Citrus Sinensis ID: 025112

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------
Protein Sequence
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGQPLLQLTM
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccccEEEccccHHHHHHHHHHccEEEEcccccccccEEEEEEEcccccHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEEEcccEEEEEcccccHHHHHHHHHcccEEEcccccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEcccccccccEEEEEEccccccccHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEEccccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEcc
Coil and Loop (DISEMBL)
maeqgeitvnptvsvvtepeprhdvsgkrrredgeiegsdpkrrAKAQDVLFRIIVpsrqigkvigkeGHRIQKIREETKATIKIADAIARHEERVIIISskdndnvvsDAENALQQIAALILkdddsnseaskVAAGHVAANTIRLLIAGSQagcligmsgqnieklrnssgativilapnqlplcasahesdrvvQISGDVPAVLNALVEIGNqlrenpprqvisispaynysairpaqpfveptsgqpllqltm
Flexible Loop (DISEMBL)
maeqgeitvnptvsvvtepeprhdvsgkrrredgeiegsdpkrrakaqdvlfriivpsrqigkvigkeghriqkireetkaTIKIADAIARHEERVIIISskdndnvvSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGnqlrenpprQVISISPAYNYSAIRpaqpfveptsgqpllqltm
Low Complexity Region (SEG)
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEtkatikiadaiaRHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGQPLLQLTM
Disordered region (IsUnstruct)
************************************************DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL***********VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR*****QVISISPAYNYSAI********************
Disordered Region (DISOPRED)
***************************************************FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI*********************TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN******************************P******
Disordered Region (DISEMBL)
MAEQGEITVNPTVSVV***************************RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD***********AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGQPLLQLTM
Disordered Region (DISPRO)
***********************************************QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD*************VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGQP******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGQPLLQLTM
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	257	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.750	0.318	0.303	7e-14
P57721	371	Poly(rC)-binding protein	yes	no	0.618	0.428	0.293	2e-12
P57722	371	Poly(rC)-binding protein	no	no	0.618	0.428	0.293	3e-12
Q61990	362	Poly(rC)-binding protein	yes	no	0.614	0.436	0.290	3e-12
Q5SF07	592	Insulin-like growth facto	no	no	0.766	0.332	0.269	3e-11
Q15366	365	Poly(rC)-binding protein	no	no	0.614	0.432	0.284	5e-11
Q0VCU0	403	Poly(rC)-binding protein	no	no	0.603	0.384	0.264	1e-10
P57723	403	Poly(rC)-binding protein	no	no	0.603	0.384	0.264	1e-10
P57724	403	Poly(rC)-binding protein	no	no	0.603	0.384	0.264	1e-10
O19048	356	Poly(rC)-binding protein	no	no	0.630	0.455	0.270	3e-10

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

 Score = 77.8 bits (190), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 64/211 (30%), Positives = 105/211 (49%), Gaps = 18/211 (8%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS--------- 100
           V++RI+ P   +G VIGK G  I  IR  TKA IK+ D +    +RVI I          
Sbjct: 36  VVYRILCPIDVVGGVIGKSGKVINAIRHNTKAKIKVFDQLHGCSQRVITIYCSVKEKQEE 95

Query: 101 ---SKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCL 157
              +K  +  +  A++AL ++   I+  D+ N+  + V          RLL+  SQ+  L
Sbjct: 96  IGFTKSENEPLCCAQDALLKVYDAIVASDEENNTKTNVDRDD--NKECRLLVPFSQSSSL 153

Query: 158 IGMSGQNIEKLRNSSGATIVILAPN-QLPLCASAHESDRVVQISGDVPAVLNALVEIGNQ 216
           IG +G+NI+++R  + A++ +++ +   P    A E D VV ISG+  +V  AL  +   
Sbjct: 154 IGKAGENIKRIRRRTRASVKVVSKDVSDPSHVCAMEYDNVVVISGEPESVKQALFAVSAI 213

Query: 217 LRENPPRQVISISPAYNYSAIRPAQPFVEPT 247
           + +  PR+ I   P  + S   PA   + P+
Sbjct: 214 MYKINPRENI---PLDSTSQDVPAASVIVPS 241

Arabidopsis thaliana (taxid: 3702)

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

 Score = 72.8 bits (177), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 95/174 (54%), Gaps = 15/174 (8%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER++ I+        +
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITGP------T 97

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DA      + A   ++D  NS ++  A       T+RL++  SQ G LIG  G  I+++R
Sbjct: 98  DAIFKAFAMIAYKFEEDIINSMSNSPATSKPPV-TLRLVVPASQCGSLIGKGGSKIKEIR 156

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
            S+GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct: 157 ESTGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 204

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

Homo sapiens (taxid: 9606)

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

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 95/174 (54%), Gaps = 15/174 (8%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER++ I+        +
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITGP------T 97

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DA      + A   ++D  NS ++  A       T+RL++  SQ G LIG  G  I+++R
Sbjct: 98  DAIFKAFAMIAYKFEEDIINSMSNSPATSKPPV-TLRLVVPASQCGSLIGKGGSKIKEIR 156

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
            S+GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct: 157 ESTGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 204

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

Mus musculus (taxid: 10090)

>sp|Q61990|PCBP2_MOUSE Poly(rC)-binding protein 2 OS=Mus musculus GN=Pcbp2 PE=1 SV=1

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/179 (29%), Positives = 100/179 (55%), Gaps = 21/179 (11%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++   N     
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN----- 66

Query: 110 DAENALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIE 166
               A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+
Sbjct: 67  ----AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIK 121

Query: 167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV 225
           ++R S+GA + + A + LP     + ++R + I+G   +++  + +I   + E+PP+ V
Sbjct: 122 EIRESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLESPPKGV 174

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitinationa and degradation.

Mus musculus (taxid: 10090)

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

 Score = 68.9 bits (167), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 110/230 (47%), Gaps = 33/230 (14%)

Query: 16  VTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKI 75
           V+ P P H     R RE G   GS    +A+  D   RI+VP++ +G +IGKEG  I+ I
Sbjct: 160 VSSPSPPH-----RAREQGHGPGSS--SQARQIDFPLRILVPTQFVGAIIGKEGLTIKNI 212

Query: 76  REETKATIKI--ADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEAS 133
            ++T++ + I   +     E+ V I ++ +  +       A + I  ++ K+ D    A 
Sbjct: 213 TKQTQSRVDIHRKENSGAAEKPVTIHATPEGTS------EACRMILEIMQKEADETKLAE 266

Query: 134 KVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHES 193
           +V         +++L      G LIG  G+N++K+ + +G  I I +   L    S +  
Sbjct: 267 EVP--------LKILAHNGFVGRLIGKEGRNLKKIEHETGTKITISSLQDL----SIYNP 314

Query: 194 DRVVQISGDVPAVLNALVEIGNQLRENPPRQVISIS------PAYNYSAI 237
           +R + + G + A  NA +EI  +LRE     +++++      P  N SA+
Sbjct: 315 ERTITVRGTIEACANAEIEIMKKLREAFENDMLAVNQQANLIPGLNLSAL 364

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

Mus musculus (taxid: 10090)

>sp|Q15366|PCBP2_HUMAN Poly(rC)-binding protein 2 OS=Homo sapiens GN=PCBP2 PE=1 SV=1

 Score = 68.6 bits (166), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 52/183 (28%), Positives = 100/183 (54%), Gaps = 25/183 (13%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++   N     
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN----- 66

Query: 110 DAENALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIE 166
               A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+
Sbjct: 67  ----AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIK 121

Query: 167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG----NQLRENPP 222
           ++R S+GA + + A + LP     + ++R + I+G   +++  + +I       L ++PP
Sbjct: 122 EIRESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLETLSQSPP 175

Query: 223 RQV 225
           + V
Sbjct: 176 KGV 178

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitinationa and degradation.

Homo sapiens (taxid: 9606)

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

 Score = 67.4 bits (163), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 46/174 (26%), Positives = 94/174 (54%), Gaps = 19/174 (10%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            R+++  +++G +IGK+G  +++IRE++ A I I++            S  +    ++ +
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG-----------SCPERITTITGS 68

Query: 112 ENALQQIAALILKDDDSNSEASKVAAGHVA--ANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
             A+    ++I    D +  A+    G+V+    T+RL+I  SQ G LIG +G  I+++R
Sbjct: 69  TAAVFHAVSMIAFKLDEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIR 128

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
            ++GA + + A + LP     + ++R V +SG   A++  + +I   + E+PP+
Sbjct: 129 ETTGAQVQV-AGDLLP-----NSTERAVTVSGVPDAIILCVRQICAVILESPPK 176

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

Bos taurus (taxid: 9913)

>sp|P57723|PCBP4_HUMAN Poly(rC)-binding protein 4 OS=Homo sapiens GN=PCBP4 PE=2 SV=1

 Score = 67.4 bits (163), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 46/174 (26%), Positives = 94/174 (54%), Gaps = 19/174 (10%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            R+++  +++G +IGK+G  +++IRE++ A I I++            S  +    ++ +
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG-----------SCPERITTITGS 68

Query: 112 ENALQQIAALILKDDDSNSEASKVAAGHVA--ANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
             A+    ++I    D +  A+    G+V+    T+RL+I  SQ G LIG +G  I+++R
Sbjct: 69  TAAVFHAVSMIAFKLDEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIR 128

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
            ++GA + + A + LP     + ++R V +SG   A++  + +I   + E+PP+
Sbjct: 129 ETTGAQVQV-AGDLLP-----NSTERAVTVSGVPDAIILCVRQICAVILESPPK 176

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

Homo sapiens (taxid: 9606)

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

 Score = 66.6 bits (161), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 46/174 (26%), Positives = 93/174 (53%), Gaps = 19/174 (10%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            R+++  +++G +IGK+G  +++IRE++ A I I++            S  +    ++ +
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG-----------SCPERITTITGS 68

Query: 112 ENALQQIAALILKDDDSNSEASKVAAGHVA--ANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
             A+    ++I    D +  A+    G V+    T+RL+I  SQ G LIG +G  I+++R
Sbjct: 69  TAAVFHAVSMIAFKLDEDLCAAPANGGSVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIR 128

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
            ++GA + + A + LP     + ++R V +SG   A++  + +I   + E+PP+
Sbjct: 129 ETTGAQVQV-AGDLLP-----NSTERAVTVSGVPDAIILCVRQICAVILESPPK 176

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

Mus musculus (taxid: 10090)

>sp|O19048|PCBP1_RABIT Poly(rC)-binding protein 1 OS=Oryctolagus cuniculus GN=PCBP1 PE=2 SV=1

 Score = 65.9 bits (159), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 99/185 (53%), Gaps = 23/185 (12%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  +++IREE+ A I I++      ER+I ++   N     
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NCPERIITLTGPTN----- 66

Query: 110 DAENALQQIAALILK--DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEK 167
               A+ +  A+I+   ++D NS  +   A      T+RL++  +Q G LIG  G  I++
Sbjct: 67  ----AIFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKE 122

Query: 168 LRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG----NQLRENPPR 223
           +R S+GA + + A + LP     + ++R + I+G   +V   + +I       L ++P  
Sbjct: 123 IRESTGAQVQV-AGDMLP-----NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQG 176

Query: 224 QVISI 228
           +V++I
Sbjct: 177 RVMTI 181

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

Oryctolagus cuniculus (taxid: 9986)

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	257
449445515	276	PREDICTED: poly(rC)-binding protein 2-li	0.926	0.862	0.763	1e-98
356530005	385	PREDICTED: KH domain-containing protein	0.863	0.576	0.807	7e-98
255541092	363	conserved hypothetical protein [Ricinus	0.957	0.677	0.736	2e-94
297734587	346	unnamed protein product [Vitis vinifera]	0.961	0.713	0.714	1e-93
359489188	343	PREDICTED: KH domain-containing protein	0.961	0.720	0.714	1e-93
307136423	331	hypothetical protein [Cucumis melo subsp	0.782	0.607	0.783	4e-82
147855522	321	hypothetical protein VITISV_031103 [Viti	0.844	0.676	0.724	1e-81
224137186	357	predicted protein [Populus trichocarpa]	0.937	0.675	0.690	2e-81
357507881	275	Poly(rC)-binding protein [Medicago trunc	0.778	0.727	0.722	3e-75
116784616	407	unknown [Picea sitchensis]	0.805	0.508	0.540	1e-50

>gi|449445515|ref|XP_004140518.1| PREDICTED: poly(rC)-binding protein 2-like [Cucumis sativus] gi|449529952|ref|XP_004171961.1| PREDICTED: poly(rC)-binding protein 2-like [Cucumis sativus]

 Score =  365 bits (936), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 187/245 (76%), Positives = 209/245 (85%), Gaps = 7/245 (2%)

Query: 20  EPRHDVSGKRRREDGEI----EGSD---PKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRI 72
           EP H V+GKRRRED  I    + SD   PKR+AKA DVLFRI+VPS+QIGKVIGK G RI
Sbjct: 32  EPGHTVTGKRRREDDLIVSNSDASDISAPKRQAKAHDVLFRIVVPSKQIGKVIGKVGCRI 91

Query: 73  QKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA 132
           QK+REETKATIKIADA+AR+EERVIIISSKDN+N V+DAE ALQQIAALILK+D S+ E 
Sbjct: 92  QKVREETKATIKIADAVARYEERVIIISSKDNENSVTDAEKALQQIAALILKEDGSSIEE 151

Query: 133 SKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHE 192
            KV  GHVAANTIRLLIAGSQAG LIG SGQNIEKLRNSSGA+I ILAPNQLPLCASAHE
Sbjct: 152 LKVGTGHVAANTIRLLIAGSQAGSLIGASGQNIEKLRNSSGASITILAPNQLPLCASAHE 211

Query: 193 SDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGQPL 252
           SDRVVQISGD+ AVL AL EIGNQLR NPPRQVIS+SP YNY+ + P Q +++PTSG+P+
Sbjct: 212 SDRVVQISGDILAVLKALEEIGNQLRVNPPRQVISVSPTYNYNTMHPPQSYMDPTSGKPI 271

Query: 253 LQLTM 257
           LQL M
Sbjct: 272 LQLIM 276

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530005|ref|XP_003533576.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  362 bits (930), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 185/229 (80%), Positives = 206/229 (89%), Gaps = 7/229 (3%)

Query: 26  SGKRRREDGEIEG--SDPK----RRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79
           SGKRRR+D E  G  S P+    +RAK QDV+FRI+VPSRQIGKVIGKEGHRIQKIRE+T
Sbjct: 73  SGKRRRDD-ENSGTASAPEQSAAKRAKGQDVIFRIVVPSRQIGKVIGKEGHRIQKIREDT 131

Query: 80  KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGH 139
           KATIKIADAIARHEERVIIISSKDND  V+DAE AL+QIA LILK+DDS+ +ASKV AGH
Sbjct: 132 KATIKIADAIARHEERVIIISSKDNDEKVTDAEKALEQIAHLILKEDDSSLDASKVTAGH 191

Query: 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI 199
           VAANTIRLLIAGSQAG LIGMSGQNIEKLR+SSGA+I +LAPNQLPLCASAHESDRVVQ+
Sbjct: 192 VAANTIRLLIAGSQAGGLIGMSGQNIEKLRDSSGASITVLAPNQLPLCASAHESDRVVQL 251

Query: 200 SGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTS 248
           SGDVPAV+ AL EIG QLRENPPRQVISISP YNY+AIRP+QP+++PTS
Sbjct: 252 SGDVPAVMKALEEIGCQLRENPPRQVISISPTYNYAAIRPSQPYLDPTS 300

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541092|ref|XP_002511610.1| conserved hypothetical protein [Ricinus communis] gi|223548790|gb|EEF50279.1| conserved hypothetical protein [Ricinus communis]

 Score =  351 bits (901), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 187/254 (73%), Positives = 215/254 (84%), Gaps = 8/254 (3%)

Query: 1   MAEQGEITVNPTVSVVTEPEPR-HDVSGKRRREDGEI----EGSDPKRRAKAQDVLFRII 55
           M + G I +N TV  V+ P P  +  + KRRR++ ++    EGS  KR AKAQDV+FRI+
Sbjct: 19  MPQPGGIPMN-TVPPVSFPPPDIYAATAKRRRDEFDVADEPEGSAAKR-AKAQDVIFRIV 76

Query: 56  VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENAL 115
           VPSRQIGKVIGK G RIQKIREETKATIKIADAIARHEERVIIISSK++D VVSDAENAL
Sbjct: 77  VPSRQIGKVIGKVGCRIQKIREETKATIKIADAIARHEERVIIISSKESDCVVSDAENAL 136

Query: 116 QQIAALILKDDDSNSEASKV-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA 174
           ++IA LILK+D+S +E+SKV  AGH+ ANTIRLLIAGSQAG LIG+SGQNIEKLRNSSGA
Sbjct: 137 KKIATLILKEDESPAESSKVVGAGHLGANTIRLLIAGSQAGSLIGVSGQNIEKLRNSSGA 196

Query: 175 TIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNY 234
           TI +LAPNQLPLCASAHESDRVVQISGDVP VL A+ EIG QLRENPP+QVISISP YNY
Sbjct: 197 TITVLAPNQLPLCASAHESDRVVQISGDVPVVLKAVEEIGCQLRENPPKQVISISPTYNY 256

Query: 235 SAIRPAQPFVEPTS 248
           + +RP QP+V+PTS
Sbjct: 257 ATVRPTQPYVDPTS 270

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734587|emb|CBI16638.3| unnamed protein product [Vitis vinifera]

 Score =  348 bits (893), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 185/259 (71%), Positives = 208/259 (80%), Gaps = 12/259 (4%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRHDVSGKRRRED---------GEI--EGSDPKRRAKAQD 49
           MA++GE+   P +     P P    S KR R+D         GE+  +   PKRRAK QD
Sbjct: 1   MAQEGEVPRTP-IPQSEAPAPSEPTSMKRPRDDDGGVIASATGEVADDHRSPKRRAKNQD 59

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           VLFRI+VPSRQIGKVIGKEG RIQKIREETKATIKIADAIARHEERVIIISSKD++NV+S
Sbjct: 60  VLFRIVVPSRQIGKVIGKEGSRIQKIREETKATIKIADAIARHEERVIIISSKDSENVIS 119

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DAENAL Q+A+LILK+DDSN++A KV  GHV AN IRLLIAGSQAGCLIGMSGQNIEKLR
Sbjct: 120 DAENALLQVASLILKEDDSNTDALKVGVGHVVANAIRLLIAGSQAGCLIGMSGQNIEKLR 179

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISIS 229
           NSSGATI IL  NQLPLCASAH+SDR+VQISGDVPAVL AL EIG QLRENPPRQVISIS
Sbjct: 180 NSSGATITILPQNQLPLCASAHDSDRMVQISGDVPAVLKALEEIGCQLRENPPRQVISIS 239

Query: 230 PAYNYSAIRPAQPFVEPTS 248
           P YN +  R +Q +++P S
Sbjct: 240 PIYNPNTNRTSQQYLDPAS 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489188|ref|XP_002272998.2| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  348 bits (893), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 185/259 (71%), Positives = 208/259 (80%), Gaps = 12/259 (4%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRHDVSGKRRRED---------GEI--EGSDPKRRAKAQD 49
           MA++GE+   P +     P P    S KR R+D         GE+  +   PKRRAK QD
Sbjct: 1   MAQEGEVPRTP-IPQSEAPAPSEPTSMKRPRDDDGGVIASATGEVADDHRSPKRRAKNQD 59

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           VLFRI+VPSRQIGKVIGKEG RIQKIREETKATIKIADAIARHEERVIIISSKD++NV+S
Sbjct: 60  VLFRIVVPSRQIGKVIGKEGSRIQKIREETKATIKIADAIARHEERVIIISSKDSENVIS 119

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DAENAL Q+A+LILK+DDSN++A KV  GHV AN IRLLIAGSQAGCLIGMSGQNIEKLR
Sbjct: 120 DAENALLQVASLILKEDDSNTDALKVGVGHVVANAIRLLIAGSQAGCLIGMSGQNIEKLR 179

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISIS 229
           NSSGATI IL  NQLPLCASAH+SDR+VQISGDVPAVL AL EIG QLRENPPRQVISIS
Sbjct: 180 NSSGATITILPQNQLPLCASAHDSDRMVQISGDVPAVLKALEEIGCQLRENPPRQVISIS 239

Query: 230 PAYNYSAIRPAQPFVEPTS 248
           P YN +  R +Q +++P S
Sbjct: 240 PIYNPNTNRTSQQYLDPAS 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136423|gb|ADN34230.1| hypothetical protein [Cucumis melo subsp. melo]

 Score =  310 bits (794), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 163/208 (78%), Positives = 178/208 (85%), Gaps = 7/208 (3%)

Query: 20  EPRHDVSGKRRREDGEI----EGSD---PKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRI 72
           EP H V+GKRRRED  I    + SD   PKR+AKA DVLFRI+VPS+QIGKVIGK G RI
Sbjct: 32  EPGHTVTGKRRREDDLIVSNSDASDVSAPKRQAKAHDVLFRIVVPSKQIGKVIGKVGCRI 91

Query: 73  QKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA 132
           QK+REETKATIKIADA+AR+EERVIIISSKDN+N V+DAE ALQQIAALILK+D S+ E 
Sbjct: 92  QKVREETKATIKIADAVARYEERVIIISSKDNENSVTDAEKALQQIAALILKEDGSSIEE 151

Query: 133 SKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHE 192
            KV  GHVAANTIRLLIAGSQAG LIG SGQNIEKLRNSSGA+I ILAPNQLPLCASAHE
Sbjct: 152 LKVGTGHVAANTIRLLIAGSQAGSLIGASGQNIEKLRNSSGASITILAPNQLPLCASAHE 211

Query: 193 SDRVVQISGDVPAVLNALVEIGNQLREN 220
           SDRVVQISGD+ AVL AL EIGNQLR+ 
Sbjct: 212 SDRVVQISGDILAVLKALEEIGNQLRKT 239

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147855522|emb|CAN83854.1| hypothetical protein VITISV_031103 [Vitis vinifera]

 Score =  308 bits (789), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 166/229 (72%), Positives = 183/229 (79%), Gaps = 12/229 (5%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRHDVSGKRRRED---------GEI--EGSDPKRRAKAQD 49
           MA++ E+   P +     P P    S KR R+D         GE+  +   PKRRAK QD
Sbjct: 1   MAQEAEVPKTP-IPQSEAPAPSESTSMKRPRDDDGGVIASATGEVADDHRSPKRRAKNQD 59

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           VLFRI+VPSRQIGKVIGKEG RIQKIREETKATIKIADAIARHEERVIIISSKD++NV+S
Sbjct: 60  VLFRIVVPSRQIGKVIGKEGSRIQKIREETKATIKIADAIARHEERVIIISSKDSENVIS 119

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DAENAL Q A+LILK+DDSN++A KV  GHV AN IRLLIAGSQAGCLIGMSGQNIEKLR
Sbjct: 120 DAENALLQXASLILKEDDSNTDALKVGVGHVVANAIRLLIAGSQAGCLIGMSGQNIEKLR 179

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218
           NSSGATI IL  NQLPLCASAH+SDR+VQISGDVPAVL AL EIG QLR
Sbjct: 180 NSSGATITILPQNQLPLCASAHDSDRMVQISGDVPAVLKALEEIGCQLR 228

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137186|ref|XP_002327061.1| predicted protein [Populus trichocarpa] gi|222835376|gb|EEE73811.1| predicted protein [Populus trichocarpa]

 Score =  308 bits (788), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 174/252 (69%), Positives = 201/252 (79%), Gaps = 11/252 (4%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRH-DVSGKRRREDGEI-EGSDPKRRAKAQDVLFRIIVPS 58
           MA+  E+ +NP+      P+     V+ KRRR+D +  E S  KR+A+A DV+FRI+VPS
Sbjct: 1   MAQPWELQLNPSPPGTELPKLNALPVTAKRRRDDFDGGETSAAKRQARA-DVIFRIVVPS 59

Query: 59  RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118
            +IGKVIGK+GHRIQKIRE+TKATIKIADA+ARHEERVIIISSK+N+N  +DAENALQ+I
Sbjct: 60  GKIGKVIGKQGHRIQKIREDTKATIKIADAVARHEERVIIISSKENENGATDAENALQRI 119

Query: 119 AALILKDDDSNSEASK-------VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171
           A LIL +DD  S A         V AGHVAANTIRLLIAGSQAG LIGMSGQNI KLRNS
Sbjct: 120 AELILNEDDGGSSAGGGVEIGKLVNAGHVAANTIRLLIAGSQAGSLIGMSGQNIVKLRNS 179

Query: 172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA 231
           SGA I +LAPNQLPLCASA+ESDRVVQISGDVP VL AL EIG QLRENPP+QVISISP+
Sbjct: 180 SGAMITVLAPNQLPLCASAYESDRVVQISGDVPVVLKALEEIGCQLRENPPKQVISISPS 239

Query: 232 YNYSAIRPAQPF 243
           YNYSA+ P Q +
Sbjct: 240 YNYSAV-PFQQY 250

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357507881|ref|XP_003624229.1| Poly(rC)-binding protein [Medicago truncatula] gi|355499244|gb|AES80447.1| Poly(rC)-binding protein [Medicago truncatula]

 Score =  287 bits (734), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 151/209 (72%), Positives = 172/209 (82%), Gaps = 9/209 (4%)

Query: 19  PEPRHDV----SGKRRREDGEIEGSDPK-----RRAKAQDVLFRIIVPSRQIGKVIGKEG 69
           P   HD     S KRRR+D ++  +        +RAK QDV+FRI+VPS+QIGKVIGKEG
Sbjct: 60  PYSTHDAGYPSSMKRRRDDEDLGTASSAELSAAKRAKGQDVIFRIVVPSKQIGKVIGKEG 119

Query: 70  HRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129
            RIQKIRE T+A IKIADAIARHEERVIIISSKDND +V+DAE AL+QIA LILK+D+S+
Sbjct: 120 CRIQKIREMTRANIKIADAIARHEERVIIISSKDNDEMVTDAEKALEQIANLILKEDNSS 179

Query: 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCAS 189
            +ASK+ AGHVAANTIRLLIAGSQAG LIGMSGQNIEKLRNSSGA I +LAP+QLPLCAS
Sbjct: 180 FDASKLTAGHVAANTIRLLIAGSQAGGLIGMSGQNIEKLRNSSGAMITVLAPSQLPLCAS 239

Query: 190 AHESDRVVQISGDVPAVLNALVEIGNQLR 218
           AHESDRVVQ+SGDV  V+ AL EIG QLR
Sbjct: 240 AHESDRVVQLSGDVSTVMKALEEIGCQLR 268

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116784616|gb|ABK23409.1| unknown [Picea sitchensis]

 Score =  205 bits (522), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 113/209 (54%), Positives = 147/209 (70%), Gaps = 2/209 (0%)

Query: 37  EGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERV 96
           +G   KR A+ +D++FRI+V S +IGKVIGK+G +I ++RE+T A IKIAD +   E+RV
Sbjct: 80  KGFRAKRAARGRDIVFRIVVASNKIGKVIGKQGSKINQLREDTGARIKIADPVTPLEDRV 139

Query: 97  IIISSKD-NDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAG 155
           IIISSK   +   S AE AL QIA +IL++   +S  +KV   HV  N +RLLIAGSQAG
Sbjct: 140 IIISSKGEEEEETSAAEQALIQIATVILEESGESSATAKVGTRHVGPNMMRLLIAGSQAG 199

Query: 156 CLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGN 215
            LIG SG+ I+++RN SGATI IL  N  P+CASA E+DR+VQISG+V  VL AL  IG 
Sbjct: 200 SLIGASGKTIKEIRNDSGATIKILPQNLSPICASASETDRLVQISGEVSQVLKALDHIGV 259

Query: 216 QLRENPPRQVISISPAYNYSAIRPAQPFV 244
            LRE+PPR+VIS  P Y Y+ + PA   +
Sbjct: 260 TLREHPPREVISTRPTY-YAGLSPANGLM 287

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	257
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.824	0.386	0.333	9.9e-23
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.677	0.363	0.292	2.4e-16
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.758	0.337	0.282	5.9e-16
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.638	0.331	0.312	1.9e-15
TAIR|locus:2056951	153	AT2G03110 "AT2G03110" [Arabido	0.494	0.830	0.355	4.4e-13
UNIPROTKB|H9L011	195	LOC426023 "Uncharacterized pro	0.603	0.794	0.278	9.1e-13
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.622	0.257	0.294	1.8e-12
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.626	0.25	0.292	3.7e-12
UNIPROTKB|F1NPL2	319	PCBP3 "Uncharacterized protein	0.603	0.485	0.273	8.6e-12
UNIPROTKB|F1NPL4	326	PCBP3 "Uncharacterized protein	0.603	0.475	0.273	9.4e-12

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

 Score = 270 (100.1 bits), Expect = 9.9e-23, P = 9.9e-23
 Identities = 76/228 (33%), Positives = 115/228 (50%)

Query:    17 TEPEPRHDVSG-KRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKI 75
             + P+  +D +G  +RR  G+   S    R    D +FR + P ++IG VIG+ G  ++++
Sbjct:    19 SRPQSDYDDNGGSKRRYRGDDRDSLVIDR---DDTVFRYLCPVKKIGSVIGRGGDIVKQL 75

Query:    76 REEXXXXXXXXXXXXRHEERVIII-SSKDNDNVVSDAENALQ--QIAALILKD----DDS 128
             R +              +ERVI I S  D  N   D E  L   Q A   + D    DD+
Sbjct:    76 RNDTRSKIRIGEAIPGCDERVITIYSPSDETNAFGDGEKVLSPAQDALFRIHDRVVADDA 135

Query:   129 NSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA 188
              SE S      V A   +LL+   Q GC++G  GQ ++ +R+ +GA I I+    +PLCA
Sbjct:   136 RSEDSPEGEKQVTA---KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPLCA 192

Query:   189 SAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSA 236
                 SD ++QISG+V  V  AL++I ++L ENP R    +S +  Y A
Sbjct:   193 L--NSDELIQISGEVLIVKKALLQIASRLHENPSRSQNLLSSSGGYPA 238

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 210 (79.0 bits), Expect = 2.4e-16, P = 2.4e-16
 Identities = 55/188 (29%), Positives = 94/188 (50%)

Query:    47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSK---- 102
             ++D ++R + P ++ G +IGK G   ++IR E              EERV+ + S     
Sbjct:    41 SEDTVYRYLCPVKKTGSIIGKGGEIAKQIRSETKSNMRINEALPGCEERVVTMYSTNEEL 100

Query:   103 ----DNDNVVSDAENALQQIAALILKD---DDSNSEASKVAAGHVAANTIRLLIAGSQAG 155
                 D+  +V  A +AL ++  +++ D   DD   + + +  G     T+R+L+   Q G
Sbjct:   101 NHFGDDGELVCPALDALFKVHDMVVADADQDDGTDDDNDL--GEKQTVTVRMLVPSDQIG 158

Query:   156 CLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGN 215
             C+IG  GQ I+ LRN + A I ++  + LP CA     D ++ I G+   V  AL ++ +
Sbjct:   159 CVIGKGGQVIQNLRNDTNAQIRVIK-DHLPACALTLSHDELLLIIGEPLVVREALYQVAS 217

Query:   216 QLRENPPR 223
              L +NP R
Sbjct:   218 LLHDNPSR 225

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 208 (78.3 bits), Expect = 5.9e-16, P = 5.9e-16
 Identities = 57/202 (28%), Positives = 104/202 (51%)

Query:    19 PEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE 78
             PE    +      ED  + G + +      + +FR++VP++++G +IG++G  I+KI EE
Sbjct:   156 PEHLESLQKSEPEEDATVGGEEKRWPGWPGETVFRMLVPAQKVGSIIGRKGDVIKKIVEE 215

Query:    79 XXXXXXXXXXXXRHEERVIIISSKDN-DNVVSDAENALQQIAALILKDDDSNSEASKVAA 137
                            ER +++S K+  ++ +  + + L ++   I+  D  + EAS+ A 
Sbjct:   216 TRARIKILDGPPGTTERAVMVSGKEEPESSLPPSMDGLLRVHMRIV--DGLDGEASQ-AP 272

Query:   138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV 197
                  +T RLL+  SQAG LIG  G  ++ ++ +S   + +L    LP+ A   + DRVV
Sbjct:   273 PPSKVST-RLLVPASQAGSLIGKQGGTVKAIQEASACIVRVLGSEDLPVFAL--QDDRVV 329

Query:   198 QISGDVPAVLNALVEIGNQLRE 219
             ++ G+  +V  AL  I + LR+
Sbjct:   330 EVVGEPTSVHRALELIASHLRK 351

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 202 (76.2 bits), Expect = 1.9e-15, P = 1.9e-15
 Identities = 54/173 (31%), Positives = 96/173 (55%)

Query:    49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNV- 107
             D +FR+IVP  ++G +IG++G  I+K+ EE               +R+++IS K+     
Sbjct:    73 DCVFRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGPVNTPDRIVLISGKEEPEAY 132

Query:   108 VSDAENALQQIAALI--LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNI 165
             +S A +A+ ++   +  L D+D +   +   AG V ++ +RLL+A +QA  LIG  G  I
Sbjct:   133 MSPAMDAVLRVFRRVSGLPDNDDDDVQN---AGSVFSS-VRLLVASTQAINLIGKQGSLI 188

Query:   166 EKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218
             + +  +SGA++ IL+  + P  A+  + +R+V + G+   +L AL  I   LR
Sbjct:   189 KSIVENSGASVRILSEEETPFYAA--QDERIVDLQGEALKILKALEAIVGHLR 239

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0048367 "shoot system development" evidence=IMP

GO:0048467 "gynoecium development" evidence=IMP

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

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 48/135 (35%), Positives = 71/135 (52%)

Query:    93 EERVIIISSKDNDNVVSDAENALQQIAALIL----KDDDSNSEASKVAAGHVAANTIRLL 148
             EER  I    DN++ V  A +AL ++  +++     DDD  ++  + + G     T+R+L
Sbjct:    22 EERNRI--EDDNEDFVCPAFDALFKVHDMVVVEEFDDDDDYNDNDEYSEGQTVV-TVRML 78

Query:   149 IAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLN 208
             +   Q G LIG  G  I+ LRN + A I +   N LP+CA A   D ++QI GD  AV  
Sbjct:    79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDN-LPMCALALSHDELLQIIGDPSAVRE 137

Query:   209 ALVEIGNQLRENPPR 223
             AL ++   L  NP R
Sbjct:   138 ALYQVAFLLYNNPSR 152

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|H9L011 LOC426023 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 49/176 (27%), Positives = 93/176 (52%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER+I ++   N        
Sbjct:    17 RLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGPTN-------- 66

Query:   113 NALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
              A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+++R
Sbjct:    67 -AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIKEIR 124

Query:   170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV 225
              S+GA + + A + LP     + ++R + I+G   +++  + +I   + E+PP+ V
Sbjct:   125 ESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLESPPKGV 174

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 179 (68.1 bits), Expect = 1.8e-12, P = 1.8e-12
 Identities = 51/173 (29%), Positives = 92/173 (53%)

Query:    48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDN-DN 106
             ++V FR++ P+ ++G +IGK G  ++ ++ E              EER+I+IS+++N + 
Sbjct:   274 EEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLER 333

Query:   107 VVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIE 166
               S A++ + ++   I+   +   E S       AA   RLL+     G L+G  G  I 
Sbjct:   334 RHSLAQDGVMRVHNRIV---EIGFEPS-------AAVVARLLVHSPYIGRLLGKGGHLIS 383

Query:   167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
             ++R ++GA+I + A +Q     S H  D +VQ+ G++  V +AL +I  +LRE
Sbjct:   384 EMRRATGASIRVFAKDQATKYESQH--DEIVQVIGNLKTVQDALFQILCRLRE 434

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 178 (67.7 bits), Expect = 3.7e-12, P = 3.7e-12
 Identities = 52/178 (29%), Positives = 97/178 (54%)

Query:    45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEER-VIIISSKD 103
             ++++ +  ++I  S +IG+VIGK G  I+ IR+              H++  VI +++ +
Sbjct:   312 SRSEKLAIKVICSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATE 371

Query:   104 N-DNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSG 162
             + D++ S A  A+     L+L++  ++ +  KV         ++LL++    GC+IG SG
Sbjct:   372 SPDDLKSMAVEAV-----LLLQEKINDEDEDKVK--------MQLLVSSKVIGCIIGKSG 418

Query:   163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220
               I ++R  + A I I   N  P CA  +  D +V+ISG+V  V +AL++I  +LR++
Sbjct:   419 SIISEIRKRTKADIHISKGNNTPKCADPN--DELVEISGEVSNVRDALIQIVLRLRDD 474

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F1NPL2 PCBP3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 173 (66.0 bits), Expect = 8.6e-12, P = 8.6e-12
 Identities = 47/172 (27%), Positives = 89/172 (51%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER++ I+        +DA 
Sbjct:    17 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEGSC--PERIVTITGP------TDA- 67

Query:   113 NALQQIAALILK-DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171
                +  + + LK ++D N+  +          T+RL++  SQ G LIG  G  I+++R S
Sbjct:    68 -IFKAFSMIALKFEEDINASMTNSTVTSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRES 126

Query:   172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
             +GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct:   127 TGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 172

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1NPL4 PCBP3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 173 (66.0 bits), Expect = 9.4e-12, P = 9.4e-12
 Identities = 47/172 (27%), Positives = 89/172 (51%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER++ I+        +DA 
Sbjct:    17 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEGSC--PERIVTITGP------TDA- 67

Query:   113 NALQQIAALILK-DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171
                +  + + LK ++D N+  +          T+RL++  SQ G LIG  G  I+++R S
Sbjct:    68 -IFKAFSMIALKFEEDINASMTNSTVTSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRES 126

Query:   172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
             +GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct:   127 TGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 172

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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00019121001 SubName- Full=Chromosome chr15 scaffold_19, whole genome shotgun sequence; (343 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	257
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-15
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	5e-10
pfam00013	59	pfam00013, KH_1, KH domain	8e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	5e-08
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-07
pfam13014	42	pfam13014, KH_3, KH domain	3e-07
pfam00013	59	pfam00013, KH_1, KH domain	5e-06
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-04
cd02134	61	cd02134, NusA_KH, NusA_K homology RNA-binding doma	3e-04
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-04
pfam13014	42	pfam13014, KH_3, KH domain	6e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	6e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	8e-04
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.001

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

 Score = 69.0 bits (170), Expect = 1e-15
 Identities = 29/70 (41%), Positives = 41/70 (58%), Gaps = 6/70 (8%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T+RLL+  SQAG +IG  G  I+++R  +GA I +   + LP       ++RVV ISG  
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVS-KSVLPGS-----TERVVTISGKP 54

Query: 204 PAVLNALVEI 213
            AV  AL+ I
Sbjct: 55  SAVQKALLLI 64

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

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

 Score = 59.8 bits (146), Expect = 3e-12
 Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 6/69 (8%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARH-EERVIIISSKDNDNVVSD 110
            R++VPS Q G +IGK G  I++IREET A I+++ ++     ERV+ IS K      S 
Sbjct: 2   LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-----PSA 56

Query: 111 AENALQQIA 119
            + AL  I 
Sbjct: 57  VQKALLLIL 65

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

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

 Score = 53.7 bits (130), Expect = 5e-10
 Identities = 27/67 (40%), Positives = 40/67 (59%), Gaps = 5/67 (7%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            R++VPS  +G++IGK G  I++IREET A IKI D+ +  EER++ I+           
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-----PEAV 56

Query: 112 ENALQQI 118
           E A + I
Sbjct: 57  EKAKELI 63

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

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

 Score = 50.3 bits (121), Expect = 8e-09
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 9/67 (13%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            RI++P  ++G++IGK G  I++IREET   I+I D     ++ V I  + +        
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD---DRDDTVTISGTPEQ------V 52

Query: 112 ENALQQI 118
           E A + I
Sbjct: 53  EKAKELI 59

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

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

 Score = 48.4 bits (116), Expect = 5e-08
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 7/70 (10%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            +++P+ ++G +IGK G  I+KI EET   I I       EERV+ I+         + E
Sbjct: 6   EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG--SEERVVEITGPP-----ENVE 58

Query: 113 NALQQIAALI 122
            A + I  ++
Sbjct: 59  KAAELILEIL 68

Length = 68

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

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 7/70 (10%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T R+L+  S  G +IG  G  I+++R  +GA I I               +R+V I+G  
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-------GSEERIVTITGTP 53

Query: 204 PAVLNALVEI 213
            AV  A   I
Sbjct: 54  EAVEKAKELI 63

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

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

 Score = 45.6 bits (109), Expect = 3e-07
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 60  QIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS 100
            +G +IGK G  I++IREET A I+I        ER++ I+
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

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

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

 Score = 42.5 bits (101), Expect = 5e-06
 Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 11/70 (15%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T R+LI   + G +IG  G NI+++R  +G  I I             + D  V ISG  
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD-----------DRDDTVTISGTP 49

Query: 204 PAVLNALVEI 213
             V  A   I
Sbjct: 50  EQVEKAKELI 59

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

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

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 10/72 (13%)

Query: 51  LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSD 110
           +  I +   +I  VIG  G  I++I EET A I I D      +  + I++ D +     
Sbjct: 552 IETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEA---- 601

Query: 111 AENALQQIAALI 122
           AE A++ I  + 
Sbjct: 602 AEAAIKMIEGIT 613

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

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

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

Query: 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85
           R++VP  Q+G  IGK G  ++   +     I I
Sbjct: 27 ARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60

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

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 9/74 (12%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TI +LI   + G +IG  G  I+K+   +G  I I  P            +RVV+I+G  
Sbjct: 4   TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG---------SEERVVEITGPP 54

Query: 204 PAVLNALVEIGNQL 217
             V  A   I   L
Sbjct: 55  ENVEKAAELILEIL 68

Length = 68

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

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 7/49 (14%)

Query: 153 QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201
             G +IG  G+ I+++R  +GA I I  P            +R+V I+G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPE-------PGSGERIVTITG 42

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

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

 Score = 36.7 bits (86), Expect = 6e-04
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P +    +IGK+G  I+KI EET   I+  D  ++ +  + I   K+N   V  A+
Sbjct: 3   EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDT-ITITGPKEN---VEKAK 58

Query: 113 NALQ 116
             + 
Sbjct: 59  EEIL 62

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

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

 Score = 40.0 bits (95), Expect = 8e-04
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 13/73 (17%)

Query: 53  RII---VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           RI    +P  +I  VIG  G  I++I EET A I I D      +  + I++ D +    
Sbjct: 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEA--- 604

Query: 110 DAENALQQIAALI 122
            AE A ++I  + 
Sbjct: 605 -AEAAKERIEGIT 616

Length = 693

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

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 10/66 (15%)

Query: 56  VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENAL 115
           +   +I  VIG  G  I+ I EET   I I D      +  + I++ D ++    A+ A 
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGES----AKKAK 607

Query: 116 QQIAAL 121
           ++I A+
Sbjct: 608 ERIEAI 613

Length = 692

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	257
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.96
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.94
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.93
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.93
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.9
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.82
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.81
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.79
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.77
PRK13763	180	putative RNA-processing protein; Provisional	99.75
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.52
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.46
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.35
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.35
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.31
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.29
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.26
COG1094	194	Predicted RNA-binding protein (contains KH domains	99.26
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.25
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.21
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.21
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.16
PF13014	43	KH_3: KH domain	99.12
PF13014	43	KH_3: KH domain	99.1
smart00322	69	KH K homology RNA-binding domain.	99.03
KOG2113	394	consensus Predicted RNA binding protein, contains	98.93
smart00322	69	KH K homology RNA-binding domain.	98.9
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.75
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.61
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.51
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.51
PRK13763	180	putative RNA-processing protein; Provisional	98.48
PRK08406	140	transcription elongation factor NusA-like protein;	98.46
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.43
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.31
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.31
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.2
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	98.14
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.02
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.8
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.78
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.77
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.66
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.64
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.64
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.49
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.43
TIGR01953	341	NusA transcription termination factor NusA. This m	97.4
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.39
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.34
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.34
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.32
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.21
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.19
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.11
KOG2113	394	consensus Predicted RNA binding protein, contains	97.08
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.06
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.05
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.05
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.05
PRK12329	449	nusA transcription elongation factor NusA; Provisi	97.01
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.9
PRK00468	75	hypothetical protein; Provisional	96.88
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.87
PRK12704	520	phosphodiesterase; Provisional	96.87
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.85
PRK00106	535	hypothetical protein; Provisional	96.85
PRK02821	77	hypothetical protein; Provisional	96.8
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.8
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.66
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.6
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	96.55
PRK01064	78	hypothetical protein; Provisional	96.36
PRK12704	520	phosphodiesterase; Provisional	96.36
COG1094	194	Predicted RNA-binding protein (contains KH domains	96.29
PRK02821	77	hypothetical protein; Provisional	96.27
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.16
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.1
PRK00468	75	hypothetical protein; Provisional	96.02
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.01
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.99
PRK00106	535	hypothetical protein; Provisional	95.97
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	95.82
KOG2874	356	consensus rRNA processing protein [Translation, ri	95.82
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.71
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.66
PRK08406	140	transcription elongation factor NusA-like protein;	95.26
PRK12705	508	hypothetical protein; Provisional	95.26
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	95.26
PRK01064	78	hypothetical protein; Provisional	95.2
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	95.02
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	94.77
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	94.0
PRK12705	508	hypothetical protein; Provisional	93.75
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	93.53
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.12
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	93.1
PRK06418	166	transcription elongation factor NusA-like protein;	93.05
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	92.89
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	92.58
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	92.52
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	92.32
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	91.6
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	91.4
COG0195	190	NusA Transcription elongation factor [Transcriptio	91.31
COG1855	604	ATPase (PilT family) [General function prediction	91.18
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	90.98
PRK12328	374	nusA transcription elongation factor NusA; Provisi	90.75
TIGR01953	341	NusA transcription termination factor NusA. This m	90.58
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	90.04
PRK13764	602	ATPase; Provisional	90.03
PRK13764	602	ATPase; Provisional	90.02
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	89.8
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	89.78
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	89.5
COG1855	604	ATPase (PilT family) [General function prediction	89.37
PRK12327	362	nusA transcription elongation factor NusA; Provisi	88.69
PRK09202	470	nusA transcription elongation factor NusA; Validat	88.41
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	87.19
PRK12329	449	nusA transcription elongation factor NusA; Provisi	86.97
PRK06418	166	transcription elongation factor NusA-like protein;	86.71
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	86.3
COG1782	637	Predicted metal-dependent RNase, consists of a met	86.22
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	85.89
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	85.85
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	85.79
COG5166	657	Uncharacterized conserved protein [Function unknow	84.27
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	84.1
COG5166	657	Uncharacterized conserved protein [Function unknow	81.79
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	81.17
KOG2874	356	consensus rRNA processing protein [Translation, ri	80.91
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	80.54
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	80.5

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

Probab=100.00  E-value=4e-33  Score=243.92  Aligned_cols=220  Identities=25%  Similarity=0.386  Sum_probs=170.6

Q ss_pred             CCCCCCCCCCCCccCCCCCCCCCCcccc-CCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc---ccCC
Q 025112           17 TEPEPRHDVSGKRRREDGEIEGSDPKRR-AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARH   92 (257)
Q Consensus        17 ~~~~~~~~~~~kr~~~~~~~~~~~~~~~-~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~   92 (257)
                      ++...+...+.||+++...+........ ..+..+++|||||+..+|.||||||++|.+|+++|||+|++++.   .|++
T Consensus         5 ~~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGT   84 (402)
T KOG2191|consen    5 VPIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGT   84 (402)
T ss_pred             CcccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCc
Confidence            4555667778899998866433222222 22345999999999999999999999999999999999999943   6899


Q ss_pred             CccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhh--ccCCCcceEEEEEeecCccceeecCCChhHHHHHH
Q 025112           93 EERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKV--AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRN  170 (257)
Q Consensus        93 ~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~--~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~  170 (257)
                      +||+|+|+|+     +..+......|.++|++..........+  .........++++||++.+|.||||+|++||.|++
T Consensus        85 TeRvcli~Gt-----~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~E  159 (402)
T KOG2191|consen   85 TERVCLIQGT-----VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQE  159 (402)
T ss_pred             cceEEEEecc-----HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHH
Confidence            9999999998     4466777788888887764432211111  01123345689999999999999999999999999


Q ss_pred             HhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCCc-c--cC----CCCCCCCCCCCCCCC
Q 025112          171 SSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV-I--SI----SPAYNYSAIRPAQPF  243 (257)
Q Consensus       171 ~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~-~--~~----~p~~~~~~~~~~~~~  243 (257)
                      ++||+|+|++..  |...  ...+|+|++.|.+++..+|+.+|+++|.|+|+..+ +  +|    .|..|+++  +|+||
T Consensus       160 qsga~iqisPqk--pt~~--sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnP--tGspy  233 (402)
T KOG2191|consen  160 QSGAWIQISPQK--PTGI--SLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNP--TGSPY  233 (402)
T ss_pred             hhCcceEecccC--CCCc--cceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCC--CCCCC
Confidence            999999998532  2222  36899999999999999999999999999999866 2  33    58999998  66766


Q ss_pred             cCCC
Q 025112          244 VEPT  247 (257)
Q Consensus       244 ~~~~  247 (257)
                      .-+.
T Consensus       234 a~~~  237 (402)
T KOG2191|consen  234 AYQA  237 (402)
T ss_pred             CCCC
Confidence            6543

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

Probab=99.96  E-value=6.5e-29  Score=212.44  Aligned_cols=193  Identities=28%  Similarity=0.434  Sum_probs=161.7

Q ss_pred             cCCCCCCCCCCCCCCCCCCccCCCCCCCCCCccccCCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc
Q 025112           10 NPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI   89 (257)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~kr~~~~~~~~~~~~~~~~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~   89 (257)
                      ++-|..++++.++.+..+||+.+|+..   +++++   ..+.++||+.+..+|+||||+|++||+|+.++++.|.|+++ 
T Consensus        14 t~q~~~~~~~~e~g~~~gkrp~~d~~~---qa~k~---~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-   86 (390)
T KOG2192|consen   14 TEQPEETFPNTETGGEFGKRPAEDMEE---QAFKR---SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-   86 (390)
T ss_pred             CCChhhcCCCCcccccccCCcchhhHH---HHhhh---cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-
Confidence            456677899999999999999999973   33333   34899999999999999999999999999999999999988 


Q ss_pred             cCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHH
Q 025112           90 ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR  169 (257)
Q Consensus        90 ~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~  169 (257)
                       +.++|+|+|+...+     .+-+-++.|.-.+.+.-.           ..+.+.++++|+.++.|.|||++|+.||+|+
T Consensus        87 -~~peri~tisad~~-----ti~~ilk~iip~lee~f~-----------~~~pce~rllihqs~ag~iigrngskikelr  149 (390)
T KOG2192|consen   87 -SGPERILTISADIE-----TIGEILKKIIPTLEEGFQ-----------LPSPCELRLLIHQSLAGGIIGRNGSKIKELR  149 (390)
T ss_pred             -CCCceeEEEeccHH-----HHHHHHHHHhhhhhhCCC-----------CCCchhhhhhhhhhhccceecccchhHHHHH
Confidence             58999999999742     344444444444443321           2345789999999999999999999999999


Q ss_pred             HHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCCcc-cCCCCC
Q 025112          170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVI-SISPAY  232 (257)
Q Consensus       170 ~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~-~~~p~~  232 (257)
                      +++.++.+|+.     .|| +++++|+|.|.|.+.+|..+++.|++.|.|.|.+++. .|+|.|
T Consensus       150 ekcsarlkift-----~c~-p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~f  207 (390)
T KOG2192|consen  150 EKCSARLKIFT-----ECC-PHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNF  207 (390)
T ss_pred             Hhhhhhhhhhh-----ccC-CCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccc
Confidence            99999999984     333 4799999999999999999999999999999999985 776666

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

Probab=99.94  E-value=9.3e-27  Score=209.56  Aligned_cols=180  Identities=26%  Similarity=0.464  Sum_probs=155.7

Q ss_pred             cCCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        44 ~~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      ....-++.+|++||..++|.||||+|+|||.|.+.|.|+|+|.+. ..|..|+.++|-|.++     .+.+||.+|+++|
T Consensus       193 ~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpE-----g~s~Ac~~ILeim  267 (584)
T KOG2193|consen  193 KQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPE-----GTSKACKMILEIM  267 (584)
T ss_pred             cccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCcc-----chHHHHHHHHHHH
Confidence            344568999999999999999999999999999999999999854 4578899999999987     5679999999999


Q ss_pred             hcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC
Q 025112          123 LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD  202 (257)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~  202 (257)
                      ..+.....-.+        .+.++++..+.+||+||||.|++||+|+++||++|.|.+-.++..    .+.+|.+++.|+
T Consensus       268 qkEA~~~k~~~--------e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~----ynpERTItVkGs  335 (584)
T KOG2193|consen  268 QKEAVDDKVAE--------EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL----YNPERTITVKGS  335 (584)
T ss_pred             HHhhhccchhh--------hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc----cCccceEEeccc
Confidence            77654332222        257899999999999999999999999999999999988666655    378999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCcccC------CCCCCCCCCCCC
Q 025112          203 VPAVLNALVEIGNQLRENPPRQVISI------SPAYNYSAIRPA  240 (257)
Q Consensus       203 ~~~v~~A~~~I~~~l~e~~~~~~~~~------~p~~~~~~~~~~  240 (257)
                      .++|..|..+|+.+|+|.++++..++      .|++|....+.+
T Consensus       336 iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f  379 (584)
T KOG2193|consen  336 IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLF  379 (584)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCC
Confidence            99999999999999999999987544      588988887665

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

Probab=99.93  E-value=7e-25  Score=206.68  Aligned_cols=165  Identities=33%  Similarity=0.558  Sum_probs=131.2

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC---
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD---  125 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~---  125 (257)
                      +.++|+|++...+|.||||+|..||+||+++.++|+|.+..+++.||+++|+|...+.....+.+|+..+++.+...   
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~  121 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE  121 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence            34489999999999999999999999999999999999998899999999999211112334455555555555432   


Q ss_pred             -CCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHH
Q 025112          126 -DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP  204 (257)
Q Consensus       126 -~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~  204 (257)
                       +....+....  ......+.+|+||.+++|+||||+|+.||+|+++|||+|.+.+. .+|.     .++|.|+|.|.++
T Consensus       122 d~~~~~d~~~~--~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~-----ster~V~IsG~~~  193 (485)
T KOG2190|consen  122 DDEAAEDNGED--ASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN-----STERAVTISGEPD  193 (485)
T ss_pred             cccccccCCcc--ccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc-----ccceeEEEcCchH
Confidence             2221111110  01114689999999999999999999999999999999999754 8887     5788999999999


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 025112          205 AVLNALVEIGNQLRENP  221 (257)
Q Consensus       205 ~v~~A~~~I~~~l~e~~  221 (257)
                      +|.+|+..|..+|++++
T Consensus       194 av~~al~~Is~~L~~~~  210 (485)
T KOG2190|consen  194 AVKKALVQISSRLLENP  210 (485)
T ss_pred             HHHHHHHHHHHHHHhcC
Confidence            99999999999999954

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

Probab=99.93  E-value=6.5e-25  Score=205.46  Aligned_cols=166  Identities=23%  Similarity=0.383  Sum_probs=137.1

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc--cCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~--~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..+++..|+||.+.+|+||||+|++||+|++++||++.+....  ..+..+.+.|+|.++     .++.|..+|+++|.+
T Consensus       136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~-----~ve~a~~lV~dil~e  210 (600)
T KOG1676|consen  136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPD-----KVEQAKQLVADILRE  210 (600)
T ss_pred             ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHH-----HHHHHHHHHHHHHHh
Confidence            4568999999999999999999999999999999999987542  123677899999975     789999999999997


Q ss_pred             CCCCCchhh-hhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025112          125 DDDSNSEAS-KVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (257)
Q Consensus       125 ~~~~~~~~~-~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~  203 (257)
                      ......-.. ....+.....+.++.||++.||.||||+|++||+|+.+||++|+|.+ |+.|.     +.+|.+.|.|+.
T Consensus       211 ~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p~-----speR~~~IiG~~  284 (600)
T KOG1676|consen  211 EDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDPS-----SPERPAQIIGTV  284 (600)
T ss_pred             cccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCCC-----CccceeeeecCH
Confidence            544332211 11111123348999999999999999999999999999999999865 45554     789999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCC
Q 025112          204 PAVLNALVEIGNQLRENPPR  223 (257)
Q Consensus       204 ~~v~~A~~~I~~~l~e~~~~  223 (257)
                      ++|++|.++|.++|.+....
T Consensus       285 d~ie~Aa~lI~eii~~~~~~  304 (600)
T KOG1676|consen  285 DQIEHAAELINEIIAEAEAG  304 (600)
T ss_pred             HHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999997665

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

Probab=99.90  E-value=3.9e-23  Score=193.59  Aligned_cols=165  Identities=22%  Similarity=0.346  Sum_probs=133.6

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEc-ccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~-~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~  127 (257)
                      ...+++.||.+.||.||||+|++||+|+.+||+||+|- +..+.+.||.+.|.|..+     .+..|-++|.++|.+...
T Consensus       229 ~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d-----~ie~Aa~lI~eii~~~~~  303 (600)
T KOG1676|consen  229 SATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVD-----QIEHAAELINEIIAEAEA  303 (600)
T ss_pred             cceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHH-----HHHHHHHHHHHHHHHHhc
Confidence            35899999999999999999999999999999999997 445578999999999965     677888888888866533


Q ss_pred             CCchhhhhccCCC-cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025112          128 SNSEASKVAAGHV-AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (257)
Q Consensus       128 ~~~~~~~~~~~~~-~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v  206 (257)
                      .+....  ..+.. ....+.+.||.+.||.||||+|++||.|..+|||++.+.+.  -|..   +..+++|+|.|++.+|
T Consensus       304 ~~~~~~--~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~---~~~ektf~IrG~~~QI  376 (600)
T KOG1676|consen  304 GAGGGM--GGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNG---NPKEKTFVIRGDKRQI  376 (600)
T ss_pred             cCCCCc--CCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCC---CccceEEEEecCcccc
Confidence            211000  01111 11278999999999999999999999999999999998754  2221   3689999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCCc
Q 025112          207 LNALVEIGNQLRENPPRQV  225 (257)
Q Consensus       207 ~~A~~~I~~~l~e~~~~~~  225 (257)
                      +.|..||.+++.+...+..
T Consensus       377 dhAk~LIr~kvg~~~~n~~  395 (600)
T KOG1676|consen  377 DHAKQLIRDKVGDIAPNTP  395 (600)
T ss_pred             hHHHHHHHHHhcccCCCCC
Confidence            9999999999999665543

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

Probab=99.82  E-value=9e-20  Score=156.45  Aligned_cols=163  Identities=26%  Similarity=0.450  Sum_probs=132.4

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEc-ccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~-~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ......+||||..+.+|.|||++|+.||.||+++.++++|- .-.|++++|+|.+.|.++     .|..+++.|++++.+
T Consensus       119 ~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k-----~v~~~i~~il~~i~e  193 (390)
T KOG2192|consen  119 LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK-----RVVECIKIILDLISE  193 (390)
T ss_pred             CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc-----hHHHHHHHHHHHhhc
Confidence            34568899999999999999999999999999999999986 456789999999999876     578899999999877


Q ss_pred             CCCC-------------Cch------------------------------------------------------------
Q 025112          125 DDDS-------------NSE------------------------------------------------------------  131 (257)
Q Consensus       125 ~~~~-------------~~~------------------------------------------------------------  131 (257)
                      ....             ..+                                                            
T Consensus       194 ~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~  273 (390)
T KOG2192|consen  194 SPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWP  273 (390)
T ss_pred             CCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCC
Confidence            4220             000                                                            


Q ss_pred             ----hh-----hh-------------ccC--------CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112          132 ----AS-----KV-------------AAG--------HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (257)
Q Consensus       132 ----~~-----~~-------------~~~--------~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~  181 (257)
                          .+     ..             .++        ..-..+.++.||.+.-|.||||+|.+|++|+.++||.|++...
T Consensus       274 saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep  353 (390)
T KOG2192|consen  274 SAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP  353 (390)
T ss_pred             CcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc
Confidence                00     00             000        0114578999999999999999999999999999999998532


Q ss_pred             CCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          182 NQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       182 ~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                        +.     ++.+|+++|+|+.++++.|.+++...++..
T Consensus       354 --le-----GsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  354 --LE-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             --CC-----CCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence              21     478999999999999999999999999854

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

Probab=99.81  E-value=1.1e-18  Score=164.92  Aligned_cols=162  Identities=34%  Similarity=0.539  Sum_probs=132.8

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC-
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD-  126 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~-  126 (257)
                      +.++||+||++++|.||||+|+.||+|+++|||+|++... .|.+++|.|+|.|.++     ++.+|+..|...|.+.. 
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~-----av~~al~~Is~~L~~~~~  211 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPD-----AVKKALVQISSRLLENPP  211 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchH-----HHHHHHHHHHHHHHhcCC
Confidence            6899999999999999999999999999999999999865 7899999999999965     89999999999998731 


Q ss_pred             ---C---------C-------------C-ch---------------------hhhhc-----------------------
Q 025112          127 ---D---------S-------------N-SE---------------------ASKVA-----------------------  136 (257)
Q Consensus       127 ---~---------~-------------~-~~---------------------~~~~~-----------------------  136 (257)
                         .         .             . ..                     ..+..                       
T Consensus       212 ~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v  291 (485)
T KOG2190|consen  212 RSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISV  291 (485)
T ss_pred             cCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEe
Confidence               1         0             0 00                     00000                       


Q ss_pred             ----cC-----------C-------------------------CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeE
Q 025112          137 ----AG-----------H-------------------------VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI  176 (257)
Q Consensus       137 ----~~-----------~-------------------------~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I  176 (257)
                          ..           .                         ...++.+++||++++|+||||+|++|.+||+.|||.|
T Consensus       292 ~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I  371 (485)
T KOG2190|consen  292 GDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASI  371 (485)
T ss_pred             ccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCce
Confidence                00           0                         1226789999999999999999999999999999999


Q ss_pred             EEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          177 VILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       177 ~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      .+...++...     ..++.++|+|...+...|.+++...+...
T Consensus       372 ~I~~~~~~~~-----~~e~~~~I~~~~~~~~~~~~~~~~~~~~~  410 (485)
T KOG2190|consen  372 SILNKEEVSG-----VREALVQITGMLREDLLAQYLIRARLSAP  410 (485)
T ss_pred             EEccccccCC-----cceeEEEecchhHHHHhhhhhcccccccC
Confidence            9987765422     68999999999999999999996666553

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.79  E-value=5.9e-19  Score=146.52  Aligned_cols=146  Identities=21%  Similarity=0.275  Sum_probs=110.6

Q ss_pred             EEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEe---ccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112           54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII---SSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (257)
Q Consensus        54 ilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I---~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~  130 (257)
                      |.||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|   ++.     ..++.+|..+|..+.......  
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d-----~~~i~kA~~~I~~i~~gf~~e--   69 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDED-----PLAVMKAREVVKAIGRGFSPE--   69 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCC-----HHHHHHHHHHHHHHHcCCCHH--
Confidence            56899999999999999999999999999999953     356888   333     347888999888877643211  


Q ss_pred             hhhhhccCCCcceEE-EEEeec---------CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE
Q 025112          131 EASKVAAGHVAANTI-RLLIAG---------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS  200 (257)
Q Consensus       131 ~~~~~~~~~~~~~~~-~l~Vp~---------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~  200 (257)
                      ++.+.. +  ..+.. -+.|+.         ..+|+|||++|++++.|++.|||+|.|.              ++.|.|.
T Consensus        70 ~A~~l~-g--d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~--------------~~~v~i~  132 (172)
T TIGR03665        70 KALKLL-D--DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY--------------GKTVGII  132 (172)
T ss_pred             HHHHhc-C--CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--------------CCEEEEE
Confidence            000000 0  01111 122332         3689999999999999999999999984              2679999


Q ss_pred             cCHHHHHHHHHHHHHHHhcCCCCCcccC
Q 025112          201 GDVPAVLNALVEIGNQLRENPPRQVISI  228 (257)
Q Consensus       201 G~~~~v~~A~~~I~~~l~e~~~~~~~~~  228 (257)
                      |++++++.|.++|.+++.+.++..+|++
T Consensus       133 G~~~~~~~A~~~i~~li~~~~~~~vy~~  160 (172)
T TIGR03665       133 GDPEQVQIAREAIEMLIEGAPHGTVYKF  160 (172)
T ss_pred             CCHHHHHHHHHHHHHHHcCCCChhHHHH
Confidence            9999999999999999988887765544

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.

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

Probab=99.77  E-value=2.8e-18  Score=155.07  Aligned_cols=160  Identities=25%  Similarity=0.385  Sum_probs=134.7

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      ..-.+++.||...+|+||||+|.+||.|-..+|+.|+|... .+...+|-|+|+|+++     +-.+|-..|..+|.+..
T Consensus       409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppe-----aqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPE-----AQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChH-----HHHhhhhhhhhhhhhhc
Confidence            45578999999999999999999999999999999999854 5668899999999975     56788899999998765


Q ss_pred             CCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025112          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (257)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v  206 (257)
                      ......+       ......+.||...+|+||||||.++++|+.-|+|.+.|+. |+-|+    .++.-+|.|.|...++
T Consensus       484 f~~Pkee-------vklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPr-dqtpd----End~vivriiGhfyat  551 (584)
T KOG2193|consen  484 FFLPKEE-------VKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPR-DQTPD----ENDQVIVRIIGHFYAT  551 (584)
T ss_pred             cCCchhh-------heeeeeeeccchhhhhhhccccccHHHHhccccceEEccc-cCCCC----ccceeeeeeechhhcc
Confidence            4432221       1246789999999999999999999999999999999864 55554    3667899999999999


Q ss_pred             HHHHHHHHHHHhcCCCCC
Q 025112          207 LNALVEIGNQLRENPPRQ  224 (257)
Q Consensus       207 ~~A~~~I~~~l~e~~~~~  224 (257)
                      +.|...|.++|.+....+
T Consensus       552 q~aQrki~~iv~qvkq~~  569 (584)
T KOG2193|consen  552 QNAQRKIAHIVNQVKQSG  569 (584)
T ss_pred             hHHHHHHHHHHHHHHHhh
Confidence            999999999999865544

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.75  E-value=1.5e-17  Score=139.10  Aligned_cols=149  Identities=21%  Similarity=0.293  Sum_probs=111.2

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEec---cCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS---SKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~---G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      ....+.||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|.   +..    ..++.+|..+|..+.....
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d----~~~i~kA~~~I~ai~~gf~   73 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGED----PLAVLKARDIVKAIGRGFS   73 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCC----HHHHHHHHHHHHHHhcCCC
Confidence            467899999999999999999999999999999999953     4567775   221    3478899999998877432


Q ss_pred             CCCchhhhhccCCCcceEEEE-Eee---------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceE
Q 025112          127 DSNSEASKVAAGHVAANTIRL-LIA---------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV  196 (257)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~l-~Vp---------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~  196 (257)
                      .+  +..+.. +  ..+..++ .+.         ...+|+|||++|++++.|++.|||+|.|.              ++.
T Consensus        74 ~e--~A~~l~-g--d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~--------------~~~  134 (180)
T PRK13763         74 PE--KALRLL-D--DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY--------------GKT  134 (180)
T ss_pred             HH--HHHHHh-C--CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc--------------CCE
Confidence            11  000000 0  0011111 111         13689999999999999999999999984              134


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcCCCCCcc
Q 025112          197 VQISGDVPAVLNALVEIGNQLRENPPRQVI  226 (257)
Q Consensus       197 V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~  226 (257)
                      |.|.|++++++.|...|.++++...+...+
T Consensus       135 v~i~G~~~~~~~A~~~I~~li~g~~~~~~~  164 (180)
T PRK13763        135 VAIIGDPEQVEIAREAIEMLIEGAPHGTVY  164 (180)
T ss_pred             EEEEeCHHHHHHHHHHHHHHHcCCCcHHHH
Confidence            999999999999999999999887766544

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.52  E-value=4.8e-14  Score=98.56  Aligned_cols=64  Identities=42%  Similarity=0.619  Sum_probs=57.2

Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG  214 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~  214 (257)
                      ++++||.+.+|+|||++|++|++|+++|||+|.+.+... +.     ..+|+|+|+|+++++.+|+.+|.
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~~-----~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-PG-----STERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-CC-----CCceEEEEEeCHHHHHHHHHhhC
Confidence            689999999999999999999999999999999975432 22     67899999999999999999873

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.46  E-value=8.2e-14  Score=97.40  Aligned_cols=63  Identities=43%  Similarity=0.679  Sum_probs=56.1

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEccccc-CCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA-RHEERVIIISSKDNDNVVSDAENALQQI  118 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~-~~~ervv~I~G~~~~~~~~~~~~A~~~I  118 (257)
                      ++||+||.+.+|+|||++|++|++|+++|||+|++.+... +..+|+|+|.|..+     ++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPS-----AVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHH-----HHHHHHHhh
Confidence            3799999999999999999999999999999999997643 67899999999954     788888776

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.35  E-value=1.6e-12  Score=89.77  Aligned_cols=61  Identities=26%  Similarity=0.332  Sum_probs=54.6

Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG  214 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~  214 (257)
                      .++.||..++|+|||++|++|++|+++|||+|.+++..         +.++.|+|+|++++|.+|..+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~---------~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG---------SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC---------CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999996532         35789999999999999998873

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=99.35  E-value=1.9e-12  Score=88.79  Aligned_cols=60  Identities=32%  Similarity=0.445  Sum_probs=53.8

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I  213 (257)
                      |.++.||..++|+|||++|++|++|+++|||+|.+++.          +.+..|+|+|++++|++|+++|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~----------~~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD----------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST----------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC----------CCcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999643          1245999999999999999886

; 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 ....

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

Probab=99.31  E-value=9.2e-12  Score=85.93  Aligned_cols=57  Identities=26%  Similarity=0.278  Sum_probs=51.8

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-HHHHHHHHHHH
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEI  213 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-~~~v~~A~~~I  213 (257)
                      ...+.||.+++|+|||++|++|++|+++|||+|.+.             .++.|+|+|+ +++++.|.++|
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~-------------~~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE-------------DDGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeC-------------CCCEEEEEeCCHHHHHHHHHHh
Confidence            568899999999999999999999999999999984             2467999998 89999999887

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

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

Probab=99.29  E-value=1.8e-11  Score=84.57  Aligned_cols=62  Identities=34%  Similarity=0.500  Sum_probs=55.3

Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I  213 (257)
                      .++.||.+++++|||++|++|++|+++|||+|.|.....       ...++.|+|.|+.+++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-------~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-------GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-------CCCceEEEEEcCHHHHHHHHHHh
Confidence            578999999999999999999999999999999975322       15689999999999999999876

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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.26  E-value=3.5e-12  Score=87.47  Aligned_cols=60  Identities=40%  Similarity=0.609  Sum_probs=51.6

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I  118 (257)
                      |++|.||.+.+|+|||++|++|++|+++|||+|+|++.  + .+..|+|+|.++     ++.+|+++|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~-----~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPE-----QVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHH-----HHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHH-----HHHHHHhhC
Confidence            57899999999999999999999999999999999876  2 455899999643     677777665

; 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 ....

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

Probab=99.26  E-value=6e-11  Score=98.70  Aligned_cols=156  Identities=19%  Similarity=0.223  Sum_probs=112.9

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~  128 (257)
                      .....+.||...++-+||+.|++.+.|++.+++++.++     +.+..|.|.....-.......+|...|..+-..+..+
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe   81 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE   81 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence            34567999999999999999999999999999999999     5567788866531111235566666666654443221


Q ss_pred             CchhhhhccCCCcceEEEE------Ee-e----cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEE
Q 025112          129 NSEASKVAAGHVAANTIRL------LI-A----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV  197 (257)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~l------~V-p----~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V  197 (257)
                      .  +.+.-   .+...+.+      .- +    ....|+|||++|.+.+.|++.|||.|.|.              ...|
T Consensus        82 ~--A~~LL---~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--------------g~tV  142 (194)
T COG1094          82 K--ALKLL---EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--------------GKTV  142 (194)
T ss_pred             H--HHHHh---cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe--------------CcEE
Confidence            1  00000   00001110      00 1    22469999999999999999999999985              4679


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhcCCCCCcccC
Q 025112          198 QISGDVPAVLNALVEIGNQLRENPPRQVISI  228 (257)
Q Consensus       198 ~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~  228 (257)
                      .|.|.+++++.|.+.|.+++...+++.++.|
T Consensus       143 aiiG~~~~v~iAr~AVemli~G~~h~~Vy~f  173 (194)
T COG1094         143 AIIGGFEQVEIAREAVEMLINGAPHGKVYKF  173 (194)
T ss_pred             EEecChhhhHHHHHHHHHHHcCCCchhHHHH
Confidence            9999999999999999999999998876644

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.25  E-value=6.3e-12  Score=86.79  Aligned_cols=60  Identities=30%  Similarity=0.450  Sum_probs=52.2

Q ss_pred             EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (257)
Q Consensus        52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I  118 (257)
                      .+|.||.++++.|||++|++|++|+++|||+|.|++..  ..++.|+|+|+++     ++..|..+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~-----~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKE-----NVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHH-----HHHHHHHHh
Confidence            57899999999999999999999999999999999763  6789999999953     566666654

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.

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

Probab=99.21  E-value=2.9e-11  Score=83.58  Aligned_cols=62  Identities=44%  Similarity=0.669  Sum_probs=53.4

Q ss_pred             EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (257)
Q Consensus        52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I  118 (257)
                      .+|.||.++++.|||++|++|++|+++|||+|.|++......++.|.|.|..+     ++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~-----~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPE-----AVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHH-----HHHHHHHHh
Confidence            68999999999999999999999999999999999765456789999999843     566666554

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.

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

Probab=99.21  E-value=9.9e-11  Score=103.67  Aligned_cols=79  Identities=30%  Similarity=0.479  Sum_probs=71.7

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ..+.++++||+..+|.||||+|++|.+||.+|||+|++.+..+ .|.     .+||+|.|+|+.+++..-.+.|.++|+|
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG-----TTeRvcli~Gt~eai~av~efI~dKire  111 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG-----TTERVCLIQGTVEALNAVHEFIADKIRE  111 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC-----ccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence            3478999999999999999999999999999999999987544 454     8999999999999999999999999999


Q ss_pred             CCCCC
Q 025112          220 NPPRQ  224 (257)
Q Consensus       220 ~~~~~  224 (257)
                      .++..
T Consensus       112 ~p~~~  116 (402)
T KOG2191|consen  112 KPQAV  116 (402)
T ss_pred             hHHhh
Confidence            87654

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

Probab=99.16  E-value=7.8e-11  Score=81.29  Aligned_cols=58  Identities=36%  Similarity=0.542  Sum_probs=48.3

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I  118 (257)
                      ...|.||.+.+|+||||+|++|++|+++|||+|++++      ++.|.|+|...    .++++|..+|
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~----~~v~~A~~~I   60 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDK----EAAEKAKKMI   60 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCH----HHHHHHHHHh
Confidence            5678999999999999999999999999999999985      35799999732    2456666554

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.

>PF13014 KH_3: KH domain

Probab=99.12  E-value=9.6e-11  Score=75.05  Aligned_cols=42  Identities=43%  Similarity=0.673  Sum_probs=38.3

Q ss_pred             cccceeccCchhHHHHHhhhCceEEEcc-cccCCCccEEEecc
Q 025112           60 QIGKVIGKEGHRIQKIREETKATIKIAD-AIARHEERVIIISS  101 (257)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~tg~~I~i~~-~~~~~~ervv~I~G  101 (257)
                      +||+|||++|++|++|+++|+|+|+|++ ..++..++.|+|+|
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            5899999999999999999999999998 45578899999987

>PF13014 KH_3: KH domain

Probab=99.10  E-value=1.8e-10  Score=73.73  Aligned_cols=43  Identities=37%  Similarity=0.652  Sum_probs=37.2

Q ss_pred             ccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc
Q 025112          153 QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG  201 (257)
Q Consensus       153 ~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G  201 (257)
                      +||+|||++|++|++|+++|||+|+|++ +..+     ++.++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~-----~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP-----GSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC-----CCCceEEEEEC
Confidence            5799999999999999999999999976 3333     37899999998

>smart00322 KH K homology RNA-binding domain

Probab=99.03  E-value=2.4e-09  Score=73.89  Aligned_cols=67  Identities=33%  Similarity=0.457  Sum_probs=59.0

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR  218 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~  218 (257)
                      .+.++.||...+|++||++|++|++|++.||++|.+....         .....|+|.|..+++..|..+|.+.+.
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~---------~~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG---------SEERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC---------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            4688999999999999999999999999999999985321         246889999999999999999988763

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

Probab=98.93  E-value=1e-09  Score=96.63  Aligned_cols=151  Identities=21%  Similarity=0.315  Sum_probs=112.5

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC-
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD-  126 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~-  126 (257)
                      +.++..+-||+..++.|.|++|.+||.|+.+|..+|+-+..   ..+.++.++|..+     +|..|.++|...-.-.. 
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~e-----dv~~aRrei~saaeH~~l   95 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHE-----DVRRARREIPSAAEHFGL   95 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCch-----hHHHHhhcCccccceeee
Confidence            67888999999999999999999999999999999999865   5568899999976     56677666555111100 


Q ss_pred             --CCCchhhhh-ccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025112          127 --DSNSEASKV-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (257)
Q Consensus       127 --~~~~~~~~~-~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~  203 (257)
                        ........+ .+...++.+.+.-+|...+|.|.|..|++|+.|++.++..|..+-+          ..+.++.++|-+
T Consensus        96 ~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~----------~~~~Vf~Vtg~~  165 (394)
T KOG2113|consen   96 IRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR----------CGEPVFCVTGAP  165 (394)
T ss_pred             eeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc----------CCCceEEEecCC
Confidence              000000000 0112456788899999999999999999999999999999987532          367899999999


Q ss_pred             HH-HHHHH-HHHHHH
Q 025112          204 PA-VLNAL-VEIGNQ  216 (257)
Q Consensus       204 ~~-v~~A~-~~I~~~  216 (257)
                      .+ +++|. +.|...
T Consensus       166 ~nC~kra~s~eie~t  180 (394)
T KOG2113|consen  166 KNCVKRARSCEIEQT  180 (394)
T ss_pred             cchhhhccccchhhh
Confidence            88 45554 444443

>smart00322 KH K homology RNA-binding domain

Probab=98.90  E-value=7.1e-09  Score=71.44  Aligned_cols=67  Identities=34%  Similarity=0.586  Sum_probs=55.9

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      ....++.||...+|.+||++|++|++|++++|++|.+....  .....+.|.|..+     ++..|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--~~~~~v~i~g~~~-----~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--SEERVVEITGPPE-----NVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--CCccEEEEEcCHH-----HHHHHHHHHHHHh
Confidence            35789999999999999999999999999999999998542  2578899999843     6777777776654

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

Probab=98.75  E-value=1.1e-08  Score=96.13  Aligned_cols=145  Identities=26%  Similarity=0.385  Sum_probs=116.4

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      ..++.++++|+...+-.||||.|++|+.|++.+++||.+.... ..++++.++.|-+.     ++..|...+++++....
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~-----~v~~a~a~~~~~~~~~~  138 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPV-----QVCKAKAAIHQILTENT  138 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCC-----CCChHHHHHHHHHhcCC
Confidence            3678999999999999999999999999999999999998542 25677777776543     45566666677665442


Q ss_pred             CCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025112          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (257)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v  206 (257)
                      .               +...+-+|...+++++|++|.++.+|+.-++++|.+-. + ..     ....+...|.|....+
T Consensus       139 p---------------vk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~-n-gr-----~g~~~~~~i~~qqk~~  196 (608)
T KOG2279|consen  139 P---------------VSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDK-N-GR-----LGLSRLIKISGQQKEV  196 (608)
T ss_pred             c---------------ccccccchhhhcccccccchhhhcchhccccccccccc-c-cc-----cccccceecccccchH
Confidence            1               35678899999999999999999999999999999742 2 11     1467888888888888


Q ss_pred             HHHHHHHHHHHhc
Q 025112          207 LNALVEIGNQLRE  219 (257)
Q Consensus       207 ~~A~~~I~~~l~e  219 (257)
                      +.|..++.+.+.+
T Consensus       197 ~~a~~~~~~~~~e  209 (608)
T KOG2279|consen  197 AAAKHLILEKVSE  209 (608)
T ss_pred             HHHHhhhhccccc
Confidence            8999999888876

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

Probab=98.61  E-value=2e-07  Score=72.86  Aligned_cols=71  Identities=21%  Similarity=0.289  Sum_probs=53.6

Q ss_pred             cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCC-----------cccCCCCCceEEEEEcCH---HHHHHHHHHHHHH
Q 025112          151 GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP-----------LCASAHESDRVVQISGDV---PAVLNALVEIGNQ  216 (257)
Q Consensus       151 ~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~~~~~~~~~r~V~I~G~~---~~v~~A~~~I~~~  216 (257)
                      .+++|.|||++|++||+|+++|||+|.|-.+....           .... .+..-.|.|++..   +++.+|.++|..+
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~-~~eplhV~I~a~~~~~e~~~~A~~~I~~l   92 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAH-LNEPLHVLITAETPPEEALAKAVEAIEEL   92 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCccccc-CCCCcEEEEEeCCcHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999986431110           0000 0233679999965   8999999999999


Q ss_pred             HhcCCC
Q 025112          217 LRENPP  222 (257)
Q Consensus       217 l~e~~~  222 (257)
                      +.+..+
T Consensus        93 l~~~~~   98 (120)
T cd02395          93 LKPAIE   98 (120)
T ss_pred             hccCCC
Confidence            996543

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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.51  E-value=1.7e-07  Score=77.95  Aligned_cols=61  Identities=25%  Similarity=0.320  Sum_probs=54.4

Q ss_pred             EEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEE---EcCHHHHHHHHHHHHHHHhc
Q 025112          147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI---SGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       147 l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I---~G~~~~v~~A~~~I~~~l~e  219 (257)
                      +.||.+.+|.|||++|++|+.|+++|||+|++..            .+..|.|   +++++++.+|..+|..+.+.
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~------------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g   65 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS------------ETGEVKIEEEDEDPLAVMKAREVVKAIGRG   65 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc------------CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence            5689999999999999999999999999999852            2356888   89999999999999998885

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.

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

Probab=98.51  E-value=3e-07  Score=71.84  Aligned_cols=72  Identities=19%  Similarity=0.368  Sum_probs=52.5

Q ss_pred             EEEecC------ccccceeccCchhHHHHHhhhCceEEEcccccC-----------------CCccEEEeccCCCCchhh
Q 025112           53 RIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAIAR-----------------HEERVIIISSKDNDNVVS  109 (257)
Q Consensus        53 rilVP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~-----------------~~ervv~I~G~~~~~~~~  109 (257)
                      |+.||.      +++|.|||++|.++|+|+++|||+|.|......                 ...--|.|++...+  ..
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~--~e   80 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPP--EE   80 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcH--HH
Confidence            455554      468999999999999999999999999954100                 12246888887511  13


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 025112          110 DAENALQQIAALILKDD  126 (257)
Q Consensus       110 ~~~~A~~~I~~~i~~~~  126 (257)
                      ++.+|+.+|..++....
T Consensus        81 ~~~~A~~~I~~ll~~~~   97 (120)
T cd02395          81 ALAKAVEAIEELLKPAI   97 (120)
T ss_pred             HHHHHHHHHHHHhccCC
Confidence            67888888888887554

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.

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.48  E-value=3.6e-07  Score=76.47  Aligned_cols=64  Identities=25%  Similarity=0.260  Sum_probs=57.4

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE----cCHHHHHHHHHHHHHHHhc
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS----GDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~----G~~~~v~~A~~~I~~~l~e  219 (257)
                      ...+.||.+.+|.|||++|++|+.|+++|||+|++..            .+..|.|.    ++++++++|.++|..++..
T Consensus         4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~------------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g   71 (180)
T PRK13763          4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS------------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG   71 (180)
T ss_pred             eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC------------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence            5788999999999999999999999999999999852            23678885    8999999999999999885

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.46  E-value=5.3e-07  Score=72.39  Aligned_cols=103  Identities=17%  Similarity=0.298  Sum_probs=72.8

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~  129 (257)
                      -.+.|+|+...+|+.||++|++|++|++..|-+|++-...   +                   +....|...+.......
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s---~-------------------d~~~fI~n~l~Pa~V~~   89 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS---D-------------------DPEEFIKNIFAPAAVRS   89 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC---C-------------------CHHHHHHHHcCCCEEEE
Confidence            4688999999999999999999999999999888887541   1                   12222333322111000


Q ss_pred             chhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEE
Q 025112          130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (257)
Q Consensus       130 ~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i  178 (257)
                      ..   . ..........+.|+....|.+|||+|.+++.++.-+|-++.+
T Consensus        90 v~---I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         90 VT---I-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EE---E-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            00   0 000112357788999999999999999999999999998876

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.43  E-value=6.7e-07  Score=89.52  Aligned_cols=146  Identities=20%  Similarity=0.285  Sum_probs=116.0

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      ...+...+-+-...+..++||+|.+|.+|++++.|.+.+...  +..+..+.++|..+     ...+|...+...+.+..
T Consensus       344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~-----~~~ka~~~v~~~~~ei~  416 (753)
T KOG2208|consen  344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSA-----NDEKAVEDVEKIIAEIL  416 (753)
T ss_pred             ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEecccc-----chhHHHHHHHHHHHhhh
Confidence            455888899999999999999999999999999999999985  46778899999865     46777777777776654


Q ss_pred             CCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhC-CeEEEeCCCCCCcccCCCCCceEEEEEcCHHH
Q 025112          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG-ATIVILAPNQLPLCASAHESDRVVQISGDVPA  205 (257)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~  205 (257)
                      .+             .....+.+|...+.++||.+|..|..|..++| .+|++...         .+....+++.|....
T Consensus       417 n~-------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~---------~~~~~~~~~~~~~~d  474 (753)
T KOG2208|consen  417 NS-------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN---------NNSSDMVTIRGISKD  474 (753)
T ss_pred             cc-------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC---------CcccccceEeccccc
Confidence            32             12467899999999999999999999999999 66665332         134566888888888


Q ss_pred             HHHHHHHHHHHHhcCC
Q 025112          206 VLNALVEIGNQLRENP  221 (257)
Q Consensus       206 v~~A~~~I~~~l~e~~  221 (257)
                      +..+..+...+..+..
T Consensus       475 v~~~~~~~~~~~~~a~  490 (753)
T KOG2208|consen  475 VEKSVSLLKALKADAK  490 (753)
T ss_pred             cchhHHHHHhhhhhhh
Confidence            8777777766666544

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.31  E-value=3.5e-06  Score=83.28  Aligned_cols=94  Identities=24%  Similarity=0.307  Sum_probs=74.2

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +..+.+++..|++.+.+..... ...    ....+....+.||.+.+|.|||+||.+||.|+++|||+|.+.        
T Consensus       548 L~~A~~g~~~Il~~m~~al~~p-~~~----s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~--------  614 (719)
T TIGR02696       548 LKQARDARLAILDVMAEAIDTP-DEM----SPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE--------  614 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCc-ccc----ccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe--------
Confidence            4566788888888886653322 111    112345788999999999999999999999999999999984        


Q ss_pred             cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e  219 (257)
                           .+..|.|.+ +.+++++|+.+|..++..
T Consensus       615 -----d~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       615 -----DDGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             -----cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence                 357799988 568999999999999995

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.

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

Probab=98.31  E-value=1.3e-06  Score=82.38  Aligned_cols=185  Identities=18%  Similarity=0.194  Sum_probs=124.1

Q ss_pred             CCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        45 ~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..+..+.+.+-+|...+++|+|++|++++.|+.-++++|.+.........+...|.+...     ....|..++.+.+.+
T Consensus       135 ~~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk-----~~~~a~~~~~~~~~e  209 (608)
T KOG2279|consen  135 TENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQK-----EVAAAKHLILEKVSE  209 (608)
T ss_pred             hcCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccc-----hHHHHHhhhhccccc
Confidence            345678889999999999999999999999999999999999764445677788888654     223444555555543


Q ss_pred             CCCCC------------------------------------chhh----hh------------------------ccC--
Q 025112          125 DDDSN------------------------------------SEAS----KV------------------------AAG--  138 (257)
Q Consensus       125 ~~~~~------------------------------------~~~~----~~------------------------~~~--  138 (257)
                      .....                                    ....    +.                        .++  
T Consensus       210 deelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~  289 (608)
T KOG2279|consen  210 DEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSF  289 (608)
T ss_pred             hhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccccc
Confidence            21100                                    0000    00                        000  


Q ss_pred             --CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH--
Q 025112          139 --HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG--  214 (257)
Q Consensus       139 --~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~--  214 (257)
                        ........+.+|...+|.+||+.|+.++.+...+++.+.|...   |.... -..-.++.+.|+..-+.+|..++.  
T Consensus       290 ~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~---pyt~~-v~~~qic~~egkqh~~n~vl~ml~~~  365 (608)
T KOG2279|consen  290 QKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ---PYTSR-VLQLQICVNEGKQHYENSVLEMLTVH  365 (608)
T ss_pred             ccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec---cccch-hhhhhhheecchhHHHHHHHhhhhcc
Confidence              1123456788999999999999999999999999999998642   32000 011256889999999999999988  


Q ss_pred             ---HHHhcCCCCCc-ccCCCCCCCCCCC
Q 025112          215 ---NQLRENPPRQV-ISISPAYNYSAIR  238 (257)
Q Consensus       215 ---~~l~e~~~~~~-~~~~p~~~~~~~~  238 (257)
                         ....|-+-.++ ++..|--++..++
T Consensus       366 ~p~~~f~eLnl~~~~~p~lps~al~~L~  393 (608)
T KOG2279|consen  366 VPDIVFAELNLNGSWYPALPSGALENLN  393 (608)
T ss_pred             CCccccccccccCccCcccCcccccccC
Confidence               44444444443 2344444444443

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.20  E-value=7.3e-06  Score=82.18  Aligned_cols=164  Identities=22%  Similarity=0.254  Sum_probs=109.5

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCch--hhHHHHHHHHHHHHH-hc-
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNV--VSDAENALQQIAALI-LK-  124 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~--~~~~~~A~~~I~~~i-~~-  124 (257)
                      -+..++.+-...++++||++|.+++.+++++.+.++|++..-..+  ...+.|..+.-.  ...++.++.++..-. .+ 
T Consensus       200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~--~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~  277 (753)
T KOG2208|consen  200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSP--SNKIDGRLNSSSSINVEIQEALTRLESEFDYDE  277 (753)
T ss_pred             eEEEEeeccccchhhhccccccccccccccceeEEEcccccccch--hhhhccccccceehhhhhHHHHHHhcChhhhhh
Confidence            388999999999999999999999999999999999996532211  122222111100  011222222221100 00 


Q ss_pred             ---------------------------CCCCCch------hh-----hhc-------------cCCCcceEEEEEeecCc
Q 025112          125 ---------------------------DDDSNSE------AS-----KVA-------------AGHVAANTIRLLIAGSQ  153 (257)
Q Consensus       125 ---------------------------~~~~~~~------~~-----~~~-------------~~~~~~~~~~l~Vp~~~  153 (257)
                                                 ......+      ..     +..             .-........+.+....
T Consensus       278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~  357 (753)
T KOG2208|consen  278 IIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEE  357 (753)
T ss_pred             hhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHh
Confidence                                       0000000      00     000             00012356778888999


Q ss_pred             cceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 025112          154 AGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (257)
Q Consensus       154 vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~  223 (257)
                      +..++|++|.+|.+|++.+.|.|.+...         ++.+..+.++|...++.+|...+...+.+-+.+
T Consensus       358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~---------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~  418 (753)
T KOG2208|consen  358 LKFVIGKKGANIEKIREESQVKIDLPKQ---------GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS  418 (753)
T ss_pred             hhhhcCCCCccHHHHHHhhhhceecccc---------cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc
Confidence            9999999999999999999999998642         256789999999999999999999999997763

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=98.14  E-value=1.1e-05  Score=64.69  Aligned_cols=103  Identities=19%  Similarity=0.281  Sum_probs=71.6

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~  130 (257)
                      -+-|+|....+|+.||++|++|++|++..|-+|++-..   +++.                   ...|...+.-......
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey---s~D~-------------------~~fI~N~l~PA~V~~V   91 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY---SENL-------------------EEFVANKLAPAEVKNV   91 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc---CCCH-------------------HHHHHHcCCCceEEEE
Confidence            68899999999999999999999999999988888754   1110                   1111111111000000


Q ss_pred             hhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEe
Q 025112          131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL  179 (257)
Q Consensus       131 ~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~  179 (257)
                         .. ....+.....+.||.+..+..|||+|.|++...+-+|-++.+.
T Consensus        92 ---~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        92 ---TV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             ---EE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence               00 0011224678889999999999999999999999999888763

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.02  E-value=1.7e-05  Score=79.09  Aligned_cols=95  Identities=22%  Similarity=0.199  Sum_probs=69.1

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +..+.+++..|++.+.+........    .....+....+.||.+.+|.|||+||++||.|+++|||+|.|.        
T Consensus       520 l~~a~~~~~~I~~~m~~~l~~~~~~----~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~--------  587 (684)
T TIGR03591       520 LEQAKEGRLHILGEMNKVISEPRAE----LSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE--------  587 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhcc----ccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe--------
Confidence            3355667777777775532211000    0111234678899999999999999999999999999999984        


Q ss_pred             cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e  219 (257)
                           .+..|.|.+ ..+.+++|..+|..+..+
T Consensus       588 -----ddG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       588 -----DDGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             -----cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence                 246677777 567899999999988775

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).

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.80  E-value=3.7e-05  Score=76.15  Aligned_cols=66  Identities=33%  Similarity=0.524  Sum_probs=56.7

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      .-...|.||.+.+|.|||+||.+||.|+++||++|+|.+      +..|.|.+...    ..+++|+.+|..+...
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~----~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADG----PSAEAARAMINAIANP  642 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCH----HHHHHHHHHHHHhhCc
Confidence            456788889999999999999999999999999999985      46788988753    3678899999888874

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.

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.78  E-value=8.4e-05  Score=62.54  Aligned_cols=103  Identities=20%  Similarity=0.297  Sum_probs=71.1

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~  130 (257)
                      .+-+++-.+.+|..||++|++|+.|+++.|-+|+|-...             ++         -...|...+.--.    
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d---------~~~fI~nal~Pa~----  130 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------ED---------PAEFIKNALAPAE----  130 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CC---------HHHHHHHhcCcce----
Confidence            566677778899999999999999999999888777541             11         0112222222000    


Q ss_pred             hhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112          131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (257)
Q Consensus       131 ~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~  180 (257)
                       ...+.-...+.....+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus       131 -v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         131 -VLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             -EeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence             0000000001126788899999999999999999999999999999964

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.77  E-value=7.5e-05  Score=75.56  Aligned_cols=99  Identities=16%  Similarity=0.195  Sum_probs=73.1

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCe-EEEeCCCCCCc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPL  186 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~  186 (257)
                      +..+.+++..|++.+.+.....-..    ..........+.||.+.+|.|||.||.+||.|.++||++ |.+.       
T Consensus       654 L~~A~~g~~~Il~~M~~~i~~pr~~----~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-------  722 (891)
T PLN00207        654 LLQAKDGRKHILAEMSKCSPPPSKR----LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-------  722 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhh----hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------
Confidence            4456777777887776543211110    111234578889999999999999999999999999999 8862       


Q ss_pred             ccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCCCC
Q 025112          187 CASAHESDRVVQISG-DVPAVLNALVEIGNQLRENPPR  223 (257)
Q Consensus       187 ~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~~~  223 (257)
                            .+-.|.|.+ +.+.+++|+++|..++.+....
T Consensus       723 ------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG  754 (891)
T PLN00207        723 ------DDGTVKITAKDLSSLEKSKAIISSLTMVPTVG  754 (891)
T ss_pred             ------CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCC
Confidence                  356788888 5689999999999998754333

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

Probab=97.66  E-value=0.00034  Score=65.72  Aligned_cols=78  Identities=21%  Similarity=0.249  Sum_probs=57.4

Q ss_pred             ceEEEEEee------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCccc---------CCCCCceEEEEEcC-HHH
Q 025112          142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA---------SAHESDRVVQISGD-VPA  205 (257)
Q Consensus       142 ~~~~~l~Vp------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~---------~~~~~~r~V~I~G~-~~~  205 (257)
                      ....+|.||      .++||.|||..|.+.|+|+++|||+|.|.-+..+-+..         .-...+=-+.|+++ .+.
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            346678887      46899999999999999999999999997421111000         00123346888886 569


Q ss_pred             HHHHHHHHHHHHhc
Q 025112          206 VLNALVEIGNQLRE  219 (257)
Q Consensus       206 v~~A~~~I~~~l~e  219 (257)
                      |++|++.|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999996

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

Probab=97.64  E-value=0.00015  Score=70.69  Aligned_cols=111  Identities=22%  Similarity=0.223  Sum_probs=81.3

Q ss_pred             EEeccCCCC---chhhHHHHHHHHHHHHHhcCCCCC-chhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHh
Q 025112           97 IIISSKDND---NVVSDAENALQQIAALILKDDDSN-SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS  172 (257)
Q Consensus        97 v~I~G~~~~---~~~~~~~~A~~~I~~~i~~~~~~~-~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t  172 (257)
                      +.|.|-...   ..+..++.|..+|+..+.+-.... .+..     ........+.|+...++-+||++|.+|++|.++|
T Consensus       507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els-----~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eet  581 (692)
T COG1185         507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELS-----PYAPRIETIKIDPDKIRDVIGPGGKTIKAITEET  581 (692)
T ss_pred             eeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh-----ccCCceEEEccCHHHHhhccCCcccchhhhhhhh
Confidence            455554432   124466777888888886643321 1111     1123467888999999999999999999999999


Q ss_pred             CCeEEEeCCCCCCcccCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcCCCCCc
Q 025112          173 GATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLRENPPRQV  225 (257)
Q Consensus       173 ga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~-~~v~~A~~~I~~~l~e~~~~~~  225 (257)
                      ||+|++.             .+..|.|.++. +.+.+|++.|.++.++......
T Consensus       582 g~~Idie-------------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~i  622 (692)
T COG1185         582 GVKIDIE-------------DDGTVKIAASDGESAKKAKERIEAITREVEVGEV  622 (692)
T ss_pred             CcEEEec-------------CCCcEEEEecchHHHHHHHHHHHHHHhhcccccE
Confidence            9999984             34668999976 7999999999999988666554

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

Probab=97.64  E-value=0.00011  Score=67.94  Aligned_cols=69  Identities=20%  Similarity=0.250  Sum_probs=56.2

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      +...+.+.|-+++||.|||++|++|++||..|+++|++..-          +.+..|+|.|...--.+|...|...++.
T Consensus        45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~----------~~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC----------DLEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc----------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            34567788999999999999999999999999999999642          4678899999988666666666554443

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.49  E-value=0.00014  Score=72.63  Aligned_cols=66  Identities=32%  Similarity=0.455  Sum_probs=53.0

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      .-...+.||.+.++.|||+||.+||+|+++|||+|+|.+      +..|.|.+...    ..+.+|..+|..+..+
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~----~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDG----EAAEAAIKMIEGITAE  615 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcH----HHHHHHHHHHHhhhcc
Confidence            456788899999999999999999999999999999985      34577777543    2567777777776543

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).

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

Probab=97.43  E-value=0.00023  Score=48.90  Aligned_cols=37  Identities=30%  Similarity=0.504  Sum_probs=34.4

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEE
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI   85 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i   85 (257)
                      +....+.|+.+.+|..|||+|.+|+.+++.++-+|++
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4678999999999999999999999999999988876

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=97.40  E-value=9.6e-05  Score=67.72  Aligned_cols=94  Identities=22%  Similarity=0.336  Sum_probs=63.7

Q ss_pred             cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025112           60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG  138 (257)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~  138 (257)
                      -+|+.||++|++|+.|.++. |=+|+|-..   +++..                   ..|...+.-.     ....+.-.
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~---s~d~~-------------------~fi~nal~Pa-----~v~~v~i~  296 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEY---SDDPA-------------------EFIANALSPA-----KVISVEVL  296 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhcCCc-----eEEEEEEE
Confidence            39999999999999999998 888887754   11110                   1111111000     00000000


Q ss_pred             CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112          139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (257)
Q Consensus       139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~  180 (257)
                      ........+.||.++.+..|||+|.|++-..+-||.+|.|.+
T Consensus       297 ~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       297 DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            001136899999999999999999999999999999999975

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.

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

Probab=97.39  E-value=0.00027  Score=66.38  Aligned_cols=72  Identities=24%  Similarity=0.386  Sum_probs=54.9

Q ss_pred             CeEEEEEecC------ccccceeccCchhHHHHHhhhCceEEEccc------c---------cCC-CccEEEeccCCCCc
Q 025112           49 DVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA------I---------ARH-EERVIIISSKDNDN  106 (257)
Q Consensus        49 ~~~~rilVP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~------~---------~~~-~ervv~I~G~~~~~  106 (257)
                      .++-|+.||.      +++|+|||..|.|.|+|+++|||||.|--.      .         ++. .+--|.|++...  
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~--  214 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ--  214 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--
Confidence            6777888886      469999999999999999999999999731      0         111 122377777654  


Q ss_pred             hhhHHHHHHHHHHHHHhc
Q 025112          107 VVSDAENALQQIAALILK  124 (257)
Q Consensus       107 ~~~~~~~A~~~I~~~i~~  124 (257)
                        +.+++|+..|..+|.+
T Consensus       215 --eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  215 --EKIKKAIAVIENLIQS  230 (554)
T ss_pred             --HHHHHHHHHHHHHHHh
Confidence              4788999999888875

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

Probab=97.34  E-value=0.00023  Score=62.05  Aligned_cols=42  Identities=26%  Similarity=0.600  Sum_probs=37.5

Q ss_pred             CCCCeEEEEEecCc------cccceeccCchhHHHHHhhhCceEEEcc
Q 025112           46 KAQDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIAD   87 (257)
Q Consensus        46 ~~~~~~~rilVP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (257)
                      +.-.++.||+||..      +||+|+|++|.++|+|+++|+|+|-|--
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG  135 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG  135 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence            44568899999986      6999999999999999999999999983

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.34  E-value=0.0007  Score=62.45  Aligned_cols=96  Identities=21%  Similarity=0.196  Sum_probs=65.3

Q ss_pred             cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025112           60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG  138 (257)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~  138 (257)
                      -+|+.||++|.+|+.|.++. |=+|+|-..   +++..                   ..|...+.-..     ...+...
T Consensus       252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~---s~D~~-------------------~fI~Nal~Pa~-----V~~V~i~  304 (374)
T PRK12328        252 PIGATVGVKGVRINAVSKELNGENIDCIEY---SNVPE-------------------IFIARALAPAI-----ISSVKIE  304 (374)
T ss_pred             hHHhhcCCCcchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhCCCce-----eeEEEEc
Confidence            49999999999999999998 788887654   11111                   11111111000     0000000


Q ss_pred             CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC
Q 025112          139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ  183 (257)
Q Consensus       139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~  183 (257)
                       .......+.||..+.+..|||+|.|++-..+-||.+|.|.+-.+
T Consensus       305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence             11236789999999999999999999999999999999986443

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.32  E-value=0.00044  Score=69.18  Aligned_cols=95  Identities=21%  Similarity=0.202  Sum_probs=69.7

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +..+.+++.+|++.+.+.........    .........+.||.+.++.+||+||.+||.|.++||+.|.+.        
T Consensus       523 l~~a~~g~~~I~~~M~~aI~~~r~~~----~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~--------  590 (693)
T PRK11824        523 LEQAKEGRLHILGKMNEAISEPRAEL----SPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE--------  590 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCChhhh----cccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC--------
Confidence            34567778888888876432211111    111223467778999999999999999999999999998862        


Q ss_pred             cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e  219 (257)
                           .+-.|.|.+ ..+.+++|..+|..+..+
T Consensus       591 -----d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        591 -----DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             -----CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence                 246688888 567999999999998875

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.21  E-value=0.00084  Score=62.01  Aligned_cols=105  Identities=25%  Similarity=0.297  Sum_probs=69.1

Q ss_pred             eEEEEEecCc-----cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           50 VLFRIIVPSR-----QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        50 ~~~rilVP~~-----~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      .-.++-|-+.     -+|+.||++|.+|+.|.++. |=+|+|-..   +++.                   ...|...+.
T Consensus       231 ~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~---s~d~-------------------~~fi~nal~  288 (362)
T PRK12327        231 DRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIIDW---SEDP-------------------AEFVANALS  288 (362)
T ss_pred             ceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhCCCeEEEEEc---CCCH-------------------HHHHHHhCC
Confidence            3445555433     49999999999999999998 888887754   1111                   011111111


Q ss_pred             cCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112          124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (257)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~  181 (257)
                      -.     ....+...........+.||.++.+..|||+|.|++-..+-||.+|.|.+.
T Consensus       289 Pa-----~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        289 PA-----KVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             Cc-----eEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            00     000000000112468999999999999999999999999999999999753

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

Probab=97.19  E-value=0.00037  Score=62.59  Aligned_cols=72  Identities=33%  Similarity=0.370  Sum_probs=58.1

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      +....++|+++..|+|||++|.|.++|+++|+++|.++.+.  .....+.|+|-.    .+.|.+|..+|..+|.+..
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~--~n~~~i~i~~~~----~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN--TNKEEIKIIGIS----RNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC--CCcceEEEeehh----HHHHHHHHHHHHHHHHhhh
Confidence            56778999999999999999999999999999999999873  334446666654    3467888888888886653

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

Probab=97.11  E-value=0.0008  Score=60.46  Aligned_cols=70  Identities=26%  Similarity=0.419  Sum_probs=57.6

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRENP  221 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~  221 (257)
                      ....+.+++...|.|||++|.+.++|+++|+|+|.++.+.         .....++|+| +.+.|.+|.+.|..+|.+.-
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 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN---------TNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC---------CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            4567889999999999999999999999999999987642         2334455555 67899999999999988854

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

Probab=97.08  E-value=0.00038  Score=61.96  Aligned_cols=65  Identities=18%  Similarity=0.242  Sum_probs=57.7

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGN  215 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~  215 (257)
                      +..+..+.||+.+++-+.|++|.+||.|+.+|.++|+-+...          .+.++.++|..+.|..|+..|..
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~----------eePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG----------EEPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC----------CCCcceeccCchhHHHHhhcCcc
Confidence            456889999999999999999999999999999999987542          35789999999999999988865

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

Probab=97.06  E-value=0.00075  Score=62.61  Aligned_cols=55  Identities=25%  Similarity=0.439  Sum_probs=48.2

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCC
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~  103 (257)
                      ..+++.+.|.|-++.||.+||++|++||.||..|+++|++...   ..+-.|+|-|..
T Consensus        43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~   97 (629)
T KOG0336|consen   43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN   97 (629)
T ss_pred             CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence            4578999999999999999999999999999999999999864   456678888864

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.05  E-value=0.0016  Score=62.17  Aligned_cols=104  Identities=25%  Similarity=0.330  Sum_probs=68.9

Q ss_pred             eEEEEEecCc-----cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           50 VLFRIIVPSR-----QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        50 ~~~rilVP~~-----~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      .-.++-|-+.     -+|+.||++|++|+.|.++. |=+|+|-..   +++..                   ..|...+.
T Consensus       231 ~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~---s~d~~-------------------~fi~nal~  288 (470)
T PRK09202        231 SRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILW---SDDPA-------------------QFIINALS  288 (470)
T ss_pred             ceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhCC
Confidence            3445555443     38999999999999999998 888887754   11111                   11111111


Q ss_pred             cCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112          124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (257)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~  181 (257)
                      -..     ...+... .......+.||..+.+..|||+|.|++-..+-||.+|.|...
T Consensus       289 pa~-----v~~v~~~-~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        289 PAE-----VSSVVVD-EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CCE-----EEEEEEe-CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            000     0000000 001368899999999999999999999999999999999863

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

Probab=97.05  E-value=0.002  Score=56.34  Aligned_cols=86  Identities=17%  Similarity=0.252  Sum_probs=59.3

Q ss_pred             CcceEEEEEeec------CccceeecCCChhHHHHHHHhCCeEEEeCCCCC------------Cccc-CCCCCceEEEEE
Q 025112          140 VAANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQL------------PLCA-SAHESDRVVQIS  200 (257)
Q Consensus       140 ~~~~~~~l~Vp~------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~------------p~~~-~~~~~~r~V~I~  200 (257)
                      ....+.+|+||-      ++||+|+|+.|.++|+|+++|||+|-|--+...            |..+ ....---.|+..
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~  168 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE  168 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence            345678888884      589999999999999999999999998632111            1100 000111467777


Q ss_pred             cCHHHH----HHHHHHHHHHHhcCCCCCc
Q 025112          201 GDVPAV----LNALVEIGNQLRENPPRQV  225 (257)
Q Consensus       201 G~~~~v----~~A~~~I~~~l~e~~~~~~  225 (257)
                      +.+..+    ..|++.|.++|.-+.+...
T Consensus       169 ~p~~ea~~rl~~AleeI~klL~P~~e~~d  197 (259)
T KOG1588|consen  169 APPAEAYARLAYALEEIKKLLVPDHEDED  197 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCCCch
Confidence            877654    4689999998887666543

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

Probab=97.05  E-value=0.0011  Score=45.38  Aligned_cols=36  Identities=31%  Similarity=0.451  Sum_probs=33.8

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEE
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i  178 (257)
                      ....+.|+....|.+|||+|.+|+.+++.+|-+|.+
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            478999999999999999999999999999998876

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.

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=97.01  E-value=0.00049  Score=64.56  Aligned_cols=94  Identities=23%  Similarity=0.292  Sum_probs=63.2

Q ss_pred             cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025112           60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG  138 (257)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~  138 (257)
                      -+|+.||++|.+|+.|.++. |=+|+|-..   +++..                   ..|...+.-.     ....+...
T Consensus       278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~y---s~Dp~-------------------~fI~NaLsPA-----~V~~V~i~  330 (449)
T PRK12329        278 PVGACIGARGSRIQAVVNELRGEKIDVIRW---SPDPA-------------------TYIANALSPA-----RVDEVRLV  330 (449)
T ss_pred             hhhccCCCCcchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhcCCc-----eeeEEEEE
Confidence            39999999999999999998 788887654   11111                   1111111000     00000000


Q ss_pred             CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112          139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (257)
Q Consensus       139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~  180 (257)
                      ........+.||.++.+..|||+|.|++-...-||.+|.|.+
T Consensus       331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            001135789999999999999999999999999999999864

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.90  E-value=0.0022  Score=55.97  Aligned_cols=68  Identities=21%  Similarity=0.207  Sum_probs=57.7

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcCCC
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLRENPP  222 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~-~~v~~A~~~I~~~l~e~~~  222 (257)
                      -+.+.||...++++||++|.+|+.|.+.|+++|.+-             .+-.|.|.+.. +++.+|..+|..+-+++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~  212 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHT  212 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence            467889999999999999999999999999999983             24668888865 5889999999888887766


Q ss_pred             CC
Q 025112          223 RQ  224 (257)
Q Consensus       223 ~~  224 (257)
                      ++
T Consensus       213 ~~  214 (235)
T PRK04163        213 SG  214 (235)
T ss_pred             cC
Confidence            65

>PRK00468 hypothetical protein; Provisional

Probab=96.88  E-value=0.0011  Score=47.52  Aligned_cols=34  Identities=35%  Similarity=0.587  Sum_probs=30.1

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhh
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t   79 (257)
                      .+..+.+++.|..+.+|+||||+|.+|+.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3456889999999999999999999999998764

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.87  E-value=0.0059  Score=59.12  Aligned_cols=65  Identities=22%  Similarity=0.344  Sum_probs=54.3

Q ss_pred             eEEEEEeec-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e  219 (257)
                      ....+.+|+ ++-|+|||+.|.||+.+..-||+.+.|-            ++...|+|+| +|-.-+-|...+..+|.+
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid------------dtp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID------------DTPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc------------CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            456677888 5679999999999999999999999982            3456788999 788888888888888876

>PRK12704 phosphodiesterase; Provisional

Probab=96.87  E-value=0.006  Score=59.12  Aligned_cols=65  Identities=22%  Similarity=0.336  Sum_probs=52.5

Q ss_pred             eEEEEEeec-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e  219 (257)
                      ....+.+|+ ++.|+|||+.|.||+.+..-||+.|.|-            ++...|.|+| +|-.-+.|...+..++.+
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid------------dtp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID------------DTPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc------------CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            355677888 5779999999999999999999999982            3456788999 677767777777777765

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.85  E-value=0.074  Score=45.25  Aligned_cols=134  Identities=14%  Similarity=0.106  Sum_probs=87.1

Q ss_pred             EEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchh
Q 025112           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA  132 (257)
Q Consensus        53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~  132 (257)
                      .+.++....-.+...+|..++.|-...||+|.+..     .+..+.|+|++.     .+..+...|.+++..-       
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~-----~~~~i~~~i~~~l~~i-------   91 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKS-----TAEYIEASINEILSNI-------   91 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHH-----HHHHHHHHHHHHHhhc-------
Confidence            44445888899999999999999888999999984     356799999864     2233333333333221       


Q ss_pred             hhhccCCCcceEEEEEeecCccceee----cCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-----CH
Q 025112          133 SKVAAGHVAANTIRLLIAGSQAGCLI----GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-----DV  203 (257)
Q Consensus       133 ~~~~~~~~~~~~~~l~Vp~~~vG~iI----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-----~~  203 (257)
                                .+..+-++.-.--..-    -.....++.|++.|++.|....            .+..+.|.+     ..
T Consensus        92 ----------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~------------~~~~~~i~~~~~~~~~  149 (210)
T PF14611_consen   92 ----------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP------------DGNKLKISWLASPENE  149 (210)
T ss_pred             ----------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC------------CCCeEEEEEEeecccc
Confidence                      1233333322111111    1235679999999999999742            233444554     56


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCc
Q 025112          204 PAVLNALVEIGNQLRENPPRQV  225 (257)
Q Consensus       204 ~~v~~A~~~I~~~l~e~~~~~~  225 (257)
                      ..++.|..++.-.+...++...
T Consensus       150 ~~~~~a~RlL~~a~~~~~~~~~  171 (210)
T PF14611_consen  150 KRADRAKRLLLWALDYNPHSQE  171 (210)
T ss_pred             chHHHHHHHHHHhccCCccccc
Confidence            7889999999999975555543

>PRK00106 hypothetical protein; Provisional

Probab=96.85  E-value=0.007  Score=58.66  Aligned_cols=65  Identities=23%  Similarity=0.387  Sum_probs=54.7

Q ss_pred             eEEEEEeec-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e  219 (257)
                      ....+.+|+ ++-|+|||+.|.||+.+..-||+.+.|-            ++...|+|+| +|-.-+-|...+..++.+
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid------------dtp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID------------DTPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc------------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            456677888 5779999999999999999999999982            3456788999 788888888888888876

>PRK02821 hypothetical protein; Provisional

Probab=96.80  E-value=0.0013  Score=47.31  Aligned_cols=35  Identities=23%  Similarity=0.423  Sum_probs=30.5

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhC
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETK   80 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg   80 (257)
                      ..+...+++.|..+.+|+||||+|.+|+.||.--.
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            34557899999999999999999999999998754

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.80  E-value=0.0013  Score=66.88  Aligned_cols=67  Identities=25%  Similarity=0.413  Sum_probs=55.9

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCce-EEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~-I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      -.-...|.||.+.++.|||.||.+||.|.++||++ |++.+      +..|.|.+...    ..+.+|..+|..+..+
T Consensus       683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~----~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDL----SSLEKSKAIISSLTMV  750 (891)
T ss_pred             CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCH----HHHHHHHHHHHHHhcC
Confidence            35677889999999999999999999999999999 88875      35688888653    4678888888888764

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

Probab=96.66  E-value=0.0033  Score=61.70  Aligned_cols=67  Identities=30%  Similarity=0.413  Sum_probs=55.0

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      .-...+.|+.+.++.+||++|.+|++|.++||++|++.+.      ..|.|.+...+    .+.+|+..|..+..+.
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~----~~~~ak~~I~~i~~e~  617 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGE----SAKKAKERIEAITREV  617 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchH----HHHHHHHHHHHHHhhc
Confidence            4456788899999999999999999999999999999843      34778787643    6778888888888554

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

Probab=96.60  E-value=0.0023  Score=45.75  Aligned_cols=32  Identities=41%  Similarity=0.637  Sum_probs=29.3

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhh
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE   78 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~   78 (257)
                      +....+++.+..+.+|.+|||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            45678999999999999999999999999876

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

Probab=96.55  E-value=0.0059  Score=51.32  Aligned_cols=157  Identities=17%  Similarity=0.174  Sum_probs=99.9

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~  130 (257)
                      +-++-||......+=--==....-|-+..+.+|.+.     ...|.|.+.-.++-....+.+++...|...+..++....
T Consensus        75 ~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmN-----lK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DA  149 (252)
T KOG3273|consen   75 TRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMN-----LKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDA  149 (252)
T ss_pred             eeeccCCcccCChHHHhhHhhhhHHHHhhhheeEee-----cccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhH
Confidence            446677776655441111111234566677777776     334556665544433356778888888888877654321


Q ss_pred             hhh----hhccC---CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025112          131 EAS----KVAAG---HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (257)
Q Consensus       131 ~~~----~~~~~---~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~  203 (257)
                      -..    .....   -.+..+++=.=-+..+|+|+|++|.+--.|++-|.++|.+.              +..|.|-|..
T Consensus       150 iALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------------d~kIHiLG~~  215 (252)
T KOG3273|consen  150 IALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------------DSKIHILGAF  215 (252)
T ss_pred             HHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec--------------CceEEEeecc
Confidence            110    00000   00001122112245689999999999999999999999874              4669999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCcc
Q 025112          204 PAVLNALVEIGNQLRENPPRQVI  226 (257)
Q Consensus       204 ~~v~~A~~~I~~~l~e~~~~~~~  226 (257)
                      +++..|...|+.+|-.+|+..+|
T Consensus       216 ~niriAR~avcsLIlGsppgkVy  238 (252)
T KOG3273|consen  216 QNIRIARDAVCSLILGSPPGKVY  238 (252)
T ss_pred             hhhHHHHHhhHhhhccCCchhHH
Confidence            99999999999999998887644

>PRK01064 hypothetical protein; Provisional

Probab=96.36  E-value=0.004  Score=44.88  Aligned_cols=34  Identities=35%  Similarity=0.677  Sum_probs=30.2

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhh
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t   79 (257)
                      ..+.+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            3466899999999999999999999999998863

>PRK12704 phosphodiesterase; Provisional

Probab=96.36  E-value=0.0099  Score=57.65  Aligned_cols=50  Identities=26%  Similarity=0.482  Sum_probs=40.7

Q ss_pred             CeEEEEEecC-ccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCC
Q 025112           49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (257)
Q Consensus        49 ~~~~rilVP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~  103 (257)
                      .++-.+-+|+ +.-|+||||.|.|||.|+.-||+.|-|++.    + .+|+|+|..
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~~~  259 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGFD  259 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----C-CeEEEecCC
Confidence            4555677788 558999999999999999999999999964    3 357788854

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

Probab=96.29  E-value=0.0097  Score=49.97  Aligned_cols=54  Identities=26%  Similarity=0.311  Sum_probs=43.4

Q ss_pred             cccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           60 QIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ..|+|||++|.+.+.|++-|+|+|.|...       .|.|-|..+     +++.|...|..++...
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------tVaiiG~~~-----~v~iAr~AVemli~G~  165 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------TVAIIGGFE-----QVEIAREAVEMLINGA  165 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeCc-------EEEEecChh-----hhHHHHHHHHHHHcCC
Confidence            47999999999999999999999999944       478888755     5666666666666543

>PRK02821 hypothetical protein; Provisional

Probab=96.27  E-value=0.0067  Score=43.62  Aligned_cols=30  Identities=23%  Similarity=0.400  Sum_probs=27.0

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHh
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSS  172 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t  172 (257)
                      ..+.+.+..+.+|+||||+|.+|+.||.--
T Consensus        31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv   60 (77)
T PRK02821         31 RTLEVRVHPDDLGKVIGRGGRTATALRTVV   60 (77)
T ss_pred             EEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence            578899999999999999999999998643

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

Probab=96.16  E-value=0.015  Score=49.17  Aligned_cols=78  Identities=19%  Similarity=0.243  Sum_probs=49.2

Q ss_pred             ceEEEEEee------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCC-------CCCce--EEEEE-cCHHH
Q 025112          142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASA-------HESDR--VVQIS-GDVPA  205 (257)
Q Consensus       142 ~~~~~l~Vp------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~-------~~~~r--~V~I~-G~~~~  205 (257)
                      .++-++.||      .++||.|||+.|++.|++++.|+|+|-|--....-.|-..       .+.+.  -+.|. -+.+.
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedk  226 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDK  226 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhh
Confidence            355677777      5689999999999999999999999998532211111100       00111  12222 23456


Q ss_pred             HHHHHHHHHHHHhc
Q 025112          206 VLNALVEIGNQLRE  219 (257)
Q Consensus       206 v~~A~~~I~~~l~e  219 (257)
                      ++++++.+...|++
T Consensus       227 i~~~ik~~~n~I~~  240 (269)
T COG5176         227 ICRLIKSQLNAIRE  240 (269)
T ss_pred             HHHHHHHHHHHHHH
Confidence            66777777777776

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.10  E-value=0.016  Score=56.14  Aligned_cols=50  Identities=26%  Similarity=0.484  Sum_probs=40.7

Q ss_pred             CCeEEEEEecC-ccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccC
Q 025112           48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK  102 (257)
Q Consensus        48 ~~~~~rilVP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~  102 (257)
                      ..++-.+-+|+ +.-|+||||.|.|||.++..|||.|-|++.    ++ .|+|++-
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----p~-~v~ls~f  252 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----PE-AVILSGF  252 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----CC-eEEecCC
Confidence            34556677888 558999999999999999999999999964    33 4668885

>PRK00468 hypothetical protein; Provisional

Probab=96.02  E-value=0.0076  Score=43.12  Aligned_cols=30  Identities=23%  Similarity=0.390  Sum_probs=26.9

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHH
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNS  171 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~  171 (257)
                      ...+++.+..+.+|+||||+|.+|+.||.-
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            367889999999999999999999999853

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

Probab=96.01  E-value=0.015  Score=49.21  Aligned_cols=42  Identities=21%  Similarity=0.447  Sum_probs=36.2

Q ss_pred             CCCeEEEEEecC------ccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           47 AQDVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        47 ~~~~~~rilVP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      +..++-++.||.      ++||+|||+.|.|.|+|+..|+|+|-|--.
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            346777888885      569999999999999999999999999743

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.99  E-value=0.012  Score=51.33  Aligned_cols=62  Identities=27%  Similarity=0.393  Sum_probs=47.6

Q ss_pred             EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      +.+.||.+.++.+||++|.+|+.|.+++++.|.+-.      +..|-|.+...    ..+.+|..+|..+-.
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~----~~~~~a~~~I~~~e~  208 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDE----EDEEIAIEAIKKIER  208 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCH----HHHHHHHHHHHHHHh
Confidence            457789999999999999999999999999999864      35688888753    234555555554433

>PRK00106 hypothetical protein; Provisional

Probab=95.97  E-value=0.021  Score=55.45  Aligned_cols=50  Identities=26%  Similarity=0.530  Sum_probs=40.9

Q ss_pred             CCeEEEEEecC-ccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccC
Q 025112           48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK  102 (257)
Q Consensus        48 ~~~~~rilVP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~  102 (257)
                      ..++-.+.+|+ +.-|+||||.|.||+.|+.-|||.|-|++.    ++ .|+|+|.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt----p~-~v~lS~f  273 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT----PE-VVVLSGF  273 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC----CC-eEEEeCC
Confidence            34566777898 558999999999999999999999999964    34 4668885

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

Probab=95.82  E-value=0.025  Score=54.43  Aligned_cols=99  Identities=19%  Similarity=0.204  Sum_probs=72.7

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +.++..|..+|++.+.+...+.-...    .........+-++.+....+||++|-+.|+|..+||+.-.+         
T Consensus       566 l~~a~~ar~~Il~~m~k~i~~Pr~~~----~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------  632 (760)
T KOG1067|consen  566 LQKAREARLQILDIMEKNINSPRGSD----KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------  632 (760)
T ss_pred             HHhhhHHHHHHHHHHHhhcCCcccCc----cccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------
Confidence            44667777888888876543321111    11234567888999999999999999999999999943333         


Q ss_pred             cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCCCCC
Q 025112          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRENPPRQ  224 (257)
Q Consensus       188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~~~~  224 (257)
                           ++..++|.- ++...++|.+.|..++......+
T Consensus       633 -----De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~  665 (760)
T KOG1067|consen  633 -----DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQD  665 (760)
T ss_pred             -----cCceEEEEecCHHHHHHHHHHHHHHhcCccccc
Confidence                 345677776 57799999999999998866654

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

Probab=95.82  E-value=0.014  Score=51.39  Aligned_cols=51  Identities=16%  Similarity=0.249  Sum_probs=45.5

Q ss_pred             ceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       155 G~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      -+|||++|++++.|+--|.|.|-|.              ...|.+.|....+..+...+.+++..
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVq--------------G~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQ--------------GNTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEee--------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence            4799999999999999999999883              36699999999999999999888875

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.71  E-value=0.0073  Score=60.54  Aligned_cols=65  Identities=34%  Similarity=0.507  Sum_probs=51.0

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      -...+.||.+.++.+||+||.+||.|.++||++|++.+      +..|.|.+...    ..+.+|..+|..+..+
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~----~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDG----EAAEAAKERIEGITAE  618 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccH----HHHHHHHHHHHHhccc
Confidence            34566679999999999999999999999999988864      34577777653    3567777777777653

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

Probab=95.66  E-value=0.014  Score=41.85  Aligned_cols=31  Identities=32%  Similarity=0.493  Sum_probs=27.4

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHH
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNS  171 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~  171 (257)
                      ....+++.+.....|+||||+|.+|+.||.-
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            3457899999999999999999999999853

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=95.26  E-value=0.017  Score=46.37  Aligned_cols=38  Identities=26%  Similarity=0.435  Sum_probs=34.1

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA   86 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~   86 (257)
                      +..+.+.|+.+..|..|||+|.|++.+++-++-+++|.
T Consensus        98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            45677889999999999999999999999999888775

>PRK12705 hypothetical protein; Provisional

Probab=95.26  E-value=0.05  Score=52.49  Aligned_cols=65  Identities=22%  Similarity=0.293  Sum_probs=46.5

Q ss_pred             eEEEEEeecC-ccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAGS-QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~~-~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e  219 (257)
                      ....+.+|++ +-|+|||+.|.||+.+...||+.+.|.   +         +...|.|.+ +|..-+.|...+..+|.+
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d---------tp~~V~ls~fdp~rreia~~~l~~Li~d  264 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---D---------TPEAVVISSFNPIRREIARLTLEKLLAD  264 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---C---------CccchhhcccCccchHHHHHHHHHHHhc
Confidence            3455667874 669999999999999999999999983   2         334466666 444555566666555554

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=95.26  E-value=0.011  Score=41.70  Aligned_cols=36  Identities=17%  Similarity=0.348  Sum_probs=30.4

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCce
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT   82 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~   82 (257)
                      .+...+.+.+..+..|.+|||+|.+++.||.-.+.-
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~   61 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAA   61 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHH
Confidence            456678888899999999999999999999876543

>PRK01064 hypothetical protein; Provisional

Probab=95.20  E-value=0.024  Score=40.82  Aligned_cols=31  Identities=26%  Similarity=0.420  Sum_probs=27.5

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHH
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNS  171 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~  171 (257)
                      ....+++.+.....|++|||+|.+|+.||.-
T Consensus        28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            3467889999999999999999999999864

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

Probab=95.02  E-value=0.041  Score=37.40  Aligned_cols=35  Identities=29%  Similarity=0.462  Sum_probs=29.0

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceE
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI   83 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I   83 (257)
                      ...+.+.+.....|.+||++|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45666777776799999999999999999988544

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

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

Probab=94.77  E-value=0.024  Score=39.91  Aligned_cols=38  Identities=34%  Similarity=0.552  Sum_probs=30.7

Q ss_pred             EEEEEecCcc-----ccceeccCchhHHHHHhhh-CceEEEccc
Q 025112           51 LFRIIVPSRQ-----IGKVIGKEGHRIQKIREET-KATIKIADA   88 (257)
Q Consensus        51 ~~rilVP~~~-----vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~   88 (257)
                      ..++.|-+..     +|..||++|..|+.|.++. |-+|++-..
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            3577778877     9999999999999999999 889888754

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

Probab=94.00  E-value=0.025  Score=58.50  Aligned_cols=73  Identities=19%  Similarity=0.139  Sum_probs=58.5

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ....-++.+|-..++++||++|.+|+.++.-||+.|.+..- ..+-.||.+.+.|.++     ..+-|-..|...+.+.
T Consensus      1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~-----~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPP-----SQRVATSPIGLPIIDP 1411 (2131)
T ss_pred             cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCCh-----hhhhhhccccceeecC
Confidence            45667889999999999999999999999999999999974 3345799999999976     4455555565555543

>PRK12705 hypothetical protein; Provisional

Probab=93.75  E-value=0.11  Score=50.26  Aligned_cols=40  Identities=28%  Similarity=0.442  Sum_probs=33.9

Q ss_pred             CeEEEEEecCc-cccceeccCchhHHHHHhhhCceEEEccc
Q 025112           49 DVLFRIIVPSR-QIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        49 ~~~~rilVP~~-~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      .++-.+-+|++ .-|+||||.|.|||.++..||+.|.|++.
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt  237 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT  237 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence            34556667774 58999999999999999999999999964

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

Probab=93.53  E-value=0.04  Score=57.06  Aligned_cols=71  Identities=23%  Similarity=0.205  Sum_probs=59.2

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ..-++.+|-....+|||++|++|+.++..||+.|++..-.  +.    ...+|.+.+.|.++.+.-|...|.-.+.+
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~----Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD----NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc----cchhhhcccCCCChhhhhhhccccceeec
Confidence            3566788888899999999999999999999999986411  22    25789999999999999998888766665

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.12  E-value=0.062  Score=37.88  Aligned_cols=32  Identities=38%  Similarity=0.547  Sum_probs=27.8

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA  174 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga  174 (257)
                      ..+.+.+..+..|.||||.|.+++.||--.+.
T Consensus        29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             eEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            47888899999999999999999999965543

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=93.10  E-value=0.054  Score=38.62  Aligned_cols=35  Identities=40%  Similarity=0.608  Sum_probs=29.8

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEE
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK   84 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~   84 (257)
                      ..+.+.+..++.|.+||++|++|++|+++.+-.+.
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            45788899999999999999999999888755543

; 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 ....

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=93.05  E-value=0.13  Score=42.33  Aligned_cols=46  Identities=20%  Similarity=0.304  Sum_probs=37.6

Q ss_pred             cccCCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           42 KRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        42 ~~~~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      ..++...+-.+-|+|-... |..|||+|.+|+++++..|-+|.+-+.
T Consensus        53 ~~k~~~~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         53 YKKAYEVDDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             EEEEEEeCCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            3444444566778888788 999999999999999999999998864

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

Probab=92.89  E-value=0.11  Score=36.53  Aligned_cols=37  Identities=19%  Similarity=0.434  Sum_probs=30.7

Q ss_pred             EEEEEeecCc-----cceeecCCChhHHHHHHHh-CCeEEEeC
Q 025112          144 TIRLLIAGSQ-----AGCLIGMSGQNIEKLRNSS-GATIVILA  180 (257)
Q Consensus       144 ~~~l~Vp~~~-----vG~iIGk~G~~Ik~I~~~t-ga~I~i~~  180 (257)
                      ...+.|-+..     +|..||++|++|+.|.++. |-+|++..
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            4567777777     8999999999999999999 99999874

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

Probab=92.58  E-value=0.22  Score=33.66  Aligned_cols=34  Identities=32%  Similarity=0.459  Sum_probs=26.8

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeE
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI  176 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I  176 (257)
                      ....+.+.....|.+||++|.+++.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            3455666665689999999999999999887544

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=92.52  E-value=0.13  Score=36.73  Aligned_cols=35  Identities=17%  Similarity=0.373  Sum_probs=28.6

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEE
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI   85 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i   85 (257)
                      .+.+.+.....|.+|||+|+++..||--.+.-++-
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            45666778899999999999999999887755543

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.

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

Probab=92.32  E-value=0.28  Score=42.60  Aligned_cols=66  Identities=20%  Similarity=0.244  Sum_probs=50.5

Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHH-HHHHHHHHHHHHHhcCCCC
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP-AVLNALVEIGNQLRENPPR  223 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~-~v~~A~~~I~~~l~e~~~~  223 (257)
                      .-+.|+...|.++||++|+.++-|.+.++|.|.+-.             .-.|-|.|..+ ....|...|..+=+|+...
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-------------NG~IWV~~~~~~~e~~~~~aI~~ie~ea~~~  214 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-------------NGRIWVDGENESLEELAIEAIRKIEREAHTS  214 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-------------CCEEEecCCCcchHHHHHHHHHHHhhhhhhh
Confidence            457899999999999999999999999999999842             35577777766 4556666666655554433

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=91.60  E-value=0.3  Score=39.26  Aligned_cols=37  Identities=22%  Similarity=0.536  Sum_probs=33.7

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~  180 (257)
                      ..-++|....+|..||++|++|+.|++..|-+|.+..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe   70 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE   70 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence            5678899999999999999999999999999999863

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.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=91.40  E-value=0.14  Score=36.46  Aligned_cols=35  Identities=34%  Similarity=0.564  Sum_probs=29.3

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEE
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV  177 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~  177 (257)
                      ....+.+..++-|.+||++|++|++|....+-.+.
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            35788899999999999999999999876655553

; 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 ....

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=91.31  E-value=0.2  Score=42.31  Aligned_cols=37  Identities=27%  Similarity=0.416  Sum_probs=35.2

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (257)
                      ...+.||.+..+..|||+|.|++.+.+-||-+++|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            7888999999999999999999999999999999984

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

Probab=91.18  E-value=0.15  Score=48.44  Aligned_cols=40  Identities=35%  Similarity=0.482  Sum_probs=35.7

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      +-...+.||..+++.+|||+|.+|++|++..|.+|+|...
T Consensus       485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            4456788899999999999999999999999999999743

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

Probab=90.98  E-value=1.8  Score=34.86  Aligned_cols=95  Identities=14%  Similarity=0.291  Sum_probs=63.9

Q ss_pred             eccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceE
Q 025112           65 IGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANT  144 (257)
Q Consensus        65 IGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~  144 (257)
                      +=.+|.-|++|-++..-+|.|-...     .   +.-        +-.+|.+.|.+++-++..-..-..       +..+
T Consensus        21 ~~~~~dli~~lAk~lrKRIvvR~dp-----s---~l~--------~~e~A~~~I~~ivP~ea~i~di~F-------d~~t   77 (145)
T cd02410          21 FAEDGDLVKDLAKDLRKRIVIRPDP-----S---VLK--------PPEEAIKIILEIVPEEAGITDIYF-------DDDT   77 (145)
T ss_pred             HhcccHHHHHHHHHHhceEEEcCCh-----h---hcC--------CHHHHHHHHHHhCCCccCceeeEe-------cCCC
Confidence            3456778888888888777775221     0   111        124688888888854422110000       0124


Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~  182 (257)
                      -++.|-...-|.+||++|.++++|..+||-.-.+.+..
T Consensus        78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            57788888889999999999999999999999987643

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=90.75  E-value=0.28  Score=45.55  Aligned_cols=41  Identities=24%  Similarity=0.244  Sum_probs=37.2

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      ......+.||.+..+..|||+|.|++-..+-||.+|+|-..
T Consensus       306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence            44578899999999999999999999999999999999843

>TIGR01953 NusA transcription termination factor NusA

Probab=90.58  E-value=0.29  Score=45.01  Aligned_cols=40  Identities=23%  Similarity=0.361  Sum_probs=36.7

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (257)
                      ......+.||.+..+..|||+|.|++...+-||.+|+|-.
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            3467899999999999999999999999999999999974

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.

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=90.04  E-value=2  Score=36.36  Aligned_cols=66  Identities=18%  Similarity=0.234  Sum_probs=55.8

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~  221 (257)
                      .+.+.++....-.+...+|..+++|....||+|.+.            .....+.|+|+...+..+...|.++++...
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~------------~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~   92 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS------------RSENRIRITGTKSTAEYIEASINEILSNIR   92 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEe------------cCCcEEEEEccHHHHHHHHHHHHHHHhhcE
Confidence            455666788888999999999999988899999985            346789999999999999999988887643

>PRK13764 ATPase; Provisional

Probab=90.03  E-value=0.24  Score=48.93  Aligned_cols=41  Identities=37%  Similarity=0.528  Sum_probs=36.7

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      .+....+.||...++.+|||+|.+|++|++..|.+|+|-..
T Consensus       479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            45567788999999999999999999999999999999743

>PRK13764 ATPase; Provisional

Probab=90.02  E-value=0.51  Score=46.66  Aligned_cols=44  Identities=20%  Similarity=0.348  Sum_probs=39.0

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP  185 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p  185 (257)
                      .....+.||...++.+|||+|.+|++|.++.|.+|.|-+.++.+
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            34688999999999999999999999999999999998765543

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

Probab=89.80  E-value=0.22  Score=42.02  Aligned_cols=56  Identities=32%  Similarity=0.440  Sum_probs=47.3

Q ss_pred             CccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           58 SRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        58 ~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      +..+|+|+||+|.+--.|+..|..+|.+.+.       .+.|-|.     +++++-|...|+.+|...
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~-----~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGA-----FQNIRIARDAVCSLILGS  232 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeec-----chhhHHHHHhhHhhhccC
Confidence            4569999999999999999999999999854       3778787     457888888899998765

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

Probab=89.78  E-value=0.36  Score=34.95  Aligned_cols=37  Identities=19%  Similarity=0.412  Sum_probs=30.9

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEc
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA   86 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~   86 (257)
                      ..+++.|....-|.+||++|++|++|+++-.-...+.
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            3478888999999999999999999999876555554

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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=89.50  E-value=0.42  Score=34.05  Aligned_cols=34  Identities=26%  Similarity=0.509  Sum_probs=27.6

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEE
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV  177 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~  177 (257)
                      ...+.+.....|.+|||.|.+++.||--.+.-++
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            4677788889999999999999999976654443

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.

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

Probab=89.37  E-value=0.3  Score=46.48  Aligned_cols=41  Identities=15%  Similarity=0.243  Sum_probs=37.0

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ  183 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~  183 (257)
                      ....+.||...++.+|||+|.+|++|+++.|.+|.+.+.+.
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            46789999999999999999999999999999999976543

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=88.69  E-value=0.5  Score=43.85  Aligned_cols=42  Identities=29%  Similarity=0.402  Sum_probs=37.8

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      +......+.||.+..+..|||+|.|++--.+-||.+|+|...
T Consensus       300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            344678999999999999999999999999999999999854

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=88.41  E-value=0.41  Score=45.98  Aligned_cols=39  Identities=26%  Similarity=0.392  Sum_probs=36.3

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (257)
                      ...+.+.||....+..|||+|.|++...+-||.+|.|-.
T Consensus       301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            358899999999999999999999999999999999974

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

Probab=87.19  E-value=1  Score=43.74  Aligned_cols=68  Identities=26%  Similarity=0.272  Sum_probs=50.5

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      .......+.|+.+....+||.+|...|+|+.|||+.-.++       |..+.|-.+..    ....+|...|..++...
T Consensus       594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~----~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQ----AAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             cCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCH----HHHHHHHHHHHHHhcCc
Confidence            4567889999999999999999999999999999544444       44566766542    24456666666666543

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=86.97  E-value=0.58  Score=44.32  Aligned_cols=41  Identities=29%  Similarity=0.433  Sum_probs=37.0

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      ......+.||.+..+..|||+|.|++--.+-||.+|+|.+.
T Consensus       333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~  373 (449)
T PRK12329        333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS  373 (449)
T ss_pred             CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence            44567899999999999999999999999999999999843

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=86.71  E-value=1.1  Score=36.96  Aligned_cols=36  Identities=19%  Similarity=0.340  Sum_probs=31.5

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~  180 (257)
                      ..-++|-... |..||++|.+++++++..|-+|.+..
T Consensus        62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            4667777777 99999999999999999999999873

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

Probab=86.30  E-value=0.68  Score=35.38  Aligned_cols=30  Identities=30%  Similarity=0.572  Sum_probs=26.0

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhC
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETK   80 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg   80 (257)
                      .+++.|-...-|.|||++|++|++|++...
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~   91 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ   91 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence            367888888999999999999999988754

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.

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

Probab=86.22  E-value=1.7  Score=41.95  Aligned_cols=98  Identities=16%  Similarity=0.296  Sum_probs=68.8

Q ss_pred             cceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCc
Q 025112           62 GKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVA  141 (257)
Q Consensus        62 g~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~  141 (257)
                      ..++=++|.-||+|-++..-+|.|-....      +          +.+-.+|.+.|.+++-++..-..-..       .
T Consensus        41 P~~~~~~~dlik~lAk~lrKRI~iR~dPs------v----------l~~~e~A~~~I~eivP~ea~i~~i~F-------d   97 (637)
T COG1782          41 PELFAKDGDLIKDLAKDLRKRIIIRPDPS------V----------LKPPEEARKIILEIVPEEAGITDIYF-------D   97 (637)
T ss_pred             HHHhccchhHHHHHHHHHhhceEeccCch------h----------cCCHHHHHHHHHHhCccccCceeEEe-------c
Confidence            34566788999999999988888763210      0          11335788888888855432111000       0


Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~  182 (257)
                      ..+-+++|-...=|.+|||+|++.++|..+||-.-+|.+..
T Consensus        98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P  138 (637)
T COG1782          98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP  138 (637)
T ss_pred             CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence            12457888888899999999999999999999988887643

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

Probab=85.89  E-value=0.83  Score=33.20  Aligned_cols=28  Identities=29%  Similarity=0.484  Sum_probs=23.8

Q ss_pred             EEEEecCccccceeccCchhHHHHHhhh
Q 025112           52 FRIIVPSRQIGKVIGKEGHRIQKIREET   79 (257)
Q Consensus        52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~t   79 (257)
                      +++.|....-|.+||++|++|++|++.-
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            5666666899999999999999998774

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.

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

Probab=85.85  E-value=2.6  Score=36.69  Aligned_cols=46  Identities=22%  Similarity=0.489  Sum_probs=38.7

Q ss_pred             EEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCC
Q 025112           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN  104 (257)
Q Consensus        53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~  104 (257)
                      -+.|++..+-++||++|+.++.|.++++|.|-+-.      +..+-|.+..+
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~------NG~IWV~~~~~  194 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ------NGRIWVDGENE  194 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec------CCEEEecCCCc
Confidence            46789999999999999999999999999999863      23467777765

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

Probab=85.79  E-value=1.2  Score=32.15  Aligned_cols=36  Identities=14%  Similarity=0.312  Sum_probs=29.0

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEE
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i  178 (257)
                      ...++.|....-|.+||++|+.|++|++.-.-...+
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            357888888899999999999999998766444443

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.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=84.27  E-value=1.2  Score=42.87  Aligned_cols=125  Identities=12%  Similarity=0.053  Sum_probs=74.7

Q ss_pred             ceeccCchhHHHHHhhhCceEEEc--ccccCCCccEEE-eccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCC
Q 025112           63 KVIGKEGHRIQKIREETKATIKIA--DAIARHEERVII-ISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGH  139 (257)
Q Consensus        63 ~IIGk~G~~Ik~I~~~tg~~I~i~--~~~~~~~ervv~-I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~  139 (257)
                      +|=||+--.+.+|++...|-+.+.  +.   .+.++.+ +.|..-     +-++++..+   ..+.              
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~---~gs~~~~~~~g~~~-----~F~k~~~~~---~~EF--------------  447 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSS---TGSIVETNGIGEKM-----SFSKKLSIP---PTEF--------------  447 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEec---CCcEEEEeccCcch-----hhHHHhcCC---cccC--------------
Confidence            677886666999999999985544  33   2224443 344321     112222111   0111              


Q ss_pred             CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCce-EEEEEcCH---HHHHHHHHHHHH
Q 025112          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR-VVQISGDV---PAVLNALVEIGN  215 (257)
Q Consensus       140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r-~V~I~G~~---~~v~~A~~~I~~  215 (257)
                        .-...+.||...|..|||-||..|.+++.+.++.|++...-.++.     +.-+ .|.|.-..   +++.-+.--+++
T Consensus       448 --pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q-----s~~~dNV~I~~PrKn~~ni~~~KNd~~~  520 (657)
T COG5166         448 --PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ-----SQWHDNVLIEAPRKNQDNISGKKNDKLD  520 (657)
T ss_pred             --chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch-----hhhhcceEEECCccCccchhcccccHHH
Confidence              124788999999999999999999999999999999764333333     2222 24444432   234444445555


Q ss_pred             HHhc
Q 025112          216 QLRE  219 (257)
Q Consensus       216 ~l~e  219 (257)
                      ++++
T Consensus       521 ~V~~  524 (657)
T COG5166         521 KVKQ  524 (657)
T ss_pred             HHhh
Confidence            5553

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

Probab=84.10  E-value=1.4  Score=35.48  Aligned_cols=37  Identities=30%  Similarity=0.459  Sum_probs=32.2

Q ss_pred             EEEecCccccceeccCchhHHHHHhhhCceEEEcccc
Q 025112           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI   89 (257)
Q Consensus        53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~   89 (257)
                      .+.|-...-|.+||++|.++++|..+||-+-.+.+..
T Consensus        79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            5666778899999999999999999999888887654

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.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=81.79  E-value=1.9  Score=41.58  Aligned_cols=129  Identities=12%  Similarity=0.150  Sum_probs=80.8

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc--ccCCCcc-EEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEER-VIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~--~~~~~er-vv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      -.+.|.||...|..|||-||..|.+++.+.++.|++...  .+.+--+ -|.|..+.++..  .+--+...+.+++.+.+
T Consensus       449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~--ni~~~KNd~~~~V~~~c  526 (657)
T COG5166         449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQD--NISGKKNDKLDKVKQQC  526 (657)
T ss_pred             hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCcc--chhcccccHHHHHhhhc
Confidence            356789999999999999999999999999999998843  1222222 266766555422  22233334444444333


Q ss_pred             CCCchh---------------------hhhccC----CCcceEEEEEeecCccceeec---CCChhHHHHHHHhCCeEEE
Q 025112          127 DSNSEA---------------------SKVAAG----HVAANTIRLLIAGSQAGCLIG---MSGQNIEKLRNSSGATIVI  178 (257)
Q Consensus       127 ~~~~~~---------------------~~~~~~----~~~~~~~~l~Vp~~~vG~iIG---k~G~~Ik~I~~~tga~I~i  178 (257)
                      ..+...                     +.+...    ........+.+|+..++..+|   -.|++|..+.....-.|..
T Consensus       527 ~f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~  606 (657)
T COG5166         527 RFNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEF  606 (657)
T ss_pred             ccccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhcccee
Confidence            211100                     000000    011234556788888999999   6788888888888888876


Q ss_pred             eC
Q 025112          179 LA  180 (257)
Q Consensus       179 ~~  180 (257)
                      ..
T Consensus       607 ~~  608 (657)
T COG5166         607 ST  608 (657)
T ss_pred             ec
Confidence            53

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

Probab=81.17  E-value=1.4  Score=38.28  Aligned_cols=31  Identities=35%  Similarity=0.529  Sum_probs=27.0

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhh
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t   79 (257)
                      ...+++.|....-|.|||++|++|++|++..
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l   80 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL   80 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence            4567888999999999999999999987763

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

Probab=80.91  E-value=3.3  Score=36.91  Aligned_cols=25  Identities=20%  Similarity=0.385  Sum_probs=23.9

Q ss_pred             cceeccCchhHHHHHhhhCceEEEc
Q 025112           62 GKVIGKEGHRIQKIREETKATIKIA   86 (257)
Q Consensus        62 g~IIGk~G~~Ik~I~~~tg~~I~i~   86 (257)
                      -++||.+|+|+|.|+=-|+|.|-|.
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVq  185 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQ  185 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEee
Confidence            5799999999999999999999998

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

Probab=80.54  E-value=5.2  Score=39.94  Aligned_cols=97  Identities=14%  Similarity=0.274  Sum_probs=65.7

Q ss_pred             ceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcc
Q 025112           63 KVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAA  142 (257)
Q Consensus        63 ~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~  142 (257)
                      ..+=.+|..||+|-++..-+|.|-...     .   +.-        +-.+|.+.|.+++-++..-..-..       +.
T Consensus        36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~-----~---~~~--------~~~~~~~~i~~~~~~~~~~~~~~f-------~~   92 (630)
T TIGR03675        36 ELFAKDDDLVKELAKKLRKRIVIRPDP-----S---VLL--------PPEEAIEKIKEIVPEEAGITDIYF-------DD   92 (630)
T ss_pred             HHhccchHHHHHHHHHhhceEEEecCh-----h---hcC--------CHHHHHHHHHHhCCCcCCceeEEe-------cC
Confidence            344567788888888888777775221     0   111        124677888888755422110000       01


Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~  182 (257)
                      .+-+++|-...-|.|||++|+++++|..+||-.-.+.+..
T Consensus        93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~  132 (630)
T TIGR03675        93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP  132 (630)
T ss_pred             CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence            2457888888899999999999999999999999987643

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.

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

Probab=80.50  E-value=2.1  Score=31.01  Aligned_cols=29  Identities=28%  Similarity=0.469  Sum_probs=23.6

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHh
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSS  172 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t  172 (257)
                      ..++.|....-|.+||++|++|++|++.-
T Consensus        39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          39 GTQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             cEEEEEEECCCCceECCCchhHHHHHHHH
Confidence            36667777888999999999999987543

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	257
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		4e-08
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		9e-05
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		2e-04
2axy_A	73	Crystal Structure Of Kh1 Domain Of Human Poly(C)-Bi		3e-04
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		3e-04

>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains Length = 160

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 86/165 (52%), Gaps = 21/165 (12%)
Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDA 111
            R+++  +++G +IGK+G  ++K+REE               ER+I ++   N       
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN------- 57
Query: 112 ENALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKL 168
             A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+++
Sbjct: 58  --AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIKEI 114
Query: 169 RNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213
           R S+GA + + A + LP     + ++R + I+G   +++  + +I
Sbjct: 115 RESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQI 153

>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains Length = 160

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 14/96 (14%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I         +  +  +R++ ++G  
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---------SEGNCPERIITLAGPT 56
Query: 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRP 239
            A+  A   I ++L E+     IS S   + +A RP
Sbjct: 57  NAIFKAFAMIIDKLEED-----ISSSMTNSTAASRP 87

>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 = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++++R  SGA I I         +  +  +R++ ++G  
Sbjct: 4   TIRLLMHGKEVGSIIGKKGESVKRIREESGARINI---------SEGNSPERIITLTGPT 54
Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 55  NAIFKAFAMIIDKLEED 71

>pdb|2AXY|A Chain A, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding Protein-2 With C-Rich Strand Of Human Telomeric Dna Length = 73

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL  G + G +IG  G++++K R  SGA I I   N    C      +R++ ++G  
Sbjct: 6   TIRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGN----CP-----ERIITLAGPT 56
Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 57  NAIFKAFAXIIDKLEED 73

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++++R  SGA I I   N    C      +R++ ++G  
Sbjct: 4   TIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN----CP-----ERIITLTGPT 54
Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 55  NAIFKAFAMIIDKLEED 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	257
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-34
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-09
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-08
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-33
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	4e-09
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-29
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	8e-12
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-29
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-26
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	9e-10
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	6e-14
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	8e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-09
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	8e-11
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-09
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	4e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	5e-08
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-09
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-08
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	9e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-08
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	1e-08
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-08
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	9e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	9e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-08
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-07
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-05
1we8_A	104	Tudor and KH domain containing protein; structural	6e-08
1we8_A	104	Tudor and KH domain containing protein; structural	2e-05
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	8e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	4e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	4e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	9e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-05
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	6e-05
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	8e-05
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	8e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	1e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	2e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	2e-04
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	5e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	6e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	6e-04

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

 Score =  121 bits (304), Expect = 2e-34
 Identities = 43/180 (23%), Positives = 84/180 (46%), Gaps = 10/180 (5%)

Query: 47  AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIISSKD 103
                 ++++PS   G +IGK G  I ++++ET ATIK++   D      ERV +I    
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 104 N--DNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMS 161
              + V       ++++   + K +  +    +       AN +++++  S AG +IG  
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122

Query: 162 GQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221
           G  ++ +   SGA + +   +Q P   +     RVV +SG+      A+  I  +++E+P
Sbjct: 123 GATVKAIMEQSGAWVQL---SQKPDGINLQN--RVVTVSGEPEQNRKAVELIIQKIQEDP 177

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

 Score = 53.3 bits (128), Expect = 5e-09
 Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
            +++LI    AG +IG  GQ I +L+  +GATI +              ++RV  I G +
Sbjct: 7   FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFY----PGTTERVCLIQGTI 62

Query: 204 PAVLNALVEIGNQLRENPPRQ 224
            A+      I  ++RE P   
Sbjct: 63  EALNAVHGFIAEKIREMPQNV 83

>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 = 52.2 bits (125), Expect = 1e-08
 Identities = 19/105 (18%), Positives = 43/105 (40%), Gaps = 7/105 (6%)

Query: 24  DVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83
           ++     + +              +    +IIVP+   G +IGK G  ++ I E++ A +
Sbjct: 78  EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWV 137

Query: 84  KIA--DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126
           +++        + RV+ +S  + +        A++ I   I +D 
Sbjct: 138 QLSQKPDGINLQNRVVTVSG-EPEQN----RKAVELIIQKIQEDP 177

>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 =  116 bits (293), Expect = 5e-33
 Identities = 46/174 (26%), Positives = 90/174 (51%), Gaps = 15/174 (8%)

Query: 46  KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND 105
           K   +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++     
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGP--- 55

Query: 106 NVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNI 165
              +    A   I   + +D  S+   S  A+      T+RL++  SQ G LIG  G  I
Sbjct: 56  --TNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPV--TLRLVVPASQCGSLIGKGGCKI 111

Query: 166 EKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
           +++R S+GA + + A + LP     + ++R + I+G   +++  + +I   + E
Sbjct: 112 KEIRESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLE 159

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

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 9/79 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I         +  +  +R++ ++G  
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---------SEGNCPERIITLAGPT 56

Query: 204 PAVLNALVEIGNQLRENPP 222
            A+  A   I ++L E+  
Sbjct: 57  NAIFKAFAMIIDKLEEDIS 75

>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 = 53.2 bits (128), Expect = 4e-09
 Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 32  EDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIA 90
           E+           A    V  R++VP+ Q G +IGK G +I++IRE T A +++A D + 
Sbjct: 71  EEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP 130

Query: 91  RHEERVIIISSKDNDNVVSDAENALQQIAALIL 123
              ER I I+     ++       ++QI  ++L
Sbjct: 131 NSTERAITIAG-IPQSI----IECVKQICVVML 158

>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 =  108 bits (271), Expect = 2e-29
 Identities = 33/179 (18%), Positives = 61/179 (34%), Gaps = 22/179 (12%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
             + +P   +G VIG+ G  I+KI+ +    I+         ER+  I+          A
Sbjct: 5   IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-----PDRA 59

Query: 112 ENALQQIAALILKDDDSNSEASKVAA-------------GHVAANTIRLLIAGSQAGCLI 158
           ++A + I  L+      N                               ++   + G +I
Sbjct: 60  QHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLII 119

Query: 159 GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217
           G  G+ I+ +   SGA I +      P  A    + ++  I G    +  A   I  ++
Sbjct: 120 GKGGETIKSISQQSGARIEL--QRNPPPNAD--PNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 61.0 bits (148), Expect = 8e-12
 Identities = 22/115 (19%), Positives = 39/115 (33%), Gaps = 7/115 (6%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
           + I + I     G +IG +G+ I+K++N +G  I     +           +R+ QI+G 
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-------GTTPERIAQITGP 55

Query: 203 VPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGQPLLQLTM 257
                +A   I + LR           P             + P  G       +
Sbjct: 56  PDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIV 110

>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 = 51.8 bits (124), Expect = 2e-08
 Identities = 18/112 (16%), Positives = 37/112 (33%), Gaps = 8/112 (7%)

Query: 14  SVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQ 73
            ++   +  +                +           F  IVP+ + G +IGK G  I+
Sbjct: 68  DLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIK 127

Query: 74  KIREETKATIKIADAIARHE---ERVIIISSKDNDNVVSDAENALQQIAALI 122
            I +++ A I++      +     ++  I       +    + A Q I   I
Sbjct: 128 SISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQI----DYARQLIEEKI 174

>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 =  107 bits (269), Expect = 3e-29
 Identities = 36/178 (20%), Positives = 77/178 (43%), Gaps = 18/178 (10%)

Query: 48  QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARH-EERVIIISSKDNDN 106
           +  + ++ +P++ +G +IGK+G  I+++     A+IKIA       + R++II+      
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPE-- 58

Query: 107 VVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIE 166
                  A  +I   + +++    +               + +  S AG +IG  G+ + 
Sbjct: 59  ---AQFKAQGRIYGKLKEENFFGPKEE-------VKLETHIRVPASAAGRVIGKGGKTVN 108

Query: 167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ 224
           +L+N + A +V+   +Q P          +V+I G   A   A  +I + L +   + 
Sbjct: 109 ELQNLTAAEVVV-PRDQTP----DENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQH 161

>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 = 50.5 bits (121), Expect = 4e-08
 Identities = 16/97 (16%), Positives = 40/97 (41%), Gaps = 5/97 (5%)

Query: 36  IEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEE 94
           ++  +     +   +   I VP+   G+VIGK G  + +++  T A + +  D      +
Sbjct: 71  LKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDEND 130

Query: 95  RVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSE 131
           +VI+             + A ++I  ++ +    + +
Sbjct: 131 QVIVKIIGHFYAS----QMAQRKIRDILAQVKQQHQK 163

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

 Score = 99.9 bits (249), Expect = 2e-26
 Identities = 30/170 (17%), Positives = 67/170 (39%), Gaps = 15/170 (8%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDNDNVVS 109
             I++P+ + G VIGK G  I++++E     + +        + ++ + I          
Sbjct: 4   QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD-----PY 58

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
             + A + +  ++ ++ D      +   G      I + +     G +IG SG+ I+K++
Sbjct: 59  KVQQACEMVMDIL-RERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQ 117

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
           N +G  I     +           +++  I G      +A   I + L+ 
Sbjct: 118 NDAGVRIQFKQDD-------GTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

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

 Score = 56.3 bits (136), Expect = 3e-10
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201
                ++I   +AG +IG  G+ I++L+  +G  ++++              D+ ++I G
Sbjct: 1   GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTN-----VDKPLRIIG 55

Query: 202 DVPAVLNALVEIGNQLRENPPRQ 224
           D   V  A   + + LRE     
Sbjct: 56  DPYKVQQACEMVMDILRERDQGG 78

>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 = 9e-10
 Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 4/89 (4%)

Query: 31  REDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90
           RE  +    D             + VP   +G VIG+ G  I+KI+ +    I+      
Sbjct: 72  RERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG 131

Query: 91  RHEERVIIIS-SKDNDNVVSDAENALQQI 118
              E++  I    D       A   +  +
Sbjct: 132 TGPEKIAHIMGPPDR---CEHAARIINDL 157

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

 Score = 64.2 bits (157), Expect = 6e-14
 Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 9/77 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I         +  +  +R++ ++G  
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---------SEGNCPERIITLAGPT 56

Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 57  NAIFKAFAMIIDKLEED 73

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

 Score = 57.3 bits (139), Expect = 2e-11
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 46  KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND 105
           K   +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++     
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGP--- 55

Query: 106 NVVSDAENALQQIAALILKD 125
              +    A   I   + +D
Sbjct: 56  --TNAIFKAFAMIIDKLEED 73

>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 = 56.2 bits (136), Expect = 8e-11
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 7/77 (9%)

Query: 47  AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKDND 105
              +  ++ +P    G +IGK G RI++IR E+ A+IKI + +   E+R+I I+ ++D  
Sbjct: 11  GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ- 69

Query: 106 NVVSDAENALQQIAALI 122
                 +NA   +   +
Sbjct: 70  -----IQNAQYLLQNSV 81

>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 = 52.3 bits (126), Expect = 2e-09
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T ++ I    AG +IG  GQ I+++R+ SGA+I I  P            DR++ I+G  
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-------LEGSEDRIITITGTQ 67

Query: 204 PAVLNALVEIGNQLRENPPRQ 224
             + NA   + N +++   + 
Sbjct: 68  DQIQNAQYLLQNSVKQYSGKF 88

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

 Score = 56.1 bits (136), Expect = 8e-11
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 7/79 (8%)

Query: 45  AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKD 103
           A    +  ++ +P    G +IGK G RI++IR E+ A+IKI + +   E+R+I I+ ++D
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 61

Query: 104 NDNVVSDAENALQQIAALI 122
                   +NA   +   +
Sbjct: 62  Q------IQNAQYLLQNSV 74

>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 = 51.5 bits (124), Expect = 3e-09
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T ++ I    AG +IG  GQ I+++R+ SGA+I I  P            DR++ I+G  
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-------LEGSEDRIITITGTQ 60

Query: 204 PAVLNALVEIGNQLRENPPRQ 224
             + NA   + N +++   + 
Sbjct: 61  DQIQNAQYLLQNSVKQYSGKF 81

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

 Score = 53.8 bits (130), Expect = 4e-10
 Identities = 19/55 (34%), Positives = 34/55 (61%)

Query: 46  KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS 100
           KAQ     + +P+  IG +IG++G +I +IR+ + A IKIA+ +    +R + I+
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTIT 55

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

 Score = 48.1 bits (115), Expect = 5e-08
 Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           +  L I     GC+IG  G  I ++R  SGA I I  P           +DR V I+G  
Sbjct: 6   SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-------VEGSTDRQVTITGSA 58

Query: 204 PAVLNALVEIGNQLRE 219
            ++  A   I  +L  
Sbjct: 59  ASISLAQYLINVRLSS 74

>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 = 52.7 bits (127), Expect = 1e-09
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKDNDNVVSDA 111
            + +P+  IG +IG++G  I +IR+ + A IKIA+ +     R + I+ S  +       
Sbjct: 9   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS------I 62

Query: 112 ENALQQIAALILKD 125
             A   I A +  +
Sbjct: 63  SLAQYLINARLSSE 76

>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 = 49.2 bits (118), Expect = 2e-08
 Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T  L I  +  GC+IG  G NI ++R  SGA I I  P           S R V I+G  
Sbjct: 7   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-------VEGSSGRQVTITGSA 59

Query: 204 PAVLNALVEIGNQLRE 219
            ++  A   I  +L  
Sbjct: 60  ASISLAQYLINARLSS 75

>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 = 9e-09
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
              ++I  S+AG +IG  G+ I++L+  +G  +V++             +D+ ++I+GD 
Sbjct: 16  VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-----TGADKPLRITGDP 70

Query: 204 PAVLNALVEIGNQLRENPPR 223
             V  A   +   +R+    
Sbjct: 71  YKVQQAKEMVLELIRDQGSG 90

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

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA--DAIARHEERVIIISSKDNDNVVSD 110
            I++P+ + G VIGK G  I++++E     + +          ++ + I+  D   V   
Sbjct: 18  EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKV--- 73

Query: 111 AENALQQIAALILKDDDSNSEA 132
            + A + +  LI       S  
Sbjct: 74  -QQAKEMVLELIRDQGSGPSSG 94

>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 = 51.6 bits (123), Expect = 1e-08
 Identities = 29/167 (17%), Positives = 52/167 (31%), Gaps = 31/167 (18%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
           + IV    +G  IG  G  IQ+ R+    T    D     +     I  +          
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD----EDTCTFHIYGE---------- 52

Query: 113 NALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172
                           + +A K A   +      + +  +  G +IG +G+ I+++ + S
Sbjct: 53  ----------------DQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKS 96

Query: 173 GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
           G   V +                 V   G   ++ NA V +   L  
Sbjct: 97  GVVRVRIEAENEKNVPQEEGMVPFV-FVGTKDSIANATVLLDYHLNY 142

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

 Score = 49.6 bits (119), Expect = 1e-08
 Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 4/77 (5%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             + + +  +  G ++G  G+ + + +  +GA I I    +          +R V I+G 
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT----RNRRVTITGS 58

Query: 203 VPAVLNALVEIGNQLRE 219
             A   A   I  ++  
Sbjct: 59  PAATQAAQYLISQRVTY 75

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

 Score = 47.3 bits (113), Expect = 9e-08
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHE---ERVIIIS 100
             + VP   +G ++GK G  + + +E T A I+I+           R + I+
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

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

 Score = 50.2 bits (120), Expect = 2e-08
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKDNDNVVSDA 111
            + VP   +G VIG+ G  I+KI+ +    I+         E++  I    D        
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDR------C 67

Query: 112 ENALQQIAALILKDDDSNS 130
           E+A + I  L+        
Sbjct: 68  EHAARIINDLLQSLRSGPP 86

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

 Score = 45.5 bits (108), Expect = 9e-07
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 135 VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESD 194
           +A G      I + +     G +IG SG+ I+K++N +G  I     +           +
Sbjct: 3   MATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-------GTGPE 55

Query: 195 RVVQISGDVPAVLNALVEIGNQLRENPPR 223
           ++  I G      +A   I + L+     
Sbjct: 56  KIAHIMGPPDRCEHAARIINDLLQSLRSG 84

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

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             + + +  +  G ++G  G+ + + +  +GA I I    +          +R V I+G 
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT----RNRRVTITGS 58

Query: 203 VPAVLNALVEIGNQLRENPPRQ 224
             A   A   I  ++      +
Sbjct: 59  PAATQAAQYLISQRVTYEQGVR 80

>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 = 46.2 bits (110), Expect = 3e-07
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIIS 100
             I VP   +G ++GK G  + + +E T A I+I+   + +     R + I+
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

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

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKDNDNVVSDA 111
              VP   +G +IG+ G +I +I++E+   I+IA       ER  +++ + ++   V  A
Sbjct: 18  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES---VQSA 74

Query: 112 ENALQQI 118
           +  L QI
Sbjct: 75  KRLLDQI 81

>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 = 40.9 bits (96), Expect = 3e-05
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T    +     G +IG  G+ I +++  SG  I I          S    +R   ++G  
Sbjct: 16  TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD-------SGGLPERSCMLTGTP 68

Query: 204 PAVLNALVEIGNQLRE 219
            +V +A   +   + +
Sbjct: 69  ESVQSAKRLLDQIVEK 84

>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 = 48.7 bits (116), Expect = 6e-08
 Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 7/103 (6%)

Query: 38  GSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEER 95
                   +   V  ++ VP R +G++IG+ G  I+ I + + A I             R
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR 62

Query: 96  VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138
           +I IS      V      A   I   + +D++     +  A+G
Sbjct: 63  LIKISG-TQKEV----AAAKHLILEKVSEDEELRKRIAHSASG 100

>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 = 2e-05
 Identities = 23/104 (22%), Positives = 40/104 (38%), Gaps = 6/104 (5%)

Query: 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCAS 189
           S  S            +L +     G +IG  G+ I  +  +SGA I     ++      
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-----G 56

Query: 190 AHESDRVVQISGDVPAVLNALVEIGNQLRENP-PRQVISISPAY 232
                R+++ISG    V  A   I  ++ E+   R+ I+ S + 
Sbjct: 57  TLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKRIAHSASG 100

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

 Score = 47.7 bits (114), Expect = 8e-08
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 136 AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR 195
           A G        ++I   +AG +IG  G+ I++L+  +G  ++++              D+
Sbjct: 7   ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN-----TNVDK 61

Query: 196 VVQISGDVPAVLNALVEIGNQLRE 219
            ++I GD   V  A   + + LRE
Sbjct: 62  PLRIIGDPYKVQQACEMVMDILRE 85

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

 Score = 45.8 bits (109), Expect = 4e-07
 Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 7/72 (9%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA--DAIARHEERVIIISSKDNDNVVSD 110
            I++P+ + G VIGK G  I++++E     + +    +   + ++ + I   D   V   
Sbjct: 17  EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKV--- 72

Query: 111 AENALQQIAALI 122
            + A + +  ++
Sbjct: 73  -QQACEMVMDIL 83

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

 Score = 46.4 bits (110), Expect = 4e-07
 Identities = 16/100 (16%), Positives = 34/100 (34%), Gaps = 4/100 (4%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             +   I   + G +IG  G+N++ +   +GA + I       L  +   + ++  I G 
Sbjct: 7   GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI----SRQLPPNGDPNFKLFIIRGS 62

Query: 203 VPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQP 242
              + +A   I  ++                   + P  P
Sbjct: 63  PQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNP 102

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

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 12/52 (23%), Positives = 27/52 (51%), Gaps = 3/52 (5%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHE---ERVIIIS 100
               +P+ + G VIG+ G  ++ I ++T A ++I+  +  +     ++ II 
Sbjct: 9   MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

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

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P      VIGK G ++Q +  +T   I+I         ++ I  +K+        E
Sbjct: 20  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-DDPSNQIKITGTKEG------IE 72

Query: 113 NALQQIAALILKDDDSNSEAS 133
            A  ++  +  + D  +  +S
Sbjct: 73  KARHEVLLISAEQDKRSGPSS 93

>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 = 37.8 bits (88), Expect = 4e-04
 Identities = 15/92 (16%), Positives = 33/92 (35%), Gaps = 9/92 (9%)

Query: 128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187
           S+  +  + A      +  + I       +IG +G+ ++ L   +   I I  P+     
Sbjct: 2   SSGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD----- 56

Query: 188 ASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
               +    ++I+G    +  A  E+     E
Sbjct: 57  ----DPSNQIKITGTKEGIEKARHEVLLISAE 84

>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 = 42.5 bits (100), Expect = 9e-06
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + +  R   ++IG  G  I+KI +E K  I+   + A     V +    +N   V +A +
Sbjct: 21  VPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN---VEEAID 77

Query: 114 ALQQIAALILKD 125
            +  +    L D
Sbjct: 78  HILNLEEEYLAD 89

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 47  AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDN 106
            +     I +  +    +IGK G  I +I+++ K +++I    +     + I        
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-SEKSNLIRIEGDPQG-- 58

Query: 107 VVSDAENALQQIAA 120
            V  A+  L ++A+
Sbjct: 59  -VQQAKRELLELAS 71

>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 = 41.3 bits (97), Expect = 2e-05
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + V  +   K+IG++G  I +IR E    I+  D    ++ +  I  +    N     E 
Sbjct: 21  VTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNT----EA 76

Query: 114 ALQQIAALILKDDDSNSEAS 133
           A   I  ++ + +  +  +S
Sbjct: 77  ARDAILRIVGELEQMSGPSS 96

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 42.9 bits (102), Expect = 6e-05
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 10/69 (14%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + VP  +  K +G  G+ ++K++ ET  TI   D      E    + +            
Sbjct: 571 VQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSA----MHE 620

Query: 114 ALQQIAALI 122
           A   I  + 
Sbjct: 621 ARDFITEIC 629

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 42.5 bits (101), Expect = 8e-05
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 10/69 (14%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           I +P+ +I +VIG  G  I++I   T A + I D      + V+ +S+ D        + 
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDGAK----IKA 623

Query: 114 ALQQIAALI 122
           A+  I ++ 
Sbjct: 624 AIDWIKSIT 632

>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 = 39.5 bits (92), Expect = 8e-05
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 8/69 (11%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + VP R +G V+G +G  I++I++ T   I       R +E V  ++    +NV    + 
Sbjct: 14  VRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPG---RDKEPVFAVTG-MPENV----DR 65

Query: 114 ALQQIAALI 122
           A ++I A I
Sbjct: 66  AREEIEAHI 74

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

 Score = 40.8 bits (95), Expect = 1e-04
 Identities = 28/187 (14%), Positives = 55/187 (29%), Gaps = 35/187 (18%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
             + V   ++G VIG  G    +I   T   I +       E  ++I+  +       + 
Sbjct: 6   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-----TENSMVIVEPEAEGIPPVNL 60

Query: 112 ENALQQIAAL-----------ILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGM 160
             A + + A+           +L++D              + N ++ +      G +IG 
Sbjct: 61  MKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIK-----GRIIGE 115

Query: 161 SGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220
            G+    +   +   I +               +  V I GD    + A   I       
Sbjct: 116 GGRARRTIEEMTDTYINV--------------GEYEVAIIGDYERAMAAKQAIEMLAEGR 161

Query: 221 PPRQVIS 227
               V  
Sbjct: 162 MHSTVYR 168

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           I +   +I  VIGK G  I+ + EET  TI+I D      +  + I++ D +     A++
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEK----AKH 613

Query: 114 ALQQIAALI 122
           A+++I  + 
Sbjct: 614 AIRRIEEIT 622

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 41.4 bits (98), Expect = 2e-04
 Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 13/73 (17%)

Query: 53  RII---VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           RII   +P  +IG+VIG +   I +I+E+T A I I D      +  I I + D      
Sbjct: 598 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPA--- 648

Query: 110 DAENALQQIAALI 122
            AE A   I  + 
Sbjct: 649 -AEAARATINGIA 660

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 38.8 bits (89), Expect = 5e-04
 Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 24/51 (47%)

Query: 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV-LNALVE 212
           Q ++KL+ S    + + A +      SA             PA+ + A +E
Sbjct: 20  QALKKLQAS----LKLYADD------SA-------------PALAIKATME 47

>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 = 37.5 bits (87), Expect = 6e-04
 Identities = 17/92 (18%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187
           S+  + K A   +   TI + +       +IG  G  I K+ +     I + AP      
Sbjct: 2   SSGSSGKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE----- 56

Query: 188 ASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
                   ++ I+G    +  A   +  +++E
Sbjct: 57  ----LQSDIIAITGLAANLDRAKAGLLERVKE 84

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

 Score = 38.9 bits (90), Expect = 6e-04
 Identities = 38/217 (17%), Positives = 72/217 (33%), Gaps = 33/217 (15%)

Query: 22  RHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81
           +     +   +DGEI   + +     +   + + +P  +I  +IGK+G   ++I + TK 
Sbjct: 7   KLMKKFENVNKDGEIVEDEDEWEEFFKQEEY-VKIPKDRIAVLIGKKGQTKKEIEKRTKT 65

Query: 82  TIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI----------LKDDDSNSE 131
            I I       E   + I+S            A   + A+           L ++    E
Sbjct: 66  KITID-----SETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLE 120

Query: 132 ASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAH 191
              +    +      L       G +IG  G+  + +   SGA++ +             
Sbjct: 121 IINLTDIIIGNEKNALPRV---RGRIIGRKGRTRQIIEEMSGASVSV------------- 164

Query: 192 ESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISI 228
              + V I G+   +  A   I    R +P   V   
Sbjct: 165 -YGKTVAIIGNPIQIEIAKTAIEKLARGSPHGSVYRY 200

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	257
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.97
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.96
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.96
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.95
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.95
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.85
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.81
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.8
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.7
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.63
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.62
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.61
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.6
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.6
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.6
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.58
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.58
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.57
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.57
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.57
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.56
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.55
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.55
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.55
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.54
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.52
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.52
1we8_A	104	Tudor and KH domain containing protein; structural	99.52
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.52
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.51
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.51
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.49
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.47
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.47
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.46
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.46
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.46
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.46
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.44
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.42
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.42
1we8_A	104	Tudor and KH domain containing protein; structural	99.4
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.39
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.39
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.38
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.38
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.38
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.36
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.36
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.34
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.31
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.27
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.26
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.22
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.21
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.97
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.94
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.87
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.85
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.75
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.73
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.7
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.64
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.57
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.52
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.39
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.36
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.34
2cxc_A	144	NUSA; transcription termination, RNA binding prote	98.13
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.08
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.88
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.83
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.54
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.28
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.13
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.07
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	96.69
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.66
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.98
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.74
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.54
2cxc_A	144	NUSA; transcription termination, RNA binding prote	92.55
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	90.52
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	89.07
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	87.96
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	86.36
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	80.88

>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=99.97  E-value=2.4e-30  Score=214.58  Aligned_cols=166  Identities=25%  Similarity=0.387  Sum_probs=134.8

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc---ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      +++++++|+||.+.+|.||||+|++|++|+++|||+|+|++.   .+++.+|+|+|+|..+     ++.+|..+|.+++.
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~-----~v~~A~~~I~~~~~   77 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE-----ALNAVHGFIAEKIR   77 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHH-----HHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHH-----HHHHHHHHHHHHHh
Confidence            567899999999999999999999999999999999999854   3568899999999843     78899999999987


Q ss_pred             cCCCCCchhhh--h-----ccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceE
Q 025112          124 KDDDSNSEASK--V-----AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV  196 (257)
Q Consensus       124 ~~~~~~~~~~~--~-----~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~  196 (257)
                      +..........  .     ........+.++.||.+++|+|||++|++|++|+++|||+|+|.+....+.     +.++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~-----~~~~~  152 (178)
T 2anr_A           78 EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGIN-----LQNRV  152 (178)
T ss_dssp             CCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC---------CCEEE
T ss_pred             ccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCC-----CCceE
Confidence            65432111000  0     001123468899999999999999999999999999999999976433332     67899


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcCCC
Q 025112          197 VQISGDVPAVLNALVEIGNQLRENPP  222 (257)
Q Consensus       197 V~I~G~~~~v~~A~~~I~~~l~e~~~  222 (257)
                      |+|+|++++|++|+++|.++|+++|+
T Consensus       153 v~I~G~~~~v~~A~~~I~~~i~e~p~  178 (178)
T 2anr_A          153 VTVSGEPEQNRKAVELIIQKIQEDPQ  178 (178)
T ss_dssp             EEEESSHHHHHHHHHHHHHHHHSCCC
T ss_pred             EEEEcCHHHHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999999874

>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=99.96  E-value=2.5e-29  Score=205.49  Aligned_cols=157  Identities=23%  Similarity=0.371  Sum_probs=132.0

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~  128 (257)
                      -+++|+||.+.+|.||||+|++||+|+++|||+|+|++. .+++.+|+|+|+|.+     ..+.+|..+|.+++.+....
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~-----e~v~~A~~~I~~~~~e~~~~   77 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPP-----EAQFKAQGRIYGKLKEENFF   77 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECH-----HHHHHHHHHHHHHHHHTTSS
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHhccccc
Confidence            478999999999999999999999999999999999975 567899999999974     37889999999998776322


Q ss_pred             CchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHH
Q 025112          129 NSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLN  208 (257)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~  208 (257)
                      ...       .....+.++.||.+++|+|||++|++|++|++.|||+|.+.. +..|.    ...++.|+|+|++++|++
T Consensus        78 ~~~-------~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~-~~~~~----~~~~~~v~I~G~~~~v~~  145 (163)
T 3krm_A           78 GPK-------EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR-DQTPD----ENDQVIVKIIGHFYASQM  145 (163)
T ss_dssp             CSS-------CCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCT-TCCCC----TTSEEEEEEEECHHHHHH
T ss_pred             ccc-------cCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECC-CCCCC----CCCceEEEEEeCHHHHHH
Confidence            111       112357799999999999999999999999999999999854 44454    144569999999999999


Q ss_pred             HHHHHHHHHhcCCCC
Q 025112          209 ALVEIGNQLRENPPR  223 (257)
Q Consensus       209 A~~~I~~~l~e~~~~  223 (257)
                      |+.+|.+++++..++
T Consensus       146 A~~~I~~~i~~~~~~  160 (163)
T 3krm_A          146 AQRKIRDILAQVKQQ  160 (163)
T ss_dssp             HHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999986554

>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=99.96  E-value=3.8e-29  Score=203.89  Aligned_cols=159  Identities=28%  Similarity=0.493  Sum_probs=131.6

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      +..++++|+||.+.+|.||||+|++||+|+++|||+|+|++.  ++++|+|+|+|+.     .++.+|+.+|.+.+.+..
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~-----~~v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPT-----NAIFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEH-----HHHHHHHHHHHHHHHHHH
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCH-----HHHHHHHHHHHHHHHhhc
Confidence            356899999999999999999999999999999999999976  5789999999984     378899999998886632


Q ss_pred             CCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025112          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (257)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v  206 (257)
                      .......  ........+.++.||.+++|+|||++|++|++|+++|||+|++.+ +..|.     +.++.|+|+|++++|
T Consensus        75 ~~~~~~~--~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~-~~~~~-----~~~~~v~I~G~~~~v  146 (160)
T 2jzx_A           75 SSSMTNS--TAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG-DMLPN-----STERAITIAGIPQSI  146 (160)
T ss_dssp             TSCCCSS--SCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC-CCSTT-----CCEEEEEEEECHHHH
T ss_pred             cccCCCC--ccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC-CCCCC-----CCceEEEEEcCHHHH
Confidence            1110000  001123468999999999999999999999999999999999854 34453     678999999999999


Q ss_pred             HHHHHHHHHHHhcC
Q 025112          207 LNALVEIGNQLREN  220 (257)
Q Consensus       207 ~~A~~~I~~~l~e~  220 (257)
                      ++|+++|.+++.|+
T Consensus       147 ~~A~~~I~~~i~e~  160 (160)
T 2jzx_A          147 IECVKQICVVMLET  160 (160)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcC
Confidence            99999999999873

>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=99.95  E-value=3.5e-28  Score=198.58  Aligned_cols=157  Identities=19%  Similarity=0.331  Sum_probs=128.2

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc--ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~--~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~  127 (257)
                      ++++|+||.+.+|.||||+|++||+|+++|||+|++.+.  .+++.+|+|+|+|.+     .++.+|+.+|.+++.+...
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~ii~e~~~   76 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDP-----YKVQQACEMVMDILRERDQ   76 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECH-----HHHHHHHHHHHHHTTCSSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHHhccC
Confidence            578999999999999999999999999999999999754  245678999999974     3788999999999876542


Q ss_pred             CCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHH
Q 025112          128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVL  207 (257)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~  207 (257)
                      ........ .+.....+.++.||.+++|+|||++|++|++|+++|||+|.|.+.+  +     .+.++.|+|+|++++++
T Consensus        77 ~~~~~~~~-~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~--~-----~~~~~~v~I~G~~~~v~  148 (164)
T 2jvz_A           77 GGFGDRNE-YGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G-----TGPEKIAHIMGPPDRCE  148 (164)
T ss_dssp             CCCSSCSS-CTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC--T-----TSSEEEEEEESCHHHHH
T ss_pred             CCCCCccc-cCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC--C-----CCCcEEEEEEcCHHHHH
Confidence            21110000 0111124578999999999999999999999999999999997542  1     25689999999999999


Q ss_pred             HHHHHHHHHHhc
Q 025112          208 NALVEIGNQLRE  219 (257)
Q Consensus       208 ~A~~~I~~~l~e  219 (257)
                      +|+.+|.+++++
T Consensus       149 ~A~~~I~~~i~~  160 (164)
T 2jvz_A          149 HAARIINDLLQS  160 (164)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh
Confidence            999999999986

>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=99.95  E-value=4.9e-28  Score=200.03  Aligned_cols=160  Identities=21%  Similarity=0.334  Sum_probs=126.6

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~  128 (257)
                      ..+++|+||.+.+|.||||+|++||+|+++|||+|+|.+..+++.+|+|+|+|..+     ++.+|+.+|.+++.+....
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~~~~~~~~~~   76 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPD-----RAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHH-----HHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHH-----HHHHHHHHHHHHHHhcccC
Confidence            56899999999999999999999999999999999998765678899999999843     7889999999888765321


Q ss_pred             Cchhh------------hhc-cCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCce
Q 025112          129 NSEAS------------KVA-AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR  195 (257)
Q Consensus       129 ~~~~~------------~~~-~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r  195 (257)
                      .....            ... .......+.++.||.+++|+|||++|++|++|++.|||+|+|.+.. .+ +.  ++.++
T Consensus        77 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~-~~-~~--~~~~~  152 (174)
T 1j4w_A           77 NPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP-PP-NA--DPNMK  152 (174)
T ss_dssp             ---------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC-TT-TS--CTTEE
T ss_pred             CCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC-CC-CC--CCCce
Confidence            10000            000 0011235789999999999999999999999999999999997532 12 11  26789


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHH
Q 025112          196 VVQISGDVPAVLNALVEIGNQL  217 (257)
Q Consensus       196 ~V~I~G~~~~v~~A~~~I~~~l  217 (257)
                      .|+|+|+++++++|+++|.++|
T Consensus       153 ~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          153 LFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEECCHHHHHHHHHHHHHhC
Confidence            9999999999999999999875

>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=99.85  E-value=4.1e-21  Score=154.01  Aligned_cols=136  Identities=20%  Similarity=0.252  Sum_probs=101.3

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEecc-CCCCchhhHHHHHHHHHHHHHhcCCC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISS-KDNDNVVSDAENALQQIAALILKDDD  127 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G-~~~~~~~~~~~~A~~~I~~~i~~~~~  127 (257)
                      .++.+|+||.+.+|++||++|++|++|++++|  |++.... ..+++ +.+.| .++     .+.+|    ..++. .  
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~-~i~~~~~p~-----~v~~~----~~~l~-~--   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCT-FHIYGEDQD-----AVKKA----RSFLE-F--   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTE-EEEEESSHH-----HHHHH----HHHHC-E--
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchh-eeeccCCHH-----HHHHH----HHhhh-c--
Confidence            57899999999999999999999999999999  5443321 13344 44544 332     23333    22221 1  


Q ss_pred             CCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCC-eEEEeCCCCCCcccCCCCCc--eEEEEEcCHH
Q 025112          128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA-TIVILAPNQLPLCASAHESD--RVVQISGDVP  204 (257)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga-~I~i~~~~~~p~~~~~~~~~--r~V~I~G~~~  204 (257)
                                     ...++.||.+++|++|||+|.+|+.|++.||+ +|+|.+.++...    ...+  +.|+|+|+++
T Consensus        67 ---------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~----~~~~~~~~vtI~G~~~  127 (144)
T 2qnd_A           67 ---------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV----PQEEGMVPFVFVGTKD  127 (144)
T ss_dssp             ---------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC----CCCTTEEEEEEEEEHH
T ss_pred             ---------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc----cccCCeeEEEEEeCHH
Confidence                           12789999999999999999999999999997 999986433210    0223  4689999999


Q ss_pred             HHHHHHHHHHHHHhc
Q 025112          205 AVLNALVEIGNQLRE  219 (257)
Q Consensus       205 ~v~~A~~~I~~~l~e  219 (257)
                      +|+.|.++|.++|++
T Consensus       128 ~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          128 SIANATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999999976

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

Probab=99.81  E-value=5e-20  Score=156.97  Aligned_cols=157  Identities=20%  Similarity=0.217  Sum_probs=118.2

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~  128 (257)
                      .-..++.||.+.+|.|||++|.+|+.|+++|||+|++..     .++.|.|.+...-....++++|..+|..+...... 
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~-  106 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSP-  106 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCH-
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCc-
Confidence            346699999999999999999999999999999999983     35678898865211134788999999998753211 


Q ss_pred             CchhhhhccCCCcceEEEEEee-----------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEE
Q 025112          129 NSEASKVAAGHVAANTIRLLIA-----------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV  197 (257)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~l~Vp-----------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V  197 (257)
                        +...... ..+.....+.++           ...+|+|||++|++|+.|++.|||+|.|.              ++.|
T Consensus       107 --e~g~~ll-~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~--------------~~~v  169 (219)
T 2e3u_A          107 --ERAFRLL-NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY--------------GKTV  169 (219)
T ss_dssp             --HHHGGGG-STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE--------------TTEE
T ss_pred             --cccceec-cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC--------------CeEE
Confidence              1000000 011111122222           13689999999999999999999999984              2569


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhcCCCCCcccC
Q 025112          198 QISGDVPAVLNALVEIGNQLRENPPRQVISI  228 (257)
Q Consensus       198 ~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~  228 (257)
                      +|.|++++++.|..+|.++|.+.++..+|.+
T Consensus       170 ~i~G~~~~i~~A~~~i~~li~g~~~~~vy~~  200 (219)
T 2e3u_A          170 AIIGNPIQIEIAKTAIEKLARGSPHGSVYRY  200 (219)
T ss_dssp             EEEECHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             EEEeCHHHHHHHHHHHHHHHcCCCcHHHHHH
Confidence            9999999999999999999999888866654

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

Probab=99.80  E-value=2.2e-19  Score=163.30  Aligned_cols=166  Identities=14%  Similarity=0.135  Sum_probs=120.7

Q ss_pred             CCCCCeEEEEEecCccccceeccCc--hhHHHHHhhhCceEEEcccc--c---CCCccEEEeccCCCCchhhHHHHHHHH
Q 025112           45 AKAQDVLFRIIVPSRQIGKVIGKEG--HRIQKIREETKATIKIADAI--A---RHEERVIIISSKDNDNVVSDAENALQQ  117 (257)
Q Consensus        45 ~~~~~~~~rilVP~~~vg~IIGk~G--~~Ik~I~~~tg~~I~i~~~~--~---~~~ervv~I~G~~~~~~~~~~~~A~~~  117 (257)
                      .+.+.+++.+.||..+|+.||||+|  ++|++|+++|||+|+|++..  .   ......|+|+|..+     ++.+|..+
T Consensus        25 ~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~e-----nVE~AR~~   99 (376)
T 3n89_A           25 INPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFG-----DVDRARML   99 (376)
T ss_dssp             CCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHH-----HHHHHHHH
T ss_pred             ecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHH-----HHHHHHHH
Confidence            4467899999999999999999999  99999999999999999764  1   12446799999965     56677776


Q ss_pred             HHHH----------------------HhcCCCC----------C-----chh----------hhh-----------c---
Q 025112          118 IAAL----------------------ILKDDDS----------N-----SEA----------SKV-----------A---  136 (257)
Q Consensus       118 I~~~----------------------i~~~~~~----------~-----~~~----------~~~-----------~---  136 (257)
                      |.++                      +......          .     .+.          ...           .   
T Consensus       100 I~~l~Pl~i~~elp~~~i~~~~l~~~I~qq~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e  179 (376)
T 3n89_A          100 MRRNCHFTVFMALSKMKMPLHELQAHVRQNPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRES  179 (376)
T ss_dssp             HHHSCEEEEEEECTTCSSCHHHHHHHHHHCCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--
T ss_pred             HHhcCCceEEEEccccccCcchhhhhhccceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhh
Confidence            6552                      2110000          0     000          000           0   


Q ss_pred             cCCCcceEEEEEeecCccceeecCCC--hhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH
Q 025112          137 AGHVAANTIRLLIAGSQAGCLIGMSG--QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG  214 (257)
Q Consensus       137 ~~~~~~~~~~l~Vp~~~vG~iIGk~G--~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~  214 (257)
                      ......++..+.|+..+|..|||++|  ..|++|+++|||+|.++..++....   ......|+|+|+.++|.+|+++|+
T Consensus       180 ~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~---~~~~~~ItItGs~e~V~~Ark~I~  256 (376)
T 3n89_A          180 PAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNET---RGNIYEIKVVGNIDNVLKARRYIM  256 (376)
T ss_dssp             CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC------------CCEEEEEEESCHHHHHHHHHHHH
T ss_pred             cccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccc---cCCceEEEEEeCHHHHHHHHHHHH
Confidence            01124578899999999999999999  5579999999999998754331110   024679999999999999999999


Q ss_pred             HHHh
Q 025112          215 NQLR  218 (257)
Q Consensus       215 ~~l~  218 (257)
                      ++|-
T Consensus       257 ~lLP  260 (376)
T 3n89_A          257 DLLP  260 (376)
T ss_dssp             HTSE
T ss_pred             hhCC
Confidence            9875

>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=99.70  E-value=8.5e-17  Score=134.03  Aligned_cols=149  Identities=17%  Similarity=0.199  Sum_probs=113.6

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~  130 (257)
                      .++++||.+.+|.|||++|++++.|++.+|++|++.     ..++.++|...........+++|...|..+.......  
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--   77 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-----TENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPE--   77 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE-----TTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHH--
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE-----cCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHH--
Confidence            368999999999999999999999999999999997     4577888873322212457899999998887765321  


Q ss_pred             hhhhhccCCCcceEEEEEee----------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE
Q 025112          131 EASKVAAGHVAANTIRLLIA----------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS  200 (257)
Q Consensus       131 ~~~~~~~~~~~~~~~~l~Vp----------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~  200 (257)
                      +..+..  ..+.....+.++          ...+|+|||++|.+|+.|+..|||+|.|.              ++.|.|.
T Consensus        78 ~A~~Ll--~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~--------------~~~v~i~  141 (191)
T 1tua_A           78 KAFRLL--EEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG--------------EYEVAII  141 (191)
T ss_dssp             HHGGGG--STTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC--------------SSEEEEE
T ss_pred             Hhhhcc--cCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc--------------CCEEEEE
Confidence            111110  011122223243          23589999999999999999999999983              2479999


Q ss_pred             cCHHHHHHHHHHHHHHHhcCCC
Q 025112          201 GDVPAVLNALVEIGNQLRENPP  222 (257)
Q Consensus       201 G~~~~v~~A~~~I~~~l~e~~~  222 (257)
                      |++++++.|...|.++|...++
T Consensus       142 G~~~~i~~Ar~~i~~li~g~~h  163 (191)
T 1tua_A          142 GDYERAMAAKQAIEMLAEGRMH  163 (191)
T ss_dssp             EEHHHHHHHHHHHHHHHTTCCH
T ss_pred             eChHHHHHHHHHHHHHHcCCCc
Confidence            9999999999999999987666

>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=99.63  E-value=4.8e-16  Score=110.23  Aligned_cols=70  Identities=34%  Similarity=0.617  Sum_probs=63.6

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ....+++||.+.+|.|||++|++|++|+++|||+|++.+.         +..+|.|+|+|+++++.+|+++|.++|+|+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~---------~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG---------NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS---------CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC---------CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            4689999999999999999999999999999999999643         146899999999999999999999999874

>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=99.62  E-value=1.3e-15  Score=108.76  Aligned_cols=72  Identities=22%  Similarity=0.390  Sum_probs=63.6

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      .+.++.||.+.+|+|||++|++|++|++.|||+|+|.+.++ .|     ++.++.|+|+|+++++++|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP-----GTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST-----TCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCC-----CCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999999976433 23     36789999999999999999999999875

>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=99.61  E-value=5.7e-16  Score=109.86  Aligned_cols=71  Identities=25%  Similarity=0.502  Sum_probs=64.6

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ...++++|+||.+.+|.||||+|++||+|+++|||+|+|++.  ++++|+|+|+|.+     .++.+|+.+|.+++.+
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 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPT-----NAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECH-----HHHHHHHHHHHHHHHC
T ss_pred             CceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCH-----HHHHHHHHHHHHHHhc
Confidence            356899999999999999999999999999999999999976  5789999999984     3789999999999875

>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=99.60  E-value=2.4e-15  Score=108.95  Aligned_cols=72  Identities=35%  Similarity=0.520  Sum_probs=63.7

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+.++.||.+++|.|||++|++|++|+++|||+|+|.+.  .+     ++.++.|+|+|+++++++|+.+|.+++.+.
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~--~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP--VE-----GSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--CT-----TCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC--CC-----CCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4688999999999999999999999999999999999642  22     267999999999999999999999999886

>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=99.60  E-value=4.1e-15  Score=107.74  Aligned_cols=72  Identities=33%  Similarity=0.521  Sum_probs=64.5

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+.++.||.+.+|+|||++|++|++|+++|||+|+|.+.  .+     ++.+|.|+|+|+++++++|+++|.+++.+.
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~--~~-----~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LE-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT--TS-----CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC--CC-----CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3688999999999999999999999999999999999632  22     257899999999999999999999999874

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

Probab=99.60  E-value=2.1e-15  Score=107.65  Aligned_cols=72  Identities=32%  Similarity=0.512  Sum_probs=64.6

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+.++.||.+++|+|||++|++|++|++.|||+|++.+.  .+     ++.++.|+|+|+++++++|+++|.+++.+.
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~--~~-----~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP--VE-----GSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC--CT-----TCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC--CC-----CCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            3678999999999999999999999999999999999642  22     367999999999999999999999999864

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

Probab=99.58  E-value=1.2e-15  Score=108.97  Aligned_cols=73  Identities=26%  Similarity=0.444  Sum_probs=66.3

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+..+++.+|.|+|+|.+     .++.+|..+|.+++.++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~-----~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSA-----ASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCH-----HHHHHHHHHHHHHHHcc
Confidence            56889999999999999999999999999999999999987777889999999984     37889999999988653

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

Probab=99.58  E-value=4.1e-15  Score=113.09  Aligned_cols=94  Identities=19%  Similarity=0.288  Sum_probs=66.3

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~  223 (257)
                      +.+|.||.+++|+||||+|++||+|+++|||+|+|.+.. .+..   +..++.|+|+|++++|++|+++|.++|.+..  
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQL-PPNG---DPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL--   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCC-CTTC---CTTEEEEEEESCHHHHHHHHHHHHHHSCSCC--
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCcc-CCCC---CCCceEEEEECCHHHHHHHHHHHHHHHhccc--
Confidence            689999999999999999999999999999999996532 2211   2568999999999999999999999998864  


Q ss_pred             CcccCCCCCCC-CCCCCCCCCcC
Q 025112          224 QVISISPAYNY-SAIRPAQPFVE  245 (257)
Q Consensus       224 ~~~~~~p~~~~-~~~~~~~~~~~  245 (257)
                        ..|.|...- ...+..+.|.+
T Consensus        82 --~~~~p~~~~~~~~~~~~~~~~  102 (107)
T 2hh2_A           82 --CPVGPGPGGPGPAGPMGPFNP  102 (107)
T ss_dssp             --CEEC-----------------
T ss_pred             --ccCCCCCCCCCCCCCCCCCCC
Confidence              245453322 22333355655

>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=99.57  E-value=3.7e-15  Score=109.15  Aligned_cols=73  Identities=22%  Similarity=0.389  Sum_probs=65.0

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      .+.++.||.+.+|+|||++|++|++|++.|||+|+|.+.++ .|     ++.++.|+|+|+++++++|+.+|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~-----g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP-----GTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBST-----TSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCC-----CCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            47899999999999999999999999999999999975432 23     267899999999999999999999999873

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

Probab=99.57  E-value=1.1e-14  Score=106.09  Aligned_cols=72  Identities=25%  Similarity=0.448  Sum_probs=63.5

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ...++.||.+.+|+|||++|++||+|+++|||+|.+.+....+     .+.+|.|+|+|+++++++|+++|.++++|
T Consensus        14 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~-----~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN-----TNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             EEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSS-----TTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             EEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCC-----CCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            5789999999999999999999999999999999996532222     26789999999999999999999999875

>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=99.57  E-value=4.7e-15  Score=107.44  Aligned_cols=73  Identities=29%  Similarity=0.505  Sum_probs=65.8

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|++..+++.+|.|+|+|++     .++++|..+|.+++.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~-----~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ-----DQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECH-----HHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999999999999999999987677889999999984     37889999999988653

>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=99.56  E-value=3.6e-15  Score=108.04  Aligned_cols=73  Identities=26%  Similarity=0.421  Sum_probs=65.0

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+..+++.+|.|+|+|.++     ++.+|..+|.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA-----SISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHH-----HHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHH-----HHHHHHHHHHHHHHhh
Confidence            467899999999999999999999999999999999999876678899999999853     7889999999988664

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

Probab=99.55  E-value=3.2e-15  Score=108.49  Aligned_cols=71  Identities=20%  Similarity=0.279  Sum_probs=63.4

Q ss_pred             CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      .+..+.++.||.+++|+||||+|++||+|+++|||+|+|++.          ..++.|+|+|+++++++|+++|.+++..
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~----------~~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR----------DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS----------SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC----------CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            345789999999999999999999999999999999999643          2368999999999999999999998776


Q ss_pred             C
Q 025112          220 N  220 (257)
Q Consensus       220 ~  220 (257)
                      .
T Consensus        77 r   77 (83)
T 2dgr_A           77 R   77 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.55  E-value=1.4e-14  Score=107.27  Aligned_cols=74  Identities=19%  Similarity=0.302  Sum_probs=65.7

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ...+.++.||.+.+|+|||++|++|++|+++|||+|+|.+..  +     +..+|.|+|+|++++|++|+.+|.+++.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~--~-----g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--G-----GLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--T-----TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC--C-----CCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            346899999999999999999999999999999999996432  2     257899999999999999999999999985


Q ss_pred             C
Q 025112          221 P  221 (257)
Q Consensus       221 ~  221 (257)
                      .
T Consensus        86 ~   86 (92)
T 1x4n_A           86 R   86 (92)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=99.55  E-value=6.9e-15  Score=109.30  Aligned_cols=76  Identities=24%  Similarity=0.420  Sum_probs=66.2

Q ss_pred             CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ++..+.++.||.+.+|+||||+|++||+|+++|||+|+|.+.....     ...+|.|+|+|+++++++|+++|.+++.+
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-----TGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS-----SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC-----CCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            3557899999999999999999999999999999999996432211     14789999999999999999999999987


Q ss_pred             C
Q 025112          220 N  220 (257)
Q Consensus       220 ~  220 (257)
                      .
T Consensus        87 ~   87 (94)
T 1x4m_A           87 Q   87 (94)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.54  E-value=9.5e-15  Score=107.44  Aligned_cols=72  Identities=33%  Similarity=0.507  Sum_probs=64.8

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+.++.||.+.+|.|||++|++|++|+++|||+|+|.+.  .+.     +.++.|+|+|+++++++|+++|.+++.+.
T Consensus        13 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~--~~~-----~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LEG-----SEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC--CSS-----SSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC--CCC-----CCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4688999999999999999999999999999999999632  232     67899999999999999999999999884

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

Probab=99.52  E-value=2.5e-14  Score=108.55  Aligned_cols=72  Identities=22%  Similarity=0.337  Sum_probs=63.9

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~  221 (257)
                      .+.++.||.+++|+||||+|++||+|+++|||+|+|.+.+  +     .+.+|.|+|+|+++++++|+++|.+++.+..
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 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G-----TGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC--S-----SSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC--C-----CCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            4689999999999999999999999999999999996432  2     2568999999999999999999999998844

>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=99.52  E-value=1.7e-14  Score=106.72  Aligned_cols=74  Identities=22%  Similarity=0.369  Sum_probs=66.5

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+..++..+|.|+|+|+++     ++++|..+|.+++.+..
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e-----~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPE-----SVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHH-----HHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHH-----HHHHHHHHHHHHHHhcc
Confidence            468899999999999999999999999999999999999876677899999999843     78899999999987653

>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=99.52  E-value=2.3e-14  Score=108.37  Aligned_cols=77  Identities=23%  Similarity=0.265  Sum_probs=66.2

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ...+.++.||.+.+|+|||++|++|++|+++|||+|+|.+..+..     .+.++.|+|+|+++++++|+++|.+++.+.
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-----~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-----LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS-----SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC-----CCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            346889999999999999999999999999999999996532211     136899999999999999999999999885


Q ss_pred             CC
Q 025112          221 PP  222 (257)
Q Consensus       221 ~~  222 (257)
                      +.
T Consensus        88 ~~   89 (104)
T 1we8_A           88 EE   89 (104)
T ss_dssp             HH
T ss_pred             hH
Confidence            53

>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=99.52  E-value=7.8e-15  Score=107.92  Aligned_cols=73  Identities=29%  Similarity=0.513  Sum_probs=66.1

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ..++++|+||.+.+|.||||+|++||+|+++|||+|+|++..+++.+|.|+|+|+++     ++++|..+|.+++.+.
T Consensus        12 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e-----~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           12 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD-----QIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHH-----HHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHH-----HHHHHHHHHHHHHHhh
Confidence            468899999999999999999999999999999999999876778899999999853     7889999999988764

>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=99.51  E-value=1.5e-14  Score=103.18  Aligned_cols=71  Identities=23%  Similarity=0.380  Sum_probs=61.9

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc---ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..+++|+||.+.+|.||||+|++|++|+++|||+|+|++.   .+++.+|.|+|+|++     .++.+|..+|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~-----~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSP-----AATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESH-----HHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCH-----HHHHHHHHHHHHHHhc
Confidence            3578999999999999999999999999999999999964   356788999999984     3788999999988754

>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=99.51  E-value=4.2e-14  Score=105.00  Aligned_cols=77  Identities=18%  Similarity=0.348  Sum_probs=67.1

Q ss_pred             CCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccccc--CCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA--RHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        45 ~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~--~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      ..++.++++|+||.+.+|.||||+|++||+|+++|||+|+|.+..+  ...+|.|+|+|+++     ++.+|+.+|.+++
T Consensus        10 ~~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~~~i   84 (94)
T 1x4m_A           10 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPY-----KVQQAKEMVLELI   84 (94)
T ss_dssp             CCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTT-----THHHHHHHHHHHH
T ss_pred             CCCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHH-----HHHHHHHHHHHHH
Confidence            3567899999999999999999999999999999999999996532  35799999999765     6889999999999


Q ss_pred             hcCC
Q 025112          123 LKDD  126 (257)
Q Consensus       123 ~~~~  126 (257)
                      .+..
T Consensus        85 ~~~~   88 (94)
T 1x4m_A           85 RDQG   88 (94)
T ss_dssp             CCCS
T ss_pred             hccC
Confidence            7653

>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=99.49  E-value=3.4e-14  Score=103.08  Aligned_cols=71  Identities=24%  Similarity=0.407  Sum_probs=62.8

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      .++.++++|.||.+.+|+||||+|++||+|+++|||+|+|+..   .++++++|+|.++     ++++|..+|.+++..
T Consensus         6 ~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~---~~~~~v~ItG~~e-----~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---DKEPVFAVTGMPE-----NVDRAREEIEAHITL   76 (83)
T ss_dssp             SCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS---SSCCEEEEEECTT-----THHHHHHHHHHHHHS
T ss_pred             CCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC---CCCCeEEEEcCHH-----HHHHHHHHHHHHHhc
Confidence            3467899999999999999999999999999999999999864   3478999999976     688999999997654

>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=99.47  E-value=1.1e-13  Score=102.85  Aligned_cols=73  Identities=18%  Similarity=0.146  Sum_probs=64.0

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ...+..+.||.+++|.|||++|++|++|+++|||+|+|++..+        ..++.|+|+|.+++|++|+++|.+++.+.
T Consensus        15 ~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~--------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA--------PDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC--------SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC--------CCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            3468999999999999999999999999999999999964311        34689999999999999999999998874


Q ss_pred             C
Q 025112          221 P  221 (257)
Q Consensus       221 ~  221 (257)
                      .
T Consensus        87 ~   87 (95)
T 2ctm_A           87 L   87 (95)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.47  E-value=1.5e-13  Score=102.65  Aligned_cols=71  Identities=15%  Similarity=0.130  Sum_probs=63.2

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ++..+.||..++|.|||++|++|++|+++|||+|+|++..+ +.     ..++.|+|+|+.+++++|+.+|..++.+
T Consensus        17 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~-~~-----~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-GN-----QPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-CS-----SCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             eeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-CC-----CCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999965322 21     3679999999999999999999999876

>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=99.46  E-value=3.8e-14  Score=103.74  Aligned_cols=70  Identities=24%  Similarity=0.383  Sum_probs=62.5

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc---ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      .+++|+||.+.+|.||||+|++|++|+++|||+|+|++.   .+++.+|.|+|+|+++     ++..|..+|.+++.+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~-----~v~~A~~~I~~~i~~   75 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA-----ATQAAQYLISQRVTY   75 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHH-----HHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHH-----HHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999964   3567899999999843     788999999998865

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

Probab=99.46  E-value=1.1e-13  Score=100.91  Aligned_cols=72  Identities=17%  Similarity=0.345  Sum_probs=62.3

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc--cCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~--~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ....++|.||.+.+|.||||+|++||+|+++|||+|+|.+..  +.+.+|.|+|+|.+     .++.+|..+|.+++.+
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~-----~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDP-----YKVQQACEMVMDILRE   85 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECH-----HHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHhcC
Confidence            457889999999999999999999999999999999999752  35679999999964     3788899999888753

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

Probab=99.46  E-value=5.5e-14  Score=106.64  Aligned_cols=72  Identities=24%  Similarity=0.345  Sum_probs=63.4

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      .+++|+||.+.++.||||+|++||+|+++|+|+|+|.+..+.+++|+|+|+|+++     ++++|..+|.+++.+..
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 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD-----RCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHH-----HHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHH-----HHHHHHHHHHHHHhccc
Confidence            3689999999999999999999999999999999999765567899999999843     78899999999887653

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

Probab=99.46  E-value=7.7e-14  Score=98.26  Aligned_cols=66  Identities=24%  Similarity=0.350  Sum_probs=59.2

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  217 (257)
                      .+..+.||.+++|.|||++|++|++|+++|||+|+|++..         ..++.|+|+|+++++++|+++|.+++
T Consensus         5 ~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g---------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS---------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC---------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC---------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999996421         35689999999999999999998864

>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=99.44  E-value=1.4e-13  Score=102.22  Aligned_cols=74  Identities=19%  Similarity=0.298  Sum_probs=64.9

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ...+.++.||.+.+|.|||++|++|++|+++|||+|+|++.+         +.++.|+|+|+++++++|..+|.+++.+.
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~---------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD---------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT---------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC---------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            346899999999999999999999999999999999996421         23579999999999999999999999885


Q ss_pred             CCC
Q 025112          221 PPR  223 (257)
Q Consensus       221 ~~~  223 (257)
                      ...
T Consensus        86 ~~~   88 (94)
T 2cte_A           86 DKR   88 (94)
T ss_dssp             HTC
T ss_pred             ccc
Confidence            444

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

Probab=99.42  E-value=1.5e-13  Score=104.44  Aligned_cols=70  Identities=23%  Similarity=0.382  Sum_probs=61.6

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc---cCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI---ARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~---~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      +++|+||.+.+|.||||+|++||+|+++|||+|+|.+..   .+..+|.|+|+|+.     .++++|+.+|.+++.+.
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~-----e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSP-----QQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCH-----HHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCH-----HHHHHHHHHHHHHHhcc
Confidence            689999999999999999999999999999999999652   23468999999974     47899999999998765

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

Probab=99.42  E-value=1.9e-13  Score=96.23  Aligned_cols=67  Identities=19%  Similarity=0.357  Sum_probs=58.3

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHH
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~  121 (257)
                      ...+..|.||.+++|.|||++|++|++|+++|||+|+|++.  +..++.|+|+|..+     ++.+|..+|.++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~--g~~~~~V~I~G~~~-----~v~~A~~~I~~i   69 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQ-----GVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSH-----HHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC--CCcccEEEEEcCHH-----HHHHHHHHHHHH
Confidence            34678999999999999999999999999999999999975  45778999999853     678888888765

>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=99.40  E-value=2.8e-13  Score=102.40  Aligned_cols=73  Identities=26%  Similarity=0.405  Sum_probs=63.2

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccC--CCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIAR--HEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~--~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ...+++|+||.+.+|.||||+|++||+|+++|||+|+|.+...+  ..++.|+|+|..+     .+.+|+.+|.+++.+.
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~-----~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK-----EVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHH-----HHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHH-----HHHHHHHHHHHHHhhC
Confidence            45789999999999999999999999999999999999975432  3689999999854     6789999999988653

>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=99.39  E-value=4.1e-13  Score=100.24  Aligned_cols=73  Identities=22%  Similarity=0.332  Sum_probs=61.6

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc-cCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI-ARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~-~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ..++++|.||.++++.||||+|++|++|+++|||+|+|++.. ++..++.|+|+|..+     ++.+|..+|..++.+.
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e-----~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK-----NTEAARDAILRIVGEL   88 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHH-----HHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHH-----HHHHHHHHHHHHHHHH
Confidence            457999999999999999999999999999999999999752 234689999999843     6778888888877543

>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=99.39  E-value=1.1e-12  Score=106.33  Aligned_cols=76  Identities=24%  Similarity=0.413  Sum_probs=66.2

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPP  222 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~  222 (257)
                      ++.+++||.+.+|.|||++|++|++|+++|||+|++.+....+.     ..+|.|+|+|++++|.+|+.+|.+++.+...
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~-----~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~   76 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT-----NVDKPLRIIGDPYKVQQACEMVMDILRERDQ   76 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSS-----SSCEEEEEEECHHHHHHHHHHHHHHTTCSSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCC-----CCceEEEEEcCHHHHHHHHHHHHHHHHhccC
Confidence            47899999999999999999999999999999999965332222     5789999999999999999999999998654


Q ss_pred             C
Q 025112          223 R  223 (257)
Q Consensus       223 ~  223 (257)
                      .
T Consensus        77 ~   77 (164)
T 2jvz_A           77 G   77 (164)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.38  E-value=6.6e-13  Score=100.34  Aligned_cols=69  Identities=20%  Similarity=0.280  Sum_probs=61.8

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      +....+.||.+++|.|||++|++|++|+++|||+|+|++..         ...+.|+|+|+++++++|+.+|..++.+
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g---------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE---------LQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT---------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC---------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            46889999999999999999999999999999999996421         2356999999999999999999999887

>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=99.38  E-value=8.1e-13  Score=108.83  Aligned_cols=79  Identities=30%  Similarity=0.471  Sum_probs=69.0

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      +.++++++||.+.+|.|||++|++|++|+++|||+|+|.+..+ .|.     ..+|.|+|+|++++|.+|..+|.+++.+
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~-----~~er~v~I~G~~~~v~~A~~~I~~~~~~   78 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPG-----TTERVCLIQGTIEALNAVHGFIAEKIRE   78 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTT-----SSEEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCC-----CCCceEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4578999999999999999999999999999999999965432 343     6789999999999999999999999998


Q ss_pred             CCCCC
Q 025112          220 NPPRQ  224 (257)
Q Consensus       220 ~~~~~  224 (257)
                      .+...
T Consensus        79 ~~~~~   83 (178)
T 2anr_A           79 MPQNV   83 (178)
T ss_dssp             CCCC-
T ss_pred             cCCcc
Confidence            76543

>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=99.38  E-value=3.3e-13  Score=100.15  Aligned_cols=73  Identities=19%  Similarity=0.307  Sum_probs=63.2

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ....++.+|.||.+.+|.|||++|.+||+|+++|||+|+|++.  +..++.|+|+|..     .++.+|..+|.+++.+.
T Consensus        13 l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~--~~~~~~V~I~G~~-----e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           13 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTK-----EGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECH-----HHHHHHHHHHHHHHHHH
T ss_pred             hCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC--CCCCCeEEEEECH-----HHHHHHHHHHHHHhhcc
Confidence            4567899999999999999999999999999999999999965  2346889999984     37889999999888654

>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=99.36  E-value=1.5e-12  Score=105.67  Aligned_cols=73  Identities=30%  Similarity=0.466  Sum_probs=65.5

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~  221 (257)
                      .+++++||.+.+|.|||++|++|++|+++|||+|+|.+. ..|.     +.+|.|+|+|+++++.+|+.+|.+++.+..
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~-~~~~-----~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~   75 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP-ETPD-----SKVRMVIITGPPEAQFKAQGRIYGKLKEEN   75 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC-SSTT-----CSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC-CCCC-----CCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            478999999999999999999999999999999999643 3343     689999999999999999999999999863

>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=99.36  E-value=8.9e-14  Score=104.73  Aligned_cols=66  Identities=17%  Similarity=0.234  Sum_probs=59.8

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHH-hCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNS-SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      .+..+.||..+|++|||++|++|++|+++ ++++|+|++            .++.|+|+|+++.|.+|..+|..++++.
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~------------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE------------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS------------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC------------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999997 499999853            3578999999999999999999999873

>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=99.34  E-value=1.7e-12  Score=106.55  Aligned_cols=73  Identities=26%  Similarity=0.374  Sum_probs=65.2

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~  221 (257)
                      ..+.+++||.+++|.|||++|++|++|+++|||+|+|.+.+  +.     ..+|.|+|+|++++|.+|+.+|.+++.+..
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~--~~-----~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~   74 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD--GT-----TPERIAQITGPPDRAQHAAEIITDLLRSVQ   74 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT--TS-----CSEEEEEEEECHHHHHHHHHHHHHHHHHHC
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC--CC-----CCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            35789999999999999999999999999999999997432  22     578999999999999999999999999864

>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=99.31  E-value=2.7e-12  Score=95.42  Aligned_cols=75  Identities=21%  Similarity=0.288  Sum_probs=63.2

Q ss_pred             CCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        45 ~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..+..+++.|.||.+.+|.|||++|++|++|+++|||+|+|++.. ...++.|+|+|.++     ++.+|+.+|..++.+
T Consensus        12 ~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-~~~~~~V~I~G~~e-----~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPE-----NVEEAIDHILNLEEE   85 (95)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHH-----HHHHHHHHHHHHHHH
T ss_pred             hhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-CCCCcEEEEEcCHH-----HHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999999998652 13578899999853     678888888888765


Q ss_pred             C
Q 025112          125 D  125 (257)
Q Consensus       125 ~  125 (257)
                      .
T Consensus        86 ~   86 (95)
T 2ctm_A           86 Y   86 (95)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.27  E-value=5e-12  Score=102.23  Aligned_cols=70  Identities=34%  Similarity=0.617  Sum_probs=63.9

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ...++++||...+|.|||++|++|++|+++|||+|+|.+.         +..+|.|+|+|+++++.+|+.+|.+++.+.
T Consensus         4 ~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~---------~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   73 (160)
T 2jzx_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG---------NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (160)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC---------TTTEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC---------CCCceEEEEEeCHHHHHHHHHHHHHHHHhh
Confidence            4689999999999999999999999999999999999743         146899999999999999999999999884

>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=99.26  E-value=3.3e-12  Score=96.45  Aligned_cols=70  Identities=20%  Similarity=0.287  Sum_probs=60.7

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      .....|.||.+.+|.|||++|++||+|+++|||+|+|++.  +...+.|+|+|..+     ++.+|..+|..++.+.
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~--g~~~~~V~I~G~~e-----~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAA-----NLDRAKAGLLERVKEL   85 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHH-----HHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC--CCCcceEEEEcCHH-----HHHHHHHHHHHHHhhH
Confidence            4789999999999999999999999999999999999975  33456899999853     6788888888887654

>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=99.25  E-value=9.6e-12  Score=92.36  Aligned_cols=72  Identities=19%  Similarity=0.236  Sum_probs=63.4

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ...+..+.||..+++.|||++|.+|++|+++| ||+|+|+..         ++..+.|+|+|+..++++|+++|.+++.+
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~---------g~~~~~V~I~G~~~~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE---------GSGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT---------TTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC---------CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            34578999999999999999999999999999 999998632         24567899999999999999999999987


Q ss_pred             CC
Q 025112          220 NP  221 (257)
Q Consensus       220 ~~  221 (257)
                      ..
T Consensus        86 ~e   87 (95)
T 2ctj_A           86 KQ   87 (95)
T ss_dssp             HS
T ss_pred             hh
Confidence            43

>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=99.22  E-value=3.6e-11  Score=90.38  Aligned_cols=67  Identities=24%  Similarity=0.343  Sum_probs=58.0

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      .++.+|.||+.+|+.|||++|++||+|++++ +++|+|++     .++.|+|+|+++     .|.+|..+|..++.+.
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~-----~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTE-----DVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHH-----HHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHH-----HHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999985 99999996     467899999954     6788888888777653

>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=99.21  E-value=9.6e-12  Score=92.36  Aligned_cols=76  Identities=21%  Similarity=0.315  Sum_probs=65.3

Q ss_pred             cCCCCCeEEEEEecCccccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        44 ~~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      +.+++..+..|.||.++++.|||++|.+|++|+++| ||+|+|++.  ++..+.|+|+|+.+     .+.+|..+|.+++
T Consensus        11 ~e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~--g~~~~~V~I~G~~~-----~v~~A~~~I~~iv   83 (95)
T 2ctj_A           11 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSS-----DVEKAKKQLLHLA   83 (95)
T ss_dssp             CCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHH-----HHHHHHHHHHHHH
T ss_pred             HHHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC--CCCcceEEEEcCHH-----HHHHHHHHHHHHH
Confidence            445677889999999999999999999999999999 999999975  45677899999853     6788899999988


Q ss_pred             hcCC
Q 025112          123 LKDD  126 (257)
Q Consensus       123 ~~~~  126 (257)
                      .+..
T Consensus        84 ~e~e   87 (95)
T 2ctj_A           84 EEKQ   87 (95)
T ss_dssp             HHHS
T ss_pred             hhhh
Confidence            7643

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

Probab=98.97  E-value=4.7e-10  Score=101.99  Aligned_cols=75  Identities=12%  Similarity=0.098  Sum_probs=61.8

Q ss_pred             CcceEEEEEeecCccceeecCCC--hhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 025112          140 VAANTIRLLIAGSQAGCLIGMSG--QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQ  216 (257)
Q Consensus       140 ~~~~~~~l~Vp~~~vG~iIGk~G--~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~  216 (257)
                      ...+++++.||..+|++||||+|  ++|++|+++|||+|+|+..+. +.. ........|+|+|.+++|++|+.+|.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~-~~~-~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSV-GGT-TPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCC-CSS-SCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcc-ccc-CCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            34679999999999999999999  999999999999999975430 000 0014567899999999999999999885

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.94  E-value=8.3e-10  Score=80.84  Aligned_cols=67  Identities=27%  Similarity=0.247  Sum_probs=58.0

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCe-EEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLR  218 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~  218 (257)
                      ..+...+.||.+.+|.+||++|++|++|++.|||+ |.+.            +.+..|+|.| +.+++++|+++|..+-.
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~------------eddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD------------EDTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE------------TTTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE------------cCCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            34688999999999999999999999999999998 9984            2358899999 88999999998866544


Q ss_pred             c
Q 025112          219 E  219 (257)
Q Consensus       219 e  219 (257)
                      .
T Consensus        81 ~   81 (91)
T 2cpq_A           81 F   81 (91)
T ss_dssp             C
T ss_pred             E
Confidence            4

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

Probab=98.87  E-value=1.4e-09  Score=86.65  Aligned_cols=69  Identities=26%  Similarity=0.342  Sum_probs=57.1

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCc-eEEEcccccC---CCcc--EEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKA-TIKIADAIAR---HEER--VIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~-~I~i~~~~~~---~~er--vv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..++.||.+.+|++|||+|.+||.|++.||+ +|+|......   ..++  .|+|+|+.     .++++|..+|.+++..
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 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTK-----DSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEH-----HHHHHHHHHHHHHHHT
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCH-----HHHHHHHHHHHHHHHh
Confidence            3889999999999999999999999999997 9999854211   2333  48899985     4788999999988864

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.85  E-value=2.2e-09  Score=78.63  Aligned_cols=53  Identities=23%  Similarity=0.329  Sum_probs=47.0

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCce-EEEcccccCCCccEEEeccCC
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKD  103 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~-I~i~~~~~~~~ervv~I~G~~  103 (257)
                      ....+...|.||.+.+|.+||++|.+|++|+++||++ |+|.+     ++..|.|.|..
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~   64 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGES   64 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESS
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECC
Confidence            3456889999999999999999999999999999998 99974     35789999964

>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=98.75  E-value=3.7e-08  Score=77.07  Aligned_cols=78  Identities=18%  Similarity=0.290  Sum_probs=60.6

Q ss_pred             ceEEEEEeecC------ccceeecCCChhHHHHHHHhCCeEEEeCCCCCCccc---------CCCCCceEEEEEc-CHHH
Q 025112          142 ANTIRLLIAGS------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA---------SAHESDRVVQISG-DVPA  205 (257)
Q Consensus       142 ~~~~~l~Vp~~------~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~---------~~~~~~r~V~I~G-~~~~  205 (257)
                      ..+.++.||..      ++|.|||++|.+||+|+++|||+|.|-.+.......         ...+.+-.|.|++ +.+.
T Consensus         6 k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~   85 (131)
T 1k1g_A            6 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   85 (131)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             eEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHH
Confidence            35789999987      889999999999999999999999996422111000         0012366899999 5789


Q ss_pred             HHHHHHHHHHHHhc
Q 025112          206 VLNALVEIGNQLRE  219 (257)
Q Consensus       206 v~~A~~~I~~~l~e  219 (257)
                      +++|+++|..+|.+
T Consensus        86 ~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           86 VKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999987

>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=98.73  E-value=2.2e-08  Score=78.39  Aligned_cols=73  Identities=21%  Similarity=0.398  Sum_probs=59.1

Q ss_pred             CCeEEEEEecCc------cccceeccCchhHHHHHhhhCceEEEccccc----------------CCCccEEEeccCCCC
Q 025112           48 QDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIADAIA----------------RHEERVIIISSKDND  105 (257)
Q Consensus        48 ~~~~~rilVP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~----------------~~~ervv~I~G~~~~  105 (257)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|.....                ..++--|.|++... 
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~-   83 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTM-   83 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSH-
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCH-
Confidence            457889999988      8899999999999999999999999985210                01255688888643 


Q ss_pred             chhhHHHHHHHHHHHHHhc
Q 025112          106 NVVSDAENALQQIAALILK  124 (257)
Q Consensus       106 ~~~~~~~~A~~~I~~~i~~  124 (257)
                         ..+.+|+.+|..++.+
T Consensus        84 ---e~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           84 ---ENVKKAVEQIRNILKQ   99 (131)
T ss_dssp             ---HHHHHHHHHHHHHHTT
T ss_pred             ---HHHHHHHHHHHHHHhc
Confidence               4788999999999875

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.70  E-value=2.1e-08  Score=77.13  Aligned_cols=72  Identities=22%  Similarity=0.128  Sum_probs=55.4

Q ss_pred             CeEEEEEecCc-------cccceeccCchhHHHHHhhhCceEEEccccc----------CCCccEEEeccCCCCchhhHH
Q 025112           49 DVLFRIIVPSR-------QIGKVIGKEGHRIQKIREETKATIKIADAIA----------RHEERVIIISSKDNDNVVSDA  111 (257)
Q Consensus        49 ~~~~rilVP~~-------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~----------~~~ervv~I~G~~~~~~~~~~  111 (257)
                      .+..||.||.+       .+|.|||++|.+||+|+++|||+|.|.....          ..++-.|.|.+...    .++
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   86 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKP----EGL   86 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSH----HHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCH----HHH
Confidence            36678888875       6999999999999999999999999973310          01344688887643    467


Q ss_pred             HHHHHHHHHHHhc
Q 025112          112 ENALQQIAALILK  124 (257)
Q Consensus       112 ~~A~~~I~~~i~~  124 (257)
                      .+|+.+|.+++..
T Consensus        87 ~~A~~~Ie~Ll~~   99 (119)
T 2yqr_A           87 AAAKKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhc
Confidence            8898888888865

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.64  E-value=7.7e-08  Score=73.96  Aligned_cols=77  Identities=13%  Similarity=0.088  Sum_probs=56.7

Q ss_pred             eEEEEEeecC-------ccceeecCCChhHHHHHHHhCCeEEEeCCCCC---CcccCCCCCceEEEEEc-CHHHHHHHHH
Q 025112          143 NTIRLLIAGS-------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQL---PLCASAHESDRVVQISG-DVPAVLNALV  211 (257)
Q Consensus       143 ~~~~l~Vp~~-------~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~---p~~~~~~~~~r~V~I~G-~~~~v~~A~~  211 (257)
                      ...+|.||-.       ++|.|||++|.+||+|+++|||+|.|-.+...   +........+-.|.|.+ +.+++++|++
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            4677888754       78999999999999999999999999532110   00000002345788886 5889999999


Q ss_pred             HHHHHHhc
Q 025112          212 EIGNQLRE  219 (257)
Q Consensus       212 ~I~~~l~e  219 (257)
                      +|.++|.+
T Consensus        92 ~Ie~Ll~~   99 (119)
T 2yqr_A           92 LCENLLQT   99 (119)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhhc
Confidence            99999986

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

Probab=98.57  E-value=6.7e-08  Score=82.00  Aligned_cols=66  Identities=21%  Similarity=0.149  Sum_probs=58.3

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-----HHHHHHHHHHHHHH
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-----VPAVLNALVEIGNQ  216 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-----~~~v~~A~~~I~~~  216 (257)
                      ....++.||.+.+|.|||++|.+|+.|+++|||+|++.            ..++.|+|.|+     ++++++|..+|..+
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~------------~~~g~V~I~~~~~t~d~~~i~kA~~~I~~i  100 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITID------------SETGEVWITSTKETEDPLAVWKARDIVLAI  100 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEEC------------TTTCEEEEEECTTCCSHHHHHHHHHHHHHH
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEE------------cCCCEEEEecCCCCCCHHHHHHHHHHHHHH
Confidence            35679999999999999999999999999999999984            23567899886     69999999999999


Q ss_pred             Hhc
Q 025112          217 LRE  219 (257)
Q Consensus       217 l~e  219 (257)
                      ++.
T Consensus       101 ~rg  103 (219)
T 2e3u_A          101 GRG  103 (219)
T ss_dssp             HTT
T ss_pred             hcc
Confidence            854

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.52  E-value=1.6e-07  Score=74.04  Aligned_cols=75  Identities=17%  Similarity=0.404  Sum_probs=55.3

Q ss_pred             eEEEEEecCcc------ccceeccCchhHHHHHhhhCceEEEcccccC------------------CCccEEEeccCCCC
Q 025112           50 VLFRIIVPSRQ------IGKVIGKEGHRIQKIREETKATIKIADAIAR------------------HEERVIIISSKDND  105 (257)
Q Consensus        50 ~~~rilVP~~~------vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~------------------~~ervv~I~G~~~~  105 (257)
                      ++-|+.||.+.      +|.|||++|.++|+|+++|||+|.|-..-..                  ...--|.|++....
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            56788999766      9999999999999999999999999853100                  01125778885432


Q ss_pred             -chhhHHHHHHHHHHHHHhc
Q 025112          106 -NVVSDAENALQQIAALILK  124 (257)
Q Consensus       106 -~~~~~~~~A~~~I~~~i~~  124 (257)
                       .....+++|+.+|.+++..
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             hhHHHHHHHHHHHHHHHCCC
Confidence             1223578899999998864

>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=98.39  E-value=5.4e-07  Score=74.79  Aligned_cols=69  Identities=16%  Similarity=0.240  Sum_probs=61.4

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE-----cCHHHHHHHHHHHHHHHh
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GDVPAVLNALVEIGNQLR  218 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~-----G~~~~v~~A~~~I~~~l~  218 (257)
                      ..++.||.+.+|.|||++|++++.|++.+|++|++.            ..++.|+|.     |++.++.+|..+|..+.+
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id------------~~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~r   72 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD------------TENSMVIVEPEAEGIPPVNLMKAAEVVKAISL   72 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE------------TTTTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE------------cCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Confidence            468999999999999999999999999999999984            346788999     999999999999999888


Q ss_pred             cCCCCC
Q 025112          219 ENPPRQ  224 (257)
Q Consensus       219 e~~~~~  224 (257)
                      .++..+
T Consensus        73 gf~~e~   78 (191)
T 1tua_A           73 GFPPEK   78 (191)
T ss_dssp             TCCHHH
T ss_pred             CCCHHH
Confidence            765443

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.36  E-value=5.4e-07  Score=71.00  Aligned_cols=78  Identities=17%  Similarity=0.232  Sum_probs=56.3

Q ss_pred             EEEEEeecC------ccceeecCCChhHHHHHHHhCCeEEEeCCCCCCc------------ccCCCCCceEEEEEcC-HH
Q 025112          144 TIRLLIAGS------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPL------------CASAHESDRVVQISGD-VP  204 (257)
Q Consensus       144 ~~~l~Vp~~------~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~------------~~~~~~~~r~V~I~G~-~~  204 (257)
                      +.+|.||..      ++|.|||++|.++|+|+++|||+|.|--+...-.            ... .+.+--|.|++. ++
T Consensus         3 ~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~-~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEH-LNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHT-TTSCCEEEEEECSCC
T ss_pred             eeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccc-cCCCcEEEEEecCch
Confidence            567888844      5999999999999999999999999964321100            000 012237889984 32


Q ss_pred             -----HHHHHHHHHHHHHhcCCC
Q 025112          205 -----AVLNALVEIGNQLRENPP  222 (257)
Q Consensus       205 -----~v~~A~~~I~~~l~e~~~  222 (257)
                           .+++|+++|..+|...++
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~~e  104 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPAAE  104 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCSS
T ss_pred             hhHHHHHHHHHHHHHHHCCCCCc
Confidence                 789999999999986443

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.34  E-value=5.2e-07  Score=87.41  Aligned_cols=93  Identities=17%  Similarity=0.178  Sum_probs=68.5

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +..+.+++..|++.+.+........    .....+....+.||.+.+|.|||+||++||.|+++|||+|.|.        
T Consensus       536 L~~A~~g~~~I~~~m~~al~~~~~~----~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~--------  603 (630)
T 3u1k_A          536 IQQASVAKKEILQIMNKTISKPRAS----RKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV--------  603 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSCCSS----CCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC--------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh----hcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc--------
Confidence            3456777788888776543321110    0112245788999999999999999999999999999999983        


Q ss_pred             cCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 025112          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQL  217 (257)
Q Consensus       188 ~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l  217 (257)
                           .+..|.|.|. .+..++|+++|..++
T Consensus       604 -----d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          604 -----DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             -----SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             -----CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence                 3467999996 578999999987664

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=98.13  E-value=1.9e-06  Score=68.22  Aligned_cols=104  Identities=16%  Similarity=0.253  Sum_probs=73.8

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~  129 (257)
                      -.+.|+|+...+|+.||++|++|+.|+++.|-+|++-...   ++        +           ...|...+.-.....
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s---~d--------~-----------~~fI~naLsPA~V~~   93 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYS---SD--------L-----------ERIVKNLFPGVKIES   93 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECC---SS--------H-----------HHHHHHHSTTSCEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcC---CC--------H-----------HHHHHHhcCCceEEE
Confidence            4689999999999999999999999999999999987541   11        0           111222221100000


Q ss_pred             chhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEe
Q 025112          130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL  179 (257)
Q Consensus       130 ~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~  179 (257)
                      .   ..... .+.....+.||.++.+..|||+|.+++-..+-||.+|.|.
T Consensus        94 V---~i~~~-~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           94 I---NVRER-NGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             E---EEEEE-TTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             E---EEeec-CCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            0   00000 1235788999999999999999999999999999988874

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=98.08  E-value=1.1e-05  Score=62.66  Aligned_cols=67  Identities=16%  Similarity=0.136  Sum_probs=58.7

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR  218 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~  218 (257)
                      ...+.+.+..++.|||++|+.|+.|+..|++.|++..-+.        ++...|+|.|++..-..|..+|..+..
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s--------~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP--------ERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT--------TSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC--------CCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            4788899999999999999999999999999999975321        457889999999999999999987664

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.88  E-value=6.6e-06  Score=80.72  Aligned_cols=100  Identities=21%  Similarity=0.241  Sum_probs=27.2

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +..+.+++..|++.+.+.....-..    .....+....+.||.+.++.|||+||.+||.|+++||++|.+.        
T Consensus       539 L~~A~~g~~~I~~~m~~al~~~r~~----~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~--------  606 (726)
T 4aid_A          539 LAQAKEGRAHILGEMNKAMDAPRAD----VGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN--------  606 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCSS----CCSSCCC--------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhh----hcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE--------
Confidence            4456777788888876653321110    1112234678889999999999999999999999999999983        


Q ss_pred             cCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCCCCC
Q 025112          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQLRENPPRQ  224 (257)
Q Consensus       188 ~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~e~~~~~  224 (257)
                           .+..|.|.+. .+.+++|+.+|..++.+....+
T Consensus       607 -----ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~  639 (726)
T 4aid_A          607 -----DDGVVKVSASDGAKIKAAIDWIKSITDEAEVGK  639 (726)
T ss_dssp             ------------CCSCHHHHHHHHHC------------
T ss_pred             -----CCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCc
Confidence                 2456778775 7799999999999887654443

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.83  E-value=5.3e-06  Score=80.39  Aligned_cols=63  Identities=25%  Similarity=0.341  Sum_probs=51.1

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHH
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~  121 (257)
                      .-...|.||.+.+|.|||+||.+||+|+++|||+|+|.+      +..|.|.|...    ..+.+|+.+|..+
T Consensus       566 p~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d------~G~V~I~~~~~----~~~~~A~~~I~~i  628 (630)
T 3u1k_A          566 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTP----SAMHEARDFITEI  628 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESSH----HHHHHHHHHTTC-
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCCH----HHHHHHHHHHHHH
Confidence            457889999999999999999999999999999999984      45789988643    2556777666544

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.54  E-value=0.00017  Score=56.02  Aligned_cols=67  Identities=16%  Similarity=0.147  Sum_probs=53.1

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      -.+.|.|.+..++.|+|++|+.|+.|+..|++.|++..-.+ +.+-.|+|.|++.     .=.++..+|..+.
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~-----~Q~rak~MI~sLA  122 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPP-----FRRDVDRMLTDLA  122 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHH-----HHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHH-----HHHHHHHHHHHHH
Confidence            45778889999999999999999999999999999996643 4567799999853     2235556665544

>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=97.28  E-value=3.7e-05  Score=65.99  Aligned_cols=106  Identities=23%  Similarity=0.250  Sum_probs=70.5

Q ss_pred             EEEEEecC-----ccccceeccCchhHHHH-HhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           51 LFRIIVPS-----RQIGKVIGKEGHRIQKI-REETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        51 ~~rilVP~-----~~vg~IIGk~G~~Ik~I-~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      -.++-|-+     +-+|+.||++|++|+.| ++-.|-+|+|-...   ++                   ....|...+.-
T Consensus       113 R~KiAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s---~d-------------------p~~fi~nalsP  170 (251)
T 2asb_A          113 RSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYD---DD-------------------PARFVANALSP  170 (251)
T ss_dssp             EEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC---SS-------------------HHHHHHHHTTT
T ss_pred             eeEEEEEcCCCCCCHHHHHhCCCchHHHHHHHHhCCCeEEEEEec---CC-------------------HHHHHHhccCC
Confidence            34555544     34999999999999999 67788888887541   11                   01122222211


Q ss_pred             CCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC
Q 025112          125 DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ  183 (257)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~  183 (257)
                      .......     ..........+.||..+.+.-|||+|.|++-..+-||.+|.|.+..+
T Consensus       171 A~V~~V~-----i~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          171 AKVVSVS-----VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             SCCSEEE-----EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             cceEEEE-----EEcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            1110000     00001146899999999999999999999999999999999976443

>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=97.13  E-value=0.00043  Score=62.57  Aligned_cols=107  Identities=23%  Similarity=0.259  Sum_probs=73.2

Q ss_pred             eEEEEEecC-----ccccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           50 VLFRIIVPS-----RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        50 ~~~rilVP~-----~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      .-.++-|-+     +-+|+.||++|++|+.|.++. |-+|+|-...   ++                   -...|...+.
T Consensus       235 ~RaKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s---~d-------------------p~~fi~nals  292 (366)
T 1k0r_A          235 HRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYD---DD-------------------PARFVANALS  292 (366)
T ss_dssp             TEEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC---SS-------------------HHHHHHHHTT
T ss_pred             CeEEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEcC---CC-------------------HHHHHHHhcC
Confidence            445666655     569999999999999999998 8888887541   11                   0112222222


Q ss_pred             cCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC
Q 025112          124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ  183 (257)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~  183 (257)
                      -.......   . . ........+.||..+.+..|||+|.|++-..+-||.+|.|.+..+
T Consensus       293 PA~V~~V~---~-~-~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  347 (366)
T 1k0r_A          293 PAKVVSVS---V-I-DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  347 (366)
T ss_dssp             TSCCSEEE---E-E-ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESSC
T ss_pred             CcceeEEE---E-E-cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHHH
Confidence            11110000   0 0 011247899999999999999999999999999999999976433

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.07  E-value=0.00012  Score=71.75  Aligned_cols=65  Identities=28%  Similarity=0.441  Sum_probs=9.3

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      -...|.||.+.++.|||+||.+||+|+++||++|+|.+      +..|.|.+...    .++.+|+.+|..++.+
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d------dG~v~I~~~~~----~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDG----AKIKAAIDWIKSITDE  634 (726)
T ss_dssp             C-------------------------------------------------CCSCH----HHHHHHHHC-------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC------CceEEEEeCCH----HHHHHHHHHHHHHhhh
Confidence            35678889999999999999999999999999999984      34578888643    3566777777766643

>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=96.69  E-value=0.002  Score=57.88  Aligned_cols=96  Identities=24%  Similarity=0.260  Sum_probs=65.5

Q ss_pred             ccccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhcc
Q 025112           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (257)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (257)
                      +-+|+.||.+|.+|+.|.++. |-+|++-...   ++                   -...|...|.-......     ..
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s---~d-------------------~~~fi~nal~Pa~v~~v-----~~  297 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWS---DD-------------------PKQLIANALAPATVIEV-----EI  297 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECC---SS-------------------HHHHHHHHTCSSCCSEE-----EE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecC---CC-------------------HHHHHHHhcCccEEEEE-----EE
Confidence            348999999999999999997 7777776441   11                   11222222211111000     00


Q ss_pred             CCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (257)
Q Consensus       138 ~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~  181 (257)
                      .........+.||..+.+.-|||+|.|++-..+-||.+|.|.+.
T Consensus       298 ~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          298 LDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            00112478999999999999999999999999999999999653

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=96.66  E-value=0.00056  Score=67.23  Aligned_cols=99  Identities=20%  Similarity=0.203  Sum_probs=12.5

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +..+.+++..|++.+.+.........+    ...+....+.||.+.++.+||++|.+|+.|.++||+.|.+.        
T Consensus       529 l~~A~~~~~~I~~~m~~al~~~~~~~~----~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~--------  596 (723)
T 3cdi_A          529 LNQAKGARLHILGVMEQAINAPRGDIS----EFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE--------  596 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHHCC------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhhhcchhcc----ccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEec--------
Confidence            345567777777777654322111100    11234567889999999999999999999999999999873        


Q ss_pred             cCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCCCC
Q 025112          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQLRENPPR  223 (257)
Q Consensus       188 ~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~e~~~~  223 (257)
                           .+..|.|.+. ....++|.++|..++.+....
T Consensus       597 -----~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG  628 (723)
T 3cdi_A          597 -----DDGTVKIAATDGEKAKHAIRRIEEITAEIEVG  628 (723)
T ss_dssp             -------------------------------------
T ss_pred             -----CCccEEEecCCHHHHHHHHHHHHHHhhhhhcC
Confidence                 2456777765 567788888887776553333

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=95.98  E-value=0.00048  Score=68.00  Aligned_cols=92  Identities=24%  Similarity=0.302  Sum_probs=35.6

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (257)
                      +..+.+++..|++.+.+..... ...    ....+....+.||.+.+|.+||++|.+||.|+++||+.|.+.        
T Consensus       568 L~~A~~~~~~I~~~m~~al~~~-~~~----~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~--------  634 (757)
T 1e3p_A          568 LKQARDARLHILDVMMEAIDTP-DEM----SPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE--------  634 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSC-CCC----CTTSCBCCCC------------------CTTCCCCCSCC-----------
T ss_pred             HHHHHHHHHHHHHHHHHHhccc-ccc----cccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEec--------
Confidence            3456677777888776543322 111    111223456789999999999999999999999999999983        


Q ss_pred             cCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 025112          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQL  217 (257)
Q Consensus       188 ~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l  217 (257)
                           .+..|.|.+. ....++|.++|..+.
T Consensus       635 -----~dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          635 -----DDGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             ----------CCCBSSHHHHCC---------
T ss_pred             -----CCceEEEecCCHHHHHHHHHHHHHhc
Confidence                 2456777764 567777776776655

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=94.74  E-value=0.0053  Score=60.36  Aligned_cols=64  Identities=31%  Similarity=0.519  Sum_probs=0.0

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      .-...+.||.+.++.+||++|.+|+.|.++||+.|++.+      +..+.|.+....    .+.+|..+|..++
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~~----~~~~a~~~i~~i~  622 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGE----KAKHAIRRIEEIT  622 (723)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCHH----HHHHHHHHHHHHh
Confidence            345677889999999999999999999999999998874      345777765432    3445555555444

>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=93.54  E-value=0.0055  Score=60.49  Aligned_cols=46  Identities=37%  Similarity=0.630  Sum_probs=16.7

Q ss_pred             EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCC
Q 025112           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (257)
Q Consensus        52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~  103 (257)
                      ..|.||.+.+|.+||++|.+||+|+++||+.|+|.+      +..|.|+...
T Consensus       600 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~  645 (757)
T 1e3p_A          600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAAD  645 (757)
T ss_dssp             CCC------------------CTTCCCCCSCC--------------CCCBSS
T ss_pred             EEEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCC
Confidence            457789999999999999999999999999999884      4567777764

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=92.55  E-value=0.079  Score=41.57  Aligned_cols=38  Identities=32%  Similarity=0.535  Sum_probs=35.3

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~  180 (257)
                      ....++|+...+|..||++|++|+.|+++.|-+|.+..
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~   73 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE   73 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE
Confidence            36889999999999999999999999999999999875

>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=90.52  E-value=0.22  Score=42.60  Aligned_cols=40  Identities=30%  Similarity=0.359  Sum_probs=36.7

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      .....+.||.++.+..|||+|.|++.-.+-||.+|+|.+.
T Consensus       183 ~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          183 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            3578999999999999999999999999999999999754

>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=89.07  E-value=0.25  Score=44.22  Aligned_cols=41  Identities=27%  Similarity=0.375  Sum_probs=37.3

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (257)
                      ++.....+.||..+.+..|||+|.|++.-.+-||.+|+|..
T Consensus       300 ~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          300 KENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             TTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            34567899999999999999999999999999999999863

>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=87.96  E-value=0.31  Score=43.92  Aligned_cols=41  Identities=29%  Similarity=0.350  Sum_probs=37.3

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      .+....+.||....+..|||+|.|++-..+-||.+|+|...
T Consensus       305 ~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          305 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             CCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            35678999999999999999999999999999999999744

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=86.36  E-value=0.35  Score=38.21  Aligned_cols=31  Identities=16%  Similarity=0.174  Sum_probs=26.8

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhC
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETK   80 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg   80 (257)
                      -++.|.+..+..|.||||.|.+++.||--+.
T Consensus        33 ~~i~i~i~ged~glLIGK~G~TL~ALQyL~~   63 (152)
T 2pt7_G           33 GVLLIDIDGEDSALLIGEKGYRYKALSYLLF   63 (152)
T ss_dssp             TEEEEEEEEGGGTTTTCGGGHHHHHHHHHHH
T ss_pred             CEEEEEEecCCcceEECCCCcchHHHHHHHH
Confidence            3567777889999999999999999998874

>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=80.88  E-value=0.63  Score=33.50  Aligned_cols=28  Identities=25%  Similarity=0.488  Sum_probs=24.3

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhh
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREE   78 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~   78 (257)
                      .+++.|....-|.|||++|..|++|+++
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            4678888899999999999999888765

---

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	257
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-08
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	6e-09
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-07
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	8e-09
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	9e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	4e-07
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	7e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	5e-08
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	5e-08
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-06
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-08
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	8e-07
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	7e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	8e-08
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	0.001
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	9e-05
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	6e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	6e-05
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	8e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	4e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-06
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-05
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	1e-04
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	3e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	6e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	9e-04

>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 = 54.0 bits (130), Expect = 1e-10
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 9/76 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I   N           +R++ ++G  
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---------CPERIITLAGPT 55

Query: 204 PAVLNALVEIGNQLRE 219
            A+  A   I ++L E
Sbjct: 56  NAIFKAFAMIIDKLEE 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 = 48.6 bits (116), Expect = 1e-08
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 7/73 (9%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++        +
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP-----TN 56

Query: 110 DAENALQQIAALI 122
               A   I   +
Sbjct: 57  AIFKAFAMIIDKL 69

>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 = 50.7 bits (121), Expect = 4e-09
 Identities = 21/96 (21%), Positives = 39/96 (40%), Gaps = 7/96 (7%)

Query: 45  AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSK 102
            +   V  ++ VP R +G++IG+ G  I+ I + + A I             R+I IS  
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 103 DNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138
                  +   A   I   + +D++     +  A+G
Sbjct: 70  -----QKEVAAAKHLILEKVSEDEELRKRIAHSASG 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 = 48.8 bits (116), Expect = 2e-08
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
             +L +     G +IG  G+ I  +  +SGA I     ++           R+++ISG  
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-----GTLLLSRLIKISGTQ 70

Query: 204 PAVLNALVEIGNQLRENPPRQ 224
             V  A   I  ++ E+   +
Sbjct: 71  KEVAAAKHLILEKVSEDEELR 91

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (118), Expect = 6e-09
 Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
              VP   +G +IG+ G +I +I++E+   I+IA       ER  +++           +
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT-----PESVQ 65

Query: 113 NALQQIAALI 122
           +A + +  ++
Sbjct: 66  SAKRLLDQIV 75

>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 = 45.2 bits (107), Expect = 2e-07
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 7/77 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T    +     G +IG  G+ I +++  SG  I I   +           +R   ++G  
Sbjct: 9   TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-------GGLPERSCMLTGTP 61

Query: 204 PAVLNALVEIGNQLREN 220
            +V +A   +   + + 
Sbjct: 62  ESVQSAKRLLDQIVEKG 78

>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 = 49.1 bits (117), Expect = 8e-09
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P+  IG +IG++G  I +IR+ + A IKIA+ +     R + I+        +   
Sbjct: 5   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS-----AASIS 59

Query: 113 NALQQIAALI 122
            A   I A +
Sbjct: 60  LAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 9e-08
 Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T  L I  +  GC+IG  G NI ++R  SGA I I  P           S R V I+G  
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-------EGSSGRQVTITGSA 55

Query: 204 PAVLNALVEIGNQL 217
            ++  A   I  +L
Sbjct: 56  ASISLAQYLINARL 69

>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 = 47.9 bits (114), Expect = 2e-08
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             + + +  +  G ++G  G+ + + +  +GA I I    +          +R V I+G 
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT----RNRRVTITGS 58

Query: 203 VPAVLNALVEIGNQL 217
             A   A   I  ++
Sbjct: 59  PAATQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (105), Expect = 4e-07
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 8/74 (10%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIISSKDNDNVV 108
             + VP   +G ++GK G  + + +E T A I+I+   + +     R + I+        
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-----P 59

Query: 109 SDAENALQQIAALI 122
           +  + A   I+  +
Sbjct: 60  AATQAAQYLISQRV 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 = 47.9 bits (114), Expect = 2e-08
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
           ++ +P    G +IGK G RI++IR E+ A+IKI + +   E+R+I I+           +
Sbjct: 7   QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-----QDQIQ 61

Query: 113 NALQQIAALI 122
           NA   +   +
Sbjct: 62  NAQYLLQNSV 71

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (110), Expect = 7e-08
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T ++ I    AG +IG  GQ I+++R+ SGA+I I  P            DR++ I+G  
Sbjct: 5   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-------EGSEDRIITITGTQ 57

Query: 204 PAVLNALVEIGNQLRE 219
             + NA   + N +++
Sbjct: 58  DQIQNAQYLLQNSVKQ 73

>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 = 46.2 bits (110), Expect = 5e-08
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 6/56 (10%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND 105
            +  + +P  +IG+VIG +   I +I+E+T A I I D      +  I I + D  
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGP 52

>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 = 46.8 bits (111), Expect = 5e-08
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
               ++   + G +IG  G+ I+ +   SGA I +          +A  + ++  I G  
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP----PPNADPNMKLFTIRGTP 57

Query: 204 PAVLNALVEI 213
             +  A   I
Sbjct: 58  QQIDYARQLI 67

>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 = 42.2 bits (99), Expect = 2e-06
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIISSKDNDNVV 108
           F  IVP+ + G +IGK G  I+ I +++ A I++       A    ++  I         
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT-----P 57

Query: 109 SDAENALQQIAALI 122
              + A Q I   I
Sbjct: 58  QQIDYARQLIEEKI 71

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 5e-08
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
             + +P   +G VIG+ G  I+KI+ +    I+         ER+  I+          A
Sbjct: 5   IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-----PDRA 59

Query: 112 ENALQQIAALI 122
           ++A + I  L+
Sbjct: 60  QHAAEIITDLL 70

>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 = 43.7 bits (103), Expect = 8e-07
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
           + I + I     G +IG +G+ I+K++N +G  I     +           +R+ QI+G 
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-------GTTPERIAQITGP 55

Query: 203 VPAVLNALVEIGNQLRE 219
                +A   I + LR 
Sbjct: 56  PDRAQHAAEIITDLLRS 72

>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 = 46.9 bits (111), Expect = 7e-08
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
              ++I  S+AG +IG  G+ I++L+  +G  +V++             +D+ ++I+GD 
Sbjct: 9   VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-----TGADKPLRITGDP 63

Query: 204 PAVLNALVEIGNQLRE 219
             V  A   +   +R+
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 = 41.9 bits (98), Expect = 4e-06
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 48  QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDND 105
            + +  I++P+ + G VIGK G  I++++E     + +          ++ + I+     
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD--- 62

Query: 106 NVVSDAENALQQIAALI 122
                 + A + +  LI
Sbjct: 63  --PYKVQQAKEMVLELI 77

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (110), Expect = 8e-08
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 4/68 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            I +  +    +IGK G  I +I+++ K +++I          + I         V  A+
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-EKSNLIRIEGDPQG---VQQAK 63

Query: 113 NALQQIAA 120
             L ++A+
Sbjct: 64  RELLELAS 71

>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 = 34.3 bits (79), Expect = 0.001
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 9/70 (12%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
            + + I       LIG SG NI ++++    ++ I             E   +++I GD 
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI---------PPDSEKSNLIRIEGDP 56

Query: 204 PAVLNALVEI 213
             V  A  E+
Sbjct: 57  QGVQQAKREL 66

>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 = 44.7 bits (106), Expect = 4e-07
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P      VIGK G ++Q +  +T   I+I         ++ I  +K+    +  A 
Sbjct: 13  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-DDPSNQIKITGTKEG---IEKAR 68

Query: 113 NALQQIAA 120
           + +  I+A
Sbjct: 69  HEVLLISA 76

>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 = 37.8 bits (88), Expect = 9e-05
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           +  + I       +IG +G+ ++ L   +   I I  P+         +    ++I+G  
Sbjct: 11  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD---------DPSNQIKITGTK 61

Query: 204 PAVLNALVEIGNQLRENPPR 223
             +  A  E+     E   R
Sbjct: 62  EGIEKARHEVLLISAEQDKR 81

>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 = 44.1 bits (104), Expect = 6e-07
 Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + V  +   K+IG++G  I +IR E    I+  D    ++ +  I  +    N     E
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNT----E 68

Query: 113 NALQQIAALI 122
            A   I  ++
Sbjct: 69  AARDAILRIV 78

>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 = 38.7 bits (90), Expect = 6e-05
 Identities = 11/76 (14%), Positives = 23/76 (30%), Gaps = 6/76 (7%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
            + + +       +IG  G  I ++R      I     +        ++    + I+G  
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD------DGNQPQDQITITGYE 64

Query: 204 PAVLNALVEIGNQLRE 219
                A   I   + E
Sbjct: 65  KNTEAARDAILRIVGE 80

>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 = 44.0 bits (104), Expect = 8e-07
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 7/70 (10%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + VP      VIG++G  I+K+ +E +  I +       +  +I I+     N+    +
Sbjct: 13  EVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITG-LAANL----D 65

Query: 113 NALQQIAALI 122
            A   +   +
Sbjct: 66  RAKAGLLERV 75

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (91), Expect = 4e-05
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 9/76 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TI + +       +IG  G  I K+ +     I + AP              ++ I+G  
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE---------LQSDIIAITGLA 61

Query: 204 PAVLNALVEIGNQLRE 219
             +  A   +  +++E
Sbjct: 62  ANLDRAKAGLLERVKE 77

>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 = 43.3 bits (102), Expect = 1e-06
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +  R   ++IG  G  I+KI +E K  I+   + A     V +    +N       E
Sbjct: 13  DVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN------VE 66

Query: 113 NALQQIAALI 122
            A+  I  L 
Sbjct: 67  EAIDHILNLE 76

>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 = 40.1 bits (94), Expect = 2e-05
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + +   ++ +VIGK+G  I+ ++ E    I +          + +   +     VS AE 
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----NGLIWVNGDRRK---VSIAEE 56

Query: 114 ALQQIAA 120
           A+  I  
Sbjct: 57  AIYLIEQ 63

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 39.0 bits (91), Expect = 4e-05
 Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 5/68 (7%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + V   ++G VIG  G    +I   T   I +       E  ++I+  +       +   
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMK 61

Query: 114 ALQQIAAL 121
           A + + A+
Sbjct: 62  AAEVVKAI 69

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 37.0 bits (86), Expect = 1e-04
 Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 7/67 (10%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           I +   ++ +VIGK     + +  ++  +I +A+         I  +     +       
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCPSRFS-EEILIE 57

Query: 114 ALQQIAA 120
           A+++I  
Sbjct: 58  AIRKIEN 64

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 6/58 (10%)

Query: 58  SRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENAL 115
            R  G++IG+ G   + I E T   I + +        V II   +       A   L
Sbjct: 21  KRIKGRIIGEGGRARRTIEEMTDTYINVGE------YEVAIIGDYERAMAAKQAIEML 72

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 3e-04
 Identities = 13/69 (18%), Positives = 22/69 (31%), Gaps = 8/69 (11%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
            +V    +G  IG  G  IQ+ R+    T          +     I  +  D V    + 
Sbjct: 12  FVVREDLMGLAIGTHGSNIQQARKVPGVTAI----ELDEDTGTFRIYGESADAV----KK 63

Query: 114 ALQQIAALI 122
           A   +  + 
Sbjct: 64  ARGFLEFVE 72

>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 = 35.6 bits (82), Expect = 6e-04
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 8/71 (11%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREE-TKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            + +P++    +IG +G  I+ I EE     I             ++I    + +V    
Sbjct: 13  EVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRG-PSSDV---- 65

Query: 112 ENALQQIAALI 122
           E A +Q+  L 
Sbjct: 66  EKAKKQLLHLA 76

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.1 bits (81), Expect = 9e-04
 Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 7/67 (10%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + +   ++ +VIG++   ++ + E+T+  I +A          I +   + D   + A  
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNEDL-EAIAVM 57

Query: 114 ALQQIAA 120
           A++ I  
Sbjct: 58  AIKIIDE 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	257
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.67
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.66
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.66
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.66
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.66
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.66
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.65
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.61
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.61
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.6
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.6
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.6
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.57
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.56
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.55
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.53
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.52
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.48
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.45
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.43
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.41
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.28
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.25
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.17
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.12
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.07
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.02
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.99
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.99
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.88
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.81
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.79
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.76
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.67
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.29
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.26
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.19
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.98
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.96
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.31
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.28
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.27
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.93
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	92.75
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	90.02
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	85.36
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	84.23
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	83.26
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	81.58
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	80.62

>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=99.67  E-value=4.8e-17  Score=113.10  Aligned_cols=69  Identities=35%  Similarity=0.615  Sum_probs=63.2

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ..+++++||++++|+|||++|++|++|+++|||+|++++.         ...+|+|+|+|++++|.+|..+|.++|+|
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~---------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG---------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS---------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC---------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            3689999999999999999999999999999999999642         14689999999999999999999999986

>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=99.66  E-value=1e-16  Score=111.39  Aligned_cols=70  Identities=20%  Similarity=0.360  Sum_probs=61.2

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  217 (257)
                      .+++.||++++|+|||++|++|++|++.|||+|+|.+... +..   ++.+|.|+|+|++++|++|.++|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~~~---~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-PNA---DPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-TTS---CTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-CCC---CCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4689999999999999999999999999999999976433 221   367899999999999999999999875

>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=99.66  E-value=5.2e-17  Score=115.80  Aligned_cols=76  Identities=24%  Similarity=0.415  Sum_probs=67.5

Q ss_pred             CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ++..+.+++||..++|+|||++|++|++|+++|||+|.|.+.+..+.     +.+|.|+|+|++++|.+|.++|.++|+|
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~-----~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT-----GADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSS-----CSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCC-----CCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            35678999999999999999999999999999999999976444333     6789999999999999999999999987


Q ss_pred             C
Q 025112          220 N  220 (257)
Q Consensus       220 ~  220 (257)
                      .
T Consensus        80 ~   80 (81)
T d1x4ma1          80 Q   80 (81)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=7.6e-17  Score=112.96  Aligned_cols=71  Identities=27%  Similarity=0.403  Sum_probs=64.2

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ...+++.||.+++|+|||++|++|++|+++|||+|+|.+.+.       +..+|.|+|+|++++|++|.++|.++|++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~-------~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-------TTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT-------SCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC-------CCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            357999999999999999999999999999999999975432       25789999999999999999999999976

>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=99.66  E-value=1.5e-16  Score=111.47  Aligned_cols=70  Identities=20%  Similarity=0.343  Sum_probs=62.5

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  217 (257)
                      .+++.||.+++|+|||++|++|++|+++|||+|+|.+.++...    +..+|.|+|+|++++|++|.++|.++|
T Consensus         4 ~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~----~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP----GTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST----TCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCC----CCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            5799999999999999999999999999999999976544322    267999999999999999999999876

>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=99.66  E-value=1.6e-16  Score=111.57  Aligned_cols=71  Identities=32%  Similarity=0.499  Sum_probs=64.0

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      .+.++.||.+++|+|||++|++|++|+++|||+|++.+.+  +     ++.+|.|+|+|++++|++|+.+|.++|+++
T Consensus         4 ~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~--~-----~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           4 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL--E-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT--S-----CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC--C-----CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999996432  2     267899999999999999999999999874

>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=99.65  E-value=1.5e-16  Score=110.29  Aligned_cols=68  Identities=37%  Similarity=0.527  Sum_probs=61.2

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  217 (257)
                      .+.++.||.+++|+|||++|++|++|+++|||+|.|.+..  +     +..+|.|+|+|++++|++|+.+|.++|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~--~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV--E-----GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC--T-----TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC--C-----CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            4789999999999999999999999999999999996432  2     257899999999999999999999886

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2e-16  Score=109.88  Aligned_cols=70  Identities=27%  Similarity=0.525  Sum_probs=63.3

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..++++|+||++.+|+||||+|++|++|+++|||+|++++.  +.++|+|+|+|+++     ++.+|..+|.+++.+
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~--~~~er~v~I~G~~~-----~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN-----AIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHH-----HHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC--CCCcceEEEEECHH-----HHHHHHHHHHHHhcC
Confidence            36789999999999999999999999999999999999875  57799999999854     789999999998864

>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=99.61  E-value=2.2e-16  Score=110.55  Aligned_cols=72  Identities=24%  Similarity=0.407  Sum_probs=65.2

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      +.+.++|.||.+.+|+||||+|++|++|+++|||+|+|++..+++.+|+|+|+|+.+     ++.+|..+|.+++.+
T Consensus         1 G~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPD-----RAQHAAEIITDLLRS   72 (74)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHH-----HHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHH-----HHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999999877778899999999854     788999999988864

>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=99.60  E-value=1.2e-15  Score=113.73  Aligned_cols=75  Identities=24%  Similarity=0.277  Sum_probs=66.1

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..++.+|.||..++|+|||++|.+|++|+++|||+|.|.+..+..     ...+|+|+|+|++++|.+|..+|.++|.+.
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-----LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS-----SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCC-----CCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            356889999999999999999999999999999999996543322     257899999999999999999999999874

>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=99.60  E-value=1e-15  Score=108.37  Aligned_cols=72  Identities=19%  Similarity=0.313  Sum_probs=65.0

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+.++.||..++|+|||++|++|++|+++|||+|.|.+.+.       ++.++.|+|+|++++|.+|..+|.++|.++
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~-------~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-------GLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT-------TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCC-------CCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            468899999999999999999999999999999999965322       267899999999999999999999999874

>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=99.60  E-value=7.8e-16  Score=107.90  Aligned_cols=71  Identities=30%  Similarity=0.541  Sum_probs=65.1

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      .++.++.||.+.+|+||||+|++|++|+++|||+|+|.+..+++.+|+|+|+|.++     ++.+|..+|.+++.+
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~-----~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD-----QIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHH-----HHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHH-----HHHHHHHHHHHHHHh
Confidence            46889999999999999999999999999999999999877788999999999854     788999999998875

>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=99.60  E-value=4.3e-16  Score=107.90  Aligned_cols=69  Identities=28%  Similarity=0.441  Sum_probs=62.8

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      +++.+|+||.+.+|+||||+|++|++|+++|||+|.|++..+++++|+|+|+|+++     ++.+|..+|.++|
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 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA-----SISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHH-----HHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHH-----HHHHHHHHHHHHc
Confidence            36889999999999999999999999999999999999887788999999999854     7889999888775

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=2.4e-15  Score=106.98  Aligned_cols=75  Identities=19%  Similarity=0.367  Sum_probs=66.3

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc--ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~--~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      .+...+.+|+||.+++|+||||+|++|++|+++|||+|.|++.  .+++.+|.|+|+|+++     ++.+|..+|.+++.
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~~~i~   78 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPY-----KVQQAKEMVLELIR   78 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTT-----THHHHHHHHHHHHC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHH-----HHHHHHHHHHHHHH
Confidence            3568899999999999999999999999999999999999854  3456799999999976     68899999999987


Q ss_pred             cC
Q 025112          124 KD  125 (257)
Q Consensus       124 ~~  125 (257)
                      +.
T Consensus        79 e~   80 (81)
T d1x4ma1          79 DQ   80 (81)
T ss_dssp             CC
T ss_pred             hc
Confidence            64

>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=99.56  E-value=1.7e-15  Score=107.29  Aligned_cols=75  Identities=21%  Similarity=0.370  Sum_probs=67.7

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ....++.+|.||.+.+|.|||++|.+|++|+++|||+|+|++..+++.+|.|+|+|+++     ++.+|..+|.+++.+.
T Consensus         4 ~~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           4 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPE-----SVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHH-----HHHHHHHHHHHHHHHT
T ss_pred             cCCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHH-----HHHHHHHHHHHHHHcc
Confidence            34578999999999999999999999999999999999999877778899999999854     7899999999998753

>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=99.55  E-value=5e-15  Score=105.33  Aligned_cols=71  Identities=18%  Similarity=0.162  Sum_probs=62.9

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+..+.||..++++|||++|++|++|+++|||+|+|++.++        ...+.|+|+|++++|++|.++|.++++|+
T Consensus         9 ~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~--------~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           9 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA--------PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC--------SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC--------CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999965432        34578999999999999999999999874

>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=99.53  E-value=1e-14  Score=104.31  Aligned_cols=71  Identities=15%  Similarity=0.150  Sum_probs=63.6

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ++..+.||..++++|||++|++|++|+++|||+|+|++.+. +     +..++.|+|+|+.++|.+|..+|.+++++
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-~-----~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G-----NQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C-----SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-C-----CCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999999965332 2     25788999999999999999999999986

>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=99.53  E-value=3.8e-15  Score=103.30  Aligned_cols=67  Identities=28%  Similarity=0.433  Sum_probs=57.9

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEccc---ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      .+.|+||++.+|+||||+|++|++|+++|||+|+|++.   .+++.+|.|+|+|+++     ++++|..+|.+++
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQ-----QIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHH-----HHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHH-----HHHHHHHHHHhhC
Confidence            46899999999999999999999999999999999743   3346789999999854     7889998888764

>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=99.52  E-value=4.5e-15  Score=103.73  Aligned_cols=68  Identities=24%  Similarity=0.404  Sum_probs=59.7

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc---ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      -.++|+||++.+|+||||+|++|++|+++|||+|+|++.   .+++.+|+|+|+|..+     ++++|..+|.+++
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA-----ATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHH-----HHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHH-----HHHHHHHHHHHHc
Confidence            358999999999999999999999999999999999853   3556799999999854     7889999888775

>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=99.52  E-value=7.3e-15  Score=104.44  Aligned_cols=70  Identities=19%  Similarity=0.296  Sum_probs=63.6

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+.++.||..++|+|||++|++|++|+++|||+|+|++.+         +.++.|+|+|++++|.+|..+|++++.+.
T Consensus         9 ~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~---------~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           9 QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD---------DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT---------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC---------CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999999999999986432         56789999999999999999999999873

>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=99.48  E-value=2.8e-14  Score=101.56  Aligned_cols=70  Identities=20%  Similarity=0.247  Sum_probs=62.2

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHH-hCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNS-SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~  220 (257)
                      ..+.++.||..+||+|||++|++|++|+++ ++|+|.+++.         ++.++.|+|+|++++|++|..+|++++.|.
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~---------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE---------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT---------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC---------CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            357899999999999999999999999977 5999998643         256789999999999999999999999874

>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=99.47  E-value=2.7e-14  Score=98.88  Aligned_cols=66  Identities=24%  Similarity=0.345  Sum_probs=59.5

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  217 (257)
                      ...++.||..++++|||++|++|++|+++|||+|+|++.         .+.++.|+|+|++++|++|..+|++++
T Consensus         5 ~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~---------~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD---------SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC---------CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC---------CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999999999999643         146789999999999999999999864

>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=99.45  E-value=4.9e-14  Score=100.75  Aligned_cols=73  Identities=22%  Similarity=0.332  Sum_probs=63.6

Q ss_pred             CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ..++++|.||..+++.|||++|++|++|+++|||+|+|++. .++..++.|+|+|+.+     ++..|..+|.+++.+.
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e-----~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK-----NTEAARDAILRIVGEL   81 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHH-----HHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHH-----HHHHHHHHHHHHHHhH
Confidence            35789999999999999999999999999999999999854 4557789999999954     7888999999888653

>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=99.45  E-value=6.2e-14  Score=104.18  Aligned_cols=74  Identities=26%  Similarity=0.393  Sum_probs=64.2

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccccc--CCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA--RHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~--~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ...++.+|+||..++|+||||+|.+||+|+++|||+|+|++..+  ...+|+|+|+|+++     .+.+|+.+|.+++.+
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~-----~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK-----EVAAAKHLILEKVSE   86 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHH-----HHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHH-----HHHHHHHHHHHHHhC
Confidence            34688999999999999999999999999999999999986532  34689999999854     789999999999966


Q ss_pred             C
Q 025112          125 D  125 (257)
Q Consensus       125 ~  125 (257)
                      .
T Consensus        87 ~   87 (104)
T d1we8a_          87 D   87 (104)
T ss_dssp             H
T ss_pred             c
Confidence            4

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=6.9e-14  Score=101.44  Aligned_cols=69  Identities=20%  Similarity=0.278  Sum_probs=62.8

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      ..+..+.||..++++|||++|++|++|+++|||+|.|++.         ++.++.|+|+|++++|++|..+|++++.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~---------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP---------ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT---------TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC---------CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999999998643         24578999999999999999999999986

>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=99.43  E-value=4.2e-14  Score=100.43  Aligned_cols=72  Identities=19%  Similarity=0.324  Sum_probs=64.1

Q ss_pred             CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      ...++..|.||..++|+|||++|.+|++|+++|||+|+|++.  ++.++.|+|+|+++     ++.+|..+|.+++.+.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~-----~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKE-----GIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHH-----HHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC--CCCCCEEEEEeCHH-----HHHHHHHHHHHHHHHH
Confidence            456889999999999999999999999999999999999865  46788999999864     7899999999988753

>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=2e-13  Score=97.36  Aligned_cols=67  Identities=21%  Similarity=0.176  Sum_probs=60.3

Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCC
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ  224 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~  224 (257)
                      .-+.||.+.+|+|||++|++|++|+++|||+|+|.             .+..|+|+|+++++++|..+|..++++....+
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~-------------~~g~v~I~G~~e~v~~A~~~I~~i~~ea~~~g   69 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVG-------------QNGLIWVNGDRRKVSIAEEAIYLIEQEAHTEG   69 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEEC-------------TTSEEEEESCHHHHHHHHHHHHHHHHCSCCSS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEEC-------------CCCEEEEEeCHHHHHHHHHHHHHHHHhcccCc
Confidence            46789999999999999999999999999999984             24579999999999999999999999876654

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=1.4e-13  Score=97.65  Aligned_cols=74  Identities=23%  Similarity=0.305  Sum_probs=62.7

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      .+..++..+.||..++++|||++|++|++|+++|||+|+|++... ..++.|+|+|+++     .+.+|..+|.+++.++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-~~~~~v~I~G~~~-----~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           6 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPE-----NVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHH-----HHHHHHHHHHHHHHHH
T ss_pred             hhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-CCCCEEEEeCCHH-----HHHHHHHHHHHHHHHH
Confidence            345677899999999999999999999999999999999986532 2356899999864     7889999999888764

>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=99.39  E-value=1.1e-13  Score=98.31  Aligned_cols=74  Identities=22%  Similarity=0.305  Sum_probs=63.9

Q ss_pred             CCCCCeEEEEEecCccccceeccCchhHHHHHhh-hCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE-TKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        45 ~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~-tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      ..++.++..|.||..+||+||||+|++|++|+++ ++|+|++++.  +..++.|+|+|+++     .+.+|..+|.+++.
T Consensus         5 e~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~--~~~~~~v~I~G~~~-----~v~~A~~~I~~~v~   77 (82)
T d2ctja1           5 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSS-----DVEKAKKQLLHLAE   77 (82)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHH-----HHHHHHHHHHHHHH
T ss_pred             hhcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC--CCCCceEEEeCCHH-----HHHHHHHHHHHHHh
Confidence            3456778999999999999999999999999988 5999999865  46789999999854     78899999999887


Q ss_pred             cC
Q 025112          124 KD  125 (257)
Q Consensus       124 ~~  125 (257)
                      +.
T Consensus        78 e~   79 (82)
T d2ctja1          78 EK   79 (82)
T ss_dssp             HH
T ss_pred             hh
Confidence            64

>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=99.37  E-value=3.3e-13  Score=93.28  Aligned_cols=67  Identities=19%  Similarity=0.346  Sum_probs=58.6

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      -....|.||..++++|||++|++|++|+++|||+|+|++.  +.+++.|+|+|+++     ++.+|..+|.++.
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~--~~~~~~v~I~G~~~-----~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQ-----GVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSH-----HHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC--CCCCCEEEEECCHH-----HHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999865  46788999999865     6888888887653

>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=99.34  E-value=1.1e-12  Score=94.87  Aligned_cols=67  Identities=16%  Similarity=0.230  Sum_probs=60.4

Q ss_pred             cceEEEEEeecCccceeecCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e  219 (257)
                      +..+..+.||..+|++|||++|++|++|++++ |++|.+++            .+..|+|+|++++|++|..+|.+++.+
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~------------~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE------------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS------------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC------------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            34689999999999999999999999999995 89999852            357799999999999999999999986

>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=99.33  E-value=4.2e-13  Score=97.18  Aligned_cols=70  Identities=20%  Similarity=0.287  Sum_probs=62.4

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      .++..|.||..+|+.|||++|.+|++|+++|||+|.|++.  ++.++.|+|+|+++     ++.+|..+|.+++.+.
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~-----~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAA-----NLDRAKAGLLERVKEL   78 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHH-----HHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC--CCCcceEEEECCHH-----HHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999865  46678999999854     7889999999888654

>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=99.28  E-value=1.2e-12  Score=92.08  Aligned_cols=64  Identities=27%  Similarity=0.295  Sum_probs=56.2

Q ss_pred             ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHH
Q 025112          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQ  216 (257)
Q Consensus       142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~  216 (257)
                      .++.++.||.+.+|+|||++|++|++|++.|||+|.+..           ..++.|+|.| +++++++|+++|..+
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~-----------~~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD-----------EDTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE-----------TTTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec-----------CCCceEEEEECCHHHHHHHHHHHHHh
Confidence            467899999999999999999999999999999998852           3457899999 699999999999543

>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=99.25  E-value=7e-12  Score=90.45  Aligned_cols=69  Identities=23%  Similarity=0.350  Sum_probs=59.3

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..+.++..+.||..+|++|||++|++|++|++++ +++|.+++     .+..|+|+|+++     .+.+|..+|.+++.+
T Consensus        17 ~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~-----~~~~v~i~G~~~-----~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          17 ANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTE-----DVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHH-----HHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-----CCceEEEeCCHH-----HHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999995 89999984     356799999865     678888888887765

>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=99.17  E-value=9.7e-12  Score=88.44  Aligned_cols=64  Identities=17%  Similarity=0.286  Sum_probs=55.2

Q ss_pred             EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (257)
Q Consensus        52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~  126 (257)
                      .-+.||.+.+|+|||++|++|++|+++|||+|+|.+      ++.|+|+|+++     ++.+|..+|..++.+..
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------~g~v~I~G~~e-----~v~~A~~~I~~i~~ea~   66 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRR-----KVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------TSEEEEESCHH-----HHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------CCEEEEEeCHH-----HHHHHHHHHHHHHHhcc
Confidence            357899999999999999999999999999999974      35799999854     68889999988887653

>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=99.12  E-value=1.9e-11  Score=85.72  Aligned_cols=65  Identities=20%  Similarity=0.212  Sum_probs=53.1

Q ss_pred             CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (257)
Q Consensus        46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I  118 (257)
                      ....++..|.||.+.+|+|||++|++|++|+++|||+|.+.+.    .++.|.|.|...    .++++|..+|
T Consensus         4 ~~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~----eav~~A~~~I   68 (78)
T d2cpqa1           4 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESA----DAVKKARGFL   68 (78)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSH----HHHHHHHHHH
T ss_pred             ccCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCH----HHHHHHHHHH
Confidence            3456788999999999999999999999999999999998753    457899999532    2566666665

>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=99.07  E-value=3.2e-12  Score=87.69  Aligned_cols=63  Identities=16%  Similarity=0.095  Sum_probs=48.7

Q ss_pred             EEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCC
Q 025112          146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLRENP  221 (257)
Q Consensus       146 ~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~e~~  221 (257)
                      -+.||.+.+|+|||++|++|++|+++|||+|.+.             .+..|+|+|. .+++++|.++|..+.+|..
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~-------------~~g~v~I~g~~~~~v~~A~~~I~~i~~ea~   67 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA-------------NNGRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEEC-------------TTSEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEc-------------CCCEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            5779999999999999999999999999999983             2356999996 6799999999988777754

>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=99.02  E-value=2.6e-10  Score=80.77  Aligned_cols=67  Identities=19%  Similarity=0.314  Sum_probs=47.8

Q ss_pred             EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (257)
Q Consensus        52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~  123 (257)
                      +.+.||.+.+|.||||+|++||+|+++|||+|+|++.     +..+.+.+........++++|...|.++.+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d-----~g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----TTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC-----CCeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            3578999999999999999999999999999999733     345666554322112244555566655544

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.99  E-value=5.2e-10  Score=79.52  Aligned_cols=67  Identities=12%  Similarity=0.062  Sum_probs=58.1

Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCCCC
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLRENPPR  223 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~e~~~~  223 (257)
                      .-+.||.+.+|.|||++|++|+.|+++|||+|.|..             +-.|.|.|. .+.+..|..+|..+.++....
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-------------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~v~   69 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-------------NGRIHLECPNEDLEAIAVMAIKIIDEEAYTS   69 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-------------TTEEEEECSCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-------------CcEEEEEeCCHHHHHHHHHHHHHHHHhchhc
Confidence            357799999999999999999999999999999941             346999995 789999999999998887655


Q ss_pred             C
Q 025112          224 Q  224 (257)
Q Consensus       224 ~  224 (257)
                      +
T Consensus        70 g   70 (87)
T d2z0sa2          70 G   70 (87)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=98.99  E-value=4.1e-10  Score=79.74  Aligned_cols=65  Identities=15%  Similarity=0.208  Sum_probs=53.5

Q ss_pred             EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEE-----EcCHHHHHHHHHHHHHHHhc
Q 025112          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI-----SGDVPAVLNALVEIGNQLRE  219 (257)
Q Consensus       145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I-----~G~~~~v~~A~~~I~~~l~e  219 (257)
                      +.+.||.+.+|.|||++|++||+|+++|||+|+|.+.            +..|.+     .|.+.++.+|.++|.++-+.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d------------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rG   72 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE------------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLG   72 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT------------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC------------CCeEEEecCCccccHHHHHHHHHHHHHHhCC
Confidence            5689999999999999999999999999999999532            233444     45788999999999988765


Q ss_pred             CC
Q 025112          220 NP  221 (257)
Q Consensus       220 ~~  221 (257)
                      +.
T Consensus        73 f~   74 (84)
T d1tuaa1          73 FP   74 (84)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=98.88  E-value=6.8e-11  Score=80.88  Aligned_cols=60  Identities=17%  Similarity=0.207  Sum_probs=40.6

Q ss_pred             EEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (257)
Q Consensus        53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i  122 (257)
                      -+.||.+.+|+||||+|++||+|+++|||+|+|.+.      ..|+|.|...+    .+..|..+|..+.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~------g~v~I~g~~~~----~v~~A~~~I~~i~   63 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRF----SEEILIEAIRKIE   63 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT------SEEEC-----C----TTCCTHHHHTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC------CEEEEEeCCHH----HHHHHHHHHHHHH
Confidence            467899999999999999999999999999999742      35899996432    3445666665443

>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=98.81  E-value=7.5e-10  Score=81.26  Aligned_cols=57  Identities=19%  Similarity=0.204  Sum_probs=49.9

Q ss_pred             cceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCC
Q 025112          154 AGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ  224 (257)
Q Consensus       154 vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~  224 (257)
                      .|+|||++|.+|+.|++.|||+|.|.              +..|.|.|+++++..|..+|.+++.+..+..
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~--------------d~~v~iig~~e~i~~A~~~Ie~li~~~e~g~   80 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVG--------------EYEVAIIGDYERAMAAKQAIEMLAEGRMHST   80 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEEC--------------SSEEEEEEEHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEe--------------CCeEEEEECchhHHHHHHHHHHHHcCCCccH
Confidence            59999999999999999999999983              2347888999999999999999998765544

>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=98.79  E-value=2.7e-10  Score=73.80  Aligned_cols=48  Identities=35%  Similarity=0.626  Sum_probs=15.9

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCC
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN  104 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~  104 (257)
                      ..+|.||.+.+|.|||+||.+||+|+++|||+|++.+      ++.|.|.|...
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~~~   51 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADG   51 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBSS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEecCc
Confidence            3578899999999999999999999999999999974      56788888654

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.76  E-value=5.6e-09  Score=74.06  Aligned_cols=63  Identities=16%  Similarity=0.228  Sum_probs=51.0

Q ss_pred             EEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (257)
Q Consensus        53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~  125 (257)
                      -+.||.+.+|.|||++|++|+.|+++|||+|.|.+.      ..|.|.|...    ..+..|..+|..+..+.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~----~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNE----DLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCH----HHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCH----HHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999743      3689999754    24566777777666544

>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=98.67  E-value=5.9e-10  Score=72.14  Aligned_cols=46  Identities=28%  Similarity=0.408  Sum_probs=14.2

Q ss_pred             EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC
Q 025112          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD  202 (257)
Q Consensus       144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~  202 (257)
                      ...+.||.+.+|.|||++|++||.|+++|||+|.+.             ++..|+|.|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~-------------ddg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE-------------DDGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC---------------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe-------------CCeEEEEEec
Confidence            457889999999999999999999999999999983             2466777664

>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=98.29  E-value=3.1e-07  Score=67.00  Aligned_cols=53  Identities=26%  Similarity=0.303  Sum_probs=43.0

Q ss_pred             cccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112           60 QIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (257)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~  124 (257)
                      ..|+|||++|.+|+.|++.|||+|.|.+.       .+.+.|..     ..+..|..+|..++.+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d~-------~v~iig~~-----e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGEY-------EVAIIGDY-----ERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECSS-------EEEEEEEH-----HHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeCC-------eEEEEECc-----hhHHHHHHHHHHHHcC
Confidence            37999999999999999999999999743       25566753     3678888888888864

>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=98.26  E-value=2.3e-06  Score=64.10  Aligned_cols=76  Identities=18%  Similarity=0.312  Sum_probs=57.0

Q ss_pred             eEEEEEeecC------ccceeecCCChhHHHHHHHhCCeEEEeCCCC----------CCcccCCCCCceEEEEEcC-HHH
Q 025112          143 NTIRLLIAGS------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQ----------LPLCASAHESDRVVQISGD-VPA  205 (257)
Q Consensus       143 ~~~~l~Vp~~------~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~----------~p~~~~~~~~~r~V~I~G~-~~~  205 (257)
                      .+.+|+||-.      ++|.|||++|+++|+|+++|||+|.|--+..          .+.... .+..=-|.|++. ++.
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~-~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPG-EDEPLHALVTANTMEN   81 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCC-SSCCEEEEEEESSHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCC-CCCCceEEEecCChhh
Confidence            4678889865      5999999999999999999999999963211          010000 023347888885 579


Q ss_pred             HHHHHHHHHHHHhc
Q 025112          206 VLNALVEIGNQLRE  219 (257)
Q Consensus       206 v~~A~~~I~~~l~e  219 (257)
                      +.+|+.+|..+|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999975

>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=98.19  E-value=2.1e-06  Score=64.39  Aligned_cols=72  Identities=21%  Similarity=0.442  Sum_probs=54.3

Q ss_pred             eEEEEEecCcc------ccceeccCchhHHHHHhhhCceEEEccc-c--------cC------CCc-cEEEeccCCCCch
Q 025112           50 VLFRIIVPSRQ------IGKVIGKEGHRIQKIREETKATIKIADA-I--------AR------HEE-RVIIISSKDNDNV  107 (257)
Q Consensus        50 ~~~rilVP~~~------vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~--------~~------~~e-rvv~I~G~~~~~~  107 (257)
                      ++-+++||.+.      +|.|||++|+++|+|+++|||+|.|--. +        .+      ..+ =-|.|++...   
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~---   79 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTM---   79 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSH---
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCCh---
Confidence            57799999876      9999999999999999999999999721 0        00      011 2366777542   


Q ss_pred             hhHHHHHHHHHHHHHhcC
Q 025112          108 VSDAENALQQIAALILKD  125 (257)
Q Consensus       108 ~~~~~~A~~~I~~~i~~~  125 (257)
                       ..+..|+.+|..++...
T Consensus        80 -~~~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          80 -ENVKKAVEQIRNILKQG   96 (122)
T ss_dssp             -HHHHHHHHHHHHHHTTT
T ss_pred             -hhHHHHHHHHHHHHHhc
Confidence             46788999999998653

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.98  E-value=7.1e-06  Score=62.20  Aligned_cols=76  Identities=18%  Similarity=0.404  Sum_probs=53.2

Q ss_pred             eEEEEEecCc------cccceeccCchhHHHHHhhhCceEEEccccc-----------------C-CCccEEEeccCCCC
Q 025112           50 VLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIADAIA-----------------R-HEERVIIISSKDND  105 (257)
Q Consensus        50 ~~~rilVP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~-----------------~-~~ervv~I~G~~~~  105 (257)
                      +.-|+.||.+      ++|.|||++|.++|+|+++|||+|.|--.-.                 . ..+==|.|++....
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            4568888854      5899999999999999999999999983210                 0 12233677775422


Q ss_pred             c-hhhHHHHHHHHHHHHHhcC
Q 025112          106 N-VVSDAENALQQIAALILKD  125 (257)
Q Consensus       106 ~-~~~~~~~A~~~I~~~i~~~  125 (257)
                      . ....+.+|+..|..++...
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p~  102 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVPA  102 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHHHcCCC
Confidence            1 1224678888888888643

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.96  E-value=7.4e-06  Score=62.09  Aligned_cols=77  Identities=17%  Similarity=0.223  Sum_probs=55.8

Q ss_pred             EEEEEeec------CccceeecCCChhHHHHHHHhCCeEEEeCCCCCC------------cccCCCCCceEEEEEcCH--
Q 025112          144 TIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP------------LCASAHESDRVVQISGDV--  203 (257)
Q Consensus       144 ~~~l~Vp~------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p------------~~~~~~~~~r~V~I~G~~--  203 (257)
                      ..+|+||.      +++|.|||++|.++|+|+++|||+|.|--+....            .... .+.+=-|.|++..  
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~-~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEH-LNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHT-TTSCCEEEEEECSCC
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcC-CCCCCEEEEEecCcH
Confidence            46788883      5789999999999999999999999986432210            0000 1234568888853  


Q ss_pred             ----HHHHHHHHHHHHHHhcCC
Q 025112          204 ----PAVLNALVEIGNQLRENP  221 (257)
Q Consensus       204 ----~~v~~A~~~I~~~l~e~~  221 (257)
                          ..+.+|..+|..+|...+
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p~~  103 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVPAA  103 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCS
T ss_pred             HHHHHHHHHHHHHHHHHcCCCc
Confidence                358899999999997644

>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=96.31  E-value=0.0014  Score=43.31  Aligned_cols=38  Identities=29%  Similarity=0.374  Sum_probs=35.2

Q ss_pred             eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (257)
Q Consensus        50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (257)
                      -.+.+.||.+..+..|||+|.|+|-..+-||.+|+|..
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            35789999999999999999999999999999999974

>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=96.28  E-value=0.0014  Score=43.22  Aligned_cols=40  Identities=30%  Similarity=0.359  Sum_probs=36.2

Q ss_pred             CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (257)
Q Consensus        49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (257)
                      .-.+.+.||.+..+..|||+|.|+|-..+-||.+|+|-..
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            3467899999999999999999999999999999999743

>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=96.27  E-value=0.0019  Score=42.64  Aligned_cols=39  Identities=28%  Similarity=0.309  Sum_probs=35.9

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~  181 (257)
                      ....+.||.++.+..|||+|.|++-..+-||.+|.|.+-
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            368899999999999999999999999999999999753

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.93  E-value=0.0029  Score=41.60  Aligned_cols=38  Identities=26%  Similarity=0.286  Sum_probs=35.6

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~  180 (257)
                      ....+.||.++....|||+|.|++-..+-||.+|.|.+
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            46889999999999999999999999999999999975

>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=92.75  E-value=0.073  Score=36.22  Aligned_cols=63  Identities=11%  Similarity=0.013  Sum_probs=48.6

Q ss_pred             EEEeecCccceeecCCCh-hHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCC
Q 025112          146 RLLIAGSQAGCLIGMSGQ-NIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLRENP  221 (257)
Q Consensus       146 ~l~Vp~~~vG~iIGk~G~-~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~e~~  221 (257)
                      -+.|+..++.+|+|++++ .++.|.+.+++.|.|-             ..-.|-|.|. ++....+...|.++-.+..
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG-------------~NGrIWi~~~~~~~~i~i~~aI~~~e~~~~   68 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG-------------LNGKIWVKCEELSNTLACYRTIMECCQKND   68 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE-------------TTTEEEEECSSHHHHHHHHHHHHHHHHHCC
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe-------------cCcEEEEECCCHHHHHHHHHHHHHHHHhCC
Confidence            456888999999999998 7899999999999984             2356788884 6666666666666555544

>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=90.02  E-value=0.054  Score=37.49  Aligned_cols=31  Identities=23%  Similarity=0.453  Sum_probs=26.9

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhhCc
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKA   81 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~   81 (257)
                      .+++.|....-|.|||++|+.|++|+++..-
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            4778889999999999999999999877543

>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=85.36  E-value=0.17  Score=34.89  Aligned_cols=30  Identities=17%  Similarity=0.386  Sum_probs=25.6

Q ss_pred             eEEEEEeecCccceeecCCChhHHHHHHHh
Q 025112          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSS  172 (257)
Q Consensus       143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t  172 (257)
                      ...++.|....-|.|||++|+.|++|++.-
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l   64 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVV   64 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHH
Confidence            357888999999999999999999997543

>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=84.23  E-value=0.12  Score=36.55  Aligned_cols=29  Identities=38%  Similarity=0.556  Sum_probs=25.8

Q ss_pred             EEEEEecCccccceeccCchhHHHHHhhh
Q 025112           51 LFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (257)
Q Consensus        51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~t   79 (257)
                      .+++.|....-|.|||++|+.|++|+++.
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            47888888999999999999999998874

>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=83.26  E-value=0.22  Score=35.56  Aligned_cols=31  Identities=32%  Similarity=0.391  Sum_probs=24.5

Q ss_pred             CeEEEEEecCcc-ccceeccCchhHHHHHhhh
Q 025112           49 DVLFRIIVPSRQ-IGKVIGKEGHRIQKIREET   79 (257)
Q Consensus        49 ~~~~rilVP~~~-vg~IIGk~G~~Ik~I~~~t   79 (257)
                      .+...|.|+... .+.|||++|++||+|..++
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            367778888766 6667799999999986654

>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=81.58  E-value=0.56  Score=31.56  Aligned_cols=45  Identities=13%  Similarity=0.104  Sum_probs=37.1

Q ss_pred             EEEecCccccceeccCch-hHHHHHhhhCceEEEcccccCCCccEEEeccCC
Q 025112           53 RIIVPSRQIGKVIGKEGH-RIQKIREETKATIKIADAIARHEERVIIISSKD  103 (257)
Q Consensus        53 rilVP~~~vg~IIGk~G~-~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~  103 (257)
                      -+.||...+..+||++++ -++.|.+.+++.|-|=.      ...|-|.|..
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~------NGrIWi~~~~   49 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL------NGKIWVKCEE   49 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET------TTEEEEECSS
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec------CcEEEEECCC
Confidence            456899999999999998 68999999999999863      3457788863

>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=80.62  E-value=0.28  Score=34.90  Aligned_cols=36  Identities=19%  Similarity=0.254  Sum_probs=26.6

Q ss_pred             eEEEEEeecC-ccceeecCCChhHHHHH--------HHhCCeEEE
Q 025112          143 NTIRLLIAGS-QAGCLIGMSGQNIEKLR--------NSSGATIVI  178 (257)
Q Consensus       143 ~~~~l~Vp~~-~vG~iIGk~G~~Ik~I~--------~~tga~I~i  178 (257)
                      ....+.|+.. +.+.|||++|++|++|.        +-+++++.+
T Consensus        49 I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~ar~~le~~~~~kV~L   93 (113)
T d1egaa2          49 INGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHL   93 (113)
T ss_dssp             EEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHTTSCEEE
T ss_pred             EEEEEEECCcchhhhhhcccchHHHHHHHHHHHHHHHHhCCCeEE
Confidence            5667778765 55899999999999885        445666543