Citrus Sinensis ID: 027432

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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---
Protein Sequence
MMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccEEEccccccHHHHHHHcccEEEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccEccccccccccccccccccccEccccHHccccccccccccccccccccccccccccccccccccccccccEEEEEHHHHHHHHHHcccccccHHHHHHcccEEEEEcccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEHHHccccccccccccccccccHHHHHcccc
Coil and Loop (DISEMBL)
mmnlpqavpapsrnmavpppasngptvvKSRMCNrlnsaegckfgdkchfahgewelgkpiaishddprafgavpgrmggryepppapgpaasfgasaTAKISVDASLAGaiigkggvnskQICRQtgaklsirdheadpnlrnielegSFEQIKQASAMVRELIVRIgpahaknpatagsaahplssnfktklcgnfakgsctfgdrchfahGAAELRKTAI
Flexible Loop (DISEMBL)
mmnlpqavpapsrnmavpppaSNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKpiaishddpRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIigkggvnskqICRQTGaklsirdheadpnlrnIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Low Complexity Region (SEG)
MMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEpppapgpaasfgasaTAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Disordered region (IsUnstruct)
********************************CNRLNSAEGCKFGDKCHFAHGEWELGKPIAISH************************************ISVDASLAGAIIGKGGVNSKQICRQTGAKL*******************FEQIKQASAMVRELIVRIGP******************NFKTKLCGNFAKGSCTFGDRCHFAHGA********
Disordered Region (DISOPRED)
************************************************************************************************SATAKISVDASLAGAIIGKGGVNSKQICRQTGAK**I********LRNIELEGSFEQIKQASAMVRELIVRIGPAHAKN**************FKTKLCGNFAKGSCTFGDRCHFAHGAA*L*****
Disordered Region (DISEMBL)
MMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHA**********HPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Disordered Region (DISPRO)
**************************VVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI**********************PA********ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP******************NFKTKLCGNFAKGSCTFGDRCHFAHG*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
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	223	2.2.26 [Sep-21-2011]
Q69XQ3	295	Zinc finger CCCH domain-c	yes	no	0.928	0.701	0.630	3e-68
Q7F8R0	300	Zinc finger CCCH domain-c	no	no	0.991	0.736	0.613	4e-65
Q7XPK1	309	Zinc finger CCCH domain-c	no	no	0.869	0.627	0.623	9e-61
Q9FG30	240	Zinc finger CCCH domain-c	yes	no	0.847	0.787	0.543	3e-51
Q9C7C3	248	Zinc finger CCCH domain-c	no	no	0.856	0.770	0.537	5e-51
Q9LT81	386	Zinc finger CCCH domain-c	no	no	0.843	0.487	0.267	2e-08
Q84UQ3	367	Zinc finger CCCH domain-c	no	no	0.147	0.089	0.588	8e-05
Q9LQM3	384	Zinc finger CCCH domain-c	no	no	0.147	0.085	0.558	0.0004
Q5PP65	252	Zinc finger CCCH domain-c	no	no	0.264	0.234	0.376	0.0004
Q96I24	572	Far upstream element-bind	yes	no	0.318	0.124	0.337	0.0007

>sp|Q69XQ3|C3H44_ORYSJ Zinc finger CCCH domain-containing protein 44 OS=Oryza sativa subsp. japonica GN=Os06g0618100 PE=2 SV=1

 Score =  258 bits (658), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 140/222 (63%), Positives = 163/222 (73%), Gaps = 15/222 (6%)

Query: 7   AVPAPSRNMAVPPPASNGP--TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAIS 64
           AV AP   M + P A NGP  + VK+RMCN+ N+AEGCK+G KCHFAHGE ELGKP+ + 
Sbjct: 76  AVAAPPGRMPLGPGAPNGPPTSSVKTRMCNKYNTAEGCKWGSKCHFAHGERELGKPMLLD 135

Query: 65  HDDPRAFGAVPGRMGGRYEPPPAPGP----AASFGASATAKISVDASLAGAIIGKGGVNS 120
           +  P   G++P      +E PP PGP     ++FGASATAKISVDASLAG IIGKGG N+
Sbjct: 136 NSMPHPMGSMP------FEAPPMPGPDIVPPSTFGASATAKISVDASLAGGIIGKGGTNT 189

Query: 121 KQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI--GPAHAKNPAT 178
           K I R TGAKL+IRD+E++PNL+NIELEG+F+QIK ASAMV ELIVRI      AKNP  
Sbjct: 190 KHISRMTGAKLAIRDNESNPNLKNIELEGTFDQIKHASAMVTELIVRISGNAPPAKNPGR 249

Query: 179 AGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK 220
              A  P  SNFKTKLC NF KGSCTFGDRCHFAHG +ELRK
Sbjct: 250 GSHAGGP-GSNFKTKLCENFNKGSCTFGDRCHFAHGESELRK 290

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q7F8R0|C3H14_ORYSJ Zinc finger CCCH domain-containing protein 14 OS=Oryza sativa subsp. japonica GN=Os02g0194200 PE=2 SV=1

 Score =  247 bits (631), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 141/230 (61%), Positives = 158/230 (68%), Gaps = 9/230 (3%)

Query: 1   MMNL--PQAVPAPSRNMAVPPPASNGPTV--VKSRMCNRLNSAEGCKFGDKCHFAHGEWE 56
           M NL  P   P P R M +     +GP    VK+R+CN+ N+AEGCK+GDKCHFAHGE E
Sbjct: 70  MTNLGGPAIAPPPGR-MPMGNAVPDGPPTPTVKTRLCNKYNTAEGCKWGDKCHFAHGERE 128

Query: 57  LGKPIAISHDDPRAFGAVP-GRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGK 115
           LGKP+ +    P   G  P G       P PA    ASFGASATAKISVDASLAG IIG+
Sbjct: 129 LGKPMLMDSSMPPPMGPRPTGHFAPPPMPSPAMSTPASFGASATAKISVDASLAGGIIGR 188

Query: 116 GGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG---PAH 172
           GGVN+KQI R TGAKL+IRDHE+D NL+NIELEG+F+QIK ASAMVRELIV IG   P  
Sbjct: 189 GGVNTKQISRVTGAKLAIRDHESDTNLKNIELEGTFDQIKNASAMVRELIVSIGGGAPPQ 248

Query: 173 AKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTA 222
            K P           SNFKTKLC NF KGSCTFGDRCHFAHG  ELRK+A
Sbjct: 249 GKKPVGGSHRGGGPGSNFKTKLCENFTKGSCTFGDRCHFAHGENELRKSA 298

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q7XPK1|C3H31_ORYSJ Zinc finger CCCH domain-containing protein 31 OS=Oryza sativa subsp. japonica GN=Os04g0665700 PE=2 SV=1

 Score =  233 bits (594), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 136/218 (62%), Positives = 152/218 (69%), Gaps = 24/218 (11%)

Query: 20  PASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMG 79
           PAS+G    K+RMC + N+AEGCKFGDKCHFAHGE ELGKP  +SH+      A+   MG
Sbjct: 100 PASSG----KTRMCTKYNTAEGCKFGDKCHFAHGERELGKPAYMSHES-----AMAPPMG 150

Query: 80  GRYEPPPAPGPAA-------SFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLS 132
           GRY   P P P A       +FGASATAKISVDASLAG IIGKGGVN+KQICR TG KLS
Sbjct: 151 GRYGGRPEPPPPAAMGPPAGNFGASATAKISVDASLAGGIIGKGGVNTKQICRVTGVKLS 210

Query: 133 IRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA--------HAKNPATAGSAAH 184
           IRDHE+D NL+NIELEG+F+QIKQAS MV ELI  I P+         A   A AG    
Sbjct: 211 IRDHESDSNLKNIELEGNFDQIKQASNMVGELIATISPSTPAKKPAGSAAGAAPAGRGGP 270

Query: 185 PLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTA 222
              SN+KTKLC NF KG+CTFGDRCHFAHG  E RK A
Sbjct: 271 GGRSNYKTKLCENFVKGTCTFGDRCHFAHGENEQRKGA 308

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9FG30|C3H52_ARATH Zinc finger CCCH domain-containing protein 52 OS=Arabidopsis thaliana GN=At5g06770 PE=2 SV=1

 Score =  201 bits (511), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 113/208 (54%), Positives = 139/208 (66%), Gaps = 19/208 (9%)

Query: 29  KSRMCNRLNSAEGCKFGDKCHFAH---GEWE-------LGKPIAISHDDPRAFGAVPGRM 78
           KS+ C +  S  GC FGD CHF H   G +        L  P++    + +  G   GR 
Sbjct: 38  KSKPCTKFFSTSGCPFGDNCHFLHYVPGGYNAAAQMTNLRPPVSQVSRNMQGSGGPGGRF 97

Query: 79  GGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA 138
            GR +P    GP + FGAS T+KISVDASLAGAIIGKGG++SKQICR+TGAKLSI+DHE 
Sbjct: 98  SGRGDP--GSGPVSIFGAS-TSKISVDASLAGAIIGKGGIHSKQICRETGAKLSIKDHER 154

Query: 139 DPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA---HPLSSNFKTKLC 195
           DPNL+ IELEG+FEQI  AS MVRELI R+G    K P   G      HP  SN+KTK+C
Sbjct: 155 DPNLKIIELEGTFEQINVASGMVRELIGRLGS--VKKPQGIGGPEGKPHP-GSNYKTKIC 211

Query: 196 GNFAKGSCTFGDRCHFAHGAAELRKTAI 223
             ++KG+CT+GDRCHFAHG +ELR++ I
Sbjct: 212 DRYSKGNCTYGDRCHFAHGESELRRSGI 239

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C7C3|C3H36_ARATH Zinc finger CCCH domain-containing protein 36 OS=Arabidopsis thaliana GN=At3g12130 PE=2 SV=1

 Score =  201 bits (510), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 115/214 (53%), Positives = 137/214 (64%), Gaps = 23/214 (10%)

Query: 29  KSRMCNRLNSAEGCKFGDKCHFAH---GEWE-------LGKPIAISHDDPRAFGAVPGRM 78
           KS+ C +  S  GC FG+ CHF H   G +        +G PI     + +  G   GR 
Sbjct: 38  KSKPCTKFFSTSGCPFGENCHFLHYVPGGYNAVSQMTNMGPPIPQVSRNMQGSGN-GGRF 96

Query: 79  GGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA 138
            GR E    PG  ++FG SATA+ SVDASLAGAIIGKGGV+SKQICRQTG KLSI+DHE 
Sbjct: 97  SGRGES--GPGHVSNFGDSATARFSVDASLAGAIIGKGGVSSKQICRQTGVKLSIQDHER 154

Query: 139 DPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA---------HPLSSN 189
           DPNL+NI LEG+ EQI +ASAMV++LI R+  A  K P                HP  SN
Sbjct: 155 DPNLKNIVLEGTLEQISEASAMVKDLIGRLNSAAKKPPGGGLGGGGGMGSEGKPHP-GSN 213

Query: 190 FKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
           FKTK+C  F+KG+CTFGDRCHFAHG AELRK+ I
Sbjct: 214 FKTKICERFSKGNCTFGDRCHFAHGEAELRKSGI 247

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LT81|C3H39_ARATH Zinc finger CCCH domain-containing protein 39 OS=Arabidopsis thaliana GN=At3g19360 PE=2 SV=1

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 89/228 (39%), Gaps = 40/228 (17%)

Query: 18  PPPASNGPTVV--KSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVP 75
           PPP + G   +  K+RMC +   A  C+ G+ C+FAHG  +L +P       P  +  + 
Sbjct: 93  PPPVNKGTANIFYKTRMCAKF-RAGTCRNGELCNFAHGIEDLRQP-------PSNWQEIV 144

Query: 76  GRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135
           G       PPPA             +     SLA  +      + K I R    +     
Sbjct: 145 G-------PPPAGQDRER--ERERERERERPSLAPVVNNNWEDDQKIILRMKLCRKFCFG 195

Query: 136 HEADPNLRNIELEGSFEQIKQASAMVREL-IVRIGPAHAKNPATA----------GSAAH 184
            E     R   +     + ++ S  +RE  ++ +G   A  P+            GS   
Sbjct: 196 EECPYGDRCNFIHEDLSKFREDSGKLRESSVISVGATAADQPSDTASNLIEVNRQGSIPV 255

Query: 185 PLSSN---------FKTKLCGNF-AKGSCTFGDRCHFAHGAAELRKTA 222
           P   N         +KT+LC  F   G C FGD+CHFAHG AEL  + 
Sbjct: 256 PAPMNNGGVVKTVYWKTRLCMKFDITGQCPFGDKCHFAHGQAELHNSV 303

Arabidopsis thaliana (taxid: 3702)

>sp|Q84UQ3|C3H56_ORYSJ Zinc finger CCCH domain-containing protein 56 OS=Oryza sativa subsp. japonica GN=Os08g0159800 PE=2 SV=1

 Score = 47.4 bits (111), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/34 (58%), Positives = 25/34 (73%), Gaps = 1/34 (2%)

Query: 188 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK 220
           SN+KT++C  +   G C FG +CHFAHGAAEL K
Sbjct: 244 SNWKTRICNKWEMTGYCPFGSKCHFAHGAAELHK 277

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9LQM3|C3H12_ARATH Zinc finger CCCH domain-containing protein 12 OS=Arabidopsis thaliana GN=At1g32360 PE=2 SV=1

 Score = 45.1 bits (105), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 25/34 (73%), Gaps = 1/34 (2%)

Query: 188 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK 220
           SN+KT++C  +   G C FG +CHFAHGAAEL +
Sbjct: 259 SNWKTRICNKWEITGYCPFGAKCHFAHGAAELHR 292

Arabidopsis thaliana (taxid: 3702)

>sp|Q5PP65|C3H28_ARATH Zinc finger CCCH domain-containing protein 28 OS=Arabidopsis thaliana GN=At2g35430 PE=2 SV=1

 Score = 45.1 bits (105), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 152 EQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSS-NFKTKLCGNF-AKGSCTFGDRC 209
           E + +AS       V +GP         G+ A  L S N+KT++C  +   G C FG  C
Sbjct: 113 ETVTEASRNRESFAVSLGPR--------GNVAQTLKSPNWKTRICNKWQTTGYCPFGSHC 164

Query: 210 HFAHGAAEL 218
           HFAHG +EL
Sbjct: 165 HFAHGPSEL 173

Arabidopsis thaliana (taxid: 3702)

>sp|Q96I24|FUBP3_HUMAN Far upstream element-binding protein 3 OS=Homo sapiens GN=FUBP3 PE=1 SV=2

 Score = 44.3 bits (103), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 95  GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSF 151
           G       +V A   G +IGKGG N K I +Q+GA + ++ +    +DPNLR   + G  
Sbjct: 352 GGVQEITYTVPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPNSDPNLRRFTIRGVP 411

Query: 152 EQIKQASAMVRELI 165
           +QI+ A  ++ E +
Sbjct: 412 QQIEVARQLIDEKV 425

May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
225441425	297	PREDICTED: zinc finger CCCH domain-conta	0.995	0.747	0.736	6e-89
255585533	295	conserved hypothetical protein [Ricinus	0.991	0.749	0.745	5e-88
255585535	295	conserved hypothetical protein [Ricinus	0.991	0.749	0.745	6e-86
449457299	305	PREDICTED: zinc finger CCCH domain-conta	0.986	0.721	0.686	5e-83
449437587	296	PREDICTED: zinc finger CCCH domain-conta	0.986	0.743	0.729	8e-83
449526573	271	PREDICTED: zinc finger CCCH domain-conta	0.986	0.811	0.729	1e-82
363807948	295	uncharacterized protein LOC100803981 [Gl	0.986	0.745	0.706	2e-80
356504859	295	PREDICTED: zinc finger CCCH domain-conta	0.982	0.742	0.698	5e-78
356504857	295	PREDICTED: zinc finger CCCH domain-conta	0.982	0.742	0.694	8e-78
255634442	295	unknown [Glycine max]	0.982	0.742	0.689	2e-77

>gi|225441425|ref|XP_002279071.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like isoform 1 [Vitis vinifera]

 Score =  332 bits (851), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 168/228 (73%), Positives = 188/228 (82%), Gaps = 6/228 (2%)

Query: 1   MMNLPQAVPAPSRNMA-VPPPASNGPTV--VKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           M N    +P  SRNMA  PPP  NG ++  VKS+MCN+ N+AEGCKFGDKCHFAHGEWEL
Sbjct: 71  MTNQAPILPPASRNMAGPPPPVPNGSSMPAVKSKMCNKFNTAEGCKFGDKCHFAHGEWEL 130

Query: 58  GKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGG 117
           GKP+A  HDDPRA G++PGR+ GR EP P  GPAASFGASATAKISVDASLAGAIIGKGG
Sbjct: 131 GKPLAPYHDDPRAMGSIPGRLAGRIEPSPT-GPAASFGASATAKISVDASLAGAIIGKGG 189

Query: 118 VNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG--PAHAKN 175
           VNSKQICRQTGAKLSIR+H++DPNLRNIELEG+FEQIK+ASAMVRELIV I   P HA+ 
Sbjct: 190 VNSKQICRQTGAKLSIREHDSDPNLRNIELEGTFEQIKEASAMVRELIVNISAMPGHART 249

Query: 176 PATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
            A  G    P +SN+KTKLC NF KGSCTFG+RCHFAHGA ELRK+AI
Sbjct: 250 TAMPGGGQAPPASNYKTKLCDNFTKGSCTFGERCHFAHGAGELRKSAI 297

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585533|ref|XP_002533457.1| conserved hypothetical protein [Ricinus communis] gi|223526690|gb|EEF28926.1| conserved hypothetical protein [Ricinus communis]

 Score =  329 bits (843), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 170/228 (74%), Positives = 183/228 (80%), Gaps = 7/228 (3%)

Query: 1   MMNLPQAVPAPSRNMAVPPPA---SNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           MMNL  AV +  RNM  P PA    + P+ VKSRMCN+ N+ EGCKFGDKC+FAHGEWEL
Sbjct: 70  MMNLGPAVTSVPRNMPAPSPAIPNGSAPSAVKSRMCNKYNTVEGCKFGDKCNFAHGEWEL 129

Query: 58  GKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGG 117
           GK +A SHDDPRAFG   GRMGGR EPPP PGPAASFGASATAKISV+ASLAGAIIGKGG
Sbjct: 130 GKSMAPSHDDPRAFGTFAGRMGGRMEPPP-PGPAASFGASATAKISVEASLAGAIIGKGG 188

Query: 118 VNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPA 177
           VNSKQICRQTGAKLSIR+HE DPNLRNIE EGSFEQIKQASAMV ELI  I   +A   A
Sbjct: 189 VNSKQICRQTGAKLSIREHETDPNLRNIEFEGSFEQIKQASAMVSELIASISSVNASAKA 248

Query: 178 T--AGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
           T   G   HP  SNFKTKLC NF+KGSCTFG RCHFAHGAAELRK+ +
Sbjct: 249 TGLTGGHGHP-GSNFKTKLCENFSKGSCTFGQRCHFAHGAAELRKSGV 295

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585535|ref|XP_002533458.1| conserved hypothetical protein [Ricinus communis] gi|223526691|gb|EEF28927.1| conserved hypothetical protein [Ricinus communis]

 Score =  322 bits (826), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 170/228 (74%), Positives = 186/228 (81%), Gaps = 7/228 (3%)

Query: 1   MMNLPQAVPAPSRNMAVPPPA---SNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           MMNL  AV +  RNM  P PA    + P+ VKSR+CN+ N+AEGCKFGDKC+FAHGEWEL
Sbjct: 70  MMNLGPAVTSIPRNMPAPSPAIPNGSAPSAVKSRLCNKYNTAEGCKFGDKCNFAHGEWEL 129

Query: 58  GKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGG 117
           GKP+  SHDDPRAFG +PGRMGGR EPPP PG AASFGASATAKISV+ASLAGAIIGKGG
Sbjct: 130 GKPVVPSHDDPRAFGTIPGRMGGRMEPPP-PGSAASFGASATAKISVEASLAGAIIGKGG 188

Query: 118 VNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPA 177
           VNSKQICRQTGAKLSIR+HE DPN+RNIE EGSFEQIKQASAMV ELI  I  A+A   A
Sbjct: 189 VNSKQICRQTGAKLSIREHETDPNVRNIEFEGSFEQIKQASAMVSELIASISSANASAKA 248

Query: 178 TA--GSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
           T   G   HP  SNFKTKLC NF+KGSCTFG RCHFAHGAAELRK+ +
Sbjct: 249 TGLIGGHGHP-GSNFKTKLCENFSKGSCTFGQRCHFAHGAAELRKSGV 295

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457299|ref|XP_004146386.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Cucumis sativus] gi|449480828|ref|XP_004156007.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Cucumis sativus]

 Score =  313 bits (801), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 164/239 (68%), Positives = 186/239 (77%), Gaps = 19/239 (7%)

Query: 1   MMNLPQAVPAPSRNMAVPPPASNG----PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWE 56
           MMNL      PSRN+A PP  +NG    P+ VK+RMCN+ N+AEGCKFGDKC+FAHGEWE
Sbjct: 70  MMNLAPVGAQPSRNIAAPPSVTNGGPSAPSQVKTRMCNKYNTAEGCKFGDKCNFAHGEWE 129

Query: 57  LGKPIAISHDDPRAFGA---------VPGRMGGRYEPPPAPGPAASFGASATAKISVDAS 107
           LG+P   SHD+PRA G          + GRMGGR + PP PGPAASFGASATAKIS+DAS
Sbjct: 130 LGRPNPPSHDNPRAMGGGGGGGGGVHMVGRMGGRMDLPP-PGPAASFGASATAKISIDAS 188

Query: 108 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 167
           LAGAIIGKGG+NSKQICRQTGAKLSIRDHE+DPNLRNIELEG+FEQI +ASAMVRELI+ 
Sbjct: 189 LAGAIIGKGGINSKQICRQTGAKLSIRDHESDPNLRNIELEGTFEQINEASAMVRELIIT 248

Query: 168 I---GPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
           +   GP  A      G A  P  SN+KTKLC NFAKGSCTFG+RCHFAHGAAELRK+ +
Sbjct: 249 VSMAGPGKASGGMGGGPA--PTGSNYKTKLCDNFAKGSCTFGERCHFAHGAAELRKSGV 305

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437587|ref|XP_004136573.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Cucumis sativus]

 Score =  312 bits (799), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 167/229 (72%), Positives = 185/229 (80%), Gaps = 9/229 (3%)

Query: 1   MMNLPQAVPAPSRNM-AVPPPASNGPTV--VKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           MMNLP A PAP RNM A PPP SNG     VKSRMCN+ NSAEGCKFGDKCHFAH EWEL
Sbjct: 71  MMNLPPAPPAP-RNMGAPPPPMSNGSATQAVKSRMCNKYNSAEGCKFGDKCHFAHAEWEL 129

Query: 58  GKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGG 117
           GKP A SHDDPR+ G +P R+  R +  P PG AASFGAS+TAKISVDASLAGAIIGKGG
Sbjct: 130 GKPSAPSHDDPRSMGHIPNRLASRMDAGP-PGLAASFGASSTAKISVDASLAGAIIGKGG 188

Query: 118 VNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI---GPAHAK 174
           +NSKQICR+TGAKLSIRDHE+DPNLRNIELEGSF+QIK+ASAMV+ELIV +   GP  + 
Sbjct: 189 INSKQICRRTGAKLSIRDHESDPNLRNIELEGSFDQIKEASAMVQELIVTVSMAGPPKSA 248

Query: 175 NPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
                G  A P  +NFKTKLC NFAKGSCTFG+RCHFAHGAAELRK+ +
Sbjct: 249 T-GATGGTAGPAGNNFKTKLCDNFAKGSCTFGERCHFAHGAAELRKSGV 296

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449526573|ref|XP_004170288.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Cucumis sativus]

 Score =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 167/229 (72%), Positives = 185/229 (80%), Gaps = 9/229 (3%)

Query: 1   MMNLPQAVPAPSRNM-AVPPPASNGPTV--VKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           MMNLP A PAP RNM A PPP SNG     VKSRMCN+ NSAEGCKFGDKCHFAH EWEL
Sbjct: 46  MMNLPPAPPAP-RNMGAPPPPMSNGSATQAVKSRMCNKYNSAEGCKFGDKCHFAHAEWEL 104

Query: 58  GKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGG 117
           GKP A SHDDPR+ G +P R+  R +  P PG AASFGAS+TAKISVDASLAGAIIGKGG
Sbjct: 105 GKPSAPSHDDPRSMGHIPNRLASRMDAGP-PGLAASFGASSTAKISVDASLAGAIIGKGG 163

Query: 118 VNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI---GPAHAK 174
           +NSKQICR+TGAKLSIRDHE+DPNLRNIELEGSF+QIK+ASAMV+ELIV +   GP  + 
Sbjct: 164 INSKQICRRTGAKLSIRDHESDPNLRNIELEGSFDQIKEASAMVQELIVTVSMAGPPKSA 223

Query: 175 NPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
                G  A P  +NFKTKLC NFAKGSCTFG+RCHFAHGAAELRK+ +
Sbjct: 224 T-GATGGTAGPAGNNFKTKLCDNFAKGSCTFGERCHFAHGAAELRKSGV 271

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807948|ref|NP_001242454.1| uncharacterized protein LOC100803981 [Glycine max] gi|255636900|gb|ACU18783.1| unknown [Glycine max]

 Score =  304 bits (778), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 161/228 (70%), Positives = 179/228 (78%), Gaps = 8/228 (3%)

Query: 1   MMNLPQAVPAPSRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELG 58
           MMNL  A P  SRN+A PPP  NG  P  VK+R+CN+ N+AEGCKFGDKCHFAHGEWELG
Sbjct: 71  MMNLTPAAPPASRNVAAPPPVPNGSAPPAVKTRICNKFNTAEGCKFGDKCHFAHGEWELG 130

Query: 59  KPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGG 117
           K IA S DD R  G    GR+ GR EPPP  GPAASFGA+ATAKISV+ASLAGAIIGKGG
Sbjct: 131 KHIAPSFDDHRTMGPTGVGRLAGRMEPPP--GPAASFGANATAKISVEASLAGAIIGKGG 188

Query: 118 VNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPA 177
           VNSKQICRQTGAKLSIR+HE+DPNLRNIELEGSF QIK+AS MV++L++ +    A    
Sbjct: 189 VNSKQICRQTGAKLSIREHESDPNLRNIELEGSFVQIKEASNMVKDLLLTL-QMSAPPKT 247

Query: 178 TAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
           T G    P S  SNFKTKLC NF KGSCTFGDRCHFAHGAAELRK+ +
Sbjct: 248 TPGVPGAPASHGSNFKTKLCENFTKGSCTFGDRCHFAHGAAELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504859|ref|XP_003521212.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]

 Score =  296 bits (757), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 160/229 (69%), Positives = 181/229 (79%), Gaps = 10/229 (4%)

Query: 1   MMNL-PQAVPAPSRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           MMNL P A P PSRN+A  P   NG  P+ VK+R+CN+ N+AEGCKFGDKCHFAHGEWEL
Sbjct: 71  MMNLTPAAPPPPSRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDKCHFAHGEWEL 130

Query: 58  GKPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKG 116
           GK IA S DD  A G    GR+ GR EPP   GPAASFGA++TAKISV+ASLAGAIIGKG
Sbjct: 131 GKHIAPSFDDHHAMGPPGAGRLAGRMEPP---GPAASFGANSTAKISVEASLAGAIIGKG 187

Query: 117 GVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNP 176
           GVNSKQICRQTGAKLSIR+HE+DPNLRNIELEGSFEQIK+AS MV++L++ +    A   
Sbjct: 188 GVNSKQICRQTGAKLSIREHESDPNLRNIELEGSFEQIKEASNMVKDLLLTL-QMSAPPK 246

Query: 177 ATAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
            T G    P S  SNFKTKLC NFAKGSCTFGDRCHFAHGA+ELRK+ +
Sbjct: 247 TTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504857|ref|XP_003521211.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]

 Score =  295 bits (756), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 159/229 (69%), Positives = 181/229 (79%), Gaps = 10/229 (4%)

Query: 1   MMNLPQAVPAP-SRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           MMNL  A P P +RN+A  P   NG  P+ VK+R+CN+ N+AEGCKFGDKCHFAHGEWEL
Sbjct: 71  MMNLTPAAPLPPTRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDKCHFAHGEWEL 130

Query: 58  GKPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKG 116
           GK IA S DD RA G    GR+ GR EPP   GPAASFGA++TAKISV+ASLAGAIIGKG
Sbjct: 131 GKHIAPSFDDHRAMGPPGAGRLAGRMEPP---GPAASFGANSTAKISVEASLAGAIIGKG 187

Query: 117 GVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNP 176
           GVNSKQICRQTGAKLSIR+HE+DPNLRNIELEGSFEQIK+AS MV++L++ +    A   
Sbjct: 188 GVNSKQICRQTGAKLSIREHESDPNLRNIELEGSFEQIKEASNMVKDLLLTL-QMSAPPK 246

Query: 177 ATAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
            T G    P S  SNFKTKLC NFAKGSCTFGDRCHFAHGA+ELRK+ +
Sbjct: 247 TTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255634442|gb|ACU17586.1| unknown [Glycine max]

 Score =  294 bits (752), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 158/229 (68%), Positives = 180/229 (78%), Gaps = 10/229 (4%)

Query: 1   MMNLPQAVPAP-SRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
           MMNL  A P P +RN+A  P   NG  P+ VK+R+CN+ N+AEGCKFGDKCHFAHGEWEL
Sbjct: 71  MMNLTPAAPLPPTRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDKCHFAHGEWEL 130

Query: 58  GKPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKG 116
           GK IA S DD RA G    GR+ GR EPP   GPAASFGA++TAKISV+ASLAGAIIGKG
Sbjct: 131 GKHIAPSFDDHRAMGPPGAGRLAGRMEPP---GPAASFGANSTAKISVEASLAGAIIGKG 187

Query: 117 GVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNP 176
           GVNSKQICRQTGAKLSIR+HE+DPN RNIELEGSFEQIK+AS MV++L++ +    A   
Sbjct: 188 GVNSKQICRQTGAKLSIREHESDPNFRNIELEGSFEQIKEASNMVKDLLLTL-QMSAPPK 246

Query: 177 ATAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
            T G    P S  SNFKTKLC NFAKGSCTFGDRCHFAHGA+ELRK+ +
Sbjct: 247 TTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
TAIR|locus:2170169	240	AT5G06770 [Arabidopsis thalian	0.847	0.787	0.509	2.3e-46
TAIR|locus:2099292	248	AT3G12130 [Arabidopsis thalian	0.856	0.770	0.518	6.2e-46
TAIR|locus:2090669	386	AT3G19360 [Arabidopsis thalian	0.197	0.113	0.458	0.00039
TAIR|locus:2028306	384	AT1G32360 [Arabidopsis thalian	0.188	0.109	0.5	2.5e-08
UNIPROTKB|G3V2D5	176	ZFP36L1 "Zinc finger protein 3	0.147	0.187	0.558	0.00049
TAIR|locus:2062476	252	AT2G35430 [Arabidopsis thalian	0.264	0.234	0.376	4.4e-07
UNIPROTKB|G3V2P5	207	ZFP36L1 "Zinc finger protein 3	0.147	0.159	0.558	0.00093
UNIPROTKB|Q6S9E0	325	ZFP36 "Tristetraprolin" [Ovis	0.228	0.156	0.415	0.00038
UNIPROTKB|P26651	326	ZFP36 "Tristetraprolin" [Homo	0.251	0.171	0.413	5.5e-05
RGD|620722	320	Zfp36 "zinc finger protein 36"	0.251	0.175	0.413	0.00016

TAIR|locus:2170169 AT5G06770 [Arabidopsis thaliana (taxid:3702)]

 Score = 486 (176.1 bits), Expect = 2.3e-46, P = 2.3e-46
 Identities = 106/208 (50%), Positives = 131/208 (62%)

Query:    29 KSRMCNRLNSAEGCKFGDKCHFAH---GEWE-------LGKPIAISHDDPRAFGAVPGRM 78
             KS+ C +  S  GC FGD CHF H   G +        L  P++    + +  G   GR 
Sbjct:    38 KSKPCTKFFSTSGCPFGDNCHFLHYVPGGYNAAAQMTNLRPPVSQVSRNMQGSGGPGGRF 97

Query:    79 GGRYEXXXXXXXXXXXXXXXTAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA 138
              GR +               T+KISVDASLAGAIIGKGG++SKQICR+TGAKLSI+DHE 
Sbjct:    98 SGRGDPGSGPVSIFGAS---TSKISVDASLAGAIIGKGGIHSKQICRETGAKLSIKDHER 154

Query:   139 DPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA---HPLSSNFKTKLC 195
             DPNL+ IELEG+FEQI  AS MVRELI R+G    K P   G      HP  SN+KTK+C
Sbjct:   155 DPNLKIIELEGTFEQINVASGMVRELIGRLGSV--KKPQGIGGPEGKPHP-GSNYKTKIC 211

Query:   196 GNFAKGSCTFGDRCHFAHGAAELRKTAI 223
               ++KG+CT+GDRCHFAHG +ELR++ I
Sbjct:   212 DRYSKGNCTYGDRCHFAHGESELRRSGI 239

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

TAIR|locus:2099292 AT3G12130 [Arabidopsis thaliana (taxid:3702)]

 Score = 482 (174.7 bits), Expect = 6.2e-46, P = 6.2e-46
 Identities = 111/214 (51%), Positives = 131/214 (61%)

Query:    29 KSRMCNRLNSAEGCKFGDKCHFAH---GEWE-------LGKPIAISHDDPRAFGAVPGRM 78
             KS+ C +  S  GC FG+ CHF H   G +        +G PI     + +  G   GR 
Sbjct:    38 KSKPCTKFFSTSGCPFGENCHFLHYVPGGYNAVSQMTNMGPPIPQVSRNMQGSGN-GGRF 96

Query:    79 GGRYEXXXXXXXXXXXXXXXTAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA 138
              GR E               TA+ SVDASLAGAIIGKGGV+SKQICRQTG KLSI+DHE 
Sbjct:    97 SGRGESGPGHVSNFGDSA--TARFSVDASLAGAIIGKGGVSSKQICRQTGVKLSIQDHER 154

Query:   139 DPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATA-------GSAA--HPLSSN 189
             DPNL+NI LEG+ EQI +ASAMV++LI R+  A  K P          GS    HP  SN
Sbjct:   155 DPNLKNIVLEGTLEQISEASAMVKDLIGRLNSAAKKPPGGGLGGGGGMGSEGKPHP-GSN 213

Query:   190 FKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 223
             FKTK+C  F+KG+CTFGDRCHFAHG AELRK+ I
Sbjct:   214 FKTKICERFSKGNCTFGDRCHFAHGEAELRKSGI 247

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

TAIR|locus:2090669 AT3G19360 [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 0.00039, P = 0.00039
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query:    14 NMAVPPPASNGPTVV----KSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
             ++ VP P +NG  V     K+R+C + +    C FGDKCHFAHG+ EL
Sbjct:   252 SIPVPAPMNNGGVVKTVYWKTRLCMKFDITGQCPFGDKCHFAHGQAEL 299

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2028306 AT1G32360 [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 2.5e-08, Sum P(2) = 2.5e-08
 Identities = 22/44 (50%), Positives = 29/44 (65%)

Query:   179 AGSAAHPLS-SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK 220
             +GS    L  SN+KT++C  +   G C FG +CHFAHGAAEL +
Sbjct:   249 SGSGIQILKPSNWKTRICNKWEITGYCPFGAKCHFAHGAAELHR 292

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS

UNIPROTKB|G3V2D5 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]

 Score = 104 (41.7 bits), Expect = 0.00049, P = 0.00049
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query:   187 SSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELR 219
             SS +KT+LC  F + G+C +GD+C FAHG  ELR
Sbjct:    90 SSRYKTELCRPFEENGACKYGDKCQFAHGIHELR 123

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0033077 "T cell differentiation in thymus" evidence=IEA

TAIR|locus:2062476 AT2G35430 [Arabidopsis thaliana (taxid:3702)]

 Score = 107 (42.7 bits), Expect = 4.4e-07, Sum P(2) = 4.4e-07
 Identities = 26/69 (37%), Positives = 35/69 (50%)

Query:   152 EQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSS-NFKTKLCGNF-AKGSCTFGDRC 209
             E + +AS       V +GP         G+ A  L S N+KT++C  +   G C FG  C
Sbjct:   113 ETVTEASRNRESFAVSLGPR--------GNVAQTLKSPNWKTRICNKWQTTGYCPFGSHC 164

Query:   210 HFAHGAAEL 218
             HFAHG +EL
Sbjct:   165 HFAHGPSEL 173

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS

UNIPROTKB|G3V2P5 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]

 Score = 104 (41.7 bits), Expect = 0.00093, P = 0.00093
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query:   187 SSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELR 219
             SS +KT+LC  F + G+C +GD+C FAHG  ELR
Sbjct:   118 SSRYKTELCRPFEENGACKYGDKCQFAHGIHELR 151

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q6S9E0 ZFP36 "Tristetraprolin" [Ovis aries (taxid:9940)]

 Score = 111 (44.1 bits), Expect = 0.00038, P = 0.00038
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query:   170 PAHAKNPATAGSAAHPL-SSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 220
             P+   +P+     A P  SS +KT+LC  F++ G C +G +C FAHG  ELR+
Sbjct:    81 PSSELSPSPTSPTATPTTSSRYKTELCRTFSESGRCRYGAKCQFAHGLGELRQ 133

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0010494 "cytoplasmic stress granule" evidence=ISS

GO:0017091 "AU-rich element binding" evidence=ISS

GO:0032680 "regulation of tumor necrosis factor production" evidence=ISS

GO:0060213 "positive regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=ISS

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=ISS

GO:0071889 "14-3-3 protein binding" evidence=ISS

UNIPROTKB|P26651 ZFP36 "Tristetraprolin" [Homo sapiens (taxid:9606)]

 Score = 118 (46.6 bits), Expect = 5.5e-05, P = 5.5e-05
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query:   164 LIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 220
             L  R+GP  + +P T+ +A     S +KT+LC  F++ G C +G +C FAHG  ELR+
Sbjct:    79 LAPRLGPELSPSP-TSPTATSTTPSRYKTELCRTFSESGRCRYGAKCQFAHGLGELRQ 135

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0035925 "mRNA 3'-UTR AU-rich region binding" evidence=IEA

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA

GO:0050728 "negative regulation of inflammatory response" evidence=IEA

GO:0050779 "RNA destabilization" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IMP;IDA

GO:0006402 "mRNA catabolic process" evidence=IDA

GO:0060213 "positive regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0019957 "C-C chemokine binding" evidence=IPI

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0019901 "protein kinase binding" evidence=IPI

GO:0006950 "response to stress" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0071889 "14-3-3 protein binding" evidence=IDA

GO:0032680 "regulation of tumor necrosis factor production" evidence=IDA

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=IDA

GO:1900153 "positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=ISS

GO:0035278 "negative regulation of translation involved in gene silencing by miRNA" evidence=ISS

GO:0003727 "single-stranded RNA binding" evidence=TAS

GO:0003729 "mRNA binding" evidence=IDA

GO:0005829 "cytosol" evidence=IDA;TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

RGD|620722 Zfp36 "zinc finger protein 36" [Rattus norvegicus (taxid:10116)]

 Score = 114 (45.2 bits), Expect = 0.00016, P = 0.00016
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query:   164 LIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 220
             L  R GP  + +P T+ +A    SS +KT+LC  +++ G C +G +C FAHG  ELR+
Sbjct:    72 LAPRPGPELSPSP-TSPTATPTTSSRYKTELCRTYSESGRCRYGAKCQFAHGPGELRQ 128

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=ISO

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA;ISO

GO:0003677 "DNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA;ISO;ISS;IDA

GO:0005737 "cytoplasm" evidence=ISO;ISS;IDA

GO:0005829 "cytosol" evidence=IEA;ISO

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0006402 "mRNA catabolic process" evidence=ISO;ISS

GO:0006950 "response to stress" evidence=IEA;ISO;ISS

GO:0007243 "intracellular protein kinase cascade" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA;ISO;ISS

GO:0017091 "AU-rich element binding" evidence=ISO;ISS

GO:0019901 "protein kinase binding" evidence=IEA;ISO

GO:0019957 "C-C chemokine binding" evidence=IEA;ISO

GO:0032680 "regulation of tumor necrosis factor production" evidence=IEA;ISO;ISS

GO:0035925 "mRNA 3'-UTR AU-rich region binding" evidence=IEA;ISO

GO:0043488 "regulation of mRNA stability" evidence=ISO

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA;ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=TAS

GO:0050728 "negative regulation of inflammatory response" evidence=IEA;ISO

GO:0050779 "RNA destabilization" evidence=IEA;ISO

GO:0060213 "positive regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA;ISO;ISS

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=IEA;ISO;ISS

GO:0071889 "14-3-3 protein binding" evidence=IEA;ISO;ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q69XQ3	C3H44_ORYSJ	No assigned EC number	0.6306	0.9282	0.7016	yes	no
Q9FG30	C3H52_ARATH	No assigned EC number	0.5432	0.8475	0.7875	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00160401 hypothetical protein (286 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	223
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-15
pfam00013	59	pfam00013, KH_1, KH domain	1e-12
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-12
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-09
pfam13014	42	pfam13014, KH_3, KH domain	2e-08
smart00356	27	smart00356, ZnF_C3H1, zinc finger	2e-07
pfam00642	27	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H t	4e-07
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	5e-06
PRK13764	602	PRK13764, PRK13764, ATPase; Provisional	2e-04
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	3e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	9e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.001
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.003
pfam00642	27	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H t	0.004

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

 Score = 66.8 bits (164), Expect = 4e-15
 Identities = 23/63 (36%), Positives = 38/63 (60%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++ V +SL G IIGKGG   K+I  +TGAK+ I D  +    R + + G+ E +++A 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 159 AMV 161
            ++
Sbjct: 61  ELI 63

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

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

 Score = 59.9 bits (146), Expect = 1e-12
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T +I +     G IIGKGG N K+I  +TG K+ I D   D     + + G+ EQ+++A 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDT----VTISGTPEQVEKAK 56

Query: 159 AMV 161
            ++
Sbjct: 57  ELI 59

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

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

 Score = 60.0 bits (146), Expect = 2e-12
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 96  ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 155
              T ++ + A   G IIGKGG   K+I  +TG K+ I         R +E+ G  E ++
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP--GSEERVVEITGPPENVE 58

Query: 156 QASAMVRELI 165
           +A+ ++ E++
Sbjct: 59  KAAELILEIL 68

Length = 68

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

 Score = 50.9 bits (123), Expect = 4e-09
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQA 157
           T ++ V +S AG+IIGKGG   K+I  +TGAK+ +          R + + G    +++A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

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

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

 Score = 48.7 bits (117), Expect = 2e-08
 Identities = 19/42 (45%), Positives = 24/42 (57%)

Query: 108 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG 149
           L GAIIGKGG   K+I  +TGAK+ I   E     R + + G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

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

>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 189 NFKTKLCGNFAKGSCTFGDRCHFAHG 214
            +KT+LC  F +G C  GDRC FAH 
Sbjct: 1   KYKTELCKFFKRGYCPRGDRCKFAHP 26

Length = 27

>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar)

 Score = 44.5 bits (106), Expect = 4e-07
 Identities = 15/26 (57%), Positives = 21/26 (80%), Gaps = 1/26 (3%)

Query: 190 FKTKLCGNFAK-GSCTFGDRCHFAHG 214
           +KT+LC  F++ G+C +GDRC FAHG
Sbjct: 1   YKTELCRFFSRTGTCKYGDRCKFAHG 26

Length = 27

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

 Score = 42.5 bits (101), Expect = 5e-06
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++ +   L   IIGK G N ++I  +TG K+   D  +  +   I + G  E +++A 
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSD--TITITGPKENVEKAK 58

Query: 159 AMVR 162
             + 
Sbjct: 59  EEIL 62

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

>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional

 Score = 41.4 bits (98), Expect = 2e-04
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-GSFEQIKQA 157
            A + V       +IGKGG   K+I ++ G  + +R  + +P     E E  + E+ K  
Sbjct: 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVTVEETK-- 539

Query: 158 SAMVRELIVRIGPAHAKNPAT 178
               + +I+ +GP +A     
Sbjct: 540 ----KHVILIVGPDYAGKTVD 556

Length = 602

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

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 11/34 (32%), Positives = 17/34 (50%)

Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135
           + +       +IG GG   K+I  +TG K+ I D
Sbjct: 6   MKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED 39

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

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

 Score = 39.6 bits (94), Expect = 9e-04
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135
           I +       +IG GG   ++I  +TGAK+ I D
Sbjct: 558 IKIPPDKIRDVIGPGGKTIREITEETGAKIDIED 591

Length = 693

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

 Score = 39.0 bits (92), Expect = 0.001
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135
            I ++      +IG GG   ++I  +TGAK+ I D
Sbjct: 554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIED 588

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

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

 Score = 37.6 bits (88), Expect = 0.003
 Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135
           T KI  D      +IG GG   K I  +TG K+ I D
Sbjct: 555 TIKIDPD--KIRDVIGPGGKTIKAITEETGVKIDIED 589

Length = 692

>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar)

 Score = 33.3 bits (77), Expect = 0.004
 Identities = 9/13 (69%), Positives = 12/13 (92%)

Query: 42 CKFGDKCHFAHGE 54
          CK+GD+C FAHG+
Sbjct: 15 CKYGDRCKFAHGQ 27

Length = 27

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	223
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	99.58
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.52
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.37
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.35
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.32
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.31
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.29
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.27
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.2
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	99.13
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.05
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.05
KOG1676	600	consensus K-homology type RNA binding proteins [RN	98.98
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.98
smart00322	69	KH K homology RNA-binding domain.	98.96
PF13014	43	KH_3: KH domain	98.9
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.83
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.82
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.68
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.61
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.58
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	98.56
PRK13763	180	putative RNA-processing protein; Provisional	98.54
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	98.51
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.48
smart00356	27	ZnF_C3H1 zinc finger.	98.4
smart00356	27	ZnF_C3H1 zinc finger.	98.38
PRK13763	180	putative RNA-processing protein; Provisional	98.33
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	98.33
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	98.29
KOG1595	528	consensus CCCH-type Zn-finger protein [General fun	98.25
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	98.22
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.98
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.77
KOG1595	528	consensus CCCH-type Zn-finger protein [General fun	97.63
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.47
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.38
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.27
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.25
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	97.18
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.81
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.69
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.62
KOG2185	486	consensus Predicted RNA-processing protein, contai	96.62
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.47
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	96.3
KOG1040	325	consensus Polyadenylation factor I complex, subuni	96.29
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	96.22
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	96.17
KOG2333	614	consensus Uncharacterized conserved protein [Gener	96.16
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	96.07
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	96.04
KOG2185	486	consensus Predicted RNA-processing protein, contai	95.76
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.55
PRK12704	520	phosphodiesterase; Provisional	95.4
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.4
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	95.36
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	95.31
PRK00106	535	hypothetical protein; Provisional	95.17
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.04
KOG2113	394	consensus Predicted RNA binding protein, contains	94.96
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	94.92
COG5152	259	Uncharacterized conserved protein, contains RING a	94.9
PRK00468	75	hypothetical protein; Provisional	94.84
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	94.77
PRK02821	77	hypothetical protein; Provisional	94.68
PRK08406	140	transcription elongation factor NusA-like protein;	94.57
COG5152	259	Uncharacterized conserved protein, contains RING a	93.83
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.79
PRK01064	78	hypothetical protein; Provisional	93.71
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	93.67
KOG1763	343	consensus Uncharacterized conserved protein, conta	93.56
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	92.97
COG1094	194	Predicted RNA-binding protein (contains KH domains	92.95
KOG1040	325	consensus Polyadenylation factor I complex, subuni	92.95
PRK12705	508	hypothetical protein; Provisional	92.71
PRK08406	140	transcription elongation factor NusA-like protein;	91.4
KOG1763	343	consensus Uncharacterized conserved protein, conta	91.16
KOG1492	377	consensus C3H1-type Zn-finger protein [General fun	90.92
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	90.79
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	90.59
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	90.54
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	90.44
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	90.22
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	89.87
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	89.77
COG5084	285	YTH1 Cleavage and polyadenylation specificity fact	89.62
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	88.75
COG0195	190	NusA Transcription elongation factor [Transcriptio	87.65
PRK13764	602	ATPase; Provisional	87.55
PRK06418	166	transcription elongation factor NusA-like protein;	87.51
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	86.8
COG1855	604	ATPase (PilT family) [General function prediction	86.01
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	85.8
TIGR01953	341	NusA transcription termination factor NusA. This m	85.03
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	85.01
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	84.68
PRK12328	374	nusA transcription elongation factor NusA; Provisi	83.62
KOG2874	356	consensus rRNA processing protein [Translation, ri	80.84
PRK09202	470	nusA transcription elongation factor NusA; Validat	80.18

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=99.58  E-value=8.4e-16  Score=138.44  Aligned_cols=40  Identities=33%  Similarity=0.711  Sum_probs=37.3

Q ss_pred             CCCCCCCccccccCcccccccCCCC-CCCCCCcccccccCC
Q 027432           20 PASNGPTVVKSRMCNRLNSAEGCKF-GDKCHFAHGEWELGK   59 (223)
Q Consensus        20 ~~~~~~~~~kt~~C~~~~~~g~C~~-g~~C~faH~~~el~~   59 (223)
                      ....++..|||.||..|...|.|.| |++|+|||+.+||+.
T Consensus       122 ~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~  162 (332)
T KOG1677|consen  122 RGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRL  162 (332)
T ss_pred             ccccCcccccCCcceeeecCccccccCchhhhcCCcccccc
Confidence            4567788999999999999999999 999999999999996

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.52  E-value=2.4e-14  Score=100.21  Aligned_cols=64  Identities=31%  Similarity=0.483  Sum_probs=58.7

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCC-CCCceEEEEcCCHHHHHHHHHHHH
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA-DPNLRNIELEGSFEQIKQASAMVR  162 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~-~~~~r~v~I~G~~~~i~~A~~lI~  162 (223)
                      +++++||.+.+|.|||++|.+|++|+++|||+|++.+... +..+|.|+|.|+++++++|..+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            4789999999999999999999999999999999976554 678899999999999999999873

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

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

Probab=99.37  E-value=1.3e-11  Score=107.61  Aligned_cols=74  Identities=31%  Similarity=0.523  Sum_probs=69.9

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      |..+|..+.||.++-|.||||||++|++|++++||.|.|.+...+..+|+++|+|+.+||+.|+.|+++.+++.
T Consensus       312 GPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  312 GPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             CceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence            55788999999999999999999999999999999999999888899999999999999999999999998754

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

Probab=99.35  E-value=1.5e-12  Score=123.28  Aligned_cols=78  Identities=33%  Similarity=0.517  Sum_probs=71.6

Q ss_pred             CCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEe-ccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCC
Q 027432           94 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  171 (223)
Q Consensus        94 ~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I-~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~  171 (223)
                      .+.+.+.+|.||.+.||+||||+|++||+|+.+||++|++ .|.++.+.||++.|.|+.++|+.|.+||.++|++.+.+
T Consensus       226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~  304 (600)
T KOG1676|consen  226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG  304 (600)
T ss_pred             ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence            4556799999999999999999999999999999999999 46666888999999999999999999999999987765

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.32  E-value=3.2e-12  Score=88.16  Aligned_cols=62  Identities=27%  Similarity=0.440  Sum_probs=56.2

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHH
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVR  162 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~  162 (223)
                      +.++.||.+++|.|||++|++|++|++++|++|++.+..  ..++.|+|+|+.+++..|+.+|.
T Consensus         1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence            367999999999999999999999999999999997654  56789999999999999999873

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.31  E-value=1.4e-12  Score=89.36  Aligned_cols=60  Identities=43%  Similarity=0.635  Sum_probs=55.2

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHH
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV  161 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI  161 (223)
                      |.++.||.+.+|.|||++|++|++|+++||++|++.+.  + ....|+|+|+.++++.|+.+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence            67899999999999999999999999999999999766  3 455999999999999999986

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

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

Probab=99.29  E-value=8.5e-12  Score=85.82  Aligned_cols=64  Identities=36%  Similarity=0.580  Sum_probs=58.5

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHH
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVR  162 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~  162 (223)
                      +.++.||.+.++.|||++|++|++|+++||++|.|.+...+..++.|+|.|+.+++..|..+|.
T Consensus         1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence            3689999999999999999999999999999999987665678899999999999999998873

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

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

Probab=99.27  E-value=8.6e-12  Score=86.45  Aligned_cols=58  Identities=26%  Similarity=0.416  Sum_probs=53.2

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCC-HHHHHHHHHHHH
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMVR  162 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~-~~~i~~A~~lI~  162 (223)
                      +..+.||.+++|.|||++|++|++|+++||++|.|.+      ++.|+|+|+ .++++.|+.+|.
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999976      357999998 999999999873

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

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

Probab=99.20  E-value=3.1e-11  Score=107.64  Aligned_cols=74  Identities=32%  Similarity=0.351  Sum_probs=66.0

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-C--CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-H--EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~--~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..+++|+||++.+|.||||||.+||.|++++|++|+|+. .  .....+|+|+++|+++++.+|..+|.++|.+.+.
T Consensus       131 ~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq  207 (402)
T KOG2191|consen  131 IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ  207 (402)
T ss_pred             cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence            356899999999999999999999999999999999973 2  3445689999999999999999999999987654

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]

Probab=99.13  E-value=2.3e-11  Score=107.38  Aligned_cols=33  Identities=39%  Similarity=0.818  Sum_probs=30.2

Q ss_pred             CcccccccCcccc-CCcCCCCCCCccccCccccC
Q 027432          187 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELR  219 (223)
Q Consensus       187 ~~~~kt~~C~~~~-~g~C~~g~~C~faH~~~elr  219 (223)
                      ..+|||+.|.+|. .|.|+||-+|.|+||.+++-
T Consensus       269 ~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~i  302 (351)
T COG5063         269 KQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDI  302 (351)
T ss_pred             ccccccCCccchhhcccCccccccccccCChhhc
Confidence            3789999999999 79999999999999998864

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

Probab=99.05  E-value=3.7e-10  Score=100.88  Aligned_cols=74  Identities=23%  Similarity=0.362  Sum_probs=67.1

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC---CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..-++|+||+..+|.||||||++|.+++.++||+|+++++   -++..||++.|.|+-+.+....++|.++|++...
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~  114 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ  114 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence            3678999999999999999999999999999999999643   3677899999999999999999999999987553

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

Probab=99.05  E-value=3.2e-10  Score=107.37  Aligned_cols=73  Identities=27%  Similarity=0.447  Sum_probs=67.8

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEec-cCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR-DHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~-~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+.+++||.+.+|.||||+|+.||+|++.|||+|+|. +..+...+|.|+|.|.+++|.+|...|..+|.+..
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~  210 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP  210 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence            45799999999999999999999999999999999994 55788889999999999999999999999998853

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

Probab=98.98  E-value=6.9e-10  Score=105.41  Aligned_cols=74  Identities=27%  Similarity=0.453  Sum_probs=65.1

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEe-ccCCCC-CCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEAD-PNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I-~~~~~~-~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+|.+|.||++++|+||||+|++||++++++|+++.+ .|.... ..++.+.|+|++++|+.|+.||.++|.+..
T Consensus       137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~  212 (600)
T KOG1676|consen  137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREED  212 (600)
T ss_pred             cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcc
Confidence            35789999999999999999999999999999999888 444433 367999999999999999999999999633

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.98  E-value=9.3e-11  Score=68.50  Aligned_cols=27  Identities=48%  Similarity=1.062  Sum_probs=22.7

Q ss_pred             cccccCcccccccCCCCCCCCCCcccc
Q 027432           28 VKSRMCNRLNSAEGCKFGDKCHFAHGE   54 (223)
Q Consensus        28 ~kt~~C~~~~~~g~C~~g~~C~faH~~   54 (223)
                      |||++|++|..+|.|+||++|+|+|++
T Consensus         1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~   27 (27)
T PF00642_consen    1 YKTKLCRFFMRTGTCPFGDKCRFAHGE   27 (27)
T ss_dssp             TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred             CccccChhhccCCccCCCCCcCccCCC
Confidence            799999999999999999999999974

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....

>smart00322 KH K homology RNA-binding domain

Probab=98.96  E-value=3.2e-09  Score=72.42  Aligned_cols=66  Identities=32%  Similarity=0.562  Sum_probs=59.1

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI  165 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i  165 (223)
                      .+.++.||...+|.|||++|.+|++|++.+|++|.+.....  ....|+|.|+.++++.|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            46889999999999999999999999999999999964432  5688999999999999999998765

>PF13014 KH_3: KH domain

Probab=98.90  E-value=1.8e-09  Score=69.48  Aligned_cols=42  Identities=43%  Similarity=0.692  Sum_probs=37.8

Q ss_pred             cccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcC
Q 027432          108 LAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEG  149 (223)
Q Consensus       108 ~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G  149 (223)
                      .+|+|||++|++|++|+++|||+|+|.+ ..++..++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            4789999999999999999999999976 56677889999987

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

Probab=98.83  E-value=6.9e-09  Score=95.39  Aligned_cols=76  Identities=26%  Similarity=0.272  Sum_probs=68.9

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC-CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCC
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  171 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~-~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~  171 (223)
                      ...++++.||...||+|||+.|.+||+|.+.+||.|+|... -++..+|.|+|+|++++.-+|+..|..+|.+...+
T Consensus       409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~  485 (584)
T KOG2193|consen  409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFF  485 (584)
T ss_pred             chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccC
Confidence            36778999999999999999999999999999999999543 46678999999999999999999999999987754

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.82  E-value=5.8e-10  Score=65.13  Aligned_cols=26  Identities=62%  Similarity=1.364  Sum_probs=21.2

Q ss_pred             cccccCcccc-CCcCCCCCCCccccCc
Q 027432          190 FKTKLCGNFA-KGSCTFGDRCHFAHGA  215 (223)
Q Consensus       190 ~kt~~C~~~~-~g~C~~g~~C~faH~~  215 (223)
                      |||++|++|. .|.|++|++|+|+|+.
T Consensus         1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~   27 (27)
T PF00642_consen    1 YKTKLCRFFMRTGTCPFGDKCRFAHGE   27 (27)
T ss_dssp             TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred             CccccChhhccCCccCCCCCcCccCCC
Confidence            7999999999 5999999999999974

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....

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

Probab=98.68  E-value=1.8e-08  Score=92.69  Aligned_cols=70  Identities=27%  Similarity=0.427  Sum_probs=64.5

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEe-ccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I-~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      -.++++||...+|+||||.|.+||+|..+|-++|.+ .....+..|++++|.|++|+..+|..+|+++|..
T Consensus       199 ~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqk  269 (584)
T KOG2193|consen  199 WPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQK  269 (584)
T ss_pred             cceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999 4556678899999999999999999999999964

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

Probab=98.61  E-value=8.7e-08  Score=75.15  Aligned_cols=70  Identities=26%  Similarity=0.374  Sum_probs=54.4

Q ss_pred             EEEEecc------ccccceecCCCcchhhhhhhcCCeEEeccCCCC-----------------CCceEEEEcC-C--HHH
Q 027432          100 AKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD-----------------PNLRNIELEG-S--FEQ  153 (223)
Q Consensus       100 ~~i~VP~------~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~-----------------~~~r~v~I~G-~--~~~  153 (223)
                      .+|+||.      +++|.|||.+|.+||+|+++|||+|.|....+.                 ...--|.|++ +  .++
T Consensus         2 ~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~   81 (120)
T cd02395           2 EKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEA   81 (120)
T ss_pred             CEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHH
Confidence            3555554      678999999999999999999999999654111                 0114677877 4  699


Q ss_pred             HHHHHHHHHhhhhhcC
Q 027432          154 IKQASAMVRELIVRIG  169 (223)
Q Consensus       154 i~~A~~lI~~~i~~~~  169 (223)
                      +++|..+|.+++....
T Consensus        82 ~~~A~~~I~~ll~~~~   97 (120)
T cd02395          82 LAKAVEAIEELLKPAI   97 (120)
T ss_pred             HHHHHHHHHHHhccCC
Confidence            9999999999998544

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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.58  E-value=5.5e-08  Score=80.65  Aligned_cols=63  Identities=24%  Similarity=0.415  Sum_probs=55.3

Q ss_pred             EEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEE---cCCHHHHHHHHHHHHhhhhhcC
Q 027432          102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIEL---EGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus       102 i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I---~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      +.||.+.+|.|||+||++|+.|+++||++|+|.+.     +..|.|   +++++++++|+.+|.++...++
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~   67 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS   67 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC
Confidence            57999999999999999999999999999999753     246777   7899999999999999877433

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

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=98.56  E-value=6.4e-08  Score=87.24  Aligned_cols=34  Identities=47%  Similarity=1.094  Sum_probs=32.0

Q ss_pred             CcccccccCcccc-CCcCCC-CCCCccccCccccCc
Q 027432          187 SSNFKTKLCGNFA-KGSCTF-GDRCHFAHGAAELRK  220 (223)
Q Consensus       187 ~~~~kt~~C~~~~-~g~C~~-g~~C~faH~~~elr~  220 (223)
                      +..|||.+|++|. .|.|+| |++|+|||+.+|||-
T Consensus       127 p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~  162 (332)
T KOG1677|consen  127 PERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRL  162 (332)
T ss_pred             cccccCCcceeeecCccccccCchhhhcCCcccccc
Confidence            5789999999999 799999 999999999999994

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.54  E-value=1.2e-07  Score=79.16  Aligned_cols=65  Identities=23%  Similarity=0.321  Sum_probs=57.8

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEc----CCHHHHHHHHHHHHhhhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE----GSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~----G~~~~i~~A~~lI~~~i~~  167 (223)
                      ....+.||.+.+|.|||++|++|+.|++++|++|+|.+.     +..|.|.    ++++++++|+.+|.+++..
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g   71 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRG   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence            356899999999999999999999999999999999753     2567784    8999999999999998874

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]

Probab=98.51  E-value=1.9e-07  Score=82.83  Aligned_cols=44  Identities=23%  Similarity=0.295  Sum_probs=36.6

Q ss_pred             CCCCCC-CccccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432           20 PASNGP-TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI   63 (223)
Q Consensus        20 ~~~~~~-~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~   63 (223)
                      ++..++ ..|||.+|..-..-+.|.|+++|.|||...+++-.-.+
T Consensus       104 ~~a~~p~g~~kt~~l~ss~~~~~~~~p~~n~fahs~~issl~~~~  148 (351)
T COG5063         104 SNANKPYGLYKTEMLRSSTEIPYCRYPDKNPFAHSKAISSLAQTH  148 (351)
T ss_pred             CCccCccccccchhhhccccccccccCCCCcCCCccccccccccC
Confidence            555566 89999999988778999999999999998888764444

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.48  E-value=1.6e-07  Score=77.81  Aligned_cols=55  Identities=29%  Similarity=0.469  Sum_probs=50.6

Q ss_pred             ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432          107 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus       107 ~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      ..+|.|||++|++++.|++.||++|+|.+       +.|.|.|++++++.|+.+|.+++...
T Consensus        98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665        98 RIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             HHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence            47899999999999999999999999974       67999999999999999999999654

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

>smart00356 ZnF_C3H1 zinc finger

Probab=98.40  E-value=1.6e-07  Score=54.09  Aligned_cols=27  Identities=52%  Similarity=1.177  Sum_probs=24.5

Q ss_pred             ccccccCccccCCcCCCCCCCccccCc
Q 027432          189 NFKTKLCGNFAKGSCTFGDRCHFAHGA  215 (223)
Q Consensus       189 ~~kt~~C~~~~~g~C~~g~~C~faH~~  215 (223)
                      .+|+.+|++|+.|.|.+|++|+|+|..
T Consensus         1 ~~k~~~C~~~~~g~C~~g~~C~~~H~~   27 (27)
T smart00356        1 KYKTELCKFFKRGYCPYGDRCKFAHPL   27 (27)
T ss_pred             CCCCCcCcCccCCCCCCCCCcCCCCcC
Confidence            368999999999999999999999963

>smart00356 ZnF_C3H1 zinc finger

Probab=98.38  E-value=2e-07  Score=53.68  Aligned_cols=26  Identities=35%  Similarity=0.856  Sum_probs=23.7

Q ss_pred             ccccccCcccccccCCCCCCCCCCccc
Q 027432           27 VVKSRMCNRLNSAEGCKFGDKCHFAHG   53 (223)
Q Consensus        27 ~~kt~~C~~~~~~g~C~~g~~C~faH~   53 (223)
                      .+|+.+|++| ..|.|++|++|+|+|.
T Consensus         1 ~~k~~~C~~~-~~g~C~~g~~C~~~H~   26 (27)
T smart00356        1 KYKTELCKFF-KRGYCPYGDRCKFAHP   26 (27)
T ss_pred             CCCCCcCcCc-cCCCCCCCCCcCCCCc
Confidence            4789999999 7799999999999995

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.33  E-value=6.6e-07  Score=74.73  Aligned_cols=56  Identities=29%  Similarity=0.457  Sum_probs=50.2

Q ss_pred             ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432          107 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus       107 ~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+|+|||++|++++.|++.||++|+|.+       +.|.|.|++++++.|..+|.+++....
T Consensus       104 r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~I~~li~g~~  159 (180)
T PRK13763        104 RIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIAREAIEMLIEGAP  159 (180)
T ss_pred             HHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence            46899999999999999999999999964       349999999999999999999996543

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

Probab=98.33  E-value=4.2e-07  Score=79.71  Aligned_cols=72  Identities=22%  Similarity=0.341  Sum_probs=65.3

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .++++|..+++|.|||++|+.||++++.+.|+++|.. -.+.+.+|+|.|.|.+..|-.+.+.|.+.|.+.+.
T Consensus       124 e~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pi  196 (390)
T KOG2192|consen  124 ELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPI  196 (390)
T ss_pred             hhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCc
Confidence            3689999999999999999999999999999999964 46778899999999999999999999999987664

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

Probab=98.29  E-value=3e-06  Score=80.60  Aligned_cols=70  Identities=23%  Similarity=0.285  Sum_probs=65.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC---------CHHHHHHHHHHHHhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG---------SFEQIKQASAMVRELIV  166 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G---------~~~~i~~A~~lI~~~i~  166 (223)
                      ..+.|++++...+|.||||.|..||+|+.++.++|.|.+...+..+|+|+|+|         ..+++.+|..+|...+.
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~  120 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE  120 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc
Confidence            34489999999999999999999999999999999999889999999999999         99999999999998766

>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=98.25  E-value=4.5e-07  Score=85.65  Aligned_cols=31  Identities=32%  Similarity=0.733  Sum_probs=28.4

Q ss_pred             CcccccccCccccCCcCCCCCCCccccCccccCc
Q 027432          187 SSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       187 ~~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      +..|||++|++-  |.|+. --|-|||..+|||.
T Consensus       266 Pa~YRT~~CkDg--~~C~R-rvCfFAH~~eqLR~  296 (528)
T KOG1595|consen  266 PARYRTRKCKDG--GYCPR-RVCFFAHSPEQLRP  296 (528)
T ss_pred             HHHhccccccCC--CCCcc-ceEeeecChHHhcc
Confidence            469999999997  89999 78999999999985

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

Probab=98.22  E-value=2.6e-06  Score=79.03  Aligned_cols=93  Identities=19%  Similarity=0.182  Sum_probs=71.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHH
Q 027432           74 VPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQ  153 (223)
Q Consensus        74 ~~~r~~g~~~~~~~~~~~~s~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~  153 (223)
                      ..+|..+|.-...++-+++..+..-..-+.|-+++||.|||+||++||.||..++++|+|.+-+.   +..|+|.|.-.-
T Consensus        23 ~v~rg~~w~g~~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~---e~kv~ifg~~~m   99 (629)
T KOG0336|consen   23 RVNRGNYWAGHRDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDL---EVKVTIFGINHM   99 (629)
T ss_pred             ecCCCCCccCCCCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCc---eeEEEEechHHH
Confidence            34555555544444444444555667788899999999999999999999999999999965433   577999999998


Q ss_pred             HHHHHHHHHhhhhhcC
Q 027432          154 IKQASAMVRELIVRIG  169 (223)
Q Consensus       154 i~~A~~lI~~~i~~~~  169 (223)
                      -.+|...|...+...+
T Consensus       100 ~~kaka~id~~~~k~e  115 (629)
T KOG0336|consen  100 RKKAKASIDRGQDKDE  115 (629)
T ss_pred             HHHHHhhHhhhhhhhh
Confidence            8899999988876443

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.98  E-value=1.5e-05  Score=78.73  Aligned_cols=65  Identities=23%  Similarity=0.306  Sum_probs=58.9

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~  167 (223)
                      ....++.||.+++|.|||.||.+||.|+++||++|.|.+      +..|.|.+ +.+++++|+.+|..++..
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            456789999999999999999999999999999999976      36788877 699999999999999984

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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.77  E-value=3.4e-05  Score=76.38  Aligned_cols=68  Identities=22%  Similarity=0.343  Sum_probs=58.1

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ....++.||.+++|.|||+||++||.|.++||++|.|.+      +..|.|.+ +.+.+++|..+|..+......
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~  618 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITAEPEV  618 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhccccc
Confidence            456789999999999999999999999999999999976      25566655 689999999999999775443

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

>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=97.63  E-value=4.5e-05  Score=72.38  Aligned_cols=31  Identities=42%  Similarity=0.905  Sum_probs=26.8

Q ss_pred             cccccccCccccCCcCCCCCCCccccCcccc
Q 027432          188 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAEL  218 (223)
Q Consensus       188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~~el  218 (223)
                      -.|.-..|-.|.+|.|..||.|.||||.-|-
T Consensus       232 yhYs~tpCPefrkG~C~rGD~CEyaHgvfEc  262 (528)
T KOG1595|consen  232 YHYSSTPCPEFRKGSCERGDSCEYAHGVFEC  262 (528)
T ss_pred             ccccCccCcccccCCCCCCCccccccceehh
Confidence            4566678999999999999999999998763

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

Probab=97.47  E-value=0.00024  Score=67.03  Aligned_cols=74  Identities=30%  Similarity=0.426  Sum_probs=56.6

Q ss_pred             cceEEEEecc------ccccceecCCCcchhhhhhhcCCeEEeccC---------CC------CCCc-eEEEEcC-CHHH
Q 027432           97 SATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDH---------EA------DPNL-RNIELEG-SFEQ  153 (223)
Q Consensus        97 ~~t~~i~VP~------~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---------~~------~~~~-r~v~I~G-~~~~  153 (223)
                      ..+.+|.||.      ++||+|||-.|.++|+|.++|||+|.|+-.         ..      ...+ =-+.|++ +.|.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            5667888884      789999999999999999999999999531         00      0011 2244555 6999


Q ss_pred             HHHHHHHHHhhhhhcCC
Q 027432          154 IKQASAMVRELIVRIGP  170 (223)
Q Consensus       154 i~~A~~lI~~~i~~~~~  170 (223)
                      |++|.++|..+|.+...
T Consensus       217 i~~Ai~vienli~~av~  233 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSAVS  233 (554)
T ss_pred             HHHHHHHHHHHHHhhcc
Confidence            99999999999987443

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.38  E-value=0.00018  Score=72.76  Aligned_cols=68  Identities=19%  Similarity=0.355  Sum_probs=59.2

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCe-EEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAK-LSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~-I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ....++.||.++++.|||.||.+||.|.+++|++ |.|.+      +..|.|.+ +.+.+++|+.+|.++..+...
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~~~~v  753 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTMVPTV  753 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhcCcCC
Confidence            4567899999999999999999999999999999 88876      35677877 799999999999999875443

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

Probab=97.27  E-value=0.0005  Score=57.94  Aligned_cols=56  Identities=30%  Similarity=0.475  Sum_probs=50.5

Q ss_pred             cccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432          108 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       108 ~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..|.|||++|.+-+.|.+-||+.|.|..       ..|.|.|.+++++.|+..|..++.....
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr~AVemli~G~~h  167 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAREAVEMLINGAPH  167 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence            4699999999999999999999999964       4699999999999999999999986553

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

Probab=97.25  E-value=0.00045  Score=67.62  Aligned_cols=69  Identities=25%  Similarity=0.379  Sum_probs=61.0

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCC-HHHHHHHHHHHHhhhhhcCCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMVRELIVRIGPA  171 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~-~~~i~~A~~lI~~~i~~~~~~  171 (223)
                      ....++.|+.+++.-+||+||.+|++|.+++|++|+|.+      +..|.|.++ .+.++.|+..|.++.++++.+
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~e~evg  620 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITREVEVG  620 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence            456788999999999999999999999999999999974      345888775 699999999999999988875

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]

Probab=97.18  E-value=0.00016  Score=65.02  Aligned_cols=28  Identities=25%  Similarity=0.609  Sum_probs=23.8

Q ss_pred             cccCccccCCcCCCCCCCccccCccccCc
Q 027432          192 TKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       192 t~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      --.|.++.+|.|.... |+|+|.-.+|+.
T Consensus        71 v~aC~Ds~kgrCsR~n-CkylHpp~hlkd   98 (331)
T KOG2494|consen   71 VIACFDSQKGRCSREN-CKYLHPPQHLKD   98 (331)
T ss_pred             EEEEeccccCccCccc-ceecCCChhhhh
Confidence            3469999999999875 999999888764

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

Probab=96.81  E-value=0.0014  Score=45.22  Aligned_cols=36  Identities=33%  Similarity=0.528  Sum_probs=33.4

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEe
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI  133 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I  133 (223)
                      ....+.|+.+..|..|||+|.||+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            678899999999999999999999999999988765

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.69  E-value=0.0016  Score=64.86  Aligned_cols=67  Identities=21%  Similarity=0.327  Sum_probs=56.8

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ....+.|+.+.++.+||.||.+||+|.+++|++|.|.+      +..|.|.+ +.+.+++|..+|..+..+...
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~~~~v  621 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITAEPEV  621 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhcccCcC
Confidence            44677889999999999999999999999999988854      35577777 689999999999999876444

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

Probab=96.62  E-value=0.0028  Score=54.06  Aligned_cols=76  Identities=21%  Similarity=0.196  Sum_probs=51.6

Q ss_pred             CCcceEEEEec------cccccceecCCCcchhhhhhhcCCeEEeccCCCC-----CCc------------eEEEEcCCH
Q 027432           95 GASATAKISVD------ASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD-----PNL------------RNIELEGSF  151 (223)
Q Consensus        95 g~~~t~~i~VP------~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~-----~~~------------r~v~I~G~~  151 (223)
                      +...+.+++||      .+.||+|||..|.++|++++.|+|+|.|.-.-..     ..+            ....+....
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adse  224 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSE  224 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchh
Confidence            45677889988      4789999999999999999999999999532110     001            111222334


Q ss_pred             HHHHHHHHHHHhhhhhcCC
Q 027432          152 EQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       152 ~~i~~A~~lI~~~i~~~~~  170 (223)
                      +.+..+...+++.|.+...
T Consensus       225 dki~~~ik~~~n~I~~a~~  243 (269)
T COG5176         225 DKICRLIKSQLNAIREARR  243 (269)
T ss_pred             hhHHHHHHHHHHHHHHHhc
Confidence            5666677777777766544

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]

Probab=96.62  E-value=0.00072  Score=62.50  Aligned_cols=30  Identities=43%  Similarity=1.015  Sum_probs=25.1

Q ss_pred             ccccCccccCCcCCCCCCCccccCc----cccCc
Q 027432          191 KTKLCGNFAKGSCTFGDRCHFAHGA----AELRK  220 (223)
Q Consensus       191 kt~~C~~~~~g~C~~g~~C~faH~~----~elr~  220 (223)
                      -.++|.+|+.|.|.|+++|||.||.    ++||+
T Consensus       139 sMkpC~ffLeg~CRF~enCRfSHG~~V~lsslr~  172 (486)
T KOG2185|consen  139 SMKPCKFFLEGRCRFGENCRFSHGLDVPLSSLRN  172 (486)
T ss_pred             hhccchHhhccccccCcccccccCcccchhhccc
Confidence            3468999999999999999999985    45554

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.47  E-value=0.0059  Score=53.02  Aligned_cols=66  Identities=15%  Similarity=0.227  Sum_probs=55.6

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      -..+.||.++++.+||++|.+|+.|.+.+++.|.|.++      ..|.|++ +.+.+..|..+|.++-++...
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~e~~~~~  212 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKIEREAHT  212 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence            46789999999999999999999999999999999652      4566766 577999999999987766543

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type

Probab=96.30  E-value=0.0025  Score=34.01  Aligned_cols=18  Identities=39%  Similarity=0.877  Sum_probs=15.3

Q ss_pred             cCcccccccCCCCCCCCCCcc
Q 027432           32 MCNRLNSAEGCKFGDKCHFAH   52 (223)
Q Consensus        32 ~C~~~~~~g~C~~g~~C~faH   52 (223)
                      +|++|..   |.++++|.|+|
T Consensus         1 ~Ck~~~~---C~~~~~C~f~H   18 (19)
T PF14608_consen    1 PCKFGPN---CTNGDNCPFSH   18 (19)
T ss_pred             CCcCcCC---CCCCCcCccCC
Confidence            4886653   99999999999

>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]

Probab=96.29  E-value=0.0039  Score=56.69  Aligned_cols=32  Identities=31%  Similarity=0.549  Sum_probs=27.9

Q ss_pred             CccccccCcccccccCCCCCCCCCCcccccccCC
Q 027432           26 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGK   59 (223)
Q Consensus        26 ~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~   59 (223)
                      ..+++.+|++|.. |.|..||.|.|+|-. +|.+
T Consensus        73 ~~~~~~vcK~~l~-glC~kgD~C~Flhe~-~~~k  104 (325)
T KOG1040|consen   73 DSRGKVVCKHWLR-GLCKKGDQCEFLHEY-DLTK  104 (325)
T ss_pred             ccCCceeehhhhh-hhhhccCcCcchhhh-hhcc
Confidence            3889999999999 899999999999965 5554

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type

Probab=96.22  E-value=0.003  Score=33.70  Aligned_cols=19  Identities=42%  Similarity=0.812  Sum_probs=16.1

Q ss_pred             cCccccCCcCCCCCCCccccC
Q 027432          194 LCGNFAKGSCTFGDRCHFAHG  214 (223)
Q Consensus       194 ~C~~~~~g~C~~g~~C~faH~  214 (223)
                      +|++|..  |+++++|.|+|.
T Consensus         1 ~Ck~~~~--C~~~~~C~f~HP   19 (19)
T PF14608_consen    1 PCKFGPN--CTNGDNCPFSHP   19 (19)
T ss_pred             CCcCcCC--CCCCCcCccCCc
Confidence            4887765  999999999994

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

Probab=96.17  E-value=0.0022  Score=66.02  Aligned_cols=74  Identities=18%  Similarity=0.174  Sum_probs=64.6

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ....++.||...+..|||+||.||..++..+|+.|.|.+ ...+..||.+.+.|.++.++.|..+|.-.|-+...
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv 1413 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDV 1413 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCc
Confidence            344678899999999999999999999999999999987 45557799999999999999999999888866554

>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]

Probab=96.16  E-value=0.0038  Score=59.24  Aligned_cols=25  Identities=40%  Similarity=1.030  Sum_probs=21.8

Q ss_pred             ccccCcccccc--cCCCCCCCCCCccc
Q 027432           29 KSRMCNRLNSA--EGCKFGDKCHFAHG   53 (223)
Q Consensus        29 kt~~C~~~~~~--g~C~~g~~C~faH~   53 (223)
                      +..||......  ..|.|||+|+|.|.
T Consensus        75 ~n~LCPsli~g~~~~C~f~d~Crf~HD  101 (614)
T KOG2333|consen   75 QNRLCPSLIQGDISKCSFGDNCRFVHD  101 (614)
T ss_pred             hhccChHhhcCCCccCccccccccccc
Confidence            46799998887  68999999999993

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

Probab=96.07  E-value=0.0042  Score=59.49  Aligned_cols=75  Identities=25%  Similarity=0.388  Sum_probs=61.0

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCC
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  171 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~  171 (223)
                      .....++.|+.+.|-.||||+|++|++|+..++++|.+.+...+ .++.-.+.|-+.++..|+.++..++.+.++.
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pv  140 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQVCKAKAAIHQILTENTPV  140 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCCCChHHHHHHHHHhcCCcc
Confidence            35567899999999999999999999999999999999754322 3444555668889999999999988776654

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

Probab=96.04  E-value=0.0029  Score=60.57  Aligned_cols=71  Identities=25%  Similarity=0.440  Sum_probs=62.5

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ...+.+|...++.|||++|++++.|+..++|+|.++........+.+.|.+...-...|+.++.+.+.+.+
T Consensus       141 k~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~ede  211 (608)
T KOG2279|consen  141 SEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDE  211 (608)
T ss_pred             cccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchh
Confidence            35678999999999999999999999999999999877666667999999988888899999999886543

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]

Probab=95.76  E-value=0.0038  Score=57.86  Aligned_cols=29  Identities=31%  Similarity=0.774  Sum_probs=24.7

Q ss_pred             cccCcccccccCCCCCCCCCCcccc----cccCC
Q 027432           30 SRMCNRLNSAEGCKFGDKCHFAHGE----WELGK   59 (223)
Q Consensus        30 t~~C~~~~~~g~C~~g~~C~faH~~----~el~~   59 (223)
                      -++|++|.. |.|+|+.+|+|.||.    ++||+
T Consensus       140 MkpC~ffLe-g~CRF~enCRfSHG~~V~lsslr~  172 (486)
T KOG2185|consen  140 MKPCKFFLE-GRCRFGENCRFSHGLDVPLSSLRN  172 (486)
T ss_pred             hccchHhhc-cccccCcccccccCcccchhhccc
Confidence            467999998 899999999999985    56665

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.55  E-value=0.029  Score=54.09  Aligned_cols=66  Identities=24%  Similarity=0.370  Sum_probs=50.1

Q ss_pred             cceEEEEecc-ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDA-SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~-~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~  167 (223)
                      .++-.+.+|+ ++-|.||||.|.||+.+..-||+.|-|+|..     ..|+|++ +|---+.|+..+..+|..
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHHc
Confidence            3455678898 5559999999999999999999999997643     3577887 565555666666666643

>PRK12704 phosphodiesterase; Provisional

Probab=95.40  E-value=0.043  Score=53.02  Aligned_cols=67  Identities=22%  Similarity=0.331  Sum_probs=51.0

Q ss_pred             cceEEEEecc-ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhc
Q 027432           97 SATAKISVDA-SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        97 ~~t~~i~VP~-~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~  168 (223)
                      .++-.+.+|+ ++-|.||||.|.||+.+..-||+.|-|+|.+     ..|.|+| ++-.-+.|...+..++...
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            3455678888 5569999999999999999999999997653     3577887 5555456777777666543

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

Probab=95.40  E-value=0.01  Score=52.00  Aligned_cols=28  Identities=32%  Similarity=0.950  Sum_probs=25.7

Q ss_pred             CcccccccCccccCCcCCCCCCCccccC
Q 027432          187 SSNFKTKLCGNFAKGSCTFGDRCHFAHG  214 (223)
Q Consensus       187 ~~~~kt~~C~~~~~g~C~~g~~C~faH~  214 (223)
                      -..|+-..|..|..+.|.+|..|.|.|-
T Consensus       147 vT~~rea~C~~~e~~~C~rG~~CnFmH~  174 (260)
T KOG2202|consen  147 VTDFREAICGQFERTECSRGGACNFMHV  174 (260)
T ss_pred             cCchhhhhhcccccccCCCCCcCcchhh
Confidence            3778999999999999999999999994

>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]

Probab=95.36  E-value=0.0083  Score=52.08  Aligned_cols=34  Identities=47%  Similarity=0.835  Sum_probs=30.0

Q ss_pred             cccccccCccccCCcCCCCCCCccccCccccCcC
Q 027432          188 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT  221 (223)
Q Consensus       188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~~  221 (223)
                      ..-||..|-.|..+.|.-|+.|.|+|+.+|.|..
T Consensus        81 vdpK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~  114 (299)
T COG5252          81 VDPKTVVCALFLNKTCAKGDACKFAHGKEEARKT  114 (299)
T ss_pred             cCchhHHHHHhccCccccCchhhhhcchHHHhhh
Confidence            3459999999999999999999999998887753

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

Probab=95.31  E-value=0.016  Score=50.87  Aligned_cols=71  Identities=30%  Similarity=0.421  Sum_probs=50.4

Q ss_pred             CcceEEEEecc------ccccceecCCCcchhhhhhhcCCeEEeccCC------------CCC--------CceEEEEcC
Q 027432           96 ASATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHE------------ADP--------NLRNIELEG  149 (223)
Q Consensus        96 ~~~t~~i~VP~------~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~------------~~~--------~~r~v~I~G  149 (223)
                      ...+.+|+||-      +.||.|||..|.++|+|+++|||+|.|.-..            .+.        -...|+..+
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~  169 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA  169 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence            35678888886      5899999999999999999999999994210            000        014566666


Q ss_pred             CHH----HHHHHHHHHHhhhh
Q 027432          150 SFE----QIKQASAMVRELIV  166 (223)
Q Consensus       150 ~~~----~i~~A~~lI~~~i~  166 (223)
                      ++.    -+..|++.|..+|.
T Consensus       170 p~~ea~~rl~~AleeI~klL~  190 (259)
T KOG1588|consen  170 PPAEAYARLAYALEEIKKLLV  190 (259)
T ss_pred             CHHHHHHHHHHHHHHHHHhcC
Confidence            654    34467777776663

>PRK00106 hypothetical protein; Provisional

Probab=95.17  E-value=0.049  Score=52.79  Aligned_cols=66  Identities=23%  Similarity=0.335  Sum_probs=51.2

Q ss_pred             cceEEEEecc-ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDA-SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~-~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~  167 (223)
                      .++-.+.+|+ ++-|.||||-|.||+.+..-||+.|-|+|.+     ..|+|+| +|---+.|+..+..++..
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            4455688898 5569999999999999999999999997643     3577888 666666666666666654

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

Probab=95.04  E-value=0.031  Score=50.72  Aligned_cols=70  Identities=24%  Similarity=0.252  Sum_probs=56.8

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEc-CCHHHHHHHHHHHHhhhhhcC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-GSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~-G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      -...+.|+++..|.|||+.|.+.+.|+++++++|.+.....  +...|+|. +..++|.+|..-|..+|....
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~--n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT--NKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC--CcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            34568999999999999999999999999999999965432  23344444 478999999999999987765

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

Probab=94.96  E-value=0.03  Score=50.56  Aligned_cols=67  Identities=16%  Similarity=0.305  Sum_probs=56.6

Q ss_pred             CCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHh
Q 027432           94 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRE  163 (223)
Q Consensus        94 ~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~  163 (223)
                      .+..-+..+.||...|+.|.|++|.+||.|+.+|..+|+-....   .+-++.++|..+.++.|+..|..
T Consensus        22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCcc
Confidence            34567788899999999999999999999999999998763221   23679999999999999998876

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

Probab=94.92  E-value=0.018  Score=48.99  Aligned_cols=58  Identities=31%  Similarity=0.474  Sum_probs=51.6

Q ss_pred             cccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432          106 ASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       106 ~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      +..+|.|+||+|.+--.|.+.|.++|.+.+       ..|-|-|.+++++.|+..|..+|...++
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGspp  234 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGSPP  234 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccCCc
Confidence            567899999999999999999999999965       3589999999999999999999976554

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=94.90  E-value=0.0097  Score=50.50  Aligned_cols=36  Identities=19%  Similarity=0.581  Sum_probs=29.2

Q ss_pred             cccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432           28 VKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI   63 (223)
Q Consensus        28 ~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~   63 (223)
                      |..-.|+.|..+|.|-|||.|.|.|..+.....+..
T Consensus       139 ~qpdVCKdyk~TGYCGYGDsCKflH~R~D~KtGWkL  174 (259)
T COG5152         139 TQPDVCKDYKETGYCGYGDSCKFLHDRSDFKTGWKL  174 (259)
T ss_pred             cCcccccchhhcccccCCchhhhhhhhhhhhccccc
Confidence            445679999999999999999999988766654333

>PRK00468 hypothetical protein; Provisional

Probab=94.84  E-value=0.024  Score=40.84  Aligned_cols=30  Identities=30%  Similarity=0.353  Sum_probs=26.8

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQ  126 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~  126 (223)
                      ...+++.|..+-+|.||||+|.+|+.|+.-
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            456789999999999999999999999874

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]

Probab=94.77  E-value=0.0067  Score=54.78  Aligned_cols=25  Identities=40%  Similarity=1.000  Sum_probs=22.4

Q ss_pred             cccCccccCCcCCCCCC-CccccCcc
Q 027432          192 TKLCGNFAKGSCTFGDR-CHFAHGAA  216 (223)
Q Consensus       192 t~~C~~~~~g~C~~g~~-C~faH~~~  216 (223)
                      -++||.|++|.|+.||+ |+|||--.
T Consensus        37 ~eVCReF~rn~C~R~d~~CkfaHP~~   62 (331)
T KOG2494|consen   37 LEVCREFLRNTCSRGDRECKFAHPPK   62 (331)
T ss_pred             HHHHHHHHhccccCCCccccccCCCC
Confidence            37899999999999999 99999544

>PRK02821 hypothetical protein; Provisional

Probab=94.68  E-value=0.028  Score=40.72  Aligned_cols=31  Identities=23%  Similarity=0.418  Sum_probs=27.5

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQT  127 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S  127 (223)
                      .....+.|..+-+|.||||+|.+|+.|+.--
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv   60 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVV   60 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence            4568899999999999999999999999753

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=94.57  E-value=0.062  Score=43.18  Aligned_cols=37  Identities=27%  Similarity=0.400  Sum_probs=33.6

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      ..+.+.|+...+|+.||++|++|+.|++..|-+|.|-
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv   68 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV   68 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence            4677888999999999999999999999999999884

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=93.83  E-value=0.022  Score=48.35  Aligned_cols=30  Identities=27%  Similarity=0.908  Sum_probs=25.7

Q ss_pred             ccccccCcccc-CCcCCCCCCCccccCcccc
Q 027432          189 NFKTKLCGNFA-KGSCTFGDRCHFAHGAAEL  218 (223)
Q Consensus       189 ~~kt~~C~~~~-~g~C~~g~~C~faH~~~el  218 (223)
                      .|.-.+|+.|. +|+|-|||.|.|.|..++.
T Consensus       138 D~qpdVCKdyk~TGYCGYGDsCKflH~R~D~  168 (259)
T COG5152         138 DTQPDVCKDYKETGYCGYGDSCKFLHDRSDF  168 (259)
T ss_pred             ecCcccccchhhcccccCCchhhhhhhhhhh
Confidence            45667899999 8999999999999987643

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

Probab=93.79  E-value=0.052  Score=39.26  Aligned_cols=30  Identities=27%  Similarity=0.365  Sum_probs=27.0

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQ  126 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~  126 (223)
                      ...+++.|..+-+|.||||+|.+|+.|+.-
T Consensus        29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             eEEEEEEECcccccceecCCChhHHHHHHH
Confidence            456889999999999999999999999864

>PRK01064 hypothetical protein; Provisional

Probab=93.71  E-value=0.066  Score=38.91  Aligned_cols=30  Identities=30%  Similarity=0.348  Sum_probs=26.8

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQ  126 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~  126 (223)
                      ....++.|..+..|.+|||+|.+|+.|+.-
T Consensus        29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             EEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            456789999999999999999999999874

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

Probab=93.67  E-value=0.16  Score=49.40  Aligned_cols=67  Identities=21%  Similarity=0.302  Sum_probs=55.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .-..++.|+.+..-.+||.+|.+.|.|..+||+.-++++       ..++|.. ++..+++|+.+|..++.....
T Consensus       596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe-------~t~~i~A~~~~am~~Ak~~I~~i~~~~~~  663 (760)
T KOG1067|consen  596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE-------GTFSIFAPTQAAMEEAKEFIDGIIKDDQV  663 (760)
T ss_pred             ceeeEEeecchhhheeecCccceeeeEeeeccceeeecC-------ceEEEEecCHHHHHHHHHHHHHHhcCccc
Confidence            345678899999999999999999999999997766653       4566766 799999999999999976443

>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]

Probab=93.56  E-value=0.016  Score=51.74  Aligned_cols=33  Identities=42%  Similarity=0.835  Sum_probs=28.8

Q ss_pred             cccccccCccccCCcCCCCCCCccccCccccCc
Q 027432          188 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      .--|+.+|-+|..|.|.-|+.|.|+|....-|+
T Consensus        88 vDPKSvvCafFk~g~C~KG~kCKFsHdl~~~~k  120 (343)
T KOG1763|consen   88 VDPKSVVCAFFKQGTCTKGDKCKFSHDLAVERK  120 (343)
T ss_pred             CCchHHHHHHHhccCCCCCCcccccchHHHhhh
Confidence            445899999999999999999999998876554

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

Probab=92.97  E-value=0.09  Score=37.20  Aligned_cols=36  Identities=33%  Similarity=0.520  Sum_probs=28.9

Q ss_pred             eEEEEecccc-----ccceecCCCcchhhhhhhc-CCeEEec
Q 027432           99 TAKISVDASL-----AGAIIGKGGVNSKQICRQT-GAKLSIR  134 (223)
Q Consensus        99 t~~i~VP~~~-----vG~IIGkgG~~Ik~I~~~S-Ga~I~I~  134 (223)
                      -.++.|-+..     +|+.||++|++|+.|.++. |.+|.|-
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            3466677766     9999999999999999999 9999883

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

Probab=92.95  E-value=0.18  Score=42.65  Aligned_cols=69  Identities=22%  Similarity=0.318  Sum_probs=55.6

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEc-----CCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-----GSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~-----G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .....+.||...++.+||+.|+..+.|.+.+++++.|+..     +..|+|.     .+|-.+.+|..+|..+=..+++
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~p   80 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPP   80 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCH
Confidence            3456799999999999999999999999999999999643     2445553     3688999999998887665554

>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]

Probab=92.95  E-value=0.033  Score=50.71  Aligned_cols=28  Identities=29%  Similarity=0.718  Sum_probs=26.1

Q ss_pred             cccccccCccccCCcCCCCCCCccccCc
Q 027432          188 SNFKTKLCGNFAKGSCTFGDRCHFAHGA  215 (223)
Q Consensus       188 ~~~kt~~C~~~~~g~C~~g~~C~faH~~  215 (223)
                      ..+++.+|++|+.|.|+.||.|-|+|-.
T Consensus        73 ~~~~~~vcK~~l~glC~kgD~C~Flhe~  100 (325)
T KOG1040|consen   73 DSRGKVVCKHWLRGLCKKGDQCEFLHEY  100 (325)
T ss_pred             ccCCceeehhhhhhhhhccCcCcchhhh
Confidence            4789999999999999999999999966

>PRK12705 hypothetical protein; Provisional

Probab=92.71  E-value=0.13  Score=49.59  Aligned_cols=41  Identities=27%  Similarity=0.414  Sum_probs=34.2

Q ss_pred             cceEEEEecccc-ccceecCCCcchhhhhhhcCCeEEeccCC
Q 027432           97 SATAKISVDASL-AGAIIGKGGVNSKQICRQTGAKLSIRDHE  137 (223)
Q Consensus        97 ~~t~~i~VP~~~-vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~  137 (223)
                      .+.-.+.+|++- -|.||||-|.||+.+...||..|-|+|..
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp  238 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP  238 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence            344567788854 49999999999999999999999997654

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=91.40  E-value=0.13  Score=41.28  Aligned_cols=38  Identities=24%  Similarity=0.281  Sum_probs=33.2

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      .....+.|+.+..|..|||+|.|++.++.-++-++.|.
T Consensus        98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            34567789999999999999999999999999887664

>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]

Probab=91.16  E-value=0.055  Score=48.42  Aligned_cols=34  Identities=32%  Similarity=0.481  Sum_probs=29.1

Q ss_pred             CccccccCcccccccCCCCCCCCCCcccccccCCC
Q 027432           26 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP   60 (223)
Q Consensus        26 ~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~   60 (223)
                      .--|+.+|-+|.. |.|.-|++|.|+|....-+..
T Consensus        88 vDPKSvvCafFk~-g~C~KG~kCKFsHdl~~~~k~  121 (343)
T KOG1763|consen   88 VDPKSVVCAFFKQ-GTCTKGDKCKFSHDLAVERKK  121 (343)
T ss_pred             CCchHHHHHHHhc-cCCCCCCcccccchHHHhhhc
Confidence            4458999998887 899999999999998877763

>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]

Probab=90.92  E-value=0.14  Score=44.49  Aligned_cols=22  Identities=32%  Similarity=0.686  Sum_probs=20.5

Q ss_pred             ccCcccccccCCCCCCCCCCcc
Q 027432           31 RMCNRLNSAEGCKFGDKCHFAH   52 (223)
Q Consensus        31 ~~C~~~~~~g~C~~g~~C~faH   52 (223)
                      -.|++|...|-|-.|..|+|.|
T Consensus       207 vycryynangicgkgaacrfvh  228 (377)
T KOG1492|consen  207 VYCRYYNANGICGKGAACRFVH  228 (377)
T ss_pred             eEEEEecCCCcccCCceeeeec
Confidence            3599999999999999999999

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

Probab=90.79  E-value=0.3  Score=32.78  Aligned_cols=34  Identities=26%  Similarity=0.318  Sum_probs=26.4

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeE
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKL  131 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I  131 (223)
                      ....+.+.....|.+||++|.+++.|+...+-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            3445555555689999999999999999887544

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

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=90.59  E-value=0.087  Score=47.16  Aligned_cols=39  Identities=21%  Similarity=0.488  Sum_probs=31.4

Q ss_pred             CCccccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432           25 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI   63 (223)
Q Consensus        25 ~~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~   63 (223)
                      ..-|---+|+.|..+|.|-|||.|.|.|........+..
T Consensus       181 ~~d~qpDicKdykeTgycg~gdSckFlh~r~DyK~GWqi  219 (313)
T KOG1813|consen  181 RIDYQPDICKDYKETGYCGYGDSCKFLHDRSDYKAGWQI  219 (313)
T ss_pred             eeecCchhhhhhHhhCcccccchhhhhhhhhhcccccee
Confidence            356777899999999999999999999987766544333

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=90.54  E-value=0.27  Score=39.64  Aligned_cols=36  Identities=31%  Similarity=0.441  Sum_probs=31.9

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      -.-+.|....+|+.||++|++|+.|++..|-+|.|-
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV   69 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI   69 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence            455788888999999999999999999999998883

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

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=90.44  E-value=0.1  Score=36.80  Aligned_cols=32  Identities=25%  Similarity=0.343  Sum_probs=27.8

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhc
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQT  127 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S  127 (223)
                      ......+.|..+..|.||||.|.+++.||.-.
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~   58 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLV   58 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHH
Confidence            35678899999999999999999999998754

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=90.22  E-value=0.44  Score=48.11  Aligned_cols=72  Identities=19%  Similarity=0.253  Sum_probs=61.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ...+.+.|-......|+||+|.+|.+|++.+.+.|.+..  .+..+..+++.|....+++|...+...+.+...
T Consensus       346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n  417 (753)
T KOG2208|consen  346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSANDEKAVEDVEKIIAEILN  417 (753)
T ss_pred             ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence            355678888999999999999999999999999999965  234467899999999999999999988887654

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=89.87  E-value=0.12  Score=36.78  Aligned_cols=34  Identities=35%  Similarity=0.462  Sum_probs=28.7

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeE
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKL  131 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I  131 (223)
                      ....+.+-.+..|.|||++|++|+.|.+...-.+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            4577889999999999999999999988765444

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

>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]

Probab=89.77  E-value=0.071  Score=46.43  Aligned_cols=36  Identities=33%  Similarity=0.531  Sum_probs=30.4

Q ss_pred             ccccccCcccccccCCCCCCCCCCcccccccCCCccc
Q 027432           27 VVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI   63 (223)
Q Consensus        27 ~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~~~~   63 (223)
                      --||..|-.|.. +.|.-|+.|.|+|+.+|.|..--.
T Consensus        82 dpK~~vcalF~~-~~c~kg~~ckF~h~~ee~r~~eK~  117 (299)
T COG5252          82 DPKTVVCALFLN-KTCAKGDACKFAHGKEEARKTEKP  117 (299)
T ss_pred             CchhHHHHHhcc-CccccCchhhhhcchHHHhhhccc
Confidence            348899999988 799999999999998888875444

>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

Probab=89.62  E-value=0.46  Score=42.57  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=27.3

Q ss_pred             CccccccCcccccccCCCCCCCCCCcccccccC
Q 027432           26 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELG   58 (223)
Q Consensus        26 ~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~   58 (223)
                      ..+..-.|++|.. |.|+-++.|.|+|+..-++
T Consensus       100 ~~~s~V~c~~~~~-g~c~s~~~c~~lh~~d~~~  131 (285)
T COG5084         100 VLSSSVVCKFFLR-GLCKSGFSCEFLHEYDLRS  131 (285)
T ss_pred             cccCCcccchhcc-ccCcCCCccccccCCCccc
Confidence            3588889999999 8999999999999765554

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=88.75  E-value=0.45  Score=33.96  Aligned_cols=33  Identities=18%  Similarity=0.296  Sum_probs=27.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGA  129 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa  129 (223)
                      .....+.|..+..|.||||.|+++..||.-...
T Consensus        23 ~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~   55 (77)
T cd02414          23 GDTVEVNISGDDIGLLIGKRGKTLDALQYLANL   55 (77)
T ss_pred             CCEEEEEEecCCCCeEECCCCccHHHHHHHHHH
Confidence            345678888899999999999999999876543

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

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=87.65  E-value=0.43  Score=40.36  Aligned_cols=37  Identities=30%  Similarity=0.402  Sum_probs=34.6

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  135 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~  135 (223)
                      ...+.||.+..+..|||+|.|++-+.+-||.++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            6788899999999999999999999999999999964

>PRK13764 ATPase; Provisional

Probab=87.55  E-value=0.47  Score=46.71  Aligned_cols=40  Identities=28%  Similarity=0.405  Sum_probs=36.3

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH  136 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~  136 (223)
                      .....+.||...++.+|||+|.+|++|.+..|.+|.|...
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            4567899999999999999999999999999999999543

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=87.51  E-value=0.93  Score=37.53  Aligned_cols=37  Identities=27%  Similarity=0.402  Sum_probs=31.6

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  135 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~  135 (223)
                      ..+-++|-... |.-|||+|.+|+.+++..|-+|.|-+
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            44567777777 99999999999999999999998843

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=86.80  E-value=0.42  Score=38.49  Aligned_cols=38  Identities=26%  Similarity=0.307  Sum_probs=33.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      .....+.|+.+..+..|||+|.|++...+-++-++.|.
T Consensus        99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            45677889999999999999999999999998887664

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

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=86.01  E-value=0.58  Score=44.78  Aligned_cols=39  Identities=28%  Similarity=0.495  Sum_probs=35.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  135 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~  135 (223)
                      .....+.||...++.+|||+|.+|++|.+..|-+|.|..
T Consensus       485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            345778999999999999999999999999999999954

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=85.80  E-value=0.78  Score=33.37  Aligned_cols=33  Identities=12%  Similarity=0.306  Sum_probs=27.7

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCe
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAK  130 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~  130 (223)
                      ...++.|-+..-|.|||++|.+|++|++.-...
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~   62 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKR   62 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHH
Confidence            347889999999999999999999998865433

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>TIGR01953 NusA transcription termination factor NusA

Probab=85.03  E-value=0.83  Score=41.96  Aligned_cols=39  Identities=26%  Similarity=0.430  Sum_probs=35.9

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  135 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~  135 (223)
                      .....+.||.+..+..|||+|.|++-..+-+|.+|.|..
T Consensus       300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            467889999999999999999999999999999999953

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

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=85.01  E-value=0.32  Score=44.69  Aligned_cols=24  Identities=33%  Similarity=0.804  Sum_probs=21.6

Q ss_pred             ccCcccccccCCCCCCCCCCccccc
Q 027432           31 RMCNRLNSAEGCKFGDKCHFAHGEW   55 (223)
Q Consensus        31 ~~C~~~~~~g~C~~g~~C~faH~~~   55 (223)
                      .+|++|.. |.|.||+.|+|.|..-
T Consensus         9 tic~~~~~-g~c~~g~~cr~~h~~~   32 (344)
T KOG1039|consen    9 TICKYYQK-GNCKFGDLCRLSHSLP   32 (344)
T ss_pred             hhhhhccc-ccccccceeeeeccCc
Confidence            67998888 8999999999999765

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=84.68  E-value=0.31  Score=43.77  Aligned_cols=30  Identities=27%  Similarity=0.958  Sum_probs=26.4

Q ss_pred             cccccccCcccc-CCcCCCCCCCccccCccc
Q 027432          188 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAE  217 (223)
Q Consensus       188 ~~~kt~~C~~~~-~g~C~~g~~C~faH~~~e  217 (223)
                      .-|.-.+|+.|. +|.|-||+.|.|-|..+.
T Consensus       182 ~d~qpDicKdykeTgycg~gdSckFlh~r~D  212 (313)
T KOG1813|consen  182 IDYQPDICKDYKETGYCGYGDSCKFLHDRSD  212 (313)
T ss_pred             eecCchhhhhhHhhCcccccchhhhhhhhhh
Confidence            567778999999 899999999999997653

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=83.62  E-value=1.2  Score=41.51  Aligned_cols=39  Identities=21%  Similarity=0.331  Sum_probs=35.9

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      ......+.||.+..++.|||+|.|++-..+-+|.+|.|.
T Consensus       306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~  344 (374)
T PRK12328        306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN  344 (374)
T ss_pred             CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence            346788999999999999999999999999999999994

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

Probab=80.84  E-value=2.5  Score=37.92  Aligned_cols=53  Identities=21%  Similarity=0.396  Sum_probs=45.9

Q ss_pred             ceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432          111 AIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       111 ~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .+||..|.++|.|.--|.+.|-|.-       ..|++.|.+..++++..++.+++....+
T Consensus       162 RLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~NiHP  214 (356)
T KOG2874|consen  162 RLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKNIHP  214 (356)
T ss_pred             HhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhccch
Confidence            5899999999999999999998853       4689999999999999999988866443

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=80.18  E-value=1.5  Score=41.94  Aligned_cols=39  Identities=28%  Similarity=0.363  Sum_probs=35.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  135 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~  135 (223)
                      .....+.||.+..+..|||+|.|++...+-+|.+|.|..
T Consensus       301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            357889999999999999999999999999999999943

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	223
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		1e-04
2hh2_A	107	Solution Structure Of The Fourth Kh Domain Of Ksrp		3e-04
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		4e-04
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		5e-04

>pdb|1J4W|A Chain A, Complex Of The Kh3 And Kh4 Domains Of Fbp With A Single_stranded 29mer Dna Oligonucleotide From The Fuse Element Of The C-Myc Oncogene Length = 174

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 109 AGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELI 165
            G IIGKGG   K I +Q+GA++ ++ +    ADPN++   + G+ +QI  A  ++ E I
Sbjct: 115 TGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp Length = 107

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQAS 158
            S+     G +IG+GG N K I +QTGA + I        DPN +   + GS +QI  A 
Sbjct: 11  FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAK 70
Query: 159 AMVRELI 165
            ++ E I
Sbjct: 71  QLIEEKI 77

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 38/64 (59%)
Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ +QI+ A 
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 159 AMVR 162
            +++
Sbjct: 75  YLLQ 78

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 38/64 (59%)
Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ +QI+ A 
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 67
Query: 159 AMVR 162
            +++
Sbjct: 68  YLLQ 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	223
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	4e-23
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-21
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-21
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-20
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-19
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-17
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-17
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	5e-17
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-16
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-15
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	8e-15
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-13
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	9e-15
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	8e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-14
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-13
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-12
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-13
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-12
1we8_A	104	Tudor and KH domain containing protein; structural	6e-13
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-12
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-12
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-11
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-11
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-10
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	4e-09
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	1e-08
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	1e-06
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	2e-06
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	2e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-08
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	4e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	6e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	5e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	7e-06
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	8e-06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	3e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	3e-04
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	9e-05
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	2e-04
2rhk_C	72	Cleavage and polyadenylation specificity factor su	4e-04
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	5e-04
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	5e-04

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 87.7 bits (218), Expect = 4e-23
 Identities = 23/74 (31%), Positives = 41/74 (55%)

Query: 92  ASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSF 151
            + G   T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ 
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 152 EQIKQASAMVRELI 165
           +QI+ A  +++  +
Sbjct: 61  DQIQNAQYLLQNSV 74

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

 Score = 83.9 bits (208), Expect = 1e-21
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 4/81 (4%)

Query: 89  GPAASFGASA----TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRN 144
           G   S+G       T ++++   LAG+IIGKGG   KQI  ++GA + I +       R 
Sbjct: 1   GSHMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRI 60

Query: 145 IELEGSFEQIKQASAMVRELI 165
           I + G+ +QI+ A  +++  +
Sbjct: 61  ITITGTQDQIQNAQYLLQNSV 81

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 83.8 bits (207), Expect = 3e-21
 Identities = 27/95 (28%), Positives = 38/95 (40%), Gaps = 3/95 (3%)

Query: 92  ASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELE 148
            +         S+     G +IG+GG N K I +QTGA + I        DPN +   + 
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 149 GSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA 183
           GS +QI  A  ++ E I          P   G A 
Sbjct: 61  GSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAG 95

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 81.0 bits (200), Expect = 4e-20
 Identities = 14/95 (14%), Positives = 33/95 (34%)

Query: 89  GPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE 148
             A          + V     G +IG+ G   K+I    G ++  +  +     +   + 
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61

Query: 149 GSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA 183
           G  ++ + A+ ++ +L+  +       P   G   
Sbjct: 62  GPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPP 96

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 78.2 bits (193), Expect = 2e-19
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 80  GRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD 139
           G++      G           +I + A  AG +IGKGG   KQ+  + G K+ +    + 
Sbjct: 1   GQFHDNANGGQN-----GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ 55

Query: 140 PNL--RNIELEGSFEQIKQASAMVRELI 165
                + + + G   +++QA  MV +++
Sbjct: 56  NTNVDKPLRIIGDPYKVQQACEMVMDIL 83

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 73.6 bits (181), Expect = 2e-17
 Identities = 17/80 (21%), Positives = 35/80 (43%)

Query: 86  PAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNI 145
                     +  T +  V   + G IIG+GG    +I +++G K+ I         R+ 
Sbjct: 3   SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62

Query: 146 ELEGSFEQIKQASAMVRELI 165
            L G+ E ++ A  ++ +++
Sbjct: 63  MLTGTPESVQSAKRLLDQIV 82

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

 Score = 72.7 bits (179), Expect = 3e-17
 Identities = 18/71 (25%), Positives = 37/71 (52%)

Query: 95  GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 154
           G+  T ++++  +L G IIG+ G N  +I + +GA++ I +     + R + + GS   I
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 62

Query: 155 KQASAMVRELI 165
             A  ++   +
Sbjct: 63  SLAQYLINARL 73

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

 Score = 71.9 bits (177), Expect = 5e-17
 Identities = 15/71 (21%), Positives = 33/71 (46%)

Query: 95  GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 154
             + + ++++   L G IIG+ G    +I + +GA++ I +       R + + GS   I
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI 61

Query: 155 KQASAMVRELI 165
             A  ++   +
Sbjct: 62  SLAQYLINVRL 72

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 71.3 bits (175), Expect = 1e-16
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 85  PPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL-- 142
                       +A  +I + AS AG +IGKGG   KQ+  + G K+ +           
Sbjct: 2   SSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGAD 61

Query: 143 RNIELEGSFEQIKQASAMVRELI 165
           + + + G   +++QA  MV ELI
Sbjct: 62  KPLRITGDPYKVQQAKEMVLELI 84

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 67.0 bits (164), Expect = 5e-15
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNL--RNIELEGSFEQIK 155
             +I+V  +L GAI+GKGG    +    TGA++ I +  E  P    R + + GS    +
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 156 QASAMVRELIVRIGPAHAKNP 176
            A  ++ + +       A NP
Sbjct: 64  AAQYLISQRVTYEQGVRASNP 84

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

 Score = 68.7 bits (168), Expect = 8e-15
 Identities = 27/104 (25%), Positives = 41/104 (39%), Gaps = 3/104 (2%)

Query: 65  HDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQIC 124
                     PG  G               G        V     G IIGKGG   K I 
Sbjct: 71  RSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSIS 130

Query: 125 RQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELI 165
           +Q+GA++ ++ +    ADPN++   + G+ +QI  A  ++ E I
Sbjct: 131 QQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 63.7 bits (155), Expect = 5e-13
 Identities = 15/93 (16%), Positives = 36/93 (38%)

Query: 97  SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ 156
           S    + +     G +IG+ G   K+I    G ++  +  +     R  ++ G  ++ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 157 ASAMVRELIVRIGPAHAKNPATAGSAAHPLSSN 189
           A+ ++ +L+  +   +   P   G        N
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGN 94

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

 Score = 68.3 bits (167), Expect = 9e-15
 Identities = 14/97 (14%), Positives = 35/97 (36%)

Query: 69  RAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTG 128
           +A   V   +  R +                  + V     G +IG+ G   K+I    G
Sbjct: 62  QACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAG 121

Query: 129 AKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 165
            ++  +  +     +   + G  ++ + A+ ++ +L+
Sbjct: 122 VRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 158

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

 Score = 60.6 bits (147), Expect = 8e-12
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL--RNIELEGSFEQIKQ 156
             +I + A  AG +IGKGG   KQ+  + G K+ +    +      + + + G   +++Q
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 157 ASAMVRELIVRIGPAHAKNPATAGSAAH 184
           A  MV +++         +    GS   
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIG 90

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 65.8 bits (161), Expect = 1e-14
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNL--RNIELEGSFEQIK 155
             +++V  +L GAI+GKGG    +    TGA++ I +  E  P    R + + GS    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 156 QASAMVRELI 165
            A  ++ + +
Sbjct: 64  AAQYLISQRV 73

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

 Score = 64.4 bits (157), Expect = 3e-13
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 2/99 (2%)

Query: 69  RAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTG 128
           +AF  +  ++             A+     T ++ V AS  G++IGKGG   K+I   TG
Sbjct: 61  KAFAMIIDKLE-EDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTG 119

Query: 129 AKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIV 166
           A++ +  D   +   R I + G  + I +    +  +++
Sbjct: 120 AQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVML 158

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

 Score = 60.2 bits (146), Expect = 7e-12
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++ +     G+IIGK G + K++  ++GA+++I +       R I L G    I +A 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAIFKAF 63

Query: 159 AMVRELIVRIGPAHAKNPATAGSAAHPL 186
           AM+ + +     +   N   A      L
Sbjct: 64  AMIIDKLEEDISSSMTNSTAASRPPVTL 91

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 64.9 bits (158), Expect = 3e-13
 Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 79  GGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI--RDH 136
                    P    +   +   KI V  S AG IIGKGG   K I  Q+GA + +  +  
Sbjct: 85  KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD 144

Query: 137 EADPNLRNIELEGSFEQIKQASAMVRELI 165
             +   R + + G  EQ ++A  ++ + I
Sbjct: 145 GINLQNRVVTVSGEPEQNRKAVELIIQKI 173

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 61.4 bits (149), Expect = 5e-12
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 3/101 (2%)

Query: 95  GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNL--RNIELEGSF 151
           G+    K+ + +  AG+IIGKGG    Q+ ++TGA + + +  +  P    R   ++G+ 
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 152 EQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKT 192
           E +      + E I  +    AK    +        +  + 
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRA 103

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 61.8 bits (150), Expect = 6e-13
 Identities = 24/103 (23%), Positives = 45/103 (43%), Gaps = 7/103 (6%)

Query: 87  APGPAASFGASA--TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL-- 142
           + G +     +     ++SV     G IIG+GG   + IC+ +GAK++         L  
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS 61

Query: 143 RNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHP 185
           R I++ G+ +++  A  ++ E +             A SA+ P
Sbjct: 62  RLIKISGTQKEVAAAKHLILEKVSE---DEELRKRIAHSASGP 101

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

 Score = 62.9 bits (153), Expect = 1e-12
 Identities = 24/108 (22%), Positives = 46/108 (42%), Gaps = 8/108 (7%)

Query: 69  RAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTG 128
           +A G + G++  + E    P             I V AS AG +IGKGG    ++   T 
Sbjct: 62  KAQGRIYGKL--KEENFFGPKE----EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTA 115

Query: 129 AKLSIRDHEADPNL--RNIELEGSFEQIKQASAMVRELIVRIGPAHAK 174
           A++ +   +         +++ G F   + A   +R+++ ++   H K
Sbjct: 116 AEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQHQK 163

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

 Score = 62.5 bits (152), Expect = 1e-12
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQA 157
             ++ + A   GAIIGK G + KQ+ R   A + I      D  +R + + G  E   +A
Sbjct: 4   MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKA 63

Query: 158 SAMVRELIVRIGPAHAKNPAT 178
              +   +        K    
Sbjct: 64  QGRIYGKLKEENFFGPKEEVK 84

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 56.1 bits (136), Expect = 4e-11
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++ +     G+IIGK G + K++  ++GA+++I +       R I L G    I +A 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPE--RIITLAGPTNAIFKAF 63

Query: 159 AMVRELI 165
           AM+ + +
Sbjct: 64  AMIIDKL 70

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 56.7 bits (137), Expect = 4e-11
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 96  ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 155
             A+A +++       +IGK G   + +  +T  K+ I   +   N   I++ G+ E I+
Sbjct: 15  TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQ--IKITGTKEGIE 72

Query: 156 QASAMVRELI 165
           +A   V  + 
Sbjct: 73  KARHEVLLIS 82

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 54.7 bits (132), Expect = 1e-10
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
             +I++D      +IGK G N  +I  Q    + I       N   I +EG  + ++QA 
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSN--LIRIEGDPQGVQQAK 63

Query: 159 AMVRELI 165
             + EL 
Sbjct: 64  RELLELA 70

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 51.1 bits (122), Expect = 4e-09
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 89  GPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE 148
           G + S G   T ++ V   + G ++G  G   K+I ++T   +     + +P      + 
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEP---VFAVT 57

Query: 149 GSFEQIKQASAMVRELI 165
           G  E + +A   +   I
Sbjct: 58  GMPENVDRAREEIEAHI 74

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 51.4 bits (123), Expect = 4e-09
 Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 1/70 (1%)

Query: 97  SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL-RNIELEGSFEQIK 155
           S    ++VD      IIG+ G    QI  +    +   D +        I + G  +  +
Sbjct: 16  SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 75

Query: 156 QASAMVRELI 165
            A   +  ++
Sbjct: 76  AARDAILRIV 85

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 14/29 (48%), Positives = 21/29 (72%), Gaps = 1/29 (3%)

Query: 187 SSNFKTKLCGNFAK-GSCTFGDRCHFAHG 214
           SS +KT+LC  +++ G C +G +C FAHG
Sbjct: 7   SSRYKTELCRTYSESGRCRYGAKCQFAHG 35

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 44.2 bits (104), Expect = 1e-06
 Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 1/35 (2%)

Query: 184 HPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAE 217
                 +KT+LC  F   G C +G RCHF H   E
Sbjct: 42  ANRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPTE 76

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 43.8 bits (103), Expect = 2e-06
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 29 KSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPR 69
          K+ +C   + +  C++G KC FAHG  EL +          
Sbjct: 11 KTELCRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTE 51

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 29 KSRMCNRLNSAEGCKFGDKCHFAHGEWE 56
          K+ +C++      C +G +CHF H   E
Sbjct: 49 KTELCHKFKLQGRCPYGSRCHFIHNPTE 76

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 50.2 bits (120), Expect = 1e-08
 Identities = 12/70 (17%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 96  ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 155
              T ++ V   L   +IG+ G   +++  +    + +   E   +   I + G    + 
Sbjct: 15  VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSD--IIAITGLAANLD 72

Query: 156 QASAMVRELI 165
           +A A + E +
Sbjct: 73  RAKAGLLERV 82

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           +  + +D  +   IIG  G   ++I  +    +        P+   + + G  E +++A 
Sbjct: 18  SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAI 76

Query: 159 AMVRELI 165
             +  L 
Sbjct: 77  DHILNLE 83

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 193 KLCGNFAKGSCTFGDRCHFAHGAAELRK 220
            +C  +  G+C  G+ C FAHG AEL +
Sbjct: 21  SICDRYMNGTCPEGNSCKFAHGNAELHE 48

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 46.5 bits (110), Expect = 6e-07
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 83  EPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGA-KLSIRDHE---- 137
           E   A   A SF   A   I V  +L G +IGK G   ++I  ++G  ++ I        
Sbjct: 52  EDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV 111

Query: 138 -ADPNLRNIELEGSFEQIKQASAMVRELI 165
             +  +      G+ + I  A+ ++   +
Sbjct: 112 PQEEGMVPFVFVGTKDSIANATVLLDYHL 140

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 5/74 (6%)

Query: 96  ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQI 154
           +    +  V   L G  IG  G N +Q  +  G    +   + D +     + G   + +
Sbjct: 2   SRFHEQFIVREDLMGLAIGTHGANIQQARKVPG----VTAIDLDEDTCTFHIYGEDQDAV 57

Query: 155 KQASAMVRELIVRI 168
           K+A + +      I
Sbjct: 58  KKARSFLEFAEDVI 71

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 44.3 bits (104), Expect = 7e-06
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 7/56 (12%)

Query: 110 GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 165
           G IIG+ G   + I   +GA +S+         + + + G+  QI+ A   + +L 
Sbjct: 141 GRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQIEIAKTAIEKLA 189

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 42.1 bits (99), Expect = 8e-06
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 4/83 (4%)

Query: 98  ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 157
           A  ++S+ A L  ++IG  G   + I  + G  + I           + + G    +++A
Sbjct: 17  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSDVEKA 75

Query: 158 SAMVRELIVRIGPAHAKNPATAG 180
              +  L         K+  ++G
Sbjct: 76  KKQLLHL---AEEKQTKSGPSSG 95

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 110 GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 165
           G IIG+GG   + I   T   +++ +         + + G +E+   A   +  L 
Sbjct: 110 GRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLA 158

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 14/79 (17%), Positives = 30/79 (37%)

Query: 95  GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 154
                  + V     GA+IG  G    +I R+TG  +++    +   +           +
Sbjct: 1   AMKPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNL 60

Query: 155 KQASAMVRELIVRIGPAHA 173
            +A+ +V+ + +   P  A
Sbjct: 61  MKAAEVVKAISLGFPPEKA 79

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1 Length = 98

 Score = 39.3 bits (91), Expect = 9e-05
 Identities = 10/40 (25%), Positives = 16/40 (40%)

Query: 180 GSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELR 219
           GS+        K +LC  +  G C   + C + HG    +
Sbjct: 1   GSSGSSGELPKKRELCKFYITGFCARAENCPYMHGDFPCK 40

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 102

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA- 157
            + ++  + L   IIGK G N  +I +Q   K+ I   E +     I LEG  E +  A 
Sbjct: 28  VSSVAAPSWLHRFIIGKKGQNLAKITQQMP-KVHIEFTEGE---DKITLEGPTEDVSVAQ 83

Query: 158 ---SAMVRELIVRIGP 170
                MV++LI R GP
Sbjct: 84  EQIEGMVKDLINRSGP 99

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 185 PLSSNFKTKLCGNFAKGSCTFGDRCHFAH 213
             SS  KT +C ++ +G C  GD+C F H
Sbjct: 3   SGSSGEKTVVCKHWLRGLCKKGDQCEFLH 31

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens} Length = 72

 Score = 37.1 bits (86), Expect = 4e-04
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 184 HPLSSNFKTKLCGNFAKGSCTFGDRCHFAH 213
           H   S  KT +C ++ +G C  GD+C F H
Sbjct: 8   HSHMSGEKTVVCKHWLRGLCKKGDQCEFLH 37

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 39.5 bits (91), Expect = 5e-04
 Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 7/76 (9%)

Query: 97  SATAKISVDASLAGAIIGKGGV--NSKQICRQTGAKLSIRDHE-----ADPNLRNIELEG 149
             T  +  ++     +    G   N   I  +T   + + D        DP  + + + G
Sbjct: 29  RVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITG 88

Query: 150 SFEQIKQASAMVRELI 165
            F  + +A  ++R   
Sbjct: 89  YFGDVDRARMLMRRNC 104

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 131

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 17/85 (20%)

Query: 108 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-----------------S 150
             G +IG  G   K I ++  AK+ IR   +    +    +G                 +
Sbjct: 23  FVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANT 82

Query: 151 FEQIKQASAMVRELIVRIGPAHAKN 175
            E +K+A   +R ++ +        
Sbjct: 83  MENVKKAVEQIRNILKQGIETPEDQ 107

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	223
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	99.77
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.64
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.64
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.62
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.62
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.6
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.59
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.59
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.59
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.59
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.57
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.55
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.55
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.55
1we8_A	104	Tudor and KH domain containing protein; structural	99.48
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.41
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.39
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.37
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.36
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.36
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.35
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.33
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.32
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.32
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.3
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.29
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.29
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.29
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.28
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	99.28
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.21
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	99.19
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.12
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.1
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	99.04
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	99.03
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.99
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.98
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	98.91
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	98.88
2rhk_C	72	Cleavage and polyadenylation specificity factor su	98.81
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.77
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.74
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.7
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	98.62
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.43
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.42
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.37
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.35
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.32
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.29
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	98.28
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	98.24
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.12
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.11
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.08
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	97.98
2rhk_C	72	Cleavage and polyadenylation specificity factor su	97.83
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	97.81
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.62
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	97.38
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	97.15
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	97.13
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	96.97
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	96.39
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	96.15
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.94
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.45
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	91.41
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	90.91
2cxc_A	144	NUSA; transcription termination, RNA binding prote	90.77
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	88.78
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	81.79
2cxc_A	144	NUSA; transcription termination, RNA binding prote	80.5

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=99.77  E-value=1.1e-19  Score=130.20  Aligned_cols=35  Identities=34%  Similarity=0.795  Sum_probs=32.1

Q ss_pred             CCccccccCcccccccCCCCCCCCCCcccccccCC
Q 027432           25 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGK   59 (223)
Q Consensus        25 ~~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~   59 (223)
                      +++|||+||++|...|.|+||++|+|+|+.+||+.
T Consensus         7 ~~~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~~   41 (77)
T 1m9o_A            7 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ   41 (77)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGG
T ss_pred             CCCccchhCHHhhhCCCcCCCCCccCCCCChhhcc
Confidence            47899999999988899999999999999988874

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.64  E-value=2.8e-16  Score=113.85  Aligned_cols=75  Identities=31%  Similarity=0.512  Sum_probs=69.3

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      +...+.++.||.+++|.||||+|++|++|+++|||+|+|.+..++..++.|+|+|+++++++|+.+|.+++.+..
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~   78 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS   78 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            456789999999999999999999999999999999999876667788999999999999999999999998754

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

Probab=99.64  E-value=2.3e-16  Score=114.19  Aligned_cols=74  Identities=24%  Similarity=0.438  Sum_probs=67.4

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      +...+.++.||.+++|.||||+|++|++|+++|||+|+|.+..++..++.|+|+|+++++++|+.+|.+++.+.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            45678999999999999999999999999999999999987666778999999999999999999999999765

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

Probab=99.62  E-value=3e-16  Score=111.98  Aligned_cols=71  Identities=21%  Similarity=0.409  Sum_probs=66.5

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      ..+.++.||.+.+|.||||||++|++|+++|||+|+|.+..++..++.|+|+|++++++.|+.+|.+++.+
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            56789999999999999999999999999999999998766777899999999999999999999999865

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.62  E-value=1e-15  Score=113.31  Aligned_cols=74  Identities=23%  Similarity=0.392  Sum_probs=68.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..+.+|.||.+++|.||||+|++|++|+++|||+|+|.+...+..++.|+|+|+++++++|+.+|.+++.+...
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~~   87 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGRS   87 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            57899999999999999999999999999999999998766667789999999999999999999999988665

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.60  E-value=9.1e-16  Score=116.62  Aligned_cols=76  Identities=14%  Similarity=0.342  Sum_probs=67.1

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAH  172 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~p  172 (223)
                      ..+.+|.||.+++|.||||+|++||+|+++|||+|+|.+...+..+|.|+|+|+++++++|+.+|.+++.+.+..+
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~g~   85 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGP   85 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC---
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhccccCC
Confidence            3578999999999999999999999999999999999766666678999999999999999999999999887653

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.59  E-value=1.6e-15  Score=107.99  Aligned_cols=70  Identities=24%  Similarity=0.395  Sum_probs=63.2

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC---CCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      .+.++.||.+.+|.||||+|++|++|++.|||+|+|.+.   .++..++.|+|+|++++++.|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999653   2456689999999999999999999999864

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.59  E-value=8.8e-16  Score=108.99  Aligned_cols=69  Identities=28%  Similarity=0.413  Sum_probs=63.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      ..+.+++||.+.+|.||||||++|++|+++|||+|+|.+.  +..+|.|+|+|+++++.+|+.+|.++|.+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            3578999999999999999999999999999999999765  45689999999999999999999999875

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=2.9e-15  Score=113.84  Aligned_cols=73  Identities=33%  Similarity=0.447  Sum_probs=65.7

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCC---CCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~---~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .+.+|.||.+++|.||||+|++||+|+++|||+|+|.+..   .+..++.|+|+|+++++++|+.+|.+++.+...
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~~   82 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLC   82 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCCC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcccc
Confidence            3789999999999999999999999999999999996542   335679999999999999999999999987653

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

Probab=99.59  E-value=8.1e-16  Score=113.13  Aligned_cols=75  Identities=31%  Similarity=0.512  Sum_probs=68.9

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      +...+.++.||.+++|.||||+|++||+|+++|||+|+|.+..++..++.|+|+|+++++++|+.+|.+++.+..
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~~   85 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS   85 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHC
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhhh
Confidence            346788999999999999999999999999999999999876667788999999999999999999999998753

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.57  E-value=3.3e-15  Score=110.95  Aligned_cols=76  Identities=32%  Similarity=0.451  Sum_probs=68.0

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCC--CCCceEEEEcCCHHHHHHHHHHHHhhhhhcCCC
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA--DPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  171 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~--~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~~  171 (223)
                      ...+.+|.||.+++|.||||+|++||+|+++|||+|+|.+...  ...+|.|+|+|++++++.|+.+|.+++.+.+..
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~   90 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQGSG   90 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCCSSC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhccCCC
Confidence            4678999999999999999999999999999999999975432  346899999999999999999999999887653

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.55  E-value=3.7e-15  Score=109.00  Aligned_cols=72  Identities=25%  Similarity=0.374  Sum_probs=65.3

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC---CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      .+.++.||.+.+|.||||||++|++|++.|||+|+|.+.   .++..++.|+|+|++++++.|+.+|.+++.+.+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQ   77 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            578999999999999999999999999999999999754   245678999999999999999999999998754

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.55  E-value=9.1e-15  Score=106.51  Aligned_cols=71  Identities=25%  Similarity=0.402  Sum_probs=63.9

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCC--CCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE--ADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~--~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      ..+.++.||.+++|.||||+|++||+|+++|||+|+|.+..  ....+|.|+|+|++++++.|+.+|.+++.+
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            46789999999999999999999999999999999996543  345689999999999999999999998853

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=4.3e-15  Score=108.18  Aligned_cols=74  Identities=19%  Similarity=0.267  Sum_probs=65.0

Q ss_pred             CCCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           93 SFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        93 s~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      +.....+.++.||.+++|+||||+|++||+|+++||++|+|...+.   ++.|+|+|+++++++|+.+|.+++....
T Consensus         5 ~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~~---~~~v~ItG~~e~v~~A~~~I~~~i~~r~   78 (83)
T 2dgr_A            5 SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK---EPVFAVTGMPENVDRAREEIEAHITLRS   78 (83)
T ss_dssp             CSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSSS---CCEEEEEECTTTHHHHHHHHHHHHHSCC
T ss_pred             CCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCCC---CCeEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            3445678999999999999999999999999999999999974332   5889999999999999999999876544

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.48  E-value=3.1e-14  Score=107.52  Aligned_cols=72  Identities=25%  Similarity=0.446  Sum_probs=64.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCC--CCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD--PNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~--~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      ..+.+|.||.+++|.||||+|++|++|+++|||+|+|.+....  ..++.|+|+|+.+++++|+.+|.+++.+.
T Consensus        14 p~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            4678999999999999999999999999999999999764432  35899999999999999999999999753

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.41  E-value=2.8e-13  Score=101.19  Aligned_cols=73  Identities=18%  Similarity=0.283  Sum_probs=65.2

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCC-CCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE-ADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~-~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+.++.||.+++|.|||+||++|+.|+++||++|+|.+.. +...++.|+|+|+.++++.|+.+|.+++.+.+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e   89 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELE   89 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999996543 33467999999999999999999999998754

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.39  E-value=3.9e-13  Score=94.75  Aligned_cols=67  Identities=25%  Similarity=0.332  Sum_probs=60.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI  165 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i  165 (223)
                      ..+.++.||.+++|.|||+||++|++|+++||++|.|.+..  ..++.|+|+|+.+++++|+.+|.+++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g--~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC--CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999997543  25689999999999999999999875

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.37  E-value=5.8e-13  Score=98.79  Aligned_cols=74  Identities=20%  Similarity=0.268  Sum_probs=64.8

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ....+.++.||.+++|.|||+||.+||+|+++||++|+|.+.+  ..++.|+|+|+++++++|+.+|.+++.+...
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~--~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~   87 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAEQDK   87 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC--CCCCeEEEEECHHHHHHHHHHHHHHhhcccc
Confidence            3456899999999999999999999999999999999997533  2357899999999999999999999987543

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

Probab=99.36  E-value=3.9e-13  Score=107.92  Aligned_cols=73  Identities=15%  Similarity=0.357  Sum_probs=66.5

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .+.++.||.+++|.||||+|.+|++|+++|||+|+|.+......++.|+|+|++++++.|+.+|.+++.+.+.
T Consensus        91 ~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~  163 (164)
T 2jvz_A           91 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRS  163 (164)
T ss_dssp             SSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhhhhC
Confidence            4578999999999999999999999999999999997766666689999999999999999999999987653

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

Probab=99.36  E-value=4.5e-13  Score=109.07  Aligned_cols=74  Identities=16%  Similarity=0.371  Sum_probs=67.5

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      +.+.+++||.+.+|.||||+|++||+|+++||++|+|.+.+.+..+|.|+|+|+++++++|+.+|.+++.+.+.
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~   75 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQA   75 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC-
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            46789999999999999999999999999999999997656667789999999999999999999999988653

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.35  E-value=1.2e-12  Score=97.41  Aligned_cols=76  Identities=14%  Similarity=0.236  Sum_probs=66.6

Q ss_pred             CCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           94 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        94 ~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .....+.++.||.+++|.|||+||++|++|+++||++|+|.+.. +.+++.|+|+|.++++++|+.+|.+++.+++.
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            34467899999999999999999999999999999999996532 23468999999999999999999999987654

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

Probab=99.33  E-value=1.1e-12  Score=105.50  Aligned_cols=72  Identities=25%  Similarity=0.324  Sum_probs=66.4

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC-CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~-~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      .+.+++||.+.+|.||||+|++|++|+++||++|+|.+. .++..+|.|+|+|+++++..|+.+|.+++.+..
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~   75 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEEN   75 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            578999999999999999999999999999999999764 467789999999999999999999999998763

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

Probab=99.32  E-value=2.1e-12  Score=103.62  Aligned_cols=73  Identities=25%  Similarity=0.378  Sum_probs=65.4

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCC--CCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE--ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~--~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .+.+++||.+.+|.||||+|++||+|+++||++|+|.+..  .+..+|.|+|+|+++++++|+.+|.+++.+.+.
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~   76 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ   76 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccC
Confidence            4789999999999999999999999999999999996432  345689999999999999999999999987653

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.32  E-value=1.2e-12  Score=106.86  Aligned_cols=73  Identities=32%  Similarity=0.398  Sum_probs=64.8

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCC--CCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE--ADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~--~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+.++.||.+++|.||||+|.+||+|+++|||+|+|.+..  ++..++.|+|+|+++++++|+.+|.+++.+.+
T Consensus       103 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          103 ANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             GGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             ceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            46889999999999999999999999999999999996543  34568999999999999999999999998743

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

Probab=99.30  E-value=1.1e-12  Score=105.06  Aligned_cols=71  Identities=27%  Similarity=0.431  Sum_probs=64.8

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      ..+.++.||.+.+|.||||+|.+|++|+++|||+|+|.+ ..++..++.|+|+|++++++.|+.+|.+++.+
T Consensus        88 ~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           88 PVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             SEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            468899999999999999999999999999999999964 34566789999999999999999999999875

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.29  E-value=2.1e-12  Score=105.41  Aligned_cols=75  Identities=24%  Similarity=0.381  Sum_probs=67.0

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC---CCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ...+.+++||.+.+|.||||+|++|++|+++||++|+|.+.   .++..+|.|+|+|+.+++.+|+.+|.+++.+...
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~   81 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQ   81 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCC
Confidence            45789999999999999999999999999999999999653   2456789999999999999999999999987543

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

Probab=99.29  E-value=2.6e-12  Score=104.50  Aligned_cols=69  Identities=33%  Similarity=0.550  Sum_probs=61.6

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCC---CCCCceEEEEcCCHHHHHHHHHHHHhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELI  165 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~---~~~~~r~v~I~G~~~~i~~A~~lI~~~i  165 (223)
                      ..+.++.||.+.+|.||||+|.+||+|+++|||+|+|.+..   .+..++.|+|+|++++++.|+.+|.++|
T Consensus       103 ~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          103 LQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             -CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            46889999999999999999999999999999999996542   2356799999999999999999999875

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.29  E-value=1.8e-12  Score=97.96  Aligned_cols=71  Identities=17%  Similarity=0.249  Sum_probs=63.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+.++.||.+++|.|||+||++|++|+++||++|.|.+...  ..+.|+|+|+.+++++|+.+|.+++.+.+
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~--~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT--TCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC--CcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            368899999999999999999999999999999999976433  34699999999999999999999997654

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

Probab=99.28  E-value=2.8e-12  Score=103.10  Aligned_cols=74  Identities=26%  Similarity=0.409  Sum_probs=64.5

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC-CCCCCc-eEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNL-RNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~-~~~~~~-r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..+.++.||.+.+|.||||+|.+|++|++.|||+|+|.+. .++..+ +.|+|+|++++++.|+.+|.+++.+...
T Consensus        84 ~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~  159 (163)
T 3krm_A           84 KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ  159 (163)
T ss_dssp             CEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHTC
T ss_pred             ceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHHH
Confidence            4567999999999999999999999999999999999643 233344 5899999999999999999999988654

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.28  E-value=3.2e-13  Score=94.33  Aligned_cols=32  Identities=34%  Similarity=0.611  Sum_probs=29.2

Q ss_pred             cccccCcccccccCCCCCCCCCCcccccccCCC
Q 027432           28 VKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP   60 (223)
Q Consensus        28 ~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~   60 (223)
                      .|++||++| ..|.|+||++|+||||++||+.+
T Consensus        18 ~k~~LC~~~-~~G~C~~G~~C~FAHG~~ELr~~   49 (69)
T 2d9m_A           18 GYFSICDRY-MNGTCPEGNSCKFAHGNAELHEW   49 (69)
T ss_dssp             SCCSBCHHH-HHSCCSSCSSCSSBSSHHHHHHH
T ss_pred             CCcccCccc-CcCCCCCCCccCCcCCHHHHhhH
Confidence            477999999 56899999999999999999985

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

Probab=99.21  E-value=6.5e-12  Score=100.66  Aligned_cols=70  Identities=27%  Similarity=0.389  Sum_probs=63.8

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      ..+.+++||.+.+|.||||+|++|++|+++||++|+|.+.  +..+|.|+|+|+.+++.+|+.+|.+++.+.
T Consensus         4 ~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   73 (160)
T 2jzx_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (160)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHHHHHHHHHHHHHHhh
Confidence            3578999999999999999999999999999999999764  356899999999999999999999998764

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=1.4e-12  Score=91.13  Aligned_cols=30  Identities=40%  Similarity=0.951  Sum_probs=28.6

Q ss_pred             ccccCccccCCcCCCCCCCccccCccccCc
Q 027432          191 KTKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       191 kt~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      |++||++|.+|.|+||++|+||||++|||.
T Consensus        19 k~~LC~~~~~G~C~~G~~C~FAHG~~ELr~   48 (69)
T 2d9m_A           19 YFSICDRYMNGTCPEGNSCKFAHGNAELHE   48 (69)
T ss_dssp             CCSBCHHHHHSCCSSCSSCSSBSSHHHHHH
T ss_pred             CcccCcccCcCCCCCCCccCCcCCHHHHhh
Confidence            669999999999999999999999999986

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.12  E-value=3.6e-11  Score=95.64  Aligned_cols=70  Identities=21%  Similarity=0.359  Sum_probs=59.2

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCC-eEEeccC-CCC--CCc--eEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGA-KLSIRDH-EAD--PNL--RNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa-~I~I~~~-~~~--~~~--r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      ...+.||.+.+|++|||+|.||+.|++.||+ +|.|... +..  ..+  +.|+|+|++++++.|+.+|.+.|...
T Consensus        68 e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~l  143 (144)
T 2qnd_A           68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYL  143 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHTC
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3789999999999999999999999999997 8999532 221  123  46999999999999999999998753

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.10  E-value=1e-10  Score=86.93  Aligned_cols=76  Identities=16%  Similarity=0.269  Sum_probs=67.3

Q ss_pred             CCCCcceEEEEeccccccceecCCCcchhhhhhhc-CCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           93 SFGASATAKISVDASLAGAIIGKGGVNSKQICRQT-GAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        93 s~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~S-Ga~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ......+..+.||.++++.|||+||.+|++|++++ |++|.|.+.  +...+.|+|.|..+++++|+.+|.+++.+.+.
T Consensus        12 e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~--g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e~   88 (95)
T 2ctj_A           12 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   88 (95)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC--CCCcceEEEEcCHHHHHHHHHHHHHHHhhhhh
Confidence            45567789999999999999999999999999999 999999653  23467899999999999999999999988764

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=99.04  E-value=1.3e-10  Score=86.90  Aligned_cols=26  Identities=19%  Similarity=0.450  Sum_probs=23.7

Q ss_pred             CccccccCcccccccCCCCCCCCCCcc
Q 027432           26 TVVKSRMCNRLNSAEGCKFGDKCHFAH   52 (223)
Q Consensus        26 ~~~kt~~C~~~~~~g~C~~g~~C~faH   52 (223)
                      ..+|+.+|++|. .|.|.+|++|.|+|
T Consensus         9 ~~~k~~lC~~f~-~G~C~~G~~C~f~H   34 (98)
T 2cqe_A            9 LPKKRELCKFYI-TGFCARAENCPYMH   34 (98)
T ss_dssp             CSCCCSBCTTTT-TTCCSCSTTCSSBS
T ss_pred             CCCCCccCcccc-cCcCCCCCCCCCCC
Confidence            358999999996 69999999999999

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.03  E-value=1.6e-10  Score=82.70  Aligned_cols=27  Identities=33%  Similarity=0.651  Sum_probs=25.1

Q ss_pred             CCccccccCcccccccCCCCCCCCCCcc
Q 027432           25 PTVVKSRMCNRLNSAEGCKFGDKCHFAH   52 (223)
Q Consensus        25 ~~~~kt~~C~~~~~~g~C~~g~~C~faH   52 (223)
                      ...+|+.+|++|.. |.|.+|++|.|+|
T Consensus         5 ~~~~k~~~C~~fl~-G~C~~G~~C~fsH   31 (77)
T 2d9n_A            5 SSGEKTVVCKHWLR-GLCKKGDQCEFLH   31 (77)
T ss_dssp             CSCCTTSBCHHHHT-TCCSCTTSSSSBC
T ss_pred             CCCCcceeCHhHcc-CcCCCCCCCCCcc
Confidence            35789999999999 9999999999999

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.99  E-value=5.6e-10  Score=83.97  Aligned_cols=68  Identities=22%  Similarity=0.334  Sum_probs=61.3

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhh-cCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~-SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      .+.+|.||..+.+.|||++|++|++|+++ ++++|.+.+     .++.|+|.|+.++|++|+..|..++.+...
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            68899999999999999999999999997 589999876     356899999999999999999999987553

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.98  E-value=2.7e-10  Score=84.02  Aligned_cols=71  Identities=21%  Similarity=0.294  Sum_probs=62.4

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhhcCCe-EEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAK-LSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~-I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ......++.||.+++|.|||+||.+|++|+++||++ |.|.+.     +..|+|.| +.+++++|+.+|..+-.....
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed-----dG~V~I~g~~~ea~~~A~~~I~~ie~~~~v   84 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED-----TGTFRIYGESADAVKKARGFLEFVEDFIQV   84 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHSCCCCCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC-----CCEEEEEECCHHHHHHHHHHHHhhheEEec
Confidence            345778999999999999999999999999999998 999642     47899999 899999999999988776554

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=98.91  E-value=5.7e-10  Score=79.19  Aligned_cols=34  Identities=50%  Similarity=1.152  Sum_probs=31.8

Q ss_pred             CcccccccCcccc-CCcCCCCCCCccccCccccCc
Q 027432          187 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       187 ~~~~kt~~C~~~~-~g~C~~g~~C~faH~~~elr~  220 (223)
                      ..+|||+||++|. .|.|++|++|+|||+.+|||.
T Consensus         7 ~~~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~~   41 (77)
T 1m9o_A            7 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ   41 (77)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGG
T ss_pred             CCCccchhCHHhhhCCCcCCCCCccCCCCChhhcc
Confidence            4789999999997 899999999999999999985

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=98.88  E-value=5.4e-10  Score=78.50  Aligned_cols=31  Identities=26%  Similarity=0.693  Sum_probs=28.1

Q ss_pred             ccccccCccccCCcCCCCCCCccccCccccCc
Q 027432          189 NFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       189 ~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      ..++.+|.+|++|.|..+ +|.|+|...+|+.
T Consensus        39 ~~~~~vC~~flkG~C~r~-~C~y~H~~~~L~~   69 (70)
T 3d2q_A           39 DNTVTVCMDYIKGRCSRE-KCKYFHPPAHLQA   69 (70)
T ss_dssp             TTEEEBCHHHHTTCCCCT-TCCSBCCCHHHHC
T ss_pred             CCcceeccccCcCCCCCC-CcCeeCCHHHHhc
Confidence            457889999999999999 9999999999975

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=98.81  E-value=1.2e-09  Score=77.12  Aligned_cols=28  Identities=32%  Similarity=0.578  Sum_probs=25.5

Q ss_pred             CCCccccccCcccccccCCCCCCCCCCcc
Q 027432           24 GPTVVKSRMCNRLNSAEGCKFGDKCHFAH   52 (223)
Q Consensus        24 ~~~~~kt~~C~~~~~~g~C~~g~~C~faH   52 (223)
                      ....+|+.+|++|.. |.|.+|++|.|+|
T Consensus        10 ~~~~~k~~vCk~fl~-G~C~~G~~C~fsH   37 (72)
T 2rhk_C           10 HMSGEKTVVCKHWLR-GLCKKGDQCEFLH   37 (72)
T ss_dssp             SSSCCCCSBCHHHHT-TCCCCGGGSSSBC
T ss_pred             cCCCCcCeeCHHHhc-CCCCCCCCCCCcc
Confidence            346789999999999 9999999999999

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.77  E-value=1.1e-08  Score=80.27  Aligned_cols=74  Identities=20%  Similarity=0.367  Sum_probs=60.3

Q ss_pred             CCcceEEEEeccc------cccceecCCCcchhhhhhhcCCeEEeccCCC----------------CCCceEEEEcC-CH
Q 027432           95 GASATAKISVDAS------LAGAIIGKGGVNSKQICRQTGAKLSIRDHEA----------------DPNLRNIELEG-SF  151 (223)
Q Consensus        95 g~~~t~~i~VP~~------~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~----------------~~~~r~v~I~G-~~  151 (223)
                      ....+.+|.||.+      ++|.|||.+|.+||+|+++|||+|.|....+                ...+--|.|++ +.
T Consensus         4 ~~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~   83 (131)
T 1k1g_A            4 ATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTM   83 (131)
T ss_dssp             -CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSH
T ss_pred             CceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCH
Confidence            3456889999988      9999999999999999999999999964211                11245677777 69


Q ss_pred             HHHHHHHHHHHhhhhhc
Q 027432          152 EQIKQASAMVRELIVRI  168 (223)
Q Consensus       152 ~~i~~A~~lI~~~i~~~  168 (223)
                      +.+++|+.+|.+++...
T Consensus        84 e~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           84 ENVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHhcc
Confidence            99999999999999763

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.74  E-value=1.4e-08  Score=78.44  Aligned_cols=73  Identities=19%  Similarity=0.206  Sum_probs=57.9

Q ss_pred             cceEEEEeccc-------cccceecCCCcchhhhhhhcCCeEEeccCCCC----------CCceEEEEc-CCHHHHHHHH
Q 027432           97 SATAKISVDAS-------LAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD----------PNLRNIELE-GSFEQIKQAS  158 (223)
Q Consensus        97 ~~t~~i~VP~~-------~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~----------~~~r~v~I~-G~~~~i~~A~  158 (223)
                      ..+.+|+||.+       ++|.|||.+|.+||+|+++|||+|.|....+.          ..+-.|.|+ .+.+++++|+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~   90 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAK   90 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHH
Confidence            56788888875       78999999999999999999999999632110          122356665 4799999999


Q ss_pred             HHHHhhhhhcC
Q 027432          159 AMVRELIVRIG  169 (223)
Q Consensus       159 ~lI~~~i~~~~  169 (223)
                      .+|.+++....
T Consensus        91 ~~Ie~Ll~~v~  101 (119)
T 2yqr_A           91 KLCENLLQTVH  101 (119)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHhhchH
Confidence            99999997643

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=98.70  E-value=1.3e-08  Score=92.48  Aligned_cols=71  Identities=17%  Similarity=0.336  Sum_probs=62.2

Q ss_pred             CCcceEEEEeccccccceecCCC--cchhhhhhhcCCeEEeccCC-----CCCCceEEEEcCCHHHHHHHHHHHHhhh
Q 027432           95 GASATAKISVDASLAGAIIGKGG--VNSKQICRQTGAKLSIRDHE-----ADPNLRNIELEGSFEQIKQASAMVRELI  165 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG--~~Ik~I~~~SGa~I~I~~~~-----~~~~~r~v~I~G~~~~i~~A~~lI~~~i  165 (223)
                      ....|.++.||....+.||||+|  +||++|+++||++|++.+.+     .......|+|+|..++|++|+..|.+++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~  104 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC  104 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSC
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcC
Confidence            45678999999999999999999  99999999999999996654     1133478999999999999999999864

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.62  E-value=3.2e-09  Score=79.35  Aligned_cols=31  Identities=26%  Similarity=0.670  Sum_probs=27.2

Q ss_pred             ccccccCccccCCcCCCCCCCccccCccccCc
Q 027432          189 NFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       189 ~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      ..++.+|.+|++|.|.++ +|+|.|...+|+.
T Consensus        53 ~~~~~vC~~flkG~C~r~-~C~y~H~~~~l~~   83 (98)
T 2e5s_A           53 DNTVTVCMDYIKGRCMRE-KCKYFHPPAHLQA   83 (98)
T ss_dssp             TCEEEBCHHHHHTCCCCT-TCCSBCCCHHHHH
T ss_pred             CCccccchhhccCCCCCC-CcCccCChHHHHH
Confidence            347789999999999999 8999999888763

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.43  E-value=7.8e-08  Score=81.49  Aligned_cols=56  Identities=25%  Similarity=0.367  Sum_probs=51.0

Q ss_pred             ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432          107 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus       107 ~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+|.||||+|.+|+.|++.||++|+|.+       +.|+|.|++++++.|+.+|.++|....
T Consensus       138 r~~GriIGk~G~tik~ie~~Tg~~I~v~~-------~~v~i~G~~~~i~~A~~~i~~li~g~~  193 (219)
T 2e3u_A          138 RVRGRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQIEIAKTAIEKLARGSP  193 (219)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHCCEEEEET-------TEEEEEECHHHHHHHHHHHHHHHTTCC
T ss_pred             hhhheeECCCchHHHHHHHHhCceEEECC-------eEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence            37899999999999999999999999964       579999999999999999999996543

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.42  E-value=1.2e-07  Score=80.39  Aligned_cols=66  Identities=17%  Similarity=0.222  Sum_probs=57.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCC-----HHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-----FEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~-----~~~i~~A~~lI~~~i~~  167 (223)
                      ..+.++.||.+.+|.|||++|.+|+.|+++||++|.|...     ++.|+|.++     ++++++|+.+|.+++..
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~-----~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg  103 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETEDPLAVWKARDIVLAIGRG  103 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCCSHHHHHHHHHHHHHHHTT
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCCCHHHHHHHHHHHHHHhcc
Confidence            3577999999999999999999999999999999999632     456777764     79999999999998853

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.37  E-value=1.7e-07  Score=74.19  Aligned_cols=71  Identities=25%  Similarity=0.352  Sum_probs=53.9

Q ss_pred             ceEEEEecccc------ccceecCCCcchhhhhhhcCCeEEeccCCCC-----------------CCc-eEEEEcC-CH-
Q 027432           98 ATAKISVDASL------AGAIIGKGGVNSKQICRQTGAKLSIRDHEAD-----------------PNL-RNIELEG-SF-  151 (223)
Q Consensus        98 ~t~~i~VP~~~------vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~-----------------~~~-r~v~I~G-~~-  151 (223)
                      -+.+|.||.+.      +|.|||.+|.++|+|+++|||+|.|....+.                 ..+ =-|.|++ ++ 
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            36788898655      9999999999999999999999999643211                 011 2456666 34 


Q ss_pred             ----HHHHHHHHHHHhhhhhc
Q 027432          152 ----EQIKQASAMVRELIVRI  168 (223)
Q Consensus       152 ----~~i~~A~~lI~~~i~~~  168 (223)
                          ..+++|+.+|..++...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             hhHHHHHHHHHHHHHHHCCCC
Confidence                38999999999998643

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=98.35  E-value=7.7e-07  Score=69.79  Aligned_cols=69  Identities=13%  Similarity=0.159  Sum_probs=62.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV  166 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~  166 (223)
                      .....+.|.+.++++|||++|+.|+.|+..|.+.|+|..-++ .++..|+|.|++..-..|+.+|..+..
T Consensus        55 ~dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           55 EDPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             SSCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            567889999999999999999999999999999999976655 378999999999999999999998764

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=98.32  E-value=4e-07  Score=75.57  Aligned_cols=67  Identities=21%  Similarity=0.328  Sum_probs=59.6

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEc-----CCHHHHHHHHHHHHhhhhhcCC
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-----GSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~-----G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ...+.||...+|.|||++|++++.|++++|++|+++.     .++.|+|.     |++.++.+|..+|.++...+++
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~   76 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPP   76 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCH
Confidence            4689999999999999999999999999999999963     35677877     9999999999999998876654

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=98.29  E-value=8.4e-07  Score=80.54  Aligned_cols=70  Identities=16%  Similarity=0.255  Sum_probs=58.0

Q ss_pred             cceEEEEeccccccceecCCCcc--hhhhhhhcCCeEEeccCCC----CCCceEEEEcCCHHHHHHHHHHHHhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVN--SKQICRQTGAKLSIRDHEA----DPNLRNIELEGSFEQIKQASAMVRELIV  166 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~--Ik~I~~~SGa~I~I~~~~~----~~~~r~v~I~G~~~~i~~A~~lI~~~i~  166 (223)
                      ..+..+.|+...+..||||+|.+  |++|+++||++|.+.+...    ......|+|+|+.++|..|+..|.++|.
T Consensus       185 ~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLP  260 (376)
T 3n89_A          185 NFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLLP  260 (376)
T ss_dssp             CEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTSE
T ss_pred             ceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhCC
Confidence            46788999999999999999955  5999999999999964322    1234789999999999999999999984

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.28  E-value=2.6e-07  Score=65.77  Aligned_cols=37  Identities=32%  Similarity=0.570  Sum_probs=31.0

Q ss_pred             CCCCcccccccCccccCCcCCCCCCCccccCccccCc
Q 027432          184 HPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       184 ~~~~~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      +|....+|+.+|++|+.|.|..|++|.|+|..++.+.
T Consensus         2 ~p~~~~~k~~~C~~fl~G~C~~G~~C~fsH~~~~~~~   38 (77)
T 2d9n_A            2 SSGSSGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKM   38 (77)
T ss_dssp             CCCCSCCTTSBCHHHHTTCCSCTTSSSSBCSCCTTTS
T ss_pred             cCCCCCCcceeCHhHccCcCCCCCCCCCccccccCcC
Confidence            3445778999999999999999999999998876544

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=98.24  E-value=4.1e-07  Score=65.83  Aligned_cols=27  Identities=26%  Similarity=0.647  Sum_probs=24.2

Q ss_pred             CCccccccCcccccccCCCCCC-CCCCcc
Q 027432           25 PTVVKSRMCNRLNSAEGCKFGD-KCHFAH   52 (223)
Q Consensus        25 ~~~~kt~~C~~~~~~g~C~~g~-~C~faH   52 (223)
                      +...|...|+.|.. |.|..|| .|+|+|
T Consensus         4 ~~~~~~~VCr~Flr-G~C~r~d~~C~f~H   31 (83)
T 3d2n_A            4 TKWLTLEVCREFQR-GTCSRPDTECKFAH   31 (83)
T ss_dssp             CGGGEEEBCTTGGG-TCCCSCTTTCSSBC
T ss_pred             cccccchhcHHHhc-CCCCCCCCCCCCcC
Confidence            34578899999999 9999997 999999

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=98.12  E-value=1.6e-06  Score=68.60  Aligned_cols=62  Identities=19%  Similarity=0.246  Sum_probs=47.3

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHH
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV  161 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI  161 (223)
                      ..+.++.||.+.+|++||++|++|+.|++++|  |.+-.... ..++.+...++++.+.+|+.++
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~-~~~~~i~~~~~p~~v~~~~~~l   64 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDE-DTCTFHIYGEDQDAVKKARSFL   64 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEET-TTTEEEEEESSHHHHHHHHHHH
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCC-CchheeeccCCHHHHHHHHHhh
Confidence            45789999999999999999999999999999  55422111 2345555566899999987654

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=98.11  E-value=9.5e-07  Score=73.32  Aligned_cols=54  Identities=22%  Similarity=0.421  Sum_probs=49.8

Q ss_pred             ccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432          107 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus       107 ~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      ..+|.||||+|.+++.|++.||++|.|.+       +.|.|.|++++++.|+..|.++|..
T Consensus       107 r~~GrIIGk~G~tik~iE~~Tg~~I~v~~-------~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          107 RIKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HHhhheeCCCccHHHHHHHHHCceEEEcC-------CEEEEEeChHHHHHHHHHHHHHHcC
Confidence            46899999999999999999999999965       3799999999999999999999964

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.08  E-value=1.5e-06  Score=83.74  Aligned_cols=63  Identities=21%  Similarity=0.324  Sum_probs=54.7

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCC-HHHHHHHHHHHHhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMVRELI  165 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~-~~~i~~A~~lI~~~i  165 (223)
                      ....++.||.+++|.|||+||.+||.|+++||++|.|.+      +..|.|.+. .+.+++|+.+|.+++
T Consensus       566 p~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          566 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            356789999999999999999999999999999999974      367888884 789999999998875

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=97.98  E-value=4e-06  Score=62.35  Aligned_cols=27  Identities=30%  Similarity=0.706  Sum_probs=23.5

Q ss_pred             cccccccCccccCCcCCCCCCCccccC
Q 027432          188 SNFKTKLCGNFAKGSCTFGDRCHFAHG  214 (223)
Q Consensus       188 ~~~kt~~C~~~~~g~C~~g~~C~faH~  214 (223)
                      ..+||.+|++|..|.|.+|++|+|+|.
T Consensus         9 ~~~k~~lC~~f~~G~C~~G~~C~f~H~   35 (98)
T 2cqe_A            9 LPKKRELCKFYITGFCARAENCPYMHG   35 (98)
T ss_dssp             CSCCCSBCTTTTTTCCSCSTTCSSBSS
T ss_pred             CCCCCccCcccccCcCCCCCCCCCCCC
Confidence            457899999998899999999999997

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=97.83  E-value=4.3e-06  Score=58.77  Aligned_cols=34  Identities=32%  Similarity=0.626  Sum_probs=28.6

Q ss_pred             CcccccccCccccCCcCCCCCCCccccCccccCc
Q 027432          187 SSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       187 ~~~~kt~~C~~~~~g~C~~g~~C~faH~~~elr~  220 (223)
                      ....|+.+|++|+.|.|..|++|.|+|..+..+.
T Consensus        11 ~~~~k~~vCk~fl~G~C~~G~~C~fsH~~~~~~~   44 (72)
T 2rhk_C           11 MSGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKM   44 (72)
T ss_dssp             SSCCCCSBCHHHHTTCCCCGGGSSSBCSCCTTSC
T ss_pred             CCCCcCeeCHHHhcCCCCCCCCCCCccccccccC
Confidence            3567899999999999999999999998765443

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=97.81  E-value=7.5e-06  Score=59.92  Aligned_cols=28  Identities=25%  Similarity=0.610  Sum_probs=24.0

Q ss_pred             ccccCccccCCcCCCCCCCccccCccccC
Q 027432          191 KTKLCGNFAKGSCTFGDRCHFAHGAAELR  219 (223)
Q Consensus       191 kt~~C~~~~~g~C~~g~~C~faH~~~elr  219 (223)
                      +...|.+|.+|.|..+ .|+|.|....|.
T Consensus        50 ~~~vC~dflkG~C~r~-~Cky~H~~~hl~   77 (89)
T 2rpp_A           50 RVIACFDSLKGRCSRE-NCKYLHPPTHLK   77 (89)
T ss_dssp             BEEBCHHHHHTCCCCT-TCCSBCCCHHHH
T ss_pred             ceeeehhhhhCcCCCC-CcceecCHHHHH
Confidence            4567999999999998 899999877664

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.62  E-value=1.3e-05  Score=78.26  Aligned_cols=68  Identities=22%  Similarity=0.316  Sum_probs=12.0

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCCC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGPA  171 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~~  171 (223)
                      ...++.||.++++.|||+||.+||+|.++||++|.|.+      +..|.|.+ +.+.+++|+.+|..++.+...+
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d------dG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG  638 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDGAKIKAAIDWIKSITDEAEVG  638 (726)
T ss_dssp             C-------------------------------------------------CCSCHHHHHHHHHC-----------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC------CceEEEEeCCHHHHHHHHHHHHHHhhhhcCC
Confidence            45678999999999999999999999999999999965      35577776 5999999999999999876654

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=97.38  E-value=4.3e-05  Score=53.18  Aligned_cols=28  Identities=32%  Similarity=0.899  Sum_probs=25.1

Q ss_pred             ccccCccccCCcCCCCC-CCccccCcccc
Q 027432          191 KTKLCGNFAKGSCTFGD-RCHFAHGAAEL  218 (223)
Q Consensus       191 kt~~C~~~~~g~C~~g~-~C~faH~~~el  218 (223)
                      |.++|++|+.|.|..|+ .|.|+|..+++
T Consensus         5 k~~vC~~f~~G~C~rg~~~C~f~H~~~~~   33 (70)
T 3d2q_A            5 RLEVCREYQRGNCNRGENDCRFAHPADST   33 (70)
T ss_dssp             EEEBCHHHHTTCCSSCTTTCSSBCCCTTS
T ss_pred             cchhCHHHhcCCCCCCCCCCCCccCcccc
Confidence            67899999999999999 59999987764

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.15  E-value=9.8e-05  Score=54.82  Aligned_cols=32  Identities=34%  Similarity=0.748  Sum_probs=28.1

Q ss_pred             CcccccccCccccCCcCCCCC-CCccccCcccc
Q 027432          187 SSNFKTKLCGNFAKGSCTFGD-RCHFAHGAAEL  218 (223)
Q Consensus       187 ~~~~kt~~C~~~~~g~C~~g~-~C~faH~~~el  218 (223)
                      ....|.++|++|+.|.|..|+ .|+|+|..+++
T Consensus        15 ~~~~k~~VCr~FlrG~C~rgd~~C~FsH~~~~~   47 (98)
T 2e5s_A           15 LRTDKLEVCREFQRGNCARGETDCRFAHPADST   47 (98)
T ss_dssp             CCSSEEEBCSHHHHTCCSSHHHHCSSBCCSSCC
T ss_pred             cChhhhhhhHHHhcCcCCCCCCCCCCcCCchhc
Confidence            355688999999999999999 89999998765

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1

Probab=97.13  E-value=0.0001  Score=47.77  Aligned_cols=28  Identities=18%  Similarity=0.513  Sum_probs=25.9

Q ss_pred             ccccccCcccccccCCCCCCCCCCcccc
Q 027432           27 VVKSRMCNRLNSAEGCKFGDKCHFAHGE   54 (223)
Q Consensus        27 ~~kt~~C~~~~~~g~C~~g~~C~faH~~   54 (223)
                      ..+|.+|..|...|.|++|.+|.|.|..
T Consensus        17 ~~~~~iC~~FSayGwCp~G~~Cp~SHDi   44 (50)
T 2fc6_A           17 PHPTSICDNFSAYGWCPLGPQCPQSHDI   44 (50)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCCC
T ss_pred             ccccchhhhccccccCCCCCCCCccccC
Confidence            3789999999999999999999999954

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=96.97  E-value=0.00038  Score=50.08  Aligned_cols=30  Identities=30%  Similarity=0.771  Sum_probs=23.7

Q ss_pred             cccccccCccccCCcCCCCC-CCccccCccc
Q 027432          188 SNFKTKLCGNFAKGSCTFGD-RCHFAHGAAE  217 (223)
Q Consensus       188 ~~~kt~~C~~~~~g~C~~g~-~C~faH~~~e  217 (223)
                      ...|..+|++|+.|.|..+| .|+|+|....
T Consensus         5 ~~~~~~VCr~FlrG~C~r~d~~C~f~H~~~~   35 (83)
T 3d2n_A            5 KWLTLEVCREFQRGTCSRPDTECKFAHPSKS   35 (83)
T ss_dssp             GGGEEEBCTTGGGTCCCSCTTTCSSBCCCTT
T ss_pred             ccccchhcHHHhcCCCCCCCCCCCCcCCCcc
Confidence            44577888888888888886 8888887653

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=96.39  E-value=0.00076  Score=49.16  Aligned_cols=30  Identities=30%  Similarity=0.782  Sum_probs=25.7

Q ss_pred             cccccccCccccCCcCCCCC-CCccccCccc
Q 027432          188 SNFKTKLCGNFAKGSCTFGD-RCHFAHGAAE  217 (223)
Q Consensus       188 ~~~kt~~C~~~~~g~C~~g~-~C~faH~~~e  217 (223)
                      ...+.++|+.|+.|.|..++ .|+|+|-.+.
T Consensus        13 ~~~~~~VCrdFlrG~C~r~d~~CrfsH~~~~   43 (89)
T 2rpp_A           13 KWLTLEVCRQFQRGTCSRSDEECKFAHPPKS   43 (89)
T ss_dssp             SSSEECBCHHHHHTCCCCCTTTSSSBCCCSS
T ss_pred             CcchhhhchHHhcCCCCCCCCCCCCcCCCcc
Confidence            34567899999999999998 9999997654

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1

Probab=96.15  E-value=0.0017  Score=42.02  Aligned_cols=28  Identities=32%  Similarity=0.771  Sum_probs=25.2

Q ss_pred             ccccccCcccc-CCcCCCCCCCccccCcc
Q 027432          189 NFKTKLCGNFA-KGSCTFGDRCHFAHGAA  216 (223)
Q Consensus       189 ~~kt~~C~~~~-~g~C~~g~~C~faH~~~  216 (223)
                      ..+|.+|+.|. -|.|++|.+|.|.|..+
T Consensus        17 ~~~~~iC~~FSayGwCp~G~~Cp~SHDiD   45 (50)
T 2fc6_A           17 PHPTSICDNFSAYGWCPLGPQCPQSHDIS   45 (50)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCCCC
T ss_pred             ccccchhhhccccccCCCCCCCCccccCC
Confidence            46899999999 79999999999999764

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.94  E-value=0.0012  Score=64.47  Aligned_cols=67  Identities=22%  Similarity=0.372  Sum_probs=0.0

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ....+.||.++++.|||+||.+|+.|.+++|+.|.|.+      +..|.|++ +.+.+++|..+|..++.+...
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~~~~~~a~~~i~~i~~~~~v  627 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEKAKHAIRRIEEITAEIEV  627 (723)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCHHHHHHHHHHHHHHhhhhhc
Confidence            45678899999999999999999999999999998864      34566665 577888898888887765554

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=95.45  E-value=0.0014  Score=64.42  Aligned_cols=61  Identities=21%  Similarity=0.271  Sum_probs=21.1

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhh
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELI  165 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i  165 (223)
                      ...+.||.+++|.|||++|.+||+|.+++|+.|.|.+      +..|.|+. +.+.++.|+.+|..+.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC--------------CCCBSSHHHHCC---------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3457899999999999999999999999999998864      35567766 5778888887877766

>3u9g_A Zinc finger CCCH-type antiviral protein 1; zinc finger protein; 1.80A {Rattus norvegicus}

Probab=91.41  E-value=0.11  Score=43.71  Aligned_cols=21  Identities=29%  Similarity=0.945  Sum_probs=17.7

Q ss_pred             cCccccCCcCCCCCCCccccCc
Q 027432          194 LCGNFAKGSCTFGDRCHFAHGA  215 (223)
Q Consensus       194 ~C~~~~~g~C~~g~~C~faH~~  215 (223)
                      +|++|..|.|+| .+|.=+|..
T Consensus       177 IC~~Fl~G~C~f-~~CkRsH~~  197 (229)
T 3u9g_A          177 ICEHFTRGNCSY-LNCLRSHNL  197 (229)
T ss_dssp             SCHHHHTTCCCC-SSCSSCCCT
T ss_pred             ccchhhcCCcCC-CCccCccCc
Confidence            588888899998 689888865

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=90.91  E-value=0.04  Score=46.80  Aligned_cols=22  Identities=41%  Similarity=0.946  Sum_probs=20.7

Q ss_pred             ccCccccCCcCCCCCCCccccC
Q 027432          193 KLCGNFAKGSCTFGDRCHFAHG  214 (223)
Q Consensus       193 ~~C~~~~~g~C~~g~~C~faH~  214 (223)
                      .+|.+|.+|.|..|+.|.|.|.
T Consensus        71 ~~C~ffakG~C~~G~~C~y~H~   92 (240)
T 3u1l_A           71 FFCLFFAKGMCCLGPKCEYLHH   92 (240)
T ss_dssp             SBCHHHHTTCCSCGGGCSSBBS
T ss_pred             eEcCccccCCCCCCCCCCccCC
Confidence            4899999999999999999995

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=90.77  E-value=0.1  Score=40.99  Aligned_cols=37  Identities=24%  Similarity=0.327  Sum_probs=34.2

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      ....+.|....+|+.||++|++|+.|.++.|-+|.|-
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV   72 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVV   72 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEE
Confidence            5678899999999999999999999999999999884

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=88.78  E-value=0.096  Score=44.44  Aligned_cols=22  Identities=27%  Similarity=0.628  Sum_probs=20.1

Q ss_pred             ccCcccccccCCCCCCCCCCccc
Q 027432           31 RMCNRLNSAEGCKFGDKCHFAHG   53 (223)
Q Consensus        31 ~~C~~~~~~g~C~~g~~C~faH~   53 (223)
                      .+|.+|.. |.|.+|+.|.|.|.
T Consensus        71 ~~C~ffak-G~C~~G~~C~y~H~   92 (240)
T 3u1l_A           71 FFCLFFAK-GMCCLGPKCEYLHH   92 (240)
T ss_dssp             SBCHHHHT-TCCSCGGGCSSBBS
T ss_pred             eEcCcccc-CCCCCCCCCCccCC
Confidence            48999988 99999999999995

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=81.79  E-value=0.56  Score=40.10  Aligned_cols=39  Identities=31%  Similarity=0.434  Sum_probs=36.0

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  135 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~  135 (223)
                      ..+..+.||.+..++-|||+|.|++.-.+-||-+|.|.+
T Consensus       183 ~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  221 (251)
T 2asb_A          183 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  221 (251)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceE
Confidence            467889999999999999999999999999999999953

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=80.50  E-value=0.16  Score=39.93  Aligned_cols=39  Identities=28%  Similarity=0.330  Sum_probs=34.3

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      ......+.||.+..++.|||+|.|++-..+-+|.+|.|.
T Consensus       101 ~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A          101 GVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             TEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             CcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            356778899999999999999999999999999887664

---

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	223
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	8e-18
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	5e-16
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	6e-16
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-15
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	3e-15
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-15
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	8e-15
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-13
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-13
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-13
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	4e-13
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	4e-13
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	3e-09
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	8e-13
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	1e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-12
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-12
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-11
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	6e-10
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	3e-08
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-09
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-08
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	6e-06
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-05
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	6e-05
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	2e-04
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	0.003
d1k1ga_	122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	0.004

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 72.9 bits (179), Expect = 8e-18
 Identities = 17/70 (24%), Positives = 35/70 (50%)

Query: 96  ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 155
           +  T +  V   + G IIG+GG    +I +++G K+ I         R+  L G+ E ++
Sbjct: 6   SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQ 65

Query: 156 QASAMVRELI 165
            A  ++ +++
Sbjct: 66  SAKRLLDQIV 75

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.0 bits (166), Expect = 5e-16
 Identities = 23/71 (32%), Positives = 40/71 (56%)

Query: 95  GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 154
           G   T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ +QI
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI 60

Query: 155 KQASAMVRELI 165
           + A  +++  +
Sbjct: 61  QNAQYLLQNSV 71

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.6 bits (165), Expect = 6e-16
 Identities = 17/68 (25%), Positives = 35/68 (51%)

Query: 98  ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 157
            T ++++  +L G IIG+ G N  +I + +GA++ I +     + R + + GS   I  A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 158 SAMVRELI 165
             ++   +
Sbjct: 62  QYLINARL 69

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.8 bits (163), Expect = 2e-15
 Identities = 12/70 (17%), Positives = 25/70 (35%), Gaps = 1/70 (1%)

Query: 97  SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIK 155
           S    ++VD      IIG+ G    QI  +    +      + +     I + G  +  +
Sbjct: 9   SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 68

Query: 156 QASAMVRELI 165
            A   +  ++
Sbjct: 69  AARDAILRIV 78

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.3 bits (162), Expect = 2e-15
 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++ +     G+IIGK G + K++  ++GA+  I   E +   R I L G    I +A 
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGAR--INISEGNCPERIITLAGPTNAIFKAF 62

Query: 159 AMVRELI 165
           AM+ + +
Sbjct: 63  AMIIDKL 69

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.0 bits (161), Expect = 3e-15
 Identities = 12/69 (17%), Positives = 31/69 (44%)

Query: 97  SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ 156
           S    + +     G +IG+ G   K+I    G ++  +  +     R  ++ G  ++ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 157 ASAMVRELI 165
           A+ ++ +L+
Sbjct: 62  AAEIITDLL 70

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.9 bits (161), Expect = 4e-15
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 92  ASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSF 151
           A     A+A +++       +IGK G   + +  +T  K+ I   +       I++ G+ 
Sbjct: 4   ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPS--NQIKITGTK 61

Query: 152 EQIKQASAMVRELI 165
           E I++A   V  + 
Sbjct: 62  EGIEKARHEVLLIS 75

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.8 bits (158), Expect = 8e-15
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI---RDHEADPNLRNIELEGSFEQIK 155
             +++V  +L GAI+GKGG    +    TGA++ I    +       R + + GS    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 156 QASAMVRELI 165
            A  ++ + +
Sbjct: 64  AAQYLISQRV 73

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.4 bits (149), Expect = 2e-13
 Identities = 11/68 (16%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 98  ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 157
            +  + +D  +   IIG  G   ++I  +    +        P+   + + G  E +++A
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPNCVTVTGLPENVEEA 68

Query: 158 SAMVRELI 165
              +  L 
Sbjct: 69  IDHILNLE 76

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.7 bits (147), Expect = 2e-13
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSI---RDHEADPNLRNIELEGSFEQIKQA 157
              V     G IIGKGG   K I +Q+GA++ +       ADPN++   + G+ +QI  A
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYA 63

Query: 158 SAMVRELI 165
             ++ E I
Sbjct: 64  RQLIEEKI 71

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.7 bits (147), Expect = 3e-13
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 96  ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL--RNIELEGSFEQ 153
            +A  +I + AS AG +IGKGG   KQ+  + G K+ +           + + + G   +
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK 65

Query: 154 IKQASAMVRELI 165
           ++QA  MV ELI
Sbjct: 66  VQQAKEMVLELI 77

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (147), Expect = 4e-13
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 98  ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 157
              +I++D      +IGK G N  +I  Q    + I           I +EG  + ++QA
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKS--NLIRIEGDPQGVQQA 62

Query: 158 SAMVRELI 165
              + EL 
Sbjct: 63  KRELLELA 70

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.4 bits (144), Expect = 4e-13
 Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 1/35 (2%)

Query: 187 SSNFKTKLCGNF-AKGSCTFGDRCHFAHGAAELRK 220
           SS +KT+LC  +   G C +G +C FAHG  ELR+
Sbjct: 4   SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ 38

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.0 bits (117), Expect = 3e-09
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 29 KSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP 60
          K+ +C   + +  C++G KC FAHG  EL + 
Sbjct: 8  KTELCRTYSESGRCRYGAKCQFAHGLGELRQA 39

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (142), Expect = 8e-13
 Identities = 17/34 (50%), Positives = 24/34 (70%), Gaps = 1/34 (2%)

Query: 187 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELR 219
           S+ +KT+LC  F   G+C +G++C FAHG  ELR
Sbjct: 1   STRYKTELCRPFEESGTCKYGEKCQFAHGFHELR 34

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (113), Expect = 1e-08
 Identities = 13/29 (44%), Positives = 18/29 (62%)

Query: 29 KSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
          K+ +C     +  CK+G+KC FAHG  EL
Sbjct: 5  KTELCRPFEESGTCKYGEKCQFAHGFHEL 33

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (144), Expect = 1e-12
 Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 99  TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
           T ++ V   L   +IG+ G   +++  +    + +   E       I + G    + +A 
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQS--DIIAITGLAANLDRAK 68

Query: 159 AMVRELI 165
           A + E +
Sbjct: 69  AGLLERV 75

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.7 bits (139), Expect = 7e-12
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 85  PPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH--EADPNL 142
                   +       ++SV     G IIG+GG   + IC+ +GAK++            
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS 61

Query: 143 RNIELEGSFEQIKQASAMVRELI 165
           R I++ G+ +++  A  ++ E +
Sbjct: 62  RLIKISGTQKEVAAAKHLILEKV 84

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (133), Expect = 4e-11
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 98  ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 157
           A  ++S+ A L  ++IG  G   + I  + G  + I           + + G    +++A
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSDVEKA 68

Query: 158 SAMVRELI 165
              +  L 
Sbjct: 69  KKQLLHLA 76

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 34

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (122), Expect = 6e-10
 Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 4/35 (11%)

Query: 184 HPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAE 217
           HP    +KT+LC  F   G C +G RCHF H A E
Sbjct: 3   HP---KYKTELCRTFHTIGFCPYGPRCHFIHNADE 34

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 34

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (110), Expect = 3e-08
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 29 KSRMCNRLNSAEGCKFGDKCHFAHGEWE 56
          K+ +C   ++   C +G +CHF H   E
Sbjct: 7  KTELCRTFHTIGFCPYGPRCHFIHNADE 34

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 49.8 bits (119), Expect = 4e-09
 Identities = 14/72 (19%), Positives = 30/72 (41%)

Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 161
           + V     GA+IG  G    +I R+TG  +++    +   +           + +A+ +V
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVV 66

Query: 162 RELIVRIGPAHA 173
           + + +   P  A
Sbjct: 67  KAISLGFPPEKA 78

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 47.4 bits (113), Expect = 3e-08
 Identities = 8/64 (12%), Positives = 25/64 (39%), Gaps = 6/64 (9%)

Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 161
           ++++ +    +IGK G   K +  +   ++ +  +        I + G   ++  A   +
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN------GLIWVNGDRRKVSIAEEAI 58

Query: 162 RELI 165
             + 
Sbjct: 59  YLIE 62

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 45.9 bits (109), Expect = 2e-07
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 9/65 (13%)

Query: 110 GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 169
           G IIG+GG   + I   T   +++ ++E       + + G +E+   A   +  L    G
Sbjct: 25  GRIIGEGGRARRTIEEMTDTYINVGEYE-------VAIIGDYERAMAAKQAIEMLAE--G 75

Query: 170 PAHAK 174
             H+ 
Sbjct: 76  RMHST 80

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 40.0 bits (94), Expect = 6e-06
 Identities = 11/40 (27%), Positives = 17/40 (42%)

Query: 96  ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135
           A     + +     G +IG       QI   TGA+++I D
Sbjct: 1   APRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED 40

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (94), Expect = 1e-05
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 5/73 (6%)

Query: 94  FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFE 152
             A+   +  V   L G  IG  G N +Q  +  G      D     +     + G S +
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESAD 59

Query: 153 QIKQASAMVRELI 165
            +K+A   +  + 
Sbjct: 60  AVKKARGFLEFVE 72

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (90), Expect = 6e-05
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 98  ATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQ 156
             + ++  + L   IIGK G N  +I +Q     +   + E       I LEG  E +  
Sbjct: 21  TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGE-----DKITLEGPTEDVSV 75

Query: 157 ASAMVRELI 165
           A   +  ++
Sbjct: 76  AQEQIEGMV 84

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 7/65 (10%), Positives = 21/65 (32%), Gaps = 7/65 (10%)

Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSF-EQIKQASAM 160
           I +       +IGK     + +  ++G  + + ++        I          +     
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFSEEILIEA 58

Query: 161 VRELI 165
           +R++ 
Sbjct: 59  IRKIE 63

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 5/34 (14%), Positives = 14/34 (41%)

Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 135
           + +  +    +IG+     K +  +T  K+ +  
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR 38

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

 Score = 34.4 bits (79), Expect = 0.003
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 24/89 (26%)

Query: 108 LAGAIIGKGGVNSKQICRQTGAKLSIR--------------------DHEADPNLRNIEL 147
             G I+G  G+ +KQ+  +TG K+ +R                    +H  +     I +
Sbjct: 18  FVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITV 77

Query: 148 EGS----FEQIKQASAMVRELIVRIGPAH 172
           E +      ++K+A   V++L+V      
Sbjct: 78  EDAQNRAELKLKRAVEEVKKLLVPAAEGE 106

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.0 bits (78), Expect = 0.004
 Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 17/85 (20%)

Query: 108 LAGAIIGKGGVNSKQICRQTGAKLSIR----------DHEADPNLRNIELE-------GS 150
             G +IG  G   K I ++  AK+ IR            +    L   +          +
Sbjct: 19  FVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANT 78

Query: 151 FEQIKQASAMVRELIVRIGPAHAKN 175
            E +K+A   +R ++ +        
Sbjct: 79  MENVKKAVEQIRNILKQGIETPEDQ 103

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	223
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.68
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.67
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.66
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.66
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.65
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.62
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.62
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.61
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.61
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.59
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.59
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.58
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.57
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.5
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.45
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.4
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.36
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.3
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.13
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.1
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.99
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.88
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.72
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.65
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.24
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	97.97
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	97.8
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.67
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	96.84
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.02
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	95.27
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.22
d2fc6a1	37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	94.32
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	86.03
d2fc6a1	37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	84.84
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	80.71

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.7e-17  Score=116.46  Aligned_cols=73  Identities=30%  Similarity=0.494  Sum_probs=68.4

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      ...|.++.||.+++|.||||+|++|++|+++|||+|+|.+...+..+|.|+|+|++++++.|+.+|.++++++
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4568899999999999999999999999999999999987777788999999999999999999999999875

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.1e-17  Score=104.06  Aligned_cols=37  Identities=32%  Similarity=0.745  Sum_probs=35.0

Q ss_pred             CCCccccccCcccccccCCCCCCCCCCcccccccCCC
Q 027432           24 GPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP   60 (223)
Q Consensus        24 ~~~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~~   60 (223)
                      .+++|||+||++|...|.|+||++|+||||++|||.+
T Consensus         3 ~~~~yKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~~   39 (40)
T d1m9oa_           3 TSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQA   39 (40)
T ss_dssp             CSSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGT
T ss_pred             CCCccccccChhhhcCCcCCCCCCCCCCCCHHHhcCC
Confidence            5689999999999999999999999999999999975

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=3.3e-17  Score=113.83  Aligned_cols=69  Identities=25%  Similarity=0.445  Sum_probs=65.1

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV  166 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~  166 (223)
                      .|.++.||++.+|.||||+|.+|++|+++||++|+|.+...+..+|.|+|+|++++++.|+.+|.++|.
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   70 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLS   70 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHcC
Confidence            588999999999999999999999999999999999887778889999999999999999999998873

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=3e-17  Score=115.00  Aligned_cols=72  Identities=17%  Similarity=0.385  Sum_probs=67.4

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      +.++++.||.+.+|+||||+|++|++|+++|||+|+|.+..++..+|.|+|+|+++++++|+.+|.++|++.
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999999987777788999999999999999999999999864

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=7.2e-18  Score=102.60  Aligned_cols=35  Identities=40%  Similarity=0.856  Sum_probs=33.1

Q ss_pred             CCccccccCcccccccCCCCCCCCCCcccccccCC
Q 027432           25 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGK   59 (223)
Q Consensus        25 ~~~~kt~~C~~~~~~g~C~~g~~C~faH~~~el~~   59 (223)
                      +++|||+||++|...|.|+||++|+||||++|||.
T Consensus         1 ~~kyKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~   35 (36)
T d1rgoa1           1 STRYKTELCRPFEESGTCKYGEKCQFAHGFHELRS   35 (36)
T ss_dssp             CTTTTSSBCHHHHHHSCCTTGGGCSSBSSGGGCCC
T ss_pred             CCCcchhhCcchhcCCcCCCCCcCCCcCCHHHccC
Confidence            47999999999999999999999999999999995

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=6.9e-17  Score=100.45  Aligned_cols=36  Identities=47%  Similarity=1.090  Sum_probs=33.5

Q ss_pred             CcccccccCcccc-CCcCCCCCCCccccCccccCcCC
Q 027432          187 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRKTA  222 (223)
Q Consensus       187 ~~~~kt~~C~~~~-~g~C~~g~~C~faH~~~elr~~~  222 (223)
                      +.+|||+||++|. .|.|+||++|+||||++|||++.
T Consensus         4 ~~~yKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~~n   40 (40)
T d1m9oa_           4 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQAN   40 (40)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGTC
T ss_pred             CCccccccChhhhcCCcCCCCCCCCCCCCHHHhcCCC
Confidence            5899999999998 69999999999999999999863

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.1e-16  Score=109.88  Aligned_cols=67  Identities=34%  Similarity=0.585  Sum_probs=60.4

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC---CCCCCceEEEEcCCHHHHHHHHHHHHhhh
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELI  165 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---~~~~~~r~v~I~G~~~~i~~A~~lI~~~i  165 (223)
                      +.++.||++.+|.||||+|++|++|++.|||+|+|.+.   ..+..+|.|+|+|+++++++|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            57899999999999999999999999999999999532   33456799999999999999999999875

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=3.4e-16  Score=109.62  Aligned_cols=69  Identities=25%  Similarity=0.409  Sum_probs=62.1

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC---CCCCCceEEEEcCCHHHHHHHHHHHHhhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIV  166 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~---~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~  166 (223)
                      .++++.||++.+|.||||+|++|++|+++|||+|+|.+.   .++..+|.|+|+|+++++++|+.+|.++|.
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   74 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHcC
Confidence            467999999999999999999999999999999999543   345678999999999999999999998873

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2.7e-17  Score=100.04  Aligned_cols=34  Identities=50%  Similarity=1.151  Sum_probs=31.8

Q ss_pred             CcccccccCcccc-CCcCCCCCCCccccCccccCc
Q 027432          187 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK  220 (223)
Q Consensus       187 ~~~~kt~~C~~~~-~g~C~~g~~C~faH~~~elr~  220 (223)
                      +++|||+||++|. .|.|+||++|+||||++|||.
T Consensus         1 ~~kyKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~   35 (36)
T d1rgoa1           1 STRYKTELCRPFEESGTCKYGEKCQFAHGFHELRS   35 (36)
T ss_dssp             CTTTTSSBCHHHHHHSCCTTGGGCSSBSSGGGCCC
T ss_pred             CCCcchhhCcchhcCCcCCCCCcCCCcCCHHHccC
Confidence            3689999999998 799999999999999999995

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=3.2e-16  Score=109.00  Aligned_cols=69  Identities=28%  Similarity=0.413  Sum_probs=63.2

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      +.|.+++||++.+|.||||+|++|++|+++|||+|+|.+.  +..+|+|+|+|+++++.+|+.+|.++|.+
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC--CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            4578999999999999999999999999999999999754  34589999999999999999999999864

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=7e-16  Score=109.18  Aligned_cols=72  Identities=24%  Similarity=0.432  Sum_probs=67.8

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      ...+.+|.||.+.+|.|||++|.+|++|++.|||+|.|.+...+..++.|+|+|++++++.|+.+|.++|.+
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            457889999999999999999999999999999999998877788899999999999999999999999986

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.1e-16  Score=96.04  Aligned_cols=33  Identities=27%  Similarity=0.664  Sum_probs=30.8

Q ss_pred             CCCccccccCcccccccCCCCCCCCCCcccccc
Q 027432           24 GPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWE   56 (223)
Q Consensus        24 ~~~~~kt~~C~~~~~~g~C~~g~~C~faH~~~e   56 (223)
                      +.++|||+||++|...|.|+||++|+||||++|
T Consensus         2 rhpkyKT~lC~~f~~~g~C~yG~~C~FaHg~~E   34 (34)
T d1rgoa2           2 RHPKYKTELCRTFHTIGFCPYGPRCHFIHNADE   34 (34)
T ss_dssp             CCTTTTCSBCHHHHHHSCCTTGGGCSSBCCSCC
T ss_pred             CCCCccchhccccCCCCcCCCCCcccCcCCCCC
Confidence            346899999999999999999999999999987

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=9.1e-16  Score=109.20  Aligned_cols=72  Identities=32%  Similarity=0.458  Sum_probs=65.2

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC--CCCCCceEEEEcCCHHHHHHHHHHHHhhhhh
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH--EADPNLRNIELEGSFEQIKQASAMVRELIVR  167 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~--~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~  167 (223)
                      ...+.+|+||.+.+|.||||+|++|++|+++|||+|+|.+.  .+...+|.|+|+|++++|++|+.+|.++|.+
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999999643  3445689999999999999999999999976

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=1.9e-14  Score=106.82  Aligned_cols=73  Identities=25%  Similarity=0.420  Sum_probs=64.9

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCC--CCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE--ADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~--~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+++|+||.+.+|.||||+|.+|++|+++|||+|+|.+..  ....+|+|+|+|++++|+.|+.+|.++|.+.+
T Consensus        14 ~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            46789999999999999999999999999999999996443  34467999999999999999999999997644

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=4e-14  Score=101.11  Aligned_cols=73  Identities=18%  Similarity=0.282  Sum_probs=65.6

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEecc-CCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~-~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+.++.||...++.|||++|++|++|+++|||+|++.+ ...+..++.|+|+|+.++|..|+.+|.+++.+.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~e   82 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELE   82 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhHh
Confidence            356889999999999999999999999999999999954 4556678999999999999999999999998753

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=3.4e-15  Score=89.33  Aligned_cols=30  Identities=50%  Similarity=1.101  Sum_probs=28.4

Q ss_pred             cccccccCcccc-CCcCCCCCCCccccCccc
Q 027432          188 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAE  217 (223)
Q Consensus       188 ~~~kt~~C~~~~-~g~C~~g~~C~faH~~~e  217 (223)
                      .+|||+||++|. .|.|+||++|+||||++|
T Consensus         4 pkyKT~lC~~f~~~g~C~yG~~C~FaHg~~E   34 (34)
T d1rgoa2           4 PKYKTELCRTFHTIGFCPYGPRCHFIHNADE   34 (34)
T ss_dssp             TTTTCSBCHHHHHHSCCTTGGGCSSBCCSCC
T ss_pred             CCccchhccccCCCCcCCCCCcccCcCCCCC
Confidence            579999999998 699999999999999987

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=1.4e-13  Score=97.73  Aligned_cols=75  Identities=21%  Similarity=0.284  Sum_probs=65.8

Q ss_pred             CCCCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           93 SFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        93 s~g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      .+....+.++.||.+.+|.|||++|.+|++|+++||++|++.+.  +...+.|+|+|+.+++++|+.+|.+++.+.+
T Consensus         5 ~~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1           5 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             HhcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC--CCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            34456789999999999999999999999999999999999643  3346889999999999999999999998743

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=3.3e-13  Score=95.68  Aligned_cols=73  Identities=16%  Similarity=0.267  Sum_probs=63.8

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      ....+.++.||...++.|||++|++|++|+++||++|++.+... .+.+.|+|+|++++|++|+.+|.++++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999999999999999965432 23568999999999999999999998874

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=1.5e-13  Score=97.14  Aligned_cols=71  Identities=23%  Similarity=0.248  Sum_probs=61.4

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ...+.++.||.+++|.|||+||++|++|+++|||+|.+.+.    .++.|+|.| +++++++|+.||..+....+.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~~~~~eV   77 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFVEDFIQV   77 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCCCCCCCC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHhheeecC
Confidence            35688999999999999999999999999999999998653    246799999 799999999999877765543

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=5.8e-13  Score=94.52  Aligned_cols=74  Identities=16%  Similarity=0.262  Sum_probs=64.1

Q ss_pred             CCcceEEEEeccccccceecCCCcchhhhhhh-cCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432           95 GASATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus        95 g~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~-SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ....+.+|.||...+|.|||++|++|++|+++ ++++|++.+.  +..++.|+|+|+++++++|+.+|.+++.+.+.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~--~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~~   81 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   81 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC--CCCCceEEEeCCHHHHHHHHHHHHHHHhhhhc
Confidence            34568999999999999999999999999987 5888888543  34568999999999999999999999987653

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=5.5e-13  Score=92.31  Aligned_cols=67  Identities=25%  Similarity=0.333  Sum_probs=60.2

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhh
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI  165 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i  165 (223)
                      ....++.||....+.|||++|++|++|+++||++|++.+.  +..++.|+|.|+++++++|+.+|.+++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~--~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC--CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            3567899999999999999999999999999999999643  345689999999999999999999875

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.30  E-value=1e-12  Score=94.09  Aligned_cols=65  Identities=12%  Similarity=0.153  Sum_probs=59.1

Q ss_pred             EEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432          100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       100 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..+.||.+++|.|||++|++|++|+++||++|+|.+      +..|+|+|++++++.|+.+|..++.+...
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------~g~v~I~G~~e~v~~A~~~I~~i~~ea~~   67 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIAEEAIYLIEQEAHT   67 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------TSEEEEESCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------CCEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            468999999999999999999999999999999964      35799999999999999999999987553

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.6e-12  Score=93.90  Aligned_cols=71  Identities=15%  Similarity=0.240  Sum_probs=63.3

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  169 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+.+|.||.+.+|.|||++|.+|++|+++||++|.+.+.  +..+..|+|+|+.++|+.|+.+|.+++.+.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~~   79 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAANLDRAKAGLLERVKELQ   79 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC--CCCcceEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999653  3346789999999999999999999997644

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.13  E-value=4.1e-12  Score=90.82  Aligned_cols=71  Identities=18%  Similarity=0.257  Sum_probs=56.1

Q ss_pred             EEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432          100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       100 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..+.||.+.+|.|||+||++||+|+++|||+|+|.+.......+.....+.+.++++|..+|.++...+++
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf~P   75 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPP   75 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHhCCCCh
Confidence            56899999999999999999999999999999996433221122233466899999999999998765554

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=7.1e-11  Score=85.16  Aligned_cols=68  Identities=22%  Similarity=0.343  Sum_probs=61.0

Q ss_pred             CcceEEEEeccccccceecCCCcchhhhhhh-cCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhc
Q 027432           96 ASATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  168 (223)
Q Consensus        96 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~-SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~  168 (223)
                      ...|..+.||....+.|||++|++|++|+++ ++++|++.+.     ...|+|+|++++|++|+.+|.+++.+.
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~-----~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG-----EDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS-----SCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC-----CceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999 4899999642     367999999999999999999999875

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.99  E-value=1.1e-11  Score=85.43  Aligned_cols=64  Identities=11%  Similarity=0.053  Sum_probs=50.2

Q ss_pred             EEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCC-HHHHHHHHHHHHhhhhhcC
Q 027432          100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMVRELIVRIG  169 (223)
Q Consensus       100 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~-~~~i~~A~~lI~~~i~~~~  169 (223)
                      ..+.||.+++|.|||++|++||.|+++||++|+|.+      +..|+|+|. .+.++.|..+|..+.++..
T Consensus         3 ~vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~------~g~v~I~g~~~~~v~~A~~~I~~i~~ea~   67 (69)
T d2je6i3           3 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             CEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT------TSEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEEChhhccceECCchhHHHHHHHHHCCEEEEcC------CCEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            357899999999999999999999999999999954      246999995 7899999999998887754

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.88  E-value=1.2e-09  Score=78.17  Aligned_cols=65  Identities=14%  Similarity=0.105  Sum_probs=57.7

Q ss_pred             EEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC-CHHHHHHHHHHHHhhhhhcCC
Q 027432          100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       100 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G-~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      ..+.||.+++|.|||+||++|+.|+++||++|.|.+.      ..|.|.| +.+.+..|..+|..+..+...
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~~~~~~A~~~I~~I~~ea~v   68 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAIKIIDEEAYT   68 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCHHHHHHHHHHHHHHHHhchh
Confidence            4688999999999999999999999999999999652      3699999 589999999999999887553

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.72  E-value=4.9e-10  Score=73.36  Aligned_cols=45  Identities=24%  Similarity=0.341  Sum_probs=13.8

Q ss_pred             eEEEEeccccccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcC
Q 027432           99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG  149 (223)
Q Consensus        99 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G  149 (223)
                      ..++.||.+++|.|||+||.+||+|+++||++|+|.+      +..|+|+|
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a   48 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGA   48 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCC
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEe
Confidence            4578999999999999999999999999999999964      35677776

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.65  E-value=5.1e-09  Score=77.20  Aligned_cols=56  Identities=21%  Similarity=0.366  Sum_probs=49.8

Q ss_pred             cccceecCCCcchhhhhhhcCCeEEeccCCCCCCceEEEEcCCHHHHHHHHHHHHhhhhhcCC
Q 027432          108 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  170 (223)
Q Consensus       108 ~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~~~~~r~v~I~G~~~~i~~A~~lI~~~i~~~~~  170 (223)
                      +.|.|||+||.+|+.|++.|||+|.|.+       ..|.|.|++++++.|+.+|.+++...+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d-------~~v~iig~~e~i~~A~~~Ie~li~~~e~   78 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAEGRMH   78 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHTTCCH
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC-------CeEEEEECchhHHHHHHHHHHHHcCCCc
Confidence            4799999999999999999999999964       2477889999999999999999987554

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=1.1e-06  Score=66.22  Aligned_cols=71  Identities=23%  Similarity=0.368  Sum_probs=54.0

Q ss_pred             ceEEEEecccc------ccceecCCCcchhhhhhhcCCeEEeccC-C--------CC------CCc-eEEEEcC-CHHHH
Q 027432           98 ATAKISVDASL------AGAIIGKGGVNSKQICRQTGAKLSIRDH-E--------AD------PNL-RNIELEG-SFEQI  154 (223)
Q Consensus        98 ~t~~i~VP~~~------vG~IIGkgG~~Ik~I~~~SGa~I~I~~~-~--------~~------~~~-r~v~I~G-~~~~i  154 (223)
                      .+.+|+||.+.      ||.|||.+|.++|+|+++|||+|.|.-. +        .+      ..+ =-|.|++ +++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            46789999764      9999999999999999999999999421 0        00      011 1244444 68999


Q ss_pred             HHHHHHHHhhhhhc
Q 027432          155 KQASAMVRELIVRI  168 (223)
Q Consensus       155 ~~A~~lI~~~i~~~  168 (223)
                      +.|+.+|.++|...
T Consensus        83 ~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          83 KKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999753

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=1.7e-06  Score=47.92  Aligned_cols=26  Identities=23%  Similarity=0.620  Sum_probs=23.4

Q ss_pred             cccccCcccccccCCCCCCCCCCcccc
Q 027432           28 VKSRMCNRLNSAEGCKFGDKCHFAHGE   54 (223)
Q Consensus        28 ~kt~~C~~~~~~g~C~~g~~C~faH~~   54 (223)
                      .|.+||++|.+ |.|..|++|.|.|++
T Consensus         4 kkkelCKfYvq-GyCtrgenC~ymH~e   29 (29)
T d2cqea2           4 KKRELCKFYIT-GFCARAENCPYMHGD   29 (29)
T ss_dssp             CCCSBCTTTTT-TCCSCSTTCSSBSSS
T ss_pred             hhhhhhhhhee-eeecCCcCcccccCC
Confidence            47899998888 899999999999974

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.80  E-value=4.8e-06  Score=46.06  Aligned_cols=25  Identities=32%  Similarity=0.842  Sum_probs=23.3

Q ss_pred             ccccCccccCCcCCCCCCCccccCc
Q 027432          191 KTKLCGNFAKGSCTFGDRCHFAHGA  215 (223)
Q Consensus       191 kt~~C~~~~~g~C~~g~~C~faH~~  215 (223)
                      |.+||++|..|.|..|++|.|-|.+
T Consensus         5 kkelCKfYvqGyCtrgenC~ymH~e   29 (29)
T d2cqea2           5 KRELCKFYITGFCARAENCPYMHGD   29 (29)
T ss_dssp             CCSBCTTTTTTCCSCSTTCSSBSSS
T ss_pred             hhhhhhhheeeeecCCcCcccccCC
Confidence            6789999999999999999999974

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.67  E-value=1.8e-05  Score=60.12  Aligned_cols=69  Identities=26%  Similarity=0.417  Sum_probs=49.6

Q ss_pred             eEEEEecc------ccccceecCCCcchhhhhhhcCCeEEeccCCC-----------------CCCc-eEEEEcC--CH-
Q 027432           99 TAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA-----------------DPNL-RNIELEG--SF-  151 (223)
Q Consensus        99 t~~i~VP~------~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~~~-----------------~~~~-r~v~I~G--~~-  151 (223)
                      +.+|+||.      +++|.|||.+|.++|+|+++|||+|.|.-..+                 ...+ ==|.|++  .. 
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~   82 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHH
Confidence            56788885      57899999999999999999999999942211                 0111 1234444  22 


Q ss_pred             ---HHHHHHHHHHHhhhhh
Q 027432          152 ---EQIKQASAMVRELIVR  167 (223)
Q Consensus       152 ---~~i~~A~~lI~~~i~~  167 (223)
                         ..++.|..+|..+|..
T Consensus        83 ~a~~kl~~A~~~I~~lL~p  101 (134)
T d2bl5a1          83 RAELKLKRAVEEVKKLLVP  101 (134)
T ss_dssp             HHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHHHcCC
Confidence               3588999999998854

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.84  E-value=0.00015  Score=46.43  Aligned_cols=22  Identities=32%  Similarity=0.804  Sum_probs=20.7

Q ss_pred             cCcccccccCCCCCCCCCCccc
Q 027432           32 MCNRLNSAEGCKFGDKCHFAHG   53 (223)
Q Consensus        32 ~C~~~~~~g~C~~g~~C~faH~   53 (223)
                      +|++|.+++.|--||+|.|.|.
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~   23 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHD   23 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCC
T ss_pred             CcceeecCCcccCCCcccccCC
Confidence            6999999999999999999993

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.02  E-value=0.0015  Score=43.50  Aligned_cols=38  Identities=32%  Similarity=0.445  Sum_probs=35.3

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEec
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  134 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~  134 (223)
                      .....+.||.+..+..|||+|.|++-..+-||-+|.|.
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~   62 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR   62 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEE
Confidence            45688999999999999999999999999999999994

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.27  E-value=0.0027  Score=40.40  Aligned_cols=21  Identities=33%  Similarity=0.833  Sum_probs=18.5

Q ss_pred             cCccccCC-cCCCCCCCccccC
Q 027432          194 LCGNFAKG-SCTFGDRCHFAHG  214 (223)
Q Consensus       194 ~C~~~~~g-~C~~g~~C~faH~  214 (223)
                      .|++|..| .|..|++|+|.|.
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~   23 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHD   23 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCC
T ss_pred             CcceeecCCcccCCCcccccCC
Confidence            59999955 7999999999994

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.22  E-value=0.004  Score=41.43  Aligned_cols=40  Identities=30%  Similarity=0.463  Sum_probs=36.2

Q ss_pred             cceEEEEeccccccceecCCCcchhhhhhhcCCeEEeccC
Q 027432           97 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH  136 (223)
Q Consensus        97 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~SGa~I~I~~~  136 (223)
                      .....+.||.+..+..|||+|.|++-..+-+|.+|.|.+.
T Consensus        26 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          26 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            4568899999999999999999999999999999999643

>d2fc6a1 g.66.1.1 (A:8-44) Target of EGR1 protein 1, TOE1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Target of EGR1 protein 1, TOE1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.32  E-value=0.0052  Score=35.42  Aligned_cols=27  Identities=19%  Similarity=0.565  Sum_probs=24.6

Q ss_pred             ccccccCcccccccCCCCCCCCCCccc
Q 027432           27 VVKSRMCNRLNSAEGCKFGDKCHFAHG   53 (223)
Q Consensus        27 ~~kt~~C~~~~~~g~C~~g~~C~faH~   53 (223)
                      .-+|.+|..|...|.||.|.+|.-.|.
T Consensus        10 ~~~~~iC~~FsAyGWCP~G~qCp~SHd   36 (37)
T d2fc6a1          10 PHPTSICDNFSAYGWCPLGPQCPQSHD   36 (37)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCC
T ss_pred             CCccchhhhhhhccccCCCCCCcccCc
Confidence            457889999999999999999999985

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.03  E-value=0.083  Score=36.73  Aligned_cols=29  Identities=14%  Similarity=0.287  Sum_probs=25.9

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQ  126 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~  126 (223)
                      ..++|.|-...-|.|||++|.+|++|++.
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~   63 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAV   63 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHH
Confidence            45789999999999999999999998864

>d2fc6a1 g.66.1.1 (A:8-44) Target of EGR1 protein 1, TOE1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Target of EGR1 protein 1, TOE1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.84  E-value=0.17  Score=28.87  Aligned_cols=26  Identities=35%  Similarity=0.827  Sum_probs=22.8

Q ss_pred             ccccccCcccc-CCcCCCCCCCccccC
Q 027432          189 NFKTKLCGNFA-KGSCTFGDRCHFAHG  214 (223)
Q Consensus       189 ~~kt~~C~~~~-~g~C~~g~~C~faH~  214 (223)
                      --+|.+|+.|. -|-|+.|..|.-.|.
T Consensus        10 ~~~~~iC~~FsAyGWCP~G~qCp~SHd   36 (37)
T d2fc6a1          10 PHPTSICDNFSAYGWCPLGPQCPQSHD   36 (37)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCC
T ss_pred             CCccchhhhhhhccccCCCCCCcccCc
Confidence            44788999999 799999999998885

>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=80.71  E-value=0.18  Score=35.61  Aligned_cols=29  Identities=21%  Similarity=0.512  Sum_probs=25.5

Q ss_pred             ceEEEEeccccccceecCCCcchhhhhhh
Q 027432           98 ATAKISVDASLAGAIIGKGGVNSKQICRQ  126 (223)
Q Consensus        98 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~  126 (223)
                      ..++|.|-+..-|+|||++|++|+.|+++
T Consensus        61 ~~i~I~I~tarPG~iIGkkG~~i~~L~~~   89 (105)
T d2uubc1          61 DNVAVTVHVAKPGVVIGRGGERIRVLREE   89 (105)
T ss_dssp             SCEECCEEESCHHHHHCSTTSHHHHHHHH
T ss_pred             CcEEEEEEECCCceEEcCCchhHHHHHHH
Confidence            45788889999999999999999988875