  Sum_probs=53.4

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEe
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLP  239 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~  239 (292)
                      .+.++|+++|+++|+.||.|..+.+..    +..+|+|||+|.+.++|..|+.. ..-+.+.||.|.+
T Consensus         7 Lp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~   74 (75)
T d2msta_           7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             CCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEE
T ss_pred             CCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEE
Confidence            456799999999999999999988742    56799999999999999999963 5566778888876

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.82  E-value=1.4e-09  Score=83.67  Aligned_cols=61  Identities=16%  Similarity=0.174  Sum_probs=52.8

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          180 DYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      .++++.|+++|++||.|.+|.|.   +++.+|+|||+|.+.++|..|+..  +.-+.+.||.|.+.
T Consensus        38 ~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          38 EFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            47789999999999999999985   267799999999999999999985  66667888888764

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.82  E-value=4.1e-09  Score=75.98  Aligned_cols=64  Identities=20%  Similarity=0.157  Sum_probs=52.8

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEec
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPL  240 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~  240 (292)
                      .+...|++.|+++|+.||+|.+|.|.  ....+|+|||+|.+.++|..|+.. ..-+.++||.|..+
T Consensus         8 lp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           8 LPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             ECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            45669999999999999999999985  255678999999999999999963 44456778887754

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=4.5e-09  Score=77.72  Aligned_cols=63  Identities=14%  Similarity=0.060  Sum_probs=54.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+++|++||+|..|.|.   +.|+|||+|.+.++|..|+.  ++.-+.+.+|.|.++.+
T Consensus         8 lp~~~~~~~l~~~F~~~G~v~~~~i~---~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           8 LPPSGSWQDLKDHMREAGDVCYADVY---RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCSSCCTTHHHHHHGGGSCEEEEEEC---TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CCCcCCHHHHHHHHhhhccccccccc---ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            45679999999999999999999883   35999999999999999996  46667788999988754

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.80  E-value=4.8e-09  Score=78.60  Aligned_cols=67  Identities=22%  Similarity=0.229  Sum_probs=55.4

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHhhc--------CCCCCCeEEEecCC
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGSVC--------GNLSNPLLVLPLQP  242 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~~~--------g~~~~pl~v~~~~~  242 (292)
                      ..+..+|++.|+++|++||+|..+.+..    +..+|+|||+|.+.++|..|+....        -+.+.+|.|.|..+
T Consensus        15 nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~   93 (98)
T d1x4ha1          15 NLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT   93 (98)
T ss_dssp             SCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCC
T ss_pred             CCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCC
Confidence            3566799999999999999999998842    4578999999999999999998532        24467899999754

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=98.80  E-value=1.3e-09  Score=81.52  Aligned_cols=71  Identities=11%  Similarity=0.098  Sum_probs=59.6

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe---cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK---SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~---~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      +|-|  ...+..+|+++|+++|+.||.|.++.|.   +++.+|+|||+|.+.++|..|+. ++..+.+.+|.|.|..
T Consensus        15 ~ifV--~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          15 NLFI--GNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             EEEE--ECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             EEEE--eCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecC
Confidence            4444  4567789999999999999999987663   37789999999999999999996 4666778999999875

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=4.1e-09  Score=76.15  Aligned_cols=50  Identities=22%  Similarity=0.472  Sum_probs=44.4

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      .+..+|+++|+++|++||+|.+|.|..    ++.+|+|||+|.+.++|..|+..
T Consensus         7 Lp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~   60 (75)
T d1x0fa1           7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK   60 (75)
T ss_dssp             CCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC
T ss_pred             CCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh
Confidence            456799999999999999999998842    56799999999999999999964

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.79  E-value=4.9e-09  Score=75.98  Aligned_cols=63  Identities=19%  Similarity=0.285  Sum_probs=52.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEe
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLP  239 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~  239 (292)
                      .+..+|++.|+++|++||+|.+|.|.    +++.+|+|||+|.+.++|..|+.. ..-+.+.+|.|.+
T Consensus         8 Lp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~   75 (77)
T d1uawa_           8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV   75 (77)
T ss_dssp             CCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEE
T ss_pred             CCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEE
Confidence            45679999999999999999999884    266899999999999999999974 4445567777764

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.79  E-value=7e-09  Score=76.25  Aligned_cols=64  Identities=22%  Similarity=0.261  Sum_probs=52.1

Q ss_pred             ecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEe
Q 022800          176 KFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLP  239 (292)
Q Consensus       176 ~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~  239 (292)
                      ..+..+|++.|.++|++||.|.+|.|.    +++.+|+|||+|.+.++|..|+.. +.-+.+.+|.|..
T Consensus        13 nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1          13 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (84)
T ss_dssp             SCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            356679999999999999999999874    266799999999999999999974 3334566666654

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=3.7e-09  Score=79.99  Aligned_cols=73  Identities=19%  Similarity=0.215  Sum_probs=60.8

Q ss_pred             ceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          168 KVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       168 ~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ++|-|.  ..+..+|++.|.++|+.||.|..+.+.    +++.+|+|||+|.+.++|..|+..  +.-..+.||.|.|..
T Consensus        19 ~tl~V~--nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          19 KVLYLK--NLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             SEEEEE--CCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CEEEEe--CCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            345443  345679999999999999999998774    367899999999999999999974  666788999999987


Q ss_pred             C
Q 022800          242 P  242 (292)
Q Consensus       242 ~  242 (292)
                      +
T Consensus        97 ~   97 (102)
T d2cpxa1          97 N   97 (102)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.75  E-value=3.1e-09  Score=79.11  Aligned_cols=62  Identities=23%  Similarity=0.232  Sum_probs=50.1

Q ss_pred             cCCCCCHHHH---HHHhcccCCeeEEEEec-------CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEE
Q 022800          177 FGEDYTAERL---REIFSEFGKVEDVVIKS-------SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVL  238 (292)
Q Consensus       177 ~~~~~t~~~L---~~~fs~yG~V~~v~i~~-------~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~  238 (292)
                      .+..+++++|   .++|++||+|.+|.|..       ....|+|||+|.+.++|..|+..  +.-+.+.||+++
T Consensus        16 Lp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          16 LSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             ECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            4556888888   67899999999999852       12348999999999999999975  566678888775

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.73  E-value=2.7e-08  Score=77.11  Aligned_cols=68  Identities=12%  Similarity=0.106  Sum_probs=52.4

Q ss_pred             EEEeee-cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCH-HHHHHHHHhh--cCCCCCCeEEEec
Q 022800          171 KVSWEK-FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATK-SAAGAATGSV--CGNLSNPLLVLPL  240 (292)
Q Consensus       171 kvKWk~-~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~-~~A~~Av~~~--~g~~~~pl~v~~~  240 (292)
                      .+..-. .+..+|++.|+++|++||+|..|.|.  +.+|+|||.|.+. ++|..|+...  ..+....+.|.|.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~--~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV--RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC--TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEe--cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            344443 56679999999999999999999994  5589999999996 7888888763  3444556666664

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.73  E-value=6.9e-09  Score=76.96  Aligned_cols=63  Identities=13%  Similarity=0.231  Sum_probs=52.3

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+++|++|| |..+.+  .+.+|+|||+|.+.++|..|+..  ..-+.+.+|.|.|..+
T Consensus        13 Lp~~~t~~~l~~lF~~~G-~~~~~~--~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_          13 LPQDSNCQEVHDLLKDYD-LKYCYV--DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCSSCCHHHHHHHTCSSC-CCCEEE--EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCccChHHHHHHHHhcC-ceeeee--eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            456799999999999999 333444  45789999999999999999974  6667899999999853

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=4.3e-09  Score=78.43  Aligned_cols=66  Identities=27%  Similarity=0.430  Sum_probs=54.4

Q ss_pred             cCCCCCHHHHH----HHhcccCCeeEEEEe-cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          177 FGEDYTAERLR----EIFSEFGKVEDVVIK-SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       177 ~~~~~t~~~L~----~~fs~yG~V~~v~i~-~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      .+..+|+++|+    .+|++||+|.+|.+. +++.+|+|||+|.+.++|..|+..  +.-..+.||.|.|..+
T Consensus        11 Lp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~   83 (91)
T d1nu4a_          11 LNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT   83 (91)
T ss_dssp             CCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSS
T ss_pred             CCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCC
Confidence            45568887775    578999999999885 355689999999999999999974  4556789999999864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=1.8e-08  Score=72.59  Aligned_cols=63  Identities=24%  Similarity=0.310  Sum_probs=51.6

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEe
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLP  239 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~  239 (292)
                      .+..+|+++|+++|++||.|..+.+..    +..+|+|||+|.+.++|..|+.. +.-+.+.+|.|..
T Consensus        10 Lp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~   77 (79)
T d1l3ka2          10 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK   77 (79)
T ss_dssp             CTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEE
T ss_pred             CCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEE
Confidence            456799999999999999999998852    56789999999999999999863 3445567777754

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.68  E-value=1e-08  Score=72.81  Aligned_cols=50  Identities=24%  Similarity=0.265  Sum_probs=44.2

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS  226 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~  226 (292)
                      .+..+|++.|+++|++||+|..+.+..    +..+|+|||+|.+.++|..|+..
T Consensus         6 Lp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~   59 (72)
T d1x4ea1           6 LQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA   59 (72)
T ss_dssp             CCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHH
Confidence            355799999999999999999988742    56799999999999999999975

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=9.9e-08  Score=72.48  Aligned_cols=71  Identities=15%  Similarity=0.117  Sum_probs=58.6

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      |.-.......|+++|+++|+.||.|..+++.    .++.+|+|||+|.+.++|..|+. +..-+.+.++.|.+..+
T Consensus        18 v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~~   93 (104)
T d1wg5a_          18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR   93 (104)
T ss_dssp             EEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECCH
Confidence            4555567789999999999999999886553    26678999999999999999986 46667788999998864

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=1.6e-08  Score=76.21  Aligned_cols=68  Identities=22%  Similarity=0.164  Sum_probs=55.3

Q ss_pred             eecCCCCCHHHHHHHhcccCCeeEEEE--------e----cCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEec
Q 022800          175 EKFGEDYTAERLREIFSEFGKVEDVVI--------K----SSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPL  240 (292)
Q Consensus       175 k~~~~~~t~~~L~~~fs~yG~V~~v~i--------~----~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~  240 (292)
                      ...+..+|++.|+++|+.||+|..+.+        .    +++.+|+|||+|.+.++|..|+..  +.-+.+.+|.|.|.
T Consensus        14 ~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a   93 (101)
T d2cpea1          14 QGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA   93 (101)
T ss_dssp             ECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECS
T ss_pred             ECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345667999999999999999864332        1    145689999999999999999975  66677899999998


Q ss_pred             CC
Q 022800          241 QP  242 (292)
Q Consensus       241 ~~  242 (292)
                      .+
T Consensus        94 ~~   95 (101)
T d2cpea1          94 RK   95 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.66  E-value=7.1e-08  Score=73.10  Aligned_cols=71  Identities=14%  Similarity=0.102  Sum_probs=55.4

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeEEEEe-c----CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVEDVVIK-S----SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~-~----~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      .|--......+|+++|+++|+.|| |..+.+. .    ++.+|+|||+|.+.++|..|+. +..-+.+.+|.|.|..+
T Consensus        17 ~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~~   93 (104)
T d1wi8a_          17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQ   93 (104)
T ss_dssp             EEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            343344667899999999999999 5565553 1    4568999999999999988775 45666788999999865

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.61  E-value=3.6e-08  Score=74.49  Aligned_cols=68  Identities=16%  Similarity=0.026  Sum_probs=56.9

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~~  242 (292)
                      |--......+++++|.++|+.||.|..|.|.   ++|+|||+|.+.++|..||..  ..-+.+.+|.|.|+.+
T Consensus        18 i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~---~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQ---KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             EEEECCCSSCCHHHHHHHHTTSSCEEEEEEE---TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             EEEECCCCCCCHHHHHHHHHhhccccccccc---ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            3334456679999999999999999999984   469999999999999999964  5566788899999764

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.59  E-value=2.7e-08  Score=72.92  Aligned_cols=69  Identities=14%  Similarity=0.170  Sum_probs=55.7

Q ss_pred             EEEeeecCCCCCHHHHHHHhcccCCeeE-EEEe---cCCCcceEEEEecCHHHHHHHHH--hhcCCCCCCeEEEe
Q 022800          171 KVSWEKFGEDYTAERLREIFSEFGKVED-VVIK---SSKKKGSALVVMATKSAAGAATG--SVCGNLSNPLLVLP  239 (292)
Q Consensus       171 kvKWk~~~~~~t~~~L~~~fs~yG~V~~-v~i~---~~k~~g~A~V~F~~~~~A~~Av~--~~~g~~~~pl~v~~  239 (292)
                      .|.-...+..+|+++|+++|+.||.|.. |.+.   ++..+|+|||+|.+.++|..|+.  +..-+.+.||.|.+
T Consensus        11 ~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1          11 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             EEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3555556778999999999999999976 3332   26679999999999999999996  46667788888875

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=4.1e-08  Score=74.36  Aligned_cols=76  Identities=17%  Similarity=0.127  Sum_probs=59.6

Q ss_pred             cceEEEEeeecCCC-------C--CHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh--hcCCCCCCe
Q 022800          167 EKVLKVSWEKFGED-------Y--TAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS--VCGNLSNPL  235 (292)
Q Consensus       167 ~~~lkvKWk~~~~~-------~--t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl  235 (292)
                      +++|.|+---....       +  .+++|++.|++||.|..|.+.....+|+|||+|.+.++|..|+..  +.-+.+.+|
T Consensus         8 ~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i   87 (99)
T d2dita1           8 ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI   87 (99)
T ss_dssp             CCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEEC
T ss_pred             ccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCEEE
Confidence            45677765532211       1  236799999999999999987777899999999999999999985  555678999


Q ss_pred             EEEecCC
Q 022800          236 LVLPLQP  242 (292)
Q Consensus       236 ~v~~~~~  242 (292)
                      .|.+..+
T Consensus        88 ~v~~~~g   94 (99)
T d2dita1          88 TAQAWDG   94 (99)
T ss_dssp             EEEECCS
T ss_pred             EEEEeCC
Confidence            9998643

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.56  E-value=1.8e-07  Score=70.81  Aligned_cols=71  Identities=17%  Similarity=0.090  Sum_probs=56.1

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEe--cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIK--SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~--~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~~  242 (292)
                      |.-...+...|+++|+++|+.||.|.-.++.  .+..+|+|||+|.+.++|..|+. +..-+.+.++.|.|..+
T Consensus        18 v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~~   91 (102)
T d1weza_          18 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNST   91 (102)
T ss_dssp             EEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECC
T ss_pred             EEEeCCCCcCCHHHHHHHHhccCcceeeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            4444566779999999999999966433333  36679999999999999999986 46667789999999764

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=1.1e-07  Score=78.10  Aligned_cols=71  Identities=21%  Similarity=0.245  Sum_probs=57.5

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeEEEEec----CCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecCC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVEDVVIKS----SKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQP  242 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~----~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~~  242 (292)
                      |-.......+|++.|+++|+.||.|..|.|..    +..+|+|||+|.+.++|..|+.. ...+.+.+|.|.|..|
T Consensus       100 i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEECCC
T ss_pred             eEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEecCC
Confidence            44444566799999999999999999997752    56789999999999999999963 3345578999998754

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.46  E-value=6.9e-08  Score=73.12  Aligned_cols=70  Identities=13%  Similarity=0.040  Sum_probs=56.2

Q ss_pred             EEeeecCCCCCHHHHHHHhcccCCeeE-EEEe---cCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEEecC
Q 022800          172 VSWEKFGEDYTAERLREIFSEFGKVED-VVIK---SSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       172 vKWk~~~~~~t~~~L~~~fs~yG~V~~-v~i~---~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~~~~  241 (292)
                      |.-.......|+++|+++|+.||.|.. |.+.   .++.+|+|||+|.+.++|..|+.- ..-+.+.+|.|.++.
T Consensus        11 v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          11 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             EEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             EEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            444556677999999999999999976 4443   256799999999999999999963 444677899998874

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.34  E-value=1.6e-07  Score=72.29  Aligned_cols=71  Identities=15%  Similarity=0.173  Sum_probs=56.5

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEE-e---cCCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVI-K---SSKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i-~---~~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      +|.|  ......+|+++|.++|+.||.|.++++ .   ++..+|+|||+|.+.++|..|+. ++.-+.+.++.|.++.
T Consensus        20 ~i~v--~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          20 CVYL--KGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             EEEE--ECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             EEEE--ecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            4444  446667999999999999999976433 2   36789999999999999999985 4666788899988764

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=8.7e-07  Score=67.26  Aligned_cols=59  Identities=15%  Similarity=0.121  Sum_probs=49.2

Q ss_pred             HHHHHHHhcccCCeeEEEEec------CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          183 AERLREIFSEFGKVEDVVIKS------SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       183 ~~~L~~~fs~yG~V~~v~i~~------~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      .++|++.|++||.|.+|.|..      ....|++||+|.+.++|..|+..  +.-+.+.++.+.+..
T Consensus        28 ~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          28 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             HHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             HHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            356899999999999999842      23468999999999999999986  555678999999874

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.25  E-value=3e-08  Score=73.38  Aligned_cols=65  Identities=11%  Similarity=0.058  Sum_probs=53.7

Q ss_pred             cCCCCCHHHHHHHhcccCCeeEEEEec---------CCCcceEEEEecCHHHHHHHHH-hhcCCCCCCeEEEecC
Q 022800          177 FGEDYTAERLREIFSEFGKVEDVVIKS---------SKKKGSALVVMATKSAAGAATG-SVCGNLSNPLLVLPLQ  241 (292)
Q Consensus       177 ~~~~~t~~~L~~~fs~yG~V~~v~i~~---------~k~~g~A~V~F~~~~~A~~Av~-~~~g~~~~pl~v~~~~  241 (292)
                      .+.++|+++|+++|+.||.|..+.+..         .+.+|+|||+|.+.++|..|+. ++.-+.+.+|.|....
T Consensus         9 Lp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_           9 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             CCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBCTT
T ss_pred             CCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECCCC
Confidence            456799999999999999998776521         4579999999999999999985 4777788999997644

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=4.3e-06  Score=68.26  Aligned_cols=71  Identities=21%  Similarity=0.218  Sum_probs=54.1

Q ss_pred             eEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEe----cCCCcceEEEEecCHHHHHHHHHhhcC-CCCCCeEEEecC
Q 022800          169 VLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIK----SSKKKGSALVVMATKSAAGAATGSVCG-NLSNPLLVLPLQ  241 (292)
Q Consensus       169 ~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~----~~k~~g~A~V~F~~~~~A~~Av~~~~g-~~~~pl~v~~~~  241 (292)
                      +|=|  ...+..+|++.|+++|++||.|.+|.+.    ++..+|+|||+|.+.++|..|+....+ ....++.+.+..
T Consensus         8 ~lfV--~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           8 KLFI--GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             EEEE--ESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             EEEE--ECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhh
Confidence            4444  3355679999999999999999999874    256789999999999999999986332 334555565544

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.14  E-value=1.8e-06  Score=62.85  Aligned_cols=43  Identities=16%  Similarity=0.171  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHH
Q 022800          180 DYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATG  225 (292)
Q Consensus       180 ~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~  225 (292)
                      ..+++ +.+.|++||+|.++.+  .+.+|+|||+|.+.++|..|+.
T Consensus        15 ~~~~~-il~~F~~~G~I~~~~~--~~~~~~~fV~f~~~~~A~~Al~   57 (81)
T d1wwha1          15 ASASY-ILLQFAQYGNILKHVM--SNTGNWMHIRYQSKLQARKALS   57 (81)
T ss_dssp             GGHHH-HHHHHHTTSCEEEEEE--CSSSSEEEEEESSHHHHHHHHT
T ss_pred             HHHHH-HHHHHHhhhhhheEEe--cCCCCEEEEEEcccHHHHHHHh
Confidence            45544 5568999999999988  4568999999999999999996

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.24  E-value=0.1  Score=36.02  Aligned_cols=58  Identities=28%  Similarity=0.239  Sum_probs=45.3

Q ss_pred             HHHHHHhcccCCeeEEEEec-CCCcceEEEEecCHHHHHHHHHh--hcCCCCCCeEEEecC
Q 022800          184 ERLREIFSEFGKVEDVVIKS-SKKKGSALVVMATKSAAGAATGS--VCGNLSNPLLVLPLQ  241 (292)
Q Consensus       184 ~~L~~~fs~yG~V~~v~i~~-~k~~g~A~V~F~~~~~A~~Av~~--~~g~~~~pl~v~~~~  241 (292)
                      ..|.++|+++|+|.+|.+.. ..-.-.|.|...+..+|.-|+..  -....+.-+.|++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            45778999999999999942 44456899999999999999975  444455667777653

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.82  E-value=0.1  Score=37.86  Aligned_cols=68  Identities=15%  Similarity=0.210  Sum_probs=49.1

Q ss_pred             cceEEEEeee----cCCCCCHHH---HHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHh-hcCCCCCCeEEE
Q 022800          167 EKVLKVSWEK----FGEDYTAER---LREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGS-VCGNLSNPLLVL  238 (292)
Q Consensus       167 ~~~lkvKWk~----~~~~~t~~~---L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~-~~g~~~~pl~v~  238 (292)
                      +-+|.|.-..    .+..|+++.   |.+.|..||+|.-|.+.    .+..+|+|.+..+|.+|+.- .....+..|+|+
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv----~d~mwVTF~dG~SAL~al~l~g~~v~G~~l~It   90 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRIN----QGQMLVTFADSHSALSVLDVDGMKVKGRAVKIS   90 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEE----TTEEEEECSCSHHHHHHHHGGGSEETTEEEEEE
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEe----CCeEEEEECCcHHHHHHhccCCeEEcceEEEEe
Confidence            4577777665    233477755   66788999999999885    34899999999999999973 444444455554

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.24  E-value=0.72  Score=33.56  Aligned_cols=54  Identities=24%  Similarity=0.461  Sum_probs=41.1

Q ss_pred             cceEEEEeeecCCCCCHHHHHHHhcccCCeeEEEEecCCCcceEEEEecCHHHHHHHHHhh
Q 022800          167 EKVLKVSWEKFGEDYTAERLREIFSEFGKVEDVVIKSSKKKGSALVVMATKSAAGAATGSV  227 (292)
Q Consensus       167 ~~~lkvKWk~~~~~~t~~~L~~~fs~yG~V~~v~i~~~k~~g~A~V~F~~~~~A~~Av~~~  227 (292)
                      +...-+...   ..+...+|.+||+.||.|.--.| ++.   +|+|.-.+.+.|..++...
T Consensus        16 dHVf~~tFP---~~Wk~~dI~~lFSpfG~V~VswI-ddT---Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          16 DHVLHVTFP---KEWKTSDLYQLFSAFGNIQISWI-DDT---SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEEECC---TTCCHHHHHHHHTTTCSCCCEEE-ETT---EEEEECSCHHHHHHHHHHH
T ss_pred             ceeEEEeCC---cccchhHHHHHhcCCCceEEEEe-cCc---eEEEEecCHHHHHHHHHHh
Confidence            334444433   34888899999999999987777 332   8999999999999888653