Citrus Sinensis ID: 022746

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290--
Protein Sequence
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQLTM
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccccEEEccccHHHHHHHHHHccEEEccccccccccEEEEEEccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEEccccEEEEEcccccHHHHHHHHHcccEEEccccccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEcccccccccEEEEEEccccccccHHHHHHHHHHHHHHccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEEccccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccEEEEEEccccccccccccc
Coil and Loop (DISEMBL)
maeqgeitvnptvsvvtepeprhdvsgkrrredgeiegsdpkrrAKAQDVLFRIIVpsrqigkvigkeGHRIQKIREETKATIKIADAIARHEERVIIISskdndnvvsDAENALQQIAALILkdddsnseaskVAAGHVAANTIRLLIAGSQagcligmsgqnieklrnssgativilapnqlplcasahesdrvvQISGDVPAVLNALVEIGNqlrenpprqvisispaynysairpaqpfveptsgysmfLMQNTRYFVTAIFAVLSSFNIFFLITtsslgqpllqltm
Flexible Loop (DISEMBL)
maeqgeitvnptvsvvtepeprhdvsgkrrredgeiegsdpkrrakaqdvlfriivpsrqigkvigkeghriqkireetkaTIKIADAIARHEERVIIISskdndnvvSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGnqlrenpprQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITtsslgqpllqltm
Low Complexity Region (SEG)
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEtkatikiadaiaRHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQLTM
Disordered region (IsUnstruct)
************************************************DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL***********VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL*********
Disordered Region (DISOPRED)
***************************************************FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL**********************TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP***********************************************************************
Disordered Region (DISEMBL)
MAEQGEITVNPTVSVV***************************RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD***********AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQLTM
Disordered Region (DISPRO)
**********************************************AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD**************VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQ*******
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQLTM
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	292	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.708	0.341	0.290	4e-14
Q61990	362	Poly(rC)-binding protein	yes	no	0.541	0.436	0.290	2e-12
P57721	371	Poly(rC)-binding protein	no	no	0.544	0.428	0.293	2e-12
P57722	371	Poly(rC)-binding protein	no	no	0.544	0.428	0.293	3e-12
Q5SF07	592	Insulin-like growth facto	no	no	0.674	0.332	0.269	3e-11
Q15366	365	Poly(rC)-binding protein	yes	no	0.541	0.432	0.284	3e-11
Q0VCU0	403	Poly(rC)-binding protein	no	no	0.530	0.384	0.264	9e-11
P57723	403	Poly(rC)-binding protein	no	no	0.530	0.384	0.264	9e-11
P57724	403	Poly(rC)-binding protein	no	no	0.530	0.384	0.264	1e-10
O19048	356	Poly(rC)-binding protein	no	no	0.554	0.455	0.270	2e-10

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

 Score = 79.0 bits (193), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 112/231 (48%), Gaps = 24/231 (10%)

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 LRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFA 267
           + +  PR+ I   P  + S   PA   + P+       + N+ Y  T  ++
Sbjct: 214 MYKINPRENI---PLDSTSQDVPAASVIVPSD------LSNSVYPQTGFYS 255

Arabidopsis thaliana (taxid: 3702)

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

 Score = 73.2 bits (178), Expect = 2e-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|P57721|PCBP3_HUMAN Poly(rC)-binding protein 3 OS=Homo sapiens GN=PCBP3 PE=2 SV=2

 Score = 73.2 bits (178), 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 = 72.8 bits (177), 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|Q5SF07|IF2B2_MOUSE Insulin-like growth factor 2 mRNA-binding protein 2 OS=Mus musculus GN=Igf2bp2 PE=1 SV=1

 Score = 69.3 bits (168), 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 = 69.3 bits (168), Expect = 3e-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 = 67.8 bits (164), Expect = 9e-11,   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 ENALQQIAALILKDDDSNSEASKVAAGHVAAN--TIRLLIAGSQAGCLIGMSGQNIEKLR 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 = 67.8 bits (164), Expect = 9e-11,   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 ENALQQIAALILKDDDSNSEASKVAAGHVAAN--TIRLLIAGSQAGCLIGMSGQNIEKLR 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 = 67.4 bits (163), 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 = 66.6 bits (161), Expect = 2e-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	292
356530005	385	PREDICTED: KH domain-containing protein	0.839	0.636	0.750	9e-99
449445515	276	PREDICTED: poly(rC)-binding protein 2-li	0.801	0.847	0.755	1e-95
255541092	363	conserved hypothetical protein [Ricinus	0.842	0.677	0.736	8e-95
359489188	343	PREDICTED: KH domain-containing protein	0.845	0.720	0.714	3e-94
297734587	346	unnamed protein product [Vitis vinifera]	0.845	0.713	0.714	4e-94
307136423	331	hypothetical protein [Cucumis melo subsp	0.684	0.604	0.787	2e-82
147855522	321	hypothetical protein VITISV_031103 [Viti	0.743	0.676	0.724	3e-82
224137186	357	predicted protein [Populus trichocarpa]	0.825	0.675	0.694	1e-81
357507881	275	Poly(rC)-binding protein [Medicago trunc	0.684	0.727	0.722	3e-75
116784616	407	unknown [Picea sitchensis]	0.736	0.528	0.533	6e-51

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

 Score =  365 bits (938), Expect = 9e-99,   Method: Compositional matrix adjust.
 Identities = 190/253 (75%), Positives = 213/253 (84%), Gaps = 8/253 (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-GYSMFLMQNT 258
           SGDVPAV+ AL EIG QLRENPPRQVISISP YNY+AIRP+QP+++PTS  Y  F M  +
Sbjct: 252 SGDVPAVMKALEEIGCQLRENPPRQVISISPTYNYAAIRPSQPYLDPTSVDYVTFEMLIS 311

Query: 259 RYFVTAIFAVLSS 271
              V  +     S
Sbjct: 312 ETMVGGLIGRCGS 324

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  355 bits (911), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 182/241 (75%), Positives = 203/241 (84%), Gaps = 7/241 (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 SDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSM 252
           SDRVVQISGD+ AVL AL EIGNQLR NPPRQVIS+SP YNY+ + P Q +++PTSG  +
Sbjct: 212 SDRVVQISGDILAVLKALEEIGNQLRVNPPRQVISVSPTYNYNTMHPPQSYMDPTSGKPI 271

Query: 253 F 253
            
Sbjct: 272 L 272

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  352 bits (904), Expect = 8e-95,   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|359489188|ref|XP_002272998.2| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  350 bits (899), Expect = 3e-94,   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|297734587|emb|CBI16638.3| unnamed protein product [Vitis vinifera]

 Score =  350 bits (898), Expect = 4e-94,   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 =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 163/207 (78%), Positives = 178/207 (85%), Gaps = 7/207 (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 SDRVVQISGDVPAVLNALVEIGNQLRE 219
           SDRVVQISGD+ AVL AL EIGNQLR+
Sbjct: 212 SDRVVQISGDILAVLKALEEIGNQLRK 238

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 =  311 bits (796), Expect = 3e-82,   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 (790), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 175/252 (69%), Positives = 202/252 (80%), 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 AALILKDDDSNS------EASK-VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171
           A LIL +DD  S      E  K 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 =  288 bits (736), 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 =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 118/221 (53%), Positives = 153/221 (69%), Gaps = 6/221 (2%)

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 QLRENPPRQVISISPAYNYSAIRPAQPF-VEPTS---GYSM 252
            LRE+PPR+VIS  P Y Y+ + PA    V P +   GY+M
Sbjct: 260 TLREHPPREVISTRPTY-YAGLSPANGLMVLPQTVLPGYNM 299

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	292
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.726	0.386	0.333	9.9e-23
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.595	0.363	0.292	2.4e-16
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.667	0.337	0.282	5.9e-16
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.561	0.331	0.312	1.2e-14
TAIR|locus:2056951	153	AT2G03110 "AT2G03110" [Arabido	0.434	0.830	0.355	6e-13
UNIPROTKB|H9L011	195	LOC426023 "Uncharacterized pro	0.530	0.794	0.278	1.4e-12
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.547	0.257	0.294	3.3e-11
UNIPROTKB|F1NPL2	319	PCBP3 "Uncharacterized protein	0.530	0.485	0.273	3.9e-11
UNIPROTKB|F1NPL4	326	PCBP3 "Uncharacterized protein	0.530	0.475	0.273	4.2e-11
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.551	0.25	0.292	4.6e-11

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 = 1.2e-14, P = 1.2e-14
 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 = 6.0e-13, P = 6.0e-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 = 1.4e-12, P = 1.4e-12
 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 = 3.3e-11, P = 3.3e-11
 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

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

 Score = 173 (66.0 bits), Expect = 3.9e-11, P = 3.9e-11
 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 = 4.2e-11, P = 4.2e-11
 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

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

 Score = 178 (67.7 bits), Expect = 4.6e-11, P = 4.6e-11
 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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	292
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-16
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-10
pfam00013	59	pfam00013, KH_1, KH domain	3e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-08
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	9e-08
pfam13014	42	pfam13014, KH_3, KH domain	2e-07
pfam00013	59	pfam00013, KH_1, KH domain	2e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-04
cd02134	61	cd02134, NusA_KH, NusA_K homology RNA-binding doma	2e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-04
pfam13014	42	pfam13014, KH_3, KH domain	3e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	3e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	7e-04
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.001
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.002
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	0.004

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

 Score = 70.6 bits (174), Expect = 5e-16
 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 = 61.3 bits (150), Expect = 1e-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 = 55.3 bits (134), Expect = 2e-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 = 52.2 bits (126), Expect = 3e-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 = 50.8 bits (122), Expect = 1e-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 = 47.9 bits (115), Expect = 9e-08
 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 = 46.4 bits (111), Expect = 2e-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 = 44.1 bits (105), Expect = 2e-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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 39.2 bits (92), Expect = 1e-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|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH)

 Score = 38.7 bits (91), Expect = 2e-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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 42.5 bits (101), 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|221895 pfam13014, KH_3, KH domain

 Score = 37.2 bits (87), Expect = 3e-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 = 37.9 bits (89), Expect = 3e-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 = 40.8 bits (97), Expect = 7e-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 = 40.3 bits (95), 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

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

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 10/68 (14%)

Query: 51  LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSD 110
           +  + +P  +I  VIG  G  I+KI EET   I I D      +  + I++ D +     
Sbjct: 3   IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKE----A 52

Query: 111 AENALQQI 118
           AE A + I
Sbjct: 53  AEKAKKMI 60

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

>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II)

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 10/43 (23%), Positives = 21/43 (48%)

Query: 42 KRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK 84
          +       +   I+V   Q G VIGK+G  I+ +++  +  ++
Sbjct: 17 EIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLR 59

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. Length = 68

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	292
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.98
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.96
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.96
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.96
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.96
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.87
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.8
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.8
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.68
PRK13763	180	putative RNA-processing protein; Provisional	99.65
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.42
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.42
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.4
PRK13763	180	putative RNA-processing protein; Provisional	99.39
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.31
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.25
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.22
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.2
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.19
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.19
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.17
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.15
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.11
PF13014	43	KH_3: KH domain	99.07
PF13014	43	KH_3: KH domain	98.98
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.94
smart00322	69	KH K homology RNA-binding domain.	98.9
smart00322	69	KH K homology RNA-binding domain.	98.82
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.73
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.55
KOG2113	394	consensus Predicted RNA binding protein, contains	98.55
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.51
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.48
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.47
PRK08406	140	transcription elongation factor NusA-like protein;	98.21
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.07
PRK08406	140	transcription elongation factor NusA-like protein;	98.06
KOG2113	394	consensus Predicted RNA binding protein, contains	97.98
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.86
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.74
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.7
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.63
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.6
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.44
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.44
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.4
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.33
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.32
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.22
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.16
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.09
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.08
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.03
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.94
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.88
TIGR01953	341	NusA transcription termination factor NusA. This m	96.8
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.69
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.65
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.65
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.61
PRK00468	75	hypothetical protein; Provisional	96.56
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.54
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.47
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.44
PRK02821	77	hypothetical protein; Provisional	96.41
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.39
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.28
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.26
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.2
PRK00468	75	hypothetical protein; Provisional	96.16
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.16
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.09
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.03
PRK01064	78	hypothetical protein; Provisional	95.96
PRK02821	77	hypothetical protein; Provisional	95.89
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.77
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.75
PRK00106	535	hypothetical protein; Provisional	95.74
PRK12704	520	phosphodiesterase; Provisional	95.67
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.45
PRK01064	78	hypothetical protein; Provisional	95.41
PRK12704	520	phosphodiesterase; Provisional	95.36
TIGR01953	341	NusA transcription termination factor NusA. This m	95.27
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.2
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.17
PRK00106	535	hypothetical protein; Provisional	95.09
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.08
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.05
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.03
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.02
PRK12328	374	nusA transcription elongation factor NusA; Provisi	94.78
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	94.51
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	94.41
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	94.18
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	93.78
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	93.78
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	93.34
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	93.01
PRK12705	508	hypothetical protein; Provisional	92.95
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	92.19
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	91.96
PRK12705	508	hypothetical protein; Provisional	91.3
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	91.19
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	90.86
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.62
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	89.74
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	89.65
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	89.45
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	89.11
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	88.91
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	88.84
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	88.53
PRK06418	166	transcription elongation factor NusA-like protein;	88.15
PRK13764	602	ATPase; Provisional	88.11
COG1855	604	ATPase (PilT family) [General function prediction	87.72
COG1855	604	ATPase (PilT family) [General function prediction	87.56
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	87.34
KOG2874	356	consensus rRNA processing protein [Translation, ri	87.0
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	86.41
PRK13764	602	ATPase; Provisional	86.41
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	85.16
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	84.9
KOG2874	356	consensus rRNA processing protein [Translation, ri	84.64
COG5166	657	Uncharacterized conserved protein [Function unknow	83.96
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	83.72
COG1782	637	Predicted metal-dependent RNase, consists of a met	83.58
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	82.97
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	80.74
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	80.72
PRK06418	166	transcription elongation factor NusA-like protein;	80.45

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

Probab=100.00  E-value=2.8e-32  Score=258.09  Aligned_cols=217  Identities=20%  Similarity=0.274  Sum_probs=173.9

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC--CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~--~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ...++..|+||.+.+|+||||+|++||+|++++||++.+-.+.  ..+..+.+.|+|.++     .++.|..+|+++|.+
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            4568999999999999999999999999999999999887542  223678899999986     688999999999997


Q ss_pred             CCCCCcch-hhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 022746          125 DDDSNSEA-SKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (292)
Q Consensus       125 ~~~~~~~~-~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~  203 (292)
                      ........ ...+.+.....+.+|.||+..||.||||+|++||+|+.+||++|+|.++ +.|.     +.+|.+.|.|+.
T Consensus       211 ~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD-d~p~-----speR~~~IiG~~  284 (600)
T KOG1676|consen  211 EDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD-DDPS-----SPERPAQIIGTV  284 (600)
T ss_pred             cccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecC-CCCC-----CccceeeeecCH
Confidence            54432211 1111122344589999999999999999999999999999999998764 4453     789999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746          204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL  283 (292)
Q Consensus       204 ~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~  283 (292)
                      +.|.+|.++|.++|........         +++    . .+.......|+|.||+..||.|||| ||+|||.|.+.|||
T Consensus       285 d~ie~Aa~lI~eii~~~~~~~~---------~~~----~-~G~P~~~~~fy~~VPa~KcGLvIGr-GGEtIK~in~qSGA  349 (600)
T KOG1676|consen  285 DQIEHAAELINEIIAEAEAGAG---------GGM----G-GGAPGLVAQFYMKVPADKCGLVIGR-GGETIKQINQQSGA  349 (600)
T ss_pred             HHHHHHHHHHHHHHHHHhccCC---------CCc----C-CCCccceeeEEEeccccccccccCC-CccchhhhcccCCc
Confidence            9999999999999988732210         000    0 0111112389999999999999999 99999999999999


Q ss_pred             CCcccc
Q 022746          284 GQPLLQ  289 (292)
Q Consensus       284 ~~~~~~  289 (292)
                      .++|-+
T Consensus       350 ~~el~r  355 (600)
T KOG1676|consen  350 RCELSR  355 (600)
T ss_pred             cccccC
Confidence            998854

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

Probab=100.00  E-value=5.3e-32  Score=233.69  Aligned_cols=248  Identities=25%  Similarity=0.357  Sum_probs=193.5

Q ss_pred             CCCCCCCCCCCCCCCCCCccCCCCccCCCCccccCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCC
Q 022746           11 PTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA   90 (292)
Q Consensus        11 ~~~~~~~~~~~~~~~~~kr~~~~~~~e~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~   90 (292)
                      +-|..++++.++.+.++||+.+|+.   .++.+.   ..+.++||+.+..+|+||||+|++||.|+.+++|.|+|++.  
T Consensus        15 ~q~~~~~~~~e~g~~~gkrp~~d~~---~qa~k~---~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--   86 (390)
T KOG2192|consen   15 EQPEETFPNTETGGEFGKRPAEDME---EQAFKR---SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--   86 (390)
T ss_pred             CChhhcCCCCcccccccCCcchhhH---HHHhhh---cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--
Confidence            3456779999999999999999993   333333   34999999999999999999999999999999999999986  


Q ss_pred             CCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHH
Q 022746           91 RHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRN  170 (292)
Q Consensus        91 ~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~  170 (292)
                      ++++|+++|+...+     -+.+-+..|.-.+.+...           ....+.++++|..+++|.|||++|+.||+|++
T Consensus        87 ~~peri~tisad~~-----ti~~ilk~iip~lee~f~-----------~~~pce~rllihqs~ag~iigrngskikelre  150 (390)
T KOG2192|consen   87 SGPERILTISADIE-----TIGEILKKIIPTLEEGFQ-----------LPSPCELRLLIHQSLAGGIIGRNGSKIKELRE  150 (390)
T ss_pred             CCCceeEEEeccHH-----HHHHHHHHHhhhhhhCCC-----------CCCchhhhhhhhhhhccceecccchhHHHHHH
Confidence            57899999999732     344444444444443322           23467899999999999999999999999999


Q ss_pred             hhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCC-CCCCCC-----CCCCC-------
Q 022746          171 SSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVI-SISPAY-----NYSAI-------  237 (292)
Q Consensus       171 ~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~-~~~p~~-----n~~~~-------  237 (292)
                      ++.|+++++.     .|+. ++++|+|.+.|.+..|..+++.|++.|.+.+.+++. .|.|.+     .|.+.       
T Consensus       151 kcsarlkift-----~c~p-~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~  224 (390)
T KOG2192|consen  151 KCSARLKIFT-----ECCP-HSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDR  224 (390)
T ss_pred             hhhhhhhhhh-----ccCC-CCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCC
Confidence            9999999974     2332 489999999999999999999999999999887753 222221     11100       


Q ss_pred             ------------------------------CCC---------C--------------------------CCCC-------
Q 022746          238 ------------------------------RPA---------Q--------------------------PFVE-------  245 (292)
Q Consensus       238 ------------------------------~~~---------~--------------------------~~~~-------  245 (292)
                                                    +++         +                          .+++       
T Consensus       225 pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~  304 (390)
T KOG2192|consen  225 PGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGY  304 (390)
T ss_pred             CCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccc
Confidence                                          000         0                          0000       


Q ss_pred             -----CCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcccc
Q 022746          246 -----PTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQ  289 (292)
Q Consensus       246 -----~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~  289 (292)
                           -.+...+..|.||.++-|.|||| ||+.|++|+..|||.+.|-|
T Consensus       305 GsYGdlGGPitTaQvtip~dlggsiigk-ggqri~~ir~esGA~Ikide  352 (390)
T KOG2192|consen  305 GSYGDLGGPITTAQVTIPKDLGGSIIGK-GGQRIKQIRHESGASIKIDE  352 (390)
T ss_pred             cccCCCCCceeeeeEecccccCcceecc-cchhhhhhhhccCceEEecC
Confidence                 01124788999999999999999 99999999999999998876

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

Probab=99.98  E-value=5.3e-31  Score=233.27  Aligned_cols=261  Identities=22%  Similarity=0.293  Sum_probs=192.0

Q ss_pred             CCCCCCCCCCCccCCCCccCCCCccccCCC-CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEcc---CCCCCC
Q 022746           18 EPEPRHDVSGKRRREDGEIEGSDPKRRAKA-QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD---AIARHE   93 (292)
Q Consensus        18 ~~~~~~~~~~kr~~~~~~~e~~~~~~~~~~-~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~---~~~~~~   93 (292)
                      +.+.+.-.|.||+++.-+.-.......... ..+++|||||+..+|.||||+|++|.+||.+|||+|+++.   ..|+++
T Consensus         6 ~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTT   85 (402)
T KOG2191|consen    6 PIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTT   85 (402)
T ss_pred             cccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCcc
Confidence            344445557888888775211222222222 2499999999999999999999999999999999999994   368999


Q ss_pred             ceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhc--ccCCCcccEEEEEeccCcceeeecCCChhHHHHHHh
Q 022746           94 ERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKV--AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS  171 (292)
Q Consensus        94 ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~--~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~  171 (292)
                      ||+|.|+|+     +.++...+..|+++|.+...........  +........++++||+..+|.||||+|++||.++++
T Consensus        86 eRvcli~Gt-----~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq  160 (402)
T KOG2191|consen   86 ERVCLIQGT-----VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ  160 (402)
T ss_pred             ceEEEEecc-----HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence            999999998     4567777888888888765432211100  011223346899999999999999999999999999


Q ss_pred             hCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCC---CCC----CCCCCCCCCCCCCCCC
Q 022746          172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV---ISI----SPAYNYSAIRPAQPFV  244 (292)
Q Consensus       172 tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~---~~~----~p~~n~~~~~~~~~~~  244 (292)
                      +||+|+++|..  |..-+  ..+|+|++.|++++..+|+.+|+++|.+++....   .+|    .|..|+++.  +.+|.
T Consensus       161 sga~iqisPqk--pt~~s--Lqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnPt--Gspya  234 (402)
T KOG2191|consen  161 SGAWIQISPQK--PTGIS--LQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNPT--GSPYA  234 (402)
T ss_pred             hCcceEecccC--CCCcc--ceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCCC--CCCCC
Confidence            99999998632  22211  5799999999999999999999999999987653   111    123333322  22222


Q ss_pred             CCC---CceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746          245 EPT---SGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL  290 (292)
Q Consensus       245 ~~~---~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~  290 (292)
                      ...   .........++....|..-|. ||.++-.|...+|+.+-+-|.
T Consensus       235 ~~~~~~~astas~~sva~~~iG~a~ga-G~~~~a~l~~~~G~l~~itq~  282 (402)
T KOG2191|consen  235 YQAHVLPASTASTISVAAGLIGGANGA-GGAFGAALSGFTGALIAITQA  282 (402)
T ss_pred             CCCccccccchhhcccccccccccccc-ccccceeeecccccceeeccc
Confidence            211   124556677999999999999 999999999999987777664

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

Probab=99.96  E-value=3.8e-29  Score=227.47  Aligned_cols=225  Identities=24%  Similarity=0.385  Sum_probs=183.5

Q ss_pred             CCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        45 ~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      ....++++|+|||..+||.||||.|++||.|...|.|+|+|... ..+..|+.++|-|+++     .+-+|+.+|+++|.
T Consensus       194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpE-----g~s~Ac~~ILeimq  268 (584)
T KOG2193|consen  194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPE-----GTSKACKMILEIMQ  268 (584)
T ss_pred             ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCcc-----chHHHHHHHHHHHH
Confidence            34567899999999999999999999999999999999999854 3577899999999987     57899999999998


Q ss_pred             cCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 022746          124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (292)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~  203 (292)
                      ++.....-.        ..+.++++..+.+||++|||.|.+||+|.++||++|.|.+-.++...    +.+|.+++.|+-
T Consensus       269 kEA~~~k~~--------~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y----npERTItVkGsi  336 (584)
T KOG2193|consen  269 KEAVDDKVA--------EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY----NPERTITVKGSI  336 (584)
T ss_pred             Hhhhccchh--------hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc----CccceEEecccH
Confidence            765432111        24468899999999999999999999999999999999876555443    579999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCC------CCCCCCCCCCCCCCCCC---------------CCCC------CCceeEEEEE
Q 022746          204 PAVLNALVEIGNQLRENPPRQV------ISISPAYNYSAIRPAQP---------------FVEP------TSGYSMFLMQ  256 (292)
Q Consensus       204 ~~v~~A~~~I~~~l~~~~~~~~------~~~~p~~n~~~~~~~~~---------------~~~~------~~~~~~~~v~  256 (292)
                      ++|..|..+|+.+|+++++.+.      ..+.|..|++.++++.+               |.++      +.+...++|.
T Consensus       337 Eac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~f  416 (584)
T KOG2193|consen  337 EACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMF  416 (584)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeee
Confidence            9999999999999999987664      23455555544432211               1111      1235778999


Q ss_pred             eccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          257 NTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       257 iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                      ||+.++|+|||| .|.+||.|.+..||-+-|
T Consensus       417 iP~~~vGAiIGk-kG~hIKql~RfagASiKI  446 (584)
T KOG2193|consen  417 IPAQAVGAIIGK-KGQHIKQLSRFAGASIKI  446 (584)
T ss_pred             ccHHHHHHHHhh-cchhHHHHHHhccceeee
Confidence            999999999999 999999999999998765

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

Probab=99.96  E-value=2.9e-28  Score=230.91  Aligned_cols=216  Identities=21%  Similarity=0.250  Sum_probs=171.9

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~  127 (292)
                      ..++.+..||..+||+||||+|+.|..|+.++||+|++.....+..+|.+.++|.++     .+..|..++-+.+.....
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe-----~v~~aK~li~evv~r~~~  126 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPE-----NVEVAKQLIGEVVSRGRP  126 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcc-----cHHHHHHhhhhhhhccCC
Confidence            567789999999999999999999999999999999988665566899999999987     577887777777655431


Q ss_pred             CCcchhhcc-cCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 022746          128 SNSEASKVA-AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (292)
Q Consensus       128 ~~~~~~~~~-~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v  206 (292)
                          ..... +.....++.++.||.+.+|+||||+|++||.|++++||++.+..+.....     ..++.+.|+|++++|
T Consensus       127 ----~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-----~~~KplritGdp~~v  197 (600)
T KOG1676|consen  127 ----PGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-----GADKPLRITGDPDKV  197 (600)
T ss_pred             ----CCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC-----CCCCceeecCCHHHH
Confidence                01111 11134568999999999999999999999999999999999876544332     467899999999999


Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCc
Q 022746          207 LNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQP  286 (292)
Q Consensus       207 ~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~  286 (292)
                      +.|..++.++|++........            ..-+........+++|.||...||.|||| +|++||.|+-.||++++
T Consensus       198 e~a~~lV~dil~e~~~~~~g~------------~~~~g~~~g~~~~~~V~VPr~~VG~IIGk-gGE~IKklq~etG~KIQ  264 (600)
T KOG1676|consen  198 EQAKQLVADILREEDDEVPGS------------GGHAGVRGGGSATREVKVPRSKVGIIIGK-GGEMIKKLQNETGAKIQ  264 (600)
T ss_pred             HHHHHHHHHHHHhcccCCCcc------------ccccCcCccccceeEEeccccceeeEEec-CchHHHHHhhccCceeE
Confidence            999999999999753221100            01111222334589999999999999999 99999999999999999


Q ss_pred             cccc
Q 022746          287 LLQL  290 (292)
Q Consensus       287 ~~~~  290 (292)
                      ++..
T Consensus       265 fkpD  268 (600)
T KOG1676|consen  265 FKPD  268 (600)
T ss_pred             eecC
Confidence            8754

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

Probab=99.96  E-value=1.1e-27  Score=229.28  Aligned_cols=257  Identities=28%  Similarity=0.409  Sum_probs=181.1

Q ss_pred             CCCCCCCCC-CCCccCCCCccCCCCccccCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCce
Q 022746           17 TEPEPRHDV-SGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEER   95 (292)
Q Consensus        17 ~~~~~~~~~-~~kr~~~~~~~e~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er   95 (292)
                      ..+....+. +.+|+...+.     ......+...++||||+...+|.||||+|..|++|+.+|.++|+|.+..+++.+|
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~-----~~~~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eR   88 (485)
T KOG2190|consen   14 STTSNVGDNGSIKRPSLGDP-----VISTGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPER   88 (485)
T ss_pred             CCcccccCCCcccccCCCCC-----cccCCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcc
Confidence            444444444 4566666553     1112233445599999999999999999999999999999999999989999999


Q ss_pred             EEEEecCCCCcchhHHHHHHHHHHHHHhcC----CCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHh
Q 022746           96 VIIISSKDNDNVVSDAENALQQIAALILKD----DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS  171 (292)
Q Consensus        96 vv~I~G~~~~~~v~~v~~A~~~I~~~i~~~----~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~  171 (292)
                      +++|+|...+.....+.+|+..+.+++...    .....+...  ......++++|+||..++|+||||+|+.||+|+++
T Consensus        89 Iiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~--~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~  166 (485)
T KOG2190|consen   89 IITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGE--DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE  166 (485)
T ss_pred             eEEEecccccccCCchHHHHHHHHHHHhhcccccccccccCCc--cccCCceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence            999999222112333445555555554432    211111110  11112578999999999999999999999999999


Q ss_pred             hCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCC------CCCCCC-CCCCCCCC--CCC-
Q 022746          172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ------VISISP-AYNYSAIR--PAQ-  241 (292)
Q Consensus       172 tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~------~~~~~p-~~n~~~~~--~~~-  241 (292)
                      |||+|++.+. .+|.     +++|.|+|.|.+++|.+|+..|..+|.+.....      ...|.| ..-.....  .+. 
T Consensus       167 TgA~I~v~~~-~lP~-----ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~  240 (485)
T KOG2190|consen  167 TGAKIRVSSD-MLPN-----STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQT  240 (485)
T ss_pred             cCceEEecCC-CCCc-----ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccC
Confidence            9999999764 8888     578999999999999999999999999964221      122223 11000000  000 


Q ss_pred             -----CCC-CCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          242 -----PFV-EPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       242 -----~~~-~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                           ++. ...+.+..+.+.+|...++.|||+ +|..|+.|+..+++-+.+
T Consensus       241 ~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~-~~~~i~~l~~~~~~~i~v  291 (485)
T KOG2190|consen  241 SPDAHPFGGIVPEEELVFKLICPSDKVGSVIGK-GGLVIRALRNETGASISV  291 (485)
T ss_pred             CcccccccccccchhhhhhhcCchhhceeeecC-CCccchhhhhhcCCceEe
Confidence                 111 112235667889999999999999 999999999999987654

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

Probab=99.96  E-value=9.7e-30  Score=231.35  Aligned_cols=231  Identities=22%  Similarity=0.293  Sum_probs=184.3

Q ss_pred             CCCCCCCCccCCCCccCCCCccccCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC---CCCCCceEE
Q 022746           21 PRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVI   97 (292)
Q Consensus        21 ~~~~~~~kr~~~~~~~e~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~ervv   97 (292)
                      +.-+..+||.+|-+..|   +....-..++++|++..+.++|++|||.|.+||+|+++||++|.|+..   .-.++||.|
T Consensus       254 Eg~s~Ac~~ILeimqkE---A~~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTI  330 (584)
T KOG2193|consen  254 EGTSKACKMILEIMQKE---AVDDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTI  330 (584)
T ss_pred             cchHHHHHHHHHHHHHh---hhccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceE
Confidence            33445678888877432   233344478999999999999999999999999999999999999853   234579999


Q ss_pred             EEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc--------------------------c-hh-----hcc-c-------
Q 022746           98 IISSKDNDNVVSDAENALQQIAALILKDDDSNS--------------------------E-AS-----KVA-A-------  137 (292)
Q Consensus        98 ~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~--------------------------~-~~-----~~~-~-------  137 (292)
                      ++.|+     ++++..|-.+|..++.+......                          . ++     .+. +       
T Consensus       331 tVkGs-----iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~h  405 (584)
T KOG2193|consen  331 TVKGS-----IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFH  405 (584)
T ss_pred             Eeccc-----HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhh
Confidence            99997     66788888889888877432110                          0 00     000 0       


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      .......+++.||...+|.|||++|.+||.|...+||.|+|.+.+ .|+     ..+|.|+|+|++++..+|...|..+|
T Consensus       406 q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE-~pd-----vseRMViItGppeaqfKAQgrifgKi  479 (584)
T KOG2193|consen  406 QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE-IPD-----VSERMVIITGPPEAQFKAQGRIFGKI  479 (584)
T ss_pred             cCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC-CCC-----cceeEEEecCChHHHHhhhhhhhhhh
Confidence            023456789999999999999999999999999999999998754 454     67999999999999999999999999


Q ss_pred             hcCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          218 RENPPRQVISISPAYNYSAIRPAQPFVEPT-SGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       218 ~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~-~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                      .+.                     +|..|+ .-.....+.||...+|+|||| ||.|+++|+..++|.|.+
T Consensus       480 kEe---------------------nf~~PkeevklethirVPs~~aGRvIGK-GGktVnELQnlt~AeV~v  528 (584)
T KOG2193|consen  480 KEE---------------------NFFLPKEEVKLETHIRVPSSAAGRVIGK-GGKTVNELQNLTSAEVVV  528 (584)
T ss_pred             hhh---------------------ccCCchhhheeeeeeeccchhhhhhhcc-ccccHHHHhccccceEEc
Confidence            987                     222232 236788899999999999999 999999999999999865

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

Probab=99.87  E-value=7.8e-22  Score=189.06  Aligned_cols=204  Identities=25%  Similarity=0.378  Sum_probs=156.8

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~  127 (292)
                      ++++||+||++++|.||||+|+.||+|+++|||+|++... .|.+.+|.|+|.|.++     ++.+|+..|...|.+...
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            7999999999999999999999999999999999999855 7999999999999864     799999999999988431


Q ss_pred             CC---cch-----h-hccc-------C-------------CCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746          128 SN---SEA-----S-KVAA-------G-------------HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (292)
Q Consensus       128 ~~---~~~-----~-~~~~-------~-------------~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i  178 (292)
                      ..   ...     + ....       +             ......+++..|...++.|+|++|..|+.|+.++|+.|.+
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            10   000     0 0000       0             0123346788999999999999999999999999999998


Q ss_pred             eCCCCCCcccCCCCCCcEEEEEcCH--H----HHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeE
Q 022746          179 LAPNQLPLCASAHESDRVVQISGDV--P----AVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSM  252 (292)
Q Consensus       179 ~~~~~~p~~~~~~~~~r~v~I~G~~--~----~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~  252 (292)
                      ...          .+++.|+++...  +    .-..|+.++...+.+...                     .+. ...++
T Consensus       292 ~~~----------~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~---------------------~~~-~~~v~  339 (485)
T KOG2190|consen  292 GDS----------RTDRIVTISARENPEDRYSMAQEALLLVQPRISENAG---------------------DDL-TQTVT  339 (485)
T ss_pred             ccc----------cCcceeeeccccCcccccccchhhhhhcccccccccc---------------------ccc-cceee
Confidence            532          234788887753  2    123344444444333311                     111 34688


Q ss_pred             EEEEeccCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746          253 FLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL  290 (292)
Q Consensus       253 ~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~  290 (292)
                      .++.||.+++|+|||| +|.+|.+|++.|||.+.|.+.
T Consensus       340 ~~l~vps~~igciiGk-~G~~iseir~~tgA~I~I~~~  376 (485)
T KOG2190|consen  340 QRLLVPSDLIGCIIGK-GGAKISEIRQRTGASISILNK  376 (485)
T ss_pred             eeeccCccccceeecc-cccchHHHHHhcCCceEEccc
Confidence            9999999999999999 999999999999999988764

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

Probab=99.80  E-value=5.2e-19  Score=153.37  Aligned_cols=161  Identities=27%  Similarity=0.444  Sum_probs=131.5

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      ..-.+||||+.+++|.|||++|+.||+|++++.|+++|-.. -|.+++|+|.|.|.++     +|..++..|++++.+..
T Consensus       121 ~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k-----~v~~~i~~il~~i~e~p  195 (390)
T KOG2192|consen  121 SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK-----RVVECIKIILDLISESP  195 (390)
T ss_pred             CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc-----hHHHHHHHHHHHhhcCC
Confidence            35678999999999999999999999999999999999743 5788999999999876     58899999999987743


Q ss_pred             CCCc-------------ch-------------------------------------------------------------
Q 022746          127 DSNS-------------EA-------------------------------------------------------------  132 (292)
Q Consensus       127 ~~~~-------------~~-------------------------------------------------------------  132 (292)
                      ....             |.                                                             
T Consensus       196 ikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~sa  275 (390)
T KOG2192|consen  196 IKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSA  275 (390)
T ss_pred             cCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCc
Confidence            2100             00                                                             


Q ss_pred             ------h--hc-------------cc--------CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCC
Q 022746          133 ------S--KV-------------AA--------GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ  183 (292)
Q Consensus       133 ------~--~~-------------~~--------~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~  183 (292)
                            .  .+             ++        ..-..++.++.||.++-|.||||+|+.|++|++++||.|.+...  
T Consensus       276 idtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep--  353 (390)
T KOG2192|consen  276 IDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP--  353 (390)
T ss_pred             CCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc--
Confidence                  0  00             00        01235688999999999999999999999999999999998532  


Q ss_pred             CCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          184 LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       184 ~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      +.     ++.+|+++|+|+.++++.|..++...++..
T Consensus       354 le-----GsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  354 LE-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             CC-----CCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence            22     378999999999999999999999998865

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

Probab=99.80  E-value=5.6e-19  Score=157.08  Aligned_cols=135  Identities=22%  Similarity=0.255  Sum_probs=111.1

Q ss_pred             CCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC-CCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP-NQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       139 ~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      ......++|+||+..+|.||||+|++|.+|+.+|||+|+++.. |.+|.     +++|+|.|+|+.+++....+.|.++|
T Consensus        35 e~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG-----TTeRvcli~Gt~eai~av~efI~dKi  109 (402)
T KOG2191|consen   35 EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG-----TTERVCLIQGTVEALNAVHEFIADKI  109 (402)
T ss_pred             CCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC-----ccceEEEEeccHHHHHHHHHHHHHHH
Confidence            3455799999999999999999999999999999999999864 45676     89999999999999999999999999


Q ss_pred             hcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc-cc
Q 022746          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL-QL  290 (292)
Q Consensus       218 ~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~-~~  290 (292)
                      ++.+......    .+.     +++..  .+....+++.||+.-+|.|||| ||.+||.|+++|||.|+|- |+
T Consensus       110 re~p~~~~k~----v~~-----~~pqt--~~r~kqikivvPNstag~iigk-ggAtiK~~~Eqsga~iqisPqk  171 (402)
T KOG2191|consen  110 REKPQAVAKP----VDI-----LQPQT--PDRIKQIKIVVPNSTAGMIIGK-GGATIKAIQEQSGAWIQISPQK  171 (402)
T ss_pred             HHhHHhhcCC----ccc-----cCCCC--ccccceeEEeccCCcccceecC-CcchHHHHHHhhCcceEecccC
Confidence            9987543210    000     00000  1123458999999999999999 9999999999999999997 64

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.68  E-value=2e-16  Score=133.35  Aligned_cols=140  Identities=21%  Similarity=0.263  Sum_probs=105.2

Q ss_pred             EEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEE---ecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746           54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII---SSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (292)
Q Consensus        54 ilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I---~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~  130 (292)
                      |.||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|   +++     ..++.+|..+|..+.......  
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            57899999999999999999999999999999963     256888   333     347889999888876642211  


Q ss_pred             chhhcccCCCcccEEEEEecc---------CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc
Q 022746          131 EASKVAAGHVAANTIRLLIAG---------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG  201 (292)
Q Consensus       131 ~~~~~~~~~~~~~~~~i~IP~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G  201 (292)
                      ++.... +. .....-+.|+.         ..+|+|||++|++++.|++.|||+|.+.              +..|.|.|
T Consensus        70 ~A~~l~-gd-~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~--------------~~~v~i~G  133 (172)
T TIGR03665        70 KALKLL-DD-DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY--------------GKTVGIIG  133 (172)
T ss_pred             HHHHhc-CC-cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--------------CCEEEEEC
Confidence            000000 00 00011122332         3689999999999999999999999983              26899999


Q ss_pred             CHHHHHHHHHHHHHHHhcCC
Q 022746          202 DVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       202 ~~~~v~~A~~~I~~~l~~~~  221 (292)
                      ++++++.|..+|.+++...+
T Consensus       134 ~~~~~~~A~~~i~~li~~~~  153 (172)
T TIGR03665       134 DPEQVQIAREAIEMLIEGAP  153 (172)
T ss_pred             CHHHHHHHHHHHHHHHcCCC
Confidence            99999999999999996663

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.65  E-value=2.3e-15  Score=127.84  Aligned_cols=143  Identities=21%  Similarity=0.283  Sum_probs=107.0

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEe---cCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS---SKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~---G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      +...+.||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|.   +..    ..++.+|..+|..+.....
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            467899999999999999999999999999999999964     3567775   222    3578899999988876422


Q ss_pred             CCCcchhhcccCCCcccEEEE-Ee----c-----cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcE
Q 022746          127 DSNSEASKVAAGHVAANTIRL-LI----A-----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV  196 (292)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~i-~I----P-----~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~  196 (292)
                      ..  +..... +  .....++ .+    +     ...+|+|||++|++++.|++.|||+|.|.              +..
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  0001111 11    1     13689999999999999999999999984              234


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          197 VQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       197 v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      |.|.|+++++..|...|..++...
T Consensus       135 v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        135 VAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             EEEEeCHHHHHHHHHHHHHHHcCC
Confidence            889999999999999999999665

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.42  E-value=5.6e-13  Score=94.42  Aligned_cols=64  Identities=44%  Similarity=0.655  Sum_probs=57.1

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I  213 (292)
                      +++|+||...+|+|||++|.+|++|+++|||+|.+.+... +.     ..+|.|+|.|+++++.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~~-----~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-PG-----STERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-CC-----CCceEEEEEeCHHHHHHHHHhh
Confidence            3689999999999999999999999999999999975432 22     5789999999999999999987

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=99.42  E-value=3.1e-13  Score=95.79  Aligned_cols=63  Identities=44%  Similarity=0.685  Sum_probs=56.4

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCC-CCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA-RHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      +++|+||.+.+|+|||++|++|++|+++|||+|++.+... +..+|+|+|+|+.     +++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKP-----SAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCH-----HHHHHHHHhh
Confidence            4799999999999999999999999999999999997643 6789999999985     4788888776

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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.40  E-value=4.4e-13  Score=113.05  Aligned_cols=112  Identities=16%  Similarity=0.211  Sum_probs=85.1

Q ss_pred             EEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEE---EcCHHHHHHHHHHHHHHHhcCCCC
Q 022746          147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI---SGDVPAVLNALVEIGNQLRENPPR  223 (292)
Q Consensus       147 i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I---~G~~~~v~~A~~~I~~~l~~~~~~  223 (292)
                      +.||.+.+|.|||++|++|+.|+++||++|++.+            .+..|.|   +++++++.+|..+|..+.......
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 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS------------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE   69 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc------------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence            5689999999999999999999999999999953            2356888   899999999999999987753111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecc---------CccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          224 QVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTR---------YFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       224 ~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~---------~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                      .+..      .           -...+....+.|+.         ...|+|||+ +|++++.|++.|||.+.+-
T Consensus        70 ~A~~------l-----------~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~-~G~t~~~ie~~t~~~i~i~  125 (172)
T TIGR03665        70 KALK------L-----------LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGE-GGKTRRIIEELTGVSISVY  125 (172)
T ss_pred             HHHH------h-----------cCCcceEEEEEhhhccCCHHHHHHHHhhhcCC-CcHHHHHHHHHHCCeEEEc
Confidence            0000      0           00122233344544         479999999 9999999999999998764

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.39  E-value=1.4e-12  Score=110.76  Aligned_cols=117  Identities=17%  Similarity=0.187  Sum_probs=87.2

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEE----cCHHHHHHHHHHHHHHHhc
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS----GDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~----G~~~~v~~A~~~I~~~l~~  219 (292)
                      ...+.||.+.+|.|||++|++|+.|+++|||+|++..            .+..|.|.    ++++++.+|..+|..++..
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            5789999999999999999999999999999999952            23678885    8999999999999998874


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEec---------cCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746          220 NPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNT---------RYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL  290 (292)
Q Consensus       220 ~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP---------~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~  290 (292)
                      .....+..   ..              ...+....+.+.         ...+|+|||+ +|++++.|++.|||.+.+...
T Consensus        72 f~~e~A~~---l~--------------gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~-~G~~~k~ie~~t~~~i~i~~~  133 (180)
T PRK13763         72 FSPEKALR---LL--------------DDDYVLEVIDLSDYGDSPNALRRIKGRIIGE-GGKTRRIIEELTGVDISVYGK  133 (180)
T ss_pred             CCHHHHHH---Hh--------------CCCceEEEEEhhhccCChhHHHHHhhheeCC-CcHHHHHHHHHHCcEEEEcCC
Confidence            21000000   00              011111222222         1479999999 999999999999999887543

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

Probab=99.31  E-value=6.7e-12  Score=118.85  Aligned_cols=217  Identities=21%  Similarity=0.325  Sum_probs=155.3

Q ss_pred             CCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        45 ~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ....++.++++|+...|-.++||.|++|+.|+..++++|.+.... ..++++..+.|.+.     ++..|...+..++..
T Consensus        63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~-----~v~~a~a~~~~~~~~  136 (608)
T KOG2279|consen   63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPV-----QVCKAKAAIHQILTE  136 (608)
T ss_pred             CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCC-----CCChHHHHHHHHHhc
Confidence            344678999999999999999999999999999999999998542 23566666776553     355566666666554


Q ss_pred             CCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHH
Q 022746          125 DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP  204 (292)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~  204 (292)
                      ..               .+...+.+|...+++|+|++|.+++.++..++|+|.+... .  .+    -..+...|.|...
T Consensus       137 ~~---------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n-g--r~----g~~~~~~i~~qqk  194 (608)
T KOG2279|consen  137 NT---------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN-G--RL----GLSRLIKISGQQK  194 (608)
T ss_pred             CC---------------cccccccchhhhcccccccchhhhcchhcccccccccccc-c--cc----ccccceecccccc
Confidence            33               2356788999999999999999999999999999998532 1  21    3467888888888


Q ss_pred             HHHHHHHHHHHHHhcCCC---------------CCCCCC------------CCCC--CC-CCCCCC--------------
Q 022746          205 AVLNALVEIGNQLRENPP---------------RQVISI------------SPAY--NY-SAIRPA--------------  240 (292)
Q Consensus       205 ~v~~A~~~I~~~l~~~~~---------------~~~~~~------------~p~~--n~-~~~~~~--------------  240 (292)
                      .+..|..++.+.+.+...               ++..+.            .+..  ++ .+..++              
T Consensus       195 ~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~  274 (608)
T KOG2279|consen  195 EVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVV  274 (608)
T ss_pred             hHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeE
Confidence            888999999888766521               111000            0000  00 000000              


Q ss_pred             ----CCCCCCC-------CceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746          241 ----QPFVEPT-------SGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL  290 (292)
Q Consensus       241 ----~~~~~~~-------~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~  290 (292)
                          ..|..+.       ......+|.||.-.+|.+||+ .|+.|+.+...|++..-|.|.
T Consensus       275 vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~-~gey~s~yssasn~~~hi~t~  334 (608)
T KOG2279|consen  275 VSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGH-AGEYLSVYSSASNHPNHIWTQ  334 (608)
T ss_pred             EecccccCCccccccccccccccceeecCcccccchhhh-hhhhhhhhhhccCccceEEec
Confidence                0011111       123567999999999999999 999999999999998777654

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.25  E-value=1.5e-11  Score=86.13  Aligned_cols=60  Identities=27%  Similarity=0.362  Sum_probs=54.2

Q ss_pred             EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I  213 (292)
                      .++.||..++++|||++|++|++|+++|||+|.+++.+         +.++.|+|+|+.++|..|..+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~---------~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG---------SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC---------CCCCEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999986432         3578999999999999999887

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

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

Probab=99.22  E-value=5.3e-11  Score=83.15  Aligned_cols=57  Identities=26%  Similarity=0.278  Sum_probs=52.0

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHH
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEI  213 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I  213 (292)
                      ...+.||.+++|+|||++|++|++|+++|||+|.+.             .++.|.|+|+ +++++.|..+|
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             2468999998 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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.20  E-value=2.3e-11  Score=84.58  Aligned_cols=60  Identities=32%  Similarity=0.445  Sum_probs=53.7

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I  213 (292)
                      |.+|.||..++++|||++|++|++|+++|||+|.+.+.          .....|+|+|++++|.+|+.+|
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 ....

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.19  E-value=9.1e-12  Score=86.64  Aligned_cols=60  Identities=40%  Similarity=0.606  Sum_probs=51.9

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      |.+|.||.+++|+|||++|++|++|+++|||.|+|++.  + ....|+|+|++     .++.+|..+|
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-ERDIVTISGSP-----EQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESH-----HHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCH-----HHHHHHHhhC
Confidence            67899999999999999999999999999999999876  3 45599999964     4677777654

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.19  E-value=1.7e-11  Score=85.81  Aligned_cols=60  Identities=30%  Similarity=0.450  Sum_probs=52.2

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      .+|.||.+++|+|||++|++|++|+++|||+|.+++..  .+++.|+|+|+++     ++..|..+|
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            67999999999999999999999999999999999763  5678999999853     567776654

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=99.17  E-value=1.5e-10  Score=81.21  Aligned_cols=62  Identities=34%  Similarity=0.484  Sum_probs=55.2

Q ss_pred             EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I  213 (292)
                      .++.||.+++++|||++|++|++|+++|||+|.+.+...  .     ..++.|.|.|+.+++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~--~-----~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS--G-----SEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC--C-----CCceEEEEEcCHHHHHHHHHHh
Confidence            589999999999999999999999999999999965332  1     4689999999999999999876

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.

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

Probab=99.15  E-value=7.8e-11  Score=82.64  Aligned_cols=62  Identities=44%  Similarity=0.665  Sum_probs=53.6

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      .+|.||..++++|||++|++|++|+++|||+|.|+....+..++.|.|.|..     .++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~-----~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTP-----EAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCH-----HHHHHHHHHh
Confidence            6899999999999999999999999999999999976545678999999984     3577776654

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

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

Probab=99.11  E-value=2.1e-10  Score=80.14  Aligned_cols=59  Identities=36%  Similarity=0.522  Sum_probs=49.2

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      .+..|.||.+++|+||||+|++|+.|+++|||+|.+++      ++.|.|+|...    .++.+|..+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~----~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDK----EAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCH----HHHHHHHHHh
Confidence            35678999999999999999999999999999999986      35799999732    3566666554

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=99.07  E-value=2.2e-10  Score=74.21  Aligned_cols=42  Identities=43%  Similarity=0.673  Sum_probs=38.4

Q ss_pred             ccceeecCCCchhhhhhhhcCcEEEEcc-CCCCCCceEEEEec
Q 022746           60 QIGKVIGKEGHRIQKIREETKATIKIAD-AIARHEERVIIISS  101 (292)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~tga~I~i~~-~~~~~~ervv~I~G  101 (292)
                      +||+|||++|++|++|+++|||+|+|++ ..++..++.|+|+|
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 45677899999987

>PF13014 KH_3: KH domain

Probab=98.98  E-value=1.2e-09  Score=70.79  Aligned_cols=43  Identities=37%  Similarity=0.629  Sum_probs=37.1

Q ss_pred             cceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc
Q 022746          153 QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG  201 (292)
Q Consensus       153 ~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G  201 (292)
                      +||+|||++|++|++|+++|||+|+|++ +..+.     +.++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~~-----~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEPG-----SNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC-ccCCC-----CCceEEEEEC
Confidence            5799999999999999999999999976 33333     6899999998

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

Probab=98.94  E-value=1.3e-08  Score=85.95  Aligned_cols=149  Identities=19%  Similarity=0.224  Sum_probs=110.2

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~  128 (292)
                      .....+.||...++.+||+.|+..+.|.+.+++++.+...     +..|.|.......+....++|...|..+-......
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 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE   81 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence            3456799999999999999999999999999999999853     46788876643223456788888777775544321


Q ss_pred             CcchhhcccCCCcccEEEE------Ee-----ccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEE
Q 022746          129 NSEASKVAAGHVAANTIRL------LI-----AGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV  197 (292)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~i------~I-----P~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v  197 (292)
                      .  +.+.-..   ...+.+      .-     -....|+|||++|.+-+-|++-|||.|.|.              ...|
T Consensus        82 ~--A~~LL~d---~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--------------g~tV  142 (194)
T COG1094          82 K--ALKLLED---DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--------------GKTV  142 (194)
T ss_pred             H--HHHHhcC---CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe--------------CcEE
Confidence            1  1110000   001110      01     123469999999999999999999999985              4689


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          198 QISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       198 ~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      .|-|.+++|..|...|..++...+
T Consensus       143 aiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         143 AIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             EEecChhhhHHHHHHHHHHHcCCC
Confidence            999999999999999999998874

>smart00322 KH K homology RNA-binding domain

Probab=98.90  E-value=1.3e-08  Score=71.41  Aligned_cols=66  Identities=33%  Similarity=0.462  Sum_probs=58.5

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      .+.++.||..+++.+||++|++|++|++.||++|.+....         .....+.|.|+.+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~---------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG---------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC---------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999999999985321         24689999999999999999998876

>smart00322 KH K homology RNA-binding domain

Probab=98.82  E-value=1.6e-08  Score=70.88  Aligned_cols=67  Identities=34%  Similarity=0.582  Sum_probs=56.1

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      .++.++.||...+|.+||++|++|++|++.||++|.+....  .....+.|.|..     .++..|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--~~~~~v~i~g~~-----~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--SEERVVEITGPP-----ENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--CCccEEEEEcCH-----HHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999998642  256889999985     36777777776654

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.73  E-value=3.2e-08  Score=100.59  Aligned_cols=196  Identities=19%  Similarity=0.169  Sum_probs=138.0

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcc--hhHHHHHHHHHHHHHh-c--
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNV--VSDAENALQQIAALIL-K--  124 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~--v~~v~~A~~~I~~~i~-~--  124 (292)
                      +..++.+....+.++||++|.+++.++.++.+.++++.....  .....|.|..+...  ...++.++.++..-.. +  
T Consensus       201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~--~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~  278 (753)
T KOG2208|consen  201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKS--SPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEI  278 (753)
T ss_pred             EEEEeeccccchhhhccccccccccccccceeEEEccccccc--chhhhhccccccceehhhhhHHHHHHhcChhhhhhh
Confidence            678999999999999999999999999999999999954211  11222222211100  1122333322211000 0  


Q ss_pred             ------CCC--CC------------------cc------hhhcc------------------cCCCcccEEEEEeccCcc
Q 022746          125 ------DDD--SN------------------SE------ASKVA------------------AGHVAANTIRLLIAGSQA  154 (292)
Q Consensus       125 ------~~~--~~------------------~~------~~~~~------------------~~~~~~~~~~i~IP~~~v  154 (292)
                            ...  ..                  ..      .....                  .-......+.+.+-..++
T Consensus       279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~  358 (753)
T KOG2208|consen  279 IYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEEL  358 (753)
T ss_pred             hhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhh
Confidence                  000  00                  00      00000                  001234667888889999


Q ss_pred             eeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q 022746          155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNY  234 (292)
Q Consensus       155 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~  234 (292)
                      ..++||+|.+|.+|++++.+.|.+...         ++.+..+.++|...++.+|...+...+.+....           
T Consensus       359 ~~v~GK~~~ni~ki~e~~~~~i~~~~~---------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~-----------  418 (753)
T KOG2208|consen  359 KFVIGKKGANIEKIREESQVKIDLPKQ---------GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS-----------  418 (753)
T ss_pred             hhhcCCCCccHHHHHHhhhhceecccc---------cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc-----------
Confidence            999999999999999999999998531         157889999999999999999999999888421           


Q ss_pred             CCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746          235 SAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL  283 (292)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~  283 (292)
                                     .....+.+|...+.++||. +|..|+.|...+++
T Consensus       419 ---------------~~~~~~~iP~k~~~~iig~-~g~~i~~I~~k~~~  451 (753)
T KOG2208|consen  419 ---------------IVKEEVQIPTKSHKRIIGT-KGALINYIMGKHGG  451 (753)
T ss_pred             ---------------cccceeecCccchhhhhcc-ccccHHHHHhhcCc
Confidence                           2456788999999999999 99999999999995

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.55  E-value=1e-07  Score=96.97  Aligned_cols=145  Identities=21%  Similarity=0.298  Sum_probs=113.2

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      .+.+.+.+-+-...+..++||+|.+|.+|++++.|.+.+...  +.++..+.++|...     ++.+|...+.....+..
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            345788888999999999999999999999999999999974  35667788888754     46777777777766654


Q ss_pred             CCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhC-CeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH
Q 022746          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG-ATIVILAPNQLPLCASAHESDRVVQISGDVPA  205 (292)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~  205 (292)
                      ..             .....+.+|...+.++||.+|..|..|.+++| .+|+... +.        +....+++.|....
T Consensus       417 n~-------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~-~~--------~~~~~~~~~~~~~d  474 (753)
T KOG2208|consen  417 NS-------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQN-NN--------NSSDMVTIRGISKD  474 (753)
T ss_pred             cc-------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCC-CC--------cccccceEeccccc
Confidence            32             12467999999999999999999999999999 5666432 21        34567888888887


Q ss_pred             HHHHHHHHHHHHhcC
Q 022746          206 VLNALVEIGNQLREN  220 (292)
Q Consensus       206 v~~A~~~I~~~l~~~  220 (292)
                      +..+..++..+..+.
T Consensus       475 v~~~~~~~~~~~~~a  489 (753)
T KOG2208|consen  475 VEKSVSLLKALKADA  489 (753)
T ss_pred             cchhHHHHHhhhhhh
Confidence            777766666665544

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

Probab=98.55  E-value=1.3e-07  Score=84.53  Aligned_cols=149  Identities=21%  Similarity=0.302  Sum_probs=109.4

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~  127 (292)
                      +.++..+-||..+++.|.|++|.+||.|+.+|..+|+-+..   ..+-++.++|..+     .|..|.+.|...-.....
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            68899999999999999999999999999999999988754   2457888999876     577777666543211111


Q ss_pred             CCcchhh---c-ccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 022746          128 SNSEASK---V-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (292)
Q Consensus       128 ~~~~~~~---~-~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~  203 (292)
                      .......   . .+....+.+..+.+|...+|.+.|..|++|+.+++.++..|.-.-.          -.+.++.++|-+
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            0000000   0 0112456788899999999999999999999999999999886422          346788899988


Q ss_pred             HH-HHHHH-HHHH
Q 022746          204 PA-VLNAL-VEIG  214 (292)
Q Consensus       204 ~~-v~~A~-~~I~  214 (292)
                      .+ +++|. +.|.
T Consensus       166 ~nC~kra~s~eie  178 (394)
T KOG2113|consen  166 KNCVKRARSCEIE  178 (394)
T ss_pred             cchhhhccccchh
Confidence            87 55555 4443

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

Probab=98.51  E-value=5.4e-08  Score=92.76  Aligned_cols=110  Identities=24%  Similarity=0.233  Sum_probs=94.5

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+..++.|+..++-+++|++|.+|+.|+..++++|.+.+. +.       ..++.-.+.|-+.++..|+..+..++.+.
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~-------g~e~~~~~~~~p~~v~~a~a~~~~~~~~~  137 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DV-------GDERVLLISGFPVQVCKAKAAIHQILTEN  137 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cC-------CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence            45678999999999999999999999999999999998543 32       34677777889999999999999999887


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          221 PPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       221 ~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                      .                            .+.....+|...+++|+|| +|++++.|...|+|+..+
T Consensus       138 ~----------------------------pvk~~lsvpqr~~~~i~gr-gget~~si~~ss~aki~~  175 (608)
T KOG2279|consen  138 T----------------------------PVSEQLSVPQRSVGRIIGR-GGETIRSICKSSGAKITC  175 (608)
T ss_pred             C----------------------------cccccccchhhhccccccc-chhhhcchhccccccccc
Confidence            3                            2455677999999999999 999999999999998753

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

Probab=98.48  E-value=4.6e-07  Score=71.82  Aligned_cols=72  Identities=19%  Similarity=0.368  Sum_probs=53.2

Q ss_pred             EEEeeC------CccceeecCCCchhhhhhhhcCcEEEEccCCCC-----------------CCceEEEEecCCCCcchh
Q 022746           53 RIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAIAR-----------------HEERVIIISSKDNDNVVS  109 (292)
Q Consensus        53 rilvp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-----------------~~ervv~I~G~~~~~~v~  109 (292)
                      |+.||.      .++|.|||++|++||+|+++|||+|.|......                 .+.-.|.|++....  -.
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            455555      568999999999999999999999999954111                 12256889987610  13


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 022746          110 DAENALQQIAALILKDD  126 (292)
Q Consensus       110 ~v~~A~~~I~~~i~~~~  126 (292)
                      ++.+|+.+|..++....
T Consensus        81 ~~~~A~~~I~~ll~~~~   97 (120)
T cd02395          81 ALAKAVEAIEELLKPAI   97 (120)
T ss_pred             HHHHHHHHHHHHhccCC
Confidence            67888888888887544

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

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

Probab=98.47  E-value=9.1e-07  Score=70.09  Aligned_cols=69  Identities=22%  Similarity=0.312  Sum_probs=52.7

Q ss_pred             cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCC-----------cccCCCCCCcEEEEEcCH---HHHHHHHHHHHHH
Q 022746          151 GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP-----------LCASAHESDRVVQISGDV---PAVLNALVEIGNQ  216 (292)
Q Consensus       151 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~~~~~~~~~r~v~I~G~~---~~v~~A~~~I~~~  216 (292)
                      .+++|.|||++|.+||+|+++|||+|.|.......           .... ....-.|.|++..   +++.+|..+|..+
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            46889999999999999999999999996431110           0000 0234678999965   8999999999999


Q ss_pred             HhcC
Q 022746          217 LREN  220 (292)
Q Consensus       217 l~~~  220 (292)
                      +...
T Consensus        93 l~~~   96 (120)
T cd02395          93 LKPA   96 (120)
T ss_pred             hccC
Confidence            9865

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.21  E-value=2.7e-06  Score=69.26  Aligned_cols=103  Identities=17%  Similarity=0.297  Sum_probs=71.9

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCC
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~  129 (292)
                      -.+.|+|+...+|+.||++|++|+.|++..|-+|.+-+..              +        ++...|.+.+.......
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            3578999999999999999999999999998777765421              1        12233344433221110


Q ss_pred             cchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746          130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (292)
Q Consensus       130 ~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i  178 (292)
                      -   .. ..........+.|+....|..|||+|++++.++.-++-.+.+
T Consensus        90 v---~I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         90 V---TI-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             E---EE-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            0   00 000112357788999999999999999999999999888776

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.07  E-value=1.9e-05  Score=79.47  Aligned_cols=94  Identities=24%  Similarity=0.306  Sum_probs=73.6

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +..+.+++..|.+.|.+..... ....    ...+....+.||.+.++.|||+||.+||.|+++||++|.+.        
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-DEMS----PYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE--------  614 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCc-cccc----cCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe--------
Confidence            4556777778888877654333 1111    12345788999999999999999999999999999999984        


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  219 (292)
                           ++..|.|.+ +.+.+.+|+.+|..++..
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                 357888888 468999999999999885

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.06  E-value=1.8e-05  Score=64.39  Aligned_cols=102  Identities=17%  Similarity=0.154  Sum_probs=73.3

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~  223 (292)
                      .+.++|+...+|..||++|++|+.|++..|-+|.+..-          +.+              +...|.+.|.-..-.
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~----------s~d--------------~~~fI~n~l~Pa~V~   88 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY----------SDD--------------PEEFIKNIFAPAAVR   88 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc----------CCC--------------HHHHHHHHcCCCEEE
Confidence            68889999999999999999999999999999998742          122              344555544333111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          224 QVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       224 ~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                      ...       .          ....+.....+.|+.+..|..||| +|+||+.++...+-...+
T Consensus        89 ~v~-------I----------~~~~~~~~~~V~V~~~d~g~aIGK-~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         89 SVT-------I----------KKKNGDKVAYVEVAPEDKGIAIGK-NGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EEE-------E----------EecCCcEEEEEEECccccchhhCC-CCHHHHHHHHHhCCccCC
Confidence            000       0          000113466788999999999999 999999999988876544

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

Probab=97.98  E-value=7.5e-06  Score=73.40  Aligned_cols=122  Identities=14%  Similarity=0.103  Sum_probs=89.1

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+..+.||..+++.+.|++|..||.|+.+|...|.-+..          ..+.++.++|..+.|..|+..|..--+..
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr----------~eePiF~vTg~~edv~~aRrei~saaeH~   93 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR----------GEEPIFPVTGRHEDVRRARREIPSAAEHF   93 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC----------CCCCcceeccCchhHHHHhhcCcccccee
Confidence            56788999999999999999999999999999999986432          24578999999999999998886522111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhC
Q 022746          221 PPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSS  282 (292)
Q Consensus       221 ~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~  282 (292)
                      -..   .+.+.+     ..+.+.+. .....+.++.+|...+|.|.|. .|.+|+.|++...
T Consensus        94 ~l~---~~s~s~-----Sgg~~~~s-~s~qt~sy~svP~rvvglvv~~-~~~ti~~iqq~tn  145 (394)
T KOG2113|consen   94 GLI---RASRSF-----SGGTNGAS-ASGQTTSYVSVPLRVVGLVVGP-KGATIKRIQQFTN  145 (394)
T ss_pred             eee---eecccc-----cCCCcccc-ccCCCceeeeccceeeeecccc-ccCccchheeccc
Confidence            000   000000     00111111 1235677888999999999999 9999999998764

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

Probab=97.86  E-value=0.00012  Score=62.02  Aligned_cols=115  Identities=17%  Similarity=0.192  Sum_probs=82.0

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-----CHHHHHHHHHHHHHHHh
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-----DVPAVLNALVEIGNQLR  218 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-----~~~~v~~A~~~I~~~l~  218 (292)
                      ...+.||...++.+||+.|...+.|.+.+++++.+.            +.+..|+|..     +|..+.+|...|..+-.
T Consensus         9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD------------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr   76 (194)
T COG1094           9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID------------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGR   76 (194)
T ss_pred             eeeeecCchhheeeecccccchHHHHhhcCeEEEEE------------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence            466899999999999999999999999999999985            3456677654     47789999998877654


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEec----------cCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          219 ENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNT----------RYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       219 ~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP----------~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                      ..+...+..+   .              ..++.-..|.+-          ...-|+|||+ +|.|-+-|++.|+|.+.+.
T Consensus        77 GF~pe~A~~L---L--------------~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~-~GkTr~~IE~lt~~~I~V~  138 (194)
T COG1094          77 GFPPEKALKL---L--------------EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGR-EGKTRRAIEELTGVYISVY  138 (194)
T ss_pred             CCCHHHHHHH---h--------------cCCcEEEEEEHHHhccCchhhhhHhhceeeCC-CchHHHHHHHHhCCeEEEe
Confidence            4321111000   0              001112222211          2457999999 9999999999999998764

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.74  E-value=8e-05  Score=75.60  Aligned_cols=95  Identities=22%  Similarity=0.196  Sum_probs=68.1

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +..+.++...|.+.|.+.........    ....+....+.||.+.++.|||+||++||.|+++|||+|.+.        
T Consensus       520 l~~a~~~~~~I~~~m~~~l~~~~~~~----~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~--------  587 (684)
T TIGR03591       520 LEQAKEGRLHILGEMNKVISEPRAEL----SPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE--------  587 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhccc----cccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe--------
Confidence            34455666677777655432211100    111345678999999999999999999999999999999984        


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  219 (292)
                           ++..|.|.+ ..+.+.+|...|..+..+
T Consensus       588 -----ddG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       588 -----DDGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             -----cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence                 345677766 567888899998888664

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

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.70  E-value=0.00017  Score=58.69  Aligned_cols=102  Identities=19%  Similarity=0.274  Sum_probs=69.3

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~  130 (292)
                      -+-|+|....+|..||++|++|+.|++..|-+|.+-+..           ..+           ...|.+.+.......-
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys-----------~D~-----------~~fI~N~l~PA~V~~V   91 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS-----------ENL-----------EEFVANKLAPAEVKNV   91 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC-----------CCH-----------HHHHHHcCCCceEEEE
Confidence            577899999999999999999999998888777765421           111           1122222221110000


Q ss_pred             chhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746          131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (292)
Q Consensus       131 ~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i  178 (292)
                         .. ....+.....+.||.+..+..|||+|.+++....-++-++.+
T Consensus        92 ---~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952        92 ---TV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI  135 (141)
T ss_pred             ---EE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence               00 000123467888999999999999999999999988887766

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.63  E-value=9.3e-05  Score=74.55  Aligned_cols=66  Identities=33%  Similarity=0.509  Sum_probs=57.1

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      .-...|.||.+.+|.|||+||.+||.|+++|||+|++.+.      ..|.|.+...    ..+.+|+.+|..+...
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 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------GTVYIGAADG----PSAEAARAMINAIANP  642 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC------cEEEEEeCCH----HHHHHHHHHHHHhhCc
Confidence            5567888999999999999999999999999999999963      6799999764    4688888888888764

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.

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

Probab=97.60  E-value=0.00025  Score=67.46  Aligned_cols=78  Identities=21%  Similarity=0.278  Sum_probs=58.3

Q ss_pred             ccEEEEEec------cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCC----------CcccCCCCCCcEEEEEcCH-H
Q 022746          142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQL----------PLCASAHESDRVVQISGDV-P  204 (292)
Q Consensus       142 ~~~~~i~IP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~----------p~~~~~~~~~r~v~I~G~~-~  204 (292)
                      ....++.||      .+|||+|||..|.+.|+|+.+|||+|.|.-+...          ..... ...+--+.|+++. +
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~-~~epLH~~Isadt~e  215 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPK-ENEPLHCLISADTQE  215 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccc-cccceeEEEecchHH
Confidence            446788888      4699999999999999999999999999752111          11000 1234557788865 7


Q ss_pred             HHHHHHHHHHHHHhcC
Q 022746          205 AVLNALVEIGNQLREN  220 (292)
Q Consensus       205 ~v~~A~~~I~~~l~~~  220 (292)
                      .|++|++.|..+|.+.
T Consensus       216 ki~~Ai~vienli~~a  231 (554)
T KOG0119|consen  216 KIKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            9999999999999873

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.44  E-value=0.00053  Score=55.80  Aligned_cols=102  Identities=15%  Similarity=0.189  Sum_probs=69.1

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~  223 (292)
                      .+-|+|....+|..||++|++|+.|++..|-+|.+..-          +.+        +      ...|.+.|.=..-.
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey----------s~D--------~------~~fI~N~l~PA~V~   89 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY----------SEN--------L------EEFVANKLAPAEVK   89 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc----------CCC--------H------HHHHHHcCCCceEE
Confidence            57788999999999999999999999999999988642          112        1      12222211111000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          224 QVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       224 ~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                      ..       +         ... .++.....+.||.+..|..||| +|+||+-..+.++-...+
T Consensus        90 ~V-------~---------i~~-~~~~~~a~V~V~~~d~~~AIGk-~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952        90 NV-------T---------VSE-FNGKKVAYVEVHPRDKGIAIGK-GGKNIERAKELAKRHHDI  135 (141)
T ss_pred             EE-------E---------EEc-CCCCEEEEEEEChhhhhhhhCC-CchhHHHHHHHhcCccCC
Confidence            00       0         000 0123567788999999999999 999999999988765543

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.

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

Probab=97.44  E-value=0.00054  Score=60.57  Aligned_cols=42  Identities=26%  Similarity=0.604  Sum_probs=37.4

Q ss_pred             CCCCCeEEEEEeeCC------ccceeecCCCchhhhhhhhcCcEEEEc
Q 022746           45 AKAQDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIA   86 (292)
Q Consensus        45 ~~~~~~~~rilvp~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~   86 (292)
                      .+.-.++.|++||..      +||.|+|++|.++|+|+++|||+|-|.
T Consensus        87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            344567889999985      799999999999999999999999998

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.40  E-value=0.00033  Score=72.19  Aligned_cols=95  Identities=17%  Similarity=0.212  Sum_probs=70.9

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCe-EEEeCCCCCCc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPL  186 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~  186 (292)
                      +..+.+++..|++.|.+.........    .........+.||.+.++.|||.||.+||.|.++||++ |.+.       
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 LLQAKDGRKHILAEMSKCSPPPSKRL----SKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-------  722 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhh----cccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------
Confidence            44556677777777766543221111    11234578899999999999999999999999999999 8862       


Q ss_pred             ccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746          187 CASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       187 ~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  219 (292)
                            ++-.|.|.+ +.+.+.+|+.+|..++.+
T Consensus       723 ------ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        723 ------DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             ------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence                  356788877 568999999999988764

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

Probab=97.33  E-value=0.0006  Score=67.65  Aligned_cols=107  Identities=20%  Similarity=0.212  Sum_probs=78.3

Q ss_pred             EEEecCCCC---cchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhC
Q 022746           97 IIISSKDND---NVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG  173 (292)
Q Consensus        97 v~I~G~~~~---~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tg  173 (292)
                      +.|.|-+..   ..+..+..|...|+..|.+........    ..........+.|+...++-+||++|++|+.|.++||
T Consensus       507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~e----ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg  582 (692)
T COG1185         507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKE----LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETG  582 (692)
T ss_pred             eeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh----hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhC
Confidence            455665442   114456677778888887654322111    1112344678899999999999999999999999999


Q ss_pred             CeEEEeCCCCCCcccCCCCCCcEEEEEcCH-HHHHHHHHHHHHHHhcC
Q 022746          174 ATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLREN  220 (292)
Q Consensus       174 a~I~i~~~~~~p~~~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~~  220 (292)
                      ++|++.             ++..|.|.++. +.+.+|+.+|..+.++.
T Consensus       583 ~~Idie-------------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         583 VKIDIE-------------DDGTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             cEEEec-------------CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence            999983             45688898887 78899999999998665

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.32  E-value=0.00027  Score=71.79  Aligned_cols=65  Identities=32%  Similarity=0.441  Sum_probs=53.3

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      .-...+.||.+.+|.|||++|++||+|+++|||+|.|.+.      ..|.|.+...    ..+.+|..+|..+..
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~----~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDG----EAAEAAIKMIEGITA  614 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcH----HHHHHHHHHHHhhhc
Confidence            4567888999999999999999999999999999999863      5688887653    356777777776644

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).

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

Probab=97.22  E-value=0.00053  Score=65.26  Aligned_cols=73  Identities=23%  Similarity=0.380  Sum_probs=57.0

Q ss_pred             CeEEEEEeeC------CccceeecCCCchhhhhhhhcCcEEEEccC------C---------CCC-CceEEEEecCCCCc
Q 022746           49 DVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA------I---------ARH-EERVIIISSKDNDN  106 (292)
Q Consensus        49 ~~~~rilvp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~------~---------~~~-~ervv~I~G~~~~~  106 (292)
                      .++-|+.||.      ++||+|||.+|.|.|+|+++|||+|.|--.      .         ++. ++--+.|++...  
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            5667888886      579999999999999999999999999731      0         111 233478888765  


Q ss_pred             chhHHHHHHHHHHHHHhcC
Q 022746          107 VVSDAENALQQIAALILKD  125 (292)
Q Consensus       107 ~v~~v~~A~~~I~~~i~~~  125 (292)
                        +.+.+|+..|..+|.+.
T Consensus       215 --eki~~Ai~vienli~~a  231 (554)
T KOG0119|consen  215 --EKIKKAIAVIENLIQSA  231 (554)
T ss_pred             --HHHHHHHHHHHHHHHhh
Confidence              57899999999998763

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.16  E-value=0.0018  Score=55.31  Aligned_cols=103  Identities=20%  Similarity=0.288  Sum_probs=69.6

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~  130 (292)
                      .+-+.+-...+|..||++|++|+.|+++.|=+|.|-+-.             ++         -...|.+.+......  
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d---------~~~fI~nal~Pa~v~--  132 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------ED---------PAEFIKNALAPAEVL--  132 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CC---------HHHHHHHhcCcceEe--
Confidence            455566667899999999999999999999666665431             11         112233333311100  


Q ss_pred             chhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746          131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (292)
Q Consensus       131 ~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  180 (292)
                         ...-.........+.||.+..+..|||+|.+++-..+-||-++.+..
T Consensus       133 ---~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         133 ---SVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             ---EEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence               00000001116888999999999999999999999999999999864

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

Probab=97.09  E-value=0.00047  Score=64.70  Aligned_cols=74  Identities=22%  Similarity=0.315  Sum_probs=55.8

Q ss_pred             cCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        44 ~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      .....++++.|.|-+++||.+||++|++|+.||..|+++|++-..   ..+-.|+|-|....  ...+.+++....+..
T Consensus        41 aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m--~~kaka~id~~~~k~  114 (629)
T KOG0336|consen   41 AAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHM--RKKAKASIDRGQDKD  114 (629)
T ss_pred             ccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHH--HHHHHhhHhhhhhhh
Confidence            345568889999999999999999999999999999999999864   34567888887542  123344444444443

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

Probab=97.08  E-value=0.00067  Score=47.15  Aligned_cols=36  Identities=31%  Similarity=0.493  Sum_probs=33.6

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEE
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI   85 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i   85 (292)
                      ....+.|+.+..|..|||+|.+|+.+++.+|-+|.+
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578999999999999999999999999999988876

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

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

Probab=97.03  E-value=0.0007  Score=61.59  Aligned_cols=72  Identities=33%  Similarity=0.385  Sum_probs=59.2

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      .+...+.+++...|+|||++|.+-++|+++|+++|.++.+  +.....+.|+|-.    ...|..|..+|..+|.+..
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~----~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGIS----RNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehh----HHHHHHHHHHHHHHHHhhh
Confidence            5667889999999999999999999999999999999976  3344457777754    4578899999988886644

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

Probab=96.94  E-value=0.0023  Score=56.62  Aligned_cols=81  Identities=17%  Similarity=0.257  Sum_probs=54.9

Q ss_pred             CcccEEEEEecc------CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCC------------cccCCC-CCCcEEEEE
Q 022746          140 VAANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP------------LCASAH-ESDRVVQIS  200 (292)
Q Consensus       140 ~~~~~~~i~IP~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p------------~~~~~~-~~~r~v~I~  200 (292)
                      ....+.+|+||.      ++||+|+|..|.++|+|+++|||+|.|--....-            ..+... .--..|...
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            345678889984      4999999999999999999999999996432111            111000 011446667


Q ss_pred             cCHH----HHHHHHHHHHHHHhcC
Q 022746          201 GDVP----AVLNALVEIGNQLREN  220 (292)
Q Consensus       201 G~~~----~v~~A~~~I~~~l~~~  220 (292)
                      +++.    .+..|++.|..+|.-.
T Consensus       169 ~p~~ea~~rl~~AleeI~klL~P~  192 (259)
T KOG1588|consen  169 APPAEAYARLAYALEEIKKLLVPD  192 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCC
Confidence            7765    3446888888877544

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.88  E-value=0.0017  Score=66.13  Aligned_cols=95  Identities=21%  Similarity=0.202  Sum_probs=68.8

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +..+.+++..|.+.|.+.........    .........+.||.+.++.+||.||.+||+|.++||+.|.+.        
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            44556777778888776543221111    111233567778999999999999999999999999988862        


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  219 (292)
                           ++..|.|.+ ..+.+.+|...|..+..+
T Consensus       591 -----d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        591 -----DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             -----CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence                 356788887 567888999999888764

>TIGR01953 NusA transcription termination factor NusA

Probab=96.80  E-value=0.0058  Score=57.02  Aligned_cols=95  Identities=23%  Similarity=0.320  Sum_probs=63.5

Q ss_pred             CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (292)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (292)
                      +-+|+.||++|++|+.|.++. |=+|.|-...             ++         -...|.+.+.......     +.-
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-------------~d---------~~~fi~nal~Pa~v~~-----v~i  295 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS-------------DD---------PAEFIANALSPAKVIS-----VEV  295 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhcCCceEEE-----EEE
Confidence            459999999999999999998 6666665321             00         0111222221111000     000


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  180 (292)
                      .........+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       296 ~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       296 LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            0001236899999999999999999999999999999999964

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.69  E-value=0.006  Score=57.23  Aligned_cols=97  Identities=21%  Similarity=0.185  Sum_probs=65.3

Q ss_pred             CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (292)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (292)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.             ++         -...|.+.+.......     +..
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-------------~D---------~~~fI~Nal~Pa~V~~-----V~i  303 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS-------------NV---------PEIFIARALAPAIISS-----VKI  303 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCceeeE-----EEE
Confidence            459999999999999999998 6666665321             10         1112222222111000     000


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCC
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ  183 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~  183 (292)
                      . .......+.||..+.+..|||+|.+++-...-||.+|.|.+-..
T Consensus       304 ~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        304 E-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             c-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence            0 11236889999999999999999999999999999999987543

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

Probab=96.65  E-value=0.003  Score=57.62  Aligned_cols=71  Identities=24%  Similarity=0.368  Sum_probs=57.3

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      ....+.++..+.++|||++|.+-++|+++|+++|.++.+..        ..+.++.+.+..++|.+|...|...+.+..
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~--------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT--------NKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC--------CcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            35678899999999999999999999999999999865431        233344445567899999999999988774

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

Probab=96.65  E-value=0.0025  Score=59.94  Aligned_cols=68  Identities=21%  Similarity=0.251  Sum_probs=55.2

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      .....|.|-+++||.+||++|+.|++||..|+++|++..-          ..+..|+|-|...--.+|...|...+..
T Consensus        46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~----------~~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC----------DLEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc----------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            4467788999999999999999999999999999999642          3578999999987666666666555443

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

Probab=96.61  E-value=0.0041  Score=43.14  Aligned_cols=36  Identities=31%  Similarity=0.451  Sum_probs=33.6

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i  178 (292)
                      ....+.|+...+|..|||+|.+|+.+++.+|-+|.+
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            478999999999999999999999999999988876

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.

>PRK00468 hypothetical protein; Provisional

Probab=96.56  E-value=0.0023  Score=46.37  Aligned_cols=34  Identities=35%  Similarity=0.587  Sum_probs=29.8

Q ss_pred             CCCCeEEEEEeeCCccceeecCCCchhhhhhhhc
Q 022746           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (292)
Q Consensus        46 ~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t   79 (292)
                      .+..+.+++.|..+.+|.||||+|.+|+.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3446789999999999999999999999999763

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.54  E-value=0.0095  Score=55.99  Aligned_cols=96  Identities=23%  Similarity=0.294  Sum_probs=64.3

Q ss_pred             CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (292)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (292)
                      +-+|+.||++|++|+.|.++. |-+|.|-...             ++         ....|.+.+.......     +..
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s-------------~d---------~~~fi~nal~Pa~v~~-----v~i  297 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS-------------ED---------PAEFVANALSPAKVVS-----VEV  297 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCceEEE-----EEE
Confidence            459999999999999999998 7666665321             00         1112222222111000     000


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  181 (292)
                      .........+.||..+.+..|||+|.+++--..-||.+|.+.+.
T Consensus       298 ~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        298 DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            00112368999999999999999999999999999999999753

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

Probab=96.47  E-value=0.006  Score=60.75  Aligned_cols=65  Identities=31%  Similarity=0.440  Sum_probs=54.2

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ...+.++.+.++-+||++|.+|++|.++|||+|++.+.      ..|.|.++..+    .+.+|+..|..+..+.
T Consensus       553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~----~~~~ak~~I~~i~~e~  617 (692)
T COG1185         553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGE----SAKKAKERIEAITREV  617 (692)
T ss_pred             eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchH----HHHHHHHHHHHHHhhc
Confidence            45677899999999999999999999999999999954      45888887653    6778888888887543

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.44  E-value=0.0028  Score=65.56  Aligned_cols=66  Identities=26%  Similarity=0.405  Sum_probs=56.1

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcE-EEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      .....|.||.+.++.|||.||.+||.|.++||+. |++.+.      -.|.|.+...    ..+.+|+.+|..+..+
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~----~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDL----SSLEKSKAIISSLTMV  750 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCH----HHHHHHHHHHHHHhcC
Confidence            5667889999999999999999999999999999 998863      5688988764    5788888888888753

>PRK02821 hypothetical protein; Provisional

Probab=96.41  E-value=0.0032  Score=45.83  Aligned_cols=35  Identities=26%  Similarity=0.438  Sum_probs=30.3

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA   81 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga   81 (292)
                      .....+++.|..+.+|.||||+|.+|+.||.--.+
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            34577899999999999999999999999987544

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.39  E-value=0.0096  Score=56.86  Aligned_cols=95  Identities=23%  Similarity=0.265  Sum_probs=63.0

Q ss_pred             CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (292)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (292)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.             ++         -...|.+.+.......     +..
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-------------~D---------p~~fI~NaLsPA~V~~-----V~i  329 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-------------PD---------PATYIANALSPARVDE-----VRL  329 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhcCCceeeE-----EEE
Confidence            459999999999999999998 6666665321             10         1112222222111000     000


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  180 (292)
                      .........+.||..+.+..|||+|.+++--..-||.+|.|..
T Consensus       330 ~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        330 VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            0001235789999999999999999999999999999999853

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.28  E-value=0.0082  Score=51.34  Aligned_cols=100  Identities=15%  Similarity=0.178  Sum_probs=67.3

Q ss_pred             EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCC
Q 022746          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ  224 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~  224 (292)
                      ..+.+-.+.+|..||++|.+|+.|+++.|-+|.+...          +.+              -...|.+.|.  |.. 
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~----------s~d--------------~~~fI~nal~--Pa~-  130 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW----------SED--------------PAEFIKNALA--PAE-  130 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe----------CCC--------------HHHHHHHhcC--cce-
Confidence            4455556788999999999999999999988887632          111              1233333333  110 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          225 VISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       225 ~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                      ...    .+..           ..+.....+.||.+.-+..||| +|.|++-+.+-+|-.+.+
T Consensus       131 v~~----V~~~-----------~~d~~~~~v~V~~~~~~~aIGk-~G~Nvrla~~Ltg~~i~I  177 (190)
T COG0195         131 VLS----VNIK-----------EDDGHVAIVVVPPDQLSLAIGK-GGQNVRLASQLTGWEIDI  177 (190)
T ss_pred             EeE----EEEE-----------eCCCcEEEEEECHHHHhhccCc-ccHHHHHHHHHhCCEEEE
Confidence            000    0000           0011267888999999999999 999999999999987655

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.26  E-value=0.013  Score=57.08  Aligned_cols=95  Identities=25%  Similarity=0.332  Sum_probs=64.0

Q ss_pred             CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (292)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (292)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.             ++         -...|.+.+.......     +-.
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-------------~d---------~~~fi~nal~pa~v~~-----v~~  297 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS-------------DD---------PAQFIINALSPAEVSS-----VVV  297 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCCEEEE-----EEE
Confidence            348999999999999999998 6666665321             10         0112222222111000     000


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  181 (292)
                      . .....+.+.||..+.+..|||+|.+++-...-||.+|.|...
T Consensus       298 ~-~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        298 D-EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             e-CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            0 012378999999999999999999999999999999999763

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

Probab=96.20  E-value=0.0049  Score=44.60  Aligned_cols=32  Identities=41%  Similarity=0.637  Sum_probs=29.3

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhh
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE   78 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~   78 (292)
                      +..+.++|-+..+.+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            45678999999999999999999999999975

>PRK00468 hypothetical protein; Provisional

Probab=96.16  E-value=0.0065  Score=43.99  Aligned_cols=31  Identities=3%  Similarity=-0.142  Sum_probs=28.5

Q ss_pred             ceeEEEEEeccCccceeeecCCCccHHHHHHh
Q 022746          249 GYSMFLMQNTRYFVTAIFAVLSSFNIFFLITT  280 (292)
Q Consensus       249 ~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~  280 (292)
                      ....+++.+..+-+|+|||| +|.+|+.||..
T Consensus        28 ~~~~~~l~v~~~D~GrVIGk-~Gr~i~AIRtv   58 (75)
T PRK00468         28 QSVILELKVAPEDMGKVIGK-QGRIAKAIRTV   58 (75)
T ss_pred             CeEEEEEEEChhhCcceecC-CChhHHHHHHH
Confidence            45788999999999999999 99999999986

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.16  E-value=0.011  Score=52.33  Aligned_cols=65  Identities=22%  Similarity=0.222  Sum_probs=54.1

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH-HHHHHHHHHHHHHHhcCC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLRENP  221 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~~~  221 (292)
                      -+.+.||..+++.+||++|.+|+.|.+++++.|.+-             .+..|.|.|.. +.+.+|...|..+-++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            467899999999999999999999999999999982             34678888865 588888888877766663

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

Probab=96.09  E-value=0.014  Score=49.92  Aligned_cols=39  Identities=28%  Similarity=0.402  Sum_probs=34.0

Q ss_pred             ccEEEEEec------cCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746          142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (292)
Q Consensus       142 ~~~~~i~IP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  180 (292)
                      ..+-+++||      .++||.|||..|.+.|+|+..|+|+|.|--
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            445677777      679999999999999999999999999864

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.03  E-value=0.011  Score=52.44  Aligned_cols=60  Identities=28%  Similarity=0.427  Sum_probs=48.6

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~  121 (292)
                      +.+.||.+.++.+||++|.+|+.|.+++++.|.+..+      ..|.|.+...    ..+.+|..+|..+
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~----~~~~~a~~~I~~~  206 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDE----EDEEIAIEAIKKI  206 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCH----HHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999864      5689999764    3455666655555

>PRK01064 hypothetical protein; Provisional

Probab=95.96  E-value=0.008  Score=43.84  Aligned_cols=33  Identities=36%  Similarity=0.708  Sum_probs=29.6

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t   79 (292)
                      .+.+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            456889999999999999999999999999854

>PRK02821 hypothetical protein; Provisional

Probab=95.89  E-value=0.0075  Score=43.86  Aligned_cols=33  Identities=6%  Similarity=-0.144  Sum_probs=29.2

Q ss_pred             eeEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746          250 YSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL  283 (292)
Q Consensus       250 ~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~  283 (292)
                      ...+++.+..+-+|+|||| +|.+|+.||..-++
T Consensus        30 ~~~i~l~v~~~D~GrVIGk-~Gr~i~AIRtlv~a   62 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGR-GGRTATALRTVVAA   62 (77)
T ss_pred             cEEEEEEEChhhCcceeCC-CCchHHHHHHHHHH
Confidence            4678999999999999999 99999999987443

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.77  E-value=0.029  Score=55.32  Aligned_cols=67  Identities=21%  Similarity=0.330  Sum_probs=51.9

Q ss_pred             ccEEEEEecc-CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746          142 ANTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       142 ~~~~~i~IP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  219 (292)
                      .+...+.+|+ +.-|+|||+.|.+|+-|..-||+.+-|.   +         +...|+|+| +|-.-.-|...|..++.+
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d---------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D---------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C---------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            3456678888 4669999999999999999999999983   2         345788888 555556677777777766


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      -
T Consensus       271 g  271 (514)
T TIGR03319       271 G  271 (514)
T ss_pred             C
Confidence            4

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

Probab=95.75  E-value=0.011  Score=50.66  Aligned_cols=41  Identities=22%  Similarity=0.449  Sum_probs=35.1

Q ss_pred             CCCeEEEEEeeC------CccceeecCCCchhhhhhhhcCcEEEEcc
Q 022746           47 AQDVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIAD   87 (292)
Q Consensus        47 ~~~~~~rilvp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~   87 (292)
                      ...++-++.||-      .+||+|||++|+++|+|+..|+|+|-|..
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            345666777774      67999999999999999999999999974

>PRK00106 hypothetical protein; Provisional

Probab=95.74  E-value=0.034  Score=54.88  Aligned_cols=67  Identities=22%  Similarity=0.368  Sum_probs=52.6

Q ss_pred             ccEEEEEecc-CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746          142 ANTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       142 ~~~~~i~IP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  219 (292)
                      .+...+.+|+ +.-|+|||+.|.+|+-|..-||+.+-|.   +         +...|+|+| +|-.-.-|...+..++.+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d---------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---D---------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---C---------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            3456678888 4669999999999999999999999983   2         345788998 566666677777777766


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      -
T Consensus       292 g  292 (535)
T PRK00106        292 G  292 (535)
T ss_pred             C
Confidence            4

>PRK12704 phosphodiesterase; Provisional

Probab=95.67  E-value=0.036  Score=54.74  Aligned_cols=67  Identities=21%  Similarity=0.322  Sum_probs=51.0

Q ss_pred             ccEEEEEecc-CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746          142 ANTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       142 ~~~~~i~IP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  219 (292)
                      .+...+.+|+ +.-|+|||+.|.+|+-|..-||+.|-|.   +         +...|.++| ++-.-.-|...+..++.+
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d---------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D---------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C---------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            3456677887 5669999999999999999999999983   2         345888999 455545667777666665


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      -
T Consensus       277 g  277 (520)
T PRK12704        277 G  277 (520)
T ss_pred             C
Confidence            5

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.45  E-value=0.029  Score=52.76  Aligned_cols=94  Identities=15%  Similarity=0.125  Sum_probs=63.5

Q ss_pred             CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746          152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP  230 (292)
Q Consensus       152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p  230 (292)
                      +-+|.+||++|.+|+.|.++. |-+|.+..-+          .+              ....|.+.|.=..-...     
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s----------~d--------------~~~fi~nal~Pa~v~~v-----  295 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS----------ED--------------PAEFVANALSPAKVVSV-----  295 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcC----------CC--------------HHHHHHHhCCCceEEEE-----
Confidence            357999999999999999888 8899987532          22              12222222211100000     


Q ss_pred             CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                                  .. ...+...+.+.||.+..+.-||| +|.||+-....+|..+.|+
T Consensus       296 ------------~i-~~~~~~~~~v~V~~~~~~~AIGk-~G~Nv~la~~L~~~~idi~  339 (362)
T PRK12327        296 ------------EV-DDEEEKAARVVVPDYQLSLAIGK-EGQNARLAARLTGWKIDIK  339 (362)
T ss_pred             ------------EE-EcCCCcEEEEEEChhhcchhhcC-CChhHHHHHHHHCCeeeEE
Confidence                        00 00112468899999999999999 9999999999999887654

>PRK01064 hypothetical protein; Provisional

Probab=95.41  E-value=0.025  Score=41.26  Aligned_cols=31  Identities=10%  Similarity=-0.005  Sum_probs=28.4

Q ss_pred             ceeEEEEEeccCccceeeecCCCccHHHHHHh
Q 022746          249 GYSMFLMQNTRYFVTAIFAVLSSFNIFFLITT  280 (292)
Q Consensus       249 ~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~  280 (292)
                      ....+++.+..+-.|.+||| +|.+|+.|+..
T Consensus        28 ~~~~~~l~v~~~D~g~vIGk-~G~~i~air~l   58 (78)
T PRK01064         28 HTIIYELTVAKPDIGKIIGK-EGRTIKAIRTL   58 (78)
T ss_pred             CEEEEEEEECcccceEEECC-CCccHHHHHHH
Confidence            46788999999999999999 99999999985

>PRK12704 phosphodiesterase; Provisional

Probab=95.36  E-value=0.035  Score=54.81  Aligned_cols=49  Identities=27%  Similarity=0.492  Sum_probs=40.3

Q ss_pred             eEEEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCC
Q 022746           50 VLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (292)
Q Consensus        50 ~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~  103 (292)
                      .+-.+-+|+ ++-|+||||.|.||+.|+.-||+.|-|.+.    + .+|+++|..
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~~~  259 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGFD  259 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----C-CeEEEecCC
Confidence            344566777 679999999999999999999999999974    2 457899854

>TIGR01953 NusA transcription termination factor NusA

Probab=95.27  E-value=0.031  Score=52.23  Aligned_cols=94  Identities=16%  Similarity=0.176  Sum_probs=63.2

Q ss_pred             CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746          152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP  230 (292)
Q Consensus       152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p  230 (292)
                      +-+|.+||++|.+|+.|.++. |-+|.+..-+          .+.              ...|.+.|.=..   ...+  
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s----------~d~--------------~~fi~nal~Pa~---v~~v--  293 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS----------DDP--------------AEFIANALSPAK---VISV--  293 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcC----------CCH--------------HHHHHHhcCCce---EEEE--
Confidence            457999999999999999988 8899987532          220              111212111000   0000  


Q ss_pred             CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                        .         ...  .+.....+.||.+..+..||| +|.|++-....+|..+.|.
T Consensus       294 --~---------i~~--~~~~~~~v~V~~~~~~~aIGk-~G~Nv~la~~l~g~~IdI~  337 (341)
T TIGR01953       294 --E---------VLD--EDKHSAEVVVPDDQLSLAIGK-GGQNVRLASKLTGWNIDVK  337 (341)
T ss_pred             --E---------EEc--CCCcEEEEEEChHHcchhhcC-CChhHHHHHHHhCCEEEEE
Confidence              0         000  012478899999999999999 9999999999999987664

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.

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

Probab=95.20  E-value=0.026  Score=40.85  Aligned_cols=31  Identities=6%  Similarity=-0.107  Sum_probs=28.4

Q ss_pred             ceeEEEEEeccCccceeeecCCCccHHHHHHh
Q 022746          249 GYSMFLMQNTRYFVTAIFAVLSSFNIFFLITT  280 (292)
Q Consensus       249 ~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~  280 (292)
                      ...++++.+...-.|.|||| +|.+|+.||..
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk-~GRti~AIRTl   58 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGK-QGRTIQAIRTL   58 (76)
T ss_pred             CeEEEEEEECcccccceecC-CChhHHHHHHH
Confidence            36788999999999999999 99999999986

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.17  E-value=0.037  Score=54.60  Aligned_cols=49  Identities=24%  Similarity=0.460  Sum_probs=40.3

Q ss_pred             CeEEEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecC
Q 022746           49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK  102 (292)
Q Consensus        49 ~~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~  102 (292)
                      ..+-.+.+|+ ++-|+||||.|.||+.++.-||+.|-|.+.    + ..|+|++.
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~f  252 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGF  252 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----C-CeEEecCC
Confidence            3444567788 679999999999999999999999999974    3 45778885

>PRK00106 hypothetical protein; Provisional

Probab=95.09  E-value=0.042  Score=54.21  Aligned_cols=50  Identities=26%  Similarity=0.529  Sum_probs=40.7

Q ss_pred             CeEEEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCC
Q 022746           49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (292)
Q Consensus        49 ~~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~  103 (292)
                      ..+-.+.+|+ ++-|+||||.|.||+.++.-||+.+-|.+.    + ..|+++|.+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt----p-~~v~lS~fd  274 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT----P-EVVVLSGFD  274 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC----C-CeEEEeCCC
Confidence            3445677788 679999999999999999999999999974    3 347788853

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.08  E-value=0.016  Score=59.28  Aligned_cols=63  Identities=35%  Similarity=0.511  Sum_probs=50.4

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      ...+.||.+.++.+||+||.+||.|.++||++|++.+.      ..|.|.+...    ..+.+|..+|..+..
T Consensus       555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~------G~v~i~~~~~----~~~~~a~~~I~~~~~  617 (693)
T PRK11824        555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD------GTVKIAATDG----EAAEAAKERIEGITA  617 (693)
T ss_pred             heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC------ceEEEEcccH----HHHHHHHHHHHHhcc
Confidence            34566699999999999999999999999999988753      5588888653    467777777777654

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.05  E-value=0.043  Score=52.51  Aligned_cols=94  Identities=16%  Similarity=0.145  Sum_probs=62.4

Q ss_pred             CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746          152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP  230 (292)
Q Consensus       152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p  230 (292)
                      +-+|.+||++|.+|+.|.++. |-+|.|..-+          .+              -...|.+.|.=..-....    
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys----------~D--------------p~~fI~NaLsPA~V~~V~----  328 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS----------PD--------------PATYIANALSPARVDEVR----  328 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC----------CC--------------HHHHHHHhcCCceeeEEE----
Confidence            457999999999999999988 8899987532          22              111222211111000000    


Q ss_pred             CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                                  ...  .+.....+.||.+..+.-||| +|.||+-....+|..+.|.
T Consensus       329 ------------i~~--~~~k~a~V~V~~~qlslAIGK-~GqNvrLAs~Ltg~~idI~  371 (449)
T PRK12329        329 ------------LVD--PEGRHAHVLVPPDQLSLAIGK-EGQNVRLAARLTGWKIDIK  371 (449)
T ss_pred             ------------EEc--CCCcEEEEEEChHhcchhhcC-CChhHHHHHHHHCCEeccc
Confidence                        000  112367899999999999999 9999999999998877653

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.03  E-value=1.2  Score=38.49  Aligned_cols=131  Identities=14%  Similarity=0.122  Sum_probs=84.8

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcc
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSE  131 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~  131 (292)
                      +.+.++....-+|...+|..++.|-...||+|.+...     +..+.|+|++.     .+..+...|.+++..-      
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~-----~~~~i~~~i~~~l~~i------   91 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKS-----TAEYIEASINEILSNI------   91 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHH-----HHHHHHHHHHHHHhhc------
Confidence            3344458888999999999999998889999999853     45799999864     3333334444443321      


Q ss_pred             hhhcccCCCcccEEEEEeccCcceeee----cCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEE-----cC
Q 022746          132 ASKVAAGHVAANTIRLLIAGSQAGCLI----GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GD  202 (292)
Q Consensus       132 ~~~~~~~~~~~~~~~i~IP~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~-----G~  202 (292)
                                 .+..+.++.-.-..--    -.....++.|++.|++.|...+.            +..+.|+     -.
T Consensus        92 -----------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~------------~~~~~i~~~~~~~~  148 (210)
T PF14611_consen   92 -----------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD------------GNKLKISWLASPEN  148 (210)
T ss_pred             -----------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC------------CCeEEEEEEeeccc
Confidence                       1334444422111111    11356789999999999997432            2234444     45


Q ss_pred             HHHHHHHHHHHHHHHhcCC
Q 022746          203 VPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       203 ~~~v~~A~~~I~~~l~~~~  221 (292)
                      ...+..|..+|..-+...+
T Consensus       149 ~~~~~~a~RlL~~a~~~~~  167 (210)
T PF14611_consen  149 EKRADRAKRLLLWALDYNP  167 (210)
T ss_pred             cchHHHHHHHHHHhccCCc
Confidence            6788889999988886443

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.02  E-value=0.028  Score=54.67  Aligned_cols=92  Identities=17%  Similarity=0.148  Sum_probs=62.8

Q ss_pred             cceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q 022746          153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA  231 (292)
Q Consensus       153 ~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~  231 (292)
                      -+|.+||++|++|+.|.++. |-+|.|..-+          .+.              ...|.+.|.-..-...      
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s----------~d~--------------~~fi~nal~pa~v~~v------  295 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWS----------DDP--------------AQFIINALSPAEVSSV------  295 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcC----------CCH--------------HHHHHHhCCCCEEEEE------
Confidence            57999999999999999887 8899987532          221              1222222211100000      


Q ss_pred             CCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          232 YNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       232 ~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                                 ..  ......+.+.||....+.-||| +|.||+-..+.+|..+.|.
T Consensus       296 -----------~~--~~~~~~~~v~V~~~~~~~AIGk-~G~Nvrla~~l~g~~idi~  338 (470)
T PRK09202        296 -----------VV--DEDEHSADVVVPDDQLSLAIGK-NGQNVRLASKLTGWKIDIM  338 (470)
T ss_pred             -----------EE--eCCCCEEEEEECcchHHHhhCC-CCeeHHHHHHHHCCeEEEE
Confidence                       00  0012377899999999999999 9999999999999887653

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=94.78  E-value=0.033  Score=52.29  Aligned_cols=93  Identities=13%  Similarity=0.122  Sum_probs=63.1

Q ss_pred             CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746          152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP  230 (292)
Q Consensus       152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p  230 (292)
                      +-+|.+||++|.+|+.|.++. |-+|.+..-+          .+              -...|.+.|.=..   ...+. 
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s----------~D--------------~~~fI~Nal~Pa~---V~~V~-  302 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS----------NV--------------PEIFIARALAPAI---ISSVK-  302 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC----------CC--------------HHHHHHHhCCCce---eeEEE-
Confidence            467999999999999999887 8899987532          22              1112222211100   00000 


Q ss_pred             CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                                   .  ..+.....+.||.+..+..||| +|.|++-..+.+|..+-|.
T Consensus       303 -------------i--~~~~~~~~V~V~~~qlslAIGk-~GqNvrLA~~LtGwkIDI~  344 (374)
T PRK12328        303 -------------I--EEEEKKAIVTLLSDQKSKAIGK-NGINIRLASMLTGYEIELN  344 (374)
T ss_pred             -------------E--cCCCcEEEEEEChHHhhhhhcC-CChhHHHHHHHhCCEEEEE
Confidence                         0  0112477889999999999999 9999999999999887654

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

Probab=94.51  E-value=0.12  Score=50.65  Aligned_cols=96  Identities=20%  Similarity=0.205  Sum_probs=71.2

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +.++.+|...|++.|.+........    ..........+.++.+....+||.+|...|+|..+||+.-.+         
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 LQKAREARLQILDIMEKNINSPRGS----DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------  632 (760)
T ss_pred             HHhhhHHHHHHHHHHHhhcCCcccC----ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------
Confidence            4556677788888887765432211    122345577889999999999999999999999999954443         


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhcCC
Q 022746          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~~  221 (292)
                           ++..++|-. ++.+..+|++.|..++.+..
T Consensus       633 -----De~t~~i~A~~~~am~~Ak~~I~~i~~~~~  662 (760)
T KOG1067|consen  633 -----DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQ  662 (760)
T ss_pred             -----cCceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence                 355777765 56788999999999987753

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=94.41  E-value=0.017  Score=41.36  Aligned_cols=35  Identities=17%  Similarity=0.352  Sum_probs=29.8

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA   81 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga   81 (292)
                      .+...+.+-+..+..|.||||+|.+++.||.-.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            44567888889999999999999999999986654

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

Probab=94.18  E-value=0.076  Score=36.63  Aligned_cols=35  Identities=29%  Similarity=0.462  Sum_probs=28.8

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEE
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI   83 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I   83 (292)
                      ...+.+.+.....|.+||++|.++++|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45566777766799999999999999999988554

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=93.78  E-value=0.048  Score=38.83  Aligned_cols=37  Identities=35%  Similarity=0.587  Sum_probs=29.5

Q ss_pred             EEEEeeCCc-----cceeecCCCchhhhhhhhc-CcEEEEccC
Q 022746           52 FRIIVPSRQ-----IGKVIGKEGHRIQKIREET-KATIKIADA   88 (292)
Q Consensus        52 ~rilvp~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~   88 (292)
                      .++.|-+..     +|..||++|++|+.|.++. |-+|++-+.
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            567777777     9999999999999999999 888877643

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

Probab=93.78  E-value=0.16  Score=41.32  Aligned_cols=85  Identities=12%  Similarity=0.029  Sum_probs=56.8

Q ss_pred             CCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH---HHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 022746          160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV---LNALVEIGNQLRENPPRQVISISPAYNYSA  236 (292)
Q Consensus       160 k~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v---~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~  236 (292)
                      .+|..|++|..+---+|.+-+                     +++..   ..|.+.|.+++-+...-...          
T Consensus        23 ~~~dli~~lAk~lrKRIvvR~---------------------dps~l~~~e~A~~~I~~ivP~ea~i~di----------   71 (145)
T cd02410          23 EDGDLVKDLAKDLRKRIVIRP---------------------DPSVLKPPEEAIKIILEIVPEEAGITDI----------   71 (145)
T ss_pred             cccHHHHHHHHHHhceEEEcC---------------------ChhhcCCHHHHHHHHHHhCCCccCceee----------
Confidence            456788888777766666633                     22222   45888888888655211100          


Q ss_pred             CCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCc
Q 022746          237 IRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQP  286 (292)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~  286 (292)
                            +++    ..+-++.|-++.-|.+||| +|.++++|...+|-.-.
T Consensus        72 ------~Fd----~~tGEV~IeaeKPG~ViGk-~g~~~reI~~~tgW~p~  110 (145)
T cd02410          72 ------YFD----DDTGEVIIEAEKPGLVIGK-GGSTLREITRETGWAPK  110 (145)
T ss_pred             ------Eec----CCCcEEEEEEcCCeEEEec-CchhHHHHHHHhCCeeE
Confidence                  011    1244677888999999999 99999999999986543

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.

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

Probab=93.34  E-value=0.034  Score=58.30  Aligned_cols=72  Identities=21%  Similarity=0.168  Sum_probs=57.5

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC-CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI-ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      ..-++.+|.....+|||++|.+|..++.-||+.|.+.... .+..||.+++.|.++     ..+-|...|.-.+.+.+
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~-----~~r~a~~~I~~~i~Dpd 1412 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPP-----SQRVATSPIGLPIIDPD 1412 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCCh-----hhhhhhccccceeecCC
Confidence            4557889999999999999999999999999999999743 345799999999986     35556665655555443

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=93.01  E-value=1.1  Score=38.60  Aligned_cols=65  Identities=18%  Similarity=0.237  Sum_probs=56.3

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+.++....-.+...+|..++.|....||+|.+..            ....+.|+|+...+..+...|.+++...
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~------------~~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR------------SENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec------------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            4566667888889999999999999888999999863            4679999999999999999999998776

>PRK12705 hypothetical protein; Provisional

Probab=92.95  E-value=0.26  Score=48.39  Aligned_cols=66  Identities=23%  Similarity=0.285  Sum_probs=44.2

Q ss_pred             cEEEEEeccC-cceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022746          143 NTIRLLIAGS-QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (292)
Q Consensus       143 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  220 (292)
                      +...+.+|++ .-|+|||+.|.+|+.+...||+.+-|.   +.|         ..|++++- +..-+.|...+..++.+.
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp---------~~V~ls~fdp~rreia~~~l~~Li~dg  265 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---DTP---------EAVVISSFNPIRREIARLTLEKLLADG  265 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---CCc---------cchhhcccCccchHHHHHHHHHHHhcC
Confidence            3456778875 559999999999999999999999984   322         34555553 233333455555554443

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=92.19  E-value=0.15  Score=36.85  Aligned_cols=35  Identities=17%  Similarity=0.373  Sum_probs=28.4

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEE
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI   85 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i   85 (292)
                      .+.+-+..+..|.+|||+|+++..||--++.-++-
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            35566678899999999999999999887755543

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

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=91.96  E-value=0.055  Score=38.73  Aligned_cols=31  Identities=3%  Similarity=-0.172  Sum_probs=27.2

Q ss_pred             eeEEEEEeccCccceeeecCCCccHHHHHHhh
Q 022746          250 YSMFLMQNTRYFVTAIFAVLSSFNIFFLITTS  281 (292)
Q Consensus       250 ~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S  281 (292)
                      ...+.+.+..+..|.|||| .|.+++.||.-.
T Consensus        28 ~~~i~v~i~~ed~g~lIGk-~G~tl~ALq~l~   58 (73)
T PF13083_consen   28 GDTIVVNIDGEDAGRLIGK-HGKTLNALQYLV   58 (73)
T ss_dssp             TTEEEEEEESCCCHHHCTT-HHHHHHHHHHHH
T ss_pred             ceEEEEEECCCccceEECC-CCeeHHHHHHHH
Confidence            4577888999999999999 999999998653

>PRK12705 hypothetical protein; Provisional

Probab=91.30  E-value=0.28  Score=48.21  Aligned_cols=46  Identities=30%  Similarity=0.472  Sum_probs=36.3

Q ss_pred             EEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecC
Q 022746           52 FRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK  102 (292)
Q Consensus        52 ~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~  102 (292)
                      -.+-+|+ ++-|+||||.|.||+.++..||+.|-|.+..     ..|++++.
T Consensus       200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~f  246 (508)
T PRK12705        200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSF  246 (508)
T ss_pred             eeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhccc
Confidence            3455566 6799999999999999999999999999742     33556654

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=91.19  E-value=0.083  Score=38.22  Aligned_cols=35  Identities=40%  Similarity=0.608  Sum_probs=29.9

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEE
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK   84 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~   84 (292)
                      ..+.+.+..+..|.|||++|++|++|.+..+-.+.
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            45778899999999999999999999988765553

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

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

Probab=90.86  E-value=0.16  Score=43.31  Aligned_cols=56  Identities=32%  Similarity=0.440  Sum_probs=47.7

Q ss_pred             CCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           58 SRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        58 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      +..+|+|+||+|.+--.|+.-|.++|.+.+.       .|.|-|.     ++++.-|...|+.++...
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            4579999999999999999999999999864       4899998     457888888888888654

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

Probab=90.62  E-value=0.21  Score=35.52  Aligned_cols=37  Identities=19%  Similarity=0.434  Sum_probs=30.2

Q ss_pred             EEEEEeccCc-----ceeeecCCChhHHHHHHhh-CCeEEEeC
Q 022746          144 TIRLLIAGSQ-----AGCLIGMSGQNIEKLRNSS-GATIVILA  180 (292)
Q Consensus       144 ~~~i~IP~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~  180 (292)
                      ...+.|-...     +|.+||++|.+|+.|.++. |-+|++..
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            4566777777     8999999999999999999 99999874

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

Probab=89.74  E-value=0.2  Score=42.83  Aligned_cols=129  Identities=18%  Similarity=0.184  Sum_probs=85.1

Q ss_pred             hhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchh-h---cccC---CCcccEEE
Q 022746           74 KIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEAS-K---VAAG---HVAANTIR  146 (292)
Q Consensus        74 ~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~-~---~~~~---~~~~~~~~  146 (292)
                      -|-+..+.+|.+.-     ..|.|.+.-..+..+.++.+++...|...+...+....-.. +   ++..   -..-.+.+
T Consensus        98 Pive~lklqiRmNl-----K~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALlrlddlflesFEi~dVKtL~  172 (252)
T KOG3273|consen   98 PIVEHLKLQIRMNL-----KARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALLRLDDLFLESFEIKDVKTLK  172 (252)
T ss_pred             HHHHhhhheeEeec-----ccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHHhhhhhhheeeeeccccccc
Confidence            34455566666652     23566666555555577888888888888876654321100 0   0000   00000111


Q ss_pred             EEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       147 i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      =.=-+..+|+|+||+|.+--.|.+.|-++|.+.              +..+.|-|..+++.-|...|+.++-..+
T Consensus       173 GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------------d~kIHiLG~~~niriAR~avcsLIlGsp  233 (252)
T KOG3273|consen  173 GDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------------DSKIHILGAFQNIRIARDAVCSLILGSP  233 (252)
T ss_pred             chhHHHHHHHhhcCCCcceeeeeccceeEEEec--------------CceEEEeecchhhHHHHHhhHhhhccCC
Confidence            111245679999999999989999999999874              4689999999999999999999988774

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

Probab=89.65  E-value=1.1  Score=39.57  Aligned_cols=45  Identities=22%  Similarity=0.508  Sum_probs=39.7

Q ss_pred             EEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCC
Q 022746           54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN  104 (292)
Q Consensus        54 ilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~  104 (292)
                      +.|++..|.++||++|+.++.|.++|+|.|-+-.+      ..|-|.+..+
T Consensus       150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~  194 (239)
T COG1097         150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE  194 (239)
T ss_pred             EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence            67899999999999999999999999999999865      3477888765

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=89.45  E-value=0.45  Score=34.41  Aligned_cols=30  Identities=3%  Similarity=-0.140  Sum_probs=24.8

Q ss_pred             EEEEEeccCccceeeecCCCccHHHHHHhhC
Q 022746          252 MFLMQNTRYFVTAIFAVLSSFNIFFLITTSS  282 (292)
Q Consensus       252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~  282 (292)
                      .+.+.+..+..|.+||| .|++++.||--.+
T Consensus        25 ~i~i~i~~~~~g~LIGk-~G~tL~AlQ~L~~   54 (77)
T cd02414          25 TVEVNISGDDIGLLIGK-RGKTLDALQYLAN   54 (77)
T ss_pred             EEEEEEecCCCCeEECC-CCccHHHHHHHHH
Confidence            45677778889999999 9999999986543

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.

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

Probab=89.11  E-value=0.41  Score=35.14  Aligned_cols=36  Identities=19%  Similarity=0.423  Sum_probs=30.6

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEc
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA   86 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~   86 (292)
                      .+++.|....-|.|||++|++|++|+++..-...+.
T Consensus        31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            378888999999999999999999999876655554

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.

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

Probab=88.91  E-value=1  Score=39.66  Aligned_cols=62  Identities=21%  Similarity=0.282  Sum_probs=46.6

Q ss_pred             EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH-HHHHHHHHHHHHhc
Q 022746          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPA-VLNALVEIGNQLRE  219 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~-v~~A~~~I~~~l~~  219 (292)
                      .-+.|+...+.++||++|+.++.|.+.|+|+|.+-             .+..|-|.|..+. ...|...|..+=.+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG-------------~NG~IWV~~~~~~~e~~~~~aI~~ie~e  210 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG-------------QNGRIWVDGENESLEELAIEAIRKIERE  210 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe-------------cCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence            55788889999999999999999999999999984             3456777777663 44455555444333

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

Probab=88.84  E-value=0.62  Score=31.91  Aligned_cols=32  Identities=13%  Similarity=-0.066  Sum_probs=25.3

Q ss_pred             eEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746          251 SMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL  283 (292)
Q Consensus       251 ~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~  283 (292)
                      ....+.+.....|.+||| +|++|+.|+...+.
T Consensus        25 ~~~~i~~~~~~~g~lIGk-~G~~l~~l~~l~~~   56 (68)
T cd02409          25 IEIIIVVARGQPGLVIGK-KGQNIRALQKLLQK   56 (68)
T ss_pred             EEEEEEECCCCCceEECC-CCccHHHHHHHHHH
Confidence            445555665568999999 99999999988763

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.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=88.53  E-value=0.2  Score=36.13  Aligned_cols=31  Identities=6%  Similarity=-0.106  Sum_probs=27.0

Q ss_pred             EEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746          252 MFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL  283 (292)
Q Consensus       252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~  283 (292)
                      ...+.+....-|.|||+ +|++|++|.+...-
T Consensus        26 ~~~i~i~~~~~~ivIGk-~G~~ik~i~~~~~k   56 (78)
T PF07650_consen   26 QIIIVIKASQPGIVIGK-KGSNIKKIREELRK   56 (78)
T ss_dssp             EEEEEEEESSHHHHHTG-GGHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCccHhHHh-hhHHHHHHHHHHHH
Confidence            56777889999999999 99999999987653

; 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=88.15  E-value=0.56  Score=39.22  Aligned_cols=38  Identities=18%  Similarity=0.308  Sum_probs=31.9

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~   88 (292)
                      --+-|+|-... |.-|||+|++|++|++..|-+|.+-+.
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            34567787777 999999999999999999988877653

>PRK13764 ATPase; Provisional

Probab=88.11  E-value=0.79  Score=46.10  Aligned_cols=44  Identities=20%  Similarity=0.348  Sum_probs=39.3

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP  185 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p  185 (292)
                      .....+.||...++.+|||+|.+|++|.++.|.+|.|.+.+..+
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            45788999999999999999999999999999999998766543

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

Probab=87.72  E-value=0.31  Score=46.96  Aligned_cols=36  Identities=36%  Similarity=0.553  Sum_probs=33.3

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEcc
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~   87 (292)
                      ..+.||...++.+|||+|.+|++|++..|.+|.+..
T Consensus       488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            567789999999999999999999999999999974

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

Probab=87.56  E-value=0.42  Score=46.08  Aligned_cols=41  Identities=15%  Similarity=0.227  Sum_probs=37.2

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  182 (292)
                      .....+.||...++.+|||+|.+|++|.++.|.+|.+.+.+
T Consensus       485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            34688999999999999999999999999999999998654

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

Probab=87.34  E-value=2.4  Score=34.51  Aligned_cols=93  Identities=14%  Similarity=0.300  Sum_probs=60.8

Q ss_pred             cCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEE
Q 022746           66 GKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTI  145 (292)
Q Consensus        66 Gk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~  145 (292)
                      =.+|.-|+.|-++..-+|.|-.+              +..  +..-.+|...|.+++-++..-..-.+       ...+-
T Consensus        22 ~~~~dli~~lAk~lrKRIvvR~d--------------ps~--l~~~e~A~~~I~~ivP~ea~i~di~F-------d~~tG   78 (145)
T cd02410          22 AEDGDLVKDLAKDLRKRIVIRPD--------------PSV--LKPPEEAIKIILEIVPEEAGITDIYF-------DDDTG   78 (145)
T ss_pred             hcccHHHHHHHHHHhceEEEcCC--------------hhh--cCCHHHHHHHHHHhCCCccCceeeEe-------cCCCc
Confidence            35567788888877766666432              110  11124677788887754422111001       01245


Q ss_pred             EEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746          146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (292)
Q Consensus       146 ~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  181 (292)
                      ++.|-...-|.+||++|.++++|..+||-.-.+...
T Consensus        79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            777888888999999999999999999998888653

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.

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

Probab=87.00  E-value=1.3  Score=39.85  Aligned_cols=52  Identities=15%  Similarity=0.226  Sum_probs=46.2

Q ss_pred             eeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       155 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      -++||.+|+++|.|+--|.|.|-|.              ...|.+.|....+..+...+.+++...
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVq--------------G~TVsaiGpfkGlkevr~IV~DcM~Ni  212 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQ--------------GNTVSAIGPFKGLKEVRKIVEDCMKNI  212 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEee--------------CcEEEeecCcchHHHHHHHHHHHHhcc
Confidence            4799999999999999999999983              358999999999999999998888774

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

Probab=86.41  E-value=1.6  Score=43.11  Aligned_cols=66  Identities=24%  Similarity=0.263  Sum_probs=49.6

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ..+...+.++.+....+||.+|-..|+|+.+||+.-.+.+       ..+.|-....    .+..+|...|..++..
T Consensus       595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe-------~t~~i~A~~~----~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE-------GTFSIFAPTQ----AAMEEAKEFIDGIIKD  660 (760)
T ss_pred             CceeeEEeecchhhheeecCccceeeeEeeeccceeeecC-------ceEEEEecCH----HHHHHHHHHHHHHhcC
Confidence            4677889999999999999999999999999996555544       4577777542    3455666666655543

>PRK13764 ATPase; Provisional

Probab=86.41  E-value=0.47  Score=47.66  Aligned_cols=38  Identities=37%  Similarity=0.537  Sum_probs=34.5

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEcc
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~   87 (292)
                      -...+.||...++.+|||+|.+|++|++..|.+|.|..
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~  518 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP  518 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence            34567889999999999999999999999999999974

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

Probab=85.16  E-value=1  Score=32.99  Aligned_cols=28  Identities=7%  Similarity=-0.155  Sum_probs=24.8

Q ss_pred             EEEEEeccCccceeeecCCCccHHHHHHh
Q 022746          252 MFLMQNTRYFVTAIFAVLSSFNIFFLITT  280 (292)
Q Consensus       252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~  280 (292)
                      .+++.|-...-|.|||+ +|++|++|++.
T Consensus        31 ~i~I~I~tarPg~vIG~-~G~~i~~L~~~   58 (81)
T cd02413          31 RTEIIIRATRTQNVLGE-KGRRIRELTSL   58 (81)
T ss_pred             eEEEEEEeCCCceEECC-CchhHHHHHHH
Confidence            46788888899999999 99999999875

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.

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

Probab=84.90  E-value=0.76  Score=35.63  Aligned_cols=30  Identities=30%  Similarity=0.592  Sum_probs=26.1

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKA   81 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga   81 (292)
                      +++.|-...-|.|||++|++|++|++....
T Consensus        63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~   92 (109)
T cd02412          63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK   92 (109)
T ss_pred             EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence            678888888999999999999999987543

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

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

Probab=84.64  E-value=1.7  Score=39.17  Aligned_cols=50  Identities=10%  Similarity=0.155  Sum_probs=35.6

Q ss_pred             ceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           62 GKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        62 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      -++||.+|++++.|+--|.|.|-|+..       .|.+-|.-     ..+.++...+.+.|.
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG~-------TVsaiGpf-----kGlkevr~IV~DcM~  210 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQGN-------TVSAIGPF-----KGLKEVRKIVEDCMK  210 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeCc-------EEEeecCc-----chHHHHHHHHHHHHh
Confidence            469999999999999999999999864       35555653     244444444444443

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=83.96  E-value=2.6  Score=41.18  Aligned_cols=143  Identities=12%  Similarity=0.093  Sum_probs=92.2

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~  130 (292)
                      .+.|.||...+-.|||.||..|.+.....++.|++....    ++     |.       +++          .  +    
T Consensus       450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~----~~-----~q-------s~~----------~--d----  497 (657)
T COG5166         450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFY----KF-----GQ-------SQW----------H--D----  497 (657)
T ss_pred             heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhh----hc-----ch-------hhh----------h--c----
Confidence            467999999999999999999999999999888877431    00     00       000          0  0    


Q ss_pred             chhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhh----CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 022746          131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS----GATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (292)
Q Consensus       131 ~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~t----ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v  206 (292)
                                   .+-+..|.+-.+.|+|++......+++.+    ...|++.+           ..-+++++.|-...+
T Consensus       498 -------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~-----------~~~sI~~v~~~~~~I  553 (657)
T COG5166         498 -------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP-----------QSTSIFTVDIYSDEI  553 (657)
T ss_pred             -------------ceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC-----------CceEEEEEcccccHH
Confidence                         24566777777889999988888888655    45666643           234588888876655


Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeee---cCCCccHHHHHHh
Q 022746          207 LNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFA---VLSSFNIFFLITT  280 (292)
Q Consensus       207 ~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIG---k~gG~~Ik~I~~~  280 (292)
                      .+-.. -...+...+                             ....+.+|.+.++.-+|   - .|++|-.+...
T Consensus       554 ~rv~k-ne~v~~~~p-----------------------------~~~~~y~~se~h~~g~gena~-R~~ni~~~t~~  599 (657)
T COG5166         554 ERVIK-NETVLLEFP-----------------------------AEMHFYVPSEIHKKGIGENAF-RGENIQRVTKL  599 (657)
T ss_pred             HHHhh-ccceEEecc-----------------------------cccccccchhhhhccCCcccc-cccchhhhhhh
Confidence            43332 111122211                             23345577788888888   4 56776665443

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

Probab=83.72  E-value=1.1  Score=33.10  Aligned_cols=28  Identities=29%  Similarity=0.484  Sum_probs=23.7

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhc
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREET   79 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~t   79 (292)
                      +++.+....-|.+||++|++|++|++..
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            5666666889999999999999998874

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=83.58  E-value=2.5  Score=41.32  Aligned_cols=91  Identities=11%  Similarity=-0.020  Sum_probs=62.8

Q ss_pred             eeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 022746          156 CLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYS  235 (292)
Q Consensus       156 ~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~  235 (292)
                      .++-+.|..|++|..+.--+|.+-++...               .   ..-+.|...|.+++-++..-....      | 
T Consensus        42 ~~~~~~~dlik~lAk~lrKRI~iR~dPsv---------------l---~~~e~A~~~I~eivP~ea~i~~i~------F-   96 (637)
T COG1782          42 ELFAKDGDLIKDLAKDLRKRIIIRPDPSV---------------L---KPPEEARKIILEIVPEEAGITDIY------F-   96 (637)
T ss_pred             HHhccchhHHHHHHHHHhhceEeccCchh---------------c---CCHHHHHHHHHHhCccccCceeEE------e-
Confidence            45567889999999999888887542110               0   112468888888886552111000      0 


Q ss_pred             CCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCC
Q 022746          236 AIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQ  285 (292)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~  285 (292)
                                   +..+-++.|-++.-|.+||| +|++.++|.+.+|-.-
T Consensus        97 -------------d~~tGEViIea~KPGlvigk-~g~~~reI~~~tgW~p  132 (637)
T COG1782          97 -------------DDDTGEVIIEAKKPGLVIGK-GGSTLREITAETGWAP  132 (637)
T ss_pred             -------------cCCCceEEEEecCCceEEec-CchHHHHHHHHhCCcc
Confidence                         11345778889999999999 9999999999988653

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

Probab=82.97  E-value=0.39  Score=50.84  Aligned_cols=74  Identities=23%  Similarity=0.195  Sum_probs=60.2

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+-++.+|-....++||++|.+|..++.-||+.|.+..-  -+.    ...+|.+.+.|.++.++.|...|.-.+.|-
T Consensus      1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~----Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD----NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred             cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc----cchhhhcccCCCChhhhhhhccccceeecC
Confidence            34456788999899999999999999999999999998541  111    146899999999999999988887666554

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

Probab=80.74  E-value=1.4  Score=38.74  Aligned_cols=31  Identities=35%  Similarity=0.529  Sum_probs=26.8

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhc
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t   79 (292)
                      ...+++.|....-|.|||++|++|++|++..
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l   80 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL   80 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence            3457888999999999999999999888764

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

Probab=80.72  E-value=3.2  Score=42.20  Aligned_cols=92  Identities=10%  Similarity=-0.030  Sum_probs=60.9

Q ss_pred             eecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 022746          157 LIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSA  236 (292)
Q Consensus       157 IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~  236 (292)
                      .+-..|..|++|..+---+|.|-++..               +.-++   .+|.+.|.+++-++..-....         
T Consensus        37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~---------------~~~~~---~~~~~~i~~~~~~~~~~~~~~---------   89 (630)
T TIGR03675        37 LFAKDDDLVKELAKKLRKRIVIRPDPS---------------VLLPP---EEAIEKIKEIVPEEAGITDIY---------   89 (630)
T ss_pred             HhccchHHHHHHHHHhhceEEEecChh---------------hcCCH---HHHHHHHHHhCCCcCCceeEE---------
Confidence            344667889999888877777743211               11111   358888888886652111000         


Q ss_pred             CCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          237 IRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                             .    +..+-+|.|-++.-|.|||| +|.++++|.+.+|-.-.+
T Consensus        90 -------f----~~~~~~v~i~~~~p~~~~~~-~~~~~~~i~~~~~w~~~~  128 (630)
T TIGR03675        90 -------F----DDVTGEVIIEAEKPGLVIGK-GGSTLREITAETGWTPKV  128 (630)
T ss_pred             -------e----cCCCceEEEEEcCCeEEEec-CcchHHHHHHHhCCeeeE
Confidence                   0    12345778889999999999 999999999999865443

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.

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=80.45  E-value=2.4  Score=35.49  Aligned_cols=36  Identities=19%  Similarity=0.340  Sum_probs=31.5

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  180 (292)
                      .+-++|-... |.-|||+|.+++.+++..|-+|.+.-
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            5667776667 99999999999999999999999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	292
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		3e-08
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		8e-05
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		1e-04
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		3e-04
2axy_A	73	Crystal Structure Of Kh1 Domain Of Human Poly(C)-Bi		5e-04

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-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 = 44.3 bits (103), Expect = 8e-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 = 43.5 bits (101), Expect = 1e-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|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1 Length = 74

Iteration: 1
 Score = 42.4 bits (98), 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

>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 = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL  G + G +IG  G++++K R  SGA I I         +  +  +R++ ++G  
Sbjct: 6   TIRLLXHGKEVGSIIGKKGESVKKXREESGARINI---------SEGNCPERIITLAGPT 56
Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 57  NAIFKAFAXIIDKLEED 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	292
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-36
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-09
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-34
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-09
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	7e-31
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	9e-09
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	8e-31
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-12
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-27
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	8e-11
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-10
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-14
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	6e-12
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-09
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-11
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-09
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	2e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	2e-08
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	5e-10
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	9e-09
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	3e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	5e-09
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	7e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-05
1we8_A	104	Tudor and KH domain containing protein; structural	9e-09
1we8_A	104	Tudor and KH domain containing protein; structural	4e-06
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-08
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-07
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	4e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	5e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	7e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	7e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	3e-05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	5e-05
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	6e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	9e-05
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	1e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	2e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	4e-04
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	3e-04
2cxc_A	144	NUSA; transcription termination, RNA binding prote	3e-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 =  126 bits (317), Expect = 6e-36
 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 = 55.2 bits (133), Expect = 1e-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 = 54.5 bits (131), Expect = 2e-09
 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 =  121 bits (306), Expect = 2e-34
 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 = 55.9 bits (135), Expect = 7e-10
 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 = 55.5 bits (134), Expect = 1e-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

>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 =  112 bits (282), Expect = 7e-31
 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 = 52.8 bits (127), Expect = 9e-09
 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

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

 Score =  112 bits (282), Expect = 8e-31
 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 = 62.2 bits (151), Expect = 5e-12
 Identities = 22/107 (20%), Positives = 38/107 (35%), Gaps = 7/107 (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 VPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSG 249
                +A   I + LR           P             + P  G
Sbjct: 56  PDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGG 102

>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 = 54.1 bits (130), Expect = 4e-09
 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

>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 =  104 bits (260), Expect = 1e-27
 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 = 58.6 bits (142), Expect = 8e-11
 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 = 57.5 bits (139), Expect = 2e-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 = 66.1 bits (162), Expect = 2e-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 = 59.2 bits (144), Expect = 6e-12
 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 = 57.7 bits (140), Expect = 3e-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 = 53.5 bits (129), Expect = 1e-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 = 57.3 bits (139), Expect = 3e-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 = 52.7 bits (127), Expect = 1e-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 = 55.4 bits (134), Expect = 2e-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 = 49.2 bits (118), Expect = 2e-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 = 54.2 bits (131), Expect = 5e-10
 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 = 50.7 bits (122), Expect = 9e-09
 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

>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 = 54.6 bits (131), Expect = 2e-09
 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

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

 Score = 52.8 bits (127), Expect = 2e-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 = 52.4 bits (126), Expect = 3e-09
 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

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

 Score = 52.5 bits (126), Expect = 3e-09
 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 = 47.5 bits (113), Expect = 2e-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

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

 Score = 51.1 bits (123), Expect = 5e-09
 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 = 48.8 bits (117), Expect = 4e-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

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

 Score = 51.3 bits (123), Expect = 7e-09
 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 = 42.4 bits (100), Expect = 1e-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 = 51.4 bits (123), Expect = 9e-09
 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 = 44.0 bits (104), Expect = 4e-06
 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

>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 = 50.8 bits (122), Expect = 1e-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 = 47.7 bits (114), Expect = 1e-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

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

 Score = 49.7 bits (119), Expect = 2e-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 = 47.7 bits (114), Expect = 1e-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 = 47.9 bits (114), Expect = 1e-07
 Identities = 16/100 (16%), Positives = 35/100 (35%), Gaps = 4/100 (4%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             +   I   + G +IG  G+N++ +   +GA + I +    P   +   + ++  I G 
Sbjct: 7   GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI-SRQLPP---NGDPNFKLFIIRGS 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 = 46.8 bits (111), Expect = 4e-07
 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 = 45.9 bits (109), Expect = 5e-07
 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 = 39.3 bits (92), Expect = 1e-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 = 44.0 bits (104), Expect = 3e-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

>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 = 42.9 bits (101), Expect = 7e-06
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHE-ERVIIIS-SKDNDNVVSDA 111
           + V  +   K+IG++G  I +IR E    I+  D    ++ +  I I+  + N       
Sbjct: 21  VTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKN------T 74

Query: 112 ENALQQIAALILKDDDSNSEAS 133
           E A   I  ++ + +  +  +S
Sbjct: 75  EAARDAILRIVGELEQMSGPSS 96

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

 Score = 42.0 bits (99), Expect = 7e-06
 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

>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 = 41.9 bits (98), Expect = 1e-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 = 43.1 bits (101), Expect = 3e-05
 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

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 43.7 bits (104), Expect = 5e-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 = 43.3 bits (103), Expect = 6e-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

>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 = 42.0 bits (98), Expect = 9e-05
 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

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 42.1 bits (100), Expect = 1e-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 = 41.8 bits (99), 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

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

 Score = 39.0 bits (91), Expect = 2e-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

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

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 4/72 (5%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + VP      VIG++G  I+K+ +E +  I +        + + I     N   +  A+ 
Sbjct: 21  VEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-ELQSDIIAITGLAAN---LDRAKA 76

Query: 114 ALQQIAALILKD 125
            L +    +  +
Sbjct: 77  GLLERVKELQAE 88

>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 = 39.5 bits (91), Expect = 3e-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

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 17/141 (12%), Positives = 49/141 (34%), Gaps = 37/141 (26%)

Query: 40  DPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII 99
           +   R          +V   + G+ IG+ G  I+ +RE                + + ++
Sbjct: 33  EENNRLI-------FLVSEGEAGRAIGRGGRLIKLLREALG-------------KNIEVV 72

Query: 100 SSKDNDNVVSDAENALQ--QIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCL 157
             + + ++    +N     +I ++ +++ +   +               + ++    G  
Sbjct: 73  --EYSSDLERIVKNLFPGVKIESINVRERNGVKQV-------------VIKVSEDDKGAA 117

Query: 158 IGMSGQNIEKLRNSSGATIVI 178
           IG  G+N+++ R        +
Sbjct: 118 IGKGGKNVKRARLVLSKLFGV 138

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	292
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.95
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.95
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.94
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.94
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.93
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.85
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.84
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.84
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.84
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.81
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.8
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.79
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.72
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.57
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.57
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.55
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.54
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.53
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.52
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.52
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.5
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.49
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.49
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.48
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.48
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.47
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.47
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.47
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.46
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.46
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.45
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.44
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.44
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.42
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.42
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.42
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.42
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.42
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.41
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.41
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.4
1we8_A	104	Tudor and KH domain containing protein; structural	99.39
1we8_A	104	Tudor and KH domain containing protein; structural	99.39
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.37
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.36
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.35
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.35
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.34
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.33
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.32
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.3
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.29
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.28
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.24
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.18
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.12
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.12
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.11
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.07
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.81
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.78
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.73
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.61
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.59
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.48
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.46
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.13
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.11
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.88
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.68
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.67
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.62
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.43
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.27
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.97
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.26
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.14
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.88
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	95.43
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	94.88
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.63
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.47
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.96
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.28
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.91
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	84.95

>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=99.95  E-value=2.5e-28  Score=206.02  Aligned_cols=165  Identities=25%  Similarity=0.383  Sum_probs=134.0

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC---CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      ..+++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.   .+++.+|+|+|+|.+     .++.+|..+|.+++.
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 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI-----EALNAVHGFIAEKIR   77 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECH-----HHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCH-----HHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999999999853   367889999999984     478899999999987


Q ss_pred             cCCCCCcchh--h-----cccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcE
Q 022746          124 KDDDSNSEAS--K-----VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV  196 (292)
Q Consensus       124 ~~~~~~~~~~--~-----~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~  196 (292)
                      +.........  .     .........+.++.||.+++|+|||++|++|++|+++|||+|.+.+.+..+.     +.++.
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            7543211000  0     0001123468999999999999999999999999999999999975443332     57899


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          197 VQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       197 v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      |+|+|++++|.+|+.+|.++|.++|
T Consensus       153 v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          153 VTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             EEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             EEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999874

>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=99.95  E-value=1.2e-27  Score=198.98  Aligned_cols=157  Identities=23%  Similarity=0.357  Sum_probs=132.3

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~  127 (292)
                      +-+++|+||.+.+|.||||+|++|++|+++|||+|+|++. .+++.+|+|+|+|++     .++.+|..+|.+++.+...
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~-----e~v~~A~~~I~~~~~e~~~   76 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPP-----EAQFKAQGRIYGKLKEENF   76 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECH-----HHHHHHHHHHHHHHHHTTS
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHhcccc
Confidence            4579999999999999999999999999999999999975 578899999999975     4788999999999877632


Q ss_pred             CCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHH
Q 022746          128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVL  207 (292)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~  207 (292)
                      ...       ......+.++.||..++|+|||++|++|++|+++|||+|.+.. +..|..    ..++.|+|+|++++|.
T Consensus        77 ~~~-------~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~-~~~~~~----~~~~~v~I~G~~~~v~  144 (163)
T 3krm_A           77 FGP-------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR-DQTPDE----NDQVIVKIIGHFYASQ  144 (163)
T ss_dssp             SCS-------SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCT-TCCCCT----TSEEEEEEEECHHHHH
T ss_pred             ccc-------ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECC-CCCCCC----CCceEEEEEeCHHHHH
Confidence            211       1123457799999999999999999999999999999999853 444541    3455899999999999


Q ss_pred             HHHHHHHHHHhcCCC
Q 022746          208 NALVEIGNQLRENPP  222 (292)
Q Consensus       208 ~A~~~I~~~l~~~~~  222 (292)
                      +|+.+|.+++.+...
T Consensus       145 ~A~~~I~~~i~~~~~  159 (163)
T 3krm_A          145 MAQRKIRDILAQVKQ  159 (163)
T ss_dssp             HHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999988643

>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=99.94  E-value=2.1e-27  Score=196.98  Aligned_cols=158  Identities=27%  Similarity=0.488  Sum_probs=131.4

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      +.+++++|+||.+.+|.||||+|++|++|+++|||+|+|++.  ++++|+|+|+|+.     .++.+|..+|.+.+.+..
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            457899999999999999999999999999999999999975  5678999999984     478899999998886632


Q ss_pred             CCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 022746          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (292)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v  206 (292)
                      ......  .........+.++.||.+++|+|||++|++|++|+++|||+|.+.+ +..|.     +.++.|+|+|++++|
T Consensus        75 ~~~~~~--~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~-~~~~~-----~~~~~v~I~G~~~~v  146 (160)
T 2jzx_A           75 SSSMTN--STAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG-DMLPN-----STERAITIAGIPQSI  146 (160)
T ss_dssp             TSCCCS--SSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC-CCSTT-----CCEEEEEEEECHHHH
T ss_pred             cccCCC--CccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC-CCCCC-----CCceEEEEEcCHHHH
Confidence            111000  0001123568999999999999999999999999999999999854 34454     678999999999999


Q ss_pred             HHHHHHHHHHHhc
Q 022746          207 LNALVEIGNQLRE  219 (292)
Q Consensus       207 ~~A~~~I~~~l~~  219 (292)
                      .+|+.+|.+++.+
T Consensus       147 ~~A~~~I~~~i~e  159 (160)
T 2jzx_A          147 IECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999999876

>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=99.94  E-value=1.8e-26  Score=191.88  Aligned_cols=158  Identities=19%  Similarity=0.313  Sum_probs=128.6

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC--CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~--~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~  127 (292)
                      ++++|+||.+.+|.||||+|++|++|+++|||+|++.+..  ++..+|+|+|+|.+     .++.+|+.+|.+++.+...
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            5789999999999999999999999999999999997542  45678999999974     4789999999999876542


Q ss_pred             CCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHH
Q 022746          128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVL  207 (292)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~  207 (292)
                      ...... ...+.....+.++.||..++|+|||++|++|++|+++|||+|.+.+.+  +.     +.++.|+|+|+++++.
T Consensus        77 ~~~~~~-~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~--~~-----~~~~~v~I~G~~~~v~  148 (164)
T 2jvz_A           77 GGFGDR-NEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--GT-----GPEKIAHIMGPPDRCE  148 (164)
T ss_dssp             CCCSSC-SSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC--TT-----SSEEEEEEESCHHHHH
T ss_pred             CCCCCc-cccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC--CC-----CCcEEEEEEcCHHHHH
Confidence            211000 001111234688999999999999999999999999999999996532  21     4689999999999999


Q ss_pred             HHHHHHHHHHhcC
Q 022746          208 NALVEIGNQLREN  220 (292)
Q Consensus       208 ~A~~~I~~~l~~~  220 (292)
                      .|+.+|.+++.+.
T Consensus       149 ~A~~~I~~~i~~~  161 (164)
T 2jvz_A          149 HAARIINDLLQSL  161 (164)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhh
Confidence            9999999998763

>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=99.93  E-value=3.7e-26  Score=192.07  Aligned_cols=160  Identities=21%  Similarity=0.331  Sum_probs=126.5

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~  128 (292)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.+..+++.+|+|+|+|++     .++.+|+.+|.+++.+....
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~~~~~~~~~   76 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPP-----DRAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECH-----HHHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCH-----HHHHHHHHHHHHHHHhcccC
Confidence            4679999999999999999999999999999999999876567889999999984     47889999999888765321


Q ss_pred             Ccchh------------hcc-cCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCc
Q 022746          129 NSEAS------------KVA-AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR  195 (292)
Q Consensus       129 ~~~~~------------~~~-~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r  195 (292)
                      .....            ... .......+.++.||.+++|+|||++|++|++|+++|||+|.+.+.. .+ +.  .+.++
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 0001245889999999999999999999999999999999997532 12 11  25789


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHH
Q 022746          196 VVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       196 ~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      .|+|+|+++++.+|+.+|.++|
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            9999999999999999998874

>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=99.85  E-value=1.4e-21  Score=162.24  Aligned_cols=120  Identities=20%  Similarity=0.222  Sum_probs=102.8

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPP  222 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  222 (292)
                      .+++|+||.+++|.|||++|++|++|+++|||+|.+.+. ..|.     +.+|.|+|+|+++++.+|+.+|.+++.+...
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~-~~~~-----~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~   76 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP-ETPD-----SKVRMVIITGPPEAQFKAQGRIYGKLKEENF   76 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC-SSTT-----CSEEEEEEEECHHHHHHHHHHHHHHHHHTTS
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC-CCCC-----CCceEEEEEcCHHHHHHHHHHHHHHHhcccc
Confidence            478999999999999999999999999999999999643 3343     6899999999999999999999999988621


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcccc
Q 022746          223 RQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQ  289 (292)
Q Consensus       223 ~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~  289 (292)
                      ..     |               ......+.+|.||..++|+|||| ||++|++|++.|||.+.+.+
T Consensus        77 ~~-----~---------------~~~~~~~~~i~vp~~~~g~iIGk-gG~~I~~i~~~tga~I~i~~  122 (163)
T 3krm_A           77 FG-----P---------------KEEVKLETHIRVPASAAGRVIGK-GGKTVNELQNLTAAEVVVPR  122 (163)
T ss_dssp             SC-----S---------------SCCCCEEEEEEEETTTHHHHHCG-GGHHHHHHHHHHCCEEECCT
T ss_pred             cc-----c---------------ccCCceEEEEEcChhheeeEEcC-CChHHHHHHHHhCCeEEECC
Confidence            10     0               01234677999999999999999 99999999999999998765

>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=99.84  E-value=1.2e-21  Score=164.55  Aligned_cols=139  Identities=20%  Similarity=0.200  Sum_probs=100.9

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      ..+.+|+||.+++|.|||++|++|++|+++|||+|+|.+.+  +.     ..+|.|+|+|++++|.+|+.+|.+++.+..
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            45789999999999999999999999999999999997532  22     568999999999999999999999998763


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC-CCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcccc
Q 022746          222 PRQVISISPAYNYSAIRPAQPFV-EPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQ  289 (292)
Q Consensus       222 ~~~~~~~~p~~n~~~~~~~~~~~-~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~  289 (292)
                      ........|...+.+ +....|. .+.....+++|.||.+++|+|||| +|.+|++|++.|||.+.+.+
T Consensus        75 ~~~~~~~~p~~~~~~-~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk-gG~~Ik~I~~~tga~I~i~~  141 (174)
T 1j4w_A           75 AGNPGGPGPGGRGRG-RGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK-GGETIKSISQQSGARIELQR  141 (174)
T ss_dssp             ------------------------------CEEEEEEETTTHHHHHCG-GGHHHHHHHHHHCCEEEEEC
T ss_pred             cCCCCCCCCCCCCCC-CCCCccccCCCCCcEEEEEEEChHHcCeeECC-CchHHHHHHHHHCCEEEECC
Confidence            211100001000000 0001111 122235788999999999999999 99999999999999998865

>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=99.84  E-value=3.3e-21  Score=159.97  Aligned_cols=127  Identities=18%  Similarity=0.214  Sum_probs=102.4

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPP  222 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  222 (292)
                      ++.+|+||.+++|+|||++|++|++|+++|||+|.+.+....+.     ..+|.|+|+|++++|.+|+.+|.+++.+...
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            47899999999999999999999999999999999865332222     5689999999999999999999999988642


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcccc
Q 022746          223 RQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQ  289 (292)
Q Consensus       223 ~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~  289 (292)
                      .+.   .+.         ..|...  ...+++|.||..++|+|||| +|.+|++|++.|||.+.+.+
T Consensus        77 ~~~---~~~---------~~~~~~--~~~~~~i~vp~~~~g~iIGk-~G~~I~~i~~~tg~~I~i~~  128 (164)
T 2jvz_A           77 GGF---GDR---------NEYGSR--IGGGIDVPVPRHSVGVVIGR-SGEMIKKIQNDAGVRIQFKQ  128 (164)
T ss_dssp             CCC---SSC---------SSCTTS--CSSSBCCEEETTTHHHHHCS-SSHHHHHHHHHTCCEEEECC
T ss_pred             CCC---CCc---------cccCCC--CCceEEEEEChhhccccCCC-CcHhHHHHHHHHCCeEEEeC
Confidence            211   111         011110  12457889999999999999 99999999999999998865

>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=99.84  E-value=1.9e-21  Score=163.76  Aligned_cols=138  Identities=21%  Similarity=0.240  Sum_probs=106.6

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCC-CCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN-QLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      ...+++|+||.+++|.||||+|++|++|+++|||+|++.+.. ..|.     +.+|.|+|+|+++++.+|+.+|.+++.+
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            467899999999999999999999999999999999996542 2343     6789999999999999999999999988


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746          220 NPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL  290 (292)
Q Consensus       220 ~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~  290 (292)
                      .+...... .+ .++   .++ ..........+.+|.||.+++|+|||| +|++|++|++.|||.+.+.+.
T Consensus        79 ~~~~~~~~-~~-~~~---~~~-~~~~~~~~~~~~~i~Vp~~~vg~iIGk-gG~~Ik~i~~~tga~I~i~~~  142 (178)
T 2anr_A           79 MPQNVAKT-EP-VSI---LQP-QTTVNPDRANQVKIIVPNSTAGLIIGK-GGATVKAIMEQSGAWVQLSQK  142 (178)
T ss_dssp             CCCC-----------------------CGGGGEEEEEEEHHHHHHHHCG-GGHHHHHHHHHSSCEEEECCC
T ss_pred             cCCccccC-Cc-ccc---cCC-ccCCCCCCceEEEEEEchhheeeeECC-CcHHHHHHHHHHCCEEEEeCC
Confidence            75432110 00 000   000 001112335789999999999999999 999999999999999988764

>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=99.81  E-value=1.2e-20  Score=156.13  Aligned_cols=123  Identities=21%  Similarity=0.322  Sum_probs=102.1

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      +.+.+|+||.+++|.|||++|++|++|+++|||+|++... .        ..+|.|+|+|+++++.+|+.+|.+++.+..
T Consensus         4 ~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-~--------~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-N--------CPERIITLAGPTNAIFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-T--------TTEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-C--------CCceEEEEEeCHHHHHHHHHHHHHHHHhhc
Confidence            5689999999999999999999999999999999999753 1        468999999999999999999999987752


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcccc
Q 022746          222 PRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQ  289 (292)
Q Consensus       222 ~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~  289 (292)
                      ....    +  +         .........+.+|.||.+++|+|||| ||.+|++|++.|||.+.+.+
T Consensus        75 ~~~~----~--~---------~~~~~~~~~~~~i~vp~~~~g~iIGk-gG~~Ik~i~~~tga~I~i~~  126 (160)
T 2jzx_A           75 SSSM----T--N---------STAASRPPVTLRLVVPASQCGSLIGK-GGCKIKEIRESTGAQVQVAG  126 (160)
T ss_dssp             TSCC----C--S---------SSCCCCCSEEEEEEEEHHHHHHHHCG-GGHHHHHHHHHHSSEECCCC
T ss_pred             cccC----C--C---------CccCCCCCEEEEEEEChhheeeEECC-CCHHHHHHHHHhCCeEEECC
Confidence            2110    0  0         00011224789999999999999999 99999999999999988764

>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=99.80  E-value=2e-19  Score=146.35  Aligned_cols=137  Identities=20%  Similarity=0.246  Sum_probs=101.1

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEec-CCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISS-KDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G-~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      ..++.+|+||.+.+|++||++|++|++|++++|+.|.....   .++. +.+.+ +++     .+.+|.    .++.- .
T Consensus         2 ~~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~---~~~~-~i~~~~~p~-----~v~~~~----~~l~~-~   67 (144)
T 2qnd_A            2 SRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE---DTCT-FHIYGEDQD-----AVKKAR----SFLEF-A   67 (144)
T ss_dssp             --CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET---TTTE-EEEEESSHH-----HHHHHH----HHHCE-E
T ss_pred             CceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC---Cchh-eeeccCCHH-----HHHHHH----Hhhhc-c
Confidence            35789999999999999999999999999999944332222   2344 44544 332     343332    22211 0


Q ss_pred             CCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCC-eEEEeCCCCCCcccCCCCCCc--EEEEEcCH
Q 022746          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA-TIVILAPNQLPLCASAHESDR--VVQISGDV  203 (292)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga-~I~i~~~~~~p~~~~~~~~~r--~v~I~G~~  203 (292)
                                       ..++.||.+++|++|||+|++|+.+++.||+ +|+|.+.++...    ..+++  .|+|+|++
T Consensus        68 -----------------e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~----~~~~~~~~vtI~G~~  126 (144)
T 2qnd_A           68 -----------------EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV----PQEEGMVPFVFVGTK  126 (144)
T ss_dssp             -----------------EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC----CCCTTEEEEEEEEEH
T ss_pred             -----------------eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc----cccCCeeEEEEEeCH
Confidence                             3789999999999999999999999999997 999986433110    02333  58999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q 022746          204 PAVLNALVEIGNQLRE  219 (292)
Q Consensus       204 ~~v~~A~~~I~~~l~~  219 (292)
                      ++|..|..+|..+|.+
T Consensus       127 ~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          127 DSIANATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999875

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

Probab=99.79  E-value=1.2e-19  Score=167.45  Aligned_cols=189  Identities=9%  Similarity=0.047  Sum_probs=132.3

Q ss_pred             CCCCeEEEEEeeCCccceeecCCC--chhhhhhhhcCcEEEEccCC-----CCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           46 KAQDVLFRIIVPSRQIGKVIGKEG--HRIQKIREETKATIKIADAI-----ARHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        46 ~~~~~~~rilvp~~~vg~IIGk~G--~~Ik~I~~~tga~I~i~~~~-----~~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      +.+.+++++.||..++++||||+|  ++|++|+++|||+|+|++..     +......|+|+|.+     ++|++|..+|
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~-----enVE~AR~~I  100 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYF-----GDVDRARMLM  100 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEH-----HHHHHHHHHH
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCH-----HHHHHHHHHH
Confidence            466899999999999999999999  99999999999999999754     11244689999995     4788888887


Q ss_pred             HHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEE
Q 022746          119 AALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQ  198 (292)
Q Consensus       119 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~  198 (292)
                      .+++                   ..++.+.+|...++.  ..-+..|.+ ++.++++|.+.+.....     +.....|+
T Consensus       101 ~~l~-------------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~-----~~~sd~V~  153 (376)
T 3n89_A          101 RRNC-------------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKN-----GIVTTYLR  153 (376)
T ss_dssp             HHSC-------------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC----------CEEEEE
T ss_pred             HhcC-------------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCccccc-----CCCCCEEE
Confidence            7642                   124556666543222  111234544 56799999985432211     02357899


Q ss_pred             EEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCC--ccHHH
Q 022746          199 ISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSS--FNIFF  276 (292)
Q Consensus       199 I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG--~~Ik~  276 (292)
                      |+|...++..|.+.+..++......+.                    .....++.+|.|+..+|..|||| +|  ..|+.
T Consensus       154 IrG~~~nv~~akeA~~~Ll~~l~~~e~--------------------~~~~~~s~~v~V~~~~H~~IIGk-~G~n~~Ikk  212 (376)
T 3n89_A          154 ITAREKNQHELIEAAKRLNEILFRESP--------------------APENNFTLHFTLSTYYVDQVLGS-SSTAQLMPV  212 (376)
T ss_dssp             EEEEGGGHHHHHHHHHHHHHHHCC--C--------------------CCSSCEEEEEEEEGGGHHHHTCC-TTSCCHHHH
T ss_pred             EEcChhhHHHHHHHHHHHHHHHHhhhc--------------------ccccceEEEEEeCHHHHHHhhcC-CCcchHHHH
Confidence            999997666555554444433211110                    01124789999999999999999 88  55699


Q ss_pred             HHHhhCCCCcc
Q 022746          277 LITTSSLGQPL  287 (292)
Q Consensus       277 I~~~S~~~~~~  287 (292)
                      |++.+|+.+.+
T Consensus       213 Ir~eTGv~I~F  223 (376)
T 3n89_A          213 IERETTTIISY  223 (376)
T ss_dssp             HHHHHTCEEEC
T ss_pred             HHHhhCCEEEC
Confidence            99999998765

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

Probab=99.72  E-value=2.4e-17  Score=142.51  Aligned_cols=150  Identities=20%  Similarity=0.235  Sum_probs=113.5

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~  128 (292)
                      +-..++.||.+.+|.|||++|++|+.|+++|||+|++...     ++.|+|.+.....+..++++|..+|..++......
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~~~e  107 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPE  107 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHH
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCcc
Confidence            3456999999999999999999999999999999999842     46789998753323457899999999987432211


Q ss_pred             CcchhhcccCCCcccEEEEEec-----------cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEE
Q 022746          129 NSEASKVAAGHVAANTIRLLIA-----------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV  197 (292)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~i~IP-----------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v  197 (292)
                        ......  ........+.++           ...+|+|||++|++|+.|++.|||+|.|.              ++.|
T Consensus       108 --~g~~ll--~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~--------------~~~v  169 (219)
T 2e3u_A          108 --RAFRLL--NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY--------------GKTV  169 (219)
T ss_dssp             --HHGGGG--STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE--------------TTEE
T ss_pred             --ccceec--cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC--------------CeEE
Confidence              000000  001111223333           23689999999999999999999999984              3579


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          198 QISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       198 ~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      +|.|+.++++.|..+|.+++...+
T Consensus       170 ~i~G~~~~i~~A~~~i~~li~g~~  193 (219)
T 2e3u_A          170 AIIGNPIQIEIAKTAIEKLARGSP  193 (219)
T ss_dssp             EEEECHHHHHHHHHHHHHHHTTCC
T ss_pred             EEEeCHHHHHHHHHHHHHHHcCCC
Confidence            999999999999999999997763

>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=99.57  E-value=1.4e-14  Score=122.31  Aligned_cols=146  Identities=18%  Similarity=0.216  Sum_probs=111.8

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcc
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSE  131 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~  131 (292)
                      .+++||.+.+|.|||++|++++.|++.+||+|+++.     .++.++|.......+..++++|...|..+.......  +
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~e--~   78 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPE--K   78 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHH--H
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHH--H
Confidence            689999999999999999999999999999999974     357788884433333567899999998887654321  1


Q ss_pred             hhhcccCCCcccEEEEEec----------cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc
Q 022746          132 ASKVAAGHVAANTIRLLIA----------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG  201 (292)
Q Consensus       132 ~~~~~~~~~~~~~~~i~IP----------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G  201 (292)
                      ....-.  .......+.++          ....|+|||++|.+++.|++.|||+|.|.              +..|.|.|
T Consensus        79 A~~Ll~--Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~--------------~~~v~i~G  142 (191)
T 1tua_A           79 AFRLLE--EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG--------------EYEVAIIG  142 (191)
T ss_dssp             HGGGGS--TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC--------------SSEEEEEE
T ss_pred             hhhccc--CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc--------------CCEEEEEe
Confidence            111100  01112223333          24689999999999999999999999983              34899999


Q ss_pred             CHHHHHHHHHHHHHHHhcC
Q 022746          202 DVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       202 ~~~~v~~A~~~I~~~l~~~  220 (292)
                      +.++++.|...|..++...
T Consensus       143 ~~~~i~~Ar~~i~~li~g~  161 (191)
T 1tua_A          143 DYERAMAAKQAIEMLAEGR  161 (191)
T ss_dssp             EHHHHHHHHHHHHHHHTTC
T ss_pred             ChHHHHHHHHHHHHHHcCC
Confidence            9999999999999999754

>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=99.57  E-value=1.7e-15  Score=108.86  Aligned_cols=71  Identities=25%  Similarity=0.502  Sum_probs=64.6

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      +..++++|+||.+.+|.||||+|++|++|+++|||+|++++.  ++++|+|+|+|++     .++.+|+.+|.+++.+
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            457899999999999999999999999999999999999976  5789999999985     4789999999999865

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

Probab=99.55  E-value=3.3e-15  Score=108.18  Aligned_cols=74  Identities=27%  Similarity=0.448  Sum_probs=66.4

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ...++++|+||.+.+|.||||+|++|++|+++|||+|++.+..++..+|.|+|+|++     .++.+|..+|.+++.++
T Consensus         2 ~~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~-----~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            2 AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSA-----ASISLAQYLINVRLSSE   75 (76)
T ss_dssp             -CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHHTTC
T ss_pred             CCceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCH-----HHHHHHHHHHHHHHHcc
Confidence            357889999999999999999999999999999999999987777889999999985     47899999999988653

>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=99.54  E-value=8.6e-15  Score=105.16  Aligned_cols=70  Identities=34%  Similarity=0.615  Sum_probs=63.5

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ....+|+||.+.+|.|||++|++|++|+++|||+|++.+. .        ..+|.|+|+|+++++.+|+.+|.++|.++
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-N--------CPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-C--------CSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-C--------CCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            5689999999999999999999999999999999999653 1        46899999999999999999999999863

>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=99.53  E-value=1.2e-14  Score=106.77  Aligned_cols=73  Identities=29%  Similarity=0.505  Sum_probs=66.0

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|++..++..+|.|+|+|++     +++.+|..+|.+++.+.
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            46889999999999999999999999999999999999987677889999999985     47899999999988653

>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=99.52  E-value=2.3e-14  Score=103.66  Aligned_cols=72  Identities=22%  Similarity=0.376  Sum_probs=63.3

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCC-CCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      .+.++.||.+++|+|||++|++|++|+++|||+|.+.+.++ .|.     +.++.|+|+|+++++.+|+.+|.+++.+
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG-----TRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTT-----CCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCC-----CceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999999975422 232     6789999999999999999999998865

>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=99.52  E-value=9.2e-15  Score=107.39  Aligned_cols=74  Identities=26%  Similarity=0.424  Sum_probs=65.6

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ...++++|+||.+.+|.||||+|++|++|+++|||+|+|.+..++..+|.|+|+|++     .++.+|..+|.+++.+.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA-----ASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHHhh
Confidence            346889999999999999999999999999999999999987677889999999986     47899999999988664

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

Probab=99.50  E-value=3e-14  Score=103.13  Aligned_cols=72  Identities=32%  Similarity=0.499  Sum_probs=64.7

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+.++.||.+++|+|||++|++|++|+++|||+|++.+.  .+.     +.++.|+|+|+++++.+|+.+|.+++.+.
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--VEG-----STDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC--CTT-----CSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC--CCC-----CCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4688999999999999999999999999999999999642  232     67999999999999999999999999764

>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=99.49  E-value=6.9e-14  Score=102.69  Aligned_cols=72  Identities=33%  Similarity=0.507  Sum_probs=64.6

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+.++.||.+++|.|||++|++|++|+++|||+|++.+.  .|.     +.+|.|+|+|+++++.+|+.+|.+++.+.
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--LEG-----SEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT--TSC-----SSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC--CCC-----CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            5688999999999999999999999999999999999642  232     57899999999999999999999999875

>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=99.49  E-value=2e-14  Score=116.68  Aligned_cols=101  Identities=17%  Similarity=0.180  Sum_probs=78.8

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      ..+.+|.||.+.+|.+||++|++|+.|++++|  |++...++        ..+..+...++++.|.+|..++    .-  
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~--------~~~~~i~~~~~p~~v~~~~~~l----~~--   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDE--------DTCTFHIYGEDQDAVKKARSFL----EF--   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEET--------TTTEEEEEESSHHHHHHHHHHH----CE--
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCC--------CchheeeccCCHHHHHHHHHhh----hc--
Confidence            45789999999999999999999999999999  44432211        2344555556799998886543    11  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCC-CCccc
Q 022746          222 PRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL-GQPLL  288 (292)
Q Consensus       222 ~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~-~~~~~  288 (292)
                                                   ...+|.||.+++|++||| +|+||+.|++.||+ .+.+-
T Consensus        67 -----------------------------~e~~v~Vp~~~~g~~IGK-~G~nIr~i~~~tG~~~I~i~  104 (144)
T 2qnd_A           67 -----------------------------AEDVIQVPRNLVGKVIGK-NGKLIQEIVDKSGVVRVRIE  104 (144)
T ss_dssp             -----------------------------EEEEEEEEGGGHHHHHCG-GGHHHHHHHHHHTCSEEEEE
T ss_pred             -----------------------------ceEEEEECHHHcCeeECC-CCHHHHHHHHHHCCEEEEEc
Confidence                                         136889999999999999 99999999999997 66543

>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=99.48  E-value=5.3e-14  Score=103.31  Aligned_cols=73  Identities=34%  Similarity=0.504  Sum_probs=64.0

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|++.+.  .+.     +.++.|+|+|+++++.+|+.+|.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~--~~~-----~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP--VEG-----SSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--CTT-----CSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC--CCC-----CCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            35689999999999999999999999999999999999642  222     67999999999999999999999999876

>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=99.48  E-value=3.4e-14  Score=102.73  Aligned_cols=71  Identities=23%  Similarity=0.380  Sum_probs=62.1

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC---CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ..+++|+||.+.+|.||||+|++|++|+++|||+|+|.+.   .+++.++.|+|+|++     .++..|..+|.+++.+
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            4678999999999999999999999999999999999964   356778999999985     4788999999888654

>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=99.47  E-value=2.1e-14  Score=107.07  Aligned_cols=74  Identities=28%  Similarity=0.500  Sum_probs=66.8

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ...++++|+||.+.+|.||||+|++|++|+++|||+|+|++..++.++|.|+|+|++     +++.+|..+|.+++.+.
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~-----e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ-----DQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEH-----HHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCH-----HHHHHHHHHHHHHHHhh
Confidence            447889999999999999999999999999999999999987777889999999985     47899999999988764

>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=99.47  E-value=7.1e-14  Score=104.86  Aligned_cols=74  Identities=22%  Similarity=0.366  Sum_probs=66.9

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|.+..++..+|.|+|+|++     .++.+|..+|.+++.+..
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 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTP-----ESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCH-----HHHHHHHHHHHHHHHhcc
Confidence            46889999999999999999999999999999999999987667789999999985     478999999999987754

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

Probab=99.47  E-value=1.9e-13  Score=100.98  Aligned_cols=73  Identities=25%  Similarity=0.440  Sum_probs=63.5

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      ....++.||.+++|+|||++|++||+|+++|||+|.+......+.     +.+|.|+|+|+++++.+|+.+|.+++.+
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~-----~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT-----NVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSST-----TSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCC-----CCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            457899999999999999999999999999999999965322122     5789999999999999999999998864

>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=99.46  E-value=1.8e-13  Score=103.01  Aligned_cols=77  Identities=18%  Similarity=0.348  Sum_probs=67.2

Q ss_pred             CCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCC--CCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA--RHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        45 ~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~--~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      .....++++|+||.+++|+||||+|++|++|+++|||+|+|.+..+  ...+|.|+|+|+++     ++.+|..+|.+++
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            3567899999999999999999999999999999999999997532  45789999999765     6899999999998


Q ss_pred             hcCC
Q 022746          123 LKDD  126 (292)
Q Consensus       123 ~~~~  126 (292)
                      .+..
T Consensus        85 ~~~~   88 (94)
T 1x4m_A           85 RDQG   88 (94)
T ss_dssp             CCCS
T ss_pred             hccC
Confidence            7654

>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=7.4e-14  Score=103.67  Aligned_cols=73  Identities=22%  Similarity=0.375  Sum_probs=64.8

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCC-CCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      .+.+|.||.+++|+|||++|++|++|+++|||+|.+.+.++ .|.     +.++.|+|+|+++++..|+.+|.+++.+.
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 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG-----TRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTT-----SCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCC-----CCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            47899999999999999999999999999999999975422 333     57899999999999999999999998774

>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=99.45  E-value=5.9e-14  Score=103.11  Aligned_cols=71  Identities=20%  Similarity=0.279  Sum_probs=63.6

Q ss_pred             CcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       140 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|++...          .+++.|+|+|+++++.+|+.+|.+++..
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            356789999999999999999999999999999999998642          2468999999999999999999998876


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      .
T Consensus        77 r   77 (83)
T 2dgr_A           77 R   77 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.44  E-value=2.2e-13  Score=102.13  Aligned_cols=74  Identities=19%  Similarity=0.289  Sum_probs=66.1

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+.+|.||.+++|+|||++|++|++|+++|||+|+|.+..  +.     ..++.|+|+|+++++.+|+.+|.+++.+.
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--GG-----LPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--TT-----CSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC--CC-----CCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            456899999999999999999999999999999999996532  22     56899999999999999999999999887


Q ss_pred             C
Q 022746          221 P  221 (292)
Q Consensus       221 ~  221 (292)
                      .
T Consensus        86 ~   86 (92)
T 1x4n_A           86 R   86 (92)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.44  E-value=1.7e-13  Score=103.15  Aligned_cols=76  Identities=24%  Similarity=0.415  Sum_probs=66.4

Q ss_pred             CcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       140 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      +...+.+|.||.+++|+||||+|++||+|+++|||+|.|........     ..+|.|+|+|+++++.+|+.+|.+++.+
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 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT-----GADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSS-----CSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCC-----CCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            45678999999999999999999999999999999999964322111     4689999999999999999999999987


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      .
T Consensus        87 ~   87 (94)
T 1x4m_A           87 Q   87 (94)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.42  E-value=1.7e-13  Score=100.67  Aligned_cols=72  Identities=24%  Similarity=0.400  Sum_probs=62.8

Q ss_pred             CCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        46 ~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ....++++|.||.+++|+||||+|++||+|+++|||+|+|+..   .++++++|+|.++     ++.+|..+|.+++...
T Consensus         6 ~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~---~~~~~v~ItG~~e-----~v~~A~~~I~~~i~~r   77 (83)
T 2dgr_A            6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---DKEPVFAVTGMPE-----NVDRAREEIEAHITLR   77 (83)
T ss_dssp             SCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS---SSCCEEEEEECTT-----THHHHHHHHHHHHHSC
T ss_pred             CCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC---CCCCeEEEEcCHH-----HHHHHHHHHHHHHhcc
Confidence            4467899999999999999999999999999999999999853   2468999999986     5889999999876543

>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=99.42  E-value=1.4e-13  Score=102.54  Aligned_cols=73  Identities=33%  Similarity=0.501  Sum_probs=65.3

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+.++.||.+++|.|||++|++|++|+++|||+|++.+.  .|.     +.++.|+|+|+++++.+|+.+|.+++.+.
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 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LEG-----SEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC--CSS-----SSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC--CCC-----CCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            45688999999999999999999999999999999999632  232     57899999999999999999999999875

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

Probab=99.42  E-value=2.8e-13  Score=100.12  Aligned_cols=72  Identities=17%  Similarity=0.338  Sum_probs=62.5

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC--CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~--~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      ....+.+|.||.+.+|.||||+|++|++|+++|||+|++.+..  +...+|.|+|+|++     .++.+|..+|.+++.
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~-----~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDP-----YKVQQACEMVMDILR   84 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECH-----HHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHhc
Confidence            3467889999999999999999999999999999999999753  35678999999964     478899999988875

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

Probab=99.42  E-value=3.4e-13  Score=103.92  Aligned_cols=74  Identities=19%  Similarity=0.272  Sum_probs=64.4

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      +.+|.||.+++|+||||+|++||+|+++|||+|+|.... .+..   ...++.|+|+|++++|.+|+.+|.+++.+..
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            789999999999999999999999999999999996532 2211   1468999999999999999999999998873

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

Probab=99.42  E-value=1.4e-13  Score=105.74  Aligned_cols=73  Identities=23%  Similarity=0.335  Sum_probs=63.9

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~  127 (292)
                      .+++|+||.+++|.||||+|++|++|+++|+|+|+|.+..+..++|+|+|+|++     +++.+|..+|.+++.+...
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~-----e~v~~A~~~I~~ii~~~~~   83 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPP-----DRCEHAARIINDLLQSLRS   83 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSH-----HHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCH-----HHHHHHHHHHHHHHhcccc
Confidence            368999999999999999999999999999999999976566789999999985     4789999999999877543

>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=99.41  E-value=9.8e-14  Score=103.01  Aligned_cols=72  Identities=24%  Similarity=0.394  Sum_probs=63.6

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC---CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      .++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.   .+++.++.|+|+|++     .++..|..+|.+++.+.
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~-----~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSP-----AATQAAQYLISQRVTYE   76 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSH-----HHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHhcc
Confidence            3578999999999999999999999999999999999964   366788999999985     47899999999988653

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

Probab=99.41  E-value=1.4e-13  Score=118.99  Aligned_cols=116  Identities=16%  Similarity=0.095  Sum_probs=88.1

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-----HHHHHHHHHHHHHH
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-----VPAVLNALVEIGNQ  216 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-----~~~v~~A~~~I~~~  216 (292)
                      .....+.||.+.+|.|||++|++|+.|+++|||+|++.            ..++.|+|.|+     ++++.+|..+|..+
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            44679999999999999999999999999999999984            24578889886     69999999999998


Q ss_pred             HhcCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecc-----------CccceeeecCCCccHHHHHHhhCCC
Q 022746          217 LRENPPR-QVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTR-----------YFVTAIFAVLSSFNIFFLITTSSLG  284 (292)
Q Consensus       217 l~~~~~~-~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~-----------~~vG~IIGk~gG~~Ik~I~~~S~~~  284 (292)
                      +...... ...-                .  .++.....+.++.           .++|+|||| +|.||+.|++.|||.
T Consensus       101 ~rg~~~e~g~~l----------------l--~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk-~G~tik~ie~~Tg~~  161 (219)
T 2e3u_A          101 GRGFSPERAFRL----------------L--NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGR-KGRTRQIIEEMSGAS  161 (219)
T ss_dssp             HTTCCHHHHGGG----------------G--STTCEEEEEEGGGCC------CHHHHHHHHHCG-GGHHHHHHHHHHCCE
T ss_pred             hccCCcccccee----------------c--cCCccceeEEcccccccCCchhhhhhhheeECC-CchHHHHHHHHhCce
Confidence            8532100 0000                0  0111222344432           368999999 999999999999999


Q ss_pred             Cccc
Q 022746          285 QPLL  288 (292)
Q Consensus       285 ~~~~  288 (292)
                      +.+-
T Consensus       162 I~v~  165 (219)
T 2e3u_A          162 VSVY  165 (219)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            8774

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

Probab=99.40  E-value=4.5e-13  Score=102.96  Aligned_cols=72  Identities=22%  Similarity=0.339  Sum_probs=63.5

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+.+|.||.+++++||||+|++||+|+++|||+|+|.+.+  +.     +.+|.|+|+|+++++++|+.+|.+++.+.
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~--~~-----~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--GT-----GPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC--SS-----SSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC--CC-----CceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            34789999999999999999999999999999999996432  11     56899999999999999999999999876

>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=99.39  E-value=6.4e-13  Score=101.90  Aligned_cols=76  Identities=24%  Similarity=0.271  Sum_probs=65.6

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+.+|.||.+++|+|||++|++|++|+++|||+|.|.+.....     .+.++.|+|+|+.+++.+|+.+|.+++.+.
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            456899999999999999999999999999999999996532211     136899999999999999999999999876


Q ss_pred             C
Q 022746          221 P  221 (292)
Q Consensus       221 ~  221 (292)
                      +
T Consensus        88 ~   88 (104)
T 1we8_A           88 E   88 (104)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.39  E-value=5.7e-13  Score=102.17  Aligned_cols=74  Identities=26%  Similarity=0.398  Sum_probs=63.9

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCC--CCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIAR--HEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~--~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ....+++|+||.+.+|.||||+|++|++|+++|||+|+|.+...+  .+++.|+|+|.++     ++.+|+.+|.+++.+
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~-----~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK-----EVAAAKHLILEKVSE   86 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHH-----HHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHH-----HHHHHHHHHHHHHhh
Confidence            346889999999999999999999999999999999999975432  3589999999864     688999999998865


Q ss_pred             C
Q 022746          125 D  125 (292)
Q Consensus       125 ~  125 (292)
                      .
T Consensus        87 ~   87 (104)
T 1we8_A           87 D   87 (104)
T ss_dssp             H
T ss_pred             C
Confidence            3

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

Probab=99.37  E-value=4.5e-13  Score=103.25  Aligned_cols=71  Identities=23%  Similarity=0.358  Sum_probs=62.0

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC---CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI---ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~---~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      +++|+||.+++|.||||+|++|++|+++|||+|+|.+..   .+..++.|+|+|+.     +++.+|+.+|.+++.+..
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSP-----QQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCH-----HHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCH-----HHHHHHHHHHHHHHhccc
Confidence            689999999999999999999999999999999999653   23468999999974     478999999999987643

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

Probab=99.36  E-value=6.9e-13  Score=94.62  Aligned_cols=67  Identities=19%  Similarity=0.357  Sum_probs=58.2

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~  121 (292)
                      ...+..|.||.+++|.|||++|++|++|+++|||+|+|++.  +..++.|+|+|.++     ++.+|..+|.++
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            35678999999999999999999999999999999999975  34678999999853     688888887765

>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=99.35  E-value=2.3e-12  Score=97.53  Aligned_cols=73  Identities=15%  Similarity=0.090  Sum_probs=63.5

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+..|.||..+++.|||++|++|++|+++|||+|+|.+. ..+.     ..++.|+|+|+.+++.+|+.+|..++.+.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~-g~~~-----~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDK-DDGN-----QPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCT-TTCS-----SCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCC-CCCC-----CCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            4589999999999999999999999999999999998643 2222     36789999999999999999999988653

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

Probab=99.35  E-value=1.9e-12  Score=97.55  Aligned_cols=73  Identities=18%  Similarity=0.148  Sum_probs=64.1

Q ss_pred             CcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       140 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      ...++..+.||.++++.|||++|++|++|+++|||+|+|++...        ..++.|+|+|+++++.+|+.+|..++.+
T Consensus        14 ~~~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           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA--------PDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC--------SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC--------CCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            34678999999999999999999999999999999999854211        2468999999999999999999999877


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      .
T Consensus        86 ~   86 (95)
T 2ctm_A           86 Y   86 (95)
T ss_dssp             H
T ss_pred             H
Confidence            5

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

Probab=99.34  E-value=1.1e-12  Score=93.62  Aligned_cols=67  Identities=24%  Similarity=0.338  Sum_probs=59.3

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      ..+..+.||.+++|.|||++|++|++|+++|||+|.+++. .        ..++.|+|+|+.+++.+|+.+|.+++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~-g--------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-S--------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-C--------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC-C--------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999998542 1        35689999999999999999998764

>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=99.33  E-value=1.5e-12  Score=97.95  Aligned_cols=72  Identities=18%  Similarity=0.288  Sum_probs=63.9

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+..+.||.+++|.|||++|++|++|+++|||+|+|.+.+         ..++.|+|+|+++++.+|+.+|..++.+.
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            456899999999999999999999999999999999985422         23579999999999999999999999876


Q ss_pred             C
Q 022746          221 P  221 (292)
Q Consensus       221 ~  221 (292)
                      .
T Consensus        86 ~   86 (94)
T 2cte_A           86 D   86 (94)
T ss_dssp             H
T ss_pred             c
Confidence            4

>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=99.32  E-value=1.6e-12  Score=98.39  Aligned_cols=73  Identities=22%  Similarity=0.328  Sum_probs=62.2

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC-CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI-ARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ..+++.|.||.+++|.||||+|++|++|+++|||+|+|++.. ++..++.|+|+|..     .++.+|..+|..++.+.
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 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYE-----KNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCH-----HHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCH-----HHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999999653 33467899999984     36788888888887654

>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=99.30  E-value=1.6e-12  Score=97.89  Aligned_cols=72  Identities=19%  Similarity=0.321  Sum_probs=62.4

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ...++.+|.||.+.+|.|||++|++|++|+++|||+|+|++.  +..++.|+|+|.+     .++.+|..+|.+++.+.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~--~~~~~~V~I~G~~-----e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTK-----EGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECH-----HHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC--CCCCCeEEEEECH-----HHHHHHHHHHHHHhhcc
Confidence            457899999999999999999999999999999999999864  2345789999984     47889999999888654

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

Probab=99.29  E-value=6.8e-12  Score=115.87  Aligned_cols=152  Identities=11%  Similarity=0.140  Sum_probs=103.5

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCC--CCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA--RHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~--~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      .+++.+.+|...++.  ..-+..|.+ ++.++++|.+.....  +.....|+|+|...+  +..+.+|+.++.+.+.+..
T Consensus       105 Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~n--v~~akeA~~~Ll~~l~~~e  179 (376)
T 3n89_A          105 HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITAREKN--QHELIEAAKRLNEILFRES  179 (376)
T ss_dssp             EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEGGG--HHHHHHHHHHHHHHHCC--
T ss_pred             CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcChhh--HHHHHHHHHHHHHHHHhhh
Confidence            456677777654433  112334555 678999999964311  113567999998764  4566777777777765542


Q ss_pred             CCCcchhhcccCCCcccEEEEEeccCcceeeecCCC--hhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHH
Q 022746          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSG--QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP  204 (292)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G--~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~  204 (292)
                      ...          ....+..+.|+..+|..|||++|  ..|++|+++|||+|.++..++... .  ......|+|+|+.+
T Consensus       180 ~~~----------~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d-~--~~~~~~ItItGs~e  246 (376)
T 3n89_A          180 PAP----------ENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNE-T--RGNIYEIKVVGNID  246 (376)
T ss_dssp             CCC----------SSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC------------CCEEEEEEESCHH
T ss_pred             ccc----------ccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCccc-c--cCCceEEEEEeCHH
Confidence            111          12468899999999999999999  567999999999999854322111 0  02457899999999


Q ss_pred             HHHHHHHHHHHHHh
Q 022746          205 AVLNALVEIGNQLR  218 (292)
Q Consensus       205 ~v~~A~~~I~~~l~  218 (292)
                      +|.+|+..|.++|-
T Consensus       247 ~V~~Ark~I~~lLP  260 (376)
T 3n89_A          247 NVLKARRYIMDLLP  260 (376)
T ss_dssp             HHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHhhCC
Confidence            99999999999983

>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=99.28  E-value=2.7e-12  Score=108.41  Aligned_cols=115  Identities=10%  Similarity=0.109  Sum_probs=90.6

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEE-----cCHHHHHHHHHHHHHHHh
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GDVPAVLNALVEIGNQLR  218 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~l~  218 (292)
                      ..++.||...+|.|||++|++++.|++.+|++|++.            ..++.|+|.     |++.++.+|..+|..+..
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            368999999999999999999999999999999995            346788888     999999999999998887


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecc----------CccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          219 ENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTR----------YFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       219 ~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~----------~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                      .....+...+               .  .++.....|.++.          ...|+|||| +|.||+.|+..|||.+.+-
T Consensus        73 gf~~e~A~~L---------------l--~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk-~G~tik~iE~~Tg~~I~v~  134 (191)
T 1tua_A           73 GFPPEKAFRL---------------L--EEDQILVVVDLKQVVGDSQNHLKRIKGRIIGE-GGRARRTIEEMTDTYINVG  134 (191)
T ss_dssp             TCCHHHHGGG---------------G--STTEEEEEEETHHHHTTCHHHHHHHHHHHHCG-GGHHHHHHHHHHTCEEEEC
T ss_pred             CCCHHHhhhc---------------c--cCcceeEEEEcccccccCchhHHHHhhheeCC-CccHHHHHHHHHCceEEEc
Confidence            6532111000               0  0123344455552          358999999 9999999999999998764

>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=99.25  E-value=5.8e-12  Score=94.88  Aligned_cols=75  Identities=23%  Similarity=0.283  Sum_probs=63.1

Q ss_pred             CCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        46 ~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ....+++.|.||.+++|.|||++|++|++|+++|||+|+|++... ..++.|+|+|.++     ++.+|..+|..++.+.
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~-~~~~~V~I~G~~e-----~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPE-----NVEEAIDHILNLEEEY   86 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHH-----HHHHHHHHHHHHHHHH
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC-CCCcEEEEEcCHH-----HHHHHHHHHHHHHHHH
Confidence            345788999999999999999999999999999999999986521 2467899999853     6888888888887664


Q ss_pred             C
Q 022746          126 D  126 (292)
Q Consensus       126 ~  126 (292)
                      .
T Consensus        87 ~   87 (95)
T 2ctm_A           87 L   87 (95)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=99.24  E-value=1e-11  Score=95.05  Aligned_cols=70  Identities=20%  Similarity=0.262  Sum_probs=61.9

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      +....|.||.+++|.|||++|++|++|+++|||+|.|.+..         ...+.|+|+|+.+++.+|+.+|..++.+.
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 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE---------LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT---------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC---------CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            46889999999999999999999999999999999986421         23469999999999999999999988664

>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=99.18  E-value=1.3e-11  Score=94.55  Aligned_cols=70  Identities=20%  Similarity=0.279  Sum_probs=60.6

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      ..+..|.||.+++|.|||++|++|++|+++|||+|+|++..  ...+.|+|+|.+     .++.+|..+|..++.+.
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 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE--LQSDIIAITGLA-----ANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT--TTCCEEEEEECH-----HHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC--CCcceEEEEcCH-----HHHHHHHHHHHHHHhhH
Confidence            57889999999999999999999999999999999999753  244689999985     36888988888887654

>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=99.12  E-value=7.7e-11  Score=88.63  Aligned_cols=71  Identities=20%  Similarity=0.249  Sum_probs=63.2

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      ...+..|.||.++++.|||++|++|++|+++| ||+|.|+. +.        +..+.|+|+|+..++.+|+.+|..++.+
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 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV-EG--------SGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC-TT--------TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCC-CC--------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            45688999999999999999999999999999 99999853 21        4567999999999999999999999987


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      .
T Consensus        86 ~   86 (95)
T 2ctj_A           86 K   86 (95)
T ss_dssp             H
T ss_pred             h
Confidence            5

>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=99.12  E-value=1.1e-10  Score=89.01  Aligned_cols=66  Identities=17%  Similarity=0.234  Sum_probs=59.5

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHh-hCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNS-SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      .+.+|.||.++|+.|||++|++|++|+++ ++++|.|+.            .++.|+|+|+++.|.+|..+|..++.+.
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 599999742            3569999999999999999999998765

>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=99.11  E-value=4.7e-11  Score=89.79  Aligned_cols=76  Identities=21%  Similarity=0.315  Sum_probs=65.2

Q ss_pred             cCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        44 ~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      +..++.++..|.||.++++.|||++|++|++|+++| ||+|+|++.  +...+.|+|+|..+     .+.+|..+|..++
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            456678889999999999999999999999999999 999999975  34567899999853     6888999999988


Q ss_pred             hcCC
Q 022746          123 LKDD  126 (292)
Q Consensus       123 ~~~~  126 (292)
                      .+..
T Consensus        84 ~e~e   87 (95)
T 2ctj_A           84 EEKQ   87 (95)
T ss_dssp             HHHS
T ss_pred             hhhh
Confidence            7644

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

Probab=99.07  E-value=4.3e-10  Score=85.66  Aligned_cols=67  Identities=24%  Similarity=0.346  Sum_probs=58.1

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhh-cCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREE-TKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      .++.+|.||++++++|||++|++|++|+++ ++++|+|++     .++.|+|+|+++     .|.+|..+|..++.+.
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            378999999999999999999999999997 599999997     357899999964     6888888888877653

>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=98.81  E-value=4.2e-09  Score=77.99  Aligned_cols=65  Identities=28%  Similarity=0.276  Sum_probs=56.6

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCe-EEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHH
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQL  217 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l  217 (292)
                      ......|.||.+.+|.+||++|++|++|+++||++ |.+.            .++..|+|.| +.+++.+|+.+|..+-
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~------------eddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD------------EDTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE------------TTTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE------------cCCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            45688999999999999999999999999999998 9994            2358999999 7899999998885543

>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=98.78  E-value=5.7e-09  Score=77.28  Aligned_cols=65  Identities=20%  Similarity=0.275  Sum_probs=52.6

Q ss_pred             CCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcE-EEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        45 ~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      .....+...|.||.+.+|.+||++|++|++|+++||++ |.+.+     ++..|+|.|...    .++.+|..+|
T Consensus        10 ~~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~~----ea~~~A~~~I   75 (91)
T 2cpq_A           10 QLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGESA----DAVKKARGFL   75 (91)
T ss_dssp             SSSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESSH----HHHHHHHHHH
T ss_pred             hccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECCH----HHHHHHHHHH
Confidence            44557889999999999999999999999999999998 99975     247899999643    3455555433

>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=1.9e-08  Score=79.91  Aligned_cols=73  Identities=21%  Similarity=0.398  Sum_probs=60.1

Q ss_pred             CCeEEEEEeeCC------ccceeecCCCchhhhhhhhcCcEEEEccCCC----------------CCCceEEEEecCCCC
Q 022746           48 QDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIADAIA----------------RHEERVIIISSKDND  105 (292)
Q Consensus        48 ~~~~~rilvp~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------------~~~ervv~I~G~~~~  105 (292)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|.....                ..++-.|.|++... 
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            468899999998      7889999999999999999999999975210                12355788999653 


Q ss_pred             cchhHHHHHHHHHHHHHhc
Q 022746          106 NVVSDAENALQQIAALILK  124 (292)
Q Consensus       106 ~~v~~v~~A~~~I~~~i~~  124 (292)
                         ..+.+|+.+|..++..
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               5789999999999876

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.61  E-value=1e-07  Score=74.20  Aligned_cols=72  Identities=22%  Similarity=0.128  Sum_probs=56.8

Q ss_pred             CeEEEEEeeCC-------ccceeecCCCchhhhhhhhcCcEEEEccCCC----------CCCceEEEEecCCCCcchhHH
Q 022746           49 DVLFRIIVPSR-------QIGKVIGKEGHRIQKIREETKATIKIADAIA----------RHEERVIIISSKDNDNVVSDA  111 (292)
Q Consensus        49 ~~~~rilvp~~-------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------~~~ervv~I~G~~~~~~v~~v  111 (292)
                      .+..||.||.+       ++|.|||++|.+||+|+++|||+|.|.....          ..++-.|.|++...    .++
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            46778998876       6899999999999999999999999973311          11345788888653    578


Q ss_pred             HHHHHHHHHHHhc
Q 022746          112 ENALQQIAALILK  124 (292)
Q Consensus       112 ~~A~~~I~~~i~~  124 (292)
                      .+|+.+|.+++..
T Consensus        87 ~~A~~~Ie~Ll~~   99 (119)
T 2yqr_A           87 AAAKKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhc
Confidence            8999998888765

>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=98.59  E-value=1.2e-07  Score=75.29  Aligned_cols=78  Identities=18%  Similarity=0.290  Sum_probs=60.4

Q ss_pred             ccEEEEEeccC------cceeeecCCChhHHHHHHhhCCeEEEeCCCCCCccc---------CCCCCCcEEEEEc-CHHH
Q 022746          142 ANTIRLLIAGS------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA---------SAHESDRVVQISG-DVPA  205 (292)
Q Consensus       142 ~~~~~i~IP~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~---------~~~~~~r~v~I~G-~~~~  205 (292)
                      ..+.++.||.+      ++|.|||++|.+||+|+++|||+|.|..........         .....+-.|.|++ +.+.
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            45789999987      889999999999999999999999996432111000         0012467888998 5789


Q ss_pred             HHHHHHHHHHHHhc
Q 022746          206 VLNALVEIGNQLRE  219 (292)
Q Consensus       206 v~~A~~~I~~~l~~  219 (292)
                      +.+|+.+|..+|.+
T Consensus        86 ~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           86 VKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999977

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.48  E-value=3.8e-07  Score=71.01  Aligned_cols=79  Identities=13%  Similarity=0.068  Sum_probs=57.1

Q ss_pred             ccEEEEEeccC-------cceeeecCCChhHHHHHHhhCCeEEEeCCCCC---CcccCCCCCCcEEEEEc-CHHHHHHHH
Q 022746          142 ANTIRLLIAGS-------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQL---PLCASAHESDRVVQISG-DVPAVLNAL  210 (292)
Q Consensus       142 ~~~~~i~IP~~-------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~---p~~~~~~~~~r~v~I~G-~~~~v~~A~  210 (292)
                      ..+.++.||.+       ++|.|||++|.+||+|+++|||+|.|......   +........+-.|.|.+ +.+++.+|+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~   90 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAK   90 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHH
Confidence            34678888854       78999999999999999999999999632110   00000002345677775 578999999


Q ss_pred             HHHHHHHhcC
Q 022746          211 VEIGNQLREN  220 (292)
Q Consensus       211 ~~I~~~l~~~  220 (292)
                      .+|.+++...
T Consensus        91 ~~Ie~Ll~~v  100 (119)
T 2yqr_A           91 KLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHhhch
Confidence            9999998753

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.46  E-value=1.8e-07  Score=74.71  Aligned_cols=76  Identities=17%  Similarity=0.398  Sum_probs=56.0

Q ss_pred             eEEEEEeeCCc------cceeecCCCchhhhhhhhcCcEEEEccCCCC------------------CCceEEEEecCCCC
Q 022746           50 VLFRIIVPSRQ------IGKVIGKEGHRIQKIREETKATIKIADAIAR------------------HEERVIIISSKDND  105 (292)
Q Consensus        50 ~~~rilvp~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~------------------~~ervv~I~G~~~~  105 (292)
                      ++-|+.||.+.      +|.|||++|.++|+|+++|||+|.|......                  .+.--|.|++....
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            56789999766      8999999999999999999999999853211                  11226888886432


Q ss_pred             -cchhHHHHHHHHHHHHHhcC
Q 022746          106 -NVVSDAENALQQIAALILKD  125 (292)
Q Consensus       106 -~~v~~v~~A~~~I~~~i~~~  125 (292)
                       .....+++|+.+|..++...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             hhHHHHHHHHHHHHHHHCCCC
Confidence             11125778888888887653

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.13  E-value=2.3e-06  Score=84.35  Aligned_cols=93  Identities=17%  Similarity=0.180  Sum_probs=68.3

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +..+.+++..|.+.+.+.........    ....+....+.||.+.++.|||+||++||.|+++|||+|.+.        
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 IQQASVAKKEILQIMNKTISKPRASR----KENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV--------  603 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSCCSSC----CTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC--------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh----cccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc--------
Confidence            34556677777777766543221111    112345788999999999999999999999999999999983        


Q ss_pred             cCCCCCCcEEEEEcC-HHHHHHHHHHHHHHH
Q 022746          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQL  217 (292)
Q Consensus       188 ~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l  217 (292)
                           ++..|.|.|+ .+...+|+.+|..++
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                 3578999887 578899999887654

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.11  E-value=2.8e-06  Score=67.85  Aligned_cols=76  Identities=17%  Similarity=0.221  Sum_probs=55.3

Q ss_pred             EEEEEeccC------cceeeecCCChhHHHHHHhhCCeEEEeCCCCCC------------cccCCCCCCcEEEEEcCH--
Q 022746          144 TIRLLIAGS------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP------------LCASAHESDRVVQISGDV--  203 (292)
Q Consensus       144 ~~~i~IP~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p------------~~~~~~~~~r~v~I~G~~--  203 (292)
                      +.++.||.+      ++|.|||++|.++|+|+++|||+|.|..+...-            .... -..+-.|.|++..  
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      599999999999999999999999997532110            0000 0223478898853  


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 022746          204 ----PAVLNALVEIGNQLREN  220 (292)
Q Consensus       204 ----~~v~~A~~~I~~~l~~~  220 (292)
                          ..+.+|+.+|..+|...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             hhHHHHHHHHHHHHHHHCCCC
Confidence                27899999999998754

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.88  E-value=3.4e-05  Score=60.54  Aligned_cols=69  Identities=16%  Similarity=0.110  Sum_probs=60.4

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...|.+....++.|+|++|+.|+.|+..|++.|++..-+.        +..-.|+|.|++..-..|..+|..+....
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s--------~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP--------ERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT--------TSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC--------CCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999975432        45788999999999999999998877543

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.68  E-value=1.9e-05  Score=63.28  Aligned_cols=104  Identities=16%  Similarity=0.265  Sum_probs=72.9

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCC
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~  129 (292)
                      -.+.|+|+...+|+.||++|++|+.|+++.|-+|.+-+...   +                   -...|.+.+.......
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~---d-------------------~~~fI~naLsPA~V~~   93 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS---D-------------------LERIVKNLFPGVKIES   93 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS---S-------------------HHHHHHHHSTTSCEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC---C-------------------HHHHHHHhcCCceEEE
Confidence            34889999999999999999999999999999988865311   0                   1112223322211000


Q ss_pred             cchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEe
Q 022746          130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL  179 (292)
Q Consensus       130 ~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  179 (292)
                      -   ..... .......+.||.++.+..|||+|.+++-...-||.+|.+.
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 1234788999999999999999999999999998887763

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.67  E-value=1.2e-05  Score=79.29  Aligned_cols=63  Identities=24%  Similarity=0.322  Sum_probs=51.6

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~  121 (292)
                      .-.+.|.||.+.+|.|||+||++||+|+++|||+|.|.+.      ..|.|.+...    .++.+|+.+|..+
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 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE------ETFSVFAPTP----SAMHEARDFITEI  628 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS------SEEEEEESSH----HHHHHHHHHTTC-
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC------cEEEEEeCCH----HHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999853      5799999653    3567777666543

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.62  E-value=2.9e-05  Score=77.49  Aligned_cols=96  Identities=22%  Similarity=0.254  Sum_probs=26.8

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +..+.+++..|.+.+.+.........    ....+....+.||.+.++.|||+||.+||.|+++||++|.+.        
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 LAQAKEGRAHILGEMNKAMDAPRADV----GDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN--------  606 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCSSC----CSSCCC--------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhh----cccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE--------
Confidence            44556777778888776543221111    112344678899999999999999999999999999999983        


Q ss_pred             cCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022746          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (292)
Q Consensus       188 ~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  220 (292)
                           ++..|.|.+. .+++.+|+..|..++.+.
T Consensus       607 -----ddG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          607 -----DDGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             ------------CCSCHHHHHHHHHC--------
T ss_pred             -----CCceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence                 3456777665 678899999998887654

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.43  E-value=0.00023  Score=55.82  Aligned_cols=67  Identities=16%  Similarity=0.147  Sum_probs=53.8

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      -++.|.+.++.++.|||++|+.|+.|+..|++.|++....+ +.+--|+|.|++.     .-.+|..+|..+.
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            35778889999999999999999999999999999997643 3566799999863     3345666666654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.27  E-value=0.00015  Score=58.08  Aligned_cols=103  Identities=21%  Similarity=0.175  Sum_probs=72.1

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPP  222 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  222 (292)
                      ..+.+.|+...+|..||++|++|+.|+++.|-+|.+..-          +.+              ....|.+.|.=.. 
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~----------s~d--------------~~~fI~naLsPA~-   90 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEY----------SSD--------------LERIVKNLFPGVK-   90 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEEC----------CSS--------------HHHHHHHHSTTSC-
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEc----------CCC--------------HHHHHHHhcCCce-
Confidence            378999999999999999999999999999999998753          223              1222333221110 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          223 RQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       223 ~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                        ...+    +.          ...++.....+.||.+..+..||| +|.|++-..+-+|..+-|
T Consensus        91 --V~~V----~i----------~~~~~~~~~~V~V~~~q~slAIGk-~G~NvrLa~~Ltg~~idI  138 (144)
T 2cxc_A           91 --IESI----NV----------RERNGVKQVVIKVSEDDKGAAIGK-GGKNVKRARLVLSKLFGV  138 (144)
T ss_dssp             --EEEE----EE----------EEETTEEEEEEEECTTTHHHHHCG-GGHHHHHHHHHHHHHHCE
T ss_pred             --EEEE----EE----------eecCCcEEEEEEEChHHhhhccCC-CCHHHHHHHHHhCCeeCc
Confidence              0000    00          000124577889999999999999 999999999888765443

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.97  E-value=0.00013  Score=72.81  Aligned_cols=64  Identities=28%  Similarity=0.426  Sum_probs=9.6

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      -...|.||.+.++.|||+||.+||+|+++||++|.+.+.      ..|.|.+...    .++.+|+.+|..+..
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd------G~v~I~~~~~----~~~~~A~~~i~~i~~  633 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD------GVVKVSASDG----AKIKAAIDWIKSITD  633 (726)
T ss_dssp             C-------------------------------------------------CCSCH----HHHHHHHHC------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC------ceEEEEeCCH----HHHHHHHHHHHHHhh
Confidence            356788999999999999999999999999999999853      5688888653    456677777766654

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=96.26  E-value=0.003  Score=54.94  Aligned_cols=98  Identities=21%  Similarity=0.251  Sum_probs=66.7

Q ss_pred             CccceeecCCCchhhhh-hhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746           59 RQIGKVIGKEGHRIQKI-REETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (292)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I-~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (292)
                      +-+|+-||++|++|+.| ++-.|-+|.|-...   ++                   ....|.+.+.......-.     .
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s---~d-------------------p~~fi~nalsPA~V~~V~-----i  178 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD---DD-------------------PARFVANALSPAKVVSVS-----V  178 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC---SS-------------------HHHHHHHHTTTSCCSEEE-----E
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEec---CC-------------------HHHHHHhccCCcceEEEE-----E
Confidence            45899999999999999 66678777776431   10                   112233333332211100     0


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCC
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ  183 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~  183 (292)
                      .......+.+.||..+.+.-|||+|.+++--..-||.+|.|....+
T Consensus       179 ~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          179 IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             EcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            0001247899999999999999999999999999999999976443

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=96.14  E-value=0.0041  Score=57.03  Aligned_cols=104  Identities=24%  Similarity=0.281  Sum_probs=71.4

Q ss_pred             EEEEeeC-----CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           52 FRIIVPS-----RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        52 ~rilvp~-----~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      .|+-|-+     +-+|+.||++|++|+.|.++. |-+|.|-...             ++         ....|.+.+...
T Consensus       237 aKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s-------------~d---------p~~fi~nalsPA  294 (366)
T 1k0r_A          237 SKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYD-------------DD---------PARFVANALSPA  294 (366)
T ss_dssp             EEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC-------------SS---------HHHHHHHHTTTS
T ss_pred             EEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhcCCc
Confidence            3555544     569999999999999999998 7777765431             11         112233333332


Q ss_pred             CCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCC
Q 022746          126 DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (292)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  182 (292)
                      ....-.  ..   ......+.+.||..+.+..|||+|.+++-...-||.+|.|....
T Consensus       295 ~V~~V~--~~---~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          295 KVVSVS--VI---DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             CCSEEE--EE---ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             ceeEEE--EE---cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            211100  00   01134789999999999999999999999999999999997643

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.88  E-value=0.0027  Score=63.54  Aligned_cols=95  Identities=21%  Similarity=0.233  Sum_probs=11.8

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +..+.++...|.+.+.+..........    ...+....+.||.+.++.+||++|.+|+.|.+++|+.|.+.        
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            344566666777777654332211111    11234577889999999999999999999999999999873        


Q ss_pred             cCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhc
Q 022746          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQLRE  219 (292)
Q Consensus       188 ~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~  219 (292)
                           .+..|.|.+. ...+.+|...|..++.+
T Consensus       597 -----~dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          597 -----DDGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             ---------------------------------
T ss_pred             -----CCccEEEecCCHHHHHHHHHHHHHHhhh
Confidence                 2456677665 45777787777666543

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=95.43  E-value=0.016  Score=52.78  Aligned_cols=95  Identities=25%  Similarity=0.284  Sum_probs=65.1

Q ss_pred             CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (292)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  137 (292)
                      +-+|+.||.+|++|+.+.++. |-+|.+-.-             +++         -...|.+.|.......-     ..
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~-------------s~d---------~~~fi~nal~Pa~v~~v-----~~  297 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKW-------------SDD---------PKQLIANALAPATVIEV-----EI  297 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC-------------CSS---------HHHHHHHHTCSSCCSEE-----EE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEec-------------CCC---------HHHHHHHhcCccEEEEE-----EE
Confidence            458999999999999999997 656655432             111         11233344332211100     00


Q ss_pred             CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (292)
Q Consensus       138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  180 (292)
                      .......+.+.||..+.+.-|||+|.+++--..-||.+|.+.+
T Consensus       298 ~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          298 LDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             EETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            0012347899999999999999999999999999999999864

>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=94.88  E-value=0.013  Score=50.87  Aligned_cols=93  Identities=15%  Similarity=0.158  Sum_probs=63.9

Q ss_pred             CcceeeecCCChhHHHH-HHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746          152 SQAGCLIGMSGQNIEKL-RNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP  230 (292)
Q Consensus       152 ~~vg~IIGk~G~~Ik~I-~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p  230 (292)
                      +-+|..||++|++|+.| ++-.|-+|.+..-          +.+              ....|.+.|.-..-....-   
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~----------s~d--------------p~~fi~nalsPA~V~~V~i---  178 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDY----------DDD--------------PARFVANALSPAKVVSVSV---  178 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC----------CSS--------------HHHHHHHHTTTSCCSEEEE---
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEe----------cCC--------------HHHHHHhccCCcceEEEEE---
Confidence            45799999999999999 7778999999753          233              2233333332211000000   


Q ss_pred             CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746          231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL  287 (292)
Q Consensus       231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~  287 (292)
                                   .+  .+.....+.||.+..+.-||| +|.||+-..+.+|..+.|
T Consensus       179 -------------~~--~~~~~a~V~V~~~qlslAIGk-~GqNvrLA~~Ltg~~idI  219 (251)
T 2asb_A          179 -------------ID--QTARAARVVVPDFQLSLAIGK-EGQNARLAARLTGWRIDI  219 (251)
T ss_dssp             -------------EE--TTTTEEEEEECGGGHHHHHCG-GGHHHHHHHHHHSCEEEE
T ss_pred             -------------Ec--CCCcEEEEEEChHHhhhhhcC-CcCcHHHHHHHHCCEecc
Confidence                         00  012367899999999999999 999999999999987655

>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=94.63  E-value=0.017  Score=52.99  Aligned_cols=102  Identities=13%  Similarity=0.133  Sum_probs=69.5

Q ss_pred             EEEEEecc-----CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          144 TIRLLIAG-----SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       144 ~~~i~IP~-----~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      ..++.|-+     +-+|.+||++|++|+.|.++. |-+|.|..-          +.+              ....|.+.|
T Consensus       236 RaKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~----------s~d--------------p~~fi~nal  291 (366)
T 1k0r_A          236 RSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDY----------DDD--------------PARFVANAL  291 (366)
T ss_dssp             EEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC----------CSS--------------HHHHHHHHT
T ss_pred             eEEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEc----------CCC--------------HHHHHHHhc
Confidence            34555544     567999999999999999998 999999753          233              223333333


Q ss_pred             hcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       218 ~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                      .-..-....-                .  ..+.....+.||.+..+..||| +|.|++-..+.+|..+.|.
T Consensus       292 sPA~V~~V~~----------------~--~~~~~~a~V~V~~~qlslAIGk-~GqNvrLA~~Ltg~~idI~  343 (366)
T 1k0r_A          292 SPAKVVSVSV----------------I--DQTARAARVVVPDFQLSLAIGK-EGQNARLAARLTGWRIDIR  343 (366)
T ss_dssp             TTSCCSEEEE----------------E--ETTTTEEEEEECGGGHHHHHCG-GGHHHHHHHHHHCCEEEEE
T ss_pred             CCcceeEEEE----------------E--cCCCcEEEEEEChHHhhhccCC-CcHHHHHHHHHHCCeeeee
Confidence            2211000000                0  0113478899999999999999 9999999999999877653

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=94.47  E-value=0.0024  Score=64.11  Aligned_cols=92  Identities=24%  Similarity=0.301  Sum_probs=34.3

Q ss_pred             hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (292)
Q Consensus       108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  187 (292)
                      +..+.+++..|.+.+.+..... ....    ...+....+.||.+.++.+||++|.+||.|++++|+.|.+.        
T Consensus       568 L~~A~~~~~~I~~~m~~al~~~-~~~~----~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~--------  634 (757)
T 1e3p_A          568 LKQARDARLHILDVMMEAIDTP-DEMS----PNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE--------  634 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSC-CCCC----TTSCBCCCC------------------CTTCCCCCSCC-----------
T ss_pred             HHHHHHHHHHHHHHHHHHhccc-cccc----ccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEec--------
Confidence            3455666677777776543322 1111    11233456789999999999999999999999999999884        


Q ss_pred             cCCCCCCcEEEEEcC-HHHHHHHHHHHHHHH
Q 022746          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQL  217 (292)
Q Consensus       188 ~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l  217 (292)
                           .+..|.|++. .....+|...|..+.
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                 2456666664 456666766665554

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=93.96  E-value=0.0099  Score=59.47  Aligned_cols=63  Identities=32%  Similarity=0.517  Sum_probs=0.0

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~  121 (292)
                      .....+.||.+.++.+||++|.+|+.|.++||+.|.+.+      +..+.|.+...    ..+.+|..+|..+
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~----~~~~~a~~~i~~i  621 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDG----EKAKHAIRRIEEI  621 (723)
T ss_dssp             -------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCH----HHHHHHHHHHHHH
Confidence            344677889999999999999999999999999998885      35688877643    2344555555444

>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=93.28  E-value=0.057  Score=49.17  Aligned_cols=94  Identities=14%  Similarity=0.098  Sum_probs=64.0

Q ss_pred             CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746          152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP  230 (292)
Q Consensus       152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p  230 (292)
                      +-+|.+||.+|.+|+.+.++. |-+|.+..-+          .+              ....|.+.|.-..-... .   
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s----------~d--------------~~~fi~nal~Pa~v~~v-~---  296 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWS----------DD--------------PKQLIANALAPATVIEV-E---  296 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECC----------SS--------------HHHHHHHHTCSSCCSEE-E---
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecC----------CC--------------HHHHHHHhcCccEEEEE-E---
Confidence            467999999999999999987 8899987532          22              12333333321100000 0   


Q ss_pred             CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746          231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL  288 (292)
Q Consensus       231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~  288 (292)
                         .         .  ..+.....+.||.+..+.-||| +|.||+--.+.+|..+.|+
T Consensus       297 ---~---------~--d~~~~~~~v~v~~~~~s~AIGk-~G~Nvrla~~Ltg~~idi~  339 (344)
T 1hh2_P          297 ---I---------L--DKENKAARVLVPPTQLSLAIGK-GGQNARLAAKLTGWKIDIK  339 (344)
T ss_dssp             ---E---------E--ETTTTEEEEEECTTSHHHHHCG-GGHHHHHHHHHHSCEEEEE
T ss_pred             ---E---------E--cCCCCEEEEEEChHHcchhhcC-CCccHHHHHHHHCCEecee
Confidence               0         0  0113478899999999999999 9999999999999876553

>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=92.91  E-value=0.009  Score=60.04  Aligned_cols=46  Identities=37%  Similarity=0.630  Sum_probs=16.9

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCC
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~  103 (292)
                      ..|.||.+.+|.+||++|.+|++|+++||+.|.+.+      +..|.|++..
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      3568888764

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=84.95  E-value=0.33  Score=38.91  Aligned_cols=30  Identities=17%  Similarity=0.216  Sum_probs=26.1

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcC
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETK   80 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tg   80 (292)
                      ++.|-+..+..|.||||.|.+++.||--+.
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~~   63 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLLF   63 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHHH
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHHH
Confidence            466667789999999999999999998874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	292
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	4e-11
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-09
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-09
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	4e-08
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-09
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-07
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	8e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	1e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	8e-07
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-08
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	3e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-08
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	9e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-08
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	6e-04
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	8e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-05
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-05
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	6e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	1e-05
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	4e-05
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	7e-05
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-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 = 55.5 bits (134), Expect = 4e-11
 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 = 50.2 bits (120), Expect = 3e-09
 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 = 52.7 bits (126), Expect = 1e-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 = 50.4 bits (120), Expect = 7e-09
 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 = 51.7 bits (124), Expect = 1e-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 = 47.5 bits (113), Expect = 4e-08
 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 = 50.2 bits (120), Expect = 3e-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 = 47.5 bits (113), Expect = 4e-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 = 49.4 bits (118), Expect = 7e-09
 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 = 46.0 bits (109), Expect = 1e-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 = 49.5 bits (118), Expect = 8e-09
 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 = 47.9 bits (114), Expect = 3e-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 = 48.1 bits (115), Expect = 1e-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

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 2e-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 = 43.8 bits (103), Expect = 8e-07
 Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 48  QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDND 105
            + +  I++P+ + G VIGK G  I++++E     + +          ++ + I+  D  
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPY 64

Query: 106 NVVSDAENALQQIAALI 122
            V    + A + +  LI
Sbjct: 65  KV----QQAKEMVLELI 77

>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 = 48.3 bits (115), Expect = 2e-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 = 45.2 bits (107), Expect = 3e-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

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.0 bits (114), Expect = 2e-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 = 43.3 bits (102), Expect = 9e-07
 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

>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 = 47.8 bits (114), Expect = 3e-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 = 35.5 bits (82), Expect = 6e-04
 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 = 46.6 bits (111), Expect = 8e-08
 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 = 39.7 bits (93), Expect = 3e-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

>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 = 46.3 bits (110), Expect = 1e-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 = 41.0 bits (96), Expect = 1e-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

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 2e-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 = 40.2 bits (94), Expect = 2e-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

>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 = 44.8 bits (106), Expect = 4e-07
 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 = 41.6 bits (98), Expect = 6e-06
 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 = 40.5 bits (95), Expect = 1e-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 = 39.0 bits (91), Expect = 4e-05
 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 = 38.9 bits (91), Expect = 7e-05
 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 = 37.9 bits (88), Expect = 1e-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 = 37.9 bits (88), Expect = 1e-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 = 37.0 bits (86), Expect = 3e-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	292
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.58
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.58
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.58
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.57
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.57
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.56
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.56
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.56
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.56
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.53
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.51
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.5
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.5
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.49
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.49
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.43
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.42
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.42
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.31
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.24
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.23
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.16
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.1
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.09
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.09
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.89
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.87
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.83
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.79
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.79
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.75
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.74
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.56
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.51
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.24
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.23
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.93
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.9
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.74
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.39
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.2
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.08
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.5
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	89.4
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	88.75
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	83.28
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	80.4
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	80.14

>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=99.58  E-value=9.6e-16  Score=107.85  Aligned_cols=69  Identities=35%  Similarity=0.613  Sum_probs=62.9

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      .++++++||..++|+|||++|++|++|+++|||+|++++. .        ..+|+|+|+|++++|.+|..+|.++|+|
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-N--------CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-C--------CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-C--------CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            4689999999999999999999999999999999998642 1        4589999999999999999999999875

>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=99.58  E-value=5.2e-16  Score=109.26  Aligned_cols=70  Identities=26%  Similarity=0.511  Sum_probs=63.2

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ..++++|+||.+.+|+||||+|++|++|+++|||+|++++.  +.++|+|+|+|++     +++.+|..+|.+++.+
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--NCPERIITLAGPT-----NAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECH-----HHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC--CCCcceEEEEECH-----HHHHHHHHHHHHHhcC
Confidence            46899999999999999999999999999999999999875  5678999999985     4799999999998764

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=1.2e-15  Score=110.15  Aligned_cols=76  Identities=24%  Similarity=0.415  Sum_probs=67.5

Q ss_pred             CcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       140 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      .+..+.+|.||..++|+|||++|++|++|+++|||+|.|.+.+..+.     +.+|.|+|+|++++|.+|..+|.++|.+
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            35678999999999999999999999999999999999975443333     5789999999999999999999999977


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      .
T Consensus        80 ~   80 (81)
T d1x4ma1          80 Q   80 (81)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.57  E-value=1.7e-15  Score=107.67  Aligned_cols=72  Identities=29%  Similarity=0.525  Sum_probs=65.6

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|++.+..+++.+|+|+|+|++     +++.+|..+|.+++.+
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~-----~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ-----DQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECH-----HHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHHHh
Confidence            35789999999999999999999999999999999999987778889999999985     4799999999998865

>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=99.57  E-value=8.6e-16  Score=107.80  Aligned_cols=69  Identities=28%  Similarity=0.448  Sum_probs=63.0

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      +.+.+|+||.+++|+||||+|++|++|+++|||+|+|++..+++++|+|+|+|++     +++.+|..+|.++|
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 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA-----ASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCH-----HHHHHHHHHHHHHc
Confidence            4688999999999999999999999999999999999987778889999999985     47899999888765

>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=99.57  E-value=2.6e-15  Score=106.43  Aligned_cols=70  Identities=20%  Similarity=0.343  Sum_probs=61.9

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      .+++.||.+++|+|||++|++|++|+++|||+|++.+.++...    .+.+|.|+|+|++++|.+|+.+|.++|
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            5799999999999999999999999999999999976443221    267899999999999999999999876

>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=99.56  E-value=2.1e-15  Score=105.73  Aligned_cols=68  Identities=37%  Similarity=0.513  Sum_probs=61.2

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      .+.+|.||.+++|+|||++|.+|++|+++|||+|.+.+..  +.     +.+|.|+|+|++++|.+|+.+|.++|
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--EG-----SSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC--TT-----CSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC--CC-----CCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            4789999999999999999999999999999999996432  22     57899999999999999999999876

>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=99.56  E-value=3e-15  Score=105.23  Aligned_cols=70  Identities=20%  Similarity=0.360  Sum_probs=60.8

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      .++|.||..++|+|||++|++|++|+++|||+|++.+... +..   .+.+|.|+|+|++++|.+|..+|.++|
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            4789999999999999999999999999999999975432 221   257899999999999999999998874

>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=99.56  E-value=2.2e-15  Score=106.79  Aligned_cols=71  Identities=27%  Similarity=0.398  Sum_probs=63.9

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      ...+++.||.+++|+|||++|++|++|+++|||+|++...+.  .     +.+|.|+|+|++++|.+|..+|.++|++
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--T-----TPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT--S-----CSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC--C-----CCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999999975432  1     5689999999999999999999999876

>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=99.56  E-value=1.1e-15  Score=108.50  Aligned_cols=71  Identities=24%  Similarity=0.409  Sum_probs=64.7

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      .+.++|.||.+++|+||||+|++|++|+++|||+|+|+...++..+|+|+|+|++     +++.+|..+|.+++..
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 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPP-----DRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECH-----HHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCH-----HHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999999987777889999999985     4789999999988764

>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=99.55  E-value=5.2e-15  Score=105.11  Aligned_cols=72  Identities=32%  Similarity=0.475  Sum_probs=64.1

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+.++.||..++|+|||++|++|++|+++|||+|.+.+.+  +.     +.+|.|+|+|++++|.+|+.+|.+++++.
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~--~~-----~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL--EG-----SEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT--SC-----SSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC--CC-----CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            45789999999999999999999999999999999996432  22     57899999999999999999999999863

>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=99.53  E-value=7.6e-15  Score=105.82  Aligned_cols=75  Identities=19%  Similarity=0.367  Sum_probs=66.1

Q ss_pred             CCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC--CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        46 ~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~--~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      .+..++.+|+||..++|+||||+|++|++|+++|||+|+|++.  .+...+|+|+|+|+++     ++.+|..+|.+++.
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            3568999999999999999999999999999999999999853  3456789999999976     58999999999986


Q ss_pred             cC
Q 022746          124 KD  125 (292)
Q Consensus       124 ~~  125 (292)
                      +.
T Consensus        79 e~   80 (81)
T d1x4ma1          79 DQ   80 (81)
T ss_dssp             CC
T ss_pred             hc
Confidence            53

>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=99.51  E-value=7.5e-15  Score=105.34  Aligned_cols=73  Identities=22%  Similarity=0.369  Sum_probs=66.8

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ...++.+|+||.+.+|+|||++|++|++|+++|||+|+|++..+++.++.|+|+|++     .++..|..+|.+++.+
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTP-----ESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHHHc
Confidence            347899999999999999999999999999999999999987778889999999986     4789999999999875

>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=99.50  E-value=9.3e-15  Score=103.52  Aligned_cols=68  Identities=24%  Similarity=0.410  Sum_probs=60.0

Q ss_pred             eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC---CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      .+++|+||.+++|+||||+|++|++|+++|||+|+|.+.   .++..+|+|+|+|++     .++.+|..+|.+++
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSP-----AATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESH-----HHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHc
Confidence            468999999999999999999999999999999999853   356679999999985     47899999888765

>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=99.50  E-value=1.9e-14  Score=103.25  Aligned_cols=73  Identities=19%  Similarity=0.300  Sum_probs=65.3

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+.+|.||..++|+|||++|.+|++|+++|||+|.+.+.+.  .     +.++.|+|+|++++|.+|..+|.++|.+.
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~--~-----~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG--G-----LPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT--T-----CSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCC--C-----CCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4568999999999999999999999999999999999965322  2     57899999999999999999999999875

>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=99.49  E-value=8.7e-15  Score=102.83  Aligned_cols=67  Identities=28%  Similarity=0.430  Sum_probs=58.0

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC---CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      .++|+||++++|+||||+|++|++|+++|||+|+|+..   .++..+|+|+|+|++     +++.+|..+|.+++
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 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTP-----QQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCH-----HHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCH-----HHHHHHHHHHHhhC
Confidence            36899999999999999999999999999999999743   335678999999985     47899998888763

>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=99.49  E-value=2.7e-14  Score=107.80  Aligned_cols=75  Identities=25%  Similarity=0.303  Sum_probs=65.8

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..++.+|.||..++|+|||++|.+|++|+++|||+|.|.+.+....     ..+|.|+|+|++++|.+|..+|.++|.+.
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 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-----LLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSS-----SSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCC-----CCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            4567899999999999999999999999999999999965433221     46899999999999999999999999765

>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=99.45  E-value=7.9e-14  Score=100.37  Aligned_cols=71  Identities=18%  Similarity=0.162  Sum_probs=62.6

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+..+.||..+|++|||++|++|++|+++|||+|.+++.++        .+.+.|+|+|++++|.+|..+|.+++++.
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            457899999999999999999999999999999999864322        24578999999999999999999998864

>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=99.43  E-value=1.7e-13  Score=99.31  Aligned_cols=73  Identities=15%  Similarity=0.118  Sum_probs=63.9

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+.++.||..++++|||++|++|++|+++|||+|.+++.+. +.     ..++.|+|+|+.++|.+|..+|.+++.+.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-~~-----~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-GN-----QPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-CS-----SCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-CC-----CCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            457899999999999999999999999999999999854322 22     57889999999999999999999998763

>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=99.42  E-value=1e-13  Score=104.52  Aligned_cols=77  Identities=25%  Similarity=0.375  Sum_probs=65.9

Q ss_pred             cCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC--CCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746           44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (292)
Q Consensus        44 ~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~--~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~  121 (292)
                      -+.+..++.+|+||..++|+||||+|.+|++|+++|||+|+|++..  ....+|+|+|+|++     .++.+|..+|.++
T Consensus         9 ~~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~~   83 (104)
T d1we8a_           9 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQ-----KEVAAAKHLILEK   83 (104)
T ss_dssp             CSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEH-----HHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCH-----HHHHHHHHHHHHH
Confidence            3445578899999999999999999999999999999999998653  23467999999985     4799999999999


Q ss_pred             HhcC
Q 022746          122 ILKD  125 (292)
Q Consensus       122 i~~~  125 (292)
                      +.+.
T Consensus        84 i~e~   87 (104)
T d1we8a_          84 VSED   87 (104)
T ss_dssp             HHHH
T ss_pred             HhCc
Confidence            8664

>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=99.42  E-value=9.4e-14  Score=99.95  Aligned_cols=71  Identities=18%  Similarity=0.295  Sum_probs=63.8

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ...+.++.||..++|+|||++|.+|++|+++|||+|.+++.+         +.++.|+|+|++++|.+|..+|.+++.+.
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~---------~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD---------DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT---------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC---------CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            346899999999999999999999999999999999985432         46789999999999999999999999874

>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=99.39  E-value=1.9e-13  Score=99.03  Aligned_cols=72  Identities=22%  Similarity=0.329  Sum_probs=63.1

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      .+++.|.||..++++|||++|++|++|+++|||+|+|++. .++..++.|+|+|+.+     +|..|..+|.+++.+.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e-----~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK-----NTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHH-----HHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHH-----HHHHHHHHHHHHHHhH
Confidence            5789999999999999999999999999999999999754 4566788999999854     7889999998888653

>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=99.38  E-value=2e-13  Score=95.67  Aligned_cols=67  Identities=24%  Similarity=0.342  Sum_probs=59.8

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  217 (292)
                      ....++.||..++++|||++|++|++|+++|||+|.+++.+         +.++.|+|+|++++|.+|..+|.++.
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~---------~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS---------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC---------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC---------CCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            34789999999999999999999999999999999985422         46789999999999999999998764

>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=99.37  E-value=1.6e-13  Score=98.68  Aligned_cols=73  Identities=19%  Similarity=0.310  Sum_probs=64.0

Q ss_pred             CCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        46 ~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      .+..++..|.||.+++|+|||++|++|++|+++|||+|+|+..  +..++.|+|+|+++     ++.+|..+|.+++.+.
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~-----~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKE-----GIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHH-----HHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC--CCCCCEEEEEeCHH-----HHHHHHHHHHHHHHHH
Confidence            3456889999999999999999999999999999999999864  45678999999864     7899999999988663

>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=99.37  E-value=3e-13  Score=97.47  Aligned_cols=70  Identities=20%  Similarity=0.255  Sum_probs=62.1

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHh-hCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNS-SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      ..+.++.||..+||+|||++|++|++|+++ ++++|.+++.+         +.++.|+|+|++++|.+|..+|.+++.+.
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~---------~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG---------SGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT---------TTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC---------CCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            457899999999999999999999999987 59999975322         46789999999999999999999999875

>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=99.34  E-value=5.7e-13  Score=97.92  Aligned_cols=70  Identities=20%  Similarity=0.262  Sum_probs=63.0

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      .++..+.||..+|+.|||++|.+|++|+++|||+|.+++.+         +.++.|+|+|++++|.+|..+|.+++.+.
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 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE---------LQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT---------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC---------CCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            56899999999999999999999999999999999985432         45779999999999999999999998763

>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=99.33  E-value=5.1e-13  Score=96.02  Aligned_cols=73  Identities=23%  Similarity=0.322  Sum_probs=62.2

Q ss_pred             CCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        46 ~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      .++.++..+.||..++++|||++|++|++|+++|||+|+|+.... ...+.|+|+|+++     +|.+|..+|.+++.+
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-~~~~~v~I~G~~~-----~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           6 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPE-----NVEEAIDHILNLEEE   78 (81)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHH-----HHHHHHHHHHHHHHH
T ss_pred             hhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-CCCCEEEEeCCHH-----HHHHHHHHHHHHHHH
Confidence            345677899999999999999999999999999999999986532 2346899999864     789999999988765

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=9.3e-13  Score=92.20  Aligned_cols=67  Identities=19%  Similarity=0.357  Sum_probs=58.7

Q ss_pred             CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (292)
Q Consensus        48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~  121 (292)
                      ....++|.||..++++|||++|++|++|+++|||+|+|++.  +.+++.|+|+|+++     ++.+|..+|.++
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~--~~~~~~v~I~G~~~-----~v~~A~~~I~~i   69 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQ-----GVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSH-----HHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC--CCCCCEEEEECCHH-----HHHHHHHHHHHH
Confidence            35678999999999999999999999999999999999864  45678999999864     788888888775

>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=99.31  E-value=4.4e-13  Score=96.58  Aligned_cols=74  Identities=22%  Similarity=0.305  Sum_probs=63.7

Q ss_pred             CCCCCeEEEEEeeCCccceeecCCCchhhhhhhh-cCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE-TKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (292)
Q Consensus        45 ~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~  123 (292)
                      ..++.++..|.||..++|+||||+|++|++|+++ ++|+|+++..  +..++.|+|+|+++     +|.+|..+|.+++.
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            3456788999999999999999999999999987 5999999864  45678999999864     78999999999887


Q ss_pred             cC
Q 022746          124 KD  125 (292)
Q Consensus       124 ~~  125 (292)
                      +.
T Consensus        78 e~   79 (82)
T d2ctja1          78 EK   79 (82)
T ss_dssp             HH
T ss_pred             hh
Confidence            64

>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=99.24  E-value=5.5e-12  Score=90.90  Aligned_cols=64  Identities=22%  Similarity=0.186  Sum_probs=58.2

Q ss_pred             EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  221 (292)
                      .-+.||.+.+|.|||++|++|+.|+++|||+|.+.             .++.|+|+|+++++..|..+|..++++..
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 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVG-------------QNGLIWVNGDRRKVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEEC-------------TTSEEEEESCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEEC-------------CCCEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            35789999999999999999999999999999983             24689999999999999999999988864

>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=99.24  E-value=1.7e-12  Score=95.22  Aligned_cols=70  Identities=20%  Similarity=0.294  Sum_probs=62.2

Q ss_pred             CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      .++..|.||..++|+|||++|.+|++|+++|||+|.|+..  +..++.|+|+|++     .+|.+|..+|.+++.+.
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--ELQSDIIAITGLA-----ANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECH-----HHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC--CCCcceEEEECCH-----HHHHHHHHHHHHHHHHH
Confidence            6889999999999999999999999999999999999864  4567899999985     47899999999888654

>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=99.23  E-value=9e-12  Score=91.08  Aligned_cols=68  Identities=18%  Similarity=0.230  Sum_probs=60.7

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  219 (292)
                      ...+..+.||..+|++|||++|++|++|++++ |++|.+.            ..+..|+|+|++++|.+|..+|.+++.+
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 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFT------------EGEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEEC------------SSSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeC------------CCCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            35689999999999999999999999999995 8999984            2357899999999999999999999876


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      .
T Consensus        87 l   87 (90)
T d2ctfa1          87 L   87 (90)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.16  E-value=1.1e-11  Score=88.04  Aligned_cols=63  Identities=29%  Similarity=0.336  Sum_probs=55.7

Q ss_pred             cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHH
Q 022746          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIG  214 (292)
Q Consensus       141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~  214 (292)
                      ...+.+|.||.+++|+|||++|++|++|+++|||+|.+..           ..++.|+|.| +++++.+|+.+|.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~-----------~~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD-----------EDTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE-----------TTTTEEEEEESSHHHHHHHHHHHS
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec-----------CCCceEEEEECCHHHHHHHHHHHH
Confidence            3457899999999999999999999999999999998753           2457899999 6999999999994

>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=99.10  E-value=1.7e-11  Score=88.28  Aligned_cols=64  Identities=17%  Similarity=0.280  Sum_probs=55.3

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~  126 (292)
                      .-+.||.+.+|+|||++|++|++|+++|||+|+|.+.      ..|+|+|+++     ++.+|..+|..++.+..
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 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN------GLIWVNGDRR-----KVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTT------SEEEEESCHH-----HHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCC------CEEEEEeCHH-----HHHHHHHHHHHHHHhcc
Confidence            3578999999999999999999999999999999753      5799999864     78899999988876643

>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=99.09  E-value=2.9e-11  Score=85.84  Aligned_cols=64  Identities=20%  Similarity=0.226  Sum_probs=53.3

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I  118 (292)
                      ...++..|.||.+++|+|||++|++|++|+++|||+|.+.+.    +++.|+|.|...    .++.+|..+|
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~----eav~~A~~~I   68 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESA----DAVKKARGFL   68 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSH----HHHHHHHHHH
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCH----HHHHHHHHHH
Confidence            456788999999999999999999999999999999998754    457899999532    3567776665

>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=99.09  E-value=6e-11  Score=86.60  Aligned_cols=68  Identities=24%  Similarity=0.363  Sum_probs=58.7

Q ss_pred             CCCeEEEEEeeCCccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ++.++..+.||..++++|||++|++|++|++++ +|+|++++.     +..|+|+|+++     +|.+|..+|.+++.+
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~-----~~~v~i~G~~~-----~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG-----EDKITLEGPTE-----DVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS-----SCEEEEEECHH-----HHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC-----CceEEEeCCHH-----HHHHHHHHHHHHHHH
Confidence            346899999999999999999999999999995 899999853     46799999864     688888888887765

>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=98.89  E-value=1e-09  Score=78.62  Aligned_cols=66  Identities=18%  Similarity=0.299  Sum_probs=48.6

Q ss_pred             EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (292)
Q Consensus        52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i  122 (292)
                      +.+.||.+.+|.||||+|++|++|+++|||+|+|.+.     +..+.+.+......-.++.+|...|.++.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d-----~g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----TTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC-----CCeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            3578999999999999999999999999999999743     24566666543322234555666665553

>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=98.87  E-value=4.9e-11  Score=82.61  Aligned_cols=62  Identities=16%  Similarity=0.102  Sum_probs=47.8

Q ss_pred             EEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022746          146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (292)
Q Consensus       146 ~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  220 (292)
                      -+.||.+.+|.|||++|++|+.|+++|||+|.+.             .+..|+|.|. .+++..|..+|..+.++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~-------------~~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA-------------NNGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEEC-------------TTSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEc-------------CCCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            5789999999999999999999999999999983             2457999996 678999999998776654

>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=98.83  E-value=7e-11  Score=81.80  Aligned_cols=59  Identities=17%  Similarity=0.225  Sum_probs=40.9

Q ss_pred             EEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (292)
Q Consensus        53 rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~  121 (292)
                      -+.||.+.+|+||||+|++|++|+++|||+|++.+.      ..|+|+|....    ++..|..+|..+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~------g~v~I~g~~~~----~v~~A~~~I~~i   62 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRF----SEEILIEAIRKI   62 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT------SEEEC-----C----TTCCTHHHHTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC------CEEEEEeCCHH----HHHHHHHHHHHH
Confidence            467899999999999999999999999999999753      46899996432    355666666544

>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=98.79  E-value=3.7e-09  Score=75.57  Aligned_cols=64  Identities=14%  Similarity=0.174  Sum_probs=52.7

Q ss_pred             EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEE-----cCHHHHHHHHHHHHHHHhc
Q 022746          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GDVPAVLNALVEIGNQLRE  219 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~l~~  219 (292)
                      +.+.||.+.+|.|||++|++||+|+++|||+|+|..            ++..|.+.     |.+.++.+|..+|.++.+.
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 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT------------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLG   72 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET------------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEc------------CCCeEEEecCCccccHHHHHHHHHHHHHHhCC
Confidence            568999999999999999999999999999999953            23444444     5688999999999887654


Q ss_pred             C
Q 022746          220 N  220 (292)
Q Consensus       220 ~  220 (292)
                      .
T Consensus        73 f   73 (84)
T d1tuaa1          73 F   73 (84)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=98.79  E-value=4.6e-09  Score=75.38  Aligned_cols=63  Identities=13%  Similarity=0.090  Sum_probs=55.5

Q ss_pred             EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022746          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  220 (292)
                      .-+.||.+.++.|||++|++|+.|+++|||+|.+.             .+..|.|.|. .+.+..|..+|..+.++.
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~-------------d~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA-------------RNGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEE-------------TTTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEEC-------------CCcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999999994             2457999995 788899999999887776

>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=98.75  E-value=3.2e-10  Score=74.16  Aligned_cols=48  Identities=35%  Similarity=0.626  Sum_probs=16.1

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCC
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN  104 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~  104 (292)
                      ...|.||.+.+|.|||++|++||.|+++|||+|++.+      +..|+|.|...
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            3578899999999999999999999999999999985      46788888654

>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=98.74  E-value=5e-09  Score=75.18  Aligned_cols=63  Identities=16%  Similarity=0.228  Sum_probs=51.6

Q ss_pred             EEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (292)
Q Consensus        53 rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~  125 (292)
                      -+.||.+.+|.|||++|++|+.|+++|||+|.|.+.      ..|.|.|...    ..+..|..+|..+..+.
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            467899999999999999999999999999999864      3699999754    35667777777665543

>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=98.56  E-value=1.8e-09  Score=70.46  Aligned_cols=46  Identities=28%  Similarity=0.408  Sum_probs=14.0

Q ss_pred             EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC
Q 022746          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD  202 (292)
Q Consensus       144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~  202 (292)
                      ...+.||.+.+|.|||++|.+||.|+++|||+|.+.             ++..|+|.|.
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             3466666664

>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=98.51  E-value=4.3e-08  Score=72.56  Aligned_cols=53  Identities=21%  Similarity=0.242  Sum_probs=47.2

Q ss_pred             ceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746          154 AGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (292)
Q Consensus       154 vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  220 (292)
                      .|+|||++|++|+.|++.|||.|.|.              +..|.|.|+++++..|..+|..++.+.
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~--------------d~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVG--------------EYEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEEC--------------SSEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEe--------------CCeEEEEECchhHHHHHHHHHHHHcCC
Confidence            58999999999999999999999983              235778899999999999999999764

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=1.8e-06  Score=65.60  Aligned_cols=73  Identities=21%  Similarity=0.408  Sum_probs=56.5

Q ss_pred             CeEEEEEeeCCc------cceeecCCCchhhhhhhhcCcEEEEccCC---------CC-------CCceEEEEecCCCCc
Q 022746           49 DVLFRIIVPSRQ------IGKVIGKEGHRIQKIREETKATIKIADAI---------AR-------HEERVIIISSKDNDN  106 (292)
Q Consensus        49 ~~~~rilvp~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~---------~~-------~~ervv~I~G~~~~~  106 (292)
                      .++-|++||.+.      +|.|||++|+++|+|+++|||+|.|--..         .+       ...--|.|++...  
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~--   79 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTM--   79 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSH--
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCCh--
Confidence            467899999875      99999999999999999999999997210         00       1123577888653  


Q ss_pred             chhHHHHHHHHHHHHHhcC
Q 022746          107 VVSDAENALQQIAALILKD  125 (292)
Q Consensus       107 ~v~~v~~A~~~I~~~i~~~  125 (292)
                        ..+..|+.+|..++...
T Consensus        80 --~~~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          80 --ENVKKAVEQIRNILKQG   96 (122)
T ss_dssp             --HHHHHHHHHHHHHHTTT
T ss_pred             --hhHHHHHHHHHHHHHhc
Confidence              57889999999998653

>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=98.23  E-value=2e-07  Score=68.89  Aligned_cols=53  Identities=26%  Similarity=0.303  Sum_probs=43.6

Q ss_pred             ccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746           60 QIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (292)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~  124 (292)
                      ..|+|||++|.+|+.|++.|||+|.|.+.       .+.|.|.+     .++..|..+|..++.+
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            47899999999999999999999999753       35666764     4688888888888864

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.93  E-value=1.8e-05  Score=59.85  Aligned_cols=77  Identities=18%  Similarity=0.334  Sum_probs=57.0

Q ss_pred             cEEEEEeccC------cceeeecCCChhHHHHHHhhCCeEEEeCCCCC-------C---cccCCCCCCcEEEEEcC-HHH
Q 022746          143 NTIRLLIAGS------QAGCLIGMSGQNIEKLRNSSGATIVILAPNQL-------P---LCASAHESDRVVQISGD-VPA  205 (292)
Q Consensus       143 ~~~~i~IP~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-------p---~~~~~~~~~r~v~I~G~-~~~  205 (292)
                      .+.+++||.+      ++|.|||++|.++|+|+++|||+|.|.-....       +   .... ....--|.|+++ .+.
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            3678888865      58999999999999999999999999643210       0   0000 023346778875 569


Q ss_pred             HHHHHHHHHHHHhcC
Q 022746          206 VLNALVEIGNQLREN  220 (292)
Q Consensus       206 v~~A~~~I~~~l~~~  220 (292)
                      +..|+.+|..+|...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999764

>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=97.90  E-value=9.1e-06  Score=62.37  Aligned_cols=76  Identities=18%  Similarity=0.392  Sum_probs=54.6

Q ss_pred             eEEEEEeeCC------ccceeecCCCchhhhhhhhcCcEEEEccCCC------------------CCCceEEEEecCCCC
Q 022746           50 VLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIADAIA------------------RHEERVIIISSKDND  105 (292)
Q Consensus        50 ~~~rilvp~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~------------------~~~ervv~I~G~~~~  105 (292)
                      +.-|++||.+      ++|.|||++|.++|+|+++|||+|.|--...                  ..++--|.|++....
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            5678888864      6899999999999999999999999983210                  012345788886432


Q ss_pred             c-chhHHHHHHHHHHHHHhcC
Q 022746          106 N-VVSDAENALQQIAALILKD  125 (292)
Q Consensus       106 ~-~v~~v~~A~~~I~~~i~~~  125 (292)
                      . ....+.+|+..|..++...
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 1234678888888887653

>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=97.74  E-value=1.6e-05  Score=61.02  Aligned_cols=76  Identities=17%  Similarity=0.224  Sum_probs=55.5

Q ss_pred             EEEEEecc------CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCC------------cccCCCCCCcEEEEEcCH--
Q 022746          144 TIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP------------LCASAHESDRVVQISGDV--  203 (292)
Q Consensus       144 ~~~i~IP~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p------------~~~~~~~~~r~v~I~G~~--  203 (292)
                      ..+++||.      +++|+|||++|.++|+|+++|||+|.|--....-            .... -..+=-|.|+++.  
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            45778883      5889999999999999999999999997543210            0000 0245668888863  


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 022746          204 ----PAVLNALVEIGNQLREN  220 (292)
Q Consensus       204 ----~~v~~A~~~I~~~l~~~  220 (292)
                          ..+.+|+.+|..+|...
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                35888999999998654

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.39  E-value=0.0034  Score=41.87  Aligned_cols=37  Identities=30%  Similarity=0.399  Sum_probs=34.6

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEcc
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~   87 (292)
                      .+.+.||.+..+.-|||+|.|++-..+-||.+|.|..
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            5788999999999999999999999999999999974

>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=95.20  E-value=0.0038  Score=41.45  Aligned_cols=38  Identities=32%  Similarity=0.398  Sum_probs=35.1

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~   88 (292)
                      .+.+.||.+..+..|||+|.|++-..+-||.+|.|...
T Consensus        27 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          27 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             EEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            57889999999999999999999999999999999743

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.08  E-value=0.0088  Score=39.74  Aligned_cols=39  Identities=28%  Similarity=0.309  Sum_probs=35.7

Q ss_pred             cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (292)
Q Consensus       143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  181 (292)
                      ..+.+.||.++.+..|||+|.+++-..+-||.+|.|...
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            368899999999999999999999999999999999653

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.50  E-value=0.013  Score=38.81  Aligned_cols=39  Identities=28%  Similarity=0.299  Sum_probs=35.7

Q ss_pred             ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (292)
Q Consensus       142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  180 (292)
                      ...+.+.||.++.+..|||+|.+++-..+-||.+|.|..
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            347889999999999999999999999999999999974

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=89.40  E-value=0.24  Score=33.92  Aligned_cols=63  Identities=11%  Similarity=0.029  Sum_probs=47.5

Q ss_pred             EEEEeccCcceeeecCCCh-hHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022746          145 IRLLIAGSQAGCLIGMSGQ-NIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (292)
Q Consensus       145 ~~i~IP~~~vg~IIGk~G~-~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  220 (292)
                      +-+.||-.++.+++|++++ .++.|.+.+++.|.|-             .+..|-|.|. .+....+...|.++-++.
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG-------------~NGrIWi~~~~~~~~i~i~~aI~~~e~~~   67 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG-------------LNGKIWVKCEELSNTLACYRTIMECCQKN   67 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE-------------TTTEEEEECSSHHHHHHHHHHHHHHHHHC
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe-------------cCcEEEEECCCHHHHHHHHHHHHHHHHhC
Confidence            3567888999999999998 7899999999999983             3467778885 566655555565554443

>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=88.75  E-value=0.052  Score=38.02  Aligned_cols=31  Identities=23%  Similarity=0.453  Sum_probs=26.8

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKA   81 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga   81 (292)
                      .+++.|....-|.|||++|+.|++|++...-
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            3778889999999999999999999877543

>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=83.28  E-value=0.12  Score=37.02  Aligned_cols=29  Identities=38%  Similarity=0.556  Sum_probs=25.6

Q ss_pred             EEEEEeeCCccceeecCCCchhhhhhhhc
Q 022746           51 LFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (292)
Q Consensus        51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~t   79 (292)
                      .+++.|....-|.|||++|+.|++|+++.
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            37788888999999999999999998864

>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=80.40  E-value=0.22  Score=34.64  Aligned_cols=28  Identities=7%  Similarity=-0.164  Sum_probs=24.7

Q ss_pred             EEEEEeccCccceeeecCCCccHHHHHHh
Q 022746          252 MFLMQNTRYFVTAIFAVLSSFNIFFLITT  280 (292)
Q Consensus       252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~  280 (292)
                      .++|.|-...-|.|||+ +|++|++|++.
T Consensus        36 ~i~I~I~tarPGivIGr-kG~~I~~L~~~   63 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGE-KGRRIRELTAV   63 (92)
T ss_dssp             CEEEEEEESCHHHHHCG-GGHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeecc-CchhHHHHHHH
Confidence            45778888999999999 99999999875

>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=80.14  E-value=0.88  Score=30.92  Aligned_cols=45  Identities=13%  Similarity=0.096  Sum_probs=38.2

Q ss_pred             EEEeeCCccceeecCCCc-hhhhhhhhcCcEEEEccCCCCCCceEEEEecCC
Q 022746           53 RIIVPSRQIGKVIGKEGH-RIQKIREETKATIKIADAIARHEERVIIISSKD  103 (292)
Q Consensus        53 rilvp~~~vg~IIGk~G~-~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~  103 (292)
                      -+-||..++..|||++++ -++.|.+.++|.|-|-.+      ..|-|.|..
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N------GrIWi~~~~   49 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN------GKIWVKCEE   49 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT------TEEEEECSS
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC------cEEEEECCC
Confidence            356888899999999998 689999999999999865      458888864