Psyllid ID: psy11065

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
Protein Sequence
MCSIEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLRSTVLANRS
Secondary Structure (PSIPRED)
cccHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEEEEccccEEEEEEcccHHHHHHHHHcccEEEEEccccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEEEEEcccccEEEEEccccHHHHHHHHHcccEEEEEccccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccc
Coil and Loop (DISEMBL)
mcsiefqqsrrwqqgigrnndnfgnmrefnengdgrggmWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQmreddpsdrrcmlsgspDQVQEARARIEELIDSVMVEqfsganfdKLRSTVLANRS
Flexible Loop (DISEMBL)
mcsiefqqsrrwqqgigrnndnfgnMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMReddpsdrrcmlsgspdQVQEARARIEELIDSVMVeqfsganfdklrstvlanrs
Low Complexity Region (SEG)
MCSIEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCvpkaavgvvigkggDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLRSTVLANRS
Disordered region (IsUnstruct)
**********************************GRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKL*****************************************LIDSVMVEQF*****************
Disordered Region (DISOPRED)
**SI********************************************VCVPKAAVGVVIGKGGDMIKKLQNETGA***************RCMLSGSPDQVQEARARIEE***************************
Disordered Region (DISEMBL)
**********RWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLRSTVLANRS
Disordered Region (DISPRO)
MCSIEFQQSRRWQQGIGRNNDN*********************WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQF*****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MCSIEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLRSTVLANRS
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	138	2.2.26 [Sep-21-2011]
Q91WJ8	651	Far upstream element-bind	yes	N/A	0.724	0.153	0.392	2e-10
Q32PX7	639	Far upstream element-bind	yes	N/A	0.615	0.133	0.437	3e-10
Q96AE4	644	Far upstream element-bind	yes	N/A	0.724	0.155	0.383	1e-09
Q96I24	572	Far upstream element-bind	no	N/A	0.463	0.111	0.478	1e-09
Q92945	711	Far upstream element-bind	no	N/A	0.5	0.097	0.428	2e-08
Q3U0V1	748	Far upstream element-bind	no	N/A	0.5	0.092	0.428	2e-08
Q99PF5	721	Far upstream element-bind	no	N/A	0.731	0.140	0.372	3e-08
Q8UVD9	769	Far upstream element-bind	no	N/A	0.731	0.131	0.363	9e-08
O19049	463	Heterogeneous nuclear rib	no	N/A	0.623	0.185	0.340	9e-07
Q9UNW9	492	RNA-binding protein Nova-	no	N/A	0.528	0.148	0.346	3e-06

>sp|Q91WJ8|FUBP1_MOUSE Far upstream element-binding protein 1 OS=Mus musculus GN=Fubp1 PE=1 SV=1

 Score = 63.9 bits (154), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/112 (39%), Positives = 64/112 (57%), Gaps = 12/112 (10%)

Query: 7   QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDM 66
           QQ++     + R+   F  +R  NE G   GG      E I V +P+ AVG+VIG+ G+M
Sbjct: 241 QQAKEMVLELIRDQGGFREVR--NEYGSRIGGN-----EGIDVPIPRFAVGIVIGRNGEM 293

Query: 67  IKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSV 116
           IKK+QN+ G R+QF   + DD +  DR   ++G PD+ Q A   I +L+ SV
Sbjct: 294 IKKIQNDAGVRIQF---KPDDGTTPDRIAQITGPPDRCQHAAEIITDLLRSV 342

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.
Mus musculus (taxid: 10090)

>sp|Q32PX7|FUBP1_RAT Far upstream element-binding protein 1 OS=Rattus norvegicus GN=Fubp1 PE=1 SV=1

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 42/96 (43%), Positives = 56/96 (58%), Gaps = 11/96 (11%)

Query: 24  GNMREF-NENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82
           G  RE  NE G   GG      E I V +P+ AVG+VIG+ G+MIKK+QN+ G R+QF  
Sbjct: 254 GGFREVRNEYGSRIGGN-----EGIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQF-- 306

Query: 83  MREDD--PSDRRCMLSGSPDQVQEARARIEELIDSV 116
            + DD    DR   ++G PD+ Q A   I +L+ SV
Sbjct: 307 -KPDDGTTPDRIAQITGPPDRCQHAAEIITDLLRSV 341

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Rattus norvegicus (taxid: 10116)

>sp|Q96AE4|FUBP1_HUMAN Far upstream element-binding protein 1 OS=Homo sapiens GN=FUBP1 PE=1 SV=3

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/112 (38%), Positives = 64/112 (57%), Gaps = 12/112 (10%)

Query: 7   QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDM 66
           QQ++     + R+   F  +R  NE G   GG      E I V +P+ AVG+VIG+ G+M
Sbjct: 245 QQAKEMVLELIRDQGGFREVR--NEYGSRIGGN-----EGIDVPIPRFAVGIVIGRNGEM 297

Query: 67  IKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSV 116
           IKK+QN+ G R+QF   + DD +  +R   ++G PD+ Q A   I +L+ SV
Sbjct: 298 IKKIQNDAGVRIQF---KPDDGTTPERIAQITGPPDRCQHAAEIITDLLRSV 346

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Homo sapiens (taxid: 9606)

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

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 45/69 (65%), Gaps = 5/69 (7%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD--PSDRRCMLSGSPDQVQE 104
           I+V VP+ AVG+VIG+ G+MIKK+QN+ G R+QF   + DD    +R   + G PD+ Q 
Sbjct: 256 IEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQF---KPDDGISPERAAQVMGPPDRCQH 312

Query: 105 ARARIEELI 113
           A   I ELI
Sbjct: 313 AAHIISELI 321

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

Homo sapiens (taxid: 9606)

>sp|Q92945|FUBP2_HUMAN Far upstream element-binding protein 2 OS=Homo sapiens GN=KHSRP PE=1 SV=4

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           I V VP+ +VGVVIG+ G+MIKK+QN+ G R+QF Q     P ++   + G PD+ + A 
Sbjct: 325 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP-EKIAHIMGPPDRCEHAA 383

Query: 107 ARIEELIDSV 116
             I +L+ S+
Sbjct: 384 RIINDLLQSL 393

Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs.

Homo sapiens (taxid: 9606)

>sp|Q3U0V1|FUBP2_MOUSE Far upstream element-binding protein 2 OS=Mus musculus GN=Khsrp PE=1 SV=2

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           I V VP+ +VGVVIG+ G+MIKK+QN+ G R+QF Q     P ++   + G PD+ + A 
Sbjct: 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP-EKIAHIMGPPDRCEHAA 384

Query: 107 ARIEELIDSV 116
             I +L+ S+
Sbjct: 385 RIINDLLQSL 394

Binds to the dendritic targeting element and may play a role in mRNA trafficking. Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs.

Mus musculus (taxid: 10090)

>sp|Q99PF5|FUBP2_RAT Far upstream element-binding protein 2 OS=Rattus norvegicus GN=Khsrp PE=1 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/110 (37%), Positives = 58/110 (52%), Gaps = 9/110 (8%)

Query: 7   QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDM 66
           QQ+      I R  D  G   + NE G   GG        I V VP+ +VGVVIG+ G+M
Sbjct: 294 QQACEMVMDILRERDQ-GGFGDRNEYGSRVGGG-------IDVPVPRHSVGVVIGRSGEM 345

Query: 67  IKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV 116
           IKK+QN+ G R+QF Q     P ++   + G PD+ + A   I +L+ S+
Sbjct: 346 IKKIQNDAGVRIQFKQDDGTGP-EKIAHIMGPPDRCEHAARIINDLLQSL 394

Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs (By similarity). Binds to the dendritic targeting element and may play a role in mRNA trafficking.

Rattus norvegicus (taxid: 10116)

>sp|Q8UVD9|FUBP2_CHICK Far upstream element-binding protein 2 OS=Gallus gallus GN=KHSRP PE=1 SV=1

 Score = 55.5 bits (132), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 40/110 (36%), Positives = 58/110 (52%), Gaps = 9/110 (8%)

Query: 7   QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDM 66
           QQ+      I R  D  G   + NE G   GG        I V VP+ +VGVVIG+ G+M
Sbjct: 356 QQACEMVMDILRERDQ-GGFGDRNEYGSRIGGG-------IDVPVPRHSVGVVIGRSGEM 407

Query: 67  IKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV 116
           IKK+QN+ G R+QF Q     P ++   + G P++ + A   I +L+ S+
Sbjct: 408 IKKIQNDAGVRIQFKQDDGTGP-EKIAHIMGPPERCEHAARIINDLLQSL 456

Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs. Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Binds to a 54-nucleotide localization signal (the 'zipcode') found in the 3'-UTR of beta-actin mRNA and may play a role in its localization.

Gallus gallus (taxid: 9031)

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

 Score = 52.4 bits (124), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 8/94 (8%)

Query: 35  GRGGMWEVTWEVI--QVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRR 92
           GRG   ++   +I  QV +PK   G +IGKGG  IK++++E+GA ++  +  E    DR 
Sbjct: 376 GRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS-EDRI 434

Query: 93  CMLSGSPDQVQEARARIEELIDSVMVEQFSGANF 126
             ++G+ DQ+Q A+  ++       V+Q+SG  F
Sbjct: 435 ITITGTQDQIQNAQYLLQN-----SVKQYSGKFF 463

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

Oryctolagus cuniculus (taxid: 9986)

>sp|Q9UNW9|NOVA2_HUMAN RNA-binding protein Nova-2 OS=Homo sapiens GN=NOVA2 PE=1 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 41  EVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPS--DRRCMLSGS 98
           E   E++++ VP+  VG ++GKGG  + + Q  TGAR+Q  +  E  P   +RR  ++GS
Sbjct: 403 ESAKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 462

Query: 99  PDQVQEARARIEELI 113
           P   Q A+  I + +
Sbjct: 463 PAATQAAQYLISQRV 477

May regulate RNA splicing or metabolism in a specific subset of developing neurons (By similarity). Binds single strand RNA.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	138
340728851	738	PREDICTED: far upstream element-binding	0.666	0.124	0.572	1e-21
350412234	736	PREDICTED: far upstream element-binding	0.666	0.125	0.572	1e-21
328783034	735	PREDICTED: far upstream element-binding	0.753	0.141	0.539	1e-21
307187117	690	Far upstream element-binding protein 1 [	0.731	0.146	0.525	2e-21
270010095	756	hypothetical protein TcasGA2_TC009450 [T	0.463	0.084	0.739	2e-21
189238744	727	PREDICTED: similar to P-element somatic	0.463	0.088	0.739	2e-21
383858339	736	PREDICTED: far upstream element-binding	0.666	0.125	0.572	2e-21
307211366	751	Far upstream element-binding protein 1 [	0.695	0.127	0.564	4e-21
322790271	744	hypothetical protein SINV_11556 [Solenop	0.615	0.114	0.565	6e-21
332023471	731	Far upstream element-binding protein 1 [	0.739	0.139	0.508	7e-21

>gi|340728851|ref|XP_003402727.1| PREDICTED: far upstream element-binding protein 1-like [Bombus terrestris]

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 59/103 (57%), Positives = 72/103 (69%), Gaps = 11/103 (10%)

Query: 18  RNND---NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74
           R ND   N+ N   FN +G G       T + ++V VP+AAVGVVIGKGGDMIKK+Q ET
Sbjct: 280 RGNDRSGNYSNDSSFN-HGSG-------TTDGVEVLVPRAAVGVVIGKGGDMIKKIQAET 331

Query: 75  GARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           GARVQF Q RED P DR+C++SG    V++ R RI+ELIDSVM
Sbjct: 332 GARVQFQQGREDGPGDRKCIVSGKHQAVEQVRQRIQELIDSVM 374

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350412234|ref|XP_003489579.1| PREDICTED: far upstream element-binding protein 1-like [Bombus impatiens]

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 59/103 (57%), Positives = 72/103 (69%), Gaps = 11/103 (10%)

Query: 18  RNND---NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74
           R ND   N+ N   FN +G G       T + ++V VP+AAVGVVIGKGGDMIKK+Q ET
Sbjct: 280 RGNDRSGNYSNDSSFN-HGSG-------TTDGVEVLVPRAAVGVVIGKGGDMIKKIQAET 331

Query: 75  GARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           GARVQF Q RED P DR+C++SG    V++ R RI+ELIDSVM
Sbjct: 332 GARVQFQQGREDGPGDRKCIVSGKHQAVEQVRQRIQELIDSVM 374

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328783034|ref|XP_624673.3| PREDICTED: far upstream element-binding protein 1-like [Apis mellifera]

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 61/113 (53%), Positives = 76/113 (67%), Gaps = 9/113 (7%)

Query: 5   EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGG 64
           E Q   R  +G  R+  N+ N   FN +G G       T + ++V VP+AAVGVVIGKGG
Sbjct: 270 EMQMFHRGSRGSDRSG-NYSNDSNFN-HGSG-------TTDGVEVLVPRAAVGVVIGKGG 320

Query: 65  DMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           DMIKK+Q ETGARVQF Q RED P DR+C++SG    V++ R RI+ELIDSVM
Sbjct: 321 DMIKKIQAETGARVQFQQGREDGPGDRKCIVSGKHQAVEQVRQRIQELIDSVM 373

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307187117|gb|EFN72361.1| Far upstream element-binding protein 1 [Camponotus floridanus]

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 61/116 (52%), Positives = 74/116 (63%), Gaps = 15/116 (12%)

Query: 5   EFQQSRRWQQGIGRNNDNFGNMREFNE---NGDGRGGMWEVTWEVIQVCVPKAAVGVVIG 61
           E Q   R  +G  R   N+ N   FN    N DG           ++V VP+AAVGVVIG
Sbjct: 268 EMQMFHRGGRGTERTG-NYSNDSSFNHGPANSDG-----------VEVLVPRAAVGVVIG 315

Query: 62  KGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           KGGDMIKK+Q E+GA+VQF Q RED P DR+C+LSG    V++AR RI+ELIDSVM
Sbjct: 316 KGGDMIKKIQAESGAKVQFQQGREDGPGDRKCLLSGKHQAVEQARQRIQELIDSVM 371

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010095|gb|EFA06543.1| hypothetical protein TcasGA2_TC009450 [Tribolium castaneum]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 59/69 (85%)

Query: 48  QVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARA 107
           +V VP+ AVGVVIGKGGDMIKK+Q ETGARVQF Q RE+ P +RRC LSG+P QV++AR 
Sbjct: 323 EVLVPRQAVGVVIGKGGDMIKKIQAETGARVQFQQAREEGPGERRCYLSGTPKQVEQARQ 382

Query: 108 RIEELIDSV 116
           RIEELIDSV
Sbjct: 383 RIEELIDSV 391

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189238744|ref|XP_972178.2| PREDICTED: similar to P-element somatic inhibitor [Tribolium castaneum]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 59/69 (85%)

Query: 48  QVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARA 107
           +V VP+ AVGVVIGKGGDMIKK+Q ETGARVQF Q RE+ P +RRC LSG+P QV++AR 
Sbjct: 294 EVLVPRQAVGVVIGKGGDMIKKIQAETGARVQFQQAREEGPGERRCYLSGTPKQVEQARQ 353

Query: 108 RIEELIDSV 116
           RIEELIDSV
Sbjct: 354 RIEELIDSV 362

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858339|ref|XP_003704659.1| PREDICTED: far upstream element-binding protein 1-like [Megachile rotundata]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 59/103 (57%), Positives = 72/103 (69%), Gaps = 11/103 (10%)

Query: 18  RNND---NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74
           R ND   ++ N   FN +G G       T + ++V VP+AAVGVVIGKGGDMIKK+Q ET
Sbjct: 279 RGNDRSGSYSNDSSFN-HGSG-------TTDGVEVLVPRAAVGVVIGKGGDMIKKIQAET 330

Query: 75  GARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           GARVQF Q RED P DR+C+LSG    V++ R RI+ELIDSVM
Sbjct: 331 GARVQFQQGREDGPGDRKCILSGKHQAVEQVRQRIQELIDSVM 373

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307211366|gb|EFN87498.1| Far upstream element-binding protein 1 [Harpegnathos saltator]

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 57/101 (56%), Positives = 72/101 (71%), Gaps = 5/101 (4%)

Query: 17  GRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGA 76
           GR ++  GN    N+NG   G       + ++V VP+AAVGVVIGKGGDMIKK+Q E+GA
Sbjct: 276 GRGSERPGNYT--NDNGFNHG---PANNDGVEVLVPRAAVGVVIGKGGDMIKKIQAESGA 330

Query: 77  RVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           +VQF Q RED P DR+C+LSG    V++AR RI+ELIDSVM
Sbjct: 331 KVQFQQGREDGPGDRKCLLSGKHQAVEQARQRIQELIDSVM 371

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322790271|gb|EFZ15270.1| hypothetical protein SINV_11556 [Solenopsis invicta]

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 56/99 (56%), Positives = 68/99 (68%), Gaps = 14/99 (14%)

Query: 22  NFGNMREFNE---NGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARV 78
           N+ N   FN    N DG           ++V VP+AAVGVVIGKGGDMIKK+Q E+GA+V
Sbjct: 296 NYSNDSGFNHGPANSDG-----------VEVLVPRAAVGVVIGKGGDMIKKIQAESGAKV 344

Query: 79  QFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           QF Q RED P DR+C+LSG    V++AR RI+ELIDSVM
Sbjct: 345 QFQQGREDGPGDRKCLLSGKHQAVEQARQRIQELIDSVM 383

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332023471|gb|EGI63714.1| Far upstream element-binding protein 1 [Acromyrmex echinatior]

 Score =  105 bits (261), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 59/116 (50%), Positives = 73/116 (62%), Gaps = 14/116 (12%)

Query: 5   EFQQSRRWQQGIGRNNDNFGNMREFNE---NGDGRGGMWEVTWEVIQVCVPKAAVGVVIG 61
           E Q   R  +G      N+ N   FN    N DG           ++V VP+AAVGVVIG
Sbjct: 266 EIQMFHRGGRGATDRTGNYSNDSGFNHGPANSDG-----------VEVLVPRAAVGVVIG 314

Query: 62  KGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
           KGGDMIKK+Q E+GA+VQF Q RE+ P DR+C+LSG    V++AR RI+ELIDSVM
Sbjct: 315 KGGDMIKKIQAESGAKVQFQQGREEGPGDRKCLLSGKHQAVEQARQRIQELIDSVM 370

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	138
FB|FBgn0014870	806	Psi "P-element somatic inhibit	0.739	0.126	0.333	2.8e-09
UNIPROTKB|Q7JPS0	796	Psi "PSI" [Drosophila sp. (tax	0.760	0.131	0.336	4.5e-09
WB|WBGene00007534	611	C12D8.1 [Caenorhabditis elegan	0.427	0.096	0.412	7.4e-07
UNIPROTKB|Q17936	611	C12D8.1 "Protein C12D8.1, isof	0.427	0.096	0.412	7.4e-07
ZFIN|ZDB-GENE-030131-4357	666	khsrp "KH-type splicing regula	0.826	0.171	0.317	5.7e-06
UNIPROTKB|C9JSZ1	232	FUBP1 "Far upstream element-bi	0.355	0.211	0.3	0.00011
UNIPROTKB|F1MX51	602	FUBP1 "Uncharacterized protein	0.724	0.166	0.321	0.00012
RGD|1591892	639	Fubp1 "far upstream element (F	0.724	0.156	0.321	0.00013
UNIPROTKB|Q32PX7	639	Fubp1 "Far upstream element-bi	0.724	0.156	0.321	0.00013
UNIPROTKB|J9P014	644	FUBP1 "Uncharacterized protein	0.724	0.155	0.321	0.00014

FB|FBgn0014870 Psi "P-element somatic inhibitor" [Drosophila melanogaster (taxid:7227)]

 Score = 148 (57.2 bits), Expect = 2.8e-09, P = 2.8e-09
 Identities = 36/108 (33%), Positives = 54/108 (50%)

Query:    13 QQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCXXXXXXXXXXXXXXDMIKKLQN 72
             Q G G      G    FN   +G GG      E  +V               DMI+K+Q 
Sbjct:   303 QGGRGGGGGGGGPGMGFNNFNNGNGG------ESTEVFVPKIAVGVVIGKGGDMIRKIQT 356

Query:    73 ETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQ 120
             E G ++QF+Q + D+  DRRC++ G+  QV +A+  I+ LI++VMV +
Sbjct:   357 ECGCKLQFIQGKNDEMGDRRCVIQGTRQQVDDAKRTIDGLIENVMVSR 404

GO:0003729 "mRNA binding" evidence=IDA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IMP;IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005685 "U1 snRNP" evidence=IPI

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0007283 "spermatogenesis" evidence=IMP

GO:0006397 "mRNA processing" evidence=IDA

GO:0048024 "regulation of mRNA splicing, via spliceosome" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q7JPS0 Psi "PSI" [Drosophila sp. (taxid:7242)]

 Score = 146 (56.5 bits), Expect = 4.5e-09, P = 4.5e-09
 Identities = 38/113 (33%), Positives = 56/113 (49%)

Query:    13 QQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCXXXXXXXXXXXXXXDMIKKLQN 72
             Q G G      G    FN   +G GG      E  +V               DMI+K+Q 
Sbjct:   290 QGGRGGGGGGGGPGMGFNNFNNGNGG------ESTEVFVPKIAVGVVIGKGGDMIRKIQT 343

Query:    73 ETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGAN 125
             E G ++QF+Q + D+  DRRC++ G+  QV +A+  I+ LI++VM  Q +G N
Sbjct:   344 ECGCKLQFIQGKNDEMGDRRCVIQGTRQQVDDAKRTIDGLIENVM--QRNGMN 394

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0003729 "mRNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0006397 "mRNA processing" evidence=IDA

GO:0007283 "spermatogenesis" evidence=IMP

GO:0048024 "regulation of mRNA splicing, via spliceosome" evidence=IMP

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IDA;IMP

GO:0005685 "U1 snRNP" evidence=IPI

WB|WBGene00007534 C12D8.1 [Caenorhabditis elegans (taxid:6239)]

 Score = 110 (43.8 bits), Expect = 7.4e-07, Sum P(2) = 7.4e-07
 Identities = 26/63 (41%), Positives = 37/63 (58%)

Query:    65 DMIKKLQNETGARVQFVQMREDDPSD-RRC-MLSGSPDQVQEARARIEELIDSVMVEQFS 122
             D IK+L  ETG ++QF    +DDPS   RC ++ G+ DQ+  A  RI EL+    ++Q  
Sbjct:   269 DTIKRLAMETGTKIQFKP--DDDPSTPERCAVIMGTRDQIYRATERITELVKKSTMQQGG 326

Query:   123 GAN 125
             G N
Sbjct:   327 GGN 329

GO:0003723 "RNA binding" evidence=IEA

GO:0016246 "RNA interference" evidence=IMP

UNIPROTKB|Q17936 C12D8.1 "Protein C12D8.1, isoform b" [Caenorhabditis elegans (taxid:6239)]

 Score = 110 (43.8 bits), Expect = 7.4e-07, Sum P(2) = 7.4e-07
 Identities = 26/63 (41%), Positives = 37/63 (58%)

Query:    65 DMIKKLQNETGARVQFVQMREDDPSD-RRC-MLSGSPDQVQEARARIEELIDSVMVEQFS 122
             D IK+L  ETG ++QF    +DDPS   RC ++ G+ DQ+  A  RI EL+    ++Q  
Sbjct:   269 DTIKRLAMETGTKIQFKP--DDDPSTPERCAVIMGTRDQIYRATERITELVKKSTMQQGG 326

Query:   123 GAN 125
             G N
Sbjct:   327 GGN 329

GO:0005515 "protein binding" evidence=IPI

ZFIN|ZDB-GENE-030131-4357 khsrp "KH-type splicing regulatory protein" [Danio rerio (taxid:7955)]

 Score = 116 (45.9 bits), Expect = 5.7e-06, P = 5.7e-06
 Identities = 39/123 (31%), Positives = 57/123 (46%)

Query:     7 QQSRRWQQGIGRNNDNFGNMR-EFNEN---GDGRGGMWEVTWEVIQVCXXXXXXXXXXXX 62
             QQ+R   Q I R  D+ G  R E+      G G GG        I+V             
Sbjct:   252 QQAREMVQEILRERDHPGFERNEYGSRMGGGGGGGGGGGGGGGGIEVPVPRHSVGVVIGR 311

Query:    63 XXDMIKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSVMVEQ 120
               +MIKK+QN+ G R+QF   + DD +  D+   + G PD+ + A + I EL+ S+ V +
Sbjct:   312 SGEMIKKIQNDAGVRIQF---KPDDGTGPDKIAHIMGPPDRCEHAASIINELLQSIRVRE 368

Query:   121 FSG 123
               G
Sbjct:   369 EGG 371

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|C9JSZ1 FUBP1 "Far upstream element-binding protein 1" [Homo sapiens (taxid:9606)]

 Score = 89 (36.4 bits), Expect = 0.00011, Sum P(2) = 0.00011
 Identities = 15/50 (30%), Positives = 32/50 (64%)

Query:    65 DMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELID 114
             + I ++Q E+G ++Q        P +R CML+G+P+ VQ A+  ++++++
Sbjct:   141 EQISRIQQESGCKIQIAPDSGGLP-ERSCMLTGTPESVQSAKRLLDQIVE 189

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1MX51 FUBP1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 103 (41.3 bits), Expect = 0.00012, P = 0.00012
 Identities = 36/112 (32%), Positives = 52/112 (46%)

Query:     7 QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCXXXXXXXXXXXXXXDM 66
             QQ++     + R+   F  +R  NE G   GG      E I V               +M
Sbjct:   202 QQAKEMVLELIRDQGGFREVR--NEYGSRIGGN-----EGIDVPIPRFAVGIVIGRNGEM 254

Query:    67 IKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSV 116
             IKK+QN+ G R+QF   + DD +  DR   ++G PD+ Q A   I +L+ SV
Sbjct:   255 IKKIQNDAGVRIQF---KPDDGTTPDRIAQITGPPDRCQHAAEIITDLLRSV 303

GO:0010628 "positive regulation of gene expression" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

RGD|1591892 Fubp1 "far upstream element (FUSE) binding protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 103 (41.3 bits), Expect = 0.00013, P = 0.00013
 Identities = 36/112 (32%), Positives = 52/112 (46%)

Query:     7 QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCXXXXXXXXXXXXXXDM 66
             QQ++     + R+   F  +R  NE G   GG      E I V               +M
Sbjct:   240 QQAKEMVLELIRDQGGFREVR--NEYGSRIGGN-----EGIDVPIPRFAVGIVIGRNGEM 292

Query:    67 IKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSV 116
             IKK+QN+ G R+QF   + DD +  DR   ++G PD+ Q A   I +L+ SV
Sbjct:   293 IKKIQNDAGVRIQF---KPDDGTTPDRIAQITGPPDRCQHAAEIITDLLRSV 341

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

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

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

GO:0010628 "positive regulation of gene expression" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q32PX7 Fubp1 "Far upstream element-binding protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 103 (41.3 bits), Expect = 0.00013, P = 0.00013
 Identities = 36/112 (32%), Positives = 52/112 (46%)

Query:     7 QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCXXXXXXXXXXXXXXDM 66
             QQ++     + R+   F  +R  NE G   GG      E I V               +M
Sbjct:   240 QQAKEMVLELIRDQGGFREVR--NEYGSRIGGN-----EGIDVPIPRFAVGIVIGRNGEM 292

Query:    67 IKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSV 116
             IKK+QN+ G R+QF   + DD +  DR   ++G PD+ Q A   I +L+ SV
Sbjct:   293 IKKIQNDAGVRIQF---KPDDGTTPDRIAQITGPPDRCQHAAEIITDLLRSV 341

GO:0010628 "positive regulation of gene expression" evidence=IEA

UNIPROTKB|J9P014 FUBP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 103 (41.3 bits), Expect = 0.00014, P = 0.00014
 Identities = 36/112 (32%), Positives = 52/112 (46%)

Query:     7 QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCXXXXXXXXXXXXXXDM 66
             QQ++     + R+   F  +R  NE G   GG      E I V               +M
Sbjct:   245 QQAKEMVLELIRDQGGFREVR--NEYGSRIGGN-----EGIDVPIPRFAVGIVIGRNGEM 297

Query:    67 IKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSV 116
             IKK+QN+ G R+QF   + DD +  DR   ++G PD+ Q A   I +L+ SV
Sbjct:   298 IKKIQNDAGVRIQF---KPDDGTTPDRIAQITGPPDRCQHAAEIITDLLRSV 346

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	138
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-16
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-16
pfam00013	59	pfam00013, KH_1, KH domain	4e-15
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	9e-15
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	5e-08
pfam13014	42	pfam13014, KH_3, KH domain	1e-07
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	6e-06
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	1e-05
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	3e-05
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	2e-04
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	0.001

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

 Score = 68.7 bits (169), Expect = 1e-16
 Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
             +V VP + VG +IGKGG  IK+++ ETGA+++          +R   ++G+P+ V++A
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPD-SGSGSEERIVTITGTPEAVEKA 59

Query: 106 RARIE 110
           +  I 
Sbjct: 60  KELIL 64

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

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

 Score = 66.6 bits (163), Expect = 8e-16
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 43  TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQV 102
               I+V +P   VG++IGKGG  IKK++ ETG ++           +R   ++G P+ V
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI---PGPGSEERVVEITGPPENV 57

Query: 103 QEARARIEELI 113
           ++A   I E++
Sbjct: 58  EKAAELILEIL 68

Length = 68

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

 Score = 64.5 bits (158), Expect = 4e-15
 Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 5/64 (7%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
             ++ +P   VG +IGKGG  IK+++ ETG +++    R+D        +SG+P+QV++A
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDD-----TVTISGTPEQVEKA 55

Query: 106 RARI 109
           +  I
Sbjct: 56  KELI 59

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

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

 Score = 63.6 bits (156), Expect = 9e-15
 Identities = 22/59 (37%), Positives = 35/59 (59%)

Query: 51  VPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI 109
           VP +  G +IGKGG  IK+++ ETGA+++  +      ++R   +SG P  VQ+A   I
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 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|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 46.4 bits (111), Expect = 5e-08
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
             +V +PK     +IGK G  I+K+  ETG +++F        SD    ++G  + V++A
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF--PDPGSKSD-TITITGPKENVEKA 57

Query: 106 RARIE 110
           +  I 
Sbjct: 58  KEEIL 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|221895 pfam13014, KH_3, KH domain

 Score = 44.9 bits (107), Expect = 1e-07
 Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 1/42 (2%)

Query: 56 VGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG 97
          VG +IGKGG+ IK+++ ETGA++Q  +  E    +R   ++G
Sbjct: 2  VGAIIGKGGETIKEIREETGAKIQIPKP-EPGSGERIVTITG 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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 43.9 bits (105), Expect = 6e-06
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 20/75 (26%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-----SPD 100
           +  + +P   +  VIG GG  I+++  ETGA++      EDD         G     + D
Sbjct: 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI----EDD---------GTVKIAATD 601

Query: 101 Q--VQEARARIEELI 113
               + A+ RIE + 
Sbjct: 602 GEAAEAAKERIEGIT 616

Length = 693

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

 Score = 40.2 bits (95), Expect = 1e-05
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSP-DQVQE 104
           +  + +P   +  VIG GG  IKK+  ETG ++      EDD       ++ S  +  ++
Sbjct: 3   IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDI----EDDG---TVYIAASDKEAAEK 55

Query: 105 ARARIE 110
           A+  IE
Sbjct: 56  AKKMIE 61

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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 10/70 (14%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGS-PDQVQ 103
           E I++      +  VIG GG +I+++  ETGA++      EDD       ++ S  +  +
Sbjct: 553 ETIKI--NPDKIRDVIGPGGKVIREITEETGAKIDI----EDDG---TVKIAASDGEAAE 603

Query: 104 EARARIEELI 113
            A   IE + 
Sbjct: 604 AAIKMIEGIT 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|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 9/81 (11%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSP-DQVQ 103
            +  + +    +  VIG GG  IK +  ETG ++      EDD +     ++ S  +  +
Sbjct: 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDI----EDDGT---VKIAASDGESAK 604

Query: 104 EARARIEELIDSVMV-EQFSG 123
           +A+ RIE +   V V E + G
Sbjct: 605 KAKERIEAITREVEVGEVYEG 625

Length = 692

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

 Score = 34.9 bits (81), Expect = 0.001
 Identities = 11/42 (26%), Positives = 20/42 (47%)

Query: 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR 84
              I + V +   G+VIGK G  I+ LQ      ++  +++
Sbjct: 23 DRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKRVK 64

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	138
KOG1676|consensus	600		99.77
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.64
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.58
KOG1676|consensus	600		99.55
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.53
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.51
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.48
KOG2192|consensus	390		99.35
KOG2191|consensus	402		99.35
smart00322	69	KH K homology RNA-binding domain.	99.31
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	99.3
KOG2190|consensus	485		99.27
PF13014	43	KH_3: KH domain	99.22
KOG2191|consensus	402		99.15
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.1
KOG0119|consensus	554		99.09
KOG2193|consensus	584		99.07
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.04
PRK13763	180	putative RNA-processing protein; Provisional	99.04
PRK13763	180	putative RNA-processing protein; Provisional	99.03
KOG2193|consensus	584		99.0
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.94
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.88
KOG2192|consensus	390		98.8
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.64
KOG1588|consensus	259		98.63
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.62
KOG2190|consensus	485		98.54
KOG0336|consensus	629		98.32
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.32
KOG1067|consensus	760		98.28
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.96
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.94
KOG2814|consensus	345		97.89
COG5176	269	MSL5 Splicing factor (branch point binding protein	97.79
PRK12704	520	phosphodiesterase; Provisional	97.61
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.61
PRK00106	535	hypothetical protein; Provisional	97.58
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.54
KOG2113|consensus	394		97.44
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.24
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	96.89
KOG2113|consensus	394		96.68
KOG2279|consensus	608		96.67
PRK12705	508	hypothetical protein; Provisional	96.65
PRK00468	75	hypothetical protein; Provisional	96.6
PRK02821	77	hypothetical protein; Provisional	96.57
KOG2279|consensus	608		96.49
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.29
PRK01064	78	hypothetical protein; Provisional	95.99
KOG4369|consensus	2131		95.81
KOG2208|consensus	753		95.78
PRK08406	140	transcription elongation factor NusA-like protein;	95.7
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	95.51
PRK08406	140	transcription elongation factor NusA-like protein;	95.38
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	95.07
COG1855	604	ATPase (PilT family) [General function prediction	94.37
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	94.37
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	94.3
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.17
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	94.08
KOG2208|consensus	753		93.98
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	93.83
KOG3273|consensus	252		93.82
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	93.79
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	93.66
PRK13764	602	ATPase; Provisional	93.39
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	93.35
KOG2874|consensus	356		92.7
COG0195	190	NusA Transcription elongation factor [Transcriptio	92.11
TIGR01953	341	NusA transcription termination factor NusA. This m	91.57
PRK12328	374	nusA transcription elongation factor NusA; Provisi	91.13
PRK06418	166	transcription elongation factor NusA-like protein;	90.97
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	89.93
PRK12327	362	nusA transcription elongation factor NusA; Provisi	89.52
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	89.05
PRK09202	470	nusA transcription elongation factor NusA; Validat	88.64
COG1782	637	Predicted metal-dependent RNase, consists of a met	88.52
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	88.1
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	87.72
PRK12329	449	nusA transcription elongation factor NusA; Provisi	86.97
COG0195	190	NusA Transcription elongation factor [Transcriptio	86.32
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	80.3

>KOG1676|consensus

Probab=99.77  E-value=4.2e-18  Score=144.46  Aligned_cols=111  Identities=34%  Similarity=0.515  Sum_probs=90.0

Q ss_pred             hHHHHHHHHHHHhhcC--CCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065          5 EFQQSRRWQQGIGRNN--DNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~--~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      +||+||.||.+|++.-  ..++   +.++.+++.+     ...+.++.||..+||.||||+|++||+|+.+||+||+|.+
T Consensus       196 ~ve~a~~lV~dil~e~~~~~~g---~~~~~g~~~g-----~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp  267 (600)
T KOG1676|consen  196 KVEQAKQLVADILREEDDEVPG---SGGHAGVRGG-----GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP  267 (600)
T ss_pred             HHHHHHHHHHHHHHhcccCCCc---cccccCcCcc-----ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec
Confidence            6899999999999952  2221   1122222211     1238999999999999999999999999999999999999


Q ss_pred             CCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCC
Q psy11065         83 MREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSG  123 (138)
Q Consensus        83 ~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~  123 (138)
                      ++++.+-+|.+.|.|++++|.+|.++|.+||++......++
T Consensus       268 Dd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~  308 (600)
T KOG1676|consen  268 DDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGG  308 (600)
T ss_pred             CCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCC
Confidence            88754449999999999999999999999999998885443

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.64  E-value=1e-15  Score=96.94  Aligned_cols=63  Identities=35%  Similarity=0.617  Sum_probs=58.1

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHH
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI  109 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I  109 (138)
                      ++|.||.+.+|.|||++|++|++|+++|||+|.+.+...+.+.+|+++|.|+++++..|..+|
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            689999999999999999999999999999999998765344489999999999999999987

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

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

Probab=99.58  E-value=7.5e-15  Score=92.11  Aligned_cols=60  Identities=28%  Similarity=0.483  Sum_probs=54.8

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecC-HHHHHHHHHHHH
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGS-PDQVQEARARIE  110 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~-~e~i~~A~~~I~  110 (138)
                      |....+.||.+++|.|||++|++|++|+++|||+|.|++       ++.|+|.|+ +++++.|+++|+
T Consensus         1 P~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             CeEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-------CCEEEEEeCCHHHHHHHHHHhC
Confidence            467899999999999999999999999999999999987       356999998 999999999873

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

>KOG1676|consensus

Probab=99.55  E-value=4.3e-14  Score=120.27  Aligned_cols=109  Identities=21%  Similarity=0.378  Sum_probs=90.4

Q ss_pred             chhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065          3 SIEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus         3 ~~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ++.|+.||.|+.++++...   ...+|.+..+.       ..++.+|.||.+++|+||||+|+|||+|++.|||++.+..
T Consensus       107 pe~v~~aK~li~evv~r~~---~~~~~~~~q~~-------~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iq  176 (600)
T KOG1676|consen  107 PENVEVAKQLIGEVVSRGR---PPGGFPDNQGS-------VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQ  176 (600)
T ss_pred             cccHHHHHHhhhhhhhccC---CCCCccccCCc-------cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEe
Confidence            6789999999999998765   33444444442       2489999999999999999999999999999999999888


Q ss_pred             CCCCCCC-CcEEEEecCHHHHHHHHHHHHHHHHhhhhccC
Q psy11065         83 MREDDPS-DRRCMLSGSPDQVQEARARIEELIDSVMVEQF  121 (138)
Q Consensus        83 ~~~~~~~-~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~  121 (138)
                      +....++ .+.+.|+|++++|+.|+.||.++|++.....+
T Consensus       177 d~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~  216 (600)
T KOG1676|consen  177 DGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVP  216 (600)
T ss_pred             cCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCC
Confidence            7764432 78899999999999999999999997444433

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.53  E-value=1.7e-14  Score=90.09  Aligned_cols=61  Identities=28%  Similarity=0.498  Sum_probs=55.9

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHH
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIE  110 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~  110 (138)
                      .++.||.++++.|||++|++|++|+++|||+|++++...+   ++.|+|.|+++++..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~---~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSK---SDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCC---CCEEEEEcCHHHHHHHHHHhC
Confidence            5899999999999999999999999999999999986532   789999999999999998873

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.51  E-value=2e-14  Score=89.20  Aligned_cols=60  Identities=37%  Similarity=0.596  Sum_probs=54.8

Q ss_pred             EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHH
Q psy11065         46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI  109 (138)
Q Consensus        46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I  109 (138)
                      |.+|.||.+.+++|||++|++|++|+++|||+|.++++.    ....++|.|+++++..|+++|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~----~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD----ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT----EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC----CcEEEEEEeCHHHHHHHHhhC
Confidence            578999999999999999999999999999999998752    156899999999999999987

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

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

Probab=99.48  E-value=2e-13  Score=85.03  Aligned_cols=62  Identities=35%  Similarity=0.669  Sum_probs=56.1

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHH
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI  109 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I  109 (138)
                      .++.||.+++++|||++|++|++|+++|||+|.|++.... ..++.+++.|+.+++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~-~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSG-SEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCC-CCceEEEEEcCHHHHHHHHHHh
Confidence            5899999999999999999999999999999999886542 3389999999999999999887

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.

>KOG2192|consensus

Probab=99.35  E-value=5.4e-12  Score=99.50  Aligned_cols=102  Identities=26%  Similarity=0.413  Sum_probs=77.5

Q ss_pred             HHHHHhhcC-CCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCC
Q psy11065         12 WQQGIGRNN-DNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSD   90 (138)
Q Consensus        12 ~v~~i~~~~-~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~   90 (138)
                      |.+.|-.++ +.|++.+++..+..|..|.   .-.+.++.||.+.-|.||||+|..|++|++++||.|.|+++.+..+ +
T Consensus       284 wqmaYePQgGs~ydysyAG~~GsYGdlGG---PitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGse-d  359 (390)
T KOG2192|consen  284 WQMAYEPQGGSGYDYSYAGGYGSYGDLGG---PITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE-D  359 (390)
T ss_pred             cccccCCCCCCCCCccccccccccCCCCC---ceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCC-c
Confidence            344444433 3445555444443443331   1256789999999999999999999999999999999988665545 9


Q ss_pred             cEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         91 RRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        91 r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      |+++|+|+.++|+.|+.+++..++.-.
T Consensus       360 rIitItGTqdQIqnAQYLlQn~Vkq~r  386 (390)
T KOG2192|consen  360 RIITITGTQDQIQNAQYLLQNSVKQYR  386 (390)
T ss_pred             eEEEEeccHHHHhhHHHHHHHHHHhhh
Confidence            999999999999999999999888443

>KOG2191|consensus

Probab=99.35  E-value=5.8e-12  Score=101.39  Aligned_cols=78  Identities=29%  Similarity=0.532  Sum_probs=72.4

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCC--CcEEEEecCHHHHHHHHHHHHHHHHhhhhccCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSVMVEQFS  122 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~--~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g  122 (138)
                      ..++|+||...+|.||||+|++|.++|++|||+|++.+..+..|+  +|+|.|.|+.+.+....++|.+.|++..+..-+
T Consensus        39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~k  118 (402)
T KOG2191|consen   39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVAK  118 (402)
T ss_pred             eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcC
Confidence            789999999999999999999999999999999999998876665  999999999999999999999999997766555

>smart00322 KH K homology RNA-binding domain

Probab=99.31  E-value=2.8e-11  Score=74.91  Aligned_cols=67  Identities=34%  Similarity=0.631  Sum_probs=59.9

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      ..+.++.||...++.+||++|++|++|++.|+++|.+.....   ....+.+.|+++++..|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~---~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS---EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC---CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999977543   2688999999999999999998765

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

Probab=99.30  E-value=8.6e-12  Score=88.14  Aligned_cols=83  Identities=24%  Similarity=0.406  Sum_probs=61.7

Q ss_pred             CccceeeccCcHHHHHHHHHhCCeEEEecCCC------------------CCCCCcEEEEecC--HHHHHHHHHHHHHHH
Q psy11065         54 AAVGVVIGKGGDMIKKLQNETGARVQFVQMRE------------------DDPSDRRCMLSGS--PDQVQEARARIEELI  113 (138)
Q Consensus        54 ~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~------------------~~~~~r~i~i~G~--~e~i~~A~~~I~~ii  113 (138)
                      .++|.|||++|++||+|+++|||+|.|.....                  ..+ .++.+.+-+  .+++.+|+.+|+.++
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~ep-lhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEP-LHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCC-cEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999987521                  111 344555556  799999999999999


Q ss_pred             HhhhhccCCCCcccchhhhhcccC
Q psy11065        114 DSVMVEQFSGANFDKLRSTVLANR  137 (138)
Q Consensus       114 ~~~~~~~~g~~~~~~l~~~~~~~~  137 (138)
                      .........--.-.+|+++++.|-
T Consensus        94 ~~~~~~~~~~~k~~ql~~la~~nG  117 (120)
T cd02395          94 KPAIEGGNDELKREQLRELALLNG  117 (120)
T ss_pred             ccCCCccchHHHHHHHHHHHHhcc
Confidence            955444112223458888888773

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.

>KOG2190|consensus

Probab=99.27  E-value=4.3e-11  Score=101.65  Aligned_cols=74  Identities=31%  Similarity=0.512  Sum_probs=69.9

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      +.+.+|+||...+|.||||+|+.||+|+++|||+|.|..+..+..++|.|+|.|.+++|.+|...|...|.+..
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~  210 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP  210 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence            58999999999999999999999999999999999999987777779999999999999999999999998854

>PF13014 KH_3: KH domain

Probab=99.22  E-value=3.3e-11  Score=70.24  Aligned_cols=43  Identities=40%  Similarity=0.699  Sum_probs=37.6

Q ss_pred             ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec
Q psy11065         55 AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG   97 (138)
Q Consensus        55 ~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G   97 (138)
                      ++|+|||++|++|++|+++|+|+|+|++...+.+.++.|+|.|
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            4799999999999999999999999999554555589999987

>KOG2191|consensus

Probab=99.15  E-value=1.2e-10  Score=93.78  Aligned_cols=74  Identities=31%  Similarity=0.511  Sum_probs=63.7

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCC--CCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRED--DPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~--~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ..+++.||+...|.||||+|.+||.|+++++|.|+|.+..+.  ..-+|++++.|++++..+|+++|.+.|.++.+
T Consensus       132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq  207 (402)
T KOG2191|consen  132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ  207 (402)
T ss_pred             ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence            458899999999999999999999999999999999842221  11289999999999999999999999887654

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.10  E-value=6.2e-10  Score=83.03  Aligned_cols=104  Identities=23%  Similarity=0.364  Sum_probs=72.7

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecC---------CccceeeccCcHHHHHHHHHh
Q psy11065          4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPK---------AAVGVVIGKGGDMIKKLQNET   74 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~---------~~vg~IIGk~G~~Ik~I~~~T   74 (138)
                      ..+.+|+++++++...-+   ...++.-  -      ........+.|+.         ..+|+|||++|++++.|+..|
T Consensus        50 ~~i~kA~~~I~~i~~gf~---~e~A~~l--~------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t  118 (172)
T TIGR03665        50 LAVMKAREVVKAIGRGFS---PEKALKL--L------DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELT  118 (172)
T ss_pred             HHHHHHHHHHHHHHcCCC---HHHHHHh--c------CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHH
Confidence            468899999999877521   0000000  0      0011223455554         368999999999999999999


Q ss_pred             CCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCCCcccchh
Q psy11065         75 GARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLR  130 (138)
Q Consensus        75 ga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~~~~~~l~  130 (138)
                      ||+|.|++        ..|.|.|++++++.|+++|.+++...    ..+..|..|+
T Consensus       119 ~~~i~i~~--------~~v~i~G~~~~~~~A~~~i~~li~~~----~~~~vy~~l~  162 (172)
T TIGR03665       119 GVSISVYG--------KTVGIIGDPEQVQIAREAIEMLIEGA----PHGTVYKFLE  162 (172)
T ss_pred             CCeEEEcC--------CEEEEECCHHHHHHHHHHHHHHHcCC----CChhHHHHHH
Confidence            99999964        46999999999999999999999433    2334455553

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.

>KOG0119|consensus

Probab=99.09  E-value=1e-09  Score=92.30  Aligned_cols=118  Identities=22%  Similarity=0.273  Sum_probs=88.4

Q ss_pred             HHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecC------CccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065         10 RRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPK------AAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus        10 k~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~------~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      .++|.+++..+..|.....|....          ....++.||.      ++||+|||..|.|.|+|+++|||||.|--.
T Consensus       113 ~e~I~~~lk~nP~fkpP~DYk~p~----------~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGk  182 (554)
T KOG0119|consen  113 HEIIEEILKLNPGFKPPADYKPPA----------KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGK  182 (554)
T ss_pred             HHHHHHHHHhCcCCCCCcccCccc----------ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecc
Confidence            467888888888887777774332          2456777765      589999999999999999999999999651


Q ss_pred             C------------C--CC--CCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCCCcc--cchhhhhcccC
Q psy11065         84 R------------E--DD--PSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANF--DKLRSTVLANR  137 (138)
Q Consensus        84 ~------------~--~~--~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~~~~--~~l~~~~~~~~  137 (138)
                      .            .  +.  ..-++.+.+-+.|.|++|+++|+.+|.+...-..+..+.  -+|||++-+|.
T Consensus       183 gSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNg  254 (554)
T KOG0119|consen  183 GSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNG  254 (554)
T ss_pred             ccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCC
Confidence            1            0  00  003556666788999999999999999966666665443  48999998874

>KOG2193|consensus

Probab=99.07  E-value=1.1e-10  Score=96.76  Aligned_cols=74  Identities=31%  Similarity=0.492  Sum_probs=66.7

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ....+++.||...||.|||++|.+||.|...+||.|.|.+..-++..+|.|+|+|++++..+|+..|...|++.
T Consensus       409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEe  482 (584)
T KOG2193|consen  409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEE  482 (584)
T ss_pred             chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhh
Confidence            45678999999999999999999999999999999999887766555999999999999999999997777664

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.04  E-value=3.3e-10  Score=84.47  Aligned_cols=61  Identities=28%  Similarity=0.506  Sum_probs=54.5

Q ss_pred             EEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEE---ecCHHHHHHHHHHHHHHHHh
Q psy11065         49 VCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCML---SGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        49 i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i---~G~~e~i~~A~~~I~~ii~~  115 (138)
                      +.||.+++|.|||++|++|+.|+++|||+|+++++      +..|.|   +++++++.+|+++|..+...
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g   65 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE------TGEVKIEEEDEDPLAVMKAREVVKAIGRG   65 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC------CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence            67999999999999999999999999999999874      234666   89999999999999998773

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=99.04  E-value=6.8e-10  Score=83.38  Aligned_cols=64  Identities=25%  Similarity=0.432  Sum_probs=57.4

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEE----ecCHHHHHHHHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCML----SGSPDQVQEARARIEELID  114 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i----~G~~e~i~~A~~~I~~ii~  114 (138)
                      ....+.||.++++.|||++|++|+.|+++|||+|+++++      +..|.|    +++++++++|+++|++++.
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE------TGEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC------CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999999874      234555    5899999999999999988

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.03  E-value=2.1e-09  Score=80.79  Aligned_cols=54  Identities=31%  Similarity=0.550  Sum_probs=48.5

Q ss_pred             CccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         54 AAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        54 ~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      ..+|+|||++|++++.|++.|||+|.|.+        +.+.+.|++++++.|++.|..++..
T Consensus       104 r~~griIG~~G~~~k~ie~~t~~~i~i~~--------~~v~i~G~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763        104 RIKGRIIGEGGKTRRIIEELTGVDISVYG--------KTVAIIGDPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             HHhhheeCCCcHHHHHHHHHHCcEEEEcC--------CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            36899999999999999999999999974        2388889999999999999999843

>KOG2193|consensus

Probab=99.00  E-value=8.7e-10  Score=91.49  Aligned_cols=78  Identities=22%  Similarity=0.379  Sum_probs=69.8

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhcc
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQ  120 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~  120 (138)
                      ..-.++++||..++|.||||.|.|||.|.+.|.|+|++....+....++.+++.+++|...+|+.+|.+++.......
T Consensus       197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~  274 (584)
T KOG2193|consen  197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDD  274 (584)
T ss_pred             cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhcc
Confidence            346789999999999999999999999999999999998876655559999999999999999999999998766543

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.94  E-value=2.3e-09  Score=94.41  Aligned_cols=95  Identities=24%  Similarity=0.319  Sum_probs=73.9

Q ss_pred             hHHHHHHHHHHHhhcCCC-CCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065          5 EFQQSRRWQQGIGRNNDN-FGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~~~-~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      .+++|++-...|++-... ..       .+   ...+...|....+.||+++++.|||++|++||.|+++|||+|+|.++
T Consensus       547 aL~~A~~g~~~Il~~m~~al~-------~p---~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~  616 (719)
T TIGR02696       547 ALKQARDARLAILDVMAEAID-------TP---DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD  616 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh-------Cc---cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC
Confidence            456777776666653311 10       00   13445578999999999999999999999999999999999999872


Q ss_pred             CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         84 REDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                            ..+.+...+.+++++|+++|+.++..
T Consensus       617 ------G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       617 ------GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             ------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence                  45566667999999999999999994

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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.88  E-value=2.6e-09  Score=94.23  Aligned_cols=96  Identities=18%  Similarity=0.230  Sum_probs=74.9

Q ss_pred             hHHHHHHHHHHHhhcC----CCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065          5 EFQQSRRWQQGIGRNN----DNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF   80 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~----~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I   80 (138)
                      .+++|++-..+|++..    ..+            ....+...|...++.||+++++.|||++|++||.|+++|||+|.|
T Consensus       519 al~~a~~~~~~I~~~m~~~l~~~------------~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i  586 (684)
T TIGR03591       519 ALEQAKEGRLHILGEMNKVISEP------------RAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDI  586 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhh------------hccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEE
Confidence            4567777777766532    111            112344577999999999999999999999999999999999999


Q ss_pred             ecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         81 VQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        81 ~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      .++      ..+.....+.+.+.+|.++|..+..+.+.
T Consensus       587 ~dd------G~V~i~~~~~~~~~~a~~~I~~~~~~~~~  618 (684)
T TIGR03591       587 EDD------GTVKIAASDGEAAEAAIKMIEGITAEPEV  618 (684)
T ss_pred             ecC------eEEEEEECcHHHHHHHHHHHHhhhccccc
Confidence            873      45666677899999999999999776443

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).

>KOG2192|consensus

Probab=98.80  E-value=6.7e-09  Score=82.15  Aligned_cols=80  Identities=23%  Similarity=0.351  Sum_probs=73.0

Q ss_pred             CCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         40 WEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        40 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      ..+.|..++++|+.+..|.|||++|+.||+|++...+++.|-..+.+.+++|++.+.|.+..|..+++.|.++|.+..-+
T Consensus       118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pik  197 (390)
T KOG2192|consen  118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIK  197 (390)
T ss_pred             CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcC
Confidence            45667899999999999999999999999999999999999999988888999999999999999999999998875443

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

Probab=98.64  E-value=5.8e-08  Score=84.73  Aligned_cols=106  Identities=18%  Similarity=0.224  Sum_probs=80.6

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065          4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      .++.|||+....|+.....-        -.......+..+|...++.|+++++..+||++|++|++|.++||++|+|.++
T Consensus       519 ~AL~QAk~aRlhIL~~M~~a--------i~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd  590 (692)
T COG1185         519 KALEQAKGARLHILIVMNEA--------ISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD  590 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHH--------HhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC
Confidence            46789999999988843110        0000113344577899999999999999999999999999999999999852


Q ss_pred             CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCC
Q psy11065         84 REDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSG  123 (138)
Q Consensus        84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~  123 (138)
                            .++.+.+-+.+.+.+|+++|+.++++.+..+..-
T Consensus       591 ------Gtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~  624 (692)
T COG1185         591 ------GTVKIAASDGESAKKAKERIEAITREVEVGEVYE  624 (692)
T ss_pred             ------CcEEEEecchHHHHHHHHHHHHHHhhcccccEEE
Confidence                  2344445566899999999999999887765443

>KOG1588|consensus

Probab=98.63  E-value=4.1e-07  Score=71.53  Aligned_cols=93  Identities=22%  Similarity=0.298  Sum_probs=65.8

Q ss_pred             ccceEEEEEecCC------ccceeeccCcHHHHHHHHHhCCeEEEecCCC-------------------CCCCCcEEEEe
Q psy11065         42 VTWEVIQVCVPKA------AVGVVIGKGGDMIKKLQNETGARVQFVQMRE-------------------DDPSDRRCMLS   96 (138)
Q Consensus        42 ~~~~~~~i~IP~~------~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-------------------~~~~~r~i~i~   96 (138)
                      +-..+.+|.||..      +||+|+|+.|.++|+|+++|+|+|.|--...                   ..+-...|...
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            3447788888876      8999999999999999999999999954321                   11113445556


Q ss_pred             cCHHHH----HHHHHHHHHHHHhhhhccCCCCcccchhhhhcccC
Q psy11065         97 GSPDQV----QEARARIEELIDSVMVEQFSGANFDKLRSTVLANR  137 (138)
Q Consensus        97 G~~e~i----~~A~~~I~~ii~~~~~~~~g~~~~~~l~~~~~~~~  137 (138)
                      .++.-+    ..|.+.|+.+|.......-   ..++||+++..|.
T Consensus       169 ~p~~ea~~rl~~AleeI~klL~P~~e~~d---k~~QL~ELa~lng  210 (259)
T KOG1588|consen  169 APPAEAYARLAYALEEIKKLLVPDHEDED---KREQLRELAILNG  210 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCCCch---HHHHHHHHhhcCC
Confidence            666433    3577777777665544443   5789999999885

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.62  E-value=3.7e-08  Score=88.64  Aligned_cols=103  Identities=16%  Similarity=0.163  Sum_probs=77.9

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCe-EEEecC
Q psy11065          5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGAR-VQFVQM   83 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~-I~I~~~   83 (138)
                      .+++|++-...|++....-        -...-..++...|....+.||+++++.|||++|++||.|+++||++ |+|.++
T Consensus       653 AL~~A~~g~~~Il~~M~~~--------i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd  724 (891)
T PLN00207        653 ALLQAKDGRKHILAEMSKC--------SPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD  724 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHH--------HhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC
Confidence            4678888887777633111        0000112344577999999999999999999999999999999999 999772


Q ss_pred             CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccC
Q psy11065         84 REDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQF  121 (138)
Q Consensus        84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~  121 (138)
                            ..+.++.-+.+++++|+++|+.++.+.+....
T Consensus       725 ------g~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~i  756 (891)
T PLN00207        725 ------GTVKITAKDLSSLEKSKAIISSLTMVPTVGDI  756 (891)
T ss_pred             ------eeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcE
Confidence                  45666667999999999999999987554433

>KOG2190|consensus

Probab=98.54  E-value=2.6e-07  Score=78.82  Aligned_cols=70  Identities=24%  Similarity=0.388  Sum_probs=61.5

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec---------CHHHHHHHHHHHHHHHHh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG---------SPDQVQEARARIEELIDS  115 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G---------~~e~i~~A~~~I~~ii~~  115 (138)
                      .+++++++...+|.||||+|..||+|+++|.++|.|.+.....+ +|++++.|         ..+++.+|.++|-....+
T Consensus        43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~-eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~  121 (485)
T KOG2190|consen   43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCP-ERIITITGNRVELNLSPATDALFKAFDMIVFKLEE  121 (485)
T ss_pred             ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCC-cceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence            44799999999999999999999999999999998887644334 99999999         999999999999777663

>KOG0336|consensus

Probab=98.32  E-value=7.8e-07  Score=74.54  Aligned_cols=70  Identities=27%  Similarity=0.405  Sum_probs=62.0

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ....|.|..++||.|||++|++||.||..|+++|+|.+..   + +..|+|-|...--.+|+..|...+...+.
T Consensus        47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~-e~kv~ifg~~~m~~kaka~id~~~~k~e~  116 (629)
T KOG0336|consen   47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---L-EVKVTIFGINHMRKKAKASIDRGQDKDER  116 (629)
T ss_pred             CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---c-eeEEEEechHHHHHHHHhhHhhhhhhhhh
Confidence            5578889999999999999999999999999999998743   2 78899999999889999999988887665

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.32  E-value=3.3e-07  Score=81.17  Aligned_cols=99  Identities=19%  Similarity=0.293  Sum_probs=72.3

Q ss_pred             hHHHHHHHHHHHhhcCC-CCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065          5 EFQQSRRWQQGIGRNND-NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~~-~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      .+++|++-...|++... ....+         -.......|....+.||.++++.+||++|++||.|.++||++|++.++
T Consensus       522 al~~a~~g~~~I~~~M~~aI~~~---------r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~  592 (693)
T PRK11824        522 ALEQAKEGRLHILGKMNEAISEP---------RAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD  592 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCC---------hhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC
Confidence            35677777777766331 11000         011233456788999999999999999999999999999999988652


Q ss_pred             CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         84 REDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                            ..+....-+.+.+++|+++|+.++.+.+.
T Consensus       593 ------G~v~i~~~~~~~~~~a~~~I~~~~~~~~v  621 (693)
T PRK11824        593 ------GTVKIAATDGEAAEAAKERIEGITAEPEV  621 (693)
T ss_pred             ------ceEEEEcccHHHHHHHHHHHHHhcccCcC
Confidence                  34555566889999999999999876443

>KOG1067|consensus

Probab=98.28  E-value=1.2e-06  Score=75.42  Aligned_cols=101  Identities=23%  Similarity=0.240  Sum_probs=79.9

Q ss_pred             hhHHHHHHHHHHHhhcCC-CCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065          4 IEFQQSRRWQQGIGRNND-NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~-~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      .++++|++...+|++... +...+.+         ......|...++.++++++..+||++|...|+|+.+||+.-++++
T Consensus       564 eal~~a~~ar~~Il~~m~k~i~~Pr~---------~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe  634 (760)
T KOG1067|consen  564 EALQKAREARLQILDIMEKNINSPRG---------SDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE  634 (760)
T ss_pred             HHHHhhhHHHHHHHHHHHhhcCCccc---------CccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeecC
Confidence            357888888888888542 2211111         122445689999999999999999999999999999997777765


Q ss_pred             CCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhcc
Q psy11065         83 MREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQ  120 (138)
Q Consensus        83 ~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~  120 (138)
                             +.+-+++-++.++++|+++|..++..++.++
T Consensus       635 -------~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~  665 (760)
T KOG1067|consen  635 -------GTFSIFAPTQAAMEEAKEFIDGIIKDDQVQD  665 (760)
T ss_pred             -------ceEEEEecCHHHHHHHHHHHHHHhcCccccc
Confidence                   6778889999999999999999999877663

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

Probab=97.96  E-value=2.6e-05  Score=59.12  Aligned_cols=54  Identities=26%  Similarity=0.440  Sum_probs=48.8

Q ss_pred             ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         55 AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        55 ~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ..|+|||++|.|.+.|++-|+|.|.|..        ..|.|.|.++++..|++.|..++.-.
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g--------~tVaiiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG--------KTVAIIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC--------cEEEEecChhhhHHHHHHHHHHHcCC
Confidence            4699999999999999999999999975        46889999999999999999998743

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.94  E-value=2.8e-05  Score=60.67  Aligned_cols=66  Identities=26%  Similarity=0.309  Sum_probs=55.2

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEe-cCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLS-GSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~-G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      ..+.||..+++.+||++|.+|+.|.+.|+++|.|..       +-.|+|. .+.+.+..|+.+|+.+-++....
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~  213 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-------NGRIWIKGPDEEDEEIAIEAIKKIEREAHTS  213 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhcc
Confidence            789999999999999999999999999999999976       2345555 56779999999998886665443

>KOG2814|consensus

Probab=97.89  E-value=2.4e-05  Score=63.47  Aligned_cols=71  Identities=28%  Similarity=0.315  Sum_probs=61.3

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      -...+.++...++.|||+.|.|.++|+++|+|+|.++.+... . +.++.+.+..++|.+|.+.|..+|.+..
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 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-K-EEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-c-ceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            345788999999999999999999999999999999986532 1 5666677799999999999999998876

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

Probab=97.79  E-value=7.1e-05  Score=57.56  Aligned_cols=92  Identities=18%  Similarity=0.205  Sum_probs=64.1

Q ss_pred             eEEEEEecC------CccceeeccCcHHHHHHHHHhCCeEEEecCCCCC--------C-C-------CcEEEEecCHHHH
Q psy11065         45 EVIQVCVPK------AAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD--------P-S-------DRRCMLSGSPDQV  102 (138)
Q Consensus        45 ~~~~i~IP~------~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~--------~-~-------~r~i~i~G~~e~i  102 (138)
                      .+.++.||.      .+||+|||+.|.|+|+++..|+|+|-|-.....-        + .       -+..+...+.+.+
T Consensus       148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki  227 (269)
T COG5176         148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKI  227 (269)
T ss_pred             ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhH
Confidence            345666664      5899999999999999999999999995432110        0 0       1234445566778


Q ss_pred             HHHHHHHHHHHHhhhhccCCCCccc--chhhhhccc
Q psy11065        103 QEARARIEELIDSVMVEQFSGANFD--KLRSTVLAN  136 (138)
Q Consensus       103 ~~A~~~I~~ii~~~~~~~~g~~~~~--~l~~~~~~~  136 (138)
                      .+++..+..+|.+...-..|.-+..  +||.++-+|
T Consensus       228 ~~~ik~~~n~I~~a~~~PeGqnDlkR~qlr~la~ln  263 (269)
T COG5176         228 CRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLN  263 (269)
T ss_pred             HHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHhc
Confidence            8888888888888777766654443  677666554

>PRK12704 phosphodiesterase; Provisional

Probab=97.61  E-value=0.00022  Score=61.57  Aligned_cols=67  Identities=30%  Similarity=0.433  Sum_probs=54.0

Q ss_pred             eEEEEEecCC-ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhh
Q psy11065         45 EVIQVCVPKA-AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        45 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ....+.+|++ +-|+|||+.|.||+.++.-||+.|.|++.++      +|++++ +|-.-+.|...++.++.+..
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp~------~v~ls~~~~~rre~a~~~l~~l~~dg~  278 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE------AVILSGFDPIRREIARLALEKLVQDGR  278 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCC------eEEEecCChhhHHHHHHHHHHHHhcCC
Confidence            5667888984 5599999999999999999999999987532      466776 77666788888888877654

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.61  E-value=0.00021  Score=61.62  Aligned_cols=67  Identities=31%  Similarity=0.445  Sum_probs=54.6

Q ss_pred             eEEEEEecCC-ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhh
Q psy11065         45 EVIQVCVPKA-AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        45 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ....+.+|++ +-|+|||+.|.||+.++.-||+.|.|++.++      .|++++ +|---+.|+..++.++.+..
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~------~v~ls~fdp~rreia~~~l~~li~dgr  272 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE------AVILSGFDPVRREIARMALEKLIQDGR  272 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCC------eEEecCCchHHHHHHHHHHHHHHHcCC
Confidence            5667889995 5599999999999999999999999987532      466666 78777888888888887643

>PRK00106 hypothetical protein; Provisional

Probab=97.58  E-value=0.00026  Score=61.28  Aligned_cols=67  Identities=31%  Similarity=0.445  Sum_probs=55.2

Q ss_pred             eEEEEEecCC-ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhh
Q psy11065         45 EVIQVCVPKA-AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        45 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ....+.+|++ +-|+|||+-|.||+.++.-||+.|.|++.++      .|++++ +|---+.|+..++.++.+..
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~------~v~lS~fdpvRReiAr~~le~Li~dgr  293 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPE------VVVLSGFDPIRREIARMTLESLIKDGR  293 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCC------eEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence            5677889994 5599999999999999999999999987543      356666 88888888888888887643

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

Probab=97.54  E-value=0.00019  Score=44.64  Aligned_cols=36  Identities=28%  Similarity=0.593  Sum_probs=33.8

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF   80 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I   80 (138)
                      ....+.||.+.+|..|||+|.+|+.+++.++-+|.|
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.

>KOG2113|consensus

Probab=97.44  E-value=0.00021  Score=57.88  Aligned_cols=66  Identities=24%  Similarity=0.291  Sum_probs=58.4

Q ss_pred             ccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHH
Q psy11065         42 VTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEE  111 (138)
Q Consensus        42 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~  111 (138)
                      +...++.+.+|...++.|.|++|.+||.|+.+|.++|.-+....    +-++.++|.++.+..|+.-|..
T Consensus        23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e----ePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE----EPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC----CCcceeccCchhHHHHhhcCcc
Confidence            35688999999999999999999999999999999998876544    4588899999999999988865

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

Probab=97.24  E-value=0.0013  Score=49.91  Aligned_cols=63  Identities=24%  Similarity=0.411  Sum_probs=53.3

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEe-----cCHHHHHHHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLS-----GSPDQVQEARARIEELI  113 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~-----G~~e~i~~A~~~I~~ii  113 (138)
                      ....+.||.+.++.+||+.|++.+.|.+.++++|.++...      ..++|.     .+|-.+++|.++|+.+-
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~------~~V~i~~~~~t~Dp~~~~ka~d~VkAIg   75 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKT------GSVTIRTTRKTEDPLALLKARDVVKAIG   75 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCC------CeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence            4567999999999999999999999999999999998743      334443     37889999999998874

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

Probab=96.89  E-value=0.0029  Score=49.56  Aligned_cols=62  Identities=27%  Similarity=0.390  Sum_probs=50.9

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHH-HHHHHHHHHHHHHh
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQ-VQEARARIEELIDS  115 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~-i~~A~~~I~~ii~~  115 (138)
                      .-+.||+.+|.++||++|+.++-|.+.|+|+|-+..       +-.|++.+..+. ...|...|..+-.+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-------NG~IWV~~~~~~~e~~~~~aI~~ie~e  210 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-------NGRIWVDGENESLEELAIEAIRKIERE  210 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-------CCEEEecCCCcchHHHHHHHHHHHhhh
Confidence            578999999999999999999999999999999987       456888887773 55566666555444

>KOG2113|consensus

Probab=96.68  E-value=0.002  Score=52.34  Aligned_cols=95  Identities=26%  Similarity=0.370  Sum_probs=73.0

Q ss_pred             HHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCC
Q psy11065          8 QSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD   87 (138)
Q Consensus         8 ~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~   87 (138)
                      -+++..+||.....+|+-..+.++..++-.++..+...+....+|...+|.|.|..|.+|+.|++.++..|.-.-...  
T Consensus        78 dv~~aRrei~saaeH~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~--  155 (394)
T KOG2113|consen   78 DVRRARREIPSAAEHFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCG--  155 (394)
T ss_pred             hHHHHhhcCccccceeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccCC--
Confidence            344555677777777876666666666666667778889999999999999999999999999999999886654332  


Q ss_pred             CCCcEEEEecCHHH-HHHHH
Q psy11065         88 PSDRRCMLSGSPDQ-VQEAR  106 (138)
Q Consensus        88 ~~~r~i~i~G~~e~-i~~A~  106 (138)
                        +.++.+.|-+.. +++|.
T Consensus       156 --~~Vf~Vtg~~~nC~kra~  173 (394)
T KOG2113|consen  156 --EPVFCVTGAPKNCVKRAR  173 (394)
T ss_pred             --CceEEEecCCcchhhhcc
Confidence              567888887766 45554

>KOG2279|consensus

Probab=96.67  E-value=0.0011  Score=57.06  Aligned_cols=75  Identities=27%  Similarity=0.365  Sum_probs=63.1

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      .+....+.+|...++.|+|++|.+++.|+..++++|.++.+..... .+...|.+.......|+.++.+.+.+.+.
T Consensus       138 ~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~-~~~~~i~~qqk~~~~a~~~~~~~~~edee  212 (608)
T KOG2279|consen  138 TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGL-SRLIKISGQQKEVAAAKHLILEKVSEDEE  212 (608)
T ss_pred             Ccccccccchhhhcccccccchhhhcchhccccccccccccccccc-ccceecccccchHHHHHhhhhccccchhH
Confidence            4467889999999999999999999999999999999988643333 67888888888888999999887776544

>PRK12705 hypothetical protein; Provisional

Probab=96.65  E-value=0.0029  Score=54.60  Aligned_cols=68  Identities=26%  Similarity=0.346  Sum_probs=49.9

Q ss_pred             eEEEEEecCCcc-ceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         45 EVIQVCVPKAAV-GVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        45 ~~~~i~IP~~~v-g~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ....+.+|++.+ |+|||+-|.||+.++..||+.|.|++.++     .++...=+|.--+.|...+..++.+..
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~-----~V~ls~fdp~rreia~~~l~~Li~dgr  266 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTPE-----AVVISSFNPIRREIARLTLEKLLADGR  266 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCcc-----chhhcccCccchHHHHHHHHHHHhcCC
Confidence            556778888555 99999999999999999999999987543     233333366666667666766665543

>PRK00468 hypothetical protein; Provisional

Probab=96.60  E-value=0.0029  Score=41.12  Aligned_cols=30  Identities=27%  Similarity=0.489  Sum_probs=26.8

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNET   74 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T   74 (138)
                      ..+++.+.++.+|.||||+|.+|+.|+.--
T Consensus        30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         30 VILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             EEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            678899999999999999999999997543

>PRK02821 hypothetical protein; Provisional

Probab=96.57  E-value=0.0024  Score=41.72  Aligned_cols=31  Identities=29%  Similarity=0.500  Sum_probs=27.8

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETG   75 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tg   75 (138)
                      ..+++.+.++.+|.||||+|.+|+.|+.--.
T Consensus        31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             EEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            6789999999999999999999999986544

>KOG2279|consensus

Probab=96.49  E-value=0.0017  Score=56.00  Aligned_cols=71  Identities=32%  Similarity=0.523  Sum_probs=58.6

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      .....++.||.+.|.+++|+.|.+|+.|++.|++||.+..+.-+  .+++-++.|-+.++..|...+..++..
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g--~e~~~~~~~~p~~v~~a~a~~~~~~~~  136 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG--DERVLLISGFPVQVCKAKAAIHQILTE  136 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC--cccchhhccCCCCCChHHHHHHHHHhc
Confidence            45788999999999999999999999999999999999775433  266666777888888888887666544

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

Probab=96.29  E-value=0.0056  Score=39.93  Aligned_cols=29  Identities=31%  Similarity=0.480  Sum_probs=26.3

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNE   73 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~   73 (138)
                      ...++.+.++.+|.||||+|.+|+.|+.-
T Consensus        30 ~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          30 VTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             EEEEEEECcccccceecCCChhHHHHHHH
Confidence            67889999999999999999999999753

>PRK01064 hypothetical protein; Provisional

Probab=95.99  E-value=0.0089  Score=39.15  Aligned_cols=30  Identities=30%  Similarity=0.522  Sum_probs=27.0

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNET   74 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T   74 (138)
                      ..+++.+..+..|.+|||+|.+|+.|+.-.
T Consensus        30 ~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         30 IIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             EEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            678899999999999999999999998743

>KOG4369|consensus

Probab=95.81  E-value=0.0024  Score=59.55  Aligned_cols=75  Identities=25%  Similarity=0.241  Sum_probs=63.8

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ...-++.+|.....+|||++|.+|+.++.-||+.|.|.+-...+-.+|.+.+.|.++....|...|...|.+...
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv 1413 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDV 1413 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCc
Confidence            355677899999999999999999999999999999988544443489999999999999999999877776443

>KOG2208|consensus

Probab=95.78  E-value=0.026  Score=50.90  Aligned_cols=71  Identities=20%  Similarity=0.407  Sum_probs=62.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ....+.|-++.+..|+||+|.+|.+|++++.|.|.+......   ...+.+.+....+.+|.+.|+.++.+...
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~---~~~v~~~~~~~~~~ka~~~v~~~~~ei~n  417 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSN---NKKVVITGVSANDEKAVEDVEKIIAEILN  417 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCC---CCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence            567889999999999999999999999999999999884433   67889999999999999999988888766

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=95.70  E-value=0.019  Score=41.57  Aligned_cols=38  Identities=32%  Similarity=0.685  Sum_probs=34.6

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ....+.|+...+|..||++|++|+.|++..|-+|.|-.
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve   69 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE   69 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence            46788889999999999999999999999999998866

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=95.51  E-value=0.0091  Score=38.04  Aligned_cols=32  Identities=31%  Similarity=0.436  Sum_probs=28.2

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGA   76 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga   76 (138)
                      ..+.+.+..+..|.||||.|.+++.||.-.+.
T Consensus        29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             eEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            57889999999999999999999999876543

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=95.38  E-value=0.017  Score=41.74  Aligned_cols=38  Identities=24%  Similarity=0.349  Sum_probs=33.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ....+.|+.+..|.+|||+|.|++.++.-++-++.|.+
T Consensus        99 ~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~~  136 (140)
T PRK08406         99 KVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDD  136 (140)
T ss_pred             EEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCeE
Confidence            45677899999999999999999999999999887754

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

Probab=95.07  E-value=0.049  Score=33.11  Aligned_cols=34  Identities=32%  Similarity=0.425  Sum_probs=27.3

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeE
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARV   78 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I   78 (138)
                      ....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4455666665689999999999999999998554

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.

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

Probab=94.37  E-value=0.041  Score=47.30  Aligned_cols=41  Identities=32%  Similarity=0.531  Sum_probs=36.8

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE   85 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~   85 (138)
                      ....+.||...++.+|||+|.+|++|++..|.+|.+.....
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            45788999999999999999999999999999999976443

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=94.37  E-value=0.033  Score=35.75  Aligned_cols=35  Identities=31%  Similarity=0.560  Sum_probs=29.4

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEE
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQ   79 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~   79 (138)
                      ....+.+.....+.|||++|++|++|.+...-.+.
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            55788889999999999999999999887765553

; 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 ....

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

Probab=94.30  E-value=0.2  Score=36.55  Aligned_cols=66  Identities=20%  Similarity=0.304  Sum_probs=48.5

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065          5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      +=+.|++.+.+++..-.+..+-  +.            .+.+-++.|-.++-|.+||++|.++++|..+||-+-.|-+.+
T Consensus        50 ~~e~A~~~I~~ivP~ea~i~di--~F------------d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          50 PPEEAIKIILEIVPEEAGITDI--YF------------DDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             CHHHHHHHHHHhCCCccCceee--Ee------------cCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            4478999999988643222000  00            113448888889999999999999999999999988887744

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.

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.17  E-value=0.37  Score=36.44  Aligned_cols=71  Identities=15%  Similarity=0.372  Sum_probs=60.5

Q ss_pred             EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCC
Q psy11065         46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFS  122 (138)
Q Consensus        46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g  122 (138)
                      ...+.++....-.+...+|..++.|....||+|.+..+      ...+.|+|+...+..+...|.+++.........
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~------~~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~   97 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS------ENRIRITGTKSTAEYIEASINEILSNIRTEEID   97 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC------CcEEEEEccHHHHHHHHHHHHHHHhhcEEEEEe
Confidence            35666678888999999999999998888999999874      567999999999999999999999887665433

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=94.08  E-value=0.099  Score=37.90  Aligned_cols=37  Identities=27%  Similarity=0.630  Sum_probs=33.9

Q ss_pred             EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ..-|.|....+|..||++|++|+.|++..|-+|.|-.
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe   70 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE   70 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence            5778899999999999999999999999999998865

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

>KOG2208|consensus

Probab=93.98  E-value=0.095  Score=47.39  Aligned_cols=90  Identities=16%  Similarity=0.193  Sum_probs=61.7

Q ss_pred             cchhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhC-CeEEE
Q psy11065          2 CSIEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETG-ARVQF   80 (138)
Q Consensus         2 ~~~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tg-a~I~I   80 (138)
                      ++-.+++|.+.++.+...-.+-                    .....+.||...+..+||.+|..|..|..+++ ..|..
T Consensus       397 ~~~~~~ka~~~v~~~~~ei~n~--------------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f  456 (753)
T KOG2208|consen  397 VSANDEKAVEDVEKIIAEILNS--------------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKF  456 (753)
T ss_pred             cccchhHHHHHHHHHHHhhhcc--------------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEec
Confidence            4556788888888877754330                    24678999999999999999999999999999 55555


Q ss_pred             ecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHH
Q psy11065         81 VQMREDDPSDRRCMLSGSPDQVQEARARIEELID  114 (138)
Q Consensus        81 ~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~  114 (138)
                      ......   ....++.+....+..+..+...+..
T Consensus       457 ~~~~~~---~~~~~~~~~~~dv~~~~~~~~~~~~  487 (753)
T KOG2208|consen  457 QNNNNS---SDMVTIRGISKDVEKSVSLLKALKA  487 (753)
T ss_pred             CCCCcc---cccceEeccccccchhHHHHHhhhh
Confidence            443322   3445556655555555555444444

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=93.83  E-value=0.062  Score=38.96  Aligned_cols=39  Identities=26%  Similarity=0.317  Sum_probs=34.4

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      .....+.||.+..+..|||+|.|++...+-++-++.|.+
T Consensus        99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~~  137 (141)
T TIGR01952        99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDD  137 (141)
T ss_pred             CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCeE
Confidence            356778899999999999999999999999998887754

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.

>KOG3273|consensus

Probab=93.82  E-value=0.036  Score=42.65  Aligned_cols=67  Identities=25%  Similarity=0.410  Sum_probs=54.5

Q ss_pred             CccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCCCcccchhhh
Q psy11065         54 AAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLRST  132 (138)
Q Consensus        54 ~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~~~~~~l~~~  132 (138)
                      ..+|+|+|++|+|--.|+..|.++|.+.+        .-|.|-|.-+.+..|+..|..+|.-    ...|-.|..||..
T Consensus       178 RAIGRiaGk~GkTkfaIEn~trtrIVlad--------~kIHiLG~~~niriAR~avcsLIlG----sppgkVy~~LR~v  244 (252)
T KOG3273|consen  178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD--------SKIHILGAFQNIRIARDAVCSLILG----SPPGKVYGNLRNV  244 (252)
T ss_pred             HHHHHhhcCCCcceeeeeccceeEEEecC--------ceEEEeecchhhHHHHHhhHhhhcc----CCchhHHHHHHHH
Confidence            46899999999999999999999999875        3588889999999999999888763    2233467777754

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=93.79  E-value=0.073  Score=34.30  Aligned_cols=36  Identities=22%  Similarity=0.427  Sum_probs=29.6

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF   80 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I   80 (138)
                      ....+.|..+..|.+|||.|.++..||--++.-++-
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            356788888999999999999999999877655443

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.

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

Probab=93.66  E-value=0.061  Score=34.28  Aligned_cols=38  Identities=34%  Similarity=0.574  Sum_probs=29.3

Q ss_pred             EEEEEecCCc-----cceeeccCcHHHHHHHHHh-CCeEEEecC
Q psy11065         46 VIQVCVPKAA-----VGVVIGKGGDMIKKLQNET-GARVQFVQM   83 (138)
Q Consensus        46 ~~~i~IP~~~-----vg~IIGk~G~~Ik~I~~~T-ga~I~I~~~   83 (138)
                      ...+-|-...     +|..||++|..|+.|+++. |-+|.|-.-
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            3455666666     8999999999999999999 899988763

>PRK13764 ATPase; Provisional

Probab=93.39  E-value=0.076  Score=46.88  Aligned_cols=41  Identities=34%  Similarity=0.565  Sum_probs=37.2

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE   85 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~   85 (138)
                      ....+.||...++.+|||+|.+|++|++..|.+|.|....+
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~  521 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE  521 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence            56789999999999999999999999999999999976443

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

Probab=93.35  E-value=0.13  Score=33.83  Aligned_cols=38  Identities=21%  Similarity=0.315  Sum_probs=31.6

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF   80 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I   80 (138)
                      ++...++.|-...-|.|||++|++|++|++.-.-...+
T Consensus        28 t~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          28 TPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             cCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            34568899999999999999999999998877655555

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.

>KOG2874|consensus

Probab=92.70  E-value=0.3  Score=39.40  Aligned_cols=52  Identities=19%  Similarity=0.252  Sum_probs=43.2

Q ss_pred             cceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         56 VGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        56 vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      .-++||++|.|+|.|+=-|.|.|-|..        ..|.+.|.-..+..+...+.+.+..
T Consensus       160 RqRLiGpng~TLKAlelLT~CYilVqG--------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  160 RQRLIGPNGSTLKALELLTNCYILVQG--------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHHhcCCCchhHHHHHHHhhcEEEeeC--------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            467999999999999999999999864        3577788888888888887777654

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=92.11  E-value=0.18  Score=38.28  Aligned_cols=37  Identities=30%  Similarity=0.482  Sum_probs=34.8

Q ss_pred             EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            6778899999999999999999999999999999976

>TIGR01953 NusA transcription termination factor NusA

Probab=91.57  E-value=0.27  Score=40.59  Aligned_cols=38  Identities=26%  Similarity=0.469  Sum_probs=35.5

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ....+.||.+..+..|||+|.|++-..+-||.+|.|..
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            46788999999999999999999999999999999976

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=91.13  E-value=0.28  Score=40.92  Aligned_cols=40  Identities=20%  Similarity=0.205  Sum_probs=36.5

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      ....+.||.+..+..|||+|.|++-..+-||.+|+|..-.
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            5678899999999999999999999999999999997643

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=90.97  E-value=0.55  Score=35.00  Aligned_cols=38  Identities=29%  Similarity=0.568  Sum_probs=32.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      ..+-|.|.... |.-||++|.+++.+++..|-+|.+-..
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            35677777777 999999999999999999999998764

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

Probab=89.93  E-value=0.34  Score=33.36  Aligned_cols=32  Identities=34%  Similarity=0.567  Sum_probs=26.7

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGA   76 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga   76 (138)
                      ..+++.|-...-|.|||++|++|++|++....
T Consensus        61 ~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~   92 (109)
T cd02412          61 DRVEVTIHTARPGIIIGKKGAGIEKLRKELQK   92 (109)
T ss_pred             CCEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence            45788888889999999999999998776543

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=89.52  E-value=0.48  Score=39.41  Aligned_cols=40  Identities=23%  Similarity=0.354  Sum_probs=36.6

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      ....+.||.+..+..|||+|.|++--.+-||.+|.|....
T Consensus       303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~  342 (362)
T PRK12327        303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES  342 (362)
T ss_pred             cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence            5688899999999999999999999999999999997743

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

Probab=89.05  E-value=0.53  Score=30.86  Aligned_cols=30  Identities=30%  Similarity=0.457  Sum_probs=24.2

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNET   74 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T   74 (138)
                      ...++.|....-|.+||++|.+|++|++.-
T Consensus        38 ~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          38 LGTQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             CcEEEEEEECCCCceECCCchhHHHHHHHH
Confidence            346777777899999999999998877654

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

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=88.64  E-value=0.44  Score=40.95  Aligned_cols=39  Identities=23%  Similarity=0.437  Sum_probs=36.1

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      ....+.||.+..+..|||+|.|++...+-||.+|.|...
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            477889999999999999999999999999999999764

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

Probab=88.52  E-value=1.4  Score=38.55  Aligned_cols=66  Identities=23%  Similarity=0.351  Sum_probs=48.1

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065          5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      +-++|++.+.+++..-.+..+- -|             ...+-++.|-..+-|.+|||+|++.++|.++||-.-.|-+.+
T Consensus        73 ~~e~A~~~I~eivP~ea~i~~i-~F-------------d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P  138 (637)
T COG1782          73 PPEEARKIILEIVPEEAGITDI-YF-------------DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP  138 (637)
T ss_pred             CHHHHHHHHHHhCccccCceeE-Ee-------------cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence            4578899999988644322110 00             113458888999999999999999999999999877776644

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

Probab=88.10  E-value=0.49  Score=37.05  Aligned_cols=40  Identities=33%  Similarity=0.436  Sum_probs=30.8

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHH----HhCC---eEEEec
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQN----ETGA---RVQFVQ   82 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~----~Tga---~I~I~~   82 (138)
                      +|...++.|....-|.|||++|++|++|++    .+|.   .|+|.+
T Consensus        49 ~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~E   95 (233)
T COG0092          49 TPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIEE   95 (233)
T ss_pred             cCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEEEE
Confidence            466788899999999999999999987655    4554   345544

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

Probab=87.72  E-value=1.3  Score=39.34  Aligned_cols=67  Identities=21%  Similarity=0.285  Sum_probs=49.5

Q ss_pred             hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065          5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      +-+.|++.+.+++..-.+..+-+ |             .+.+-++.|-..+-|.||||+|.++++|.++||-+-.|.+.+
T Consensus        67 ~~~~~~~~i~~~~~~~~~~~~~~-f-------------~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~  132 (630)
T TIGR03675        67 PPEEAIEKIKEIVPEEAGITDIY-F-------------DDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP  132 (630)
T ss_pred             CHHHHHHHHHHhCCCcCCceeEE-e-------------cCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence            45789999999886443220000 0             123458889999999999999999999999999988887754


Q ss_pred             C
Q psy11065         85 E   85 (138)
Q Consensus        85 ~   85 (138)
                      .
T Consensus       133 ~  133 (630)
T TIGR03675       133 P  133 (630)
T ss_pred             C
Confidence            3

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.

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=86.97  E-value=0.68  Score=39.52  Aligned_cols=38  Identities=24%  Similarity=0.398  Sum_probs=35.3

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ....+.||.+..+..|||+|.|++--.+-||.+|.|..
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            45788999999999999999999999999999999976

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=86.32  E-value=1  Score=34.21  Aligned_cols=38  Identities=32%  Similarity=0.545  Sum_probs=31.9

Q ss_pred             EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065         46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus        46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      ...+.+-.+.+|..||++|.+|+.|+++.|-+|.|-.-
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~  114 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW  114 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence            35556667788999999999999999999988888653

>TIGR00436 era GTP-binding protein Era

Probab=80.30  E-value=2.8  Score=32.81  Aligned_cols=29  Identities=28%  Similarity=0.436  Sum_probs=21.6

Q ss_pred             eEEEEEecCCcc-ceeeccCcHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAV-GVVIGKGGDMIKKLQNE   73 (138)
Q Consensus        45 ~~~~i~IP~~~v-g~IIGk~G~~Ik~I~~~   73 (138)
                      ....+.|+.+.. +.|||++|++||+|..+
T Consensus       221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~  250 (270)
T TIGR00436       221 IHALISVERESQKKIIIGKNGSMIKAIGIA  250 (270)
T ss_pred             EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence            455666665544 88999999999887644

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	138
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		2e-04

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 5/54 (9%)
Query: 65  DMIKKLQNETGARVQFVQMREDD--PSDRRCMLSGSPDQVQEARARIEELIDSV 116
           +MIKK+QN+ G R+QF   + DD    +R   ++G PD+ Q A   I +L+ SV
Sbjct: 23  EMIKKIQNDAGVRIQF---KPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	138
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-24
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-20
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	8e-18
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-20
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-15
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	7e-20
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	8e-20
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-20
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-17
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	8e-20
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-19
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	5e-19
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-19
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-19
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-17
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	8e-19
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	8e-19
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-18
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-16
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	5e-18
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-18
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-16
1we8_A	104	Tudor and KH domain containing protein; structural	3e-16
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-16
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	6e-16
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-15
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	4e-14
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	6e-14
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	6e-14
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-12
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	4e-09
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	1e-08
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	3e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	2e-08
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	3e-08
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-08
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	2e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	8e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	7e-06
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	2e-06
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	7e-06
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	8e-06
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	1e-05
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	6e-04

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

 Score = 88.7 bits (220), Expect = 4e-24
 Identities = 30/71 (42%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           I V VP+ +VGVVIG+ G+MIKK+QN+ G R+QF Q     P ++   + G PD+ + A 
Sbjct: 13  IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP-EKIAHIMGPPDRCEHAA 71

Query: 107 ARIEELIDSVM 117
             I +L+ S+ 
Sbjct: 72  RIINDLLQSLR 82

>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 = 81.4 bits (201), Expect = 1e-20
 Identities = 31/91 (34%), Positives = 46/91 (50%), Gaps = 1/91 (1%)

Query: 27  REFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRED 86
                    R          I V VP+ +VGVVIG+ G+MIKK+QN+ G R+QF Q    
Sbjct: 73  ERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT 132

Query: 87  DPSDRRCMLSGSPDQVQEARARIEELIDSVM 117
            P ++   + G PD+ + A   I +L+ S+ 
Sbjct: 133 GP-EKIAHIMGPPDRCEHAARIINDLLQSLR 162

>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 = 74.1 bits (182), Expect = 8e-18
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDP-SDRRCMLSGSPDQVQE 104
           V ++ +P    G+VIGKGG+ IK+LQ   G ++  +Q    +   D+   + G P +VQ+
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 105 ARARIEELIDS 115
           A   + +++  
Sbjct: 63  ACEMVMDILRE 73

>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 = 80.3 bits (198), Expect = 4e-20
 Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 1/81 (1%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
            +I V +P+ AVG+VIG+ G+MIKK+QN+ G R+QF       P +R   ++G PD+ Q 
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP-ERIAQITGPPDRAQH 61

Query: 105 ARARIEELIDSVMVEQFSGAN 125
           A   I +L+ SV      G  
Sbjct: 62  AAEIITDLLRSVQAGNPGGPG 82

>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 = 67.2 bits (164), Expect = 3e-15
 Identities = 26/99 (26%), Positives = 41/99 (41%), Gaps = 2/99 (2%)

Query: 17  GRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGA 76
           G         R                 +     VP    G++IGKGG+ IK +  ++GA
Sbjct: 76  GNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGA 135

Query: 77  RVQFVQMRE--DDPSDRRCMLSGSPDQVQEARARIEELI 113
           R++  +      DP+ +   + G+P Q+  AR  IEE I
Sbjct: 136 RIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>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 = 76.9 bits (190), Expect = 7e-20
 Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
              ++ +P   +G +IG+ G  I +++  +GA+++ +    +  S R+  ++GS   +  
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIK-IANPVEGSSGRQVTITGSAASISL 64

Query: 105 ARARIEELIDSVMVEQFSGAN 125
           A+  I   + S   E+  G +
Sbjct: 65  AQYLINARLSS---EKGMGCS 82

>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 = 77.0 bits (190), Expect = 8e-20
 Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
            QV +PK   G +IGKGG  IK++++E+GA ++ +    +   DR   ++G+ DQ+Q A+
Sbjct: 16  TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIK-IDEPLEGSEDRIITITGTQDQIQNAQ 74

Query: 107 ARIEELIDS 115
             ++  +  
Sbjct: 75  YLLQNSVKQ 83

>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 = 79.0 bits (195), Expect = 8e-20
 Identities = 23/89 (25%), Positives = 38/89 (42%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
           E++QV +P  AVG +IGK G  IK+L     A ++       D   R  +++G P+   +
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFK 62

Query: 105 ARARIEELIDSVMVEQFSGANFDKLRSTV 133
           A+ RI   +              +    V
Sbjct: 63  AQGRIYGKLKEENFFGPKEEVKLETHIRV 91

>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 = 71.3 bits (175), Expect = 8e-17
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRC-MLSGSPDQVQEA 105
             + VP +A G VIGKGG  + +LQN T A V   + +  D +D+    + G     Q A
Sbjct: 87  THIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMA 146

Query: 106 RARIEELIDSVM 117
           + +I +++  V 
Sbjct: 147 QRKIRDILAQVK 158

>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 = 76.5 bits (189), Expect = 8e-20
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDP--SDRRCMLSGSPDQV 102
           E++++ VP+  VG ++GKGG  + + Q  TGAR+Q  +  E  P   +RR  ++GSP   
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 103 QEARARIEELIDS 115
           Q A+  I + +  
Sbjct: 63  QAAQYLISQRVTY 75

>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 = 75.8 bits (187), Expect = 2e-19
 Identities = 26/80 (32%), Positives = 47/80 (58%), Gaps = 6/80 (7%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
            QV +PK   G +IGKGG  IK++++E+GA ++ +    +   DR   ++G+ DQ+Q A+
Sbjct: 9   TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIK-IDEPLEGSEDRIITITGTQDQIQNAQ 67

Query: 107 ARIEELIDSVMVEQFSGANF 126
             ++  +     +Q+SG  F
Sbjct: 68  YLLQNSV-----KQYSGKFF 82

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

 Score = 74.7 bits (184), Expect = 5e-19
 Identities = 24/87 (27%), Positives = 47/87 (54%), Gaps = 6/87 (6%)

Query: 28  EFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ-MRED 86
           +F++N +G          V ++ +P    G+VIGKGG+ IK+LQ   G ++  +Q   ++
Sbjct: 2   QFHDNANGGQNG-----TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN 56

Query: 87  DPSDRRCMLSGSPDQVQEARARIEELI 113
              D+   + G P +VQ+A   + +++
Sbjct: 57  TNVDKPLRIIGDPYKVQQACEMVMDIL 83

>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 = 74.7 bits (184), Expect = 5e-19
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDP--SDRRCMLSGSPDQV 102
           E++++ VP+  VG ++GKGG  + + Q  TGAR+Q  +  E  P   +RR  ++GSP   
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 103 QEARARIEELIDS 115
           Q A+  I + +  
Sbjct: 63  QAAQYLISQRVTY 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 = 76.3 bits (188), Expect = 7e-19
 Identities = 21/88 (23%), Positives = 41/88 (46%)

Query: 26  MREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE 85
           + E   +              +++ VP +  G +IGKGG  IK+++  TGA+VQ      
Sbjct: 70  LEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDML 129

Query: 86  DDPSDRRCMLSGSPDQVQEARARIEELI 113
            + ++R   ++G P  + E   +I  ++
Sbjct: 130 PNSTERAITIAGIPQSIIECVKQICVVM 157

>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 = 71.3 bits (175), Expect = 7e-17
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
            I++ +    VG +IGK G+ +KK++ E+GAR+      E +  +R   L+G  + + +A
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---SEGNCPERIITLAGPTNAIFKA 62

Query: 106 RARIEELIDSVMVEQFSGANFDK 128
            A I + ++  +    + +    
Sbjct: 63  FAMIIDKLEEDISSSMTNSTAAS 85

>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 = 74.8 bits (184), Expect = 8e-19
 Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
            +  VP   VG +IG+GG+ I ++Q E+G ++Q        P +R CML+G+P+ VQ A+
Sbjct: 17  EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP-ERSCMLTGTPESVQSAK 75

Query: 107 ARIEELIDSVMVEQFSG 123
             ++++++       SG
Sbjct: 76  RLLDQIVEKGRSGPSSG 92

>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 = 74.8 bits (184), Expect = 8e-19
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPS-DRRCMLSGSPDQVQ 103
            V ++ +P +  G+VIGKGG+ IK+LQ   G ++  +Q    +   D+   ++G P +VQ
Sbjct: 15  AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQ 74

Query: 104 EARARIEELIDS 115
           +A+  + ELI  
Sbjct: 75  QAKEMVLELIRD 86

>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 = 76.0 bits (187), Expect = 1e-18
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDP--SDRRCMLSGSPDQVQ 103
            ++V +P  A G +IGKGG  I +LQ ETGA ++  + ++  P  ++R C++ G+ + + 
Sbjct: 7   FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALN 66

Query: 104 EARARIEELIDSVM 117
                I E I  + 
Sbjct: 67  AVHGFIAEKIREMP 80

>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 = 71.0 bits (174), Expect = 1e-16
 Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 18  RNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGAR 77
           R         E       +  +       +++ VP +  G++IGKGG  +K +  ++GA 
Sbjct: 77  REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAW 136

Query: 78  VQFVQ-MREDDPSDRRCMLSGSPDQVQEARARIEELI 113
           VQ  Q     +  +R   +SG P+Q ++A   I + I
Sbjct: 137 VQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKI 173

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

 Score = 73.0 bits (179), Expect = 5e-18
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE--DDPSDRRCMLSGSPDQVQE 104
           +   +P    G+VIG+GG+ +K +  +TGA V+  +      DP+ +  ++ GSP Q+  
Sbjct: 9   MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDH 68

Query: 105 ARARIEELIDS 115
           A+  IEE I+ 
Sbjct: 69  AKQLIEEKIEG 79

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

 Score = 71.9 bits (177), Expect = 6e-18
 Identities = 15/69 (21%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
            ++ +P   +G +IG+ G  I +++  +GA+++ +    +  +DR+  ++GS   +  A+
Sbjct: 7   HELTIPNDLIGCIIGRQGAKINEIRQMSGAQIK-IANPVEGSTDRQVTITGSAASISLAQ 65

Query: 107 ARIEELIDS 115
             I   + S
Sbjct: 66  YLINVRLSS 74

>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 = 68.1 bits (167), Expect = 2e-16
 Identities = 20/69 (28%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
            I++ +    VG +IGK G+ +KK++ E+GAR   + + E +  +R   L+G  + + +A
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGAR---INISEGNCPERIITLAGPTNAIFKA 62

Query: 106 RARIEELID 114
            A I + ++
Sbjct: 63  FAMIIDKLE 71

>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 = 68.3 bits (167), Expect = 3e-16
 Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 1/86 (1%)

Query: 36  RGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPS-DRRCM 94
            G + E T    Q+ VP+ +VG +IG+GG+ I+ +   +GA++   +  E      R   
Sbjct: 6   SGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIK 65

Query: 95  LSGSPDQVQEARARIEELIDSVMVEQ 120
           +SG+  +V  A+  I E +      +
Sbjct: 66  ISGTQKEVAAAKHLILEKVSEDEELR 91

>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 = 67.4 bits (165), Expect = 4e-16
 Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
              V +PK     VIGK G+ ++ L+ +T  ++Q    R DDPS+ +  ++G+ + +++A
Sbjct: 18  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSN-QIKITGTKEGIEKA 74

Query: 106 RARIEELID 114
           R  +  +  
Sbjct: 75  RHEVLLISA 83

>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 = 67.2 bits (164), Expect = 6e-16
 Identities = 13/70 (18%), Positives = 30/70 (42%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           + V V       +IG+ G +I +++ E    +QF    + +    +  ++G     + AR
Sbjct: 19  LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAAR 78

Query: 107 ARIEELIDSV 116
             I  ++  +
Sbjct: 79  DAILRIVGEL 88

>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 = 66.1 bits (161), Expect = 1e-15
 Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           IQV VP   VG+V+G  G  IK++Q  T   +           +    ++G P+ V  AR
Sbjct: 12  IQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVT----PGRDKEPVFAVTGMPENVDRAR 67

Query: 107 ARIEELI 113
             IE  I
Sbjct: 68  EEIEAHI 74

>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 = 62.5 bits (152), Expect = 4e-14
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
             V +       +IG  G  I+K+ +E    ++F   +   P      ++G P+ V+EA 
Sbjct: 19  EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFP--QSGAPDPNCVTVTGLPENVEEAI 76

Query: 107 ARIEELIDSVMVE 119
             I  L +  + +
Sbjct: 77  DHILNLEEEYLAD 89

>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 = 62.5 bits (152), Expect = 6e-14
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           I+V VP      VIG+ G  I+K+ +E    +       +  SD    ++G    +  A+
Sbjct: 19  IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSD-IIAITGLAANLDRAK 75

Query: 107 ARIEELIDSVMVEQF 121
           A + E +  +  EQ 
Sbjct: 76  AGLLERVKELQAEQE 90

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

 Score = 61.2 bits (149), Expect = 6e-14
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
           + +++ +       +IGK G  I +++++    V+      D        + G P  VQ+
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP---DSEKSNLIRIEGDPQGVQQ 61

Query: 105 ARARIEELI 113
           A+  + EL 
Sbjct: 62  AKRELLELA 70

>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 = 58.1 bits (140), Expect = 7e-12
 Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 41  EVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGA-RVQFVQMREDDPSDRRCM----L 95
            + +    + VP+  VG VIGK G +I+++ +++G  RV+     E +      M     
Sbjct: 63  FLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVF 122

Query: 96  SGSPDQVQEARARIEELIDSV 116
            G+ D +  A   ++  ++ +
Sbjct: 123 VGTKDSIANATVLLDYHLNYL 143

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSP-DQVQE 104
             Q  V +  +G+ IG  G  I++ +   G     V   + D       + G   D V++
Sbjct: 5   HEQFIVREDLMGLAIGTHGANIQQARKVPG-----VTAIDLDEDTCTFHIYGEDQDAVKK 59

Query: 105 ARARIEELIDSVMV 118
           AR+ +E   D + V
Sbjct: 60  ARSFLEFAEDVIQV 73

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

 Score = 51.5 bits (122), Expect = 1e-08
 Identities = 12/74 (16%), Positives = 24/74 (32%), Gaps = 6/74 (8%)

Query: 46  VIQVCVPKAAVGVVIGKGGDM--IKKLQNETGARVQF----VQMREDDPSDRRCMLSGSP 99
            + +        ++    GD   +  +  ET   +Q     V     DP  ++  ++G  
Sbjct: 31  TLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYF 90

Query: 100 DQVQEARARIEELI 113
             V  AR  +    
Sbjct: 91  GDVDRARMLMRRNC 104

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

 Score = 41.5 bits (96), Expect = 3e-05
 Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 5/72 (6%)

Query: 47  IQVCVPKAAVGVVIGK--GGDMIKKLQNETGARVQF--VQMREDDPSDRRCM-LSGSPDQ 101
           +   +    V  V+G      ++  ++ ET   + +     R +   +   + + G+ D 
Sbjct: 188 LHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDN 247

Query: 102 VQEARARIEELI 113
           V +AR  I +L+
Sbjct: 248 VLKARRYIMDLL 259

>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 = 50.1 bits (119), Expect = 2e-08
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
           +   V +PK  + V+IGK G   K+++  T  ++       +         +  P  V +
Sbjct: 34  QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVW-ITSTKETEDPLAVWK 92

Query: 105 ARARIEELIDSVMVEQ 120
           AR  +  +      E+
Sbjct: 93  ARDIVLAIGRGFSPER 108

>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 = 49.7 bits (118), Expect = 3e-08
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 8/64 (12%)

Query: 51  VPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIE 110
                 G +IG+ G   + ++  +GA V            +   + G+P Q++ A+  IE
Sbjct: 135 ALPRVRGRIIGRKGRTRQIIEEMSGASVSV--------YGKTVAIIGNPIQIEIAKTAIE 186

Query: 111 ELID 114
           +L  
Sbjct: 187 KLAR 190

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

 Score = 47.9 bits (114), Expect = 2e-08
 Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 4/69 (5%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNE-TGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
           ++V +P      +IG  G +I+ +  E  G  + F    E   SD   ++ G    V++A
Sbjct: 19  VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHF--PVEGSGSD-TVVIRGPSSDVEKA 75

Query: 106 RARIEELID 114
           + ++  L +
Sbjct: 76  KKQLLHLAE 84

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
           +I V +P   +G VIG    MI ++Q +TGA +      EDD +    + +      + A
Sbjct: 599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI----EDDGTIY--IGAADGPAAEAA 652

Query: 106 RARIEELIDSVMVE 119
           RA I  + +    E
Sbjct: 653 RATINGIANPTSPE 666

>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 = 45.0 bits (106), Expect = 8e-07
 Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 52  PKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEE 111
            K   G +IG+GG   + ++  T   +           +    + G  ++   A+  IE 
Sbjct: 105 LKRIKGRIIGEGGRARRTIEEMTDTYINV--------GEYEVAIIGDYERAMAAKQAIEM 156

Query: 112 LID 114
           L +
Sbjct: 157 LAE 159

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

 Score = 42.7 bits (100), Expect = 7e-06
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 1/76 (1%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
             I V V    +G VIG  G++  ++   TG  +                    P  + +
Sbjct: 4   PRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-ENSMVIVEPEAEGIPPVNLMK 62

Query: 105 ARARIEELIDSVMVEQ 120
           A   ++ +      E+
Sbjct: 63  AAEVVKAISLGFPPEK 78

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

 Score = 44.8 bits (107), Expect = 2e-06
 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 6/68 (8%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
           V  V VP +     +G GG  +KKLQ ETG  +       D+ +    + + +P  + EA
Sbjct: 568 VETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQ----VDEETFS--VFAPTPSAMHEA 621

Query: 106 RARIEELI 113
           R  I E+ 
Sbjct: 622 RDFITEIC 629

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

 Score = 42.2 bits (99), Expect = 3e-06
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
           V  V  P      +IGK G  + K+  +       V +   +  D +  L G  + V  A
Sbjct: 28  VSSVAAPSWLHRFIIGKKGQNLAKITQQMPK----VHIEFTEGED-KITLEGPTEDVSVA 82

Query: 106 RARIEELID 114
           + +IE ++ 
Sbjct: 83  QEQIEGMVK 91

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

 Score = 43.3 bits (103), Expect = 7e-06
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
           +  + +    +  VIGKGG +I+ L  ETG  ++     EDD + +  + +   ++ + A
Sbjct: 561 IHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEI----EDDGTVK--IAATDGEKAKHA 614

Query: 106 RARIEELIDSVMV 118
             RIEE+   + V
Sbjct: 615 IRRIEEITAEIEV 627

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
           +  + +P   +  VIG GG +I+++   TGA+V       DD   +  + +    +++ A
Sbjct: 571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDI----NDDGVVK--VSASDGAKIKAA 624

Query: 106 RARIEELIDSVMV 118
              I+ + D   V
Sbjct: 625 IDWIKSITDEAEV 637

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 119

 Score = 40.7 bits (95), Expect = 1e-05
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 10/75 (13%)

Query: 56  VGVVIGKGGDMIKKLQNETGARVQ-------FVQMREDDPSDRR--CMLSG-SPDQVQEA 105
              V G G   ++ +Q ETGA+V         ++      +       +S   P+ +  A
Sbjct: 30  KEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA 89

Query: 106 RARIEELIDSVMVEQ 120
           +   E L+ +V  E 
Sbjct: 90  KKLCENLLQTVHAEY 104

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

 Score = 36.8 bits (85), Expect = 6e-04
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 16/78 (20%)

Query: 56  VGVVIGKGGDMIKKLQNETGARVQFV---------------QMREDDPSDRRCMLSG-SP 99
           VG++IG  G+ +K ++ E  A++                  QM   +      +++  + 
Sbjct: 24  VGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTM 83

Query: 100 DQVQEARARIEELIDSVM 117
           + V++A  +I  ++   +
Sbjct: 84  ENVKKAVEQIRNILKQGI 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	138
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.79
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.76
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.75
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.74
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.74
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.74
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.73
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.73
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.72
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.72
1we8_A	104	Tudor and KH domain containing protein; structural	99.72
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.72
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.7
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.69
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.68
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.68
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.67
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.67
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.66
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.66
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.65
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.65
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.65
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.63
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.56
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.53
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.53
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.51
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	99.51
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.5
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.5
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	99.41
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.38
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.32
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.3
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	99.16
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.1
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.07
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	99.06
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.05
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.9
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.84
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.76
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.74
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.56
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.45
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	97.87
2cxc_A	144	NUSA; transcription termination, RNA binding prote	94.66
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	93.1
2cxc_A	144	NUSA; transcription termination, RNA binding prote	92.18
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	90.89
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	90.56
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	89.12
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	88.97
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	87.33
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	87.3
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	80.98

>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=99.79  E-value=5.9e-19  Score=118.11  Aligned_cols=81  Identities=27%  Similarity=0.545  Sum_probs=71.1

Q ss_pred             CCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         40 WEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        40 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      .+....+.+|.||.+++|.|||++|++|++|+++|||+|+|+++.+. ..++.|+|.|+++++++|+.+|++++.+.+..
T Consensus        10 ~~~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g-~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~~~   88 (92)
T 1x4n_A           10 QQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG-LPERSCMLTGTPESVQSAKRLLDQIVEKGRSG   88 (92)
T ss_dssp             CCCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTT-CSEEEEEEEECHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCC-CCccEEEEEeCHHHHHHHHHHHHHHHHhcccC
Confidence            34566899999999999999999999999999999999999886432 23799999999999999999999999987764


Q ss_pred             cC
Q psy11065        120 QF  121 (138)
Q Consensus       120 ~~  121 (138)
                      ..
T Consensus        89 p~   90 (92)
T 1x4n_A           89 PS   90 (92)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.76  E-value=1.3e-18  Score=116.93  Aligned_cols=79  Identities=30%  Similarity=0.498  Sum_probs=69.3

Q ss_pred             CccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCC-CCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         41 EVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRED-DPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        41 ~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~-~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      .+...+.+|.||.+++|.||||+|++||+|+++|||+|+|+++..+ ...++.|+|.|++++++.|+.+|++++.+.+..
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~   90 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQGSG   90 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCCSSC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhccCCC
Confidence            3556899999999999999999999999999999999999886542 123899999999999999999999999876543

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

Probab=99.75  E-value=2.2e-18  Score=118.36  Aligned_cols=79  Identities=38%  Similarity=0.603  Sum_probs=65.4

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCC
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSG  123 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~  123 (138)
                      +.+.+|.||.++++.||||+|++||+|+++|+|+|+|+++....+ +|.|+|.|+++++++|+.+|++++.+.+....++
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~-er~V~I~G~~e~v~~A~~~I~~ii~~~~~g~~g~   88 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP-EKIAHIMGPPDRCEHAARIINDLLQSLRSGPPGP   88 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSS-EEEEEEESSHHHHHHHHHHHHHHHHHHC------
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCc-eeEEEEEeCHHHHHHHHHHHHHHHhccccCCCCC
Confidence            357899999999999999999999999999999999987543323 7999999999999999999999999988765444

>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=99.74  E-value=2.2e-18  Score=114.63  Aligned_cols=73  Identities=32%  Similarity=0.536  Sum_probs=65.8

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ...+.+|.||.+++|.||||+|++|++|+++|||+|+|++... ...++.|+|.|+++++++|+.+|++++.+.
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 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-GSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCC-CCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4588999999999999999999999999999999999987432 233899999999999999999999999875

>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=99.74  E-value=3e-18  Score=110.07  Aligned_cols=70  Identities=27%  Similarity=0.430  Sum_probs=64.6

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      .+...+|+||.+++|.|||++|++|++|+++|||+|+|+++..+   +|.++|.|+++++.+|+.+|.+++.+
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~---er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP---ERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCS---EEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCCCC---cEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999999999999986332   89999999999999999999999876

>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=99.74  E-value=1.8e-17  Score=108.55  Aligned_cols=73  Identities=32%  Similarity=0.530  Sum_probs=65.4

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ..+.+|.||.+++|.||||+|++|++|+++|||+|+|++... .+.++.|+|.|+++++++|+.+|++++.+..
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~   78 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-GSEDRIITITGTQDQIQNAQYLLQNSVKQYS   78 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTS-CSSEEEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCC-CCCceEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            478999999999999999999999999999999999987532 2337999999999999999999999998753

>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=99.73  E-value=8.3e-18  Score=110.11  Aligned_cols=72  Identities=22%  Similarity=0.426  Sum_probs=64.0

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|+|++... ...++.|+|.|+++++++|+.+|.+++.+.
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~-~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE-GSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCT-TCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCC-CCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            478999999999999999999999999999999999987532 233899999999999999999999999876

>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=99.73  E-value=2.9e-18  Score=112.96  Aligned_cols=74  Identities=30%  Similarity=0.358  Sum_probs=65.7

Q ss_pred             CCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         39 MWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        39 ~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ++.+...+.+|.||.+++|+||||+|++||+|+++|||+|+|++..+    +++++|+|+++++++|+.+|.+++...
T Consensus         4 ~~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~~----~~~v~ItG~~e~v~~A~~~I~~~i~~r   77 (83)
T 2dgr_A            4 GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK----EPVFAVTGMPENVDRAREEIEAHITLR   77 (83)
T ss_dssp             CCSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSSS----CCEEEEEECTTTHHHHHHHHHHHHHSC
T ss_pred             CCCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCCC----CCeEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            34566789999999999999999999999999999999999986432    689999999999999999999976643

>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=99.72  E-value=1.1e-17  Score=107.72  Aligned_cols=71  Identities=34%  Similarity=0.580  Sum_probs=62.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCC--CCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRED--DPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~--~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      .+.+|.||.+++|.|||++|++|++|+++|||+|+|+++.++  ...++.|+|.|+++++..|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999986432  22379999999999999999999998764

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

Probab=99.72  E-value=7.7e-18  Score=108.71  Aligned_cols=73  Identities=21%  Similarity=0.421  Sum_probs=65.3

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|++.. +.+.++.|+|.|+++++..|+.+|.+++.+.
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV-EGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCC-TTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCC-CCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            347899999999999999999999999999999999998743 3334899999999999999999999998753

>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=99.72  E-value=4e-17  Score=111.43  Aligned_cols=81  Identities=28%  Similarity=0.391  Sum_probs=70.2

Q ss_pred             CCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCC-CCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         37 GGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD-PSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        37 ~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~-~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      .......|.+.+|.||.+++|.|||++|++|++|+++|||+|+|++..... +.++.|+|.|+++++++|+.+|.+++.+
T Consensus         7 ~~~s~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T 1we8_A            7 GILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             CCCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            345567889999999999999999999999999999999999998754321 1279999999999999999999999976


Q ss_pred             hh
Q psy11065        116 VM  117 (138)
Q Consensus       116 ~~  117 (138)
                      ..
T Consensus        87 ~~   88 (104)
T 1we8_A           87 DE   88 (104)
T ss_dssp             HH
T ss_pred             Ch
Confidence            43

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

Probab=99.72  E-value=5.3e-17  Score=106.95  Aligned_cols=72  Identities=29%  Similarity=0.541  Sum_probs=64.2

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC-CCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE-DDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      ....+|.||.+++|.||||+|++||+|+++|||+|+|+++.. +...++.|+|.|++++++.|+++|++++.+
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            378899999999999999999999999999999999988643 223388999999999999999999999864

>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=99.70  E-value=2.1e-17  Score=109.31  Aligned_cols=75  Identities=32%  Similarity=0.537  Sum_probs=66.3

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC--CCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE--DDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~--~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      .+.+|.||.+++|.|||++|++|++|+++|||+|+|+++.+  +...++.|+|.|+++++..|+.+|.+++.+....
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~   79 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGV   79 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccc
Confidence            57899999999999999999999999999999999998543  2223799999999999999999999999886554

>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=99.69  E-value=3.1e-16  Score=113.79  Aligned_cols=103  Identities=26%  Similarity=0.297  Sum_probs=82.5

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065          4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      ..+..|+.++.+++.....+.+              ......+.+|.||.+++|.|||++|++|++|+++|||+|.|+++
T Consensus        58 e~v~~A~~~I~~~~~e~~~~~~--------------~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~  123 (163)
T 3krm_A           58 EAQFKAQGRIYGKLKEENFFGP--------------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRD  123 (163)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSCS--------------SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTT
T ss_pred             HHHHHHHHHHHHHHhccccccc--------------ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCC
Confidence            4678899999998876533211              11224677999999999999999999999999999999999876


Q ss_pred             CCCCCCC-cEEEEecCHHHHHHHHHHHHHHHHhhhhcc
Q psy11065         84 REDDPSD-RRCMLSGSPDQVQEARARIEELIDSVMVEQ  120 (138)
Q Consensus        84 ~~~~~~~-r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~  120 (138)
                      ..+..++ +.++|.|+++++..|+.+|.+++.+.++.+
T Consensus       124 ~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~~~  161 (163)
T 3krm_A          124 QTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQH  161 (163)
T ss_dssp             CCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHTC--
T ss_pred             CCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHHHhh
Confidence            5443333 489999999999999999999999987765

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

Probab=99.68  E-value=5.7e-17  Score=111.25  Aligned_cols=73  Identities=30%  Similarity=0.580  Sum_probs=65.7

Q ss_pred             EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCC--CCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD--PSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~--~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      +.+|.||.+++|.||||+|++||+|+++|||+|+|.++.++.  ..++.|+|.|+++++++|+.+|++++.+...
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~~   82 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLC   82 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcccc
Confidence            689999999999999999999999999999999999865322  2379999999999999999999999998764

>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=99.68  E-value=2.2e-16  Score=114.33  Aligned_cols=104  Identities=36%  Similarity=0.557  Sum_probs=82.3

Q ss_pred             hhHHHHHHHHHHHhhcCC--CCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEe
Q psy11065          4 IEFQQSRRWQQGIGRNND--NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFV   81 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~--~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~   81 (138)
                      .+|++|++++.+++....  +|.+...++.          ....+.+|.||.+++|.|||++|++|++|+++|||+|.|+
T Consensus        58 ~~v~~A~~~I~~ii~e~~~~~~~~~~~~~~----------~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~  127 (164)
T 2jvz_A           58 YKVQQACEMVMDILRERDQGGFGDRNEYGS----------RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFK  127 (164)
T ss_dssp             HHHHHHHHHHHHHTTCSSSCCCSSCSSCTT----------SCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEEC
T ss_pred             HHHHHHHHHHHHHHHhccCCCCCCccccCC----------CCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEe
Confidence            468999999999988653  2222111111          0123578999999999999999999999999999999998


Q ss_pred             cCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         82 QMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        82 ~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      +.... +.++.++|.|+++++..|+.+|.+++.+.+.
T Consensus       128 ~~~~~-~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~  163 (164)
T 2jvz_A          128 QDDGT-GPEKIAHIMGPPDRCEHAARIINDLLQSLRS  163 (164)
T ss_dssp             CCCTT-SSEEEEEEESCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCC-CCcEEEEEEcCHHHHHHHHHHHHHHHhhhhC
Confidence            75432 3379999999999999999999999988653

>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=99.67  E-value=1e-16  Score=107.54  Aligned_cols=77  Identities=19%  Similarity=0.315  Sum_probs=68.2

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCC
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFS  122 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g  122 (138)
                      ...+.+|.||.+++|.|||++|++||+|+++|||+|+|++..++   ++.|+|.|+++++.+|+.+|.+++.+.....+.
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~---~~~V~I~G~~e~v~~A~~~I~~i~~~~~~~~~~   91 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP---SNQIKITGTKEGIEKARHEVLLISAEQDKRSGP   91 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSS---CCEEEEEECHHHHHHHHHHHHHHHHHHHTCCSC
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCCC---CCeEEEEECHHHHHHHHHHHHHHhhcccccccc
Confidence            34789999999999999999999999999999999999875432   578999999999999999999999988766543

>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=99.67  E-value=1.9e-16  Score=107.00  Aligned_cols=76  Identities=17%  Similarity=0.276  Sum_probs=67.5

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      ..+.+|.||+++++.|||++|++|++|+++|||+|+|+++..+...++.|+|.|+++++..|+.+|..++.+.+..
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~~   91 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELEQM   91 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHhh
Confidence            3689999999999999999999999999999999999886543323789999999999999999999999886653

>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=99.66  E-value=4.6e-16  Score=104.72  Aligned_cols=76  Identities=22%  Similarity=0.338  Sum_probs=67.6

Q ss_pred             ccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         42 VTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        42 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      ..+.+.+|.||+++++.|||++|++|++|+++|||+|+|+++..  .+.+.|+|.|+++++++|+++|..++.+.++.
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~~~~   89 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA--PDPNCVTVTGLPENVEEAIDHILNLEEEYLAD   89 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC--SCTTEEEEESCHHHHHHHHHHHHHHHHHHHTS
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC--CCCcEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Confidence            34588999999999999999999999999999999999987543  22679999999999999999999999887763

>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=99.66  E-value=3.4e-16  Score=114.88  Aligned_cols=110  Identities=26%  Similarity=0.420  Sum_probs=76.4

Q ss_pred             hhHHHHHHHHHHHhhcCC--CCCCCcCCCCCCCCCCCCCC----ccceEEEEEecCCccceeeccCcHHHHHHHHHhCCe
Q psy11065          4 IEFQQSRRWQQGIGRNND--NFGNMREFNENGDGRGGMWE----VTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGAR   77 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~--~~~~~~~~~~~~~g~~~~~~----~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~   77 (138)
                      ..|++|+++|.+++....  .|+....++.+.+...+.|.    ....+.+|.||.+++|.||||+|++|++|+++|||+
T Consensus        57 ~~v~~A~~~I~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~  136 (174)
T 1j4w_A           57 DRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGAR  136 (174)
T ss_dssp             HHHHHHHHHHHHHHHHHC-----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCE
T ss_pred             HHHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCE
Confidence            478999999999987542  12111000000000001111    123688999999999999999999999999999999


Q ss_pred             EEEecCCCCC--CCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         78 VQFVQMREDD--PSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        78 I~I~~~~~~~--~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      |+|++...+.  +.++.|+|.|+++++..|+.+|+++|
T Consensus       137 I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          137 IELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            9998864322  33799999999999999999999874

>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=99.65  E-value=4.1e-16  Score=114.74  Aligned_cols=113  Identities=21%  Similarity=0.239  Sum_probs=80.5

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065          4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      ..|.+|++++.+++......................+.....+.+|.||.+++|.|||++|++||+|+++|||+|.|.+.
T Consensus        63 ~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~  142 (178)
T 2anr_A           63 EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQK  142 (178)
T ss_dssp             HHHHHHHHHHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCC
T ss_pred             HHHHHHHHHHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCC
Confidence            46899999999998765332110000000000001112334789999999999999999999999999999999999875


Q ss_pred             CC-CCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         84 RE-DDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        84 ~~-~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      .. +.+.++.|+|.|+++++.+|+.+|.+++.+.
T Consensus       143 ~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          143 PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             C----CCEEEEEEESSHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhC
Confidence            42 2233799999999999999999999998864

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

Probab=99.65  E-value=1.5e-16  Score=101.66  Aligned_cols=67  Identities=21%  Similarity=0.362  Sum_probs=61.2

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      ..+.+|.||+++++.|||++|++|++|+++|||+|+|+++...   ++.|+|.|+++++++|+++|.+++
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 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK---SNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSS---SEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCCCc---ccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4788999999999999999999999999999999999886542   689999999999999999998864

>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=99.65  E-value=4e-16  Score=112.88  Aligned_cols=103  Identities=19%  Similarity=0.217  Sum_probs=81.0

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065          4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      .+|+.|+.++.+++......  ...       ........+.+.++.||.+++|.|||++|++|++|+++|||+|.|+++
T Consensus        57 ~~v~~A~~~I~~~i~e~~~~--~~~-------~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~  127 (160)
T 2jzx_A           57 NAIFKAFAMIIDKLEEDISS--SMT-------NSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD  127 (160)
T ss_dssp             HHHHHHHHHHHHHHHHHHTS--CCC-------SSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC
T ss_pred             HHHHHHHHHHHHHHHhhccc--cCC-------CCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC
Confidence            46889999998877642110  000       000112235899999999999999999999999999999999999875


Q ss_pred             CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         84 REDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      ..+.+.++.|+|.|+++++..|+.+|.+++.+
T Consensus       128 ~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          128 MLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             CSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            54445589999999999999999999999876

>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=99.63  E-value=6.6e-16  Score=105.53  Aligned_cols=74  Identities=20%  Similarity=0.253  Sum_probs=66.6

Q ss_pred             ccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         42 VTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        42 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ..|.+.+|.||.++++.|||++|++|++|+++|||+|+|+++...   .+.|+|.|+++++..|+.+|..++.+.+.
T Consensus        14 ~ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~---~~~V~I~G~~e~v~~A~~~I~~i~~e~e~   87 (104)
T 2ctk_A           14 LVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQ---SDIIAITGLAANLDRAKAGLLERVKELQA   87 (104)
T ss_dssp             SSCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTT---CCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCCC---cceEEEEcCHHHHHHHHHHHHHHHhhHHH
Confidence            356899999999999999999999999999999999999875432   56899999999999999999999988664

>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=99.56  E-value=7.7e-15  Score=106.38  Aligned_cols=73  Identities=30%  Similarity=0.485  Sum_probs=66.5

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      +.+++|+||.+++|.|||++|++|++|+++|||+|+|+++..+...+|+|+|.|+++++..|+.+|.+++.+.
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~   74 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEE   74 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            4689999999999999999999999999999999999886544444899999999999999999999998876

>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=99.53  E-value=1.4e-14  Score=106.22  Aligned_cols=74  Identities=41%  Similarity=0.700  Sum_probs=65.0

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      .+.+|+||.+++|.||||+|++||+|+++|||+|+|.+.... ..+++|+|.|+++++.+|+.+|.+++.+....
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~-~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~   76 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGT-TPERIAQITGPPDRAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTS-CSEEEEEEEECHHHHHHHHHHHHHHHHHHC--
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCC-CCccEEEEEeCHHHHHHHHHHHHHHHHhcccC
Confidence            678999999999999999999999999999999999864322 23799999999999999999999999987643

>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=99.53  E-value=1.7e-14  Score=97.11  Aligned_cols=76  Identities=17%  Similarity=0.363  Sum_probs=67.3

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHh-CCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccC
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET-GARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQF  121 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T-ga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~  121 (138)
                      ...+..|.||+++++.|||++|++|++|+++| ||+|+|+++...   .+.|+|.|+.+++++|+++|+.++.+.+...+
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~---~~~V~I~G~~~~v~~A~~~I~~iv~e~e~~~~   91 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSG---SDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSG   91 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTT---CCEEEEESCHHHHHHHHHHHHHHHHHHSCCSS
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCC---cceEEEEcCHHHHHHHHHHHHHHHhhhhhccc
Confidence            34789999999999999999999999999999 999999875432   67899999999999999999999998775543

>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=99.51  E-value=4.3e-14  Score=102.21  Aligned_cols=75  Identities=28%  Similarity=0.505  Sum_probs=65.7

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC-CCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE-DDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      .+.+|.||.+++|.|||++|++||+|+++|||+|++.++.. +...++.++|.|+++++..|+.+|.+++.+....
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~   77 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQG   77 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSC
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCC
Confidence            57899999999999999999999999999999999976532 2223789999999999999999999999876643

>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=99.51  E-value=5.9e-14  Score=99.51  Aligned_cols=95  Identities=19%  Similarity=0.275  Sum_probs=72.9

Q ss_pred             cceEEEEEecCC------ccceeeccCcHHHHHHHHHhCCeEEEecCCC----------------CCCCCcEEEEecCHH
Q psy11065         43 TWEVIQVCVPKA------AVGVVIGKGGDMIKKLQNETGARVQFVQMRE----------------DDPSDRRCMLSGSPD  100 (138)
Q Consensus        43 ~~~~~~i~IP~~------~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~----------------~~~~~r~i~i~G~~e  100 (138)
                      ...+.++.||.+      ++|.|||++|++||+|+++|||+|.|.....                .+...++.+..-+.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            347889999998      8899999999999999999999999976210                001145555566899


Q ss_pred             HHHHHHHHHHHHHHhhhhccCCCC--cccchhhhhcccC
Q psy11065        101 QVQEARARIEELIDSVMVEQFSGA--NFDKLRSTVLANR  137 (138)
Q Consensus       101 ~i~~A~~~I~~ii~~~~~~~~g~~--~~~~l~~~~~~~~  137 (138)
                      .+++|+++|+.++.+......+.-  ...+||++++.|-
T Consensus        85 ~~~~A~~~I~~ll~~~~~~p~~~d~~k~~Ql~eLa~~nG  123 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNG  123 (131)
T ss_dssp             HHHHHHHHHHHHHTTTTSCCTTSSGGGGGGGHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHcC
Confidence            999999999999987443333333  4459999999883

>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=99.50  E-value=2.7e-14  Score=104.97  Aligned_cols=75  Identities=29%  Similarity=0.568  Sum_probs=66.0

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC--CCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE--DDPSDRRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~--~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ...+++|.||.+++|.||||+|++|++|+++|||+|+|.+..+  +...+|+++|.|+++++.+|+.+|.+++.+..
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~   80 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMP   80 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            4588999999999999999999999999999999999987542  22238999999999999999999999997754

>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=99.50  E-value=2.7e-14  Score=103.19  Aligned_cols=73  Identities=26%  Similarity=0.406  Sum_probs=66.3

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      .+.+.+|.||.+++|.|||++|++|++|+++|||+|+|++...+   ++.++|.|+++++.+|+.+|.+++.+...
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~---~r~v~I~G~~~~v~~A~~~I~~~i~e~~~   75 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP---ERIITLAGPTNAIFKAFAMIIDKLEEDIS   75 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTTT---EEEEEEEEEHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCCCC---ceEEEEEeCHHHHHHHHHHHHHHHHhhcc
Confidence            56899999999999999999999999999999999999985332   89999999999999999999999887643

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

Probab=99.41  E-value=1.4e-12  Score=91.09  Aligned_cols=74  Identities=22%  Similarity=0.248  Sum_probs=60.7

Q ss_pred             ceEEEEEecCC-------ccceeeccCcHHHHHHHHHhCCeEEEecCCC-----------CCCCCcEEEEecCHHHHHHH
Q psy11065         44 WEVIQVCVPKA-------AVGVVIGKGGDMIKKLQNETGARVQFVQMRE-----------DDPSDRRCMLSGSPDQVQEA  105 (138)
Q Consensus        44 ~~~~~i~IP~~-------~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-----------~~~~~r~i~i~G~~e~i~~A  105 (138)
                      ....++.||.+       ++|.|||++|++||+|+++|||+|.|.....           ..+ .++.+.+.+++++++|
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   89 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEP-MYIYISHPKPEGLAAA   89 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSB-CEEEEEESSHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCC-cEEEEEeCCHHHHHHH
Confidence            46778888765       7899999999999999999999999973311           111 5777778899999999


Q ss_pred             HHHHHHHHHhhhh
Q psy11065        106 RARIEELIDSVMV  118 (138)
Q Consensus       106 ~~~I~~ii~~~~~  118 (138)
                      +++|++++.+...
T Consensus        90 ~~~Ie~Ll~~v~~  102 (119)
T 2yqr_A           90 KKLCENLLQTVHA  102 (119)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHhhchHH
Confidence            9999999987654

>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=99.38  E-value=1.7e-12  Score=88.27  Aligned_cols=72  Identities=21%  Similarity=0.408  Sum_probs=64.7

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHH-hCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNE-TGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFS  122 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~-Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g  122 (138)
                      .+.+|.||..+++.|||++|++|++|+++ ++++|++++   .   ++.|+|.|+++.|.+|+..|+.++.+.......
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~---~---~~~ItI~G~~~~V~~a~~~I~~~v~el~~~~~~   99 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---G---EDKITLEGPTEDVSVAQEQIEGMVKDLINRSGP   99 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---S---SCEEEEEECHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC---C---CCEEEEECCHHHHHHHHHHHHHHHHHHHhhccc
Confidence            78999999999999999999999999997 589999987   2   578999999999999999999999987765443

>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=99.32  E-value=2.2e-12  Score=92.50  Aligned_cols=70  Identities=26%  Similarity=0.513  Sum_probs=60.1

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCC-eEEEecCCCCC-C-CC--cEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGA-RVQFVQMREDD-P-SD--RRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga-~I~I~~~~~~~-~-~~--r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      .++.||.+.+|++|||+|.||+.|++.||+ +|+|.++.+.. + .+  +.++|.|++++++.|+.+|+..|.+.
T Consensus        69 ~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~l  143 (144)
T 2qnd_A           69 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYL  143 (144)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            789999999999999999999999999997 99998754331 1 13  35899999999999999999998753

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.30  E-value=4.9e-13  Score=89.22  Aligned_cols=72  Identities=22%  Similarity=0.289  Sum_probs=61.1

Q ss_pred             ccceEEEEEecCCccceeeccCcHHHHHHHHHhCCe-EEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhhhc
Q psy11065         42 VTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGAR-VQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        42 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~-I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      ..+...+|.||+++++.|||++|++|++|+++||++ |.|.++      +..|.|.| +.+++++|+++|+.+......+
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed------dG~V~I~g~~~ea~~~A~~~I~~ie~~~~vp   85 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED------TGTFRIYGESADAVKKARGFLEFVEDFIQVP   85 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT------TTEEEEEESSHHHHHHHHHHHSCCCCCCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC------CCEEEEEECCHHHHHHHHHHHHhhheEEecC
Confidence            345889999999999999999999999999999998 999752      35688888 9999999999997765544433

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

Probab=99.16  E-value=3.1e-11  Score=86.33  Aligned_cols=90  Identities=19%  Similarity=0.255  Sum_probs=63.7

Q ss_pred             eEEEEEecCCc------cceeeccCcHHHHHHHHHhCCeEEEecCCCC----------------CCC-CcEEEEec-CHH
Q psy11065         45 EVIQVCVPKAA------VGVVIGKGGDMIKKLQNETGARVQFVQMRED----------------DPS-DRRCMLSG-SPD  100 (138)
Q Consensus        45 ~~~~i~IP~~~------vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~----------------~~~-~r~i~i~G-~~e  100 (138)
                      ...++.||.+.      +|.|||++|.++|+|+++|||+|.|......                ... .--|.|++ +++
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            45778888665      9999999999999999999999999864310                000 11334444 443


Q ss_pred             -----HHHHHHHHHHHHHHhhhhccCCCC--cccchhhhhcccC
Q psy11065        101 -----QVQEARARIEELIDSVMVEQFSGA--NFDKLRSTVLANR  137 (138)
Q Consensus       101 -----~i~~A~~~I~~ii~~~~~~~~g~~--~~~~l~~~~~~~~  137 (138)
                           .+++|+++|+.++.....   +..  ...+||++++.|-
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~~e---~~de~K~~QL~eLA~lNG  122 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPAAE---GEDSLKKMKLMELAILNG  122 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCSS---SSSHHHHHHHTGGGSSST
T ss_pred             hhHHHHHHHHHHHHHHHCCCCCc---chhHHHHHHHHHHHHhcC
Confidence                 789999999999864321   222  3348999999883

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

Probab=99.10  E-value=6.2e-11  Score=96.72  Aligned_cols=71  Identities=15%  Similarity=0.222  Sum_probs=62.0

Q ss_pred             ccceEEEEEecCCccceeeccCc--HHHHHHHHHhCCeEEEecCC--C--CCCCCcEEEEecCHHHHHHHHHHHHHH
Q psy11065         42 VTWEVIQVCVPKAAVGVVIGKGG--DMIKKLQNETGARVQFVQMR--E--DDPSDRRCMLSGSPDQVQEARARIEEL  112 (138)
Q Consensus        42 ~~~~~~~i~IP~~~vg~IIGk~G--~~Ik~I~~~Tga~I~I~~~~--~--~~~~~r~i~i~G~~e~i~~A~~~I~~i  112 (138)
                      ....+.++.||..+++.||||+|  ++|++|+++|||+|++++..  .  +......|+|+|.+++|++|+..|.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            35689999999999999999999  99999999999999998765  1  112267899999999999999999885

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

Probab=99.07  E-value=6.1e-10  Score=84.97  Aligned_cols=93  Identities=22%  Similarity=0.306  Sum_probs=68.5

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecC-----------CccceeeccCcHHHHHHHH
Q psy11065          4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPK-----------AAVGVVIGKGGDMIKKLQN   72 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~-----------~~vg~IIGk~G~~Ik~I~~   72 (138)
                      .++++|+++|.++....+.   ..+..-        ..+......+.|+.           ..+|+||||+|+||+.|++
T Consensus        88 ~~i~kA~~~I~~i~rg~~~---e~g~~l--------l~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~  156 (219)
T 2e3u_A           88 LAVWKARDIVLAIGRGFSP---ERAFRL--------LNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEE  156 (219)
T ss_dssp             HHHHHHHHHHHHHHTTCCH---HHHGGG--------GSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCCc---ccccee--------ccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHH
Confidence            6789999999999853210   000000        00111233455542           2689999999999999999


Q ss_pred             HhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         73 ETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        73 ~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      .|||+|.|.+        +.+.|.|++++++.|+.+|.+++..
T Consensus       157 ~Tg~~I~v~~--------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          157 MSGASVSVYG--------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHCCEEEEET--------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             HhCceEEECC--------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            9999999964        4699999999999999999999954

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

Probab=99.06  E-value=1.1e-10  Score=100.74  Aligned_cols=94  Identities=28%  Similarity=0.281  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC
Q psy11065          6 FQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE   85 (138)
Q Consensus         6 ~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~   85 (138)
                      +++|++-..+|++.+...        -......+...+|....+.||+++++.|||++|++||.|+++|||+|.|.++  
T Consensus       536 L~~A~~g~~~I~~~m~~a--------l~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~--  605 (630)
T 3u1k_A          536 IQQASVAKKEILQIMNKT--------ISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE--  605 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHH--------CSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--
T ss_pred             HHHHHHHHHHHHHHHHHH--------HHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC--
Confidence            567777777776633110        0000112344567899999999999999999999999999999999999862  


Q ss_pred             CCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         86 DDPSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        86 ~~~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                          .++.+...+++++++|+++|++++
T Consensus       606 ----G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          606 ----ETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             ----SEEEEEESSHHHHHHHHHHTTC--
T ss_pred             ----cEEEEEeCCHHHHHHHHHHHHHHh
Confidence                344444556899999999998876

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

Probab=99.05  E-value=2e-10  Score=87.59  Aligned_cols=69  Identities=22%  Similarity=0.271  Sum_probs=57.8

Q ss_pred             CCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecC-----HHHHHHHHHHHHHHHH
Q psy11065         40 WEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGS-----PDQVQEARARIEELID  114 (138)
Q Consensus        40 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~-----~e~i~~A~~~I~~ii~  114 (138)
                      +..+|...++.||+++++.|||++|++|+.|+++|||+|+|+.+      +..++|.++     ++++++|+++|.+++.
T Consensus        29 s~~aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~------~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           29 EEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE------TGEVWITSTKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             ----CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT------TCEEEEEECTTCCSHHHHHHHHHHHHHHHT
T ss_pred             CCCCCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC------CCEEEEecCCCCCCHHHHHHHHHHHHHHhc
Confidence            34567889999999999999999999999999999999999842      345677664     7999999999999983

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

Probab=98.90  E-value=4e-09  Score=86.03  Aligned_cols=69  Identities=17%  Similarity=0.264  Sum_probs=57.2

Q ss_pred             eEEEEEecCCccceeeccCc--HHHHHHHHHhCCeEEEecCCCCC---CCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGG--DMIKKLQNETGARVQFVQMREDD---PSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G--~~Ik~I~~~Tga~I~I~~~~~~~---~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      .+.++.|+...+..|||++|  ..|++|+++|||+|.+++..+..   .....|+|.|+.++|..|++.|.++|
T Consensus       186 ~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          186 FTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             EEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             eEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            68899999999999999998  67799999999999998754321   12468999999999999999999885

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

Probab=98.84  E-value=1e-09  Score=95.93  Aligned_cols=104  Identities=17%  Similarity=0.271  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHhhcCCC-CCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065          6 FQQSRRWQQGIGRNNDN-FGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus         6 ~~~ak~~v~~i~~~~~~-~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      +++|++-..+|++.... ...         .-..+...+|....+.||+++++.|||++|++||.|+++||++|.|.++ 
T Consensus       539 L~~A~~g~~~I~~~m~~al~~---------~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd-  608 (726)
T 4aid_A          539 LAQAKEGRAHILGEMNKAMDA---------PRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD-  608 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSS---------CCSSCCSSCCC---------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHh---------hhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC-
Confidence            67777777777764321 100         0112344567899999999999999999999999999999999999862 


Q ss_pred             CCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCCC
Q psy11065         85 EDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGA  124 (138)
Q Consensus        85 ~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~~  124 (138)
                           ..+.+...+.+++++|+++|+.++.+.+..+.--|
T Consensus       609 -----G~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G  643 (726)
T 4aid_A          609 -----GVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDG  643 (726)
T ss_dssp             ----------CCSCHHHHHHHHHC----------------
T ss_pred             -----ceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEE
Confidence                 45556667899999999999999988776654443

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

Probab=98.76  E-value=1.9e-08  Score=75.21  Aligned_cols=92  Identities=16%  Similarity=0.250  Sum_probs=68.7

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecC----------CccceeeccCcHHHHHHHHH
Q psy11065          4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPK----------AAVGVVIGKGGDMIKKLQNE   73 (138)
Q Consensus         4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~----------~~vg~IIGk~G~~Ik~I~~~   73 (138)
                      ..+.+|+++|.++...-+   ...+..-        ..+......|.|+.          ..+|+|||++|.||+.|+..
T Consensus        58 ~~i~KA~dlI~ai~rgf~---~e~A~~L--------l~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~  126 (191)
T 1tua_A           58 VNLMKAAEVVKAISLGFP---PEKAFRL--------LEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEM  126 (191)
T ss_dssp             HHHHHHHHHHHHHHHTCC---HHHHGGG--------GSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCC---HHHhhhc--------ccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHH
Confidence            467899999999887532   1111100        00112345566653          35899999999999999999


Q ss_pred             hCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHH
Q psy11065         74 TGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELID  114 (138)
Q Consensus        74 Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~  114 (138)
                      |||+|.|.+        +.+.+.|+++.++.|+..|.+++.
T Consensus       127 Tg~~I~v~~--------~~v~i~G~~~~i~~Ar~~i~~li~  159 (191)
T 1tua_A          127 TDTYINVGE--------YEVAIIGDYERAMAAKQAIEMLAE  159 (191)
T ss_dssp             HTCEEEECS--------SEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HCceEEEcC--------CEEEEEeChHHHHHHHHHHHHHHc
Confidence            999999965        368999999999999999999995

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

Probab=98.74  E-value=1.6e-08  Score=75.65  Aligned_cols=64  Identities=19%  Similarity=0.279  Sum_probs=57.8

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEe-----cCHHHHHHHHHHHHHHHHhh
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLS-----GSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~-----G~~e~i~~A~~~I~~ii~~~  116 (138)
                      .++.||.+.+|.|||++|++++.|++.++++|+++..      ++.+++.     |++.++.+|.++|.++....
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~------~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf   74 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   74 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC------CCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCC
Confidence            6899999999999999999999999999999999753      5667777     99999999999999988743

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

Probab=98.56  E-value=8e-08  Score=68.57  Aligned_cols=61  Identities=23%  Similarity=0.328  Sum_probs=48.4

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI  109 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I  109 (138)
                      .+.+|.||.+.+|.+||++|++|+.|++++|  |++.... +++ +.++...++|+.+..|+.++
T Consensus         4 ~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~-~~~i~~~~~p~~v~~~~~~l   64 (144)
T 2qnd_A            4 FHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDT-CTFHIYGEDQDAVKKARSFL   64 (144)
T ss_dssp             CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTT-TEEEEEESSHHHHHHHHHHH
T ss_pred             eEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCc-hheeeccCCHHHHHHHHHhh
Confidence            5789999999999999999999999999999  4443322 122 56777778899999987643

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

Probab=98.45  E-value=7.3e-07  Score=63.09  Aligned_cols=73  Identities=12%  Similarity=0.183  Sum_probs=64.2

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      .....|.|....++.|||++|+.|+.|+..|++.|+|..-..  ++...|+|.|++..-..|+.+|..+..--++
T Consensus        55 ~dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s--~g~tEVtIfG~~~~Q~rak~MI~sLA~~hr~  127 (140)
T 3v69_A           55 EDPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP--ERRAEIWIFGPPPFRRDVDRMLTDLAHYCRM  127 (140)
T ss_dssp             SSCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT--TSCEEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC--CCcEEEEEECCHHHHHHHHHHHHHHHHHHHH
Confidence            356789999999999999999999999999999999987633  3589999999999999999999998775443

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

Probab=98.14  E-value=2.7e-07  Score=80.79  Aligned_cols=78  Identities=23%  Similarity=0.348  Sum_probs=0.0

Q ss_pred             CccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhcc
Q psy11065         41 EVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQ  120 (138)
Q Consensus        41 ~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~  120 (138)
                      ..+|....+.||+++++.+||++|++|+.|.++||+.|+|.++      ..+.+...+.+.+.+|.++|+.++.+.+..+
T Consensus       556 ~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~d------g~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~  629 (723)
T 3cdi_A          556 EFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDD------GTVKIAATDGEKAKHAIRRIEEITAEIEVGR  629 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecCC------ccEEEecCCHHHHHHHHHHHHHHhhhhhcCc
Confidence            4467899999999999999999999999999999999999862      3455556677888999999999887666554


Q ss_pred             CCCC
Q psy11065        121 FSGA  124 (138)
Q Consensus       121 ~g~~  124 (138)
                      .--|
T Consensus       630 i~~G  633 (723)
T 3cdi_A          630 VYTG  633 (723)
T ss_dssp             ----
T ss_pred             EEEE
Confidence            4333

>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=97.87  E-value=3.3e-07  Score=80.60  Aligned_cols=93  Identities=23%  Similarity=0.259  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHHHhhcCCC-CCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065          5 EFQQSRRWQQGIGRNNDN-FGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus         5 ~~~~ak~~v~~i~~~~~~-~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      .+++|++...+|++.... ....          ..+....|....+.||+++++.+||++|++||.|+++||+.|.|.++
T Consensus       567 aL~~A~~~~~~I~~~m~~al~~~----------~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~d  636 (757)
T 1e3p_A          567 ALKQARDARLHILDVMMEAIDTP----------DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD  636 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSSC----------CCCCTTSCBCCCC------------------CTTCCCCCSCC-----
T ss_pred             HHHHHHHHHHHHHHHHHHHhccc----------ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecCC
Confidence            356777777776663311 1000          12233456778899999999999999999999999999999999851


Q ss_pred             CCCCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         84 REDDPSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                            ..+.+...+.+...+|.++|+.+.
T Consensus       637 ------G~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          637 ------GTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             ---------CCCBSSHHHHCC---------
T ss_pred             ------ceEEEecCCHHHHHHHHHHHHHhc
Confidence                  344444567788888988888877

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

Probab=94.66  E-value=0.036  Score=39.29  Aligned_cols=40  Identities=28%  Similarity=0.534  Sum_probs=36.2

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      ....+.|+...+|..||++|++|+.|+++.|-+|.|-.-.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s   75 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYS   75 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECC
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcC
Confidence            5678999999999999999999999999999999887643

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=93.10  E-value=0.24  Score=37.32  Aligned_cols=59  Identities=31%  Similarity=0.331  Sum_probs=47.6

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHH
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEEL  112 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~i  112 (138)
                      .-+.++...+.+++|+++..++.|.+.+++.|.+-.       +-.|+|.++......+...|..+
T Consensus       138 ~v~~vs~~~v~rl~~~~~~~l~~l~~~~~~ei~vG~-------NG~IWi~~~~~~~~~~~~ai~~~  196 (229)
T 2ba0_A          138 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-------NGLIWVNGDRRKVSIAEEAIYLI  196 (229)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-------TSEEEEESCHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHhHHHhcCCchHHHHhcccCCeEEEEEC-------CcEEEEeCCchhHHHHHHHHHHH
Confidence            567899999999999999999999999999999976       45789998877555555445433

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

Probab=92.18  E-value=0.033  Score=39.47  Aligned_cols=38  Identities=21%  Similarity=0.318  Sum_probs=34.4

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ   82 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~   82 (138)
                      ....+.||.+..+..|||+|.+++-..+-||.+|.|..
T Consensus       103 ~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~~  140 (144)
T 2cxc_A          103 KQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEK  140 (144)
T ss_dssp             EEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEEE
T ss_pred             EEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCceE
Confidence            56778999999999999999999999999999888754

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

Probab=90.89  E-value=0.2  Score=38.53  Aligned_cols=41  Identities=24%  Similarity=0.327  Sum_probs=37.0

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE   85 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~   85 (138)
                      ....+.||.+..+.-|||+|.|++--.+-||.+|.|.....
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            46788999999999999999999999999999999977543

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=90.56  E-value=1.3  Score=33.27  Aligned_cols=59  Identities=25%  Similarity=0.272  Sum_probs=47.1

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHH
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEEL  112 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~i  112 (138)
                      .-+.++...+..++|+++..++.|.+.++++|.+-.       +..|+|.+ +++.+..+...|..+
T Consensus       150 ~vv~vs~~~~~rl~~~~~~~l~~l~~~~~~~i~vG~-------NG~IWi~~~~~~~~~~~~~ai~~~  209 (235)
T 2z0s_A          150 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-------NGRIHLECPNEDLEAIAVMAIKII  209 (235)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-------TTEEEEECSCHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHhHHHhcCcchHHHHhcccCCeEEEEeC-------CCEEEEecCCHHHHHHHHHHHHHH
Confidence            567899999999999999999999989999999977       44677775 665666555555544

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

Probab=89.12  E-value=0.33  Score=39.29  Aligned_cols=41  Identities=24%  Similarity=0.327  Sum_probs=37.2

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE   85 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~   85 (138)
                      ....+.||.+..+..|||+|.|++-..+-||.+|.|.....
T Consensus       307 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  347 (366)
T 1k0r_A          307 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  347 (366)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESSC
T ss_pred             cEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHHH
Confidence            56888999999999999999999999999999999977543

>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=88.97  E-value=0.43  Score=38.30  Aligned_cols=39  Identities=26%  Similarity=0.469  Sum_probs=35.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      ....+.||.+..+.-|||+|.|++--.+-||.+|.|...
T Consensus       303 ~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          303 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            467889999999999999999999999999999999763

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

Probab=87.33  E-value=0.3  Score=34.80  Aligned_cols=31  Identities=19%  Similarity=0.176  Sum_probs=26.6

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETG   75 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tg   75 (138)
                      .++.+.|..+..|.+|||.|.|++.||--+.
T Consensus        33 ~~i~i~i~ged~glLIGK~G~TL~ALQyL~~   63 (152)
T 2pt7_G           33 GVLLIDIDGEDSALLIGEKGYRYKALSYLLF   63 (152)
T ss_dssp             TEEEEEEEEGGGTTTTCGGGHHHHHHHHHHH
T ss_pred             CEEEEEEecCCcceEECCCCcchHHHHHHHH
Confidence            3577888899999999999999999987663

>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1

Probab=87.30  E-value=0.23  Score=32.38  Aligned_cols=30  Identities=20%  Similarity=0.277  Sum_probs=24.3

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHH
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQN   72 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~   72 (138)
                      ++...++.|....-|.|||++|..|++|++
T Consensus        33 ~~~~i~I~I~tarPg~vIGkkG~~Ie~L~~   62 (92)
T 1wh9_A           33 TPTRTEIIILATRTQNVLGEKGRRIRELTA   62 (92)
T ss_dssp             CSSCEEEEEEESCHHHHHCGGGHHHHHHHH
T ss_pred             CCCeEEEEEEeCCCceEEcCCcHHHHHHHH
Confidence            345678888889999999999998877544

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=80.98  E-value=1.7  Score=31.42  Aligned_cols=58  Identities=12%  Similarity=0.029  Sum_probs=44.6

Q ss_pred             EEEEecCCccceeeccCcH-HHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHH
Q psy11065         47 IQVCVPKAAVGVVIGKGGD-MIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEE  111 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~-~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~  111 (138)
                      .-+.||..++.+++++.+. .++.|.+.+++.|.+-.       +-.|+|.+ ++.....+...|..
T Consensus        93 ~l~~v~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~-------NG~IWi~~~~~~~~~~v~~aI~~  152 (175)
T 2ja9_A           93 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-------NGKIWVKCEELSNTLACYRTIME  152 (175)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-------TTEEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEEEcHHHhhHHhcCCCcchHHhhhccCCeEEEEEC-------CcEEEEecCCHHHHHHHHHHHHH
Confidence            6789999999999998888 99999989999999987       34677775 55444444455554

---

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	138
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-18
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-17
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	6e-17
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-16
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	6e-16
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-15
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-15
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-15
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	8e-15
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-14
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-14
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-14
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-14
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	5e-14
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-11
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-11
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-10
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-09
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	8e-09
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	8e-09
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	4e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	4e-07
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	9e-07

>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 = 71.8 bits (176), Expect = 2e-18
 Identities = 31/72 (43%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
            +I V +P+ AVG+VIG+ G+MIKK+QN+ G R+QF       P +R   ++G PD+ Q 
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP-ERIAQITGPPDRAQH 61

Query: 105 ARARIEELIDSV 116
           A   I +L+ SV
Sbjct: 62  AAEIITDLLRSV 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 = 69.1 bits (169), Expect = 3e-17
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDP--SDRRCMLSGSPDQV 102
           E++++ VP+  VG ++GKGG  + + Q  TGAR+Q  +  E  P   +RR  ++GSP   
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 103 QEARARIEELI 113
           Q A+  I + +
Sbjct: 63  QAAQYLISQRV 73

>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 = 68.3 bits (167), Expect = 6e-17
 Identities = 23/67 (34%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 48  QVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARA 107
           +  VP   VG +IG+GG+ I ++Q E+G ++Q        P +R CML+G+P+ VQ A+ 
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP-ERSCMLTGTPESVQSAKR 69

Query: 108 RIEELID 114
            ++++++
Sbjct: 70  LLDQIVE 76

>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 = 65.6 bits (160), Expect = 5e-16
 Identities = 19/68 (27%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           I++ +    VG +IGK G+ +KK++ E+GAR+   +    +  +R   L+G  + + +A 
Sbjct: 6   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISE---GNCPERIITLAGPTNAIFKAF 62

Query: 107 ARIEELID 114
           A I + ++
Sbjct: 63  AMIIDKLE 70

>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 = 65.6 bits (160), Expect = 6e-16
 Identities = 13/70 (18%), Positives = 30/70 (42%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           + V V       +IG+ G +I +++ E    +QF    + +    +  ++G     + AR
Sbjct: 12  LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAAR 71

Query: 107 ARIEELIDSV 116
             I  ++  +
Sbjct: 72  DAILRIVGEL 81

>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 = 64.9 bits (158), Expect = 1e-15
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDP--SDRRCMLSGSPDQV 102
           +     VP    G++IGKGG+ IK +  ++GAR++  +    +   + +   + G+P Q+
Sbjct: 1   QEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQI 60

Query: 103 QEARARIEELI 113
             AR  IEE I
Sbjct: 61  DYARQLIEEKI 71

>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 = 64.3 bits (157), Expect = 2e-15
 Identities = 15/68 (22%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
             V +PK     VIGK G+ ++ L+ +T  ++Q       D    +  ++G+ + +++AR
Sbjct: 12  ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI---PRPDDPSNQIKITGTKEGIEKAR 68

Query: 107 ARIEELID 114
             +  +  
Sbjct: 69  HEVLLISA 76

>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 = 63.7 bits (155), Expect = 3e-15
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 41  EVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPD 100
           + T E+    +P   +G +IG+ G  I +++  +GA+++      +  S R+  ++GS  
Sbjct: 1   QTTHELT---IPNNLIGCIIGRQGANINEIRQMSGAQIKIAN-PVEGSSGRQVTITGSAA 56

Query: 101 QVQEARARIEELI 113
            +  A+  I   +
Sbjct: 57  SISLAQYLINARL 69

>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 = 62.9 bits (153), Expect = 8e-15
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           I+V VP      VIG+ G  I+K+ +E    +        +       ++G    +  A+
Sbjct: 12  IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA---PELQSDIIAITGLAANLDRAK 68

Query: 107 ARIEELIDSVMVEQ 120
           A + E +  +  EQ
Sbjct: 69  AGLLERVKELQAEQ 82

>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 = 62.2 bits (151), Expect = 1e-14
 Identities = 25/76 (32%), Positives = 45/76 (59%), Gaps = 6/76 (7%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
            QV +PK   G +IGKGG  IK++++E+GA ++  +  E    DR   ++G+ DQ+Q A+
Sbjct: 6   TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE-DRIITITGTQDQIQNAQ 64

Query: 107 ARIEELIDSVMVEQFS 122
             ++  +     +Q+S
Sbjct: 65  YLLQNSV-----KQYS 75

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.7 bits (152), Expect = 2e-14
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ-MREDDPSDRRCMLSGSPDQVQE 104
             Q+ VP+ +VG +IG+GG+ I+ +   +GA++   +         R   +SG+  +V  
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAA 75

Query: 105 ARARIEELIDSVM 117
           A+  I E +    
Sbjct: 76  AKHLILEKVSEDE 88

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

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

 Score = 61.4 bits (149), Expect = 3e-14
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
             V +       +IG  G  I+K+ +E    ++F   +   P      ++G P+ V+EA 
Sbjct: 12  EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF--PQSGAPDPNCVTVTGLPENVEEAI 69

Query: 107 ARIEELIDSVM 117
             I  L +  +
Sbjct: 70  DHILNLEEEYL 80

>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 = 61.1 bits (148), Expect = 4e-14
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 7/84 (8%)

Query: 32  NGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPS-D 90
           +GDG G       E++   +P +  G+VIGKGG+ IK+LQ   G ++  +Q    +   D
Sbjct: 1   HGDGPG---NAVQEIM---IPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGAD 54

Query: 91  RRCMLSGSPDQVQEARARIEELID 114
           +   ++G P +VQ+A+  + ELI 
Sbjct: 55  KPLRITGDPYKVQQAKEMVLELIR 78

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

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

 Score = 60.5 bits (147), Expect = 5e-14
 Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 3/67 (4%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           +++ +       +IGK G  I +++++    V+      D        + G P  VQ+A+
Sbjct: 7   VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP---DSEKSNLIRIEGDPQGVQQAK 63

Query: 107 ARIEELI 113
             + EL 
Sbjct: 64  RELLELA 70

>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 = 55.1 bits (133), Expect = 1e-11
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 9/70 (12%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
            ++ +    A V  VIGK G MIK L++E   ++   Q       +    ++G   +V  
Sbjct: 3   RIVAI--NPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-------NGLIWVNGDRRKVSI 53

Query: 105 ARARIEELID 114
           A   I  +  
Sbjct: 54  AEEAIYLIEQ 63

>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 = 53.3 bits (128), Expect = 4e-11
 Identities = 13/69 (18%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNE-TGARVQFVQMREDDPSDRRCMLSGSPDQVQEA 105
           ++V +P      +IG  G +I+ +  E  G  + F     +       ++ G    V++A
Sbjct: 12  VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHF---PVEGSGSDTVVIRGPSSDVEKA 68

Query: 106 RARIEELID 114
           + ++  L +
Sbjct: 69  KKQLLHLAE 77

>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 = 51.8 bits (124), Expect = 1e-10
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 4/71 (5%)

Query: 48  QVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARA 107
           +  V +  +G+ IG  G  I++ +   G          D+ +    +   S D V++AR 
Sbjct: 11  EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIE----LDEDTGTFRIYGESADAVKKARG 66

Query: 108 RIEELIDSVMV 118
            +E + D + V
Sbjct: 67  FLEFVEDFIQV 77

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 49.4 bits (118), Expect = 2e-09
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 5/70 (7%)

Query: 47  IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEAR 106
           I V V    +G VIG  G++  ++   TG  +       D  +    +   +        
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITV-----DTENSMVIVEPEAEGIPPVNL 59

Query: 107 ARIEELIDSV 116
            +  E++ ++
Sbjct: 60  MKAAEVVKAI 69

>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 = 47.8 bits (114), Expect = 8e-09
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 8/66 (12%)

Query: 53  KAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEEL 112
           K   G +IG+GG   + ++  T   +           +    + G  ++   A+  IE L
Sbjct: 21  KRIKGRIIGEGGRARRTIEEMTDTYINV--------GEYEVAIIGDYERAMAAKQAIEML 72

Query: 113 IDSVMV 118
            +  M 
Sbjct: 73  AEGRMH 78

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 47.5 bits (113), Expect = 8e-09
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 46  VIQVCVPKAAVGVVIGKGGDMIKKLQNE-TGARVQFVQMREDDPSDRRCMLSGSPDQVQE 104
           V  V  P      +IGK G  + K+  +     ++F         + +  L G  + V  
Sbjct: 22  VSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEF------TEGEDKITLEGPTEDVSV 75

Query: 105 ARARIEELIDSVM 117
           A+ +IE ++  ++
Sbjct: 76  AQEQIEGMVKDLI 88

>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 = 45.1 bits (107), Expect = 4e-08
 Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 8/70 (11%)

Query: 51  VPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARI 109
           +    V  VIGK   M + L +++G  +           + R   +  S    +     I
Sbjct: 7   IMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-------NGRIWATCPSRFSEEILIEAI 59

Query: 110 EELIDSVMVE 119
            ++ +   ++
Sbjct: 60  RKIENESHIK 69

>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 = 42.3 bits (100), Expect = 4e-07
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 4/42 (9%)

Query: 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD 87
          +I V +P   +G VIG    MI ++Q +TGA +      EDD
Sbjct: 4  IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI----EDD 41

>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 = 42.0 bits (99), Expect = 9e-07
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 10/69 (14%)

Query: 45  EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQ 103
           +++++    A V  VIG+   M+K L+ +T  ++   +       + R  L   + D   
Sbjct: 3   KIVEI--SPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-------NGRIHLECPNEDLEA 53

Query: 104 EARARIEEL 112
            A   I+ +
Sbjct: 54  IAVMAIKII 62

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	138
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.76
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.76
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.75
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.74
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.74
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.74
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.72
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.72
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.71
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.68
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.66
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.63
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.63
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.61
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.59
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.53
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	99.4
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.38
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.37
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	99.27
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	99.19
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.06
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.82
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.84
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	96.73
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.55
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	93.42
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	87.76
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	87.1
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	84.27

>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=99.76  E-value=1.5e-18  Score=116.86  Aligned_cols=83  Identities=28%  Similarity=0.374  Sum_probs=71.8

Q ss_pred             CCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCC-CCCcEEEEecCHHHHHHHHHHHHHHHH
Q psy11065         36 RGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD-PSDRRCMLSGSPDQVQEARARIEELID  114 (138)
Q Consensus        36 ~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~-~~~r~i~i~G~~e~i~~A~~~I~~ii~  114 (138)
                      .+.....++.+.+|.||..++|+|||++|.+|++|+++|||+|.|++..... +.+|+++|+|++++|.+|+.+|.+++.
T Consensus         6 ~~~~~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   85 (104)
T d1we8a_           6 SGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             CCCCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             CCccCCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Confidence            3345677889999999999999999999999999999999999997754322 237899999999999999999999998


Q ss_pred             hhhh
Q psy11065        115 SVMV  118 (138)
Q Consensus       115 ~~~~  118 (138)
                      +...
T Consensus        86 e~~~   89 (104)
T d1we8a_          86 EDEE   89 (104)
T ss_dssp             HHHH
T ss_pred             CcHH
Confidence            7553

>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=99.76  E-value=5.6e-19  Score=112.11  Aligned_cols=71  Identities=44%  Similarity=0.771  Sum_probs=65.2

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ..++|.||.+++|+|||++|++|++|+++|||+|+|++..+..+ +++++|.|+++++..|+.+|.+++++.
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~-~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP-ERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCS-EEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCC-eeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999999987654433 899999999999999999999999875

>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=99.75  E-value=4.1e-18  Score=108.14  Aligned_cols=71  Identities=32%  Similarity=0.559  Sum_probs=64.4

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      .+.++.||.+.+|+|||++|++|++|+++|||+|+|.++.+. .++++++|.|+++++..|+.+|.+++++.
T Consensus         4 ~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~-~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           4 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG-SEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSC-SSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            678999999999999999999999999999999999765433 33899999999999999999999999874

>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=99.74  E-value=1.6e-18  Score=109.29  Aligned_cols=69  Identities=28%  Similarity=0.436  Sum_probs=63.9

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      +.+.+|.||...+|.|||++|++|++|+++|||+|+++++..+   +|+++|.|+++++.+|..+|.++++|
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 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP---ERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCS---EEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCCCC---cceEEEEECHHHHHHHHHHHHHHhcC
Confidence            4789999999999999999999999999999999999875443   89999999999999999999999875

>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=99.74  E-value=2.9e-18  Score=108.02  Aligned_cols=68  Identities=34%  Similarity=0.632  Sum_probs=60.6

Q ss_pred             EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCC--CCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD--PSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~--~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      ..+|.||.+.+|.|||++|++|++|+++|||+|+|+++.++.  +.+|.++|.|+++++++|+++|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            468999999999999999999999999999999998765433  33789999999999999999998864

>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=99.74  E-value=3.2e-18  Score=107.65  Aligned_cols=68  Identities=22%  Similarity=0.460  Sum_probs=61.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      .+.+|.||.+.+|+|||++|++|++|+++|||+|.|++.... +.+|.++|.|++++++.|+.+|.+.|
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 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEG-SSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTT-CSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCC-CCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            578999999999999999999999999999999999775543 34899999999999999999998876

>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=99.72  E-value=6.1e-18  Score=108.44  Aligned_cols=73  Identities=30%  Similarity=0.648  Sum_probs=66.3

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ...+.+|.||...+|.|||++|.+|++|+++|||+|.|++.... ..++.++|.|+++++..|+.+|.++|.+.
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 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG-LPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTT-CSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            45789999999999999999999999999999999999875543 33899999999999999999999999875

>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=99.72  E-value=8.3e-18  Score=106.68  Aligned_cols=69  Identities=35%  Similarity=0.587  Sum_probs=61.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCC--CCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD--PSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~--~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      ...++.||.+++|.|||++|++|++|+++|||+|+|.++.+..  +++|.++|.|+++++..|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            4679999999999999999999999999999999998765432  33899999999999999999998875

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

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

Probab=99.71  E-value=5.5e-18  Score=109.26  Aligned_cols=73  Identities=33%  Similarity=0.587  Sum_probs=65.3

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC-CCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE-DDPSDRRCMLSGSPDQVQEARARIEELIDS  115 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~  115 (138)
                      ...+.+|.||..++|.|||++|++|++|+++|||+|.|.+... +...+|.++|.|++++|.+|+.+|.+++++
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4589999999999999999999999999999999999987532 233489999999999999999999999865

>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=99.68  E-value=7.2e-17  Score=104.54  Aligned_cols=73  Identities=18%  Similarity=0.318  Sum_probs=66.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      .+.+|.||..+++.|||++|++|++|+++|||+|++++.+....+++.|+|.|++++|..|+.+|.+++.+.+
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~e   82 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELE   82 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhHh
Confidence            4689999999999999999999999999999999998766655558899999999999999999999998865

>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=99.66  E-value=8.4e-17  Score=103.65  Aligned_cols=73  Identities=21%  Similarity=0.351  Sum_probs=66.1

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ...+.++.||..++++|||++|.+|++|+++|||+|++++....   .+.++|.|+++++.+|+.+|.+++.+...
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~---~~~v~I~G~~~~v~~A~~~I~~iv~e~~~   80 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP---SNQIKITGTKEGIEKARHEVLLISAEQDK   80 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSS---CCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCCCC---CCEEEEEeCHHHHHHHHHHHHHHHHHHhc
Confidence            34789999999999999999999999999999999999875443   78999999999999999999999988653

>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=99.63  E-value=3.5e-16  Score=100.66  Aligned_cols=71  Identities=24%  Similarity=0.325  Sum_probs=63.9

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV  116 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~  116 (138)
                      ..+.++.||..+++.|||++|++|++|+++|||+|++++..+..  .+.|+|.|++++|.+|+++|.+++++.
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 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD--PNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSC--TTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCC--CCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            36789999999999999999999999999999999998755432  578999999999999999999999874

>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=99.63  E-value=4.8e-16  Score=102.00  Aligned_cols=76  Identities=21%  Similarity=0.262  Sum_probs=67.9

Q ss_pred             CccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065         41 EVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE  119 (138)
Q Consensus        41 ~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~  119 (138)
                      ...+.+.+|.||..+++.|||++|.+|++|+++|||+|.+++....   ...|+|.|++++|..|+.+|.+++.+.+..
T Consensus         6 ~~~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~---~~~v~I~G~~~~V~~A~~~I~~~v~e~~~~   81 (91)
T d2ctka1           6 ALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQ---SDIIAITGLAANLDRAKAGLLERVKELQAE   81 (91)
T ss_dssp             CSSCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTT---CCEEEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhCCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCCCC---cceEEEECCHHHHHHHHHHHHHHHHHHHHH
Confidence            4457899999999999999999999999999999999999875443   779999999999999999999999876543

>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=99.62  E-value=3.1e-16  Score=101.07  Aligned_cols=72  Identities=18%  Similarity=0.395  Sum_probs=64.5

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHH-hCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNE-TGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~-Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ..+.+|.||..++|+|||++|++|++|+++ ++|+|++++....   ++.|+|.|++++|.+|+.+|.+++++.+.
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~---~~~v~I~G~~~~v~~A~~~I~~~v~e~~~   81 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSG---SDTVVIRGPSSDVEKAKKQLLHLAEEKQT   81 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTT---CCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCC---CceEEEeCCHHHHHHHHHHHHHHHhhhhc
Confidence            367899999999999999999999999977 5999999875443   78999999999999999999999998764

>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=99.61  E-value=2.9e-16  Score=98.75  Aligned_cols=66  Identities=21%  Similarity=0.372  Sum_probs=60.4

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELI  113 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii  113 (138)
                      ...++.||..++++|||++|++|++|+++|||+|.++++...   ++.|+|.|+++++.+|+++|.+++
T Consensus         5 ~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~---~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK---SNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSS---SEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCCCC---CCEEEEECCHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999999999999875433   789999999999999999998874

>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=99.59  E-value=1.2e-15  Score=99.05  Aligned_cols=65  Identities=28%  Similarity=0.286  Sum_probs=59.7

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ..+.||++++|.|||++|++|++|+++|||+|+|++       +..|+|.|+++++..|+.+|+.++++...
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-------~g~v~I~G~~e~v~~A~~~I~~i~~ea~~   67 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-------NGLIWVNGDRRKVSIAEEAIYLIEQEAHT   67 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-------TSEEEEESCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-------CCEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            478999999999999999999999999999999976       45799999999999999999999887654

>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=99.53  E-value=7.7e-16  Score=98.67  Aligned_cols=68  Identities=22%  Similarity=0.254  Sum_probs=58.2

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhh
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSV  116 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~  116 (138)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|.+.++.     ...+.|.| +++++++|+.+|+.+....
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~~-----~g~v~I~g~~~eav~~A~~~Ie~~~~~~   75 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED-----TGTFRIYGESADAVKKARGFLEFVEDFI   75 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHSCCCCCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecCC-----CceEEEEECCHHHHHHHHHHHHHhheee
Confidence            36889999999999999999999999999999999987642     45677777 7999999999997665443

>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=99.53  E-value=1.5e-14  Score=94.70  Aligned_cols=70  Identities=21%  Similarity=0.443  Sum_probs=63.3

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHh-CCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET-GARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T-ga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ...+.++.||..++++|||++|++|++|++++ +++|.++++      +..++|.|++++|+.|+++|++++.+...
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~------~~~v~i~G~~~~ve~Ak~~I~~iv~el~~   89 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG------EDKITLEGPTEDVSVAQEQIEGMVKDLIN   89 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS------SCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC------CceEEEeCCHHHHHHHHHHHHHHHHHHhc
Confidence            34899999999999999999999999999995 899999763      56799999999999999999999998654

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.40  E-value=5.1e-13  Score=86.86  Aligned_cols=65  Identities=23%  Similarity=0.242  Sum_probs=57.8

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhhh
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVMV  118 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~~  118 (138)
                      ..+.||+++++.|||++|++|+.|+++|||+|.|.+       +..|+|.| +.+.+..|+.+|+.+..+...
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~v   68 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-------NGRIHLECPNEDLEAIAVMAIKIIDEEAYT   68 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-------TTEEEEECSCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-------CcEEEEEeCCHHHHHHHHHHHHHHHHhchh
Confidence            468999999999999999999999999999999976       33578888 689999999999999887654

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.38  E-value=5e-15  Score=92.72  Aligned_cols=64  Identities=19%  Similarity=0.198  Sum_probs=50.1

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhh
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ..+.||++++|.|||++|++||+|+++|||+|+|++       +..++|.| +++.++.|+++|+.+.++.+
T Consensus         3 ~vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~-------~g~v~I~g~~~~~v~~A~~~I~~i~~ea~   67 (69)
T d2je6i3           3 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-------NGRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             CEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT-------TSEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEEChhhccceECCchhHHHHHHHHHCCEEEEcC-------CCEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            368999999999999999999999999999999975       34578888 57899999999998877654

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.37  E-value=6.4e-14  Score=90.72  Aligned_cols=62  Identities=19%  Similarity=0.278  Sum_probs=51.0

Q ss_pred             EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEE-----ecCHHHHHHHHHHHHHHHH
Q psy11065         47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCML-----SGSPDQVQEARARIEELID  114 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i-----~G~~e~i~~A~~~I~~ii~  114 (138)
                      +.+.||.+++|.|||++|++||+|+++|||+|+|+++..      .+.+     .+.+.++++|.++|.++..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g------~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENS------MVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTT------EEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCC------eEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            479999999999999999999999999999999976432      2333     4567888888888887744

>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=99.27  E-value=1.1e-11  Score=85.04  Aligned_cols=92  Identities=20%  Similarity=0.316  Sum_probs=71.0

Q ss_pred             eEEEEEecCCc------cceeeccCcHHHHHHHHHhCCeEEEecCCC-----------------CCCCCcEEEEecCHHH
Q psy11065         45 EVIQVCVPKAA------VGVVIGKGGDMIKKLQNETGARVQFVQMRE-----------------DDPSDRRCMLSGSPDQ  101 (138)
Q Consensus        45 ~~~~i~IP~~~------vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-----------------~~~~~r~i~i~G~~e~  101 (138)
                      .+.++.||.+.      +|.|||++|+++|+|+++|||+|.|--...                 ..| -++++..-+++.
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~ep-LHv~I~a~~~~~   81 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEP-LHALVTANTMEN   81 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCC-EEEEEEESSHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCC-ceEEEecCChhh
Confidence            57789999875      899999999999999999999999954211                 111 366666778899


Q ss_pred             HHHHHHHHHHHHHhhhhccCCCC--cccchhhhhcccC
Q psy11065        102 VQEARARIEELIDSVMVEQFSGA--NFDKLRSTVLANR  137 (138)
Q Consensus       102 i~~A~~~I~~ii~~~~~~~~g~~--~~~~l~~~~~~~~  137 (138)
                      +..|+.+|+.+|.+.-.......  .-.+||++++.|-
T Consensus        82 ~~~A~~~i~~ll~~~~~~~e~~d~~k~~Ql~eLa~lnG  119 (122)
T d1k1ga_          82 VKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNG  119 (122)
T ss_dssp             HHHHHHHHHHHHTTTTSCCTTSSGGGGGGGHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHhcC
Confidence            99999999999976544433333  3448999998874

>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=99.19  E-value=4.4e-13  Score=79.85  Aligned_cols=47  Identities=30%  Similarity=0.512  Sum_probs=14.9

Q ss_pred             ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec
Q psy11065         44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG   97 (138)
Q Consensus        44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G   97 (138)
                      |...+|.||.+++|.|||++|++||.|+++|||+|+|.+       +..|.|.+
T Consensus         2 P~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d-------dg~v~I~a   48 (54)
T d1e3ha4           2 PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-------DGTIYIGA   48 (54)
T ss_dssp             CBCC---------------------CHHHHSCCCC---------------CCCC
T ss_pred             CeEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC-------CeEEEEEe
Confidence            567889999999999999999999999999999999976       34455555

>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=99.06  E-value=7.1e-11  Score=78.86  Aligned_cols=55  Identities=22%  Similarity=0.367  Sum_probs=48.1

Q ss_pred             ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065         55 AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM  117 (138)
Q Consensus        55 ~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~  117 (138)
                      ..|+|||++|++|+.|++.|||+|.|.+       . .+.+.|+++++..|+++|+.++...+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d-------~-~v~iig~~e~i~~A~~~Ie~li~~~e   77 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE-------Y-EVAIIGDYERAMAAKQAIEMLAEGRM   77 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-------S-EEEEEEEHHHHHHHHHHHHHHHTTCC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC-------C-eEEEEECchhHHHHHHHHHHHHcCCC
Confidence            4799999999999999999999999965       2 35667899999999999999997643

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.82  E-value=1.7e-09  Score=74.97  Aligned_cols=91  Identities=18%  Similarity=0.208  Sum_probs=61.6

Q ss_pred             eEEEEEecCC------ccceeeccCcHHHHHHHHHhCCeEEEecCCC-------------------CCCCCcEEEEecCH
Q psy11065         45 EVIQVCVPKA------AVGVVIGKGGDMIKKLQNETGARVQFVQMRE-------------------DDPSDRRCMLSGSP   99 (138)
Q Consensus        45 ~~~~i~IP~~------~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-------------------~~~~~r~i~i~G~~   99 (138)
                      ...++.||.+      ++|.|||++|.++|+|+++|||+|.|--...                   ..+ -++.+..-++
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~ep-LHv~I~a~~~   80 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNED-LHVLITVEDA   80 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSC-CEEEEEECSC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCC-CEEEEEecCc
Confidence            3567788754      7899999999999999999999999965321                   112 3444333333


Q ss_pred             -----HHHHHHHHHHHHHHHhhhhccCCCCcccchhhhhcccC
Q psy11065        100 -----DQVQEARARIEELIDSVMVEQFSGANFDKLRSTVLANR  137 (138)
Q Consensus       100 -----e~i~~A~~~I~~ii~~~~~~~~g~~~~~~l~~~~~~~~  137 (138)
                           ..+..|+++|+.++....... ---.-.+||++++.|-
T Consensus        81 ~~~a~~kl~~A~~~I~~lL~p~~e~~-de~k~~QL~eLa~lNG  122 (134)
T d2bl5a1          81 QNRAELKLKRAVEEVKKLLVPAAEGE-DSLKKMKLMELAILNG  122 (134)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCSSSS-SHHHHHHHTGGGSSST
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCccch-HHHHHHHHHHHHHhcC
Confidence                 357889999999885432111 0113348889988873

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.84  E-value=0.00057  Score=41.15  Aligned_cols=40  Identities=25%  Similarity=0.339  Sum_probs=36.8

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR   84 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~   84 (138)
                      ....+.||.+..+..|||+|.|++-..+-||.+|+|..+.
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            5688899999999999999999999999999999998754

>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=96.73  E-value=0.0011  Score=41.65  Aligned_cols=62  Identities=11%  Similarity=0.019  Sum_probs=50.6

Q ss_pred             EEEEecCCccceeeccCcH-HHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHh
Q psy11065         47 IQVCVPKAAVGVVIGKGGD-MIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDS  115 (138)
Q Consensus        47 ~~i~IP~~~vg~IIGk~G~-~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~  115 (138)
                      .-+.||..++..+||++++ .++.|.+.+++.|.|..       .-.|+|.+ +++....+...|..+-.+
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~-------NGrIWi~~~~~~~~i~i~~aI~~~e~~   66 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-------NGKIWVKCEELSNTLACYRTIMECCQK   66 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-------TTEEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec-------CcEEEEECCCHHHHHHHHHHHHHHHHh
Confidence            4678999999999999998 89999999999999987       45688888 567777666667655443

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=96.55  E-value=0.0014  Score=39.44  Aligned_cols=39  Identities=26%  Similarity=0.469  Sum_probs=35.9

Q ss_pred             eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065         45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM   83 (138)
Q Consensus        45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~   83 (138)
                      ....+.||.+..+..|||+|.|++-..+-||.+|+|...
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            467889999999999999999999999999999999763

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.42  E-value=0.014  Score=36.90  Aligned_cols=33  Identities=18%  Similarity=0.223  Sum_probs=27.5

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHhC
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETG   75 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tg   75 (138)
                      ++...++.|....-|.|||++|+.|++|++.-.
T Consensus        33 t~~~i~I~I~tarPGivIGrkG~~I~~L~~~l~   65 (92)
T d1wh9a_          33 TPTRTEIIILATRTQNVLGEKGRRIRELTAVVQ   65 (92)
T ss_dssp             CSSCEEEEEEESCHHHHHCGGGHHHHHHHHHHH
T ss_pred             CCCeEEEEEEeCCCceeeccCchhHHHHHHHHH
Confidence            445678899999999999999999998876543

>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=87.76  E-value=0.052  Score=34.77  Aligned_cols=32  Identities=41%  Similarity=0.612  Sum_probs=26.5

Q ss_pred             cceEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065         43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET   74 (138)
Q Consensus        43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T   74 (138)
                      ++...++.|....-|.|||++|+.|+.|.++-
T Consensus        59 ~~~~i~I~I~tarPG~iIGkkG~~i~~L~~~l   90 (105)
T d2uubc1          59 AADNVAVTVHVAKPGVVIGRGGERIRVLREEL   90 (105)
T ss_dssp             SSSCEECCEEESCHHHHHCSTTSHHHHHHHHH
T ss_pred             ccCcEEEEEEECCCceEEcCCchhHHHHHHHH
Confidence            34558888999999999999999998877654

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.10  E-value=0.13  Score=33.24  Aligned_cols=30  Identities=27%  Similarity=0.277  Sum_probs=22.8

Q ss_pred             eEEEEEecCCcc-ceeeccCcHHHHHHHHHh
Q psy11065         45 EVIQVCVPKAAV-GVVIGKGGDMIKKLQNET   74 (138)
Q Consensus        45 ~~~~i~IP~~~v-g~IIGk~G~~Ik~I~~~T   74 (138)
                      ....+.|+.+.. +.|||++|++||+|...+
T Consensus        49 I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          49 INGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             EEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            556677777655 888999999998876543

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=84.27  E-value=0.21  Score=32.45  Aligned_cols=36  Identities=28%  Similarity=0.474  Sum_probs=25.9

Q ss_pred             eEEEEEecCCcc-ceeeccCcHHHHHH--------HHHhCCeEEE
Q psy11065         45 EVIQVCVPKAAV-GVVIGKGGDMIKKL--------QNETGARVQF   80 (138)
Q Consensus        45 ~~~~i~IP~~~v-g~IIGk~G~~Ik~I--------~~~Tga~I~I   80 (138)
                      ....+.|+.+.. +.|||++|++||+|        ++.++++|.+
T Consensus        50 I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~aR~~le~~~~~kV~L   94 (118)
T d1wf3a2          50 IKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYL   94 (118)
T ss_dssp             EEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHTSEEEE
T ss_pred             EEEEEEeCccchhhhhhccCchhHHHHHHHHHHHHHHHhCCCeEE
Confidence            455677777655 78899999999865        4556666654