Psyllid ID: psy7546

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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
Protein Sequence
MEFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA
Secondary Structure (PSIPRED)
cHHHHHHHHHccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHHccEEEEccccccccEEEEEEcccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEEEEEEEccccEEEEEccccccHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cEEEEcccHHcccccccccEEEEEEEEEcccccEEEcccccEHHHHHHHcccEEEEcccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEEEEccccccEEcccccHHHHHHHHccc
Coil and Loop (DISEMBL)
MEFFIQQLSNfkrfrggpndveLRLLIPsrvagsvigkggsniaRLRNdfkasvtvpdcpgpeRILTIFAELENGLKVIEEVLPALDEIRQKygkgrggedggdgyngggvgglgkddydiRLIVHQsqagciigkggtkIKELRDTFDA
Flexible Loop (DISEMBL)
MEFFIQQLsnfkrfrggpnDVELRLLIpsrvagsvigkGGSNIARLRNDFKasvtvpdcpgPERILTIFAELENGLKVIEEVLPALDEIRQKYgkgrggedggdgynGGGVGGLGKDDYDIRLIVHQsqagciigkggtkiKELRDTFDA
Low Complexity Region (SEG)
MEFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQkygkgrggedggdgyngggvgglgkddydIRLIVHQSQAGCiigkggtkikELRDTFDA
Disordered region (IsUnstruct)
***FIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYG*********DGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKI*********
Disordered Region (DISOPRED)
*EF********************RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR*****************************DIRLIVHQSQAGCIIGKGGTKIKELRD****
Disordered Region (DISEMBL)
MEFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA
Disordered Region (DISPRO)
MEFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGR******************KDDYDIRLIVHQSQAGCIIGKGGTKIKE*RD****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA
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	150	2.2.26 [Sep-21-2011]
Q5ZIQ3	427	Heterogeneous nuclear rib	yes	N/A	0.813	0.285	0.429	9e-23
Q5R5H8	464	Heterogeneous nuclear rib	yes	N/A	0.94	0.303	0.428	6e-22
Q4R4M6	464	Heterogeneous nuclear rib	N/A	N/A	0.94	0.303	0.428	6e-22
Q3T0D0	464	Heterogeneous nuclear rib	yes	N/A	0.94	0.303	0.428	6e-22
P61980	463	Heterogeneous nuclear rib	yes	N/A	0.94	0.304	0.428	6e-22
P61979	463	Heterogeneous nuclear rib	yes	N/A	0.94	0.304	0.428	6e-22
P61978	463	Heterogeneous nuclear rib	yes	N/A	0.94	0.304	0.428	6e-22
O19049	463	Heterogeneous nuclear rib	yes	N/A	0.94	0.304	0.428	6e-22
P57724	403	Poly(rC)-binding protein	no	N/A	0.78	0.290	0.328	5e-11
Q0VCU0	403	Poly(rC)-binding protein	no	N/A	0.78	0.290	0.328	7e-11

>sp|Q5ZIQ3|HNRPK_CHICK Heterogeneous nuclear ribonucleoprotein K OS=Gallus gallus GN=HNRNPK PE=2 SV=1

 Score =  105 bits (262), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 61/142 (42%), Positives = 86/142 (60%), Gaps = 20/142 (14%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 24  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 83

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLI 124
           IL+I A+ E   +++++++P L+E +               Y G         D ++RL+
Sbjct: 84  ILSISADTETIGEILKKIIPTLEEYQH--------------YKGSDF------DCELRLL 123

Query: 125 VHQSQAGCIIGKGGTKIKELRD 146
           +HQS AG IIG  G KIKELR+
Sbjct: 124 IHQSLAGGIIGVKGAKIKELRE 145

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.
Gallus gallus (taxid: 9031)

>sp|Q5R5H8|HNRPK_PONAB Heterogeneous nuclear ribonucleoprotein K OS=Pongo abelii GN=HNRNPK PE=2 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 27  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 86

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE-----DGGDGYNGGGVGGLGKDDY 119
           IL+I A++E   +++++++P L+E  Q        +     D  +  N     G    D 
Sbjct: 87  ILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG-SDFDC 145

Query: 120 DIRLIVHQSQAGCIIGKGGTKIKELRD 146
           ++RL++HQS AG IIG  G KIKELR+
Sbjct: 146 ELRLLIHQSLAGGIIGVKGAKIKELRE 172

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Pongo abelii (taxid: 9601)

>sp|Q4R4M6|HNRPK_MACFA Heterogeneous nuclear ribonucleoprotein K OS=Macaca fascicularis GN=HNRNPK PE=2 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 27  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 86

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE-----DGGDGYNGGGVGGLGKDDY 119
           IL+I A++E   +++++++P L+E  Q        +     D  +  N     G    D 
Sbjct: 87  ILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG-SDFDC 145

Query: 120 DIRLIVHQSQAGCIIGKGGTKIKELRD 146
           ++RL++HQS AG IIG  G KIKELR+
Sbjct: 146 ELRLLIHQSLAGGIIGVKGAKIKELRE 172

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Macaca fascicularis (taxid: 9541)

>sp|Q3T0D0|HNRPK_BOVIN Heterogeneous nuclear ribonucleoprotein K OS=Bos taurus GN=HNRNPK PE=2 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 27  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 86

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE-----DGGDGYNGGGVGGLGKDDY 119
           IL+I A++E   +++++++P L+E  Q        +     D  +  N     G    D 
Sbjct: 87  ILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG-SDFDC 145

Query: 120 DIRLIVHQSQAGCIIGKGGTKIKELRD 146
           ++RL++HQS AG IIG  G KIKELR+
Sbjct: 146 ELRLLIHQSLAGGIIGVKGAKIKELRE 172

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Bos taurus (taxid: 9913)

>sp|P61980|HNRPK_RAT Heterogeneous nuclear ribonucleoprotein K OS=Rattus norvegicus GN=Hnrnpk PE=1 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 27  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 86

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE-----DGGDGYNGGGVGGLGKDDY 119
           IL+I A++E   +++++++P L+E  Q        +     D  +  N     G    D 
Sbjct: 87  ILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG-SDFDC 145

Query: 120 DIRLIVHQSQAGCIIGKGGTKIKELRD 146
           ++RL++HQS AG IIG  G KIKELR+
Sbjct: 146 ELRLLIHQSLAGGIIGVKGAKIKELRE 172

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Rattus norvegicus (taxid: 10116)

>sp|P61979|HNRPK_MOUSE Heterogeneous nuclear ribonucleoprotein K OS=Mus musculus GN=Hnrnpk PE=1 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 27  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 86

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE-----DGGDGYNGGGVGGLGKDDY 119
           IL+I A++E   +++++++P L+E  Q        +     D  +  N     G    D 
Sbjct: 87  ILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG-SDFDC 145

Query: 120 DIRLIVHQSQAGCIIGKGGTKIKELRD 146
           ++RL++HQS AG IIG  G KIKELR+
Sbjct: 146 ELRLLIHQSLAGGIIGVKGAKIKELRE 172

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Mus musculus (taxid: 10090)

>sp|P61978|HNRPK_HUMAN Heterogeneous nuclear ribonucleoprotein K OS=Homo sapiens GN=HNRNPK PE=1 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 27  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 86

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE-----DGGDGYNGGGVGGLGKDDY 119
           IL+I A++E   +++++++P L+E  Q        +     D  +  N     G    D 
Sbjct: 87  ILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG-SDFDC 145

Query: 120 DIRLIVHQSQAGCIIGKGGTKIKELRD 146
           ++RL++HQS AG IIG  G KIKELR+
Sbjct: 146 ELRLLIHQSLAGGIIGVKGAKIKELRE 172

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Homo sapiens (taxid: 9606)

>sp|O19049|HNRPK_RABIT Heterogeneous nuclear ribonucleoprotein K OS=Oryctolagus cuniculus GN=HNRNPK PE=2 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 63/147 (42%), Positives = 90/147 (61%), Gaps = 6/147 (4%)

Query: 5   IQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPER 64
           +++   FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPER
Sbjct: 27  MEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPER 86

Query: 65  ILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE-----DGGDGYNGGGVGGLGKDDY 119
           IL+I A++E   +++++++P L+E  Q        +     D  +  N     G    D 
Sbjct: 87  ILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHFKG-SDFDC 145

Query: 120 DIRLIVHQSQAGCIIGKGGTKIKELRD 146
           ++RL++HQS AG IIG  G KIKELR+
Sbjct: 146 ELRLLIHQSLAGGIIGVKGAKIKELRE 172

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Oryctolagus cuniculus (taxid: 9986)

>sp|P57724|PCBP4_MOUSE Poly(rC)-binding protein 4 OS=Mus musculus GN=Pcbp4 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 63/131 (48%), Gaps = 14/131 (10%)

Query: 20  DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVI 79
            + LR+L+  +  GS+IGK G  + R+R    A +T+ +   PERI TI          +
Sbjct: 17  TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAV 76

Query: 80  EEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGT 139
             +   LDE           +      NGG V    +    +RL++  SQ G +IGK GT
Sbjct: 77  SMIAFKLDE-----------DLCAAPANGGSV---SRPPVTLRLVIPASQCGSLIGKAGT 122

Query: 140 KIKELRDTFDA 150
           KIKE+R+T  A
Sbjct: 123 KIKEIRETTGA 133

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

Mus musculus (taxid: 10090)

>sp|Q0VCU0|PCBP4_BOVIN Poly(rC)-binding protein 4 OS=Bos taurus GN=PCBP4 PE=2 SV=1

 Score = 66.2 bits (160), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 63/131 (48%), Gaps = 14/131 (10%)

Query: 20  DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVI 79
            + LR+L+  +  GS+IGK G  + R+R    A +T+ +   PERI TI          +
Sbjct: 17  TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAV 76

Query: 80  EEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGT 139
             +   LDE           +      NGG V    +    +RL++  SQ G +IGK GT
Sbjct: 77  SMIAFKLDE-----------DLCAAPANGGNV---SRPPVTLRLVIPASQCGSLIGKAGT 122

Query: 140 KIKELRDTFDA 150
           KIKE+R+T  A
Sbjct: 123 KIKEIRETTGA 133

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

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	150
307185703	143	Heterogeneous nuclear ribonucleoprotein	0.8	0.839	0.546	4e-33
328702411	428	PREDICTED: heterogeneous nuclear ribonuc	0.873	0.306	0.580	6e-33
328702409	426	PREDICTED: heterogeneous nuclear ribonuc	0.873	0.307	0.580	7e-33
383849051	460	PREDICTED: heterogeneous nuclear ribonuc	0.793	0.258	0.528	5e-32
307204634	139	Heterogeneous nuclear ribonucleoprotein	0.773	0.834	0.532	6e-32
328781397	482	PREDICTED: heterogeneous nuclear ribonuc	0.766	0.238	0.536	9e-32
350409768	439	PREDICTED: heterogeneous nuclear ribonuc	0.793	0.271	0.528	1e-31
332027896	172	Heterogeneous nuclear ribonucleoprotein	0.773	0.674	0.525	2e-31
340718655	466	PREDICTED: heterogeneous nuclear ribonuc	0.766	0.246	0.536	9e-31
189238821	414	PREDICTED: similar to heterogeneous nucl	0.773	0.280	0.503	2e-29

>gi|307185703|gb|EFN71619.1| Heterogeneous nuclear ribonucleoprotein K [Camponotus floridanus]

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 76/139 (54%), Positives = 96/139 (69%), Gaps = 19/139 (13%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI 68
           S  KR+R G  D ELRLLIPS+VAGS+IGKGG NI +LR+ +KAS+ VPDCPGPER+LTI
Sbjct: 18  SPHKRYRQG--DDELRLLIPSKVAGSIIGKGGQNITKLRSQYKASIIVPDCPGPERVLTI 75

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQS 128
            ++L   L+V+ EV+P L+E R + G   G                  D+ D+R++VHQS
Sbjct: 76  SSDLPTVLQVLNEVVPNLEETRFQNGSRHGS-----------------DEIDVRMLVHQS 118

Query: 129 QAGCIIGKGGTKIKELRDT 147
           QAGCIIGKGG KIKELR+ 
Sbjct: 119 QAGCIIGKGGLKIKELREV 137

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328702411|ref|XP_003241892.1| PREDICTED: heterogeneous nuclear ribonucleoprotein K-like isoform 2 [Acyrthosiphon pisum]

 Score =  145 bits (366), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 79/136 (58%), Positives = 100/136 (73%), Gaps = 5/136 (3%)

Query: 11  FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
           FKR + GP+D+ELR+LIPS+VAGS+IGKGG NI+RLR D+ A+VTVPDCPGPERILTI +
Sbjct: 15  FKRPKMGPDDIELRVLIPSKVAGSIIGKGGFNISRLRTDYNATVTVPDCPGPERILTIIS 74

Query: 71  ELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQA 130
             +N LKV+ EV+  L++     G  R    G  G  G      G+ D D+R++VHQSQA
Sbjct: 75  SNDNALKVLGEVMGNLED-----GGSRFKRGGAGGGQGNNDNQGGETDVDVRMLVHQSQA 129

Query: 131 GCIIGKGGTKIKELRD 146
           GCIIGKGG K+KELR+
Sbjct: 130 GCIIGKGGLKVKELRE 145

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328702409|ref|XP_001943097.2| PREDICTED: heterogeneous nuclear ribonucleoprotein K-like isoform 1 [Acyrthosiphon pisum] gi|328702413|ref|XP_003241893.1| PREDICTED: heterogeneous nuclear ribonucleoprotein K-like isoform 3 [Acyrthosiphon pisum]

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 79/136 (58%), Positives = 100/136 (73%), Gaps = 5/136 (3%)

Query: 11  FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
           FKR + GP+D+ELR+LIPS+VAGS+IGKGG NI+RLR D+ A+VTVPDCPGPERILTI +
Sbjct: 13  FKRPKMGPDDIELRVLIPSKVAGSIIGKGGFNISRLRTDYNATVTVPDCPGPERILTIIS 72

Query: 71  ELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQA 130
             +N LKV+ EV+  L++     G  R    G  G  G      G+ D D+R++VHQSQA
Sbjct: 73  SNDNALKVLGEVMGNLED-----GGSRFKRGGAGGGQGNNDNQGGETDVDVRMLVHQSQA 127

Query: 131 GCIIGKGGTKIKELRD 146
           GCIIGKGG K+KELR+
Sbjct: 128 GCIIGKGGLKVKELRE 143

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849051|ref|XP_003700160.1| PREDICTED: heterogeneous nuclear ribonucleoprotein K-like [Megachile rotundata]

 Score =  142 bits (358), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 75/142 (52%), Positives = 96/142 (67%), Gaps = 23/142 (16%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI 68
           S  KR+R G  D ELRLLIPS+VAGS+IGKGG NI +LR+ +KAS+ VPDCPGPER+LTI
Sbjct: 37  SPHKRYRQG--DDELRLLIPSKVAGSIIGKGGQNITKLRSQYKASIIVPDCPGPERVLTI 94

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQS 128
            ++L   L+V+ EV+P L+E   ++                     G D+ D+R++VHQS
Sbjct: 95  SSDLPTVLQVLNEVVPNLEENGSRH---------------------GSDEIDVRMLVHQS 133

Query: 129 QAGCIIGKGGTKIKELRDTFDA 150
           QAGCIIGKGG KIKELR+   A
Sbjct: 134 QAGCIIGKGGLKIKELREKTGA 155

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307204634|gb|EFN83256.1| Heterogeneous nuclear ribonucleoprotein K [Harpegnathos saltator]

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 74/139 (53%), Positives = 95/139 (68%), Gaps = 23/139 (16%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI 68
           S  KR+R G  D ELRLLIPS+VAGS+IGKGG NI +LR+ +KAS+ VPDCPGPER+LTI
Sbjct: 18  SPHKRYRQG--DDELRLLIPSKVAGSIIGKGGQNITKLRSQYKASIIVPDCPGPERVLTI 75

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQS 128
            ++L   L+V+ EV+P L+E   ++                     G D+ D+R++VHQS
Sbjct: 76  SSDLPTVLQVLNEVVPNLEENGSRH---------------------GSDEIDVRMLVHQS 114

Query: 129 QAGCIIGKGGTKIKELRDT 147
           QAGCIIGKGG KIKELR+ 
Sbjct: 115 QAGCIIGKGGLKIKELREV 133

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328781397|ref|XP_392536.4| PREDICTED: heterogeneous nuclear ribonucleoprotein K [Apis mellifera]

 Score =  141 bits (355), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 74/138 (53%), Positives = 95/138 (68%), Gaps = 23/138 (16%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI 68
           S  KR+R G  D ELRLLIPS+VAGS+IGKGG NI +LR+ +KAS+ VPDCPGPER+LTI
Sbjct: 72  SPHKRYRQG--DDELRLLIPSKVAGSIIGKGGQNITKLRSQYKASIIVPDCPGPERVLTI 129

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQS 128
            ++L   L+V+ EV+P L+E   ++                     G D+ D+R++VHQS
Sbjct: 130 SSDLPTVLQVLNEVVPNLEENGSRH---------------------GSDEIDVRMLVHQS 168

Query: 129 QAGCIIGKGGTKIKELRD 146
           QAGCIIGKGG KIKELR+
Sbjct: 169 QAGCIIGKGGLKIKELRE 186

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350409768|ref|XP_003488838.1| PREDICTED: heterogeneous nuclear ribonucleoprotein K-like [Bombus impatiens]

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 75/142 (52%), Positives = 96/142 (67%), Gaps = 23/142 (16%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI 68
           S  KR+R G  D ELRLLIPS+VAGS+IGKGG NI +LR+ +KAS+ VPDCPGPER+LTI
Sbjct: 65  SPHKRYRQG--DDELRLLIPSKVAGSIIGKGGQNITKLRSQYKASIIVPDCPGPERVLTI 122

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQS 128
            ++L   L+V+ EV+P L+E   ++                     G D+ D+R++VHQS
Sbjct: 123 SSDLPTVLQVLNEVVPNLEENGSRH---------------------GSDEIDVRMLVHQS 161

Query: 129 QAGCIIGKGGTKIKELRDTFDA 150
           QAGCIIGKGG KIKELR+   A
Sbjct: 162 QAGCIIGKGGLKIKELREKTGA 183

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332027896|gb|EGI67951.1| Heterogeneous nuclear ribonucleoprotein K [Acromyrmex echinatior]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 73/139 (52%), Positives = 94/139 (67%), Gaps = 23/139 (16%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI 68
           S  KR+R G  D ELRLLIPS+VAGS+IGKGG NI +LR+ +KAS+ VPDCPGPER+LTI
Sbjct: 18  SPHKRYRQG--DDELRLLIPSKVAGSIIGKGGQNITKLRSQYKASIIVPDCPGPERVLTI 75

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQS 128
            ++L   L+V+ EV+P L+E   ++                     G D+ D+R++VHQS
Sbjct: 76  SSDLPTVLQVLNEVVPNLEENGSRH---------------------GSDEIDVRMLVHQS 114

Query: 129 QAGCIIGKGGTKIKELRDT 147
           QAGCIIGK G KIKELR+ 
Sbjct: 115 QAGCIIGKAGLKIKELREV 133

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340718655|ref|XP_003397779.1| PREDICTED: heterogeneous nuclear ribonucleoprotein K-like [Bombus terrestris]

 Score =  138 bits (347), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 74/138 (53%), Positives = 95/138 (68%), Gaps = 23/138 (16%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI 68
           S  KR+R G  D ELRLLIPS+VAGS+IGKGG NI +LR+ +KAS+ VPDCPGPER+LTI
Sbjct: 51  SPHKRYRQG--DDELRLLIPSKVAGSIIGKGGQNITKLRSQYKASIIVPDCPGPERVLTI 108

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQS 128
            ++L   L+V+ EV+P L+E   ++                     G D+ D+R++VHQS
Sbjct: 109 SSDLPTVLQVLNEVVPNLEENGSRH---------------------GSDEIDVRMLVHQS 147

Query: 129 QAGCIIGKGGTKIKELRD 146
           QAGCIIGKGG KIKELR+
Sbjct: 148 QAGCIIGKGGLKIKELRE 165

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189238821|ref|XP_968538.2| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein k [Tribolium castaneum] gi|270010156|gb|EFA06604.1| hypothetical protein TcasGA2_TC009519 [Tribolium castaneum]

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 70/139 (50%), Positives = 95/139 (68%), Gaps = 23/139 (16%)

Query: 12  KRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE 71
           KR R G  D E+RLLIPS+VAGS+IGKGG NI +LR+ +KAS+TVPDCPGPER+LT+ ++
Sbjct: 14  KRSRRG--DEEVRLLIPSKVAGSIIGKGGQNITKLRSQYKASITVPDCPGPERMLTLSSD 71

Query: 72  LENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAG 131
           L+    ++ +V+P L+E                  NGG V G   ++ D+R+++HQSQAG
Sbjct: 72  LDTICNIVTDVVPNLEE------------------NGGRVNG---NELDLRMMIHQSQAG 110

Query: 132 CIIGKGGTKIKELRDTFDA 150
           C+IGK G KIKELR+   A
Sbjct: 111 CVIGKAGYKIKELREKTGA 129

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

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	150
UNIPROTKB|Q5T6W2	379	HNRNPK "Heterogeneous nuclear	0.52	0.205	0.525	3.8e-19
UNIPROTKB|E1C453	426	HNRNPK "Heterogeneous nuclear	0.52	0.183	0.525	8.2e-19
UNIPROTKB|I3LQS0	444	HNRNPK "Uncharacterized protei	0.52	0.175	0.525	1e-18
UNIPROTKB|P61978	463	HNRNPK "Heterogeneous nuclear	0.52	0.168	0.525	1.3e-18
MGI|MGI:99894	463	Hnrnpk "heterogeneous nuclear	0.52	0.168	0.525	1.3e-18
RGD|71058	463	Hnrnpk "heterogeneous nuclear	0.52	0.168	0.525	1.3e-18
UNIPROTKB|Q3T0D0	464	HNRNPK "Heterogeneous nuclear	0.52	0.168	0.525	1.3e-18
UNIPROTKB|H9L0I0	426	HNRPK "Uncharacterized protein	0.52	0.183	0.525	1.8e-18
UNIPROTKB|Q5ZIQ3	427	HNRNPK "Heterogeneous nuclear	0.52	0.182	0.525	1.8e-18
UNIPROTKB|H9L242	427	HNRPK "Uncharacterized protein	0.52	0.182	0.525	1.8e-18

UNIPROTKB|Q5T6W2 HNRNPK "Heterogeneous nuclear ribonucleoprotein K" [Homo sapiens (taxid:9606)]

 Score = 207 (77.9 bits), Expect = 3.8e-19, Sum P(2) = 3.8e-19
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    33 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 92

Query:    71 ELENGLKVIEEVLPALDE 88
             ++E   +++++++P L+E
Sbjct:    93 DIETIGEILKKIIPTLEE 110

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|E1C453 HNRNPK "Heterogeneous nuclear ribonucleoprotein K" [Gallus gallus (taxid:9031)]

 Score = 207 (77.9 bits), Expect = 8.2e-19, Sum P(2) = 8.2e-19
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    30 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 89

Query:    71 ELENGLKVIEEVLPALDE 88
             ++E   +++++++P L+E
Sbjct:    90 DIETIGEILKKIIPTLEE 107

GO:0003723 "RNA binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0010988 "regulation of low-density lipoprotein particle clearance" evidence=IEA

GO:0045716 "positive regulation of low-density lipoprotein particle receptor biosynthetic process" evidence=IEA

GO:0048260 "positive regulation of receptor-mediated endocytosis" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0072369 "regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|I3LQS0 HNRNPK "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 207 (77.9 bits), Expect = 1.0e-18, Sum P(2) = 1.0e-18
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    36 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 95

Query:    71 ELENGLKVIEEVLPALDE 88
             ++E   +++++++P L+E
Sbjct:    96 DIETIGEILKKIIPTLEE 113

GO:0072369 "regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0048260 "positive regulation of receptor-mediated endocytosis" evidence=IEA

GO:0045716 "positive regulation of low-density lipoprotein particle receptor biosynthetic process" evidence=IEA

GO:0010988 "regulation of low-density lipoprotein particle clearance" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P61978 HNRNPK "Heterogeneous nuclear ribonucleoprotein K" [Homo sapiens (taxid:9606)]

 Score = 207 (77.9 bits), Expect = 1.3e-18, Sum P(2) = 1.3e-18
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    33 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 92

Query:    71 ELENGLKVIEEVLPALDE 88
             ++E   +++++++P L+E
Sbjct:    93 DIETIGEILKKIIPTLEE 110

GO:0003723 "RNA binding" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

GO:0006396 "RNA processing" evidence=TAS

GO:0007165 "signal transduction" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0045716 "positive regulation of low-density lipoprotein particle receptor biosynthetic process" evidence=IMP

GO:0072369 "regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0048260 "positive regulation of receptor-mediated endocytosis" evidence=IMP

GO:0010988 "regulation of low-density lipoprotein particle clearance" evidence=IMP

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=IMP

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IMP

GO:0003697 "single-stranded DNA binding" evidence=TAS

GO:0000790 "nuclear chromatin" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:99894 Hnrnpk "heterogeneous nuclear ribonucleoprotein K" [Mus musculus (taxid:10090)]

 Score = 207 (77.9 bits), Expect = 1.3e-18, Sum P(2) = 1.3e-18
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    33 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 92

Query:    71 ELENGLKVIEEVLPALDE 88
             ++E   +++++++P L+E
Sbjct:    93 DIETIGEILKKIIPTLEE 110

GO:0000790 "nuclear chromatin" evidence=ISO

GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=ISO

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=ISO

GO:0003723 "RNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0010988 "regulation of low-density lipoprotein particle clearance" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0042981 "regulation of apoptotic process" evidence=IMP

GO:0045716 "positive regulation of low-density lipoprotein particle receptor biosynthetic process" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0048260 "positive regulation of receptor-mediated endocytosis" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:0072369 "regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

RGD|71058 Hnrnpk "heterogeneous nuclear ribonucleoprotein K" [Rattus norvegicus (taxid:10116)]

 Score = 207 (77.9 bits), Expect = 1.3e-18, Sum P(2) = 1.3e-18
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    33 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 92

Query:    71 ELENGLKVIEEVLPALDE 88
             ++E   +++++++P L+E
Sbjct:    93 DIETIGEILKKIIPTLEE 110

GO:0000790 "nuclear chromatin" evidence=IEA;ISO

GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=IEA;ISO

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA;ISO

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0010988 "regulation of low-density lipoprotein particle clearance" evidence=IEA;ISO

GO:0042981 "regulation of apoptotic process" evidence=ISO

GO:0045716 "positive regulation of low-density lipoprotein particle receptor biosynthetic process" evidence=IEA;ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0048260 "positive regulation of receptor-mediated endocytosis" evidence=IEA;ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

GO:0072369 "regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q3T0D0 HNRNPK "Heterogeneous nuclear ribonucleoprotein K" [Bos taurus (taxid:9913)]

 Score = 207 (77.9 bits), Expect = 1.3e-18, Sum P(2) = 1.3e-18
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    33 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 92

Query:    71 ELENGLKVIEEVLPALDE 88
             ++E   +++++++P L+E
Sbjct:    93 DIETIGEILKKIIPTLEE 110

GO:0005737 "cytoplasm" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0072369 "regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0048260 "positive regulation of receptor-mediated endocytosis" evidence=IEA

GO:0045716 "positive regulation of low-density lipoprotein particle receptor biosynthetic process" evidence=IEA

GO:0010988 "regulation of low-density lipoprotein particle clearance" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|H9L0I0 HNRPK "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 204 (76.9 bits), Expect = 1.8e-18, Sum P(2) = 1.8e-18
 Identities = 41/78 (52%), Positives = 57/78 (73%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    30 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 89

Query:    71 ELENGLKVIEEVLPALDE 88
             + E   +++++++P L+E
Sbjct:    90 DTETIGEILKKIIPTLEE 107

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q5ZIQ3 HNRNPK "Heterogeneous nuclear ribonucleoprotein K" [Gallus gallus (taxid:9031)]

 Score = 204 (76.9 bits), Expect = 1.8e-18, Sum P(2) = 1.8e-18
 Identities = 41/78 (52%), Positives = 57/78 (73%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    30 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 89

Query:    71 ELENGLKVIEEVLPALDE 88
             + E   +++++++P L+E
Sbjct:    90 DTETIGEILKKIIPTLEE 107

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|H9L242 HNRPK "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 204 (76.9 bits), Expect = 1.8e-18, Sum P(2) = 1.8e-18
 Identities = 41/78 (52%), Positives = 57/78 (73%)

Query:    11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
             FKR R     VELR+L+ S+ AG+VIGKGG NI  LR D+ ASV+VPD  GPERIL+I A
Sbjct:    30 FKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISA 89

Query:    71 ELENGLKVIEEVLPALDE 88
             + E   +++++++P L+E
Sbjct:    90 DTETIGEILKKIIPTLEE 107

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	150
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-15
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-11
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-11
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-09
pfam00013	59	pfam00013, KH_1, KH domain	4e-09
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	3e-06
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-05
pfam13014	42	pfam13014, KH_3, KH domain	8e-05
pfam00013	59	pfam00013, KH_1, KH domain	2e-04
smart00322	68	smart00322, KH, K homology RNA-binding domain	0.001

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

 Score = 65.2 bits (160), Expect = 4e-15
 Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 3/65 (4%)

Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV---PDCPGPERILTIFAELENGLKV 78
           LRLL+PS  AGS+IGKGGS I  +R +  A + V         ER++TI  +     K 
Sbjct: 1  TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

Query: 79 IEEVL 83
          +  +L
Sbjct: 61 LLLIL 65

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

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

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 21/65 (32%), Positives = 34/65 (52%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKV 78
          + V + +LIP+   G +IGKGGS I ++  +    + +P     ER++ I    EN  K 
Sbjct: 1  DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKA 60

Query: 79 IEEVL 83
           E +L
Sbjct: 61 AELIL 65

Length = 68

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

 Score = 54.5 bits (132), Expect = 4e-11
 Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTIFAELENGLKVI 79
            R+L+PS + G +IGKGGS I  +R +  A + +PD      ERI+TI    E   K  
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 80 EEVL 83
          E +L
Sbjct: 61 ELIL 64

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

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

 Score = 49.8 bits (120), Expect = 3e-09
 Identities = 17/26 (65%), Positives = 22/26 (84%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
           +RL+V  SQAG IIGKGG+ IKE+R+
Sbjct: 2   LRLLVPSSQAGSIIGKGGSTIKEIRE 27

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

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

 Score = 49.5 bits (119), Expect = 4e-09
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEE 81
            R+LIP    G +IGKGGSNI  +R +    + +PD    +  +TI    E   K  E 
Sbjct: 1  TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD--DRDDTVTISGTPEQVEKAKEL 58

Query: 82 V 82
          +
Sbjct: 59 I 59

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

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

 Score = 42.1 bits (100), Expect = 3e-06
 Identities = 19/62 (30%), Positives = 29/62 (46%)

Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEE 81
             + IP ++   +IGK GSNI ++  +    +  PD       +TI    EN  K  EE
Sbjct: 1  TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEE 60

Query: 82 VL 83
          +L
Sbjct: 61 IL 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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 39.5 bits (93), Expect = 3e-05
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
            R++V  S  G IIGKGG+ IKE+R+   A
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGA 31

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

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

 Score = 37.5 bits (88), Expect = 8e-05
 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 2/39 (5%)

Query: 32 AGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTI 68
           G++IGKGG  I  +R +  A + +P       ERI+TI
Sbjct: 2  VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTI 40

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

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

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 12/30 (40%), Positives = 19/30 (63%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
            R+++   + G IIGKGG+ IKE+R+    
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGV 31

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 = 35.3 bits (82), Expect = 0.001
 Identities = 10/30 (33%), Positives = 18/30 (60%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
           I +++   + G IIGKGG+ IK++ +    
Sbjct: 5   IEVLIPADKVGLIIGKGGSTIKKIEEETGV 34

Length = 68

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	150
KOG2191|consensus	402		99.92
KOG2190|consensus	485		99.86
KOG1676|consensus	600		99.86
KOG1676|consensus	600		99.83
KOG2192|consensus	390		99.79
KOG2193|consensus	584		99.78
KOG2190|consensus	485		99.73
KOG2193|consensus	584		99.67
KOG2192|consensus	390		99.66
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.66
KOG2191|consensus	402		99.58
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.55
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.53
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.48
PRK13763	180	putative RNA-processing protein; Provisional	99.47
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.46
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.45
smart00322	69	KH K homology RNA-binding domain.	99.31
PF13014	43	KH_3: KH domain	99.28
KOG2279|consensus	608		98.91
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.76
PRK08406	140	transcription elongation factor NusA-like protein;	98.73
KOG2113|consensus	394		98.65
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.55
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.55
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	98.52
PRK13763	180	putative RNA-processing protein; Provisional	98.49
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	98.36
KOG2208|consensus	753		98.35
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.34
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.27
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	98.27
KOG0336|consensus	629		98.27
PF13014	43	KH_3: KH domain	98.15
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.95
smart00322	69	KH K homology RNA-binding domain.	97.94
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.88
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.86
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.84
KOG0119|consensus	554		97.84
KOG2279|consensus	608		97.81
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.7
KOG2814|consensus	345		97.63
KOG1588|consensus	259		97.59
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.49
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.2
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.14
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.14
COG5176	269	MSL5 Splicing factor (branch point binding protein	97.1
PRK00468	75	hypothetical protein; Provisional	97.08
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.07
TIGR01953	341	NusA transcription termination factor NusA. This m	97.06
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.04
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.04
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.97
PRK00468	75	hypothetical protein; Provisional	96.97
PRK12704	520	phosphodiesterase; Provisional	96.97
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.96
PRK02821	77	hypothetical protein; Provisional	96.95
PRK00106	535	hypothetical protein; Provisional	96.94
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.93
PRK02821	77	hypothetical protein; Provisional	96.92
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.89
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.88
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.83
PRK01064	78	hypothetical protein; Provisional	96.82
PRK01064	78	hypothetical protein; Provisional	96.8
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.57
PRK08406	140	transcription elongation factor NusA-like protein;	96.35
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.27
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.25
KOG2208|consensus	753		96.25
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	96.1
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	95.86
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	95.64
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	95.64
KOG0336|consensus	629		95.4
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	95.27
PRK12705	508	hypothetical protein; Provisional	95.21
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	95.18
COG1782	637	Predicted metal-dependent RNase, consists of a met	95.17
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	95.17
PRK06418	166	transcription elongation factor NusA-like protein;	95.0
KOG4369|consensus	2131		94.91
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	94.77
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	94.76
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.62
PRK00106	535	hypothetical protein; Provisional	94.48
PRK12704	520	phosphodiesterase; Provisional	94.45
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	94.44
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	94.27
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	94.26
KOG3273|consensus	252		93.99
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	93.86
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	93.64
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	93.46
COG0195	190	NusA Transcription elongation factor [Transcriptio	93.38
KOG1588|consensus	259		93.28
KOG0119|consensus	554		93.19
PRK12705	508	hypothetical protein; Provisional	93.07
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	92.92
COG5176	269	MSL5 Splicing factor (branch point binding protein	92.75
KOG1067|consensus	760		92.52
COG1855	604	ATPase (PilT family) [General function prediction	92.22
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	92.12
PRK12328	374	nusA transcription elongation factor NusA; Provisi	91.96
KOG2113|consensus	394		91.83
TIGR01953	341	NusA transcription termination factor NusA. This m	91.75
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	91.6
KOG2874|consensus	356		91.53
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	91.45
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	91.43
PRK09202	470	nusA transcription elongation factor NusA; Validat	91.08
PRK12327	362	nusA transcription elongation factor NusA; Provisi	90.76
PRK13764	602	ATPase; Provisional	90.74
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	89.77
PRK12329	449	nusA transcription elongation factor NusA; Provisi	89.17
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	89.14
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	88.66
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	88.18
KOG1067|consensus	760		88.07
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	87.78
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	87.77
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	87.37
PRK00089	292	era GTPase Era; Reviewed	85.57
COG1159	298	Era GTPase [General function prediction only]	85.17
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	85.17
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	85.16
PRK15494	339	era GTPase Era; Provisional	84.68
PRK06418	166	transcription elongation factor NusA-like protein;	83.79
PTZ00084	220	40S ribosomal protein S3; Provisional	83.78
COG1847	208	Jag Predicted RNA-binding protein [General functio	82.64
COG5166	657	Uncharacterized conserved protein [Function unknow	82.52
PRK00089	292	era GTPase Era; Reviewed	81.95
PRK15494	339	era GTPase Era; Provisional	81.53
CHL00048	214	rps3 ribosomal protein S3	81.47
KOG1423|consensus	379		80.98
TIGR01008	195	rpsC_E_A ribosomal protein S3, eukaryotic/archaeal	80.93
PRK04191	207	rps3p 30S ribosomal protein S3P; Reviewed	80.05

>KOG2191|consensus

Probab=99.92  E-value=6e-24  Score=164.02  Aligned_cols=131  Identities=34%  Similarity=0.464  Sum_probs=108.6

Q ss_pred             ccCCCCCCCCC-ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC----CC-CCceEEEecChHHHHHHHHHH
Q psy7546           9 SNFKRFRGGPN-DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC----PG-PERILTIFAELENGLKVIEEV   82 (150)
Q Consensus         9 ~~~~~~~~~~~-~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----~~-~ervv~I~G~~~~v~~A~~~i   82 (150)
                      ...+|.....+ .+.+++|||+..+|.||||+|++|.+||++|||+|+++++    |+ +||+|.|+|+.+++......|
T Consensus        26 ~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI  105 (402)
T KOG2191|consen   26 GSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFI  105 (402)
T ss_pred             cccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHH
Confidence            34555555544 4999999999999999999999999999999999999975    45 999999999999999999999


Q ss_pred             HHHHHHhhhhcCCCCCC-CCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          83 LPALDEIRQKYGKGRGG-EDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        83 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+++.+.++........ .+..           .+....+++++|++.+|.||||+|++||.+++++||
T Consensus       106 ~dKire~p~~~~k~v~~~~pqt-----------~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga  163 (402)
T KOG2191|consen  106 ADKIREKPQAVAKPVDILQPQT-----------PDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGA  163 (402)
T ss_pred             HHHHHHhHHhhcCCccccCCCC-----------ccccceeEEeccCCcccceecCCcchHHHHHHhhCc
Confidence            99999988665442111 1110           134456999999999999999999999999999986

>KOG2190|consensus

Probab=99.86  E-value=2.4e-21  Score=159.41  Aligned_cols=119  Identities=31%  Similarity=0.504  Sum_probs=99.8

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--CCCCceEEEec---------ChHHHHHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--PGPERILTIFA---------ELENGLKVIEEVLPAL   86 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~~~ervv~I~G---------~~~~v~~A~~~i~~~~   86 (150)
                      +...++||||+..++|.||||+|..||+|+.+|.++|++.+.  +++||+++|+|         ..+++.+|..+|...+
T Consensus        40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~  119 (485)
T KOG2190|consen   40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKL  119 (485)
T ss_pred             CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcc
Confidence            455668999999999999999999999999999998888875  36999999999         9999999999999988


Q ss_pred             HHhhhhcCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          87 DEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +++.....++             + ......+.+++|+||.+++|+||||+|+.||+|+++|||
T Consensus       120 ~~d~~~~~d~-------------~-~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA  169 (485)
T KOG2190|consen  120 EEDDEAAEDN-------------G-EDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGA  169 (485)
T ss_pred             cccccccccC-------------C-ccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCc
Confidence            7543322221             0 011123689999999999999999999999999999997

>KOG1676|consensus

Probab=99.86  E-value=2.2e-21  Score=159.30  Aligned_cols=117  Identities=26%  Similarity=0.412  Sum_probs=97.6

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC---CCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCC
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC---PGPERILTIFAELENGLKVIEEVLPALDEIRQKYGK   95 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~---~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~   95 (150)
                      ...++++.||.+.||.||||+|++||+|+.+||++|+|...   ++.||.+.|.|+++.+++|...|.+++.+.......
T Consensus       228 ~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~  307 (600)
T KOG1676|consen  228 GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGG  307 (600)
T ss_pred             ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCC
Confidence            34599999999999999999999999999999999999743   369999999999999999998888888876432110


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCce--EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          96 GRGGEDGGDGYNGGGVGGLGKDDY--DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                             .-+        .+..-.  .+.+.||++.+|+||||+|++||.|.++|||
T Consensus       308 -------~~~--------~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA  349 (600)
T KOG1676|consen  308 -------GMG--------GGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGA  349 (600)
T ss_pred             -------CcC--------CCCccceeeEEEeccccccccccCCCccchhhhcccCCc
Confidence                   000        111222  7889999999999999999999999999998

>KOG1676|consensus

Probab=99.83  E-value=8.6e-20  Score=150.03  Aligned_cols=122  Identities=27%  Similarity=0.385  Sum_probs=98.8

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHHHhhhhc
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALDEIRQKY   93 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~   93 (150)
                      +.+++.+|+||++.+|+||||+|++||+||+.+||++.+..+.    ...+-+.|+|+++.++.|..++.+.|.+.....
T Consensus       136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~  215 (600)
T KOG1676|consen  136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEV  215 (600)
T ss_pred             ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCC
Confidence            4678999999999999999999999999999999999987653    367889999999999999999999999732111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          94 GKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      . .+.     ..+..     ......+.++.||.+.||.||||+|++||+|+.+|||
T Consensus       216 ~-g~~-----~~~g~-----~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~  261 (600)
T KOG1676|consen  216 P-GSG-----GHAGV-----RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGA  261 (600)
T ss_pred             C-ccc-----cccCc-----CccccceeEEeccccceeeEEecCchHHHHHhhccCc
Confidence            0 000     00000     0123348999999999999999999999999999997

>KOG2192|consensus

Probab=99.79  E-value=3.1e-19  Score=135.03  Aligned_cols=109  Identities=52%  Similarity=0.830  Sum_probs=98.6

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCC
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRG   98 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~   98 (150)
                      ..+.+++|+.+..+|+||||+|++||.|+.+.+|+|++++++.++|+++|+.+.+.+-+-+..|+..+++.++       
T Consensus        46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f~-------  118 (390)
T KOG2192|consen   46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGFQ-------  118 (390)
T ss_pred             cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCC-------
Confidence            4589999999999999999999999999999999999999999999999999999988888888888887442       


Q ss_pred             CCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          99 GEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                                      ...+..++|+|.++++|.|||++|++||+|++.+.|
T Consensus       119 ----------------~~~pce~rllihqs~ag~iigrngskikelrekcsa  154 (390)
T KOG2192|consen  119 ----------------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSA  154 (390)
T ss_pred             ----------------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhh
Confidence                            246678999999999999999999999999998765

>KOG2193|consensus

Probab=99.78  E-value=1.7e-19  Score=143.37  Aligned_cols=117  Identities=28%  Similarity=0.449  Sum_probs=102.1

Q ss_pred             CCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHHhhh
Q psy7546          15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDEIRQ   91 (150)
Q Consensus        15 ~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~   91 (150)
                      -..++...++|.||...+|+||||+|.+||+|-.++||.|+|...  + ..+|+|+|+|+++..++|...|..++.+...
T Consensus       405 hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf  484 (584)
T KOG2193|consen  405 HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF  484 (584)
T ss_pred             hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence            344577889999999999999999999999999999999999754  3 4899999999999999999999999988643


Q ss_pred             hcCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          92 KYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+.                   +.-.....+.||++.+|.||||||.++++|+..|+|
T Consensus       485 ~~Pk-------------------eevklethirVPs~~aGRvIGKGGktVnELQnlt~A  524 (584)
T KOG2193|consen  485 FLPK-------------------EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSA  524 (584)
T ss_pred             CCch-------------------hhheeeeeeeccchhhhhhhccccccHHHHhccccc
Confidence            2221                   235567889999999999999999999999999997

>KOG2190|consensus

Probab=99.73  E-value=3.5e-17  Score=134.90  Aligned_cols=131  Identities=32%  Similarity=0.430  Sum_probs=101.4

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcC--
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDEIRQKYG--   94 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~--   94 (150)
                      ++++||+||++++|.||||+|..||+|+++|||+|++...  | +++|.|+|.|.++.+.+|+..|+..|.+......  
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~  216 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPP  216 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCC
Confidence            6899999999999999999999999999999999999976  4 7999999999999999999999999999652211  


Q ss_pred             CCC---CCC--C-CC---CCCCC------CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          95 KGR---GGE--D-GG---DGYNG------GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        95 ~~~---~~~--~-~~---~~~~~------~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+   |-+  + ..   +....      +......+.+..+++.+|.+.++.|+|++|..|+.++..+|+
T Consensus       217 ~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~  287 (485)
T KOG2190|consen  217 LVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGA  287 (485)
T ss_pred             CCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCC
Confidence            111   111  0 00   00000      000111124456788999999999999999999999999986

>KOG2193|consensus

Probab=99.67  E-value=4.7e-17  Score=129.60  Aligned_cols=113  Identities=23%  Similarity=0.445  Sum_probs=100.1

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C--CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcC
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P--GPERILTIFAELENGLKVIEEVLPALDEIRQKYG   94 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~   94 (150)
                      .-.+.+|++||...+|.||||.|++||.|.+.|-|+|-|-.- +  ..|++++|.++++...+|+.+|++.+........
T Consensus       196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k  275 (584)
T KOG2193|consen  196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDK  275 (584)
T ss_pred             ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhccc
Confidence            457899999999999999999999999999999999988742 2  3899999999999999999999999988664332


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          95 KGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .                    ..++..+++.-+.++|.+|||.|++||+|.+.||.
T Consensus       276 ~--------------------~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgT  311 (584)
T KOG2193|consen  276 V--------------------AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGT  311 (584)
T ss_pred             h--------------------hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCC
Confidence            2                    36678889999999999999999999999999984

>KOG2192|consensus

Probab=99.66  E-value=3.5e-16  Score=118.54  Aligned_cols=75  Identities=31%  Similarity=0.478  Sum_probs=67.7

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ..++.+.+||||+.+.+|.|||++|..||.|++++.+++++-..  | +++|+|.+.|.+.+|..++..|++.+.+.+
T Consensus       118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~p  195 (390)
T KOG2192|consen  118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESP  195 (390)
T ss_pred             CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCC
Confidence            34677999999999999999999999999999999999988643  4 699999999999999999999999998843

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.66  E-value=2.9e-16  Score=96.76  Aligned_cols=61  Identities=39%  Similarity=0.585  Sum_probs=56.8

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC---CCCceEEEecChHHHHHHHHHH
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP---GPERILTIFAELENGLKVIEEV   82 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~---~~ervv~I~G~~~~v~~A~~~i   82 (150)
                      +++|+||.+.+|.|||++|++|++|+++|||+|++.+..   .++|+|+|.|+++++.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            479999999999999999999999999999999998753   5899999999999999999876

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

>KOG2191|consensus

Probab=99.58  E-value=5.2e-15  Score=114.79  Aligned_cols=129  Identities=22%  Similarity=0.270  Sum_probs=96.7

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C----CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P----GPERILTIFAELENGLKVIEEVLPALDEIRQKYGKG   96 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~----~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~   96 (150)
                      .+++++|++.+|.||||+|++||.++|++||+|++++. +    ..||+|++.|.+++..+|+.+|+.++.++++.....
T Consensus       133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scl  212 (402)
T KOG2191|consen  133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCL  212 (402)
T ss_pred             eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCccccee
Confidence            38999999999999999999999999999999999943 2    389999999999999999999999999988654321


Q ss_pred             --CCCCC--CCCCCCCCCCC-----CCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          97 --RGGED--GGDGYNGGGVG-----GLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        97 --~~~~~--~~~~~~~~~~~-----~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                        +|...  +.-++++.+.+     ...+.......-++..+.|..-|.+|.+.-.+-..+|+
T Consensus       213 n~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~  275 (402)
T KOG2191|consen  213 NISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGA  275 (402)
T ss_pred             ccchhcccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeeccccc
Confidence              22221  11223322221     11223345567788889999999988887777666653

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.55  E-value=1.1e-14  Score=88.66  Aligned_cols=60  Identities=30%  Similarity=0.400  Sum_probs=56.5

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHH
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEV   82 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i   82 (150)
                      .+|.||.+.+|.|||++|++|++|+++|||+|.+++...+++.|+|+|+.+++..|..+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHh
Confidence            578999999999999999999999999999999998777899999999999999998776

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=99.53  E-value=9.6e-15  Score=88.41  Aligned_cols=60  Identities=30%  Similarity=0.460  Sum_probs=55.0

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHH
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEV   82 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i   82 (150)
                      |.+|.||.+.+|.|||++|.+|++|+++|||+|++++.+ .+..|+|.|+++++.+|..+|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-CcEEEEEEeCHHHHHHHHhhC
Confidence            678999999999999999999999999999999999774 445999999999999998765

; 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 ....

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.48  E-value=6.3e-14  Score=101.90  Aligned_cols=104  Identities=21%  Similarity=0.276  Sum_probs=76.5

Q ss_pred             EEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEE---ecChHHHHHHHHHHHHHHHHh-hhh-cCCCCCC
Q psy7546          25 LLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI---FAELENGLKVIEEVLPALDEI-RQK-YGKGRGG   99 (150)
Q Consensus        25 l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I---~G~~~~v~~A~~~i~~~~~~~-~~~-~~~~~~~   99 (150)
                      |.||.+.+|.|||++|++|+.|+++||++|.+.+.   +..|.|   +++++++.+|...|....... +.. ....   
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~---   75 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE---TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLL---   75 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC---CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhc---
Confidence            56899999999999999999999999999999974   245777   789999999998877644421 100 0000   


Q ss_pred             CCCCCCCCCCCCCCCCCCceEEE-EEEec---------CceeEEeecCCchHHHHHHhhCC
Q psy7546         100 EDGGDGYNGGGVGGLGKDDYDIR-LIVHQ---------SQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~-l~vp~---------~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                                      ...++.. +.|+.         ..+|.|||++|++++.|++.|||
T Consensus        76 ----------------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~  120 (172)
T TIGR03665        76 ----------------DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGV  120 (172)
T ss_pred             ----------------CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCC
Confidence                            0111111 22222         36899999999999999999996

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.47  E-value=1.8e-13  Score=100.22  Aligned_cols=108  Identities=19%  Similarity=0.210  Sum_probs=79.2

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEE----ecChHHHHHHHHHHHHHHHHh-hhh-cC
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI----FAELENGLKVIEEVLPALDEI-RQK-YG   94 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I----~G~~~~v~~A~~~i~~~~~~~-~~~-~~   94 (150)
                      ....+.||.+.+|.|||++|++|+.|+++||++|++.+.   +..|.|    +++++.+.+|..+|....... +.. ..
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~   79 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALR   79 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHH
Confidence            567899999999999999999999999999999999975   356677    489999999998877655420 100 00


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCceEEEE-EE---------ecCceeEEeecCCchHHHHHHhhCC
Q psy7546          95 KGRGGEDGGDGYNGGGVGGLGKDDYDIRL-IV---------HQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~v---------p~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..                   ...+...+ .+         ....+|.|||++|++++.|++.||+
T Consensus        80 l~-------------------gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~  126 (180)
T PRK13763         80 LL-------------------DDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGV  126 (180)
T ss_pred             Hh-------------------CCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCc
Confidence            00                   01111111 01         1136899999999999999999986

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

Probab=99.46  E-value=3.7e-13  Score=82.08  Aligned_cols=61  Identities=39%  Similarity=0.610  Sum_probs=55.7

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHH
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEV   82 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i   82 (150)
                      +.+|.||...++.|||++|++|++|+++|||+|.+++..  .+++.|.|.|+.+++..|..+|
T Consensus         1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence            368999999999999999999999999999999999764  5889999999999999988765

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=99.45  E-value=4.9e-13  Score=81.31  Aligned_cols=58  Identities=22%  Similarity=0.313  Sum_probs=52.3

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC-hHHHHHHHHHH
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE-LENGLKVIEEV   82 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-~~~v~~A~~~i   82 (150)
                      .+..|.||.+.+|.|||++|++|++|+++|||+|.+++    ++.|.|.|+ ++++..|..+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~----~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC----CCEEEEEeCCHHHHHHHHHHh
Confidence            45678999999999999999999999999999999987    467999998 88999888765

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.

>smart00322 KH K homology RNA-binding domain

Probab=99.31  E-value=2e-11  Score=74.40  Aligned_cols=67  Identities=33%  Similarity=0.540  Sum_probs=60.6

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPAL   86 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~   86 (150)
                      ..+.++.||...+|.+||++|.+|++|++.||++|.+.........+.|.|+.+++..|...|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999999876667899999999999999988887654

>PF13014 KH_3: KH domain

Probab=99.28  E-value=8.5e-12  Score=70.56  Aligned_cols=40  Identities=38%  Similarity=0.664  Sum_probs=36.6

Q ss_pred             ccceEecCCchHHHHHHHHhCCeEEecC---CCCCCceEEEec
Q psy7546          31 VAGSVIGKGGSNIARLRNDFKASVTVPD---CPGPERILTIFA   70 (150)
Q Consensus        31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~---~~~~ervv~I~G   70 (150)
                      ++|.|||++|.+|++|+++|||+|+|++   .++++|.|+|+|
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            4799999999999999999999999998   336899999987

>KOG2279|consensus

Probab=98.91  E-value=7.9e-10  Score=91.04  Aligned_cols=107  Identities=29%  Similarity=0.431  Sum_probs=96.6

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCC
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGLKVIEEVLPALDEIRQKYGK   95 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~   95 (150)
                      .++++..+++||...|-+++|+.|.+|+.|++.++++|.+.... +.++.-.+.|.+..+..|...++.++.+       
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~-------  136 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE-------  136 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc-------
Confidence            35788999999999999999999999999999999999998765 5788888888999999999999988886       


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          96 GRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                                          ..++...+.+|...++.++|++|.++..++.-++|
T Consensus       137 --------------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~a  171 (608)
T KOG2279|consen  137 --------------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGA  171 (608)
T ss_pred             --------------------CCcccccccchhhhcccccccchhhhcchhccccc
Confidence                                46677889999999999999999999999988876

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

Probab=98.76  E-value=5.9e-08  Score=66.59  Aligned_cols=59  Identities=20%  Similarity=0.282  Sum_probs=46.7

Q ss_pred             CccceEecCCchHHHHHHHHhCCeEEecCCCC-------------------CCceEEEecCh---HHHHHHHHHHHHHHH
Q psy7546          30 RVAGSVIGKGGSNIARLRNDFKASVTVPDCPG-------------------PERILTIFAEL---ENGLKVIEEVLPALD   87 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~-------------------~ervv~I~G~~---~~v~~A~~~i~~~~~   87 (150)
                      +.+|.|||++|.++|+|+++|||+|.|.+..|                   ..--|.|+++.   +.+.+|+.+|...+.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            56899999999999999999999999986421                   11457777755   788888888777766


Q ss_pred             H
Q psy7546          88 E   88 (150)
Q Consensus        88 ~   88 (150)
                      .
T Consensus        95 ~   95 (120)
T cd02395          95 P   95 (120)
T ss_pred             c
Confidence            4

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.73  E-value=1.6e-08  Score=71.15  Aligned_cols=98  Identities=19%  Similarity=0.264  Sum_probs=67.8

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCC
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE  100 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~  100 (150)
                      -.+.++|+...+|+.||++|++|+.|++..|-+|.+-+..            +...   ..+.+.+....-..-..    
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s------------~d~~---~fI~n~l~Pa~V~~v~I----   92 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS------------DDPE---EFIKNIFAPAAVRSVTI----   92 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC------------CCHH---HHHHHHcCCCEEEEEEE----
Confidence            4567889999999999999999999999999988887642            1111   12222222110000000    


Q ss_pred             CCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         101 DGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                                  ..........+.|+....|..|||+|.+++.++..+|
T Consensus        93 ------------~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~  129 (140)
T PRK08406         93 ------------KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAK  129 (140)
T ss_pred             ------------EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhC
Confidence                        0012345677889999999999999999999998876

>KOG2113|consensus

Probab=98.65  E-value=3.2e-08  Score=76.91  Aligned_cols=122  Identities=19%  Similarity=0.294  Sum_probs=91.2

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCC
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRG   98 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~   98 (150)
                      +.++..+-+|..+++.+.|++|.+||.|+.+|..+|+-+..+ .|-++.++|..++++.|..+|-..-+....... ..+
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~-eePiF~vTg~~edv~~aRrei~saaeH~~l~~~-s~s  101 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG-EEPIFPVTGRHEDVRRARREIPSAAEHFGLIRA-SRS  101 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC-CCCcceeccCchhHHHHhhcCccccceeeeeee-ccc
Confidence            889999999999999999999999999999999999877554 557899999999999998777654443211100 001


Q ss_pred             CCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546          99 GEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      +..+.+.+       ..+...+...-+|...+|+|.|..|++|+.+++.+.
T Consensus       102 ~Sgg~~~~-------s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tn  145 (394)
T KOG2113|consen  102 FSGGTNGA-------SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTN  145 (394)
T ss_pred             ccCCCccc-------cccCCCceeeeccceeeeeccccccCccchheeccc
Confidence            11111111       113455667788999999999999999999998653

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

Probab=98.55  E-value=8.4e-08  Score=58.16  Aligned_cols=32  Identities=19%  Similarity=0.282  Sum_probs=29.8

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....+.||.+++|+|||++|++|++|+++|||
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~   33 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGV   33 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCC
Confidence            46779999999999999999999999999996

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.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.55  E-value=1.3e-07  Score=68.84  Aligned_cols=53  Identities=19%  Similarity=0.286  Sum_probs=48.9

Q ss_pred             ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ..|.|||++|++++.|++.|||+|.+++     +.|.|.|+++++..|...|..++..
T Consensus        99 ~~griIG~~G~t~~~ie~~t~~~i~i~~-----~~v~i~G~~~~~~~A~~~i~~li~~  151 (172)
T TIGR03665        99 IKGRIIGEGGKTRRIIEELTGVSISVYG-----KTVGIIGDPEQVQIAREAIEMLIEG  151 (172)
T ss_pred             HHhhhcCCCcHHHHHHHHHHCCeEEEcC-----CEEEEECCHHHHHHHHHHHHHHHcC
Confidence            6899999999999999999999999986     5699999999999999999888854

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.

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=98.52  E-value=6.7e-08  Score=59.22  Aligned_cols=31  Identities=58%  Similarity=0.909  Sum_probs=29.4

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +.++.||++.+|+|||++|++|++|++.|||
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga   31 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGA   31 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCC
Confidence            3689999999999999999999999999997

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.49  E-value=3.1e-07  Score=67.29  Aligned_cols=53  Identities=17%  Similarity=0.244  Sum_probs=47.7

Q ss_pred             ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      .+|.|||++|++++.|++.|||+|.+++.     .|.|.|+++++..|...|...+..
T Consensus       105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-----~v~i~G~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763        105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-----TVAIIGDPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             HhhheeCCCcHHHHHHHHHHCcEEEEcCC-----EEEEEeCHHHHHHHHHHHHHHHcC
Confidence            68999999999999999999999999864     388999999999999888887754

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=98.36  E-value=4e-07  Score=64.09  Aligned_cols=97  Identities=24%  Similarity=0.294  Sum_probs=65.8

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGED  101 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~  101 (150)
                      -+=|+|....+|..||++|.+|+.|++..|-+|.+-+..            ++...   .+.+.+.     |.....-. 
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys------------~D~~~---fI~N~l~-----PA~V~~V~-   92 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS------------ENLEE---FVANKLA-----PAEVKNVT-   92 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC------------CCHHH---HHHHcCC-----CceEEEEE-
Confidence            556888999999999999999999999999888886642            11111   1111111     11000000 


Q ss_pred             CCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         102 GGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                                ....+......+.||.+..+..|||+|.+++...+.+|
T Consensus        93 ----------i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~  130 (141)
T TIGR01952        93 ----------VSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAK  130 (141)
T ss_pred             ----------EEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhc
Confidence                      00002345677889999999999999999999988876

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.

>KOG2208|consensus

Probab=98.35  E-value=1.2e-06  Score=76.55  Aligned_cols=105  Identities=21%  Similarity=0.274  Sum_probs=93.9

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCC
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGG   99 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~   99 (150)
                      .+...+-+-...+..++||+|.++.++++++.+.+.+....+++..+.++|...++.+|...+...+.+...        
T Consensus       346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n--------  417 (753)
T KOG2208|consen  346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIAEILN--------  417 (753)
T ss_pred             ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHHhhhc--------
Confidence            366777888899999999999999999999999999999777889999999999999999999999888652        


Q ss_pred             CCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         100 EDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                                       ......+.+|...+..+||.+|+.|+.|...+|
T Consensus       418 -----------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~  450 (753)
T KOG2208|consen  418 -----------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHG  450 (753)
T ss_pred             -----------------ccccceeecCccchhhhhccccccHHHHHhhcC
Confidence                             245666899999999999999999999999876

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=98.34  E-value=8.3e-08  Score=57.70  Aligned_cols=31  Identities=39%  Similarity=0.537  Sum_probs=29.5

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      |.++.||.+++|+|||++|++|++|+++|||
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~   31 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGV   31 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTS
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCe
Confidence            5789999999999999999999999999986

; 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=98.27  E-value=7.9e-07  Score=53.72  Aligned_cols=30  Identities=50%  Similarity=0.756  Sum_probs=28.3

Q ss_pred             EEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .++.||..++++|||++|++|++|++.||+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~   31 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGA   31 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCC
Confidence            578999999999999999999999999985

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.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=98.27  E-value=4.1e-07  Score=55.01  Aligned_cols=30  Identities=20%  Similarity=0.350  Sum_probs=28.4

Q ss_pred             EEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+.||.+++++|||++|++|++|++.||+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~   31 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGV   31 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCC
Confidence            578999999999999999999999999986

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.

>KOG0336|consensus

Probab=98.27  E-value=2.3e-06  Score=69.46  Aligned_cols=74  Identities=30%  Similarity=0.432  Sum_probs=61.1

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      .+.++.+++|.+-+..||.|||++|.+||+||.+|+++|++..+. .+-.|+|.|...--.+|.+.|-..+..+.
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~-~e~kv~ifg~~~m~~kaka~id~~~~k~e  115 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD-LEVKVTIFGINHMRKKAKASIDRGQDKDE  115 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC-ceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence            346788999999999999999999999999999999999999875 56678899987776677666655555443

>PF13014 KH_3: KH domain

Probab=98.15  E-value=1.5e-06  Score=48.87  Aligned_cols=22  Identities=55%  Similarity=0.844  Sum_probs=20.8

Q ss_pred             ceeEEeecCCchHHHHHHhhCC
Q psy7546         129 QAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       129 ~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ++|+|||++|++|++|+++|||
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~   22 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGA   22 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCc
Confidence            5899999999999999999997

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.95  E-value=3e-05  Score=67.14  Aligned_cols=64  Identities=19%  Similarity=0.223  Sum_probs=53.4

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD   87 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~   87 (150)
                      .-...|.||.+++|.|||+||.+||.|+++||++|.+.+.    ..|.|.+ +.+.+.+|+.+|.....
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~----G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD----GTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC----cEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            4567788999999999999999999999999999999984    4677766 56677788877766665

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.

>smart00322 KH K homology RNA-binding domain

Probab=97.94  E-value=1.3e-05  Score=48.17  Aligned_cols=32  Identities=31%  Similarity=0.643  Sum_probs=29.8

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.++.||...+|++||++|++|++|++.||+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~   34 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGV   34 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCC
Confidence            56789999999999999999999999999985

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

Probab=97.88  E-value=1.8e-05  Score=58.14  Aligned_cols=112  Identities=20%  Similarity=0.227  Sum_probs=72.5

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-----ChHHHHHHHHHHHHHHHHhhhhc
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-----ELENGLKVIEEVLPALDEIRQKY   93 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-----~~~~v~~A~~~i~~~~~~~~~~~   93 (150)
                      ....+.+.||.+.++.+||+.|++.+.|.+.+++++.++...   ..|.|..     +|..+.+|...+ .++..-++..
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~---~~V~i~~~~~t~Dp~~~~ka~d~V-kAIgrGF~pe   81 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKT---GSVTIRTTRKTEDPLALLKARDVV-KAIGRGFPPE   81 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCC---CeEEEEecCCCCChHHHHHHHHHH-HHHhcCCCHH
Confidence            445677999999999999999999999999999999998653   4555543     456666666333 3333211100


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCceEEEE------EE-e----cCceeEEeecCCchHHHHHHhhCC
Q psy7546          94 GKGRGGEDGGDGYNGGGVGGLGKDDYDIRL------IV-H----QSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l------~v-p----~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....               .- .....+.+      .- +    ....|.|||++|.+-+.|++.||+
T Consensus        82 ~A~~---------------LL-~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~  133 (194)
T COG1094          82 KALK---------------LL-EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGV  133 (194)
T ss_pred             HHHH---------------Hh-cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCC
Confidence            0000               00 01111111      11 1    124699999999999999999985

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.86  E-value=3e-05  Score=67.36  Aligned_cols=66  Identities=20%  Similarity=0.168  Sum_probs=52.2

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD   87 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~   87 (150)
                      --.-...+.||.+.+|.|||+||.+||.|+++|||+|.+.+.    -.|.|.+ ..+.+.+|...|.....
T Consensus       548 ~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd----G~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       548 YAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD----GTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             cCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC----eEEEEEECcHHHHHHHHHHHHhhhc
Confidence            345677788999999999999999999999999999999874    3455544 56667777766665543

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).

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.84  E-value=1.2e-05  Score=59.24  Aligned_cols=93  Identities=20%  Similarity=0.245  Sum_probs=62.0

Q ss_pred             EEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCC
Q psy7546          25 LLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGD  104 (150)
Q Consensus        25 l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~  104 (150)
                      +.+-.+.+|..||++|.+|+.|+++.|-+|.+-...            ++....+   .+.+.     +.....-     
T Consensus        80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s------------~d~~~fI---~nal~-----Pa~v~~V-----  134 (190)
T COG0195          80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS------------EDPAEFI---KNALA-----PAEVLSV-----  134 (190)
T ss_pred             eecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC------------CCHHHHH---HHhcC-----cceEeEE-----
Confidence            444457899999999999999999999888776542            1122222   22222     1100000     


Q ss_pred             CCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         105 GYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                             .-...+.....+.||.+..+.+|||+|.+++.+.+.||
T Consensus       135 -------~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg  172 (190)
T COG0195         135 -------NIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTG  172 (190)
T ss_pred             -------EEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhC
Confidence                   00000122788889999999999999999999999987

>KOG0119|consensus

Probab=97.84  E-value=8.7e-05  Score=61.17  Aligned_cols=70  Identities=21%  Similarity=0.269  Sum_probs=52.5

Q ss_pred             ceEEEEEeeC------CccceEecCCchHHHHHHHHhCCeEEecCC----------------C-C-CCceEEEec-ChHH
Q psy7546          20 DVELRLLIPS------RVAGSVIGKGGSNIARLRNDFKASVTVPDC----------------P-G-PERILTIFA-ELEN   74 (150)
Q Consensus        20 ~~~~~l~vp~------~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----------------~-~-~ervv~I~G-~~~~   74 (150)
                      .++-++.||-      +.||+|||..|.+.|+|+++|||+|.|-..                + . .+--|.|++ +-+.
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            5677888885      459999999999999999999999999531                1 1 122366665 4566


Q ss_pred             HHHHHHHHHHHHHHh
Q psy7546          75 GLKVIEEVLPALDEI   89 (150)
Q Consensus        75 v~~A~~~i~~~~~~~   89 (150)
                      |.+|++.|..++...
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            888888887777763

>KOG2279|consensus

Probab=97.81  E-value=2.7e-05  Score=64.80  Aligned_cols=133  Identities=18%  Similarity=0.212  Sum_probs=93.7

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHhhhhc--
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEIRQKY--   93 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~--   93 (150)
                      ...+...+.+|...++.++|++|+++..++.-++++|.+..+.  +..++..|.+..+....|..++...++++....  
T Consensus       137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~  216 (608)
T KOG2279|consen  137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKR  216 (608)
T ss_pred             CCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhh
Confidence            3456777889999999999999999999999999999999874  578999999988888778877777766543211  


Q ss_pred             ---------CC----CCCCC----------------------CCCCCCCCCCC-------------------CCCCCCce
Q psy7546          94 ---------GK----GRGGE----------------------DGGDGYNGGGV-------------------GGLGKDDY  119 (150)
Q Consensus        94 ---------~~----~~~~~----------------------~~~~~~~~~~~-------------------~~~~~~~~  119 (150)
                               +.    +..+.                      ++.+..+..+.                   ........
T Consensus       217 ~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~  296 (608)
T KOG2279|consen  217 IAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALA  296 (608)
T ss_pred             chhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccc
Confidence                     00    00000                      00000000000                   01112334


Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.+|...+|.+||+.|++++.+...|++
T Consensus       297 i~e~e~p~~lsg~lig~~gey~s~yssasn~  327 (608)
T KOG2279|consen  297 IPEMEMPEILSGDLIGHAGEYLSVYSSASNH  327 (608)
T ss_pred             cceeecCcccccchhhhhhhhhhhhhhccCc
Confidence            4678899999999999999999999998874

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

Probab=97.70  E-value=8.6e-05  Score=44.85  Aligned_cols=37  Identities=24%  Similarity=0.498  Sum_probs=34.0

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEe
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV   56 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i   56 (150)
                      .....+.||.+.+|.+|||+|.+|+.+++.+|-+|.+
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4788899999999999999999999999999988765

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.

>KOG2814|consensus

Probab=97.63  E-value=9.7e-05  Score=58.19  Aligned_cols=70  Identities=21%  Similarity=0.310  Sum_probs=58.9

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ...-+.+++...|+|||++|.+-++|+++|+++|.++... ..+.++.+.+..+.|.+|...|...+...-
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 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            4556889999999999999999999999999999999876 355566666788889999888888877654

>KOG1588|consensus

Probab=97.59  E-value=0.0001  Score=56.35  Aligned_cols=42  Identities=21%  Similarity=0.589  Sum_probs=36.3

Q ss_pred             CCCCceEEEEEeeCC------ccceEecCCchHHHHHHHHhCCeEEec
Q psy7546          16 GGPNDVELRLLIPSR------VAGSVIGKGGSNIARLRNDFKASVTVP   57 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~------~vg~IIGk~G~~Ik~l~~~tg~~I~i~   57 (150)
                      ..+-.++.+++||-.      .||.|+|++|.++|+|+++|||+|-|-
T Consensus        87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            334567788999965      599999999999999999999999995

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

Probab=97.49  E-value=0.00031  Score=51.68  Aligned_cols=53  Identities=17%  Similarity=0.211  Sum_probs=48.0

Q ss_pred             ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ..|.|||++|.+-+.|++-|||+|.+.+..     |.|-|.++++.-|...|..++..
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t-----VaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYGKT-----VAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeCcE-----EEEecChhhhHHHHHHHHHHHcC
Confidence            368999999999999999999999999864     99999999999999888888764

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.20  E-value=0.00096  Score=58.05  Aligned_cols=35  Identities=23%  Similarity=0.317  Sum_probs=32.1

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+....+.||.+.+|.|||+||.+||.|+++|||
T Consensus       575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~  609 (719)
T TIGR02696       575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGA  609 (719)
T ss_pred             CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCC
Confidence            35677889999999999999999999999999996

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.

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

Probab=97.14  E-value=0.0007  Score=40.82  Aligned_cols=32  Identities=28%  Similarity=0.514  Sum_probs=29.5

Q ss_pred             ceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      .....+.||...+|.+|||+|.+|+.+++.+|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~   55 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLG   55 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence            46888999999999999999999999998876

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.14  E-value=0.00045  Score=55.82  Aligned_cols=88  Identities=18%  Similarity=0.236  Sum_probs=59.3

Q ss_pred             CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546          30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG  108 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (150)
                      +-+|+.||++|.+|+.+.++. |-+|.+-...            ++...   .|.+.+.-     .....-         
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s------------~d~~~---fi~nal~P-----a~v~~v---------  295 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS------------EDPAE---FVANALSP-----AKVVSV---------  295 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhCCC-----ceEEEE---------
Confidence            569999999999999999998 7888776542            11111   22222211     000000         


Q ss_pred             CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                         ...........+.||.+..+..|||+|.+++.....||
T Consensus       296 ---~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~  333 (362)
T PRK12327        296 ---EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTG  333 (362)
T ss_pred             ---EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHC
Confidence               00002335788999999999999999999999999887

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

Probab=97.10  E-value=0.0015  Score=48.62  Aligned_cols=40  Identities=23%  Similarity=0.446  Sum_probs=33.8

Q ss_pred             CceEEEEEeeC------CccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          19 NDVELRLLIPS------RVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        19 ~~~~~~l~vp~------~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      ..++-++.||-      +.||++||+.|.+.|+|++.|+|+|-|-.
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            34566777774      56999999999999999999999999864

>PRK00468 hypothetical protein; Provisional

Probab=97.08  E-value=0.0008  Score=42.34  Aligned_cols=35  Identities=31%  Similarity=0.420  Sum_probs=30.5

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDF   50 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t   50 (150)
                      ..++.+.+++.+..+-+|.||||+|.+|+.||.-.
T Consensus        25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            34566889999999999999999999999999753

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.07  E-value=0.0008  Score=58.64  Aligned_cols=34  Identities=21%  Similarity=0.323  Sum_probs=31.8

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+...++.||.+.+|.|||++|++||+|+++|||
T Consensus       549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~  582 (684)
T TIGR03591       549 APRIETIKINPDKIRDVIGPGGKVIREITEETGA  582 (684)
T ss_pred             CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCC
Confidence            5677889999999999999999999999999996

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).

>TIGR01953 NusA transcription termination factor NusA

Probab=97.06  E-value=0.00057  Score=54.82  Aligned_cols=106  Identities=18%  Similarity=0.251  Sum_probs=66.1

Q ss_pred             CCCCCCCCceEEEEEeeC-CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          12 KRFRGGPNDVELRLLIPS-RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        12 ~~~~~~~~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      .|.++.-..+.+.-.-|. +-+|+.||++|.+|+.|.++. |-+|.+-...            ++...   .|.+.+.- 
T Consensus       224 aR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s------------~d~~~---fi~nal~P-  287 (341)
T TIGR01953       224 AREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYS------------DDPAE---FIANALSP-  287 (341)
T ss_pred             eeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhcCC-
Confidence            344443333333333333 569999999999999999998 7888776542            11111   12222211 


Q ss_pred             hhhcCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546          90 RQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                          .....-            .-.........+.||.+..+..|||+|.+++.....||
T Consensus       288 ----a~v~~v------------~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g  331 (341)
T TIGR01953       288 ----AKVISV------------EVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTG  331 (341)
T ss_pred             ----ceEEEE------------EEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhC
Confidence                000000            00001335788999999999999999999999999988

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.04  E-value=0.0019  Score=49.20  Aligned_cols=59  Identities=24%  Similarity=0.170  Sum_probs=46.9

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChH-HHHHHHHHHHHH
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELE-NGLKVIEEVLPA   85 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~-~v~~A~~~i~~~   85 (150)
                      +.+.||.+.++.+||++|.+|+.|.+++++.|.+-.+    -.|.|.+... .+.+|...|...
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N----G~VwI~~~~~~~~~~a~~~I~~~  206 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN----GRIWIKGPDEEDEEIAIEAIKKI  206 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC----cEEEEeeCCHHHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999764    4688877665 555555444443

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.04  E-value=0.00074  Score=59.98  Aligned_cols=65  Identities=14%  Similarity=0.153  Sum_probs=52.5

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCe-EEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKAS-VTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD   87 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~-I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~   87 (150)
                      -.....|.||.++++.|||.||.+||.|+++||+. |.+.+.    -.|.|.+ +.+.+.+|+..|.....
T Consensus       683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd----g~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD----GTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC----eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            45677889999999999999999999999999999 888874    3466655 56777778777666654

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.97  E-value=0.0028  Score=53.56  Aligned_cols=49  Identities=20%  Similarity=0.386  Sum_probs=41.3

Q ss_pred             CceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec
Q psy7546          19 NDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA   70 (150)
Q Consensus        19 ~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G   70 (150)
                      +..+--+.+|+ +.-|.||||.|.|||.|+.-||+.+-|++.|   ..|++++
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp---~~v~ls~  251 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---EAVILSG  251 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC---CeEEecC
Confidence            44555688898 5679999999999999999999999999976   5566776

>PRK00468 hypothetical protein; Provisional

Probab=96.97  E-value=0.00074  Score=42.49  Aligned_cols=32  Identities=28%  Similarity=0.413  Sum_probs=28.6

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      ......++.+..+-+|.||||+|.+|+.|+..
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            35578899999999999999999999999865

>PRK12704 phosphodiesterase; Provisional

Probab=96.97  E-value=0.0028  Score=53.67  Aligned_cols=49  Identities=20%  Similarity=0.386  Sum_probs=41.2

Q ss_pred             CceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec
Q psy7546          19 NDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA   70 (150)
Q Consensus        19 ~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G   70 (150)
                      +..+--+.+|+ +.-|.||||.|.|||.|+.-||+.+-|++.|   .+|.++|
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp---~~v~ls~  257 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---EAVILSG  257 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC---CeEEEec
Confidence            44555677898 5689999999999999999999999999976   5666777

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.96  E-value=0.00054  Score=55.36  Aligned_cols=87  Identities=14%  Similarity=0.153  Sum_probs=58.7

Q ss_pred             CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546          30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG  108 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (150)
                      +-+|+.||++|.+|+.|.++. |-+|.+-...            ++...   .|.+.+.-     .....-.        
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s------------~D~~~---fI~Nal~P-----a~V~~V~--------  302 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS------------NVPEI---FIARALAP-----AIISSVK--------  302 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhCCC-----ceeeEEE--------
Confidence            559999999999999999998 7888776542            11111   12222211     0000000        


Q ss_pred             CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                           -........+.||.+..+..|||+|.+++...+.||
T Consensus       303 -----i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtG  338 (374)
T PRK12328        303 -----IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTG  338 (374)
T ss_pred             -----EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhC
Confidence                 001335778899999999999999999999999988

>PRK02821 hypothetical protein; Provisional

Probab=96.95  E-value=0.00081  Score=42.51  Aligned_cols=32  Identities=28%  Similarity=0.536  Sum_probs=28.4

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ......|.+..+-+|.||||+|.+|+.|+..-
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv   60 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV   60 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence            45778999999999999999999999998753

>PRK00106 hypothetical protein; Provisional

Probab=96.94  E-value=0.0034  Score=53.17  Aligned_cols=50  Identities=22%  Similarity=0.440  Sum_probs=41.8

Q ss_pred             CCceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec
Q psy7546          18 PNDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA   70 (150)
Q Consensus        18 ~~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G   70 (150)
                      .+..+--+.+|+ +.-|.||||.|.||+.|+.-||+.+-|++.|   ..|+++|
T Consensus       222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp---~~v~lS~  272 (535)
T PRK00106        222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP---EVVVLSG  272 (535)
T ss_pred             hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC---CeEEEeC
Confidence            345556688898 5679999999999999999999999999976   4566777

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

Probab=96.93  E-value=0.0021  Score=55.29  Aligned_cols=65  Identities=22%  Similarity=0.223  Sum_probs=52.1

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecCh-HHHHHHHHHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAEL-ENGLKVIEEVLPALDE   88 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~-~~v~~A~~~i~~~~~~   88 (150)
                      +-...+-++.+.+..+||++|.+|+.|.++||++|.+.+.+    .|.|.++. +.+.+|+..|.....+
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG----tv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG----TVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC----cEEEEecchHHHHHHHHHHHHHHhh
Confidence            34566888999999999999999999999999999999643    46666654 6677777777766654

>PRK02821 hypothetical protein; Provisional

Probab=96.92  E-value=0.0012  Score=41.68  Aligned_cols=36  Identities=28%  Similarity=0.411  Sum_probs=30.6

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKA   52 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~   52 (150)
                      ..+...+++.+..+-+|.||||+|.+|+.||.-..+
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            345578999999999999999999999999976543

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.89  E-value=0.00074  Score=55.57  Aligned_cols=88  Identities=18%  Similarity=0.229  Sum_probs=58.4

Q ss_pred             CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546          30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG  108 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (150)
                      +-+|+.||++|.+|+.|.++. |-+|.+-...            ++...   .|.+.+.-     .......        
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys------------~Dp~~---fI~NaLsP-----A~V~~V~--------  328 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS------------PDPAT---YIANALSP-----ARVDEVR--------  328 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhcCC-----ceeeEEE--------
Confidence            559999999999999999998 7888776542            11111   12222211     0000000        


Q ss_pred             CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                          -.........+.||.+..+..|||+|.+++.....||
T Consensus       329 ----i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg  365 (449)
T PRK12329        329 ----LVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTG  365 (449)
T ss_pred             ----EEcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHC
Confidence                0001334678999999999999999999999999887

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

Probab=96.88  E-value=0.0016  Score=41.01  Aligned_cols=32  Identities=31%  Similarity=0.482  Sum_probs=29.3

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRND   49 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~   49 (150)
                      +....+++.+..+-+|.||||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            66788999999999999999999999999975

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.83  E-value=0.0007  Score=56.50  Aligned_cols=87  Identities=17%  Similarity=0.290  Sum_probs=58.8

Q ss_pred             CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546          30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG  108 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (150)
                      +-+|+.||++|.+|+.|.++. |-+|-+-...            ++..   ..|.+.+.-     .....-.        
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s------------~d~~---~fi~nal~p-----a~v~~v~--------  296 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS------------DDPA---QFIINALSP-----AEVSSVV--------  296 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC------------CCHH---HHHHHhCCC-----CEEEEEE--------
Confidence            459999999999999999998 7888776542            1111   122222221     0000000        


Q ss_pred             CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                           -........+.||....+..|||+|.+++...+.||
T Consensus       297 -----~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g  332 (470)
T PRK09202        297 -----VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTG  332 (470)
T ss_pred             -----EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHC
Confidence                 001234788999999999999999999999999987

>PRK01064 hypothetical protein; Provisional

Probab=96.82  E-value=0.002  Score=40.82  Aligned_cols=35  Identities=26%  Similarity=0.458  Sum_probs=30.6

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDF   50 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t   50 (150)
                      ...+.+.+++.+...-.|.+|||+|.+|+.||.-.
T Consensus        25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             eCCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            34577899999999999999999999999999753

>PRK01064 hypothetical protein; Provisional

Probab=96.80  E-value=0.0016  Score=41.23  Aligned_cols=33  Identities=33%  Similarity=0.470  Sum_probs=29.1

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ......++.+..+..|.+|||+|.+|+.|+...
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            466788899999999999999999999998753

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

Probab=96.57  E-value=0.003  Score=39.74  Aligned_cols=32  Identities=31%  Similarity=0.494  Sum_probs=28.5

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      +.....+|.+..+-+|.||||+|.+|+.|+..
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            45677899999999999999999999999864

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=96.35  E-value=0.0042  Score=43.75  Aligned_cols=39  Identities=26%  Similarity=0.335  Sum_probs=33.5

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEec
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP   57 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~   57 (150)
                      +.-.+.+.|+.+..|.+|||+|.+++.++.-++-++.+.
T Consensus        97 ~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         97 GDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             CcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            345667789999999999999999999999999877664

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.27  E-value=0.0042  Score=54.33  Aligned_cols=63  Identities=22%  Similarity=0.250  Sum_probs=48.3

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD   87 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~   87 (150)
                      -...+.||.+.++.+||+||.+||.|+++||++|.+.+.    -.|.|.+ ..+.+.+|...|.....
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~----G~v~i~~~~~~~~~~a~~~I~~~~~  617 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD----GTVKIAATDGEAAEAAKERIEGITA  617 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC----ceEEEEcccHHHHHHHHHHHHHhcc
Confidence            445566799999999999999999999999998888653    3466655 45667777766665553

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.25  E-value=0.0051  Score=54.85  Aligned_cols=35  Identities=23%  Similarity=0.316  Sum_probs=32.2

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+....+.||.+.++.|||.||.+||.|.++||+
T Consensus       682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~  716 (891)
T PLN00207        682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGV  716 (891)
T ss_pred             cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCC
Confidence            35678889999999999999999999999999986

>KOG2208|consensus

Probab=96.25  E-value=0.0032  Score=55.44  Aligned_cols=103  Identities=20%  Similarity=0.290  Sum_probs=73.8

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCC
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGR   97 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~   97 (150)
                      ....+.+..+|...+-.+.|.+|..+++++...+..+.+++.+...+.-.   ..........++.+...+         
T Consensus       637 ~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~---~~~~~~~~~~e~~~~~~~---------  704 (753)
T KOG2208|consen  637 SAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNT---IHVSGEKMQSEIAKIALE---------  704 (753)
T ss_pred             ccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCc---chhhhhhhhhhhcccccc---------
Confidence            45566779999999999999999999999999999999998763211110   111111111111111111         


Q ss_pred             CCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546          98 GGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                                       .....+..+.+|.++++.+||++|++++.+...++
T Consensus       705 -----------------~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~  739 (753)
T KOG2208|consen  705 -----------------AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFN  739 (753)
T ss_pred             -----------------cccceeeEEeccHHHhhhccCCCCccHHHHHHHhc
Confidence                             14667888999999999999999999999988875

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=96.10  E-value=0.005  Score=38.73  Aligned_cols=35  Identities=20%  Similarity=0.246  Sum_probs=27.3

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEE
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVT   55 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~   55 (150)
                      -.+.+-+..+..|.+|||.|++++.||--++.-++
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            34556667788999999999999999976664443

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=95.86  E-value=0.0045  Score=38.47  Aligned_cols=35  Identities=26%  Similarity=0.336  Sum_probs=29.6

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKA   52 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~   52 (150)
                      .+...+.+-+..+..|.||||.|.+++.||.-.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            55677788889999999999999999999976543

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=95.64  E-value=0.032  Score=39.35  Aligned_cols=86  Identities=21%  Similarity=0.367  Sum_probs=57.2

Q ss_pred             ecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCCCC
Q psy7546          36 IGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLG  115 (150)
Q Consensus        36 IGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (150)
                      +-..|..|++|-++.--+|.+-.+++      +   ...-++|...|.+.+.+....           .+.        .
T Consensus        21 ~~~~~dli~~lAk~lrKRIvvR~dps------~---l~~~e~A~~~I~~ivP~ea~i-----------~di--------~   72 (145)
T cd02410          21 FAEDGDLVKDLAKDLRKRIVIRPDPS------V---LKPPEEAIKIILEIVPEEAGI-----------TDI--------Y   72 (145)
T ss_pred             HhcccHHHHHHHHHHhceEEEcCChh------h---cCCHHHHHHHHHHhCCCccCc-----------eee--------E
Confidence            33567888999988888888865431      0   011134665666655432100           000        1


Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      .+..+-.+.|-...-|.+||++|.++++|..+||
T Consensus        73 Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tg  106 (145)
T cd02410          73 FDDDTGEVIIEAEKPGLVIGKGGSTLREITRETG  106 (145)
T ss_pred             ecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhC
Confidence            2455677888899999999999999999999987

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

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

Probab=95.64  E-value=0.027  Score=33.63  Aligned_cols=35  Identities=29%  Similarity=0.491  Sum_probs=28.1

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeE
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASV   54 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I   54 (150)
                      .....+.+.....|.+||++|.+++.++..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45556666666789999999999999999988554

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.

>KOG0336|consensus

Probab=95.40  E-value=0.0085  Score=49.25  Aligned_cols=37  Identities=24%  Similarity=0.615  Sum_probs=31.8

Q ss_pred             CCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         113 GLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       113 ~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      +.+..+...-+.+.+.++|.|||++|++|+.||..|.
T Consensus        41 aag~~e~plcf~iks~mvg~vigrggskik~iq~~tn   77 (629)
T KOG0336|consen   41 AAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTN   77 (629)
T ss_pred             ccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccc
Confidence            3445677778889999999999999999999998875

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=95.27  E-value=0.0044  Score=38.52  Aligned_cols=33  Identities=27%  Similarity=0.422  Sum_probs=28.8

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      .......+.+..+..|.||||.|.+++.||...
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~   58 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLV   58 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHH
Confidence            356678889999999999999999999998754

>PRK12705 hypothetical protein; Provisional

Probab=95.21  E-value=0.03  Score=47.28  Aligned_cols=42  Identities=26%  Similarity=0.411  Sum_probs=35.9

Q ss_pred             CceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCC
Q psy7546          19 NDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCP   60 (150)
Q Consensus        19 ~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~   60 (150)
                      +..+--+.+|+ +.-|.||||.|.+||.++..||+.+-|++.|
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp  238 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP  238 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence            44455577887 5689999999999999999999999999876

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

Probab=95.18  E-value=0.088  Score=40.12  Aligned_cols=46  Identities=26%  Similarity=0.291  Sum_probs=39.1

Q ss_pred             EEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHH
Q psy7546          25 LLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELEN   74 (150)
Q Consensus        25 l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~   74 (150)
                      +.||...|-.+||++|..++.|.++|+|+|-+-.+.    .|.|.+..+.
T Consensus       150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG----~IWV~~~~~~  195 (239)
T COG1097         150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG----RIWVDGENES  195 (239)
T ss_pred             EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC----EEEecCCCcc
Confidence            568888899999999999999999999999998753    5777776664

>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]

Probab=95.17  E-value=0.042  Score=46.19  Aligned_cols=88  Identities=22%  Similarity=0.325  Sum_probs=61.7

Q ss_pred             eEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCC
Q psy7546          34 SVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGG  113 (150)
Q Consensus        34 ~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (150)
                      ..+-+.|+.||+|-++.--+|.+-.+|+.         ...-+.|...|.+.+.+......           .       
T Consensus        42 ~~~~~~~dlik~lAk~lrKRI~iR~dPsv---------l~~~e~A~~~I~eivP~ea~i~~-----------i-------   94 (637)
T COG1782          42 ELFAKDGDLIKDLAKDLRKRIIIRPDPSV---------LKPPEEARKIILEIVPEEAGITD-----------I-------   94 (637)
T ss_pred             HHhccchhHHHHHHHHHhhceEeccCchh---------cCCHHHHHHHHHHhCccccCcee-----------E-------
Confidence            35678899999999999999988766521         11224566666666544321110           0       


Q ss_pred             CCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         114 LGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       114 ~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                       .....+-.+.|-...-|.+|||+|++.++|.++||
T Consensus        95 -~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tg  129 (637)
T COG1782          95 -YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETG  129 (637)
T ss_pred             -EecCCCceEEEEecCCceEEecCchHHHHHHHHhC
Confidence             02445667889999999999999999999999987

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

Probab=95.17  E-value=0.015  Score=35.96  Aligned_cols=37  Identities=24%  Similarity=0.447  Sum_probs=28.3

Q ss_pred             EEEEeeCCc-----cceEecCCchHHHHHHHHh-CCeEEecCC
Q psy7546          23 LRLLIPSRV-----AGSVIGKGGSNIARLRNDF-KASVTVPDC   59 (150)
Q Consensus        23 ~~l~vp~~~-----vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~   59 (150)
                      ..+.|-+..     +|..||++|.+|+.|.++. |-+|.+-+.
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            345555555     9999999999999999999 899988654

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=95.00  E-value=0.031  Score=40.44  Aligned_cols=35  Identities=31%  Similarity=0.344  Sum_probs=30.4

Q ss_pred             EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC
Q psy7546          24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC   59 (150)
Q Consensus        24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~   59 (150)
                      =|+|.... |..|||+|.++++|++..|-+|.+-+.
T Consensus        64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             EEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            35666666 999999999999999999999999764

>KOG4369|consensus

Probab=94.91  E-value=0.014  Score=53.27  Aligned_cols=65  Identities=20%  Similarity=0.139  Sum_probs=55.6

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C--CCCceEEEecChHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P--GPERILTIFAELENGLKVIEEV   82 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~--~~ervv~I~G~~~~v~~A~~~i   82 (150)
                      .+.-..++-+|......|||++|.+|..++.-||+.|.+.+- +  -.||.+.+.|+++.+.-|...|
T Consensus      1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I 1404 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPI 1404 (2131)
T ss_pred             CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccc
Confidence            455667788999999999999999999999999999999872 2  4899999999999998776433

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=94.77  E-value=0.025  Score=49.57  Aligned_cols=34  Identities=21%  Similarity=0.318  Sum_probs=29.8

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+....+.||.+.++.+||.||.+||.|.++||+
T Consensus       552 ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~  585 (693)
T PRK11824        552 APRIETIKIPPDKIRDVIGPGGKTIREITEETGA  585 (693)
T ss_pred             CchheeecCCHHHHHHHhcCCchhHHHHHHHHCC
Confidence            4455667789999999999999999999999986

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=94.76  E-value=0.015  Score=36.43  Aligned_cols=35  Identities=31%  Similarity=0.610  Sum_probs=29.2

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEE
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVT   55 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~   55 (150)
                      ....+.+...+.|.|||++|++|++|.++..-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            34568888999999999999999999987765553

; 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 ....

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.62  E-value=0.059  Score=45.71  Aligned_cols=34  Identities=21%  Similarity=0.291  Sum_probs=28.8

Q ss_pred             CceEEEEEEecC-ceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQS-QAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ......+.+|++ +.|.||||.|.+|+.+...||.
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgv  236 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGV  236 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCc
Confidence            445666789995 5699999999999999999984

>PRK00106 hypothetical protein; Provisional

Probab=94.48  E-value=0.073  Score=45.28  Aligned_cols=34  Identities=21%  Similarity=0.323  Sum_probs=28.9

Q ss_pred             CceEEEEEEecC-ceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQS-QAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ......+.+|++ +.|.||||.|.+|+.+...||.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGv  257 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGI  257 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCc
Confidence            445666889995 5699999999999999999984

>PRK12704 phosphodiesterase; Provisional

Probab=94.45  E-value=0.067  Score=45.44  Aligned_cols=34  Identities=21%  Similarity=0.291  Sum_probs=28.5

Q ss_pred             CceEEEEEEecC-ceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQS-QAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ......+.+|++ +.|.||||.|.+|+.+...||.
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgv  242 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGV  242 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCC
Confidence            445566788995 5699999999999999999984

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

Probab=94.44  E-value=0.064  Score=31.92  Aligned_cols=31  Identities=32%  Similarity=0.641  Sum_probs=24.4

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      ....+.+.....|.+||++|.+++.++..++
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~   55 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQ   55 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHH
Confidence            4455555555689999999999999998764

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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=94.27  E-value=0.063  Score=33.65  Aligned_cols=30  Identities=20%  Similarity=0.358  Sum_probs=25.1

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ....+.+..+..|.+|||.|.+++.||-.+
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~   53 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLA   53 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHH
Confidence            356677888899999999999999998654

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

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=94.26  E-value=0.014  Score=36.59  Aligned_cols=30  Identities=37%  Similarity=0.722  Sum_probs=26.4

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ....+.+..++.|.+||++|++|++|.+..
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~   54 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREEL   54 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHH
Confidence            457788899999999999999999998764

; 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 ....

>KOG3273|consensus

Probab=93.99  E-value=0.024  Score=42.11  Aligned_cols=54  Identities=20%  Similarity=0.328  Sum_probs=49.2

Q ss_pred             CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          30 RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ..+|.|+||+|.+--.|++.|-++|.+.+..     +.|-|..+++.-|...+|.++--
T Consensus       178 RAIGRiaGk~GkTkfaIEn~trtrIVlad~k-----IHiLG~~~niriAR~avcsLIlG  231 (252)
T KOG3273|consen  178 RAIGRIAGKGGKTKFAIENVTRTRIVLADSK-----IHILGAFQNIRIARDAVCSLILG  231 (252)
T ss_pred             HHHHHhhcCCCcceeeeeccceeEEEecCce-----EEEeecchhhHHHHHhhHhhhcc
Confidence            4689999999999999999999999999864     89999999999999999998864

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

Probab=93.86  E-value=0.099  Score=33.29  Aligned_cols=34  Identities=18%  Similarity=0.325  Sum_probs=29.4

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCCeEEe
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV   56 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i   56 (150)
                      .++.+....-|.|||++|+.|++|+++..-...+
T Consensus        32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            7788888899999999999999999887665555

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=93.64  E-value=0.059  Score=37.97  Aligned_cols=40  Identities=28%  Similarity=0.331  Sum_probs=33.9

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEec
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP   57 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~   57 (150)
                      ++.....+.||.+..+..|||+|.+++...+-++-++.+.
T Consensus        97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            3456677889999999999999999999999998877554

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.

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

Probab=93.46  E-value=0.1  Score=45.20  Aligned_cols=34  Identities=18%  Similarity=0.280  Sum_probs=31.3

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+...++.++.+.++-+||++|++|++|.++|||
T Consensus       550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~  583 (692)
T COG1185         550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGV  583 (692)
T ss_pred             CCceEEEccCHHHHhhccCCcccchhhhhhhhCc
Confidence            5567789999999999999999999999999996

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=93.38  E-value=0.091  Score=38.86  Aligned_cols=38  Identities=18%  Similarity=0.257  Sum_probs=35.1

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC   59 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~   59 (150)
                      .+.+.||.++.+.+|||+|.+++...+-||-++.+...
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~  180 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI  180 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence            78888999999999999999999999999999988653

>KOG1588|consensus

Probab=93.28  E-value=0.096  Score=40.35  Aligned_cols=34  Identities=21%  Similarity=0.352  Sum_probs=29.1

Q ss_pred             CceEEEEEEecC------ceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQS------QAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~------~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.++.||-.      +||.|+|..|.++|+|+++||.
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgC  129 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGC  129 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCC
Confidence            456777888765      7999999999999999999984

>KOG0119|consensus

Probab=93.19  E-value=0.067  Score=44.63  Aligned_cols=33  Identities=24%  Similarity=0.316  Sum_probs=28.0

Q ss_pred             ceEEEEEEec------CceeEEeecCCchHHHHHHhhCC
Q psy7546         118 DYDIRLIVHQ------SQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       118 ~~~~~l~vp~------~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+-++.||.      +++|+|||..|.+.|+|+++|||
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgA  175 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGA  175 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCC
Confidence            4556666665      47999999999999999999998

>PRK12705 hypothetical protein; Provisional

Probab=93.07  E-value=0.16  Score=42.98  Aligned_cols=34  Identities=21%  Similarity=0.270  Sum_probs=28.0

Q ss_pred             CceEEEEEEecCc-eeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQ-AGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~-~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ......+.+|++- .|.||||.|.+|+.+...||.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGv  230 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGV  230 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCC
Confidence            4445567788864 699999999999999999984

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=92.92  E-value=1.8  Score=32.10  Aligned_cols=64  Identities=14%  Similarity=0.119  Sum_probs=50.9

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      +.+.++....-++...+|..++.|-...|++|.+...   +..+.|+|+...+..+...|...+...
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~---~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS---ENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC---CcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            3444557788899999999999998888999999874   468999999888877766666666553

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

Probab=92.75  E-value=0.099  Score=39.14  Aligned_cols=34  Identities=24%  Similarity=0.454  Sum_probs=27.1

Q ss_pred             CceEEEEEEec------CceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQ------SQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~------~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..++-++-||-      .++|++||..|+++|+|++.|+|
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~a  185 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRA  185 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCC
Confidence            34455555553      47999999999999999999987

>KOG1067|consensus

Probab=92.52  E-value=0.22  Score=42.58  Aligned_cols=69  Identities=17%  Similarity=0.157  Sum_probs=52.8

Q ss_pred             CCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHHH
Q psy7546          15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALDE   88 (150)
Q Consensus        15 ~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~~   88 (150)
                      ......+...+.++.++...+||.+|...|+|+.+||+.-++++.     .+.|.. +....++|.+.|...+..
T Consensus       591 ~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe~-----t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  591 DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDEG-----TFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeecCc-----eEEEEecCHHHHHHHHHHHHHHhcC
Confidence            344567788899999999999999999999999999976666654     255544 556677888777666554

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

Probab=92.22  E-value=0.092  Score=43.91  Aligned_cols=37  Identities=24%  Similarity=0.451  Sum_probs=33.2

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC   59 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~   59 (150)
                      ..+.+|...++.+|||+|.+|++|.+..|.+|.+...
T Consensus       488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            4477899999999999999999999999999998653

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=92.12  E-value=0.3  Score=42.48  Aligned_cols=87  Identities=20%  Similarity=0.331  Sum_probs=57.8

Q ss_pred             EecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCCC
Q psy7546          35 VIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGL  114 (150)
Q Consensus        35 IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (150)
                      .+-..|..||+|-++.--+|.+-.+|+      +   ...-++|...|.+.+.+....           .+.        
T Consensus        37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~------~---~~~~~~~~~~i~~~~~~~~~~-----------~~~--------   88 (630)
T TIGR03675        37 LFAKDDDLVKELAKKLRKRIVIRPDPS------V---LLPPEEAIEKIKEIVPEEAGI-----------TDI--------   88 (630)
T ss_pred             HhccchHHHHHHHHHhhceEEEecChh------h---cCCHHHHHHHHHHhCCCcCCc-----------eeE--------
Confidence            445677888999888888888865442      0   011134555555555432110           000        


Q ss_pred             CCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         115 GKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       115 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      -.+..+-.+.|-...-|.||||+|+++++|..+||
T Consensus        89 ~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~  123 (630)
T TIGR03675        89 YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETG  123 (630)
T ss_pred             EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhC
Confidence            12455677889999999999999999999999987

This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=91.96  E-value=0.19  Score=40.94  Aligned_cols=41  Identities=17%  Similarity=0.151  Sum_probs=36.6

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      ++.-...+.||.++.++.|||+|.+++-..+-||.+|.|-.
T Consensus       305 ~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        305 EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            34457789999999999999999999999999999999964

>KOG2113|consensus

Probab=91.83  E-value=0.2  Score=39.69  Aligned_cols=59  Identities=20%  Similarity=0.333  Sum_probs=48.9

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHH
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGL   76 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~   76 (150)
                      .+...+...-+|-..+|+|.|.+|++|+.+|+.++..|.-.-. +.+.+..++|.++++.
T Consensus       111 ~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-~~~~Vf~Vtg~~~nC~  169 (394)
T KOG2113|consen  111 ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-CGEPVFCVTGAPKNCV  169 (394)
T ss_pred             ccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-CCCceEEEecCCcchh
Confidence            4666777788899999999999999999999999998876532 4678888999888833

>TIGR01953 NusA transcription termination factor NusA

Probab=91.75  E-value=0.2  Score=40.32  Aligned_cols=40  Identities=20%  Similarity=0.309  Sum_probs=36.1

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      +.-.+.+.||.++.+..|||+|.+++-...-||.+|.+..
T Consensus       299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            4457889999999999999999999999999999998753

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.

>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3

Probab=91.60  E-value=0.21  Score=33.55  Aligned_cols=30  Identities=30%  Similarity=0.617  Sum_probs=25.2

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKA   52 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~   52 (150)
                      +++.+....-|.|||++|+.|++|++....
T Consensus        63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~   92 (109)
T cd02412          63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK   92 (109)
T ss_pred             EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence            567777788899999999999999976543

S3 is part of the head region of the 30S 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.

>KOG2874|consensus

Probab=91.53  E-value=0.46  Score=37.16  Aligned_cols=50  Identities=16%  Similarity=0.182  Sum_probs=41.8

Q ss_pred             eEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          34 SVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        34 ~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      .+||.+|.++|.|+--|.|.|-+....     |.+.|+...+..+...+.+++.+
T Consensus       162 RLiGpng~TLKAlelLT~CYilVqG~T-----VsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  162 RLIGPNGSTLKALELLTNCYILVQGNT-----VSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HhcCCCchhHHHHHHHhhcEEEeeCcE-----EEeecCcchHHHHHHHHHHHHhc
Confidence            489999999999999999999998753     78888888887777666666654

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

Probab=91.45  E-value=0.3  Score=31.09  Aligned_cols=29  Identities=21%  Similarity=0.503  Sum_probs=25.2

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      ..+++.|-...-|.+||++|+.|++|++.
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~   58 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSL   58 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHH
Confidence            35778888889999999999999999764

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.

>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein

Probab=91.43  E-value=0.29  Score=31.28  Aligned_cols=28  Identities=36%  Similarity=0.573  Sum_probs=23.2

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDF   50 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~t   50 (150)
                      .++.+....-|.+||++|++|++|++..
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHHH
Confidence            5566666788999999999999998764

S3 is part of the head region of the 30S 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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=91.08  E-value=0.19  Score=42.18  Aligned_cols=38  Identities=16%  Similarity=0.216  Sum_probs=35.2

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      -.+.+.||.++.+..|||+|.+++...+-||.+|.+..
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            47889999999999999999999999999999998864

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=90.76  E-value=0.3  Score=39.67  Aligned_cols=41  Identities=17%  Similarity=0.225  Sum_probs=36.6

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      ++.-.+.+.||.++.++.|||+|.+++--..-||.+|.+..
T Consensus       300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            34457889999999999999999999999999999998864

>PRK13764 ATPase; Provisional

Probab=90.74  E-value=0.19  Score=43.44  Aligned_cols=37  Identities=24%  Similarity=0.499  Sum_probs=33.3

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      ..-+.||...++.+|||+|.+|++|.+..|.+|.+-.
T Consensus       482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~  518 (602)
T PRK13764        482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP  518 (602)
T ss_pred             eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence            4457899999999999999999999999999999864

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

Probab=89.77  E-value=0.38  Score=36.58  Aligned_cols=30  Identities=43%  Similarity=0.606  Sum_probs=25.8

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRND   49 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~   49 (150)
                      ....++.|....-|.|||++|++|++|+++
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~   79 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE   79 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence            446678888899999999999999998865

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=89.17  E-value=0.38  Score=39.98  Aligned_cols=41  Identities=22%  Similarity=0.332  Sum_probs=36.5

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      ++.-.+.+.||.++.++.|||+|.+++--..-||.+|.|..
T Consensus       332 ~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        332 PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            34456789999999999999999999999999999998865

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=89.14  E-value=0.73  Score=32.58  Aligned_cols=37  Identities=30%  Similarity=0.499  Sum_probs=32.0

Q ss_pred             EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC
Q psy7546          24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP   60 (150)
Q Consensus        24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~   60 (150)
                      ++.|-...-|.+||++|.+++.|..+||-.-.+...|
T Consensus        79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            4566678889999999999999999999988887664

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=88.66  E-value=0.2  Score=38.18  Aligned_cols=30  Identities=20%  Similarity=0.328  Sum_probs=27.3

Q ss_pred             EEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+.||.++++.+||++|.+|+.|.+.|++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~  176 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGC  176 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCc
Confidence            557899999999999999999999998874

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

Probab=88.18  E-value=0.29  Score=30.17  Aligned_cols=29  Identities=28%  Similarity=0.602  Sum_probs=23.6

Q ss_pred             EEEEEEecCc-----eeEEeecCCchHHHHHHhh
Q psy7546         120 DIRLIVHQSQ-----AGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       120 ~~~l~vp~~~-----~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ...+.|-+..     +|..||++|++|+.|.++.
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L   37 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEEL   37 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHT
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHh
Confidence            4556777776     8999999999999999886

>KOG1067|consensus

Probab=88.07  E-value=0.46  Score=40.67  Aligned_cols=35  Identities=26%  Similarity=0.234  Sum_probs=32.2

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+....|.++++....+||.+|-..|.|+.+|||
T Consensus       594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGa  628 (760)
T KOG1067|consen  594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGA  628 (760)
T ss_pred             cCceeeEEeecchhhheeecCccceeeeEeeeccc
Confidence            46678889999999999999999999999999996

>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein

Probab=87.78  E-value=0.73  Score=29.39  Aligned_cols=27  Identities=30%  Similarity=0.719  Sum_probs=22.4

Q ss_pred             EEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         121 IRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      .++.+-...-|.+||++|++|+++++.
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~   66 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEI   66 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHH
Confidence            556666688899999999999998764

S3 is part of the head region of the 30S 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.

>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3

Probab=87.77  E-value=0.53  Score=31.54  Aligned_cols=28  Identities=36%  Similarity=0.717  Sum_probs=24.2

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      .+++.+-...-|.|||+.|+.|++|++.
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~   89 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKE   89 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHH
Confidence            4677788888899999999999999875

S3 is part of the head region of the 30S 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.

>TIGR00436 era GTP-binding protein Era

Probab=87.37  E-value=0.48  Score=36.53  Aligned_cols=30  Identities=33%  Similarity=0.376  Sum_probs=23.2

Q ss_pred             eEEEEEEec-CceeEEeecCCchHHHHHHhh
Q psy7546         119 YDIRLIVHQ-SQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       119 ~~~~l~vp~-~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ....+.|.. ++.+.|||++|++||+|....
T Consensus       221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a  251 (270)
T TIGR00436       221 IHALISVERESQKKIIIGKNGSMIKAIGIAA  251 (270)
T ss_pred             EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence            455666754 467999999999999997653

Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.

>PRK00089 era GTPase Era; Reviewed

Probab=85.57  E-value=0.7  Score=35.85  Aligned_cols=30  Identities=37%  Similarity=0.607  Sum_probs=22.5

Q ss_pred             eEEEEEEe-cCceeEEeecCCchHHHHHHhh
Q psy7546         119 YDIRLIVH-QSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       119 ~~~~l~vp-~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      +...+.|. .++.+.|||++|++||+|....
T Consensus       226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a  256 (292)
T PRK00089        226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA  256 (292)
T ss_pred             EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence            34455564 4467999999999999997653

>COG1159 Era GTPase [General function prediction only]

Probab=85.17  E-value=0.66  Score=36.62  Aligned_cols=29  Identities=34%  Similarity=0.563  Sum_probs=22.2

Q ss_pred             eEEEEEEecC-ceeEEeecCCchHHHHHHh
Q psy7546         119 YDIRLIVHQS-QAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       119 ~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~  147 (150)
                      ....+.|+.+ +-|.||||+|++||+|-..
T Consensus       229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~  258 (298)
T COG1159         229 IHATIYVERESQKGIIIGKNGAMIKKIGTA  258 (298)
T ss_pred             EEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence            3444666554 6899999999999999654

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

Probab=85.17  E-value=1  Score=34.26  Aligned_cols=30  Identities=33%  Similarity=0.664  Sum_probs=25.8

Q ss_pred             ceEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      +..+++.|-...=|.|||++|+.|++|+..
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~   79 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE   79 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence            456778888899999999999999998764

>TIGR00436 era GTP-binding protein Era

Probab=85.16  E-value=1.4  Score=33.89  Aligned_cols=29  Identities=21%  Similarity=0.275  Sum_probs=23.8

Q ss_pred             eEEEEEeeC-CccceEecCCchHHHHHHHH
Q psy7546          21 VELRLLIPS-RVAGSVIGKGGSNIARLRND   49 (150)
Q Consensus        21 ~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~   49 (150)
                      +...++|.. ++-+.|||++|+.||+|..+
T Consensus       221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~  250 (270)
T TIGR00436       221 IHALISVERESQKKIIIGKNGSMIKAIGIA  250 (270)
T ss_pred             EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence            566678884 77899999999999998754

Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.

>PRK15494 era GTPase Era; Provisional

Probab=84.68  E-value=0.78  Score=36.77  Aligned_cols=29  Identities=31%  Similarity=0.516  Sum_probs=22.6

Q ss_pred             eEEEEEEecC-ceeEEeecCCchHHHHHHh
Q psy7546         119 YDIRLIVHQS-QAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       119 ~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~  147 (150)
                      +...+.|..+ +.+.|||++|++||+|...
T Consensus       273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~  302 (339)
T PRK15494        273 INQVIVVSRESYKTIILGKNGSKIKEIGAK  302 (339)
T ss_pred             EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence            3455667554 6799999999999999765

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=83.79  E-value=1.4  Score=31.93  Aligned_cols=29  Identities=31%  Similarity=0.408  Sum_probs=24.3

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      .+-++|.... |..|||+|++++.+++..|
T Consensus        62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lg   90 (166)
T PRK06418         62 LVILLVTSGP-RIPIGKGGKIAKALSRKLG   90 (166)
T ss_pred             EEEEEEeCCC-cccccccchHHHHHHHHhC
Confidence            4556776666 9999999999999998766

>PTZ00084 40S ribosomal protein S3; Provisional

Probab=83.78  E-value=2.2  Score=32.31  Aligned_cols=30  Identities=20%  Similarity=0.368  Sum_probs=25.1

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKA   52 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~   52 (150)
                      .++.+....-|.|||++|..|++|+++..-
T Consensus        46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k   75 (220)
T PTZ00084         46 TEIIIRATRTREVLGDKGRRIRELTSLLQK   75 (220)
T ss_pred             EEEEEEECCCccEEcCCchHHHHHHHHHHH
Confidence            667777788899999999999999877543

>COG1847 Jag Predicted RNA-binding protein [General function prediction only]

Probab=82.64  E-value=0.74  Score=34.45  Aligned_cols=39  Identities=21%  Similarity=0.241  Sum_probs=30.7

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEe
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV   56 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i   56 (150)
                      .+.-.+.+-+..+..+.+||+.|.++..||--++..++-
T Consensus        88 ~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~  126 (208)
T COG1847          88 EEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK  126 (208)
T ss_pred             ecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence            344556666777779999999999999999887766655

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=82.52  E-value=1.8  Score=36.72  Aligned_cols=31  Identities=32%  Similarity=0.450  Sum_probs=26.2

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      ....+.||..++-.|||.||..|++.....+
T Consensus       449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~  479 (657)
T COG5166         449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHA  479 (657)
T ss_pred             hheEEEeecccceeeeccCchhhHHhhhhhh
Confidence            3566889999999999999999998876543

>PRK00089 era GTPase Era; Reviewed

Probab=81.95  E-value=2.3  Score=32.97  Aligned_cols=36  Identities=22%  Similarity=0.525  Sum_probs=26.9

Q ss_pred             eEEEEEee-CCccceEecCCchHHHHHHHH--------hCCeEEe
Q psy7546          21 VELRLLIP-SRVAGSVIGKGGSNIARLRND--------FKASVTV   56 (150)
Q Consensus        21 ~~~~l~vp-~~~vg~IIGk~G~~Ik~l~~~--------tg~~I~i   56 (150)
                      +...+.|. .++-+.|||++|+.||+|...        .|++|.+
T Consensus       226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l  270 (292)
T PRK00089        226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL  270 (292)
T ss_pred             EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence            55567777 477899999999999988643        5655554

>PRK15494 era GTPase Era; Provisional

Probab=81.53  E-value=2.3  Score=34.05  Aligned_cols=29  Identities=17%  Similarity=0.408  Sum_probs=23.5

Q ss_pred             eEEEEEeeC-CccceEecCCchHHHHHHHH
Q psy7546          21 VELRLLIPS-RVAGSVIGKGGSNIARLRND   49 (150)
Q Consensus        21 ~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~   49 (150)
                      +...++|.. ++-+.|||++|+.||+|..+
T Consensus       273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~  302 (339)
T PRK15494        273 INQVIVVSRESYKTIILGKNGSKIKEIGAK  302 (339)
T ss_pred             EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence            556688885 77899999999999988643

>CHL00048 rps3 ribosomal protein S3

Probab=81.47  E-value=3.2  Score=31.30  Aligned_cols=29  Identities=17%  Similarity=0.339  Sum_probs=24.6

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDF   50 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t   50 (150)
                      ..++.+....-|.|||++|++|++|++..
T Consensus        67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L   95 (214)
T CHL00048         67 LIQVIIYTGFPKLLIERKGRGIEELQINL   95 (214)
T ss_pred             eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence            46677777788999999999999999775

>KOG1423|consensus

Probab=80.98  E-value=1.8  Score=34.71  Aligned_cols=34  Identities=21%  Similarity=0.388  Sum_probs=27.6

Q ss_pred             CCceEEEEEeeC-CccceEecCCchHHHHHHHHhC
Q psy7546          18 PNDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFK   51 (150)
Q Consensus        18 ~~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg   51 (150)
                      ...+..+++||. +..-+||||||..|++|-++.+
T Consensus       325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~  359 (379)
T KOG1423|consen  325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN  359 (379)
T ss_pred             EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence            346677899996 6788899999999999977654

>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type

Probab=80.93  E-value=2.3  Score=31.60  Aligned_cols=30  Identities=30%  Similarity=0.581  Sum_probs=25.2

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFK   51 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg   51 (150)
                      ..++.+....-|.|||++|..|++|+++..
T Consensus        39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~   68 (195)
T TIGR01008        39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ   68 (195)
T ss_pred             cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence            367778888889999999999999987643

This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.

>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed

Probab=80.05  E-value=2.5  Score=31.68  Aligned_cols=30  Identities=37%  Similarity=0.580  Sum_probs=24.3

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKA   52 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~   52 (150)
                      .++.+....-|.+||++|++|+++++...-
T Consensus        42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk   71 (207)
T PRK04191         42 TRITIYAERPGMVIGRGGKNIRELTEILEK   71 (207)
T ss_pred             EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence            556666678899999999999999977543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	150
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		2e-04
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		5e-04

>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of Poly(C)-Binding Protein 1 To Its Affinity And Specificity For C-Rich Oligonucleotides Length = 76

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 36/66 (54%)
Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEV 82
          +RLL+  +  GS+IGK G ++ R+R +  A + + +   PERI+T+        K    +
Sbjct: 5  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSPERIITLTGPTNAIFKAFAMI 64
Query: 83 LPALDE 88
          +  L+E
Sbjct: 65 IDKLEE 70

>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1 Length = 74

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 36/66 (54%)
Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEV 82
          +RLL+  +  GS+IGK G ++ R+R +  A + + +   PERI+T+        K    +
Sbjct: 5  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMI 64
Query: 83 LPALDE 88
          +  L+E
Sbjct: 65 IDKLEE 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	150
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-32
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-10
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-31
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	9e-11
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-29
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-09
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	5e-27
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-11
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-05
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-25
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-10
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-18
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-07
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	7e-05
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-05
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-04
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-08
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-04
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-08
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	9e-04
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	4e-08
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-06
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	5e-08
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-04
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	7e-08
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-05
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	8e-05
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	3e-07
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	6e-07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-06
1we8_A	104	Tudor and KH domain containing protein; structural	5e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-05
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	6e-05

>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 =  110 bits (277), Expect = 7e-32
 Identities = 36/131 (27%), Positives = 62/131 (47%), Gaps = 14/131 (10%)

Query: 20  DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVI 79
            + +RLL+  +  GS+IGK G ++ ++R +  A + + +   PERI+T+        K  
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAF 63

Query: 80  EEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGT 139
             ++  L+E                  +        +    +RL+V  SQ G +IGKGG 
Sbjct: 64  AMIIDKLEE--------------DISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGC 109

Query: 140 KIKELRDTFDA 150
           KIKE+R++  A
Sbjct: 110 KIKEIRESTGA 120

>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 = 55.2 bits (133), Expect = 1e-10
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 15  RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP---ERILTIFAE 71
                 V LRL++P+   GS+IGKGG  I  +R    A V V     P   ER +TI   
Sbjct: 83  AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGI 142

Query: 72  LENGLKVIEEVLPALDE 88
            ++ ++ ++++   + E
Sbjct: 143 PQSIIECVKQICVVMLE 159

>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 =  109 bits (273), Expect = 3e-31
 Identities = 37/139 (26%), Positives = 58/139 (41%), Gaps = 10/139 (7%)

Query: 17  GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG-----PERILTIFAE 71
             +   L++LIPS  AGS+IGKGG  I +L+ +  A++ +           ER+  I   
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 72  LENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAG 131
           +E    V   +   + E+ Q   K                         +++IV  S AG
Sbjct: 62  IEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDR-----ANQVKIIVPNSTAG 116

Query: 132 CIIGKGGTKIKELRDTFDA 150
            IIGKGG  +K + +   A
Sbjct: 117 LIIGKGGATVKAIMEQSGA 135

>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 = 56.0 bits (135), Expect = 9e-11
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 4/80 (5%)

Query: 16  GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV---PDCPGP-ERILTIFAE 71
                 ++++++P+  AG +IGKGG+ +  +     A V +   PD      R++T+  E
Sbjct: 99  NPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGE 158

Query: 72  LENGLKVIEEVLPALDEIRQ 91
            E   K +E ++  + E  Q
Sbjct: 159 PEQNRKAVELIIQKIQEDPQ 178

>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 =  103 bits (259), Expect = 4e-29
 Identities = 35/134 (26%), Positives = 48/134 (35%), Gaps = 3/134 (2%)

Query: 20  DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV--PDCPGPERILTIFAELENGLK 77
              + + IP    G VIG+ G  I +++ND    +     D   PERI  I    +    
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 78  VIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYD-IRLIVHQSQAGCIIGK 136
             E +   L  ++     G G    G G   G               IV   + G IIGK
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 137 GGTKIKELRDTFDA 150
           GG  IK +     A
Sbjct: 122 GGETIKSISQQSGA 135

>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 = 51.4 bits (123), Expect = 4e-09
 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 12/82 (14%)

Query: 16  GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTIFA 70
                 E   ++P+   G +IGKGG  I  +     A + +   P P      ++ TI  
Sbjct: 99  PPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG 158

Query: 71  ELENGLKVIEEVLPALDEIRQK 92
             +        +  A   I +K
Sbjct: 159 TPQQ-------IDYARQLIEEK 173

>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 = 97.9 bits (244), Expect = 5e-27
 Identities = 31/134 (23%), Positives = 52/134 (38%), Gaps = 22/134 (16%)

Query: 20  DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP---ERILTIFAELENGL 76
              +++ IP++  G++IGK G +I +L     AS+ +     P    R++ I    E   
Sbjct: 2   QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQF 61

Query: 77  KVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGK 136
           K    +   L E                       G   +   +  + V  S AG +IGK
Sbjct: 62  KAQGRIYGKLKE-------------------ENFFGPKEEVKLETHIRVPASAAGRVIGK 102

Query: 137 GGTKIKELRDTFDA 150
           GG  + EL++   A
Sbjct: 103 GGKTVNELQNLTAA 116

>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 = 55.9 bits (135), Expect = 8e-11
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 16  GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP----ERILTI--- 68
                +E  + +P+  AG VIGKGG  +  L+N   A V VP    P    + I+ I   
Sbjct: 80  KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGH 139

Query: 69  FAELENGLKVIEEVLPALDEIRQK 92
           F   +   + I ++L  + +  QK
Sbjct: 140 FYASQMAQRKIRDILAQVKQQHQK 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 = 40.5 bits (95), Expect = 4e-05
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
           +   +++ +     G IIGK G  IK+L     A
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASA 34

>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 = 94.1 bits (234), Expect = 2e-25
 Identities = 27/132 (20%), Positives = 49/132 (37%), Gaps = 17/132 (12%)

Query: 23  LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTIFAELENGLKV 78
             ++IP+  AG VIGKGG  I +L+      + +          ++ L I  +     + 
Sbjct: 4   QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQA 63

Query: 79  IEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGG 138
            E V+  L              +   G  G       +    I + V +   G +IG+ G
Sbjct: 64  CEMVMDIL-------------RERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSG 110

Query: 139 TKIKELRDTFDA 150
             IK++++    
Sbjct: 111 EMIKKIQNDAGV 122

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

 Score = 55.2 bits (133), Expect = 2e-10
 Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 2/92 (2%)

Query: 1   MEFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP 60
           +    Q     +   G      + + +P    G VIG+ G  I +++ND    +      
Sbjct: 71  LRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD 130

Query: 61  G--PERILTIFAELENGLKVIEEVLPALDEIR 90
           G  PE+I  I    +        +   L  +R
Sbjct: 131 GTGPEKIAHIMGPPDRCEHAARIINDLLQSLR 162

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

 Score = 73.5 bits (181), Expect = 2e-18
 Identities = 19/69 (27%), Positives = 37/69 (53%)

Query: 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVI 79
           + +RLL+  +  GS+IGK G ++ ++R +  A + + +   PERI+T+        K  
Sbjct: 4  TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAF 63

Query: 80 EEVLPALDE 88
            ++  L+E
Sbjct: 64 AMIIDKLEE 72

>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 = 45.7 bits (109), Expect = 1e-07
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
              IRL++H  + G IIGK G  +K++R+   A
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGA 36

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

 Score = 51.3 bits (123), Expect = 1e-09
 Identities = 24/99 (24%), Positives = 36/99 (36%), Gaps = 2/99 (2%)

Query: 16  GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV--PDCPGPERILTIFAELE 73
           G      + + +P    G VIG+ G  I +++ND    +     D  GPE+I  I    +
Sbjct: 6   GSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD 65

Query: 74  NGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVG 112
                   +   L  +R       GG     G  G G G
Sbjct: 66  RCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRG 104

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

 Score = 39.0 bits (91), Expect = 7e-05
 Identities = 9/38 (23%), Positives = 19/38 (50%)

Query: 109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRD 146
           G +    +    I + V +   G +IG+ G  IK++++
Sbjct: 1   GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQN 38

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

 Score = 50.0 bits (120), Expect = 2e-09
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTI--- 68
          GG N     ++IP+  AG VIGKGG  I +L+      + +          ++ L I   
Sbjct: 9  GGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD 68

Query: 69 FAELENGLKVIEEVL 83
            +++   +++ ++L
Sbjct: 69 PYKVQQACEMVMDIL 83

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

 Score = 39.6 bits (93), Expect = 2e-05
 Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 106 YNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDT 147
           ++    GG  ++     +++   +AG +IGKGG  IK+L++ 
Sbjct: 3   FHDNANGG--QNGTVQEIMIPAGKAGLVIGKGGETIKQLQER 42

>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 = 50.5 bits (121), Expect = 3e-09
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTIFAE 71
           GP +    ++IP+  AG VIGKGG  I +L+      + +    P   G ++ L I  +
Sbjct: 10 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD 69

Query: 72 LENGLKVIEEVLPALDEIRQKYGKG 96
               +  E VL  + +       G
Sbjct: 70 PYKVQQAKEMVLELIRDQGSGPSSG 94

>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 = 41.2 bits (97), Expect = 7e-06
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 105 GYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRD 146
           G +G    G G  +    +++  S+AG +IGKGG  IK+L++
Sbjct: 1   GSSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQE 42

>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 = 50.1 bits (120), Expect = 4e-09
 Identities = 19/80 (23%), Positives = 26/80 (32%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKV 78
                + IP      VIGK G  +  L       + +P    P   + I    E   K 
Sbjct: 15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKA 74

Query: 79 IEEVLPALDEIRQKYGKGRG 98
            EVL    E  ++ G   G
Sbjct: 75 RHEVLLISAEQDKRSGPSSG 94

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

 Score = 48.3 bits (115), Expect = 2e-08
 Identities = 21/101 (20%), Positives = 37/101 (36%), Gaps = 8/101 (7%)

Query: 17  GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTI--- 68
                E+   IP+   G VIG+GG N+  +     A V +     P      ++  I   
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGS 62

Query: 69  FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGG 109
             ++++  ++IEE +            G G       +N G
Sbjct: 63  PQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPG 103

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

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 6/26 (23%), Positives = 13/26 (50%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
           +   +   + G +IG+GG  +K +  
Sbjct: 9   MTFSIPTHKCGLVIGRGGENVKAINQ 34

>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 = 47.3 bits (113), Expect = 3e-08
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
            +     L IP+ + G +IG+ G+NI  +R    A + + +       R +TI
Sbjct: 2  LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 55

>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 = 36.1 bits (84), Expect = 4e-04
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
             L +  +  GCIIG+ G  I E+R
Sbjct: 8   HELTIPNNLIGCIIGRQGANINEIR 32

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

 Score = 46.9 bits (112), Expect = 3e-08
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 2/53 (3%)

Query: 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
                 L IP+ + G +IG+ G+ I  +R    A + + +      +R +TI
Sbjct: 2  AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTI 54

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

 Score = 35.3 bits (82), Expect = 9e-04
 Identities = 11/27 (40%), Positives = 14/27 (51%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147
             L +     GCIIG+ G KI E+R  
Sbjct: 7   HELTIPNDLIGCIIGRQGAKINEIRQM 33

>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 = 46.9 bits (112), Expect = 4e-08
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 2/54 (3%)

Query: 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
          G   +  ++ IP  +AGS+IGKGG  I ++R++  AS+ + +      +RI+TI
Sbjct: 10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63

>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 = 43.5 bits (103), Expect = 1e-06
 Identities = 14/39 (35%), Positives = 22/39 (56%)

Query: 107 NGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELR 145
           +    G LG      ++ + +  AG IIGKGG +IK++R
Sbjct: 2   SHMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIR 40

>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 = 46.9 bits (112), Expect = 5e-08
 Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
               +  ++ IP  +AGS+IGKGG  I ++R++  AS+ + +      +RI+TI
Sbjct: 2  AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 56

>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 = 36.9 bits (86), Expect = 2e-04
 Identities = 11/25 (44%), Positives = 18/25 (72%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
            ++ + +  AG IIGKGG +IK++R
Sbjct: 9   TQVTIPKDLAGSIIGKGGQRIKQIR 33

>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 = 46.6 bits (111), Expect = 7e-08
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 9/97 (9%)

Query: 9   SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERIL 66
           S     +   + +     +P  + G +IG+GG  I+R++ +    + +    G  PER  
Sbjct: 3   SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62

Query: 67  TIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGG 103
            +    E+       V  A   + Q   KGR G   G
Sbjct: 63  MLTGTPES-------VQSAKRLLDQIVEKGRSGPSSG 92

>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 = 45.3 bits (108), Expect = 1e-07
 Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 5/51 (9%)

Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTI 68
          + + +P  + G+++GKGG  +   +    A + +            R +TI
Sbjct: 5  VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

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

 Score = 38.8 bits (91), Expect = 4e-05
 Identities = 8/26 (30%), Positives = 16/26 (61%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
           + + V ++  G I+GKGG  + E ++
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQE 30

>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 = 45.4 bits (108), Expect = 1e-07
 Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 5/51 (9%)

Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTI 68
          + + +P  + G+++GKGG  +   +    A + +            R +TI
Sbjct: 5  VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

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

 Score = 38.5 bits (90), Expect = 8e-05
 Identities = 8/27 (29%), Positives = 16/27 (59%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147
           + + V ++  G I+GKGG  + E ++ 
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQEL 31

>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 = 45.2 bits (107), Expect = 3e-07
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 3/83 (3%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP---DCPGPERILTIFAELENG 75
             +L + +  +    +IG+ G+ I ++R +   ++  P   D   P+  +TI    +N 
Sbjct: 15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNT 74

Query: 76 LKVIEEVLPALDEIRQKYGKGRG 98
              + +L  + E+ Q  G   G
Sbjct: 75 EAARDAILRIVGELEQMSGPSSG 97

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

 Score = 44.3 bits (105), Expect = 3e-07
 Identities = 15/63 (23%), Positives = 31/63 (49%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIE 80
            + + I  +    +IGK G+NI R+++ +K SV +P       ++ I  + +   +   
Sbjct: 5  DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKR 64

Query: 81 EVL 83
          E+L
Sbjct: 65 ELL 67

>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 = 44.6 bits (105), Expect = 4e-07
 Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 8/87 (9%)

Query: 16  GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENG 75
                  +++ +P RV G V+G  G+ I R++      +  P     E +  +    EN 
Sbjct: 5   SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPG-RDKEPVFAVTGMPEN- 62

Query: 76  LKVIEEVLPALDEIRQKYGKGRGGEDG 102
                 V  A +EI        G   G
Sbjct: 63  ------VDRAREEIEAHITLRSGPSSG 83

>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 = 44.4 bits (105), Expect = 6e-07
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 1/82 (1%)

Query: 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGL 76
             V   + +  RV   +IG  G  I ++ ++FK  +  P         +T+    EN  
Sbjct: 14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVE 73

Query: 77 KVIEEVLPALDEIRQKYGKGRG 98
          + I+ +L   +E     G   G
Sbjct: 74 EAIDHILNLEEEYLADSGPSSG 95

>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 = 43.2 bits (102), Expect = 1e-06
 Identities = 16/73 (21%), Positives = 35/73 (47%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIE 80
          V + + +P  +   VIG+ GS I ++ ++F+ ++ VP       I+ I     N  +   
Sbjct: 17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKA 76

Query: 81 EVLPALDEIRQKY 93
           +L  + E++ + 
Sbjct: 77 GLLERVKELQAEQ 89

>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 = 41.7 bits (98), Expect = 5e-06
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 7/90 (7%)

Query: 21  VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTIF---AELE 73
           V  +L +P R  G +IG+GG  I  +     A +T            R++ I     E+ 
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVA 74

Query: 74  NGLKVIEEVLPALDEIRQKYGKGRGGEDGG 103
               +I E +   +E+R++      G   G
Sbjct: 75  AAKHLILEKVSEDEELRKRIAHSASGPSSG 104

>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 = 2e-05
 Identities = 23/123 (18%), Positives = 41/123 (33%), Gaps = 35/123 (28%)

Query: 24  RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVL 83
           + ++   + G  IG  G+NI + R      VT  D         I+ E ++ +K     L
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARK--VPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFL 64

Query: 84  PALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKE 143
                                            +  +  + V ++  G +IGK G  I+E
Sbjct: 65  ---------------------------------EFAEDVIQVPRNLVGKVIGKNGKLIQE 91

Query: 144 LRD 146
           + D
Sbjct: 92  IVD 94

>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 = 39.0 bits (91), Expect = 6e-05
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLK 77
          N  E+ + IP+++  S+IG  G  I  +  +     +  P        + I     +  K
Sbjct: 15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEK 74

Query: 78 VIEEVLPALDEIRQKYGKGRG 98
            +++L   +E + K G   G
Sbjct: 75 AKKQLLHLAEEKQTKSGPSSG 95

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	150
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.92
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.91
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.9
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.9
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.77
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.71
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.7
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.68
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.68
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.68
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.68
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.67
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.67
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.66
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.66
1we8_A	104	Tudor and KH domain containing protein; structural	99.64
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.64
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.63
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.63
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.62
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.62
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.61
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.61
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.59
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.53
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.51
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.48
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.47
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.47
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.44
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.43
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.43
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.42
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.35
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.21
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.09
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.9
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.88
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.75
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	98.67
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	98.66
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.65
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	98.64
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	98.63
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	98.63
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	98.61
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	98.6
1we8_A	104	Tudor and KH domain containing protein; structural	98.59
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.59
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	98.55
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	98.54
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	98.54
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	98.47
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	98.44
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	98.43
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	98.36
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	98.31
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.29
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.28
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	98.27
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.25
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.13
2cxc_A	144	NUSA; transcription termination, RNA binding prote	98.03
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.01
2cpq_A	91	FragIle X mental retardation syndrome related prot	97.92
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	97.83
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	97.66
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.51
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	97.08
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.06
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.49
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.44
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	96.43
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.34
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	95.74
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.33
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	93.84
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.77
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.48
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.31
2cxc_A	144	NUSA; transcription termination, RNA binding prote	92.76
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	91.35
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	90.21
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	89.51
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	89.39
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	88.81
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	83.33
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	80.01

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

Probab=99.93  E-value=1.1e-25  Score=160.95  Aligned_cols=112  Identities=27%  Similarity=0.382  Sum_probs=98.1

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCC
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDEIRQKYGKG   96 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~   96 (150)
                      +.+++|+||.+.+|.||||+|++|++|+++|||+|++++.  + +++|+|+|+|+++++.+|..+|...+.+.....+  
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~~--   79 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGP--   79 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSSCS--
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccccc--
Confidence            4689999999999999999999999999999999999974  2 5899999999999999999999998887521110  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          97 RGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                                       ......+.+|.||.+++|+||||+|++|++|++.|||
T Consensus        80 -----------------~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga  116 (163)
T 3krm_A           80 -----------------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAA  116 (163)
T ss_dssp             -----------------SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCC
T ss_pred             -----------------ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCC
Confidence                             1135567899999999999999999999999999997

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

Probab=99.92  E-value=7.4e-26  Score=161.43  Aligned_cols=119  Identities=30%  Similarity=0.507  Sum_probs=102.7

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCC
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGR   97 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~   97 (150)
                      +..++++|+||.+.+|.||||+|++|++|+++|||+|++++..+++|.|+|+|+++++.+|..+|...+.+.......++
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~~~~~~   81 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEEDISSSMTNS   81 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHTSCCCSS
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhhccccCCCC
Confidence            35689999999999999999999999999999999999998777899999999999999999999999887653221100


Q ss_pred             CCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          98 GGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                                    ........+.++.||.+++|+||||+|++|++|+++|||
T Consensus        82 --------------~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga  120 (160)
T 2jzx_A           82 --------------TAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGA  120 (160)
T ss_dssp             --------------SCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSS
T ss_pred             --------------ccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCC
Confidence                          011235689999999999999999999999999999997

>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=99.91  E-value=2.2e-25  Score=161.53  Aligned_cols=129  Identities=29%  Similarity=0.389  Sum_probs=99.1

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC----C-CCCceEEEecChHHHHHHHHHHHHHHHHhhh
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC----P-GPERILTIFAELENGLKVIEEVLPALDEIRQ   91 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~   91 (150)
                      .+++++++|+||.+.+|.||||+|++|++|+++|||+|++++.    + +++|+|+|+|+++++.+|..+|...+.+...
T Consensus         2 l~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~   81 (178)
T 2anr_A            2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQ   81 (178)
T ss_dssp             -CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCC
Confidence            3678999999999999999999999999999999999999864    2 5889999999999999999999888765432


Q ss_pred             hcCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          92 KYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ........     .+..+..........+.+|.||.+++|+||||+|++|++|++.|||
T Consensus        82 ~~~~~~~~-----~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga  135 (178)
T 2anr_A           82 NVAKTEPV-----SILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGA  135 (178)
T ss_dssp             C----------------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSC
T ss_pred             ccccCCcc-----cccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCC
Confidence            11100000     0000000011234578999999999999999999999999999997

>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=99.90  E-value=2.8e-24  Score=153.56  Aligned_cols=117  Identities=25%  Similarity=0.364  Sum_probs=95.3

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCC
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALDEIRQKYGKG   96 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~   96 (150)
                      ++++|+||.+.+|.||||+|++||+|+++|||+|++++..    +++|+|+|+|+++++.+|..+|...+.+....    
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~----   77 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQG----   77 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSC----
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCC----
Confidence            6789999999999999999999999999999999997542    47899999999999999999998887653211    


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          97 RGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                        +......|..       ....+.++.||.+++|+||||+|++|++|+++|||
T Consensus        78 --~~~~~~~~~~-------~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~  122 (164)
T 2jvz_A           78 --GFGDRNEYGS-------RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGV  122 (164)
T ss_dssp             --CCSSCSSCTT-------SCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCC
T ss_pred             --CCCCccccCC-------CCCceEEEEEChhhccccCCCCcHhHHHHHHHHCC
Confidence              0000011111       12356789999999999999999999999999997

>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=99.90  E-value=4.3e-24  Score=154.31  Aligned_cols=130  Identities=28%  Similarity=0.398  Sum_probs=95.9

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C-CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCC
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P-GPERILTIFAELENGLKVIEEVLPALDEIRQKYGKG   96 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~   96 (150)
                      +..+++|+||.+.+|.||||+|++||+|+++|||+|++++. + +++|+|+|+|+++++.+|+.+|...+.+........
T Consensus         1 g~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~   80 (174)
T 1j4w_A            1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPGG   80 (174)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC------
T ss_pred             CCeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCCCC
Confidence            35789999999999999999999999999999999999853 2 588999999999999999999998887753211000


Q ss_pred             CCCCCCCCCCCCCC---CCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          97 RGGEDGGDGYNGGG---VGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        97 ~~~~~~~~~~~~~~---~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                       .+ +....+....   ...+.....+.+|.||.+++|+||||+|++|++|+++|||
T Consensus        81 -~~-p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga  135 (174)
T 1j4w_A           81 -PG-PGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGA  135 (174)
T ss_dssp             -------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCC
T ss_pred             -CC-CCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCC
Confidence             00 0000000000   0001123468899999999999999999999999999997

>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=99.77  E-value=3.4e-19  Score=111.44  Aligned_cols=71  Identities=27%  Similarity=0.511  Sum_probs=66.7

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      +..++++|+||.+.+|.||||+|++||+|+++|||+|++++..+++|+|+|+|+++++.+|..+|...+.+
T Consensus         2 ~~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             CceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            35689999999999999999999999999999999999998877899999999999999999999998875

>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=99.71  E-value=5.3e-17  Score=103.57  Aligned_cols=73  Identities=25%  Similarity=0.385  Sum_probs=66.7

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      .+.++++|.||.+.+|.||||+|++|++|+++|||+|++++..  +++|.|+|+|+++++.+|..+|...+.+..
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            4678999999999999999999999999999999999999752  478999999999999999999999888753

>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=99.70  E-value=2.1e-17  Score=105.42  Aligned_cols=73  Identities=21%  Similarity=0.242  Sum_probs=65.5

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C-CCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P-GPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      ....++++|.||.+.+|.||||+|++|++|+++|||+|++++. + +++|.|+|+|+++++.+|..+|...+.+.
T Consensus         2 ~g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            2 LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             CTTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4567899999999999999999999999999999999999974 2 47999999999999999999999887664

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

Probab=99.68  E-value=3.1e-17  Score=103.16  Aligned_cols=71  Identities=20%  Similarity=0.275  Sum_probs=64.3

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C-CCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P-GPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~-~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      +..++++|.||.+.+|.||||+|++|++|+++|||+|++++. + +++|.|+|+|+++++.+|..+|...+.+
T Consensus         2 ~~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            2 AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             -CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             CCceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            357899999999999999999999999999999999999974 2 4799999999999999999999888754

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

Probab=99.68  E-value=1e-16  Score=102.91  Aligned_cols=76  Identities=26%  Similarity=0.375  Sum_probs=67.8

Q ss_pred             CCCCCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHH
Q psy7546          12 KRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALD   87 (150)
Q Consensus        12 ~~~~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~   87 (150)
                      .+|..+++..+.+|.||.+.+|.||||+|++||+|+++|||+|.+++..    +.+|.|+|+|+++++.+|..+|...+.
T Consensus         5 ~~~~~g~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A            5 DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SSCCCSCSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCCCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            3467778889999999999999999999999999999999999998742    478999999999999999988877653

>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=99.68  E-value=5.9e-17  Score=104.89  Aligned_cols=76  Identities=25%  Similarity=0.356  Sum_probs=67.5

Q ss_pred             CCCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          14 FRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        14 ~~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      +......++++|.||.+.+|.||||+|++||+|+++|||+|++++..  +++|.|+|+|+++++.+|..+|...+.+.
T Consensus         7 ~~~~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A            7 GDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             ---CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            34456789999999999999999999999999999999999998752  47899999999999999999999988875

>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=99.68  E-value=4.7e-17  Score=103.97  Aligned_cols=72  Identities=21%  Similarity=0.361  Sum_probs=65.3

Q ss_pred             CCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHH
Q psy7546          15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALD   87 (150)
Q Consensus        15 ~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~   87 (150)
                      ++.++..+.+|.||.+.+|+||||+|++||+||++|||+|+++... ++++++|+|+++++++|..+|...+.
T Consensus         4 ~~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~-~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A            4 GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD-KEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             CCSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS-SCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             CCCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC-CCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            4567889999999999999999999999999999999999998643 47999999999999999999988654

>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=99.67  E-value=5.9e-17  Score=105.93  Aligned_cols=73  Identities=27%  Similarity=0.432  Sum_probs=67.2

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      .+++.++++|+||.+.+|.||||+|++||+|+++|||+|++++..    +++|+|+|+|+++++.+|+.+|...+.+
T Consensus        10 ~~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           10 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             CCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999999999998753    4799999999999999999999988865

>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=99.67  E-value=1.4e-16  Score=103.75  Aligned_cols=73  Identities=18%  Similarity=0.284  Sum_probs=66.9

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ...++++|.||.+.+|.||||+|++|++|+++|||+|+|++..  .++|.|+|+|+++++.+|..+|...+.+..
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            5679999999999999999999999999999999999999763  478999999999999999999999888743

>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=99.66  E-value=1.2e-16  Score=100.47  Aligned_cols=68  Identities=16%  Similarity=0.293  Sum_probs=61.6

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC----C-CCCceEEEecChHHHHHHHHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC----P-GPERILTIFAELENGLKVIEEVLPALD   87 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----~-~~ervv~I~G~~~~v~~A~~~i~~~~~   87 (150)
                      ..+++|.||.+.+|.||||+|++|++|+++|||+|++++.    + +++|.|+|+|+++++.+|..+|...+.
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   74 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999999999999974    2 478999999999999999998887654

>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=99.66  E-value=4.1e-17  Score=114.48  Aligned_cols=97  Identities=19%  Similarity=0.196  Sum_probs=76.0

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCC
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRG   98 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~   98 (150)
                      ..++.+|+||.+.+|++||++|++|++|++++|+++.... ..+++.+...++++.+.+|..++    .           
T Consensus         2 ~~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~-~~~~~~i~~~~~p~~v~~~~~~l----~-----------   65 (144)
T 2qnd_A            2 SRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD-EDTCTFHIYGEDQDAVKKARSFL----E-----------   65 (144)
T ss_dssp             --CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEE-TTTTEEEEEESSHHHHHHHHHHH----C-----------
T ss_pred             CceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccC-CCchheeeccCCHHHHHHHHHhh----h-----------
Confidence            3578999999999999999999999999999994433222 23566666667788887764321    1           


Q ss_pred             CCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546          99 GEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                                         .....+.||.+++|++|||+|.+|+.+++.|||
T Consensus        66 -------------------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~   98 (144)
T 2qnd_A           66 -------------------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV   98 (144)
T ss_dssp             -------------------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTC
T ss_pred             -------------------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCC
Confidence                               012779999999999999999999999999995

>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=99.64  E-value=8.2e-16  Score=102.22  Aligned_cols=79  Identities=20%  Similarity=0.251  Sum_probs=68.7

Q ss_pred             CCCCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          13 RFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        13 ~~~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      +.-......+++|.||.+.+|.||||+|++||+|+++|||+|++++..    .++|.|+|.|+.+++.+|+.+|...+.+
T Consensus         7 ~~~s~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T 1we8_A            7 GILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             CCCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            334445668899999999999999999999999999999999999753    2589999999999999999999998876


Q ss_pred             hhh
Q psy7546          89 IRQ   91 (150)
Q Consensus        89 ~~~   91 (150)
                      .+.
T Consensus        87 ~~~   89 (104)
T 1we8_A           87 DEE   89 (104)
T ss_dssp             HHH
T ss_pred             ChH
Confidence            553

>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=99.64  E-value=2.9e-16  Score=101.20  Aligned_cols=71  Identities=15%  Similarity=0.262  Sum_probs=64.6

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC----C-CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC----P-GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ..+++|.||.+.+|.||||+|++|++|+++|||+|++++.    + +++|.|+|+|+++++.+|..+|...+.+..
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQ   77 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            3678999999999999999999999999999999999974    2 378999999999999999999999887754

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

Probab=99.63  E-value=5.4e-16  Score=103.39  Aligned_cols=70  Identities=23%  Similarity=0.399  Sum_probs=63.4

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      -+++|+||.+.+|.||||+|++||+|+++|||+|+|++..  +++|.|+|+|+++++.+|..+|...+.+..
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            4789999999999999999999999999999999998643  478999999999999999999998887754

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

Probab=99.63  E-value=7.2e-16  Score=95.71  Aligned_cols=68  Identities=22%  Similarity=0.357  Sum_probs=61.9

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPA   85 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~   85 (150)
                      +...+..|.||.+.+|.|||++|++|++|+++|||+|+|++...++|.|+|+|+.+++.+|..+|...
T Consensus         2 ~~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            2 NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             CceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEcCHHHHHHHHHHHHHH
Confidence            35678899999999999999999999999999999999998766789999999999999999888654

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

Probab=99.62  E-value=1.5e-15  Score=120.68  Aligned_cols=134  Identities=11%  Similarity=0.146  Sum_probs=97.4

Q ss_pred             CCCCCceEEEEEeeCCccceEecCCc--hHHHHHHHHhCCeEEecCCC-------CCCceEEEecChHHHHHHHHHHHHH
Q psy7546          15 RGGPNDVELRLLIPSRVAGSVIGKGG--SNIARLRNDFKASVTVPDCP-------GPERILTIFAELENGLKVIEEVLPA   85 (150)
Q Consensus        15 ~~~~~~~~~~l~vp~~~vg~IIGk~G--~~Ik~l~~~tg~~I~i~~~~-------~~ervv~I~G~~~~v~~A~~~i~~~   85 (150)
                      ....+.++.++.||...++.||||+|  ++|++|+++|||+|+|++.+       .....|+|+|.+++|++|...|...
T Consensus        24 e~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           24 EINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             CCCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             EecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            44578999999999999999999999  99999999999999999754       2457899999999999999988763


Q ss_pred             ------------------HHHhhhhcCCCCCCCC----CCCCCCC--------CCCC------------------C---C
Q psy7546          86 ------------------LDEIRQKYGKGRGGED----GGDGYNG--------GGVG------------------G---L  114 (150)
Q Consensus        86 ------------------~~~~~~~~~~~~~~~~----~~~~~~~--------~~~~------------------~---~  114 (150)
                                        +......  ...++..    ..+..++        .|..                  .   .
T Consensus       104 ~Pl~i~~elp~~~i~~~~l~~~I~q--q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e~~  181 (376)
T 3n89_A          104 CHFTVFMALSKMKMPLHELQAHVRQ--NPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPA  181 (376)
T ss_dssp             CEEEEEEECTTCSSCHHHHHHHHHH--CCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--CC
T ss_pred             CCceEEEEccccccCcchhhhhhcc--ceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhhcc
Confidence                              1111111  0111110    0011000        0000                  1   1


Q ss_pred             CCCceEEEEEEecCceeEEeecCC--chHHHHHHhhCC
Q psy7546         115 GKDDYDIRLIVHQSQAGCIIGKGG--TKIKELRDTFDA  150 (150)
Q Consensus       115 ~~~~~~~~l~vp~~~~g~iIGk~G--~~Ik~i~~~tGA  150 (150)
                      ....++..+.|+..++..|||++|  ..|++|+++|||
T Consensus       182 ~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv  219 (376)
T 3n89_A          182 PENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTT  219 (376)
T ss_dssp             CSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTC
T ss_pred             cccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCC
Confidence            124688999999999999999999  566999999997

>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=99.62  E-value=1.5e-15  Score=99.17  Aligned_cols=75  Identities=23%  Similarity=0.234  Sum_probs=67.7

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ...+.++.+|.||.+.+|.|||++|++||+|+++|||+|+|++...+++.|+|+|+++++.+|..+|...+.+..
T Consensus        12 ~l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           12 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             HhCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            345679999999999999999999999999999999999999765567899999999999999999988887754

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

Probab=99.61  E-value=6.6e-16  Score=103.18  Aligned_cols=69  Identities=19%  Similarity=0.254  Sum_probs=63.0

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-----CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-----GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-----~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      +++|+||.+.+|.||||+|++||+|+++|||+|+|++..     .++|.|+|+|+++++.+|+.+|...+.+..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            789999999999999999999999999999999999753     267999999999999999999998887643

>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=99.61  E-value=3.8e-15  Score=97.45  Aligned_cols=76  Identities=21%  Similarity=0.288  Sum_probs=68.6

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-CCCceEEEecChHHHHHHHHHHHHHHHHhhh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGLKVIEEVLPALDEIRQ   91 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~   91 (150)
                      ...+.++..|.||.+.+|.|||++|++|++|+++|||+|+|++.. .++|.|+|+|.++++.+|+.+|...+.+...
T Consensus        12 ~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             hhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            446779999999999999999999999999999999999998764 3678999999999999999999998887664

>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=99.59  E-value=6.8e-15  Score=96.59  Aligned_cols=73  Identities=21%  Similarity=0.376  Sum_probs=65.3

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC---CCCceEEEecChHHHHHHHHHHHHHHHHhhh
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP---GPERILTIFAELENGLKVIEEVLPALDEIRQ   91 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~---~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~   91 (150)
                      ..++..|.||.+.+|.|||++|++|++|+++|||+|+|++..   ..+|.|+|+|+.+++.+|..+|...+.+...
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~   90 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELEQ   90 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHh
Confidence            457999999999999999999999999999999999999754   2679999999999999999999888776543

>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=99.53  E-value=1.6e-14  Score=95.97  Aligned_cols=71  Identities=23%  Similarity=0.360  Sum_probs=64.1

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ..+..|.||.+.+|.|||++|++|++|+++|||+|+|++.....+.|+|+|+.+++.+|+.+|...+.+..
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 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            37889999999999999999999999999999999999876566799999999999999998888776643

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

Probab=99.51  E-value=1.8e-14  Score=107.31  Aligned_cols=111  Identities=19%  Similarity=0.160  Sum_probs=79.3

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC-----hHHHHHHHHHHHHHHHHhhhhcCC
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE-----LENGLKVIEEVLPALDEIRQKYGK   95 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-----~~~v~~A~~~i~~~~~~~~~~~~~   95 (150)
                      -..++.||.+.+|.|||++|++|+.|+++||++|.++..   ++.|.|.++     ++++.+|..+|.............
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~---~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~g~  110 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE---TGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAF  110 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT---TCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHHHG
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC---CCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCccccc
Confidence            456899999999999999999999999999999999843   456788775     599999998888765210000000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCceEEEEEEe-----------cCceeEEeecCCchHHHHHHhhCC
Q psy7546          96 GRGGEDGGDGYNGGGVGGLGKDDYDIRLIVH-----------QSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp-----------~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .                ...+......+.++           ...+|+||||+|++|+.|++.||+
T Consensus       111 ~----------------ll~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~  160 (219)
T 2e3u_A          111 R----------------LLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGA  160 (219)
T ss_dssp             G----------------GGSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             e----------------eccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCc
Confidence            0                00011111122222           126899999999999999999996

>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=99.48  E-value=8.5e-14  Score=90.96  Aligned_cols=79  Identities=18%  Similarity=0.181  Sum_probs=70.8

Q ss_pred             CCCCCCCCCceEEEEEeeCCccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          11 FKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        11 ~~~~~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      ........+.++..|.||.+.++.|||++|.+|++|+++| ||+|.|++..+..+.|+|+|+.+.+.+|+.+|...+.+.
T Consensus         7 ~~i~~e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A            7 GSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             CCCCCCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            3445667889999999999999999999999999999999 999999987667789999999999999999998887763

>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=99.47  E-value=5.3e-14  Score=99.77  Aligned_cols=71  Identities=32%  Similarity=0.513  Sum_probs=64.7

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ....+++|+||.+.+|.||||+|.+|++|+++|||+|++++.  + +.++.|+|+|+++++.+|+.+|...+.+
T Consensus        86 ~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           86 RPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             CCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            346899999999999999999999999999999999999864  2 4789999999999999999999888765

>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=99.47  E-value=2.6e-14  Score=103.15  Aligned_cols=71  Identities=25%  Similarity=0.471  Sum_probs=65.2

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      ...+++|+||.+.+|.||||+|++||+|+++|||+|++++.+    +.+|.|+|+|+++++.+|+.+|...+.+.
T Consensus       102 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          102 RANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             GGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHSC
T ss_pred             CceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhC
Confidence            457899999999999999999999999999999999998753    47899999999999999999999998864

>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=99.44  E-value=2.4e-13  Score=96.63  Aligned_cols=73  Identities=26%  Similarity=0.415  Sum_probs=64.5

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC---C-CCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP---G-PERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~---~-~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ....+.+|.||.+.+|.||||+|++|++|+++|||+|++++..   + .++.|+|+|+++++.+|..+|...+.+..
T Consensus        82 ~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~  158 (163)
T 3krm_A           82 EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVK  158 (163)
T ss_dssp             CCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999998652   2 34589999999999999999999988754

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

Probab=99.43  E-value=5.1e-13  Score=88.35  Aligned_cols=71  Identities=18%  Similarity=0.249  Sum_probs=63.9

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHH-hCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhh
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRND-FKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQK   92 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~-tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~   92 (150)
                      +.++.+|.||...++.|||++|++|++|+++ ++++|+|++   .++.|+|.|+++.|.+|..+|...+.+....
T Consensus        25 ~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~---~~~~ItI~G~~~~V~~a~~~I~~~v~el~~~   96 (102)
T 2ctf_A           25 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---GEDKITLEGPTEDVSVAQEQIEGMVKDLINR   96 (102)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---SSCEEEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC---CCCEEEEECCHHHHHHHHHHHHHHHHHHHhh
Confidence            3478999999999999999999999999997 589999998   4689999999999999999998888776544

>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=99.43  E-value=1.6e-13  Score=98.59  Aligned_cols=67  Identities=19%  Similarity=0.296  Sum_probs=59.8

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-----CCCceEEEecChHHHHHHHHHHHHH
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-----GPERILTIFAELENGLKVIEEVLPA   85 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-----~~ervv~I~G~~~~v~~A~~~i~~~   85 (150)
                      +..+++|.||.+.+|.||||+|++||+|+++|||+|++++..     +.+|.|+|.|+++++.+|..+|...
T Consensus       102 ~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~  173 (174)
T 1j4w_A          102 GLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK  173 (174)
T ss_dssp             --CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999998752     4679999999999999999888765

>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=99.42  E-value=1.6e-13  Score=97.45  Aligned_cols=70  Identities=21%  Similarity=0.377  Sum_probs=63.1

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      ..+++|.||.+.+|.||||+|++|++|+++|||+|++++..  +.+|.|+|+|+++++.+|..+|...+.+.
T Consensus        90 ~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A           90 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             SSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            35689999999999999999999999999999999998653  36899999999999999999998888764

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

Probab=99.35  E-value=8.2e-13  Score=96.29  Aligned_cols=110  Identities=19%  Similarity=0.209  Sum_probs=80.8

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEe-----cChHHHHHHHHHHHHHHHHhhhhcCCC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIF-----AELENGLKVIEEVLPALDEIRQKYGKG   96 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~-----G~~~~v~~A~~~i~~~~~~~~~~~~~~   96 (150)
                      .++++||.+.+|.|||++|++++.|++.+|++|+++.   .++.|+|.     |++..+.+|...|..............
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~---~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~e~A~~   81 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT---ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAFR   81 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET---TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHHHGG
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc---CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHHHhhh
Confidence            3689999999999999999999999999999999975   36778887     899999999988865544211000000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCceEEEEEEe----------cCceeEEeecCCchHHHHHHhhCC
Q psy7546          97 RGGEDGGDGYNGGGVGGLGKDDYDIRLIVH----------QSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp----------~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                                      ...++.....+.++          ...+|.||||+|.+++.|++.||+
T Consensus        82 ----------------Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~  129 (191)
T 1tua_A           82 ----------------LLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDT  129 (191)
T ss_dssp             ----------------GGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTC
T ss_pred             ----------------cccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCc
Confidence                            00012122223333          235899999999999999999986

>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=99.21  E-value=1.3e-11  Score=86.35  Aligned_cols=67  Identities=18%  Similarity=0.179  Sum_probs=57.9

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCC-eEEecCCC-----CCCc--eEEEecChHHHHHHHHHHHHHHHH
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKA-SVTVPDCP-----GPER--ILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~-~I~i~~~~-----~~er--vv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ..++.||.+++|++|||+|.+||.+++.||+ +|+|+..+     .+++  .|+|.|+++++..|..+|...+.+
T Consensus        68 e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3889999999999999999999999999997 99998532     2344  488999999999999999888764

>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=99.09  E-value=8e-11  Score=75.87  Aligned_cols=63  Identities=16%  Similarity=0.201  Sum_probs=54.3

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCe-EEecCCCCCCceEEEec-ChHHHHHHHHHH
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKAS-VTVPDCPGPERILTIFA-ELENGLKVIEEV   82 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~-I~i~~~~~~ervv~I~G-~~~~v~~A~~~i   82 (150)
                      -...+...|.||.+.+|.|||++|.+|++|+++||++ |.+.+.   +..|.|.| +.+.+.+|..+|
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed---dG~V~I~g~~~ea~~~A~~~I   75 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED---TGTFRIYGESADAVKKARGFL   75 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT---TTEEEEEESSHHHHHHHHHHH
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC---CCEEEEEECCHHHHHHHHHHH
Confidence            3456889999999999999999999999999999998 999862   47899999 777787777554

>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=98.90  E-value=2.5e-09  Score=73.48  Aligned_cols=70  Identities=20%  Similarity=0.343  Sum_probs=56.3

Q ss_pred             CceEEEEEeeCC------ccceEecCCchHHHHHHHHhCCeEEecCCC------------------CCCceEEEec-ChH
Q psy7546          19 NDVELRLLIPSR------VAGSVIGKGGSNIARLRNDFKASVTVPDCP------------------GPERILTIFA-ELE   73 (150)
Q Consensus        19 ~~~~~~l~vp~~------~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~------------------~~ervv~I~G-~~~   73 (150)
                      ..++.++.||.+      .+|.|||++|.+||+|+++|||+|.+....                  ..+--|.|++ +.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            457899999988      789999999999999999999999997521                  1234566766 577


Q ss_pred             HHHHHHHHHHHHHHH
Q psy7546          74 NGLKVIEEVLPALDE   88 (150)
Q Consensus        74 ~v~~A~~~i~~~~~~   88 (150)
                      .+.+|+.+|...+..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            788888888887765

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.88  E-value=7.2e-09  Score=69.99  Aligned_cols=69  Identities=17%  Similarity=0.083  Sum_probs=53.6

Q ss_pred             ceEEEEEeeCC-------ccceEecCCchHHHHHHHHhCCeEEecCCCC------------C-CceEEEecChHHHHHHH
Q psy7546          20 DVELRLLIPSR-------VAGSVIGKGGSNIARLRNDFKASVTVPDCPG------------P-ERILTIFAELENGLKVI   79 (150)
Q Consensus        20 ~~~~~l~vp~~-------~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~------------~-ervv~I~G~~~~v~~A~   79 (150)
                      .++.++.||-+       .+|.|||++|.+||+|+++|||+|.|....|            . .++.....+.+.+.+|+
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            47788988865       6899999999999999999999999973211            2 23444456788899999


Q ss_pred             HHHHHHHHH
Q psy7546          80 EEVLPALDE   88 (150)
Q Consensus        80 ~~i~~~~~~   88 (150)
                      .+|..++..
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            887777655

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

Probab=98.75  E-value=9.1e-09  Score=81.78  Aligned_cols=71  Identities=13%  Similarity=0.223  Sum_probs=59.6

Q ss_pred             CCceEEEEEeeCCccceEecCCc--hHHHHHHHHhCCeEEecCCCC------CCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGG--SNIARLRNDFKASVTVPDCPG------PERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G--~~Ik~l~~~tg~~I~i~~~~~------~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ...++..|.|+..++..|||++|  ..|++|+++||++|.|++.+.      ....|+|+|..++|.+|...|...+.=
T Consensus       183 ~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLPv  261 (376)
T 3n89_A          183 ENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLLPI  261 (376)
T ss_dssp             SSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTSEE
T ss_pred             ccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhCCE
Confidence            45689999999999999999999  567999999999999996532      346899999999999999998887643

>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=98.67  E-value=3.2e-09  Score=65.76  Aligned_cols=34  Identities=38%  Similarity=0.671  Sum_probs=32.4

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.+|+||++.+|+||||+|++|++|+++|||
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga   36 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGA   36 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCC
Confidence            5678999999999999999999999999999997

>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=98.66  E-value=4.8e-09  Score=66.60  Aligned_cols=35  Identities=20%  Similarity=0.352  Sum_probs=33.1

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +...+.++.||.+++|+||||+|++||+|+++|||
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga   41 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHT   41 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTC
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCC
Confidence            56789999999999999999999999999999997

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.65  E-value=3.6e-08  Score=68.24  Aligned_cols=67  Identities=19%  Similarity=0.291  Sum_probs=49.8

Q ss_pred             eEEEEEeeCCc------cceEecCCchHHHHHHHHhCCeEEecCCCC--------------------CCceEEEecC-hH
Q psy7546          21 VELRLLIPSRV------AGSVIGKGGSNIARLRNDFKASVTVPDCPG--------------------PERILTIFAE-LE   73 (150)
Q Consensus        21 ~~~~l~vp~~~------vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~--------------------~ervv~I~G~-~~   73 (150)
                      ++.++.||-+.      +|.|||++|.++|+|+++|||+|.|....|                    .+--|.|++. ++
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            56788899655      999999999999999999999999985321                    1114667763 33


Q ss_pred             -----HHHHHHHHHHHHHH
Q psy7546          74 -----NGLKVIEEVLPALD   87 (150)
Q Consensus        74 -----~v~~A~~~i~~~~~   87 (150)
                           .+.+|+.+|...+.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                 56677766666554

>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=98.64  E-value=7.6e-09  Score=65.40  Aligned_cols=35  Identities=31%  Similarity=0.567  Sum_probs=32.8

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....+.+|.||.+++|+||||+|++|++|+++|||
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga   37 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGA   37 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCC
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCC
Confidence            36688999999999999999999999999999997

>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=98.63  E-value=1.2e-08  Score=64.46  Aligned_cols=35  Identities=34%  Similarity=0.547  Sum_probs=32.9

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+..+.++.||.+++|+||||+|++|++|+++|||
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga   38 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA   38 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCC
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCC
Confidence            35789999999999999999999999999999997

>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=98.63  E-value=9.5e-09  Score=63.92  Aligned_cols=32  Identities=28%  Similarity=0.493  Sum_probs=30.5

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.++.||.+++|+||||+|++|++|++.|||
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga   34 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGA   34 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCC
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCC
Confidence            57889999999999999999999999999997

>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=98.61  E-value=1.5e-08  Score=65.49  Aligned_cols=35  Identities=23%  Similarity=0.415  Sum_probs=32.8

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....+.+|.||.+++|+||||+|++|++|+++|||
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga   46 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGC   46 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCC
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCC
Confidence            35688999999999999999999999999999997

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

Probab=98.60  E-value=6e-09  Score=64.93  Aligned_cols=34  Identities=35%  Similarity=0.614  Sum_probs=32.3

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.+|.||.+++|+||||+|++|++|++.|||
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga   36 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGA   36 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCC
Confidence            5678999999999999999999999999999997

>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=98.59  E-value=2.5e-08  Score=65.83  Aligned_cols=35  Identities=31%  Similarity=0.418  Sum_probs=32.9

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+.+.+|.||.+++|+||||+|++|++|+++|||
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga   46 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGA   46 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCC
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCC
Confidence            46788999999999999999999999999999997

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

Probab=98.59  E-value=2.2e-08  Score=74.43  Aligned_cols=54  Identities=19%  Similarity=0.144  Sum_probs=49.5

Q ss_pred             ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      .+|.||||+|.+|+.|++.|||+|.+++     +.|.|.|+.+++..|..+|+.++...
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~~-----~~v~i~G~~~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVYG-----KTVAIIGNPIQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEET-----TEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             hhheeECCCchHHHHHHHHhCceEEECC-----eEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence            6899999999999999999999999986     46999999999999999999998653

>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=98.55  E-value=1e-08  Score=65.80  Aligned_cols=35  Identities=34%  Similarity=0.547  Sum_probs=33.3

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....+.++.||.+++|+||||+|++|++|+++|||
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga   45 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA   45 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCC
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCC
Confidence            57789999999999999999999999999999997

>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=98.54  E-value=3.2e-08  Score=64.12  Aligned_cols=35  Identities=31%  Similarity=0.556  Sum_probs=33.3

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +...+.+|.||.+++|+||||+|++|++|+++|||
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga   46 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGV   46 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTS
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCC
Confidence            57789999999999999999999999999999997

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

Probab=98.54  E-value=2.4e-08  Score=63.51  Aligned_cols=35  Identities=29%  Similarity=0.562  Sum_probs=32.5

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....+.+|.||.+++|+||||+|++|++|+++|||
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga   45 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGV   45 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCC
Confidence            35678899999999999999999999999999997

>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=98.47  E-value=1.8e-08  Score=64.36  Aligned_cols=32  Identities=28%  Similarity=0.493  Sum_probs=30.5

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.++.||.+++|+||||+|++|++|++.|||
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga   34 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGA   34 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCC
Confidence            57889999999999999999999999999997

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

Probab=98.44  E-value=6.7e-08  Score=59.41  Aligned_cols=34  Identities=18%  Similarity=0.391  Sum_probs=31.9

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.++.||.+++|.|||++|++|++|+++|||
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~   36 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKV   36 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCC
Confidence            5678899999999999999999999999999996

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

Probab=98.43  E-value=5.2e-08  Score=64.60  Aligned_cols=31  Identities=23%  Similarity=0.592  Sum_probs=30.1

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +.+|.||.+++|+||||+|++||+|+++|||
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa   38 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGA   38 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSS
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCC
Confidence            7899999999999999999999999999997

>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=98.36  E-value=1.1e-07  Score=61.54  Aligned_cols=35  Identities=17%  Similarity=0.340  Sum_probs=32.6

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...++.++.||.+++|.|||++|++|++|+++|||
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~   48 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTAT   48 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTC
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCC
Confidence            35688999999999999999999999999999996

>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=98.31  E-value=1.7e-07  Score=61.11  Aligned_cols=34  Identities=24%  Similarity=0.413  Sum_probs=32.0

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+..+.||.+++|.|||++|++|++|+++|||
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~   48 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDV   48 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTC
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCC
Confidence            4578999999999999999999999999999996

>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=98.29  E-value=3.4e-07  Score=66.55  Aligned_cols=53  Identities=15%  Similarity=0.322  Sum_probs=48.3

Q ss_pred             ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ..|.||||+|.+++.|++.|||+|.+++.     .|.|.|+++++..|...|..++..
T Consensus       108 ~~GrIIGk~G~tik~iE~~Tg~~I~v~~~-----~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          108 IKGRIIGEGGRARRTIEEMTDTYINVGEY-----EVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECSS-----EEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhhheeCCCccHHHHHHHHHCceEEEcCC-----EEEEEeChHHHHHHHHHHHHHHcC
Confidence            48999999999999999999999999874     699999999999999888888864

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=98.28  E-value=1.7e-06  Score=59.06  Aligned_cols=69  Identities=17%  Similarity=0.131  Sum_probs=60.5

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-CCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      -++.|.+.+..++.|+|++|+.|+.|+..|++.|++.... +++--|+|.|++..-.+|..+|....+..
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999754 46777999999999999998888777654

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

Probab=98.27  E-value=1.7e-07  Score=62.03  Aligned_cols=33  Identities=24%  Similarity=0.449  Sum_probs=30.1

Q ss_pred             ceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+.+|.||.+++|+||||+|++||+|+++|||
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGa   42 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGV   42 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTC
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCc
Confidence            457899999999999999999999999999997

>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=98.25  E-value=2.2e-07  Score=60.30  Aligned_cols=35  Identities=20%  Similarity=0.331  Sum_probs=32.9

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...++.++.||.+++|.|||++|++|++|+++|||
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~   48 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKV   48 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTC
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCC
Confidence            46789999999999999999999999999999986

>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=98.13  E-value=3.7e-07  Score=60.20  Aligned_cols=34  Identities=24%  Similarity=0.390  Sum_probs=32.0

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.+..+.||.+++|.|||++|++|++|+++||+
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~   48 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEV   48 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCC
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCC
Confidence            4588999999999999999999999999999996

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=98.03  E-value=3.7e-07  Score=63.47  Aligned_cols=98  Identities=26%  Similarity=0.324  Sum_probs=68.3

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCC
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE  100 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~  100 (150)
                      -.+.++|+...+|+.||++|.+|+.+++++|-+|.+-+...         ++..      .|.+.+.     |.....-.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~---------d~~~------fI~naLs-----PA~V~~V~   95 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS---------DLER------IVKNLFP-----GVKIESIN   95 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS---------SHHH------HHHHHST-----TSCEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC---------CHHH------HHHHhcC-----CceEEEEE
Confidence            45778999999999999999999999999999998876431         1111      1222211     11100000


Q ss_pred             CCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         101 DGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                                 ....+......+.||.+..+..|||+|.+++-..+.||
T Consensus        96 -----------i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg  133 (144)
T 2cxc_A           96 -----------VRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLS  133 (144)
T ss_dssp             -----------EEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHH
T ss_pred             -----------EeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhC
Confidence                       00002456788899999999999999999999998886

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.01  E-value=5.3e-06  Score=70.09  Aligned_cols=61  Identities=16%  Similarity=0.279  Sum_probs=51.1

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC-hHHHHHHHHHHH
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE-LENGLKVIEEVL   83 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-~~~v~~A~~~i~   83 (150)
                      -.-...|-||.+.+|.|||+||.+||.|+++|||+|.+.+.    -.|.|.++ .+...+|+.+|.
T Consensus       565 ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~----G~V~I~~~~~~~~~~A~~~I~  626 (630)
T 3u1k_A          565 GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE----ETFSVFAPTPSAMHEARDFIT  626 (630)
T ss_dssp             CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS----SEEEEEESSHHHHHHHHHHTT
T ss_pred             CCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC----cEEEEEeCCHHHHHHHHHHHH
Confidence            34577899999999999999999999999999999999863    57888775 466777776654

>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=97.92  E-value=9.5e-07  Score=56.73  Aligned_cols=35  Identities=20%  Similarity=0.395  Sum_probs=32.7

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .......+.||.+++|.+||++|++|++|+++|||
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv   46 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGV   46 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTE
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCC
Confidence            46688999999999999999999999999999996

>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=97.83  E-value=2.4e-06  Score=55.32  Aligned_cols=35  Identities=11%  Similarity=0.275  Sum_probs=32.5

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhh-CC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF-DA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t-GA  150 (150)
                      +...+..|.||.++++.|||++|++|++|+++| |+
T Consensus        14 ~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv   49 (95)
T 2ctj_A           14 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGV   49 (95)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSC
T ss_pred             hhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCC
Confidence            567899999999999999999999999999999 65

>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=97.66  E-value=1e-05  Score=52.96  Aligned_cols=32  Identities=16%  Similarity=0.155  Sum_probs=29.2

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ...+.+|.||+++++.|||++|++|++|++.+
T Consensus        25 ~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~   56 (102)
T 2ctf_A           25 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQM   56 (102)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHC
T ss_pred             CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHc
Confidence            34789999999999999999999999999974

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.51  E-value=2.8e-05  Score=66.57  Aligned_cols=64  Identities=22%  Similarity=0.222  Sum_probs=9.3

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD   87 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~   87 (150)
                      .-...|.||.++++.|||+||.+||.|+++||++|.+.+.    -.|.|.+ +.+...+|+..|.....
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd----G~v~I~~~~~~~~~~A~~~i~~i~~  633 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD----GVVKVSASDGAKIKAAIDWIKSITD  633 (726)
T ss_dssp             CC-----------------------------------------------CCSCHHHHHHHHHC------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC----ceEEEEeCCHHHHHHHHHHHHHHhh
Confidence            3466788999999999999999999999999999999863    3456655 46667777766655543

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.08  E-value=0.00012  Score=49.20  Aligned_cols=34  Identities=15%  Similarity=0.122  Sum_probs=29.2

Q ss_pred             CceEEEEEEecC-------ceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQS-------QAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~-------~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.+|.||..       ++|.|||++|.+||+|+++|||
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~   50 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGA   50 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCC
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCC
Confidence            456777877765       6899999999999999999997

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.06  E-value=0.00032  Score=59.32  Aligned_cols=34  Identities=21%  Similarity=0.261  Sum_probs=31.8

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+....+.||.+.+|.|||+||++||.|+++||+
T Consensus       565 ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~  598 (630)
T 3u1k_A          565 GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGV  598 (630)
T ss_dssp             CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             CCeEEEEEeChhHhheeECCCChhHHHHHHHHCC
Confidence            5668889999999999999999999999999996

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.49  E-value=0.0014  Score=56.15  Aligned_cols=34  Identities=24%  Similarity=0.280  Sum_probs=1.4

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+....+.||.+.++.|||+||.+||.|+++|||
T Consensus       568 ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~  601 (726)
T 4aid_A          568 APKIETINIPTDKIREVIGSGGKVIREIVATTGA  601 (726)
T ss_dssp             CCC-------------------------------
T ss_pred             CCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCC
Confidence            4456789999999999999999999999999996

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=96.44  E-value=0.00026  Score=53.22  Aligned_cols=88  Identities=18%  Similarity=0.169  Sum_probs=58.7

Q ss_pred             CccceEecCCchHHHHH-HHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546          30 RVAGSVIGKGGSNIARL-RNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG  108 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l-~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (150)
                      +-+|+.||++|.+|+.| ++-.|-+|-+-....            +..   ..|.+.+.     |.....-.        
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~------------dp~---~fi~nals-----PA~V~~V~--------  177 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD------------DPA---RFVANALS-----PAKVVSVS--------  177 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS------------SHH---HHHHHHTT-----TSCCSEEE--------
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecC------------CHH---HHHHhccC-----CcceEEEE--------
Confidence            55999999999999999 666788888865421            111   12222222     11110000        


Q ss_pred             CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                          ..........+.||.++.+..|||+|.+++...+.||
T Consensus       178 ----i~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg  214 (251)
T 2asb_A          178 ----VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTG  214 (251)
T ss_dssp             ----EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHS
T ss_pred             ----EEcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHC
Confidence                0001235788999999999999999999999999887

>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=96.43  E-value=0.00034  Score=47.75  Aligned_cols=24  Identities=25%  Similarity=0.486  Sum_probs=22.1

Q ss_pred             cCceeEEeecCCchHHHHHHhhCC
Q psy7546         127 QSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       127 ~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+++|.|||++|.+||+|+++|||
T Consensus        21 ~n~iG~IIGP~G~tiK~Iq~eTG~   44 (131)
T 1k1g_A           21 INFVGLLIGPRGNTLKNIEKECNA   44 (131)
T ss_dssp             HHHHHHHHCSSSHHHHHHHHHSCC
T ss_pred             cceeeeEECCCcHHHHHHHHHHCC
Confidence            357899999999999999999997

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=96.34  E-value=0.00084  Score=53.10  Aligned_cols=88  Identities=18%  Similarity=0.217  Sum_probs=60.2

Q ss_pred             CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546          30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG  108 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (150)
                      +-+|+.||++|.+|+.|.++. |-+|.+-...            ++..   ..|.+.+.     |.....-.        
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s------------~dp~---~fi~nals-----PA~V~~V~--------  300 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD------------DDPA---RFVANALS-----PAKVVSVS--------  300 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC------------SSHH---HHHHHHTT-----TSCCSEEE--------
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC------------CCHH---HHHHHhcC-----CcceeEEE--------
Confidence            568999999999999999999 8888886542            1111   12222221     11110000        


Q ss_pred             CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                          ..........+.||....+..|||+|.+++...+.||
T Consensus       301 ----~~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg  337 (366)
T 1k0r_A          301 ----VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTG  337 (366)
T ss_dssp             ----EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHC
T ss_pred             ----EEcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHC
Confidence                0002345788999999999999999999999999987

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=95.74  E-value=0.0025  Score=50.08  Aligned_cols=88  Identities=25%  Similarity=0.319  Sum_probs=59.5

Q ss_pred             CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546          30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG  108 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (150)
                      +-+|+.||.+|.+|+.+.++. |-+|-+-...            ++..   ..|.+.+.     |.....-.        
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s------------~d~~---~fi~nal~-----Pa~v~~v~--------  296 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWS------------DDPK---QLIANALA-----PATVIEVE--------  296 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECC------------SSHH---HHHHHHTC-----SSCCSEEE--------
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecC------------CCHH---HHHHHhcC-----ccEEEEEE--------
Confidence            458999999999999999998 6888776442            1111   12222221     11100000        


Q ss_pred             CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                          ..........+.||..+.+..|||+|.+++...+.||
T Consensus       297 ----~~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg  333 (344)
T 1hh2_P          297 ----ILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTG  333 (344)
T ss_dssp             ----EEETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHS
T ss_pred             ----EEcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHC
Confidence                0002345788999999999999999999999999887

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.33  E-value=0.0027  Score=54.44  Aligned_cols=60  Identities=25%  Similarity=0.285  Sum_probs=0.0

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVL   83 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~   83 (150)
                      .-...+.+|.++++.+||++|.+|+.|.++||+.|.+.+.    ..+.|.+ ..+...+|...|.
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~d----g~v~I~~~~~~~~~~a~~~i~  619 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDD----GTVKIAATDGEKAKHAIRRIE  619 (723)
T ss_dssp             -----------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecCC----ccEEEecCCHHHHHHHHHHHH
Confidence            3456678899999999999999999999999999988763    3455544 3444555544443

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=93.84  E-value=0.014  Score=39.83  Aligned_cols=32  Identities=25%  Similarity=0.342  Sum_probs=28.7

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...-+.+.++.++.|+|++|+.|++|+..|.|
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqT   87 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHT   87 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTS
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcce
Confidence            45667899999999999999999999999875

>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=93.77  E-value=0.0029  Score=54.53  Aligned_cols=56  Identities=23%  Similarity=0.296  Sum_probs=17.7

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC-hHHHHHHHHHH
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE-LENGLKVIEEV   82 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-~~~v~~A~~~i   82 (150)
                      ..|.||.+.+|.+||++|.+||.|++++|+.|.+.+    +..|.|+.. .....+|...|
T Consensus       600 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~----dG~v~Is~~~~~~~~~a~~~i  656 (757)
T 1e3p_A          600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----DGTIYIGAADGPAAEAARATI  656 (757)
T ss_dssp             CCC------------------CTTCCCCCSCC------------CCCBSSHHHHCC-----
T ss_pred             EEEEEChHHeehcccccceeeehhhHhhCCEEEecC----CceEEEecCCHHHHHHHHHHH
Confidence            457799999999999999999999999999998885    345566553 34444444333

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=93.48  E-value=0.035  Score=47.70  Aligned_cols=34  Identities=21%  Similarity=0.337  Sum_probs=0.0

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+....+.||.+.++.+||++|.+|+.|.++||+
T Consensus       558 ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~  591 (723)
T 3cdi_A          558 APRIHTIKINPDKIKDVIGKGGSVIRALTEETGT  591 (723)
T ss_dssp             ----------------------------------
T ss_pred             CceEEEEEECHHHhcccccccceeeeeeehhhCc
Confidence            4556778999999999999999999999999986

>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=93.31  E-value=0.018  Score=49.61  Aligned_cols=33  Identities=18%  Similarity=0.263  Sum_probs=11.4

Q ss_pred             ceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +....+.||.+.+|.+||++|.+||.|++.|||
T Consensus       597 p~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~  629 (757)
T 1e3p_A          597 PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGA  629 (757)
T ss_dssp             CBCCCC------------------CTTCCCCCS
T ss_pred             ceeEEEEEChHHeehcccccceeeehhhHhhCC
Confidence            344568899999999999999999999999986

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=92.76  E-value=0.022  Score=39.31  Aligned_cols=40  Identities=25%  Similarity=0.355  Sum_probs=34.8

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEec
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP   57 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~   57 (150)
                      ++.-.+.+.||.++.+..|||+|.+++-..+-||.++.+.
T Consensus       100 ~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A          100 NGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             TTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             CCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            3456788999999999999999999999999999877654

>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=91.35  E-value=0.097  Score=39.25  Aligned_cols=39  Identities=18%  Similarity=0.184  Sum_probs=35.6

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      .-...+.||.++.++.|||+|.|++.-..-||.+|.+..
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            356889999999999999999999999999999999864

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=90.21  E-value=0.16  Score=39.83  Aligned_cols=39  Identities=23%  Similarity=0.330  Sum_probs=35.5

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEec
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP   57 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~   57 (150)
                      +.-...+.||.++.++.|||+|.|++.-..-||.+|.+.
T Consensus       301 ~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~  339 (344)
T 1hh2_P          301 ENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK  339 (344)
T ss_dssp             TTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEecee
Confidence            455788999999999999999999999999999999875

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=89.51  E-value=0.18  Score=39.86  Aligned_cols=40  Identities=18%  Similarity=0.184  Sum_probs=36.4

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      +.-.+.+.||.++.++.|||+|.+++-...-||.+|.|..
T Consensus       305 ~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  344 (366)
T 1k0r_A          305 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  344 (366)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEE
T ss_pred             CCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeE
Confidence            4567889999999999999999999999999999999864

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=89.39  E-value=0.14  Score=35.57  Aligned_cols=66  Identities=23%  Similarity=0.157  Sum_probs=39.5

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCce-EEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERI-LTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~erv-v~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ++.+-+..+..|.+|||.|.+++.||--+...++-..  . .++ +-+.+=.+.-.+.+..+...+.+..
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~~~~vn~~~--~-~~V~LDve~YRerReetL~~lA~~~A~kV  100 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHPTY--G-YSIRLEISTFLQNQEKVMDTQLQSVIMTV  100 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHHHHH--S-CEEEEEETTHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHHHHHhhhcC--C-ceEEEEhHHhHHHHHHHHHHHHHHHHHHH
Confidence            4556667888999999999999999965532222111  0 111 2234444555555656655555544

>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1

Probab=88.81  E-value=0.14  Score=32.42  Aligned_cols=28  Identities=21%  Similarity=0.361  Sum_probs=23.5

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHH
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRND   49 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~   49 (150)
                      ..++.|....-|.|||++|+.|++|+.+
T Consensus        36 ~i~I~I~tarPg~vIGkkG~~Ie~L~~~   63 (92)
T 1wh9_A           36 RTEIIILATRTQNVLGEKGRRIRELTAV   63 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHH
T ss_pred             eEEEEEEeCCCceEEcCCcHHHHHHHHH
Confidence            4567788888899999999999988765

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=83.33  E-value=0.36  Score=33.43  Aligned_cols=29  Identities=17%  Similarity=0.295  Sum_probs=24.9

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ++.+.+..+..|.+|||.|.+++.||-.+
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~   62 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLL   62 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHH
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHH
Confidence            56677888999999999999999998654

>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1

Probab=80.01  E-value=0.43  Score=30.16  Aligned_cols=29  Identities=21%  Similarity=0.480  Sum_probs=24.1

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      ..+++.|-...-|.|||++|+.|++|+..
T Consensus        35 ~~i~I~I~tarPg~vIGkkG~~Ie~L~~~   63 (92)
T 1wh9_A           35 TRTEIIILATRTQNVLGEKGRRIRELTAV   63 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceEEcCCcHHHHHHHHH
Confidence            45777888888899999999999988764

---

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	150
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-06
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-10
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.003
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	4e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	6e-04
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	0.001
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-09
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-04
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-04
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-04
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-09
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-04
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-08
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-04
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-08
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-08
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-08
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.001
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	0.002

>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 = 63.6 bits (155), Expect = 5e-15
 Identities = 19/68 (27%), Positives = 37/68 (54%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIE 80
          + +RLL+  +  GS+IGK G ++ ++R +  A + + +   PERI+T+        K   
Sbjct: 4  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFA 63

Query: 81 EVLPALDE 88
           ++  L+E
Sbjct: 64 MIIDKLEE 71

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (98), Expect = 1e-06
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
           IRL++H  + G IIGK G  +K++R+   A
Sbjct: 6   IRLLMHGKEVGSIIGKKGESVKKMREESGA 35

>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 = 52.4 bits (126), Expect = 1e-10
 Identities = 17/74 (22%), Positives = 24/74 (32%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKV 78
                + IP      VIGK G  +  L       + +P    P   + I    E   K 
Sbjct: 8  TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKA 67

Query: 79 IEEVLPALDEIRQK 92
            EVL    E  ++
Sbjct: 68 RHEVLLISAEQDKR 81

>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 = 32.8 bits (75), Expect = 0.003
 Identities = 6/30 (20%), Positives = 13/30 (43%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
             + + +     +IGK G K+++L      
Sbjct: 12  ATVAIPKEHHRFVIGKNGEKLQDLELKTAT 41

>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 = 52.1 bits (125), Expect = 2e-10
 Identities = 16/72 (22%), Positives = 35/72 (48%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIE 80
          V + + +P  +   VIG+ GS I ++ ++F+ ++ VP       I+ I     N  +   
Sbjct: 10 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKA 69

Query: 81 EVLPALDEIRQK 92
           +L  + E++ +
Sbjct: 70 GLLERVKELQAE 81

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.0 bits (122), Expect = 4e-10
 Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTIFAELENGLKV 78
          +     +P  + G +IG+GG  I+R++ +    + +    G  PER   +    E+    
Sbjct: 8  MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSA 67

Query: 79 IEEVLPALDEIR 90
             +   +++ R
Sbjct: 68 KRLLDQIVEKGR 79

>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 = 34.4 bits (79), Expect = 6e-04
 Identities = 8/29 (27%), Positives = 12/29 (41%)

Query: 122 RLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
              V     G IIG+GG +I  ++     
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGC 39

>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 = 50.0 bits (119), Expect = 1e-09
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 7/86 (8%)

Query: 21  VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD----CPGPERILTIFAELEN-- 74
           V  +L +P R  G +IG+GG  I  +     A +T            R++ I    +   
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVA 74

Query: 75  -GLKVIEEVLPALDEIRQKYGKGRGG 99
               +I E +   +E+R++      G
Sbjct: 75  AAKHLILEKVSEDEELRKRIAHSASG 100

>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 = 34.2 bits (78), Expect = 0.001
 Identities = 11/30 (36%), Positives = 15/30 (50%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
            +L V Q   G IIG+GG  I+ +     A
Sbjct: 17  EQLSVPQRSVGRIIGRGGETIRSICKASGA 46

>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 = 48.8 bits (116), Expect = 3e-09
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC----PGPERILTIFAEL 72
          GP +    ++IP+  AG VIGKGG  I +L+      + +        G ++ L I  + 
Sbjct: 4  GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDP 63

Query: 73 ENGLKVIEEVLPALDE 88
              +  E VL  + +
Sbjct: 64 YKVQQAKEMVLELIRD 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (81), Expect = 3e-04
 Identities = 11/30 (36%), Positives = 19/30 (63%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
             +++  S+AG +IGKGG  IK+L++    
Sbjct: 10  QEIMIPASKAGLVIGKGGETIKQLQERAGV 39

>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 = 48.4 bits (115), Expect = 3e-09
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 12/76 (15%)

Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTIFAELENGL 76
          E   ++P+   G +IGKGG  I  +     A + +   P P      ++ TI    +   
Sbjct: 2  EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ-- 59

Query: 77 KVIEEVLPALDEIRQK 92
               +  A   I +K
Sbjct: 60 -----IDYARQLIEEK 70

>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 = 35.6 bits (82), Expect = 2e-04
 Identities = 12/30 (40%), Positives = 14/30 (46%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
              IV   + G IIGKGG  IK +     A
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGA 32

>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 = 48.3 bits (115), Expect = 3e-09
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTIFAELENGL 76
            +  ++ IP  +AGS+IGKGG  I ++R++  AS+ + +      +RI+TI    +   
Sbjct: 2  PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQ 61

Query: 77 KVIEEVLPALDE 88
               +  ++ +
Sbjct: 62 NAQYLLQNSVKQ 73

>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 = 36.0 bits (83), Expect = 2e-04
 Identities = 12/30 (40%), Positives = 19/30 (63%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
            ++ + +  AG IIGKGG +IK++R    A
Sbjct: 6   TQVTIPKDLAGSIIGKGGQRIKQIRHESGA 35

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (115), Expect = 3e-09
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 9/72 (12%)

Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIE 80
            L IP+ + G +IG+ G+NI  +R    A + + +       R +TI     +      
Sbjct: 4  HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS------ 57

Query: 81 EVLPALDEIRQK 92
           +  A   I  +
Sbjct: 58 -ISLAQYLINAR 68

>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 = 36.3 bits (84), Expect = 1e-04
 Identities = 11/30 (36%), Positives = 15/30 (50%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
             L +  +  GCIIG+ G  I E+R    A
Sbjct: 4   HELTIPNNLIGCIIGRQGANINEIRQMSGA 33

>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 = 48.7 bits (116), Expect = 4e-09
 Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP---ERILTIFAELENGLK 77
           +L + +  +    +IG+ G+ I ++R +   ++  PD       +  +TI    +N   
Sbjct: 10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEA 69

Query: 78 VIEEVLPALDEIRQ 91
            + +L  + E+ Q
Sbjct: 70 ARDAILRIVGELEQ 83

>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 = 46.8 bits (111), Expect = 1e-08
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIE 80
          + + IP    G VIG+ G  I +++ND    +         PERI  I    +      E
Sbjct: 5  IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAE 64

Query: 81 EVLPALDEIR 90
           +   L  ++
Sbjct: 65 IITDLLRSVQ 74

>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 = 35.2 bits (81), Expect = 4e-04
 Identities = 7/32 (21%), Positives = 17/32 (53%)

Query: 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
           + I + + +   G +IG+ G  IK++++    
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGV 34

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 1e-08
 Identities = 13/75 (17%), Positives = 26/75 (34%), Gaps = 12/75 (16%)

Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTIFAELENGLK 77
          + + +P  + G+++GKGG  +   +    A + +            R +TI         
Sbjct: 5  VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA--- 61

Query: 78 VIEEVLPALDEIRQK 92
                 A   I Q+
Sbjct: 62 ----TQAAQYLISQR 72

>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 = 37.9 bits (88), Expect = 3e-05
 Identities = 9/30 (30%), Positives = 17/30 (56%)

Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
           + + V ++  G I+GKGG  + E ++   A
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGA 34

>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 = 46.7 bits (111), Expect = 1e-08
 Identities = 15/63 (23%), Positives = 31/63 (49%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIE 80
            + + I  +    +IGK G+NI R+++ +K SV +P       ++ I  + +   +   
Sbjct: 5  DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKR 64

Query: 81 EVL 83
          E+L
Sbjct: 65 ELL 67

>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 = 46.3 bits (110), Expect = 2e-08
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD-CPGPERILTIFAELENGLK 77
            V   + +  RV   +IG  G  I ++ ++FK  +  P         +T+    EN  +
Sbjct: 8  QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEE 67

Query: 78 VIEEVL 83
           I+ +L
Sbjct: 68 AIDHIL 73

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 4e-08
 Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLK 77
          N  E+ + IP+++  S+IG  G  I  +  +     +  P        + I     +  K
Sbjct: 8  NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEK 67

Query: 78 VIEEVLPALDEIRQK 92
            +++L   +E + K
Sbjct: 68 AKKQLLHLAEEKQTK 82

>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 = 36.3 bits (84), Expect = 2e-04
 Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 4/56 (7%)

Query: 27 IPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEV 82
          I       VIGK GS I  L+++    + V        ++ +  +        E +
Sbjct: 7  INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ----NGLIWVNGDRRKVSIAEEAI 58

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 33.1 bits (76), Expect = 0.001
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70
           + IP    G VIG     I +++ D  A +T+ D    +  + I A
Sbjct: 6  TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----DGTIYIGA 48

>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 = 33.3 bits (76), Expect = 0.002
 Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVI 79
              +  PS +   +IGK G N+A++     K  +   +    E  +T+    E+     
Sbjct: 21 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---GEDKITLEGPTEDVSVAQ 77

Query: 80 EEVLPALDEIRQK 92
          E++   + ++  +
Sbjct: 78 EQIEGMVKDLINR 90

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	150
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.79
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.74
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.73
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.73
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.72
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.71
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.71
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.7
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.67
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.67
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.66
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.63
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.62
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.58
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.42
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.41
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.15
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.05
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	99.02
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.97
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.77
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	98.68
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	98.67
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	98.65
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	98.65
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	98.62
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	98.62
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	98.61
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.57
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	98.51
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.49
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.47
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	98.4
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.33
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.32
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.29
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.29
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.23
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.19
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.09
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.05
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.04
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.0
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.8
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	97.77
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	96.56
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.45
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.4
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.57
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.41
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	93.77
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	90.4
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	90.15
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	89.59
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	89.58
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	89.51
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	88.34
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	87.4
d2qalc1	105	Ribosomal protein S3 N-terminal domain {Escherichi	83.06
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	81.85
d2asba2	79	Transcription factor NusA, C-terminal domains {Myc	81.01

>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=99.79  E-value=4e-20  Score=113.59  Aligned_cols=70  Identities=27%  Similarity=0.523  Sum_probs=65.8

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      -.++++|+||++.+|.||||+|++|++|+++|||+|++++..+++|+|+|+|+++++.+|..+|.+.+++
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCCCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            3589999999999999999999999999999999999998878899999999999999999999988763

>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=99.74  E-value=3.4e-18  Score=105.80  Aligned_cols=71  Identities=25%  Similarity=0.404  Sum_probs=65.4

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      +.++.+|.||.+.+|.|||++|++|++|+++|||+|++++..  +++|+|+|+|+++++.+|..+|...+++.
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            467899999999999999999999999999999999998653  58899999999999999999999988864

>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=99.73  E-value=2.1e-18  Score=106.55  Aligned_cols=71  Identities=24%  Similarity=0.349  Sum_probs=64.8

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      +...++|.||.+.+|.||||+|++|++|+++|||+|++++.+  +++|+|+|+|+++++.+|..+|.+.+++.
T Consensus         1 G~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999999998653  48899999999999999999999888753

>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=99.73  E-value=2.6e-18  Score=105.08  Aligned_cols=67  Identities=22%  Similarity=0.292  Sum_probs=61.1

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHH
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPAL   86 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~   86 (150)
                      +.+.+|.||.+.+|.||||+|++|++|+++|||+|++++..  +++|+|+|+|+++++.+|..+|...+
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            36899999999999999999999999999999999998653  58899999999999999998887654

>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=99.72  E-value=4.4e-18  Score=104.32  Aligned_cols=64  Identities=20%  Similarity=0.336  Sum_probs=58.2

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-----CCCceEEEecChHHHHHHHHHHHHH
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-----GPERILTIFAELENGLKVIEEVLPA   85 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-----~~ervv~I~G~~~~v~~A~~~i~~~   85 (150)
                      .++|+||++.+|.||||+|++|++|+++|||+|++++..     .++|+|+|+|+++++.+|..+|.+.
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~   70 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK   70 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhh
Confidence            478999999999999999999999999999999997532     3789999999999999999988765

>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=99.71  E-value=4.3e-18  Score=106.91  Aligned_cols=72  Identities=28%  Similarity=0.446  Sum_probs=65.6

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC----CCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC----PGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      ++..++.+|+||.+.+|.||||+|++|++|+++|||+|++++.    ++.+|+|+|+|++++|.+|..+|...+.+
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            5688999999999999999999999999999999999999753    25789999999999999999999887754

>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=99.71  E-value=1.1e-17  Score=103.29  Aligned_cols=66  Identities=15%  Similarity=0.253  Sum_probs=59.6

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-----CCCceEEEecChHHHHHHHHHHHHHH
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-----GPERILTIFAELENGLKVIEEVLPAL   86 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-----~~ervv~I~G~~~~v~~A~~~i~~~~   86 (150)
                      ..++|+||++.+|.||||+|++|++|+++|||+|++++.+     +++|+|+|+|+++++.+|..+|.+.+
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            4689999999999999999999999999999999998542     47899999999999999999887653

>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=99.70  E-value=1.8e-17  Score=103.52  Aligned_cols=72  Identities=17%  Similarity=0.282  Sum_probs=66.6

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      .+..++.+|.||.+.+|.|||++|.+|++|+++|||+|++++.+  +++|.|+|+|+++++.+|..+|...+++
T Consensus         4 ~~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           4 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            45679999999999999999999999999999999999998753  4889999999999999999999998886

>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=99.67  E-value=7.2e-17  Score=105.76  Aligned_cols=76  Identities=21%  Similarity=0.253  Sum_probs=67.4

Q ss_pred             CCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        15 ~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ......++.+|+||...+|.||||+|.+|++|+++|||+|+|++..    ..+|+|+|+|++++|.+|..+|...+.+..
T Consensus         9 ~~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_           9 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             CSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            3445568999999999999999999999999999999999997542    368999999999999999999999997654

>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=99.67  E-value=8.5e-17  Score=100.87  Aligned_cols=74  Identities=23%  Similarity=0.241  Sum_probs=68.4

Q ss_pred             CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      -...++.+|.||...+|.|||++|.+|++|+++|||+|+|++..+.++.|+|+|+++++.+|..+|...+++..
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            45678999999999999999999999999999999999999877788999999999999999999999888753

>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=99.66  E-value=1.4e-16  Score=99.82  Aligned_cols=75  Identities=21%  Similarity=0.302  Sum_probs=68.0

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCC-CCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG-PERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~-~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ...+.++..+.||...++.|||++|.+|++|+++|||+|+|++... +++.|+|+|++++|.+|..+|.+.+++..
T Consensus         5 e~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           5 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            4567788999999999999999999999999999999999987653 57899999999999999999999988764

>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=99.63  E-value=2.8e-16  Score=98.63  Aligned_cols=74  Identities=19%  Similarity=0.206  Sum_probs=67.8

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHH-hCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRND-FKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEI   89 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~-tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~   89 (150)
                      ..++.++.+|.||...+|.||||+|++|++|+++ ++++|++++..+.++.|+|+|++++|.+|..+|...+++.
T Consensus         5 e~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           5 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hhcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            4567789999999999999999999999999987 5899999987778899999999999999999999988875

>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=99.62  E-value=5.4e-16  Score=97.74  Aligned_cols=71  Identities=20%  Similarity=0.373  Sum_probs=64.5

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC---CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP---GPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~---~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      .++.+|.||...++.|||++|++|++|+++|||+|+|++.+   .+++.|+|.|+.++|.+|..+|...+.+..
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            47889999999999999999999999999999999998643   478999999999999999999999887753

>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=99.62  E-value=4.6e-16  Score=95.11  Aligned_cols=67  Identities=22%  Similarity=0.366  Sum_probs=61.8

Q ss_pred             CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHH
Q psy7546          19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPA   85 (150)
Q Consensus        19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~   85 (150)
                      ...+.+|.||...++.|||++|++|++|+++|||+|+|++..++++.|+|+|+++++.+|..+|.+.
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEECCHHHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999998777889999999999999999888764

>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=99.58  E-value=1.6e-15  Score=96.97  Aligned_cols=71  Identities=23%  Similarity=0.360  Sum_probs=65.7

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      .++..|.||...++.|||++|.+|++|+++|||+|.|++..+.++.|+|+|++++|.+|..+|...+.+..
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 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQ   79 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCCCCcceEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            58899999999999999999999999999999999999877788899999999999999999988877643

>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=99.46  E-value=1.3e-13  Score=87.75  Aligned_cols=72  Identities=18%  Similarity=0.246  Sum_probs=64.3

Q ss_pred             CCCCceEEEEEeeCCccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546          16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR   90 (150)
Q Consensus        16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~   90 (150)
                      ...+.++..+.||...++.|||++|++|++|++++ |++|++++.   +..|+|+|++++|++|..+|...+.+..
T Consensus        16 ~~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~---~~~v~i~G~~~~ve~Ak~~I~~iv~el~   88 (90)
T d2ctfa1          16 KANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG---EDKITLEGPTEDVSVAQEQIEGMVKDLI   88 (90)
T ss_dssp             CCCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS---SCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC---CceEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            34567999999999999999999999999999995 799999863   5789999999999999999998888754

>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=99.42  E-value=6.6e-14  Score=86.73  Aligned_cols=63  Identities=17%  Similarity=0.186  Sum_probs=56.0

Q ss_pred             CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHH
Q psy7546          18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEV   82 (150)
Q Consensus        18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i   82 (150)
                      ...++.+|.||.+.+|+|||++|++|++|+++|||+|.+.+.  .++.|.|.| +++++.+|..+|
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~--~~g~v~I~g~~~eav~~A~~~I   68 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--DTGTFRIYGESADAVKKARGFL   68 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--TTTEEEEEESSHHHHHHHHHHH
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC--CCceEEEEECCHHHHHHHHHHH
Confidence            456788999999999999999999999999999999998764  357899998 689999999777

>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=99.41  E-value=9.8e-14  Score=87.09  Aligned_cols=61  Identities=20%  Similarity=0.219  Sum_probs=55.2

Q ss_pred             EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      -+.||.+.+|.|||++|++|++|+++|||+|++++    +..|+|.|+++++.+|..+|.....+
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~----~g~v~I~G~~e~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ----NGLIWVNGDRRKVSIAEEAIYLIEQE   64 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT----TSEEEEESCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC----CCEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999976    35799999999999999888777664

>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=99.15  E-value=5e-12  Score=79.04  Aligned_cols=61  Identities=20%  Similarity=0.065  Sum_probs=45.8

Q ss_pred             EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCC--CceEEEecChHHHHHHHHHHHH
Q psy7546          24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP--ERILTIFAELENGLKVIEEVLP   84 (150)
Q Consensus        24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~--ervv~I~G~~~~v~~A~~~i~~   84 (150)
                      .+-||.+.+|.|||++|++||+|+++|||+|++++..+.  .+.....+.+.++.+|...|..
T Consensus         6 ~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~a   68 (84)
T d1tuaa1           6 YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKA   68 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHH
T ss_pred             EEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999754321  1111224566777777755544

>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=99.05  E-value=5.4e-12  Score=76.14  Aligned_cols=58  Identities=19%  Similarity=0.053  Sum_probs=43.3

Q ss_pred             EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC-hHHHHHHHHHHHHH
Q psy7546          24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE-LENGLKVIEEVLPA   85 (150)
Q Consensus        24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-~~~v~~A~~~i~~~   85 (150)
                      -+.||.+.+|.||||+|++||+|+++|||+|++.+.    ..|+|.|. .+++.+|..+|...
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~----g~v~I~g~~~~~v~~A~~~I~~i   62 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN----GRIWATCPSRFSEEILIEAIRKI   62 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT----SEEEC-----CTTCCTHHHHTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC----CEEEEEeCCHHHHHHHHHHHHHH
Confidence            367899999999999999999999999999999763    46899995 67888888777543

>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=99.02  E-value=2.4e-10  Score=71.54  Aligned_cols=60  Identities=12%  Similarity=0.046  Sum_probs=49.7

Q ss_pred             EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC-hHHHHHHHHHHHHHHH
Q psy7546          24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE-LENGLKVIEEVLPALD   87 (150)
Q Consensus        24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-~~~v~~A~~~i~~~~~   87 (150)
                      -+-||.+.+|.|||++|++|+.|+++|||+|.+.++    -.|+|.|. .+.+..|..+|.....
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~----G~V~I~g~~~~~~~~A~~~I~~I~~   64 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN----GRIHLECPNEDLEAIAVMAIKIIDE   64 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT----TEEEEECSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC----cEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            367899999999999999999999999999999864    36899996 5667777766655444

>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=98.97  E-value=1.9e-11  Score=69.95  Aligned_cols=46  Identities=28%  Similarity=0.393  Sum_probs=14.1

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE   71 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~   71 (150)
                      ...|.||.+.+|.|||++|.+||+|+++|||+|.+.+    +..|.|.|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d----dg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----DGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC----CeEEEEEec
Confidence            4578899999999999999999999999999999986    356666664

>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=98.77  E-value=2.2e-09  Score=69.13  Aligned_cols=52  Identities=15%  Similarity=0.323  Sum_probs=45.5

Q ss_pred             cceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546          32 AGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE   88 (150)
Q Consensus        32 vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~   88 (150)
                      .|.|||++|.+|+.|++.|||+|.+.+..     |.+.|+++++..|..+|..++..
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d~~-----v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGEYE-----VAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECSSE-----EEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeCCe-----EEEEECchhHHHHHHHHHHHHcC
Confidence            68899999999999999999999997642     66678999999999888877754

>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=98.68  E-value=3.2e-09  Score=64.45  Aligned_cols=34  Identities=35%  Similarity=0.574  Sum_probs=31.9

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +..+.++.||.+++|+||||+|++|++|+++|||
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga   35 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA   35 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCC
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCC
Confidence            4568899999999999999999999999999997

>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=98.67  E-value=1.5e-09  Score=65.40  Aligned_cols=34  Identities=38%  Similarity=0.671  Sum_probs=32.1

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.+.+|+||++++|+||||+|++|++|++.|||
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga   35 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGA   35 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCC
Confidence            4678999999999999999999999999999997

>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=98.65  E-value=2.4e-09  Score=64.34  Aligned_cols=32  Identities=34%  Similarity=0.617  Sum_probs=30.6

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.+|.||.+++|+||||+|++|++|+++|||
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga   33 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGA   33 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCC
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCc
Confidence            57899999999999999999999999999997

>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=98.65  E-value=3.6e-09  Score=64.19  Aligned_cols=32  Identities=28%  Similarity=0.493  Sum_probs=30.2

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..++|.||++++|+||||+|++|++|+++|||
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga   34 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGA   34 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCC
Confidence            46789999999999999999999999999997

>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=98.62  E-value=2.3e-09  Score=65.06  Aligned_cols=33  Identities=21%  Similarity=0.395  Sum_probs=31.1

Q ss_pred             ceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+++.||.+++|+||||+|++|++|+++|||
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga   34 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGV   34 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCC
Confidence            457899999999999999999999999999997

>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=98.62  E-value=3.4e-09  Score=63.76  Aligned_cols=31  Identities=39%  Similarity=0.662  Sum_probs=29.3

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+|.||++++|+||||+|++|++|++.|||
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga   32 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGA   32 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCc
Confidence            4679999999999999999999999999997

>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=98.61  E-value=4.7e-09  Score=64.73  Aligned_cols=35  Identities=31%  Similarity=0.556  Sum_probs=33.3

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +...+.+|.||..++|+||||+|++|++|+++|||
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga   39 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGV   39 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTS
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCC
Confidence            57789999999999999999999999999999997

>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=98.57  E-value=6.1e-08  Score=64.06  Aligned_cols=70  Identities=21%  Similarity=0.330  Sum_probs=52.5

Q ss_pred             ceEEEEEeeCCc------cceEecCCchHHHHHHHHhCCeEEecCC-------------C----CCC-ceEEEec-ChHH
Q psy7546          20 DVELRLLIPSRV------AGSVIGKGGSNIARLRNDFKASVTVPDC-------------P----GPE-RILTIFA-ELEN   74 (150)
Q Consensus        20 ~~~~~l~vp~~~------vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-------------~----~~e-rvv~I~G-~~~~   74 (150)
                      .++.+++||-+.      +|.|||++|.++|+|+++|||+|.|-..             +    .++ --|.|++ +.+.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            467889999776      9999999999999999999999999421             0    112 1244544 5667


Q ss_pred             HHHHHHHHHHHHHHh
Q psy7546          75 GLKVIEEVLPALDEI   89 (150)
Q Consensus        75 v~~A~~~i~~~~~~~   89 (150)
                      +.+|+.++...+...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            888888888887653

>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=98.51  E-value=2.8e-08  Score=63.99  Aligned_cols=35  Identities=31%  Similarity=0.418  Sum_probs=33.0

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..+++.+|.||..++|+||||+|++|++|+++|||
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga   46 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGA   46 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCC
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCC
Confidence            46688999999999999999999999999999997

>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=98.49  E-value=7.2e-09  Score=58.95  Aligned_cols=31  Identities=19%  Similarity=0.307  Sum_probs=8.6

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..++.||.+.+|.|||++|++||.|+++|||
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga   34 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGA   34 (54)
T ss_dssp             CC---------------------CHHHHSCC
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCC
Confidence            4568999999999999999999999999997

>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=98.47  E-value=7.4e-09  Score=63.46  Aligned_cols=35  Identities=20%  Similarity=0.395  Sum_probs=32.7

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...++.++.||.+++|+|||++|++|++|++.|||
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa   39 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGV   39 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTE
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCc
Confidence            46678899999999999999999999999999997

>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=98.40  E-value=3.3e-08  Score=60.43  Aligned_cols=35  Identities=23%  Similarity=0.415  Sum_probs=33.0

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....+.++.||.+++|+|||++|++|++|++.|||
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~   39 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGC   39 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCC
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCC
Confidence            46789999999999999999999999999999997

>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=98.33  E-value=7e-08  Score=59.27  Aligned_cols=35  Identities=17%  Similarity=0.340  Sum_probs=32.6

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ....+.++.||.+++|+|||++|++|++|++.|||
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~   41 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTAT   41 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTC
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCC
Confidence            35678999999999999999999999999999996

>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=98.32  E-value=9.5e-08  Score=57.22  Aligned_cols=34  Identities=18%  Similarity=0.391  Sum_probs=31.7

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.++.||..+++.|||++|++|++|+++|||
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~   36 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKV   36 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCC
Confidence            4568899999999999999999999999999986

>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=98.29  E-value=8.8e-08  Score=59.17  Aligned_cols=34  Identities=24%  Similarity=0.413  Sum_probs=31.5

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...+.++.||..++++|||++|++|++|+++|||
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~   41 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDV   41 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTC
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCC
Confidence            4567899999999999999999999999999997

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.29  E-value=3.6e-08  Score=61.05  Aligned_cols=30  Identities=23%  Similarity=0.339  Sum_probs=28.2

Q ss_pred             EEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      +.+.||.+.+|.|||++|++|++|+++|||
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~   34 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGT   34 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTE
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCC
Confidence            358999999999999999999999999996

>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=98.23  E-value=1e-06  Score=58.80  Aligned_cols=38  Identities=18%  Similarity=0.434  Sum_probs=33.3

Q ss_pred             eEEEEEeeC------CccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          21 VELRLLIPS------RVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        21 ~~~~l~vp~------~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      +..+++||-      +.+|.|||++|.++|+|+++|||+|.|-.
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrG   45 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRG   45 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEES
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEe
Confidence            567888884      45899999999999999999999999953

>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=98.19  E-value=1.6e-07  Score=57.55  Aligned_cols=35  Identities=20%  Similarity=0.331  Sum_probs=32.3

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ...++..+.||..+++.|||++|++|++|++.||+
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~   41 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKV   41 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTC
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCC
Confidence            35677899999999999999999999999999986

>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=98.09  E-value=2e-07  Score=57.26  Aligned_cols=33  Identities=12%  Similarity=0.290  Sum_probs=30.1

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      +...+.++.||..++|+||||+|++|++|++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~   39 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEEC   39 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHc
Confidence            456789999999999999999999999999875

>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=98.05  E-value=2.4e-07  Score=57.28  Aligned_cols=29  Identities=28%  Similarity=0.488  Sum_probs=27.6

Q ss_pred             EEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         122 RLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       122 ~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      -+.||.+++|.|||++|++|++|+++|||
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~   32 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDV   32 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTC
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCC
Confidence            47899999999999999999999999997

>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=98.04  E-value=3.1e-07  Score=57.47  Aligned_cols=34  Identities=24%  Similarity=0.390  Sum_probs=32.1

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.+..+.||..+++.|||++|++|++|++.||+
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~   41 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEV   41 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCC
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCC
Confidence            5688999999999999999999999999999986

>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=98.00  E-value=2.2e-07  Score=55.31  Aligned_cols=29  Identities=14%  Similarity=0.166  Sum_probs=25.6

Q ss_pred             EEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         122 RLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       122 ~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      -+.||...+|.||||+|++|++|+++||+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~   32 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGC   32 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC--
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCC
Confidence            37899999999999999999999999986

>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=97.80  E-value=2.8e-06  Score=52.91  Aligned_cols=33  Identities=15%  Similarity=0.159  Sum_probs=30.5

Q ss_pred             CCceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546         116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      ....+..+.||..+++.|||++|++|++|++++
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~   50 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQM   50 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHC
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHc
Confidence            356899999999999999999999999999985

>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=97.77  E-value=2e-06  Score=53.21  Aligned_cols=29  Identities=14%  Similarity=0.281  Sum_probs=27.4

Q ss_pred             EEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546         122 RLIVHQSQAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       122 ~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      .+.||.+.+|.|||++|++|+.|+++|||
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~   32 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTEC   32 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCC
Confidence            47899999999999999999999999996

>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=96.56  E-value=0.00012  Score=46.46  Aligned_cols=22  Identities=32%  Similarity=0.593  Sum_probs=20.6

Q ss_pred             ceeEEeecCCchHHHHHHhhCC
Q psy7546         129 QAGCIIGKGGTKIKELRDTFDA  150 (150)
Q Consensus       129 ~~g~iIGk~G~~Ik~i~~~tGA  150 (150)
                      ..|.|||++|.+|+.|++.|||
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~   44 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDT   44 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTC
T ss_pred             HhcceeCCCcHHHHHHHHHHCC
Confidence            4799999999999999999997

>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=96.45  E-value=0.00084  Score=39.08  Aligned_cols=38  Identities=24%  Similarity=0.306  Sum_probs=34.4

Q ss_pred             eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      -.+.+.||.++.+..|||+|.++|-..+-||.+|.+..
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            35778999999999999999999999999999998853

>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=96.40  E-value=0.00082  Score=39.02  Aligned_cols=39  Identities=18%  Similarity=0.184  Sum_probs=35.1

Q ss_pred             ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546          20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD   58 (150)
Q Consensus        20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~   58 (150)
                      .-.+.+.||.++.+..|||+|.+++-..+-||.+|.+..
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            346778999999999999999999999999999998863

>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=94.57  E-value=0.0049  Score=35.67  Aligned_cols=32  Identities=25%  Similarity=0.352  Sum_probs=29.1

Q ss_pred             ceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      .....+.||.+..+..|||+|.+++-..+.||
T Consensus        26 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg   57 (68)
T d1hh2p3          26 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTG   57 (68)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHS
T ss_pred             CCEEEEEECcccccccccCCcchHHHHHHHHC
Confidence            34688999999999999999999999999887

>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=94.41  E-value=0.0051  Score=35.47  Aligned_cols=33  Identities=21%  Similarity=0.208  Sum_probs=29.8

Q ss_pred             CceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546         117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD  149 (150)
Q Consensus       117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG  149 (150)
                      ......+.||.++....|||+|.+++-..+.||
T Consensus        24 ~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg   56 (67)
T d2asba3          24 TARAARVVVPDFQLSLAIGKEGQNARLAARLTG   56 (67)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHS
T ss_pred             CCcEEEEEECcccccchhcCCceeHHHHHHHHC
Confidence            345788999999999999999999999999987

>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=93.77  E-value=0.0095  Score=36.46  Aligned_cols=31  Identities=19%  Similarity=0.339  Sum_probs=26.5

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKA   52 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~   52 (150)
                      ..++.|....-|.|||++|+.|++|+++..-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k   66 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQK   66 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHH
Confidence            4668889999999999999999999976543

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

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: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.40  E-value=0.036  Score=34.97  Aligned_cols=30  Identities=23%  Similarity=0.370  Sum_probs=24.9

Q ss_pred             ceEEEEEeeC-CccceEecCCchHHHHHHHH
Q psy7546          20 DVELRLLIPS-RVAGSVIGKGGSNIARLRND   49 (150)
Q Consensus        20 ~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~   49 (150)
                      .+...+.|+. ++.+.|||++|++||+|...
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~   78 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIE   78 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHH
Confidence            4667788886 67899999999999998754

>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=90.15  E-value=0.03  Score=34.90  Aligned_cols=29  Identities=31%  Similarity=0.613  Sum_probs=25.0

Q ss_pred             EEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546          22 ELRLLIPSRVAGSVIGKGGSNIARLRNDF   50 (150)
Q Consensus        22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t   50 (150)
                      .+++.|....-|.|||++|+.|++|+++.
T Consensus        62 ~i~I~I~tarPG~iIGkkG~~i~~L~~~l   90 (105)
T d2uubc1          62 NVAVTVHVAKPGVVIGRGGERIRVLREEL   90 (105)
T ss_dssp             CEECCEEESCHHHHHCSTTSHHHHHHHHH
T ss_pred             cEEEEEEECCCceEEcCCchhHHHHHHHH
Confidence            36777888899999999999999998764

>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=89.59  E-value=0.038  Score=33.66  Aligned_cols=29  Identities=21%  Similarity=0.480  Sum_probs=25.3

Q ss_pred             eEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         119 YDIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      ..+++.|-...-|.|||++|+.|++|++.
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            35778899999999999999999999764

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=89.58  E-value=0.32  Score=28.80  Aligned_cols=57  Identities=14%  Similarity=0.083  Sum_probs=42.9

Q ss_pred             EEeeCCccceEecCCch-HHHHHHHHhCCeEEecCCCCCCceEEEecC-hHHHHHHHHHHHHH
Q psy7546          25 LLIPSRVAGSVIGKGGS-NIARLRNDFKASVTVPDCPGPERILTIFAE-LENGLKVIEEVLPA   85 (150)
Q Consensus        25 l~vp~~~vg~IIGk~G~-~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-~~~v~~A~~~i~~~   85 (150)
                      +-||-..+..++|+++. .++.|.+.+++.|-+-.+.    .|.|.|. ++....+...|...
T Consensus         5 ~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NG----rIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           5 IDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNG----KIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTT----EEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecCc----EEEEECCCHHHHHHHHHHHHHH
Confidence            45777888899999998 7899999999999998763    6888885 45554444444333

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

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: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.51  E-value=0.032  Score=35.23  Aligned_cols=31  Identities=29%  Similarity=0.403  Sum_probs=25.0

Q ss_pred             ceEEEEEEecC-ceeEEeecCCchHHHHHHhh
Q psy7546         118 DYDIRLIVHQS-QAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       118 ~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      .....+.|+.. +.+.|||++|++|++|...+
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            36677888766 46999999999999997654

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-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: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=88.34  E-value=0.064  Score=34.07  Aligned_cols=37  Identities=22%  Similarity=0.328  Sum_probs=27.7

Q ss_pred             ceEEEEEeeC-CccceEecCCchHHHHHHH--------HhCCeEEe
Q psy7546          20 DVELRLLIPS-RVAGSVIGKGGSNIARLRN--------DFKASVTV   56 (150)
Q Consensus        20 ~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~--------~tg~~I~i   56 (150)
                      .+...+.|+. ++-+.|||++|++||+|..        -++++|.+
T Consensus        49 ~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~aR~~le~~~~~kV~L   94 (118)
T d1wf3a2          49 YIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYL   94 (118)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHTSEEEE
T ss_pred             EEEEEEEeCccchhhhhhccCchhHHHHHHHHHHHHHHHhCCCeEE
Confidence            3466688886 6788999999999997764        45666644

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-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: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=87.40  E-value=0.054  Score=34.44  Aligned_cols=31  Identities=35%  Similarity=0.512  Sum_probs=24.4

Q ss_pred             ceEEEEEEecC-ceeEEeecCCchHHHHHHhh
Q psy7546         118 DYDIRLIVHQS-QAGCIIGKGGTKIKELRDTF  148 (150)
Q Consensus       118 ~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~t  148 (150)
                      .....+.|+.. +.+.|||++|++|++|...+
T Consensus        49 ~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~a   80 (118)
T d1wf3a2          49 YIKAILYVERPSQKAIVIGEGGRKIKEIGQAT   80 (118)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEEeCccchhhhhhccCchhHHHHHHHH
Confidence            34666778766 46999999999999997653

>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal domain {Escherichia coli [TaxId: 562]}

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: Escherichia coli [TaxId: 562]

Probab=83.06  E-value=0.11  Score=32.28  Aligned_cols=28  Identities=36%  Similarity=0.625  Sum_probs=23.5

Q ss_pred             EEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546          23 LRLLIPSRVAGSVIGKGGSNIARLRNDF   50 (150)
Q Consensus        23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~t   50 (150)
                      +++.|....-|.|||++|+.|.+|+++.
T Consensus        63 i~V~I~tarPGviIG~~G~~i~~L~~~l   90 (105)
T d2qalc1          63 IRVTIHTARPGIVIGKKGEDVEKLRKVV   90 (105)
T ss_dssp             BCCEEEESCHHHHHCTTSHHHHHHHHHH
T ss_pred             EEEEEEeCCCccEeccCcccHHHHHHHH
Confidence            5567777889999999999999988653

>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=81.85  E-value=0.12  Score=31.99  Aligned_cols=28  Identities=36%  Similarity=0.852  Sum_probs=24.3

Q ss_pred             EEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546         120 DIRLIVHQSQAGCIIGKGGTKIKELRDT  147 (150)
Q Consensus       120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~  147 (150)
                      .+++.|-...-|.|||++|+.|+.|++.
T Consensus        62 ~i~I~I~tarPG~iIGkkG~~i~~L~~~   89 (105)
T d2uubc1          62 NVAVTVHVAKPGVVIGRGGERIRVLREE   89 (105)
T ss_dssp             CEECCEEESCHHHHHCSTTSHHHHHHHH
T ss_pred             cEEEEEEECCCceEEcCCchhHHHHHHH
Confidence            4777888889999999999999998764

>d2asba2 d.52.3.1 (A:184-262) 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=81.01  E-value=0.22  Score=29.10  Aligned_cols=27  Identities=15%  Similarity=0.448  Sum_probs=22.8

Q ss_pred             CccceEecCCchHHHHHHHHhC-CeEEe
Q psy7546          30 RVAGSVIGKGGSNIARLRNDFK-ASVTV   56 (150)
Q Consensus        30 ~~vg~IIGk~G~~Ik~l~~~tg-~~I~i   56 (150)
                      +-+|+.||.+|.+|+.+.++.+ -+|.+
T Consensus        47 DpvGacvG~~GsRI~~I~~eL~gEkIDi   74 (79)
T d2asba2          47 NAKGACIGPMGQRVRNVMSELSGEKIDI   74 (79)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEE
T ss_pred             CceeEEECCCccHHHHHHHHhCCceEEE
Confidence            5599999999999999999876 55554