Citrus Sinensis ID: 039634

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------
Protein Sequence
MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHccEEEEcccccccccccccccccccccccEEEEEEEccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHcccEEEEEEcccccccccccccccccccccEEEEEEcccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MTPEVDLLIKFKvsingcpytytSLSIKVeikdkpgyehlneplhmlveaefpeVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGtlreespsmspsmspsmspfnnagmkcaetgr
Flexible Loop (DISEMBL)
MTPEVDLLIKFkvsingcpyTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLreespsmspsmspsmspfnnagMKCAETGR
Low Complexity Region (SEG)
MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLREEspsmspsmspsmspFNNAGMKCAETGR
Disordered region (IsUnstruct)
****VDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAIL**********************************
Disordered Region (DISOPRED)
MTPEVDLLIKFKVSING**************************LHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILN*********************************
Disordered Region (DISEMBL)
MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLR************SMSPFNNAGMKCAETGR
Disordered Region (DISPRO)
***EVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLR*****************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR
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	127	2.2.26 [Sep-21-2011]
Q8GWR3	298	KH domain-containing prot	yes	no	0.913	0.389	0.603	6e-31
Q75GR5	281	KH domain-containing prot	no	no	0.732	0.330	0.602	7e-28
Q9FKT4	315	KH domain-containing prot	no	no	0.716	0.288	0.621	8e-25
Q0WLR1	308	KH domain-containing prot	no	no	0.716	0.295	0.621	9e-25
Q8GYR4	283	KH domain-containing prot	no	no	0.740	0.332	0.561	1e-22
Q9ZVI3	286	KH domain-containing prot	no	no	0.708	0.314	0.559	2e-21
Q6IRN2	342	Protein quaking-B OS=Xeno	N/A	no	0.614	0.228	0.432	6e-09
Q32NN2	341	Protein quaking-A OS=Xeno	N/A	no	0.614	0.228	0.432	7e-09
Q6P104	319	Protein quaking-B OS=Dani	yes	no	0.614	0.244	0.432	8e-09
Q5W9D5	341	Protein quaking OS=Sus sc	yes	no	0.614	0.228	0.432	8e-09

>sp|Q8GWR3|QKIL5_ARATH KH domain-containing protein At1g09660 OS=Arabidopsis thaliana GN=At1g09660 PE=2 SV=1

 Score =  132 bits (332), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 73/121 (60%), Positives = 90/121 (74%), Gaps = 5/121 (4%)

Query: 4   EVDLLIKFKVSINGCPYTYTSLSIKVE-IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLD 62
            V+L    +V I G        ++K E +K KPGYEHL EPLH+L+EAE PE IINS L+
Sbjct: 177 RVELATHCRVFIRG--RGSVKDTVKEEKLKGKPGYEHLCEPLHVLIEAELPEDIINSRLE 234

Query: 63  HAVAILENLLKPVDESLDHYKKQQLRELAILNGTLREE--SPSMSPSMSPSMSPFNNAGM 120
           HAV  LE+LLKP+DES+DHYK++QL+ELA LNGTLREE  SPS+SP +SPSMSPFN+   
Sbjct: 235 HAVHFLESLLKPMDESMDHYKREQLKELAALNGTLREESPSPSLSPCLSPSMSPFNSKRA 294

Query: 121 K 121
           K
Sbjct: 295 K 295

Arabidopsis thaliana (taxid: 3702)

>sp|Q75GR5|SPIN1_ORYSJ KH domain-containing protein SPIN1 OS=Oryza sativa subsp. japonica GN=SPIN1 PE=1 SV=1

 Score =  122 bits (306), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 59/98 (60%), Positives = 77/98 (78%), Gaps = 5/98 (5%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           +++ KPGYEHL++PLH+L+EAEFP  II++ L HA  ++E LLKPVDES D YK+QQLRE
Sbjct: 189 KLRGKPGYEHLSDPLHILIEAEFPASIIDARLRHAQEVIEELLKPVDESQDFYKRQQLRE 248

Query: 90  LAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR 127
           LA+LN TLRE+SP        S+SPF+N GMK A+TG+
Sbjct: 249 LAMLNSTLREDSPHPG-----SVSPFSNGGMKRAKTGQ 281

Involved in flowering time control. Binds DNA and RNA in vitro.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9FKT4|QKIL2_ARATH KH domain-containing protein At5g56140 OS=Arabidopsis thaliana GN=At5g56140 PE=2 SV=1

 Score =  112 bits (279), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 59/95 (62%), Positives = 75/95 (78%), Gaps = 4/95 (4%)

Query: 31  IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLREL 90
           ++ KPGYEHLNEPLH+LVEAE P  I+++ L  A  IL++LL P++E+ D YKKQQLREL
Sbjct: 222 MRGKPGYEHLNEPLHILVEAELPIEIVDARLMQAREILDDLLTPMEETHDMYKKQQLREL 281

Query: 91  AILNGTLREESPSMSPSMSPSMSPFNNAGMKCAET 125
           A+LNGTLREE    SP MS S+SP+N+ GMK A+T
Sbjct: 282 ALLNGTLREEG---SP-MSGSVSPYNSLGMKRAKT 312

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WLR1|QKIL1_ARATH KH domain-containing protein At4g26480 OS=Arabidopsis thaliana GN=At4g26480 PE=2 SV=1

 Score =  112 bits (279), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 59/95 (62%), Positives = 75/95 (78%), Gaps = 4/95 (4%)

Query: 31  IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLREL 90
           ++ KPGYEHLNEPLH+LVEAE P  I+++ L  A  IL++LL PV+E+ D YKKQQLREL
Sbjct: 216 MRGKPGYEHLNEPLHILVEAELPIEIVDARLMQAREILDDLLTPVEETHDFYKKQQLREL 275

Query: 91  AILNGTLREESPSMSPSMSPSMSPFNNAGMKCAET 125
           A+LNG+LREE    SP MS S+SP+N+ GMK A+T
Sbjct: 276 ALLNGSLREEG---SP-MSGSISPYNSLGMKRAKT 306

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GYR4|QKIL4_ARATH KH domain-containing protein At3g08620 OS=Arabidopsis thaliana GN=At3g08620 PE=2 SV=1

 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 55/98 (56%), Positives = 70/98 (71%), Gaps = 4/98 (4%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           ++K KPGYEHLNE LH+L+EA+ P  I++  L  A  I+E L+KPVDES D+ K+QQLRE
Sbjct: 190 KLKGKPGYEHLNEQLHILIEADLPIDIVDIKLRQAQEIIEELVKPVDESQDYIKRQQLRE 249

Query: 90  LAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR 127
           LA+LN  LRE     SP  S S+SPFN+  MK  +TGR
Sbjct: 250 LALLNSNLREN----SPGPSGSVSPFNSNAMKRPKTGR 283

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZVI3|QKIL3_ARATH KH domain-containing protein At2g38610 OS=Arabidopsis thaliana GN=At2g38610 PE=1 SV=1

 Score =  100 bits (250), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 52/93 (55%), Positives = 67/93 (72%), Gaps = 3/93 (3%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           +++ +PGYEHLNE LH+L+EA+ P  I+   L  A  I+E LLKPVDES D  K+QQLRE
Sbjct: 191 KLRGRPGYEHLNEQLHILIEADLPASIVEIRLRQAQEIIEELLKPVDESQDFIKRQQLRE 250

Query: 90  LAILNG-TLREESPSMSPSMSPSMSPFNNAGMK 121
           LA+LN   LREESP   PS   S+SPFN++G +
Sbjct: 251 LALLNSNNLREESP--GPSGGGSVSPFNSSGKR 281

Arabidopsis thaliana (taxid: 3702)

>sp|Q6IRN2|QKIB_XENLA Protein quaking-B OS=Xenopus laevis GN=qki-b PE=1 SV=1

 Score = 59.3 bits (142), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 49/81 (60%), Gaps = 3/81 (3%)

Query: 32  KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
           + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct: 140 RGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 199

Query: 92  ILNGTLRE---ESPSMSPSMS 109
           ILNGT R+   +SP+++ S++
Sbjct: 200 ILNGTYRDANLKSPALAFSLA 220

RNA-binding protein that plays a central role in myelinization. Binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence. Acts by regulating pre-mRNA splicing, mRNA export, mRNA stability and protein translation. Required to protect and promote stability of mRNAs which promotes oligodendrocyte differentiation. Participates in mRNA transport by regulating the nuclear export of MBP mRNA. Also involved in regulation of mRNA splicing of some pre-mRNA. Acts as a translational repressor.

Xenopus laevis (taxid: 8355)

>sp|Q32NN2|QKIA_XENLA Protein quaking-A OS=Xenopus laevis GN=qki-a PE=1 SV=2

 Score = 59.3 bits (142), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 49/81 (60%), Gaps = 3/81 (3%)

Query: 32  KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
           + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct: 140 RGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 199

Query: 92  ILNGTLRE---ESPSMSPSMS 109
           ILNGT R+   +SP+++ S++
Sbjct: 200 ILNGTYRDANLKSPALAFSLA 220

RNA-binding protein that plays a central role in myelinization. Binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence. Acts by regulating pre-mRNA splicing, mRNA export, mRNA stability and protein translation. Required to protect and promote stability of mRNAs which promotes oligodendrocyte differentiation. Participates in mRNA transport by regulating the nuclear export of MBP mRNA. Also involved in regulation of mRNA splicing of some pre-mRNA. Acts as a translational repressor (By similarity). Essential for notochord development.

Xenopus laevis (taxid: 8355)

>sp|Q6P104|QKIB_DANRE Protein quaking-B OS=Danio rerio GN=qkib PE=2 SV=1

 Score = 59.3 bits (142), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 49/81 (60%), Gaps = 3/81 (3%)

Query: 32  KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
           + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct: 139 RGKPNWEHLNEDLHVLITVEDSQNRAEIKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 198

Query: 92  ILNGTLRE---ESPSMSPSMS 109
           ILNGT R+   +SP+++ S++
Sbjct: 199 ILNGTYRDANIKSPALAFSLA 219

RNA-binding protein that plays a central role in myelinization. Binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence. Acts by regulating pre-mRNA splicing, mRNA export, mRNA stability and protein translation. Required to protect and promote stability of mRNAs which promotes oligodendrocyte differentiation. Participates in mRNA transport by regulating the nuclear export of MBP mRNA. Also involved in regulation of mRNA splicing of some pre-mRNA. Acts as a translational repressor.

Danio rerio (taxid: 7955)

>sp|Q5W9D5|QKI_PIG Protein quaking OS=Sus scrofa GN=QKI PE=2 SV=1

 Score = 58.9 bits (141), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 49/81 (60%), Gaps = 3/81 (3%)

Query: 32  KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
           + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct: 139 RGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 198

Query: 92  ILNGTLRE---ESPSMSPSMS 109
           ILNGT R+   +SP+++ S++
Sbjct: 199 ILNGTYRDANIKSPALAFSLA 219

RNA-binding protein that plays a central role in myelinization. Binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence. Acts by regulating pre-mRNA splicing, mRNA export, mRNA stability and protein translation. Required to protect and promote stability of mRNAs such as MBP and CDKN1B which promotes oligodendrocyte differentiation. Participates in mRNA transport by regulating the nuclear export of MBP mRNA. Also involved in regulation of mRNA splicing of MAG pre-mRNA. Acts as a translational repressor.

Sus scrofa (taxid: 9823)

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	127
115441499	290	Os01g0886300 [Oryza sativa Japonica Grou	0.755	0.331	0.744	7e-35
242090563	292	hypothetical protein SORBIDRAFT_09g02064	0.755	0.328	0.744	9e-35
357445253	312	KH domain-containing protein [Medicago t	0.968	0.394	0.733	1e-34
358248858	275	uncharacterized protein LOC100796731 [Gl	0.960	0.443	0.739	4e-34
255635453	274	unknown [Glycine max]	0.960	0.445	0.739	4e-34
357126240	288	PREDICTED: KH domain-containing protein	0.787	0.347	0.728	8e-34
414879338	293	TPA: hypothetical protein ZEAMMB73_28287	0.984	0.426	0.583	3e-33
226494061	285	hypothetical protein [Zea mays] gi|19470	0.755	0.336	0.714	4e-33
242055227	293	hypothetical protein SORBIDRAFT_03g04209	0.755	0.327	0.714	6e-33
224129440	294	predicted protein [Populus trichocarpa]	0.968	0.418	0.733	7e-33

>gi|115441499|ref|NP_001045029.1| Os01g0886300 [Oryza sativa Japonica Group] gi|56784311|dbj|BAD82237.1| QUAKING isoform 5-like [Oryza sativa Japonica Group] gi|56785233|dbj|BAD82121.1| QUAKING isoform 5-like [Oryza sativa Japonica Group] gi|113534560|dbj|BAF06943.1| Os01g0886300 [Oryza sativa Japonica Group] gi|125528639|gb|EAY76753.1| hypothetical protein OsI_04709 [Oryza sativa Indica Group] gi|125572899|gb|EAZ14414.1| hypothetical protein OsJ_04338 [Oryza sativa Japonica Group] gi|215694363|dbj|BAG89356.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 73/98 (74%), Positives = 88/98 (89%), Gaps = 2/98 (2%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           +++DKPGYEHLNEPLH+LVEAEFP  II++ L+ AV ILE+LLKP+DES+D+YKKQQLRE
Sbjct: 195 KLRDKPGYEHLNEPLHVLVEAEFPADIIDTRLNQAVTILEDLLKPIDESMDYYKKQQLRE 254

Query: 90  LAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR 127
           LAILNGTLREESP  SP +SPS+SPFN+ GMK A+TGR
Sbjct: 255 LAILNGTLREESP--SPHLSPSVSPFNSTGMKRAKTGR 290

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242090563|ref|XP_002441114.1| hypothetical protein SORBIDRAFT_09g020640 [Sorghum bicolor] gi|241946399|gb|EES19544.1| hypothetical protein SORBIDRAFT_09g020640 [Sorghum bicolor]

 Score =  151 bits (381), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 73/98 (74%), Positives = 89/98 (90%), Gaps = 2/98 (2%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           +++DKPGYEHLN+PLH+LVEAEFP  I+++ L+ AVAILE+LLKPVDES+D+YKKQQLRE
Sbjct: 197 KLRDKPGYEHLNDPLHVLVEAEFPADIVDARLNQAVAILEDLLKPVDESMDYYKKQQLRE 256

Query: 90  LAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR 127
           LAILNGTLREESP  SP +SPS+SPFN+ GMK A+TGR
Sbjct: 257 LAILNGTLREESP--SPYLSPSVSPFNSTGMKRAKTGR 292

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357445253|ref|XP_003592904.1| KH domain-containing protein [Medicago truncatula] gi|92893883|gb|ABE91933.1| KH [Medicago truncatula] gi|355481952|gb|AES63155.1| KH domain-containing protein [Medicago truncatula]

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/124 (73%), Positives = 105/124 (84%), Gaps = 1/124 (0%)

Query: 4   EVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDH 63
            V+ + + +V I GC     S+  + ++KDKPGYEHL EPLH+LVEAEFPE IINS LDH
Sbjct: 190 RVEAMTECRVYIRGCGSVKDSIK-EEKLKDKPGYEHLKEPLHLLVEAEFPEDIINSRLDH 248

Query: 64  AVAILENLLKPVDESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCA 123
           AVA+LENLLKPVDESLDHYKKQQLRELA++NGTLREESPSMSPSMSPSMSPFN+ GMK A
Sbjct: 249 AVAVLENLLKPVDESLDHYKKQQLRELAMINGTLREESPSMSPSMSPSMSPFNSNGMKRA 308

Query: 124 ETGR 127
           +TGR
Sbjct: 309 KTGR 312

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248858|ref|NP_001239952.1| uncharacterized protein LOC100796731 [Glycine max] gi|255641182|gb|ACU20868.1| unknown [Glycine max]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 91/123 (73%), Positives = 105/123 (85%), Gaps = 1/123 (0%)

Query: 5   VDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHA 64
           V+ + + +V I GC     S+  + ++K+KPGYEHL EPLH+LVEAEFPE IIN+ LDHA
Sbjct: 154 VEAMTECRVYIRGCGSVKDSIK-EEKLKEKPGYEHLKEPLHVLVEAEFPEDIINARLDHA 212

Query: 65  VAILENLLKPVDESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAE 124
           VAILENLLKPVDESLDHYKKQQLRELA+LNGTLREESPSMSPSMSPSMSPFN+ GMK A+
Sbjct: 213 VAILENLLKPVDESLDHYKKQQLRELAMLNGTLREESPSMSPSMSPSMSPFNSTGMKRAK 272

Query: 125 TGR 127
           TGR
Sbjct: 273 TGR 275

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255635453|gb|ACU18079.1| unknown [Glycine max]

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 91/123 (73%), Positives = 105/123 (85%), Gaps = 1/123 (0%)

Query: 5   VDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHA 64
           V+ + + +V I GC     S+  + ++K+KPGYEHL EPLH+LVEAEFPE IIN+ LDHA
Sbjct: 153 VEAMTECRVYIRGCGSVKDSIK-EEKLKEKPGYEHLKEPLHVLVEAEFPEDIINARLDHA 211

Query: 65  VAILENLLKPVDESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAE 124
           VAILENLLKPVDESLDHYKKQQLRELA+LNGTLREESPSMSPSMSPSMSPFN+ GMK A+
Sbjct: 212 VAILENLLKPVDESLDHYKKQQLRELAMLNGTLREESPSMSPSMSPSMSPFNSTGMKRAK 271

Query: 125 TGR 127
           TGR
Sbjct: 272 TGR 274

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357126240|ref|XP_003564796.1| PREDICTED: KH domain-containing protein At1g09660-like [Brachypodium distachyon]

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 75/103 (72%), Positives = 90/103 (87%), Gaps = 3/103 (2%)

Query: 26  SIKVE-IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKK 84
           S+K E ++DKP YEHLNEPLH+LVEAEFP  II++ L+ AV ILE+LLKP+DES+D+YKK
Sbjct: 188 SVKEEKLRDKPEYEHLNEPLHVLVEAEFPADIIDARLNQAVTILEDLLKPIDESMDYYKK 247

Query: 85  QQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR 127
           QQLRELAILNGTLREESP  SP +SPS+SPFN+ GMK A+TGR
Sbjct: 248 QQLRELAILNGTLREESP--SPHLSPSLSPFNSTGMKRAKTGR 288

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414879338|tpg|DAA56469.1| TPA: hypothetical protein ZEAMMB73_282873 [Zea mays]

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 77/132 (58%), Positives = 97/132 (73%), Gaps = 7/132 (5%)

Query: 1   MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIK-----DKPGYEHLNEPLHMLVEAEFPEV 55
           + P  + L + + S     Y     S+K  +K     DKPGYEHLNE LH+LVEAEFP  
Sbjct: 164 LGPRGNSLKRVEASTQCRVYIRGRGSVKDSVKEDKLRDKPGYEHLNEQLHVLVEAEFPAD 223

Query: 56  IINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPF 115
           +++  L+ AV+ILE+LLKP+DES+D+YKKQQLRELAILNGTLREESP  SP +SPS+SPF
Sbjct: 224 MVDVRLNQAVSILEDLLKPIDESMDYYKKQQLRELAILNGTLREESP--SPHLSPSVSPF 281

Query: 116 NNAGMKCAETGR 127
           N+ GMK A+TGR
Sbjct: 282 NSTGMKRAKTGR 293

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226494061|ref|NP_001142049.1| hypothetical protein [Zea mays] gi|194706914|gb|ACF87541.1| unknown [Zea mays] gi|414879339|tpg|DAA56470.1| TPA: hypothetical protein ZEAMMB73_282873 [Zea mays]

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 70/98 (71%), Positives = 87/98 (88%), Gaps = 2/98 (2%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           +++DKPGYEHLNE LH+LVEAEFP  +++  L+ AV+ILE+LLKP+DES+D+YKKQQLRE
Sbjct: 190 KLRDKPGYEHLNEQLHVLVEAEFPADMVDVRLNQAVSILEDLLKPIDESMDYYKKQQLRE 249

Query: 90  LAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR 127
           LAILNGTLREESP  SP +SPS+SPFN+ GMK A+TGR
Sbjct: 250 LAILNGTLREESP--SPHLSPSVSPFNSTGMKRAKTGR 285

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242055227|ref|XP_002456759.1| hypothetical protein SORBIDRAFT_03g042090 [Sorghum bicolor] gi|241928734|gb|EES01879.1| hypothetical protein SORBIDRAFT_03g042090 [Sorghum bicolor]

 Score =  145 bits (366), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 70/98 (71%), Positives = 87/98 (88%), Gaps = 2/98 (2%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           +++DKPGYEHLNE LH+LVEAEFP  ++++ L+ AV+ILE+LLKP+DES+D YKKQQLRE
Sbjct: 198 KLRDKPGYEHLNEQLHVLVEAEFPVDMVDARLNQAVSILEDLLKPIDESMDFYKKQQLRE 257

Query: 90  LAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETGR 127
           LAILNGTLREESP  SP +SPS+SPFN+ GMK A+TGR
Sbjct: 258 LAILNGTLREESP--SPHLSPSVSPFNSTGMKRAKTGR 293

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224129440|ref|XP_002328717.1| predicted protein [Populus trichocarpa] gi|222839015|gb|EEE77366.1| predicted protein [Populus trichocarpa]

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 91/124 (73%), Positives = 103/124 (83%), Gaps = 1/124 (0%)

Query: 4   EVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDH 63
            V+ L   +V I G      SL  + ++KDKPGYEHLNEPLH+LVEAEFPE IIN+ L+H
Sbjct: 172 RVEALTDCRVYIRGKGSVKDSLK-EEKLKDKPGYEHLNEPLHVLVEAEFPEDIINARLEH 230

Query: 64  AVAILENLLKPVDESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCA 123
           A+ ILE+LLKPVDESLDHYKKQQLRELA+LNGTLREESPSMSPSMSPSMSPFN AGMK A
Sbjct: 231 AITILESLLKPVDESLDHYKKQQLRELALLNGTLREESPSMSPSMSPSMSPFNTAGMKRA 290

Query: 124 ETGR 127
           +TGR
Sbjct: 291 KTGR 294

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	127
TAIR|locus:2024326	298	AT1G09660 "AT1G09660" [Arabido	0.590	0.251	0.710	2e-24
UNIPROTKB|Q75GR5	281	SPIN1 "KH domain-containing pr	0.732	0.330	0.551	6.1e-23
TAIR|locus:2161845	315	AT5G56140 "AT5G56140" [Arabido	0.748	0.301	0.55	1e-20
TAIR|locus:2077818	283	AT3G08620 "AT3G08620" [Arabido	0.740	0.332	0.5	1.4e-18
TAIR|locus:2064097	286	AT2G38610 "AT2G38610" [Arabido	0.740	0.328	0.489	6.7e-17
TAIR|locus:2176222	804	AT5G51300 [Arabidopsis thalian	0.433	0.068	0.566	6.3e-10
UNIPROTKB|F5GXS8	160	QKI "Protein quaking" [Homo sa	0.535	0.425	0.470	1.1e-09
UNIPROTKB|F5GYM3	170	QKI "Protein quaking" [Homo sa	0.535	0.4	0.470	1.1e-09
UNIPROTKB|J9NVZ6	286	QKI "Protein quaking" [Canis l	0.535	0.237	0.470	3.1e-09
UNIPROTKB|F1PLY2	310	QKI "Protein quaking" [Canis l	0.535	0.219	0.470	3.9e-09

TAIR|locus:2024326 AT1G09660 "AT1G09660" [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 54/76 (71%), Positives = 66/76 (86%)

Query:    26 SIKVE-IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKK 84
             ++K E +K KPGYEHL EPLH+L+EAE PE IINS L+HAV  LE+LLKP+DES+DHYK+
Sbjct:   197 TVKEEKLKGKPGYEHLCEPLHVLIEAELPEDIINSRLEHAVHFLESLLKPMDESMDHYKR 256

Query:    85 QQLRELAILNGTLREE 100
             +QL+ELA LNGTLREE
Sbjct:   257 EQLKELAALNGTLREE 272

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q75GR5 SPIN1 "KH domain-containing protein SPIN1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 265 (98.3 bits), Expect = 6.1e-23, P = 6.1e-23
 Identities = 54/98 (55%), Positives = 71/98 (72%)

Query:    30 EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
             +++ KPGYEHL++PLH+L+EAEFP  II++ L HA  ++E LLKPVDES D YK+QQLRE
Sbjct:   189 KLRGKPGYEHLSDPLHILIEAEFPASIIDARLRHAQEVIEELLKPVDESQDFYKRQQLRE 248

Query:    90 LAILNGTLREEXXXXXXXXXXXXXXFNNAGMKCAETGR 127
             LA+LN TLRE+              F+N GMK A+TG+
Sbjct:   249 LAMLNSTLREDSPHPGSVSP-----FSNGGMKRAKTGQ 281

GO:0003677 "DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0048577 "negative regulation of short-day photoperiodism, flowering" evidence=IMP

GO:0048579 "negative regulation of long-day photoperiodism, flowering" evidence=IMP

TAIR|locus:2161845 AT5G56140 "AT5G56140" [Arabidopsis thaliana (taxid:3702)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 55/100 (55%), Positives = 70/100 (70%)

Query:    27 IKVEI-KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQ 85
             IK E+ + KPGYEHLNEPLH+LVEAE P  I+++ L  A  IL++LL P++E+ D YKKQ
Sbjct:   217 IKEEMMRGKPGYEHLNEPLHILVEAELPIEIVDARLMQAREILDDLLTPMEETHDMYKKQ 276

Query:    86 QLRELAILNGTLREEXXXXXXXXXXXXXXFNNAGMKCAET 125
             QLRELA+LNGTLREE              +N+ GMK A+T
Sbjct:   277 QLRELALLNGTLREEGSPMSGSVSP----YNSLGMKRAKT 312

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2077818 AT3G08620 "AT3G08620" [Arabidopsis thaliana (taxid:3702)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 49/98 (50%), Positives = 63/98 (64%)

Query:    30 EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
             ++K KPGYEHLNE LH+L+EA+ P  I++  L  A  I+E L+KPVDES D+ K+QQLRE
Sbjct:   190 KLKGKPGYEHLNEQLHILIEADLPIDIVDIKLRQAQEIIEELVKPVDESQDYIKRQQLRE 249

Query:    90 LAILNGTLREEXXXXXXXXXXXXXXFNNAGMKCAETGR 127
             LA+LN  LRE               FN+  MK  +TGR
Sbjct:   250 LALLNSNLRENSPGPSGSVSP----FNSNAMKRPKTGR 283

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0010048 "vernalization response" evidence=RCA

TAIR|locus:2064097 AT2G38610 "AT2G38610" [Arabidopsis thaliana (taxid:3702)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 48/98 (48%), Positives = 62/98 (63%)

Query:    30 EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
             +++ +PGYEHLNE LH+L+EA+ P  I+   L  A  I+E LLKPVDES D  K+QQLRE
Sbjct:   191 KLRGRPGYEHLNEQLHILIEADLPASIVEIRLRQAQEIIEELLKPVDESQDFIKRQQLRE 250

Query:    90 LAILNGT-LREEXXXXXXXXXXXXXXFNNAGMKCAETG 126
             LA+LN   LREE              FN++G K  +TG
Sbjct:   251 LALLNSNNLREESPGPSGGGSVSP--FNSSG-KRPKTG 285

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2176222 AT5G51300 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 6.3e-10, P = 6.3e-10
 Identities = 34/60 (56%), Positives = 44/60 (73%)

Query:    41 NEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELAILNGTLREE 100
             NE LH+LVEAE  E      L+ A  ++E LL+PVDE L+ +K+QQLRELA LNGT+R+E
Sbjct:   306 NEDLHVLVEAETQEA-----LEAAAGMVEKLLQPVDEVLNEHKRQQLRELATLNGTIRDE 360

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

UNIPROTKB|F5GXS8 QKI "Protein quaking" [Homo sapiens (taxid:9606)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 32/68 (47%), Positives = 40/68 (58%)

Query:    32 KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
             + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct:    84 RGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 143

Query:    92 ILNGTLRE 99
             ILNGT R+
Sbjct:   144 ILNGTYRD 151

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F5GYM3 QKI "Protein quaking" [Homo sapiens (taxid:9606)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 32/68 (47%), Positives = 40/68 (58%)

Query:    32 KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
             + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct:    84 RGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 143

Query:    92 ILNGTLRE 99
             ILNGT R+
Sbjct:   144 ILNGTYRD 151

GO:0003723 "RNA binding" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

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

GO:0042552 "myelination" evidence=IEA

GO:0042692 "muscle cell differentiation" evidence=IEA

GO:0042759 "long-chain fatty acid biosynthetic process" evidence=IEA

UNIPROTKB|J9NVZ6 QKI "Protein quaking" [Canis lupus familiaris (taxid:9615)]

 Score = 140 (54.3 bits), Expect = 3.1e-09, P = 3.1e-09
 Identities = 32/68 (47%), Positives = 40/68 (58%)

Query:    32 KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
             + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct:    84 RGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 143

Query:    92 ILNGTLRE 99
             ILNGT R+
Sbjct:   144 ILNGTYRD 151

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1PLY2 QKI "Protein quaking" [Canis lupus familiaris (taxid:9615)]

 Score = 140 (54.3 bits), Expect = 3.9e-09, P = 3.9e-09
 Identities = 32/68 (47%), Positives = 40/68 (58%)

Query:    32 KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
             + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK QL ELA
Sbjct:   113 RGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLVPAAEGEDSLKKMQLMELA 172

Query:    92 ILNGTLRE 99
             ILNGT R+
Sbjct:   173 ILNGTYRD 180

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: OsI_04709 Os01g0886300 (290 aa) (Oryza sativa Indica)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	127
cd02395	120	cd02395, SF1_like-KH, Splicing factor 1 (SF1) K ho	3e-19

>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

 Score = 76.5 bits (189), Expect = 3e-19
 Identities = 37/72 (51%), Positives = 43/72 (59%), Gaps = 4/72 (5%)

Query: 28  KVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESL-DHYKKQQ 86
           K E    P Y HLNEPLH+L+ AE P       L  AV  +E LLKP  E   D  K++Q
Sbjct: 52  KEEELRGPKYAHLNEPLHVLITAETPPEE---ALAKAVEAIEELLKPAIEGGNDELKREQ 108

Query: 87  LRELAILNGTLR 98
           LRELA+LNGT R
Sbjct: 109 LRELALLNGTYR 120

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. Length = 120

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	127
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	100.0
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	99.95
KOG0119	554	consensus Splicing factor 1/branch point binding p	99.91
COG5176	269	MSL5 Splicing factor (branch point binding protein	99.69
KOG1960	531	consensus Predicted RNA-binding protein, contains	95.7
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	95.33
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	95.27
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	93.3
smart00322	69	KH K homology RNA-binding domain.	93.07
KOG1676	600	consensus K-homology type RNA binding proteins [RN	92.26
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	91.56
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	91.06
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	90.05
PRK13763	180	putative RNA-processing protein; Provisional	88.73
PF13014	43	KH_3: KH domain	87.94
PRK13763	180	putative RNA-processing protein; Provisional	86.93
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	84.83
KOG1960	531	consensus Predicted RNA-binding protein, contains	81.41
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	80.14

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

Probab=100.00  E-value=2.6e-36  Score=244.63  Aligned_cols=117  Identities=38%  Similarity=0.525  Sum_probs=104.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccc-----cCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVE-----IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVD   76 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~-----~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~   76 (127)
                      +||||++|||||+|||||      |+||.     .+++|+|+|+++||||+|++++++.+|+.+|++|++.|++||+|.+
T Consensus       120 lkrLe~eTgCki~IrGrg------SmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~  193 (259)
T KOG1588|consen  120 LKRLEEETGCKIMIRGRG------SMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDH  193 (259)
T ss_pred             HHHHHHHHCCeEEEecCC------cccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCC
Confidence            799999999999999999      99988     6789999999999999999999999999999999999999999999


Q ss_pred             cchhHHHHHHHHHHHHHhCcccCCCCCCCCCCCCCCCCCCcccccccccC
Q 039634           77 ESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETG  126 (127)
Q Consensus        77 e~~delK~~QL~eLA~lNGt~r~~~~~~~~~~~~~~~p~~~~~~~~~~~~  126 (127)
                      ++.|  |++||+|||++||||..+....++...++++||+..+++|++++
T Consensus       194 e~~d--k~~QL~ELa~lngt~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~  241 (259)
T KOG1588|consen  194 EDED--KREQLRELAILNGTYLRSESRKPSGGNGRGVPGNSAGGKRGKTG  241 (259)
T ss_pred             CCch--HHHHHHHHhhcCCccccccccccCCCCCcCCCCCCCCcccccCC
Confidence            8877  99999999999999654444333333368999999999999875

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

Probab=99.95  E-value=2.3e-27  Score=173.52  Aligned_cols=88  Identities=48%  Similarity=0.670  Sum_probs=78.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCC----CCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKD----KPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDE   77 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~----~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e   77 (127)
                      +|+||++|||+|.|||+|      |+|++...    .+.|+|++|||||+|+|+++   |.+++++|+++|+.||.++.+
T Consensus        28 iK~i~~eTg~kI~Irg~g------s~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~---~~e~~~~A~~~I~~ll~~~~~   98 (120)
T cd02395          28 LKQLEKETGAKISIRGKG------SMKDGKKEEELRGPKYAHLNEPLHVLITAETP---PEEALAKAVEAIEELLKPAIE   98 (120)
T ss_pred             HHHHHHHHCCEEEEecCc------ccccccccccccCcccccCCCCcEEEEEeCCc---HHHHHHHHHHHHHHHhccCCC
Confidence            699999999999999999      88877211    27899999999999999996   346799999999999999877


Q ss_pred             c-hhHHHHHHHHHHHHHhCccc
Q 039634           78 S-LDHYKKQQLRELAILNGTLR   98 (127)
Q Consensus        78 ~-~delK~~QL~eLA~lNGt~r   98 (127)
                      + .|++|++||+|||++|||||
T Consensus        99 ~~~~~~k~~ql~~la~~nGt~~  120 (120)
T cd02395          99 GGNDELKREQLRELALLNGTYR  120 (120)
T ss_pred             ccchHHHHHHHHHHHHhcccCC
Confidence            6 99999999999999999996

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.

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

Probab=99.91  E-value=1.1e-24  Score=189.28  Aligned_cols=91  Identities=38%  Similarity=0.552  Sum_probs=80.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCcccccccc--CCCCCCC-CCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC---CC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEI--KDKPGYE-HLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK---PV   75 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~--~~~~~~e-h~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~---p~   75 (127)
                      ||+||+||||||+|||||      |+|||+  .++..|. ..+|||||+|+|+++++     |++|+++|+.||.   .+
T Consensus       166 qK~lE~etgAKI~IRGkg------SvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek-----i~~Ai~vienli~~av~~  234 (554)
T KOG0119|consen  166 QKRLERETGAKIAIRGKG------SVKEGKGRSDDLSYIPKENEPLHCLISADTQEK-----IKKAIAVIENLIQSAVSV  234 (554)
T ss_pred             HHHHHHHhCCeEEEeccc------cccccccCCcccccccccccceeEEEecchHHH-----HHHHHHHHHHHHHhhccC
Confidence            799999999999999999      999995  2234442 47899999999999765     9999999999998   58


Q ss_pred             CcchhHHHHHHHHHHHHHhCcccCCCCC
Q 039634           76 DESLDHYKKQQLRELAILNGTLREESPS  103 (127)
Q Consensus        76 ~e~~delK~~QL~eLA~lNGt~r~~~~~  103 (127)
                      +|+++++|+.||+|||.+|||+|++++.
T Consensus       235 ~e~~n~l~~~Qlrela~lNgt~r~~d~~  262 (554)
T KOG0119|consen  235 PEGQNDLKRLQLRELARLNGTLRDDDNR  262 (554)
T ss_pred             ccccccccHHHHHHHHHhCCCCCccccc
Confidence            9999999999999999999999998843

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

Probab=99.69  E-value=2.1e-17  Score=132.41  Aligned_cols=91  Identities=26%  Similarity=0.367  Sum_probs=71.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCcccccccc-CC--CCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCcc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEI-KD--KPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDES   78 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~-~~--~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e~   78 (127)
                      ||+||+.|+|||.|||+|      |+|++. +.  .++.....++||+||+++....+|.. +.-....|.+.-. +|+|
T Consensus       176 lk~le~~s~akIaIRG~g------svKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~-ik~~~n~I~~a~~-~PeG  247 (269)
T COG5176         176 LKQLERISRAKIAIRGSG------SVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRL-IKSQLNAIREARR-NPEG  247 (269)
T ss_pred             HHHHHHHhCCeEEEeccc------ccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHH-HHHHHHHHHHHhc-CCcc
Confidence            799999999999999999      999982 22  23344578999999999997765433 2334444555555 6899


Q ss_pred             hhHHHHHHHHHHHHHhCcccCC
Q 039634           79 LDHYKKQQLRELAILNGTLREE  100 (127)
Q Consensus        79 ~delK~~QL~eLA~lNGt~r~~  100 (127)
                      ++++|+-||++||.+|||+|++
T Consensus       248 qnDlkR~qlr~la~lngtlr~d  269 (269)
T COG5176         248 QNDLKRFQLRWLAHLNGTLRAD  269 (269)
T ss_pred             cchHHHHHHHHHHHhcceecCC
Confidence            9999999999999999999864

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]

Probab=95.70  E-value=0.0057  Score=53.77  Aligned_cols=61  Identities=18%  Similarity=0.032  Sum_probs=47.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVD   76 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~   76 (127)
                      |..+|.||+.++.||||||+     -.|...   +.| .+|||.++|+....+.     +.+|+.++.+|+.-+.
T Consensus       237 La~~~ie~~i~~l~~Gr~SG-----~iEP~~---G~E-snEPMYI~i~h~~~~g-----~~~A~r~~~nl~~~v~  297 (531)
T KOG1960|consen  237 LALQEIESWINPLIDGRRSG-----RREPNE---GNE-SNEPMYIFSTHGNGNG-----ENGAPRRKWNLEEKVY  297 (531)
T ss_pred             hhhhhhhhhhhhhhcccccc-----ccCccc---ccc-cCCceeEEeecCCchh-----hccchhHHHhHHHHHH
Confidence            34578899999999999943     234432   333 7999999999999765     8899999999998653

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

Probab=95.33  E-value=0.035  Score=35.64  Aligned_cols=38  Identities=16%  Similarity=0.142  Sum_probs=28.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHH
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILE   69 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie   69 (127)
                      +|+||++|||+|.|--.|                         .|.|+|.+++.     ++.|.++|+
T Consensus        24 ik~I~~~tg~~I~i~~~g-------------------------~v~I~G~~~~~-----v~~A~~~I~   61 (61)
T cd02393          24 IKKIIEETGVKIDIEDDG-------------------------TVYIAASDKEA-----AEKAKKMIE   61 (61)
T ss_pred             HHHHHHHHCCEEEeCCCC-------------------------EEEEEeCCHHH-----HHHHHHHhC
Confidence            689999999999874322                         38899987544     788888774

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=95.27  E-value=0.036  Score=34.58  Aligned_cols=39  Identities=18%  Similarity=0.233  Sum_probs=29.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL   68 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I   68 (127)
                      +|+||++|||+|.|...                      ++.-.|.|+| +++     .+++|.++|
T Consensus        22 i~~I~~~t~~~I~i~~~----------------------~~~~~v~I~G-~~~-----~v~~A~~~I   60 (60)
T PF00013_consen   22 IKEIEEETGVKIQIPDD----------------------DERDIVTISG-SPE-----QVEKAKKMI   60 (60)
T ss_dssp             HHHHHHHHTSEEEEEST----------------------TEEEEEEEEE-SHH-----HHHHHHHHH
T ss_pred             HHHhhhhcCeEEEEcCC----------------------CCcEEEEEEe-CHH-----HHHHHHhhC
Confidence            68999999999999552                      1335788999 543     478888765

; 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=93.30  E-value=0.26  Score=30.40  Aligned_cols=42  Identities=14%  Similarity=0.106  Sum_probs=30.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL   68 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I   68 (127)
                      +++|+++|||+|.|...+      +             ...+-.|.|.|..      ..+..|..+|
T Consensus        22 i~~I~~~s~~~I~i~~~~------~-------------~~~~~~v~i~G~~------~~v~~a~~~i   63 (64)
T cd00105          22 IKEIREETGAKIKIPDSG------S-------------GSEERIVTITGTP------EAVEKAKELI   63 (64)
T ss_pred             HHHHHHHHCCEEEEcCCC------C-------------CCCceEEEEEcCH------HHHHHHHHHh
Confidence            688999999999998755      1             2244668888883      3477777765

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.

>smart00322 KH K homology RNA-binding domain

Probab=93.07  E-value=0.32  Score=29.33  Aligned_cols=44  Identities=14%  Similarity=0.142  Sum_probs=32.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      ++.|++.|||+|.|.+.+      +               ..-.|.|.|+.      ..+..|...|.+.+
T Consensus        25 i~~i~~~~~~~i~~~~~~------~---------------~~~~v~i~g~~------~~v~~a~~~i~~~~   68 (69)
T smart00322       25 IKKIEEETGVKIDIPEDG------S---------------EERVVEITGPP------ENVEKAAELILEIL   68 (69)
T ss_pred             HHHHHHHHCCEEEECCCC------C---------------CccEEEEEcCH------HHHHHHHHHHHHHh
Confidence            578999999999998755      1               23568888873      23677887777665

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

Probab=92.26  E-value=0.24  Score=45.20  Aligned_cols=50  Identities=12%  Similarity=0.253  Sum_probs=34.7

Q ss_pred             CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      |+|+|+.|||+||+|+=--              +|.  ..+-+  +.|.|..      .++.+|.++|.+||.-
T Consensus       251 ~IKklq~etG~KIQfkpDd--------------~p~--speR~--~~IiG~~------d~ie~Aa~lI~eii~~  300 (600)
T KOG1676|consen  251 MIKKLQNETGAKIQFKPDD--------------DPS--SPERP--AQIIGTV------DQIEHAAELINEIIAE  300 (600)
T ss_pred             HHHHHhhccCceeEeecCC--------------CCC--Cccce--eeeecCH------HHHHHHHHHHHHHHHH
Confidence            7899999999999997632              121  01122  3345543      4689999999999874

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=91.56  E-value=0.41  Score=29.89  Aligned_cols=40  Identities=5%  Similarity=-0.017  Sum_probs=28.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL   68 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I   68 (127)
                      +++|+++|||+|.|-..+                     +.+=.|.|.|+.      +.+..|.++|
T Consensus        22 i~~i~~~~g~~I~i~~~~---------------------~~~~~v~I~G~~------~~v~~A~~~i   61 (62)
T cd02394          22 IRKIMEETGVKIRFPDPG---------------------SKSDTITITGPK------ENVEKAKEEI   61 (62)
T ss_pred             HHHHHHHhCCEEEcCCCC---------------------CCCCEEEEEcCH------HHHHHHHHHh
Confidence            688999999999987543                     122358899883      3477887765

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.

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=91.06  E-value=0.64  Score=29.67  Aligned_cols=43  Identities=14%  Similarity=0.174  Sum_probs=28.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL   68 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I   68 (127)
                      +++|+++|||+|.|.-..      .        +   ..++. -|.|+|..      ..+..|..+|
T Consensus        22 i~~i~~~tga~I~i~~~~------~--------~---~~~~r-~v~I~G~~------~~v~~A~~~I   64 (65)
T cd02396          22 IKEIREETGAKIRVSKSV------L--------P---GSTER-VVTISGKP------SAVQKALLLI   64 (65)
T ss_pred             HHHHHHHHCCEEEEcCCC------C--------C---CCCce-EEEEEeCH------HHHHHHHHhh
Confidence            689999999999995433      1        1   12233 47777774      3467887776

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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=90.05  E-value=0.47  Score=36.27  Aligned_cols=41  Identities=17%  Similarity=0.180  Sum_probs=32.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      .+.||..|||+|.|-|+                          .|.|.| ++     .+++.|.+.|+.||.-
T Consensus       111 ~~~ie~~t~~~i~i~~~--------------------------~v~i~G-~~-----~~~~~A~~~i~~li~~  151 (172)
T TIGR03665       111 RRIIEELTGVSISVYGK--------------------------TVGIIG-DP-----EQVQIAREAIEMLIEG  151 (172)
T ss_pred             HHHHHHHHCCeEEEcCC--------------------------EEEEEC-CH-----HHHHHHHHHHHHHHcC
Confidence            57899999999998641                          377888 54     3489999999999964

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=88.73  E-value=0.91  Score=35.00  Aligned_cols=44  Identities=18%  Similarity=0.210  Sum_probs=34.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEE---ecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVE---AEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~---a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      .|.|+++|||+|.|.-..                        =.|.|.   +.++..     +.+|+++|+.++..
T Consensus        25 Ik~I~e~tg~~I~i~~~~------------------------g~V~I~~~~~~d~~~-----i~kA~~~I~ai~~g   71 (180)
T PRK13763         25 KKEIEERTGVKLEIDSET------------------------GEVIIEPTDGEDPLA-----VLKARDIVKAIGRG   71 (180)
T ss_pred             HHHHHHHHCcEEEEECCC------------------------CeEEEEeCCCCCHHH-----HHHHHHHHHHHhcC
Confidence            588999999999997641                        145566   566544     89999999999985

>PF13014 KH_3: KH domain

Probab=87.94  E-value=0.31  Score=28.75  Aligned_cols=16  Identities=19%  Similarity=0.077  Sum_probs=14.6

Q ss_pred             chhhhhhcCcEEEEec
Q 039634            2 TPEVDLLIKFKVSING   17 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRG   17 (127)
                      +++|+++|||+|.|--
T Consensus        13 I~~I~~~tg~~I~i~~   28 (43)
T PF13014_consen   13 IKEIREETGAKIQIPP   28 (43)
T ss_pred             HHHHHHHhCcEEEECC
Confidence            6899999999999976

>PRK13763 putative RNA-processing protein; Provisional

Probab=86.93  E-value=1.1  Score=34.59  Aligned_cols=41  Identities=17%  Similarity=0.224  Sum_probs=31.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      .|.||..|||+|.|-|+                          .|.|.| ++     .+++.|.+.|+.|+.-
T Consensus       117 ~k~ie~~t~~~i~i~~~--------------------------~v~i~G-~~-----~~~~~A~~~I~~li~g  157 (180)
T PRK13763        117 RRIIEELTGVDISVYGK--------------------------TVAIIG-DP-----EQVEIAREAIEMLIEG  157 (180)
T ss_pred             HHHHHHHHCcEEEEcCC--------------------------EEEEEe-CH-----HHHHHHHHHHHHHHcC
Confidence            57899999999998541                          166777 43     3489999999999964

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=84.83  E-value=1.9  Score=40.34  Aligned_cols=43  Identities=14%  Similarity=0.149  Sum_probs=36.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      .|.|+++|||+|.|--.|                         +|.|.|.+.+     .+++|+++|+.+..+
T Consensus       600 I~~i~~~tg~~Idi~d~G-------------------------~V~I~a~d~~-----~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       600 INQIQDETGAEISIEDDG-------------------------TVYIGAADGP-----SAEAARAMINAIANP  642 (719)
T ss_pred             HHHHHHHHCCEEEEecCc-------------------------EEEEEeCCHH-----HHHHHHHHHHHhhCc
Confidence            588999999999886655                         6889999864     489999999999995

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.

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]

Probab=81.41  E-value=0.78  Score=40.74  Aligned_cols=64  Identities=20%  Similarity=0.385  Sum_probs=50.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCcch
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESL   79 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e~~   79 (127)
                      +|.++.++-+++.|.|-||+|    + +.   -+..+ .++|.||-|...++..     |+.|.-++++++-||+...
T Consensus       317 ~~~~~~~~~~~~~~~g~~s~~----i-~p---~~~~~-~~~p~~~~~~~~~~~~-----~~~~~~~~~~~i~~v~~qy  380 (531)
T KOG1960|consen  317 VKHIQQETRTRVQIKGQGSAF----I-EP---STNRE-SDEPIHLCIMSHDPNA-----IQRAKVLCEDLIASVHQQY  380 (531)
T ss_pred             ccccCCCCCcceeccCcccee----e-cC---CCCCC-CCCCcccccccCChhh-----hhhhhhcccccCCcccccC
Confidence            467889999999999999664    2 22   13333 7899999999999766     7788999999999987543

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=80.14  E-value=3.9  Score=31.19  Aligned_cols=43  Identities=16%  Similarity=0.200  Sum_probs=32.8

Q ss_pred             chhhhhhcCcEEEEecC-CCCCCccccccccCCCCCCCCCCCCceEEE--EecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGC-PYTYTSLSIKVEIKDKPGYEHLNEPLHMLV--EAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGk-G~~~~~~S~Kd~~~~~~~~eh~~epLHVlI--~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      .|+||++|||+|.|--. |                         .|.|  .+.++.     .+.+|.++|+.+...
T Consensus        20 Ik~I~~~tgv~I~Id~~~g-------------------------~V~I~~~t~d~~-----~i~kA~~~I~~i~~g   65 (172)
T TIGR03665        20 KKEIEERTGVKLDIDSETG-------------------------EVKIEEEDEDPL-----AVMKAREVVKAIGRG   65 (172)
T ss_pred             HHHHHHHhCcEEEEEcCCc-------------------------eEEEecCCCCHH-----HHHHHHHHHHHHHcC
Confidence            58899999999998753 2                         3556  445554     489999999998885

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	127
2bl5_A	140	Solution Structure Of The Kh-Qua2 Region Of The Xen		1e-08
1k1g_A	131	Structural Basis For Recognition Of The Intron Bran		1e-04

>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus Star-Gsg Quaking Protein Length = 140

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 40/68 (58%)
Query: 32  KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRELA 91
           + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK +L ELA
Sbjct: 59  RGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELA 118
Query: 92  ILNGTLRE 99
           ILNGT R+
Sbjct: 119 ILNGTYRD 126

>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site Rna By Splicing Factor 1 Length = 131

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 28  KVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP---VDESLDHYKK 84
           KV  KD       +EPLH LV A   E +       AV  + N+LK      E  +  +K
Sbjct: 58  KVGRKDGQMLPGEDEPLHALVTANTMENV-----KKAVEQIRNILKQGIETPEDQNDLRK 112
Query: 85  QQLRELAILNGTLREE 100
            QLRELA LNGTLRE+
Sbjct: 113 MQLRELARLNGTLRED 128
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	127
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	3e-25
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	2e-22
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	1e-10

>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 = 84.5 bits (209), Expect = 2e-22
 Identities = 35/94 (37%), Positives = 44/94 (46%), Gaps = 11/94 (11%)

Query: 12  KVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENL 71
           K+ I G     +    KV  KD       +EPLH LV A   E      +  AV  + N+
Sbjct: 45  KIMIRG---KGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME-----NVKKAVEQIRNI 96

Query: 72  LK---PVDESLDHYKKQQLRELAILNGTLREESP 102
           LK      E  +  +K QLRELA LNGTLRE+  
Sbjct: 97  LKQGIETPEDQNDLRKMQLRELARLNGTLREDDN 130

>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 = 53.8 bits (129), Expect = 1e-10
 Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 5/56 (8%)

Query: 31  IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQ 86
             +        EP+++ +    PE      L  A  + ENLL+ V      +  Q 
Sbjct: 61  CIEPASGREAFEPMYIYISHPKPE-----GLAAAKKLCENLLQTVHAEYSRFVNQI 111

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	127
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	100.0
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	99.96
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	99.67
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	97.22
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	97.03
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	96.85
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	96.69
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	96.65
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	96.62
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	96.3
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	96.17
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	96.17
1we8_A	104	Tudor and KH domain containing protein; structural	96.05
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	96.05
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	96.0
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	95.87
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	95.83
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	95.57
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	95.53
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	95.12
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	95.07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	95.05
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	94.62
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	94.51
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	94.27
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	93.41
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	92.75
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	92.51
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	92.02
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	89.83
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	89.6
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	88.94
1tua_A	191	Hypothetical protein APE0754; structural genomics,	88.35
2cpq_A	91	FragIle X mental retardation syndrome related prot	88.33
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	88.01
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	86.58
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	86.11
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	84.18

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

Probab=100.00  E-value=8.3e-36  Score=222.44  Aligned_cols=96  Identities=35%  Similarity=0.485  Sum_probs=91.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccc-----cCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVE-----IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVD   76 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~-----~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~   76 (127)
                      +|+||++|||||+|||||      |+||+     .+|+|+|+|++|||||+|+|++++++|+++|++|+++|++||.|++
T Consensus        30 ~K~ie~eTg~kI~IrGkG------S~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I~~lL~p~~  103 (140)
T 2bl5_A           30 AKQLEAETGCKIMVRGKG------SMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAA  103 (140)
T ss_dssp             HHHHHHHHSEEEEEESTT------SSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHHHHSSCCS
T ss_pred             HHHHHHHHCCeEEEecCC------CcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHHHHHCCCCC
Confidence            799999999999999999      88876     4678999999999999999999999999999999999999999999


Q ss_pred             cchhHHHHHHHHHHHHHhCcccCCCCC
Q 039634           77 ESLDHYKKQQLRELAILNGTLREESPS  103 (127)
Q Consensus        77 e~~delK~~QL~eLA~lNGt~r~~~~~  103 (127)
                      +++|++|++||+|||+||||||+++++
T Consensus       104 e~~de~K~~QL~eLA~lNGt~r~~~~~  130 (140)
T 2bl5_A          104 EGEDSLKKMKLMELAILNGTYRDANLK  130 (140)
T ss_dssp             SSSSHHHHHHHTGGGSSSTTTSGGGGS
T ss_pred             cchhHHHHHHHHHHHHhcCCcCCCccc
Confidence            999999999999999999999998776

>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=99.96  E-value=1.6e-29  Score=186.02  Aligned_cols=90  Identities=37%  Similarity=0.442  Sum_probs=77.0

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCC---CCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC---C
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDK---PGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP---V   75 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~---~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p---~   75 (127)
                      +|+||+||||||.|||+|      |+|++..+.   ..|+|++|||||+|+|++++     .|++|+++|+.||.+   +
T Consensus        35 iK~Iq~eTG~kI~Irgkg------S~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e-----~~~~A~~~I~~ll~~~~~~  103 (131)
T 1k1g_A           35 LKNIEKECNAKIMIRGKG------SVKEGKVGRKDGQMLPGEDEPLHALVTANTME-----NVKKAVEQIRNILKQGIET  103 (131)
T ss_dssp             HHHHHHHSCCEEEEEEST------TSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH-----HHHHHHHHHHHHHTTTTSC
T ss_pred             HHHHHHHHCCeEEecCCc------ccccccccccccccccccCCCeEEEEEECCHH-----HHHHHHHHHHHHHhccCCC
Confidence            699999999999999999      888874332   34678999999999999965     499999999999975   7


Q ss_pred             CcchhHHHHHHHHHHHHHhCcccCCCC
Q 039634           76 DESLDHYKKQQLRELAILNGTLREESP  102 (127)
Q Consensus        76 ~e~~delK~~QL~eLA~lNGt~r~~~~  102 (127)
                      |+++|++|++||+|||+||||||++++
T Consensus       104 p~~~d~~k~~Ql~eLa~~nGt~r~~~~  130 (131)
T 1k1g_A          104 PEDQNDLRKMQLRELARLNGTLREDDN  130 (131)
T ss_dssp             CTTSSGGGGGGGHHHHHHHTCCC----
T ss_pred             CccHHHHHHHHHHHHHHHcCcCCCcCC
Confidence            899999999999999999999998764

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

Probab=99.67  E-value=4.2e-17  Score=118.28  Aligned_cols=71  Identities=25%  Similarity=0.304  Sum_probs=60.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCcchhH
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDH   81 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e~~de   81 (127)
                      +|+||+||||||.|||+|      |.+..  +..+ ++++|||||+|+|++++.     +++|+++|++||.++.+..++
T Consensus        41 iK~I~~eTG~kI~I~G~g------S~~~e--~~~~-~e~~e~l~V~I~a~~~e~-----i~~A~~~Ie~Ll~~v~~~~~~  106 (119)
T 2yqr_A           41 LQHIQIETGAKVFLRGKG------SGCIE--PASG-REAFEPMYIYISHPKPEG-----LAAAKKLCENLLQTVHAEYSR  106 (119)
T ss_dssp             HHHHHHHHCCEEEEESBT------TTCCC--TTTS-SCCSSBCEEEEEESSHHH-----HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEEecCC------ccccc--cccc-cccCCCcEEEEEeCCHHH-----HHHHHHHHHHHhhchHHHHHH
Confidence            699999999999999999      65522  1122 358999999999999755     899999999999999888899


Q ss_pred             HHHHH
Q 039634           82 YKKQQ   86 (127)
Q Consensus        82 lK~~Q   86 (127)
                      +|++|
T Consensus       107 ~~~q~  111 (119)
T 2yqr_A          107 FVNQI  111 (119)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            98876

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

Probab=97.22  E-value=0.00071  Score=44.84  Aligned_cols=49  Identities=12%  Similarity=0.064  Sum_probs=38.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|...|      +.       +    .+.+-+|.|+| +++     .+++|+++|+.++.
T Consensus        36 Ik~I~~~tga~I~i~~~~------~~-------~----~~~er~v~I~G-~~~-----~v~~A~~~I~~i~~   84 (85)
T 2opv_A           36 IKQLQERAGVKMILIQDG------SQ-------N----TNVDKPLRIIG-DPY-----KVQQACEMVMDILR   84 (85)
T ss_dssp             HHHHHHHHTCEEEECSSS------CS-------S----TTSCEEEEEEE-CHH-----HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCEEEEcCCC------CC-------C----CCCceEEEEEe-CHH-----HHHHHHHHHHHHhc
Confidence            689999999999998876      21       1    23456799999 654     48999999999874

>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=97.03  E-value=0.0015  Score=44.17  Aligned_cols=50  Identities=8%  Similarity=0.036  Sum_probs=38.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      +|+|+++|||+|.|-..|      ..         +  ...+-.|.|+| +++.     +++|+++|+++|..
T Consensus        37 Ik~I~~~tga~I~I~~~~------~~---------~--~~~~r~v~I~G-~~~~-----v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           37 IKQLQERAGVKMVMIQDG------PQ---------N--TGADKPLRITG-DPYK-----VQQAKEMVLELIRD   86 (94)
T ss_dssp             HHHHHHHHTSEEEECCSC------CC---------S--SCSCEEEEEEE-CTTT-----HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHCCeEEecCCC------CC---------C--CCCceEEEEEe-CHHH-----HHHHHHHHHHHHhc
Confidence            689999999999998766      11         0  12346799999 5543     89999999999974

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

Probab=96.85  E-value=0.0012  Score=46.06  Aligned_cols=47  Identities=13%  Similarity=0.182  Sum_probs=35.8

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|.-.+               +    .+.+-.|.|++. ++     .+++|+++|++++.
T Consensus        33 Ik~I~~~TGakI~I~~~~---------------~----~~~er~V~I~G~-~e-----~v~~A~~~I~~ii~   79 (106)
T 2hh3_A           33 IKKIQNDAGVRIQFKQDD---------------G----TGPEKIAHIMGP-PD-----RCEHAARIINDLLQ   79 (106)
T ss_dssp             HHHHHHHHTCEEEECSSC---------------S----SSSEEEEEEESS-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcEEEEecCC---------------C----CCceeEEEEEeC-HH-----HHHHHHHHHHHHHh
Confidence            689999999999997533               1    123467899986 43     48999999999876

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

Probab=96.69  E-value=0.0031  Score=43.67  Aligned_cols=51  Identities=16%  Similarity=0.196  Sum_probs=37.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      +|+|+++|||+|.|....      .        +. . ...+-.|.|+| +++     .+++|+++|+++|.-
T Consensus        29 Ik~I~~~TGa~I~I~~~~------~--------~~-~-~~~~r~V~I~G-~~e-----~v~~A~~~I~~~i~e   79 (107)
T 2hh2_A           29 VKAINQQTGAFVEISRQL------P--------PN-G-DPNFKLFIIRG-SPQ-----QIDHAKQLIEEKIEG   79 (107)
T ss_dssp             HHHHHHHSSSEEEECCCC------C--------TT-C-CTTEEEEEEES-CHH-----HHHHHHHHHHHHSCS
T ss_pred             HHHHHHHhCCEEEEcCcc------C--------CC-C-CCCceEEEEEC-CHH-----HHHHHHHHHHHHHhc
Confidence            689999999999998754      1        11 0 12335688998 543     489999999999874

>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=96.65  E-value=0.0034  Score=40.26  Aligned_cols=50  Identities=14%  Similarity=0.205  Sum_probs=37.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|...+      ...      ++    ..+-.|.|+|. ++     .+.+|..+|+.++.
T Consensus        25 Ik~I~~~tga~I~i~~~~------~~~------~~----~~~~~v~I~G~-~~-----~v~~A~~~I~~~i~   74 (76)
T 1dtj_A           25 LVEYQELTGARIQISKKG------EFL------PG----TRNRRVTITGS-PA-----ATQAAQYLISQRVT   74 (76)
T ss_dssp             HHHHHHHHCCEEEECCTT------CCS------TT----CCEEEEEEEES-HH-----HHHHHHHHHHHHCC
T ss_pred             HHHHHHHhCCEEEECcCC------CCC------CC----CceeEEEEEeC-HH-----HHHHHHHHHHHHHh
Confidence            589999999999998765      111      11    23467889986 43     48999999999875

>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=96.62  E-value=0.003  Score=42.44  Aligned_cols=48  Identities=15%  Similarity=0.236  Sum_probs=36.2

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      +|+|+++|||+|.|....               ++    ..+-.|.|+|. ++     .+++|+++|++++..
T Consensus        37 Ik~I~~~tga~I~I~~~~---------------~g----~~~r~v~I~G~-~e-----~v~~A~~~I~~~i~~   84 (92)
T 1x4n_A           37 ISRIQQESGCKIQIAPDS---------------GG----LPERSCMLTGT-PE-----SVQSAKRLLDQIVEK   84 (92)
T ss_dssp             HHHHHHHSCCEEEECSCC---------------TT----CSEEEEEEEEC-HH-----HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEEcCCC---------------CC----CCccEEEEEeC-HH-----HHHHHHHHHHHHHHh
Confidence            589999999999998643               11    12357889986 43     488999999998763

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

Probab=96.30  E-value=0.0067  Score=39.07  Aligned_cols=47  Identities=11%  Similarity=0.149  Sum_probs=35.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-...               ++    ..+=.|.|+|. ++     .+.+|.++|+++|.
T Consensus        27 Ik~I~~~tga~I~i~~~~---------------~~----~~~~~v~I~G~-~~-----~v~~A~~~I~~~i~   73 (76)
T 2p2r_A           27 INEIRQMSGAQIKIANPV---------------EG----STDRQVTITGS-AA-----SISLAQYLINVRLS   73 (76)
T ss_dssp             HHHHHHHHCCEEEECCCC---------------TT----CSEEEEEEEEC-HH-----HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCEEEEcCCC---------------CC----CCeEEEEEEeC-HH-----HHHHHHHHHHHHHH
Confidence            589999999999997522               11    23357899996 43     48999999999886

>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=96.17  E-value=0.0074  Score=39.47  Aligned_cols=48  Identities=8%  Similarity=0.071  Sum_probs=36.0

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      +|+|+++|||+|.|-...               +    ...+=.|.|+|..      ..+++|+++|++++..
T Consensus        28 Ik~I~~~sga~I~i~~~~---------------~----~~~~r~v~I~G~~------~~v~~A~~~I~~~i~~   75 (82)
T 1wvn_A           28 INEIRQMSGAQIKIANPV---------------E----GSSGRQVTITGSA------ASISLAQYLINARLSS   75 (82)
T ss_dssp             HHHHHHHHCCEEEECCCC---------------T----TCSEEEEEEEECH------HHHHHHHHHHHHHTC-
T ss_pred             HHHHHHHhCCEEEEecCC---------------C----CCCceEEEEEcCH------HHHHHHHHHHHHHHHh
Confidence            589999999999997522               1    1233578899865      2489999999999873

>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=96.17  E-value=0.008  Score=39.37  Aligned_cols=47  Identities=15%  Similarity=0.184  Sum_probs=34.8

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|...-               ++    ..+-.|.|+|. ++     .+++|.++|++++.
T Consensus        29 Ik~I~~~tga~I~i~~~~---------------~~----~~~~~v~I~G~-~~-----~v~~A~~~I~~~i~   75 (82)
T 1zzk_A           29 IKQIRHESGASIKIDEPL---------------EG----SEDRIITITGT-QD-----QIQNAQYLLQNSVK   75 (82)
T ss_dssp             HHHHHHHHCCEEEECCTT---------------SC----SSEEEEEEEEC-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEEcCCC---------------CC----CCceEEEEEeC-HH-----HHHHHHHHHHHHHH
Confidence            589999999999996421               11    12357889994 43     48999999999875

>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=96.05  E-value=0.008  Score=41.20  Aligned_cols=49  Identities=8%  Similarity=-0.025  Sum_probs=37.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-...               .+.  ..++=.|.|+|...      .+++|+++|+.++.
T Consensus        37 Ik~I~~~tga~I~I~~~~---------------~~~--~~~~~~V~I~G~~~------~v~~A~~~I~~~i~   85 (104)
T 1we8_A           37 IRSICKASGAKITCDKES---------------EGT--LLLSRLIKISGTQK------EVAAAKHLILEKVS   85 (104)
T ss_dssp             HHHHHHHHCCEEEECCSS---------------CCS--SSSEEEEEEEEEHH------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEEecCC---------------CCC--CCCcceEEEEcCHH------HHHHHHHHHHHHHh
Confidence            689999999999997654               110  12346799998763      48999999999986

>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=96.05  E-value=0.0095  Score=39.65  Aligned_cols=47  Identities=15%  Similarity=0.184  Sum_probs=34.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|...-               ++    ..+=.|.|+|. ++     .+++|+++|++++.
T Consensus        36 Ik~I~~~tga~I~I~~~~---------------~~----~~~~~v~I~G~-~e-----~v~~A~~~I~~~i~   82 (89)
T 1j5k_A           36 IKQIRHESGASIKIDEPL---------------EG----SEDRIITITGT-QD-----QIQNAQYLLQNSVK   82 (89)
T ss_dssp             HHHHHHHTCCEEEECSCC---------------SS----SSEEEEEEEEE-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCeEEecCCC---------------CC----CCccEEEEEcC-HH-----HHHHHHHHHHHHHH
Confidence            589999999999996421               11    12346889987 43     47899999998875

>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=96.00  E-value=0.0091  Score=39.44  Aligned_cols=50  Identities=14%  Similarity=0.205  Sum_probs=37.2

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-..+      ...      ++    ..+=.|.|+|. ++     .+.+|..+|+.+|.
T Consensus        25 Ik~I~~~tga~I~I~~~~------~~~------~g----~~~r~v~I~G~-~~-----~v~~A~~~I~~~i~   74 (87)
T 1ec6_A           25 LVEYQELTGARIQISKKG------EFL------PG----TRNRRVTITGS-PA-----ATQAAQYLISQRVT   74 (87)
T ss_dssp             HHHHHHHHCCEEEECCTT------CBS------TT----SCEEEEEEESS-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEEccCC------CCC------CC----CCceEEEEEcC-HH-----HHHHHHHHHHHHHh
Confidence            589999999999998755      211      11    13357889986 43     48999999999986

>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=95.87  E-value=0.0066  Score=40.98  Aligned_cols=45  Identities=11%  Similarity=0.093  Sum_probs=34.0

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-..+                     +++=.|.|+|. ++.     +++|.++|+.++.
T Consensus        39 Ik~I~~etg~~I~i~~~~---------------------~~~~~V~I~G~-~e~-----v~~A~~~I~~i~~   83 (94)
T 2cte_A           39 LQDLELKTATKIQIPRPD---------------------DPSNQIKITGT-KEG-----IEKARHEVLLISA   83 (94)
T ss_dssp             HHHHHHHTTCCCBCCCTT---------------------SSCCEEEEEEC-HHH-----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEeCCCC---------------------CCCCeEEEEEC-HHH-----HHHHHHHHHHHhh
Confidence            589999999999986433                     01137899998 544     7899999988875

>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=95.83  E-value=0.013  Score=39.12  Aligned_cols=44  Identities=16%  Similarity=0.131  Sum_probs=33.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+||++|||+|.|-.++                     +++ .|.|+|... .     +++|+.+|+.++.
T Consensus        32 Ik~Iqe~Tga~I~I~~~~---------------------~~~-~v~ItG~~e-~-----v~~A~~~I~~~i~   75 (83)
T 2dgr_A           32 IKRIQQRTHTYIVTPGRD---------------------KEP-VFAVTGMPE-N-----VDRAREEIEAHIT   75 (83)
T ss_dssp             HHHHHHHTTCEEECCCSS---------------------SCC-EEEEEECTT-T-----HHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCeEEecCCC---------------------CCC-eEEEEcCHH-H-----HHHHHHHHHHHHh
Confidence            689999999999996533                     122 377888763 3     7899999998754

>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=95.57  E-value=0.019  Score=36.90  Aligned_cols=45  Identities=9%  Similarity=0.073  Sum_probs=34.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-..|      +               .+=-|.|+|. ++.     +.+|.++|.++|.
T Consensus        27 Ik~I~~~tga~I~i~~~~------~---------------~er~v~I~G~-~~~-----v~~A~~~I~~~l~   71 (73)
T 2axy_A           27 VKKMREESGARINISEGN------C---------------PERIITLAGP-TNA-----IFKAFAMIIDKLE   71 (73)
T ss_dssp             HHHHHHHHCCEEEECSSC------C---------------SEEEEEEEEC-HHH-----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEEecCC------C---------------CcEEEEEEeC-HHH-----HHHHHHHHHHHHh
Confidence            589999999999997644      1               1235888988 543     7899999998875

>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=95.53  E-value=0.017  Score=41.50  Aligned_cols=50  Identities=14%  Similarity=0.115  Sum_probs=37.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      +|+|+++|||+|.|-..|              .|+   .++.-.|.|+| +++     .+++|.++|+++|.-
T Consensus       107 I~~i~~~tga~I~i~~~~--------------~~~---~~~~~~v~I~G-~~~-----~v~~A~~~I~~~i~~  156 (163)
T 3krm_A          107 VNELQNLTAAEVVVPRDQ--------------TPD---ENDQVIVKIIG-HFY-----ASQMAQRKIRDILAQ  156 (163)
T ss_dssp             HHHHHHHHCCEEECCTTC--------------CCC---TTSEEEEEEEE-CHH-----HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCeEEECCCC--------------CCC---CCCceEEEEEe-CHH-----HHHHHHHHHHHHHHH
Confidence            588999999999997655              121   34445789999 543     489999999999873

>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=95.12  E-value=0.024  Score=38.56  Aligned_cols=49  Identities=4%  Similarity=0.051  Sum_probs=35.1

Q ss_pred             CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      ++|+|+++|||+|.|--.|      .        ++    ..+=-|.|+|. ++     .+++|.++|+.++.
T Consensus        38 ~Ik~I~~etg~~I~i~~~g------~--------~~----~~~~~V~I~G~-~e-----~v~~A~~~I~~iv~   86 (97)
T 2ctl_A           38 VITQIRLEHDVNIQFPDKD------D--------GN----QPQDQITITGY-EK-----NTEAARDAILRIVG   86 (97)
T ss_dssp             HHHHHHHHHTCEEECCCTT------T--------CS----SCSSEEEEESC-HH-----HHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHCCEEEecCCC------C--------CC----CCccEEEEEeC-HH-----HHHHHHHHHHHHHH
Confidence            3689999999999996655      1        11    12245889986 43     37888888888764

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

Probab=95.07  E-value=0.044  Score=34.98  Aligned_cols=44  Identities=16%  Similarity=0.083  Sum_probs=33.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      +++|+++|||+|.|--.|      +               .+=-|.|+|.. +     .+++|.++|+.++
T Consensus        27 I~~I~e~tg~~I~i~~~g------~---------------~~~~V~I~G~~-~-----~v~~A~~~I~~i~   70 (71)
T 1vig_A           27 INRIKDQYKVSVRIPPDS------E---------------KSNLIRIEGDP-Q-----GVQQAKRELLELA   70 (71)
T ss_dssp             HHHHHHHTCCEEECCCCC------S---------------SSEEEEEEESS-H-----HHHHHHHHHHHTC
T ss_pred             HHHHHHHHCCEEEECCCC------C---------------cccEEEEEcCH-H-----HHHHHHHHHHHHh
Confidence            689999999999996544      1               11258899984 3     3899999999875

>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=95.05  E-value=0.031  Score=37.93  Aligned_cols=46  Identities=17%  Similarity=0.211  Sum_probs=33.8

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-..|      +              ..+=.|.|+|. +++     +++|+++|+.|+.
T Consensus        39 Ir~I~e~tg~~I~i~~~g------~--------------~~~~~V~I~G~-~e~-----v~~A~~~I~~i~~   84 (95)
T 2ctm_A           39 IRKIMDEFKVDIRFPQSG------A--------------PDPNCVTVTGL-PEN-----VEEAIDHILNLEE   84 (95)
T ss_dssp             HHHHHHHHTCEEECCCTT------C--------------SCTTEEEEESC-HHH-----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCeEEecCCC------C--------------CCCcEEEEEcC-HHH-----HHHHHHHHHHHHH
Confidence            589999999999997665      1              11246889987 333     7888888888754

>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=94.62  E-value=0.059  Score=39.17  Aligned_cols=49  Identities=12%  Similarity=0.196  Sum_probs=34.8

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      +|+|+++|||+|.|-...      .        + .. ...+=.|.|+| ++     ..+.+|.++|+++|
T Consensus       126 Ik~I~~~tga~I~i~~~~------~--------~-~~-~~~~~~v~I~G-~~-----~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          126 IKSISQQSGARIELQRNP------P--------P-NA-DPNMKLFTIRG-TP-----QQIDYARQLIEEKI  174 (174)
T ss_dssp             HHHHHHHHCCEEEEECCC------T--------T-TS-CTTEEEEEEEC-CH-----HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCCEEEECCCC------C--------C-CC-CCCceEEEEEC-CH-----HHHHHHHHHHHHhC
Confidence            589999999999998754      1        1 11 12234688888 44     34899999999875

>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=94.51  E-value=0.046  Score=37.59  Aligned_cols=45  Identities=13%  Similarity=0.011  Sum_probs=35.0

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|--.|      +               ++=.|.|+|.. +     .+++|+++|+.++.
T Consensus        39 Ir~I~eetg~~I~I~~~g------~---------------~~~~V~I~G~~-e-----~v~~A~~~I~~i~~   83 (104)
T 2ctk_A           39 IRKMMDEFEVNIHVPAPE------L---------------QSDIIAITGLA-A-----NLDRAKAGLLERVK   83 (104)
T ss_dssp             HHHHHHHTCCEEECCCTT------T---------------TCCEEEEEECH-H-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEecCCC------C---------------CcceEEEEcCH-H-----HHHHHHHHHHHHHh
Confidence            689999999999996555      1               01279999974 3     38999999999876

>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=94.27  E-value=0.056  Score=38.51  Aligned_cols=47  Identities=13%  Similarity=0.182  Sum_probs=35.2

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-...               +    ...+=.|.|+|. ++     .+++|..+|+.+|.
T Consensus       113 I~~i~~~tg~~I~i~~~~---------------~----~~~~~~v~I~G~-~~-----~v~~A~~~I~~~i~  159 (164)
T 2jvz_A          113 IKKIQNDAGVRIQFKQDD---------------G----TGPEKIAHIMGP-PD-----RCEHAARIINDLLQ  159 (164)
T ss_dssp             HHHHHHHTCCEEEECCCC---------------T----TSSEEEEEEESC-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCeEEEeCCC---------------C----CCCcEEEEEEcC-HH-----HHHHHHHHHHHHHh
Confidence            689999999999996543               1    112356888886 43     48999999999875

>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=93.41  E-value=0.11  Score=37.60  Aligned_cols=48  Identities=13%  Similarity=0.187  Sum_probs=34.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      +|+|+++|||+|.|...-               +    ...+-.|.|+|. ++     .+.+|.++|.++|..
T Consensus        25 Ik~i~~~tg~~I~i~~~~---------------~----~~~~r~v~I~G~-~~-----~v~~A~~~I~~~~~~   72 (174)
T 1j4w_A           25 IKKIQNDAGVRIQFKPDD---------------G----TTPERIAQITGP-PD-----RAQHAAEIITDLLRS   72 (174)
T ss_dssp             HHHHHHHHCCEEEEECCT---------------T----SCSEEEEEEEEC-HH-----HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEEecCC---------------C----CCCccEEEEEeC-HH-----HHHHHHHHHHHHHHh
Confidence            689999999999996421               1    112346788887 33     478999999888763

>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=92.75  E-value=0.24  Score=35.11  Aligned_cols=51  Identities=12%  Similarity=0.051  Sum_probs=36.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPV   75 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~   75 (127)
                      +|+|+++|||+|.|--.+      +.       +    ...+-.|.|+| ++     ..+.+|..+|..++...
T Consensus        24 Ik~i~~~tg~~I~i~~~~------~~-------~----~~~~r~v~I~G-~~-----~~v~~A~~~I~~ii~e~   74 (164)
T 2jvz_A           24 IKQLQERAGVKMILIQDG------SQ-------N----TNVDKPLRIIG-DP-----YKVQQACEMVMDILRER   74 (164)
T ss_dssp             HHHHHHTSCSEEEECCCT------TS-------S----SSSCEEEEEEE-CH-----HHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHhCCeEEEecCC------CC-------C----CCCceEEEEEc-CH-----HHHHHHHHHHHHHHHhc
Confidence            689999999999995433      11       1    12335788898 43     34889999999998853

>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=92.51  E-value=0.13  Score=36.72  Aligned_cols=48  Identities=13%  Similarity=0.173  Sum_probs=34.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|.+..              .|+    ..+=.|.|+| +++     .+.+|.++|.++|.
T Consensus       111 Ik~i~~~tga~I~i~~~~--------------~~~----~~~~~v~I~G-~~~-----~v~~A~~~I~~~i~  158 (160)
T 2jzx_A          111 IKEIRESTGAQVQVAGDM--------------LPN----STERAITIAG-IPQ-----SIIECVKQICVVML  158 (160)
T ss_dssp             HHHHHHHHSSEECCCCCC--------------STT----CCEEEEEEEE-CHH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCeEEECCCC--------------CCC----CCceEEEEEc-CHH-----HHHHHHHHHHHHHh
Confidence            589999999999997632              121    2335688999 443     48899999888763

>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=92.02  E-value=0.19  Score=36.46  Aligned_cols=52  Identities=10%  Similarity=0.196  Sum_probs=35.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPV   75 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~   75 (127)
                      +|+|+++|||+|.|--.+      ..-      ++   ..+ =.|.|+|. +     +.+.+|.++|.+++.-.
T Consensus        28 Ik~i~~~tg~~I~i~~~~------~~~------~~---~~e-r~v~I~G~-~-----~~v~~A~~~I~~~~~~~   79 (178)
T 2anr_A           28 IVQLQKETGATIKLSKSK------DFY------PG---TTE-RVCLIQGT-I-----EALNAVHGFIAEKIREM   79 (178)
T ss_dssp             HHHHHHHHCCEEEECCTT------CBC------TT---SSE-EEEEEEEC-H-----HHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHhCCeEEEecCC------CCC------CC---CCC-ceEEEEeC-H-----HHHHHHHHHHHHHHhcc
Confidence            589999999999997544      110      11   112 24778886 2     24788999999888753

>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=89.83  E-value=0.32  Score=32.92  Aligned_cols=45  Identities=9%  Similarity=-0.058  Sum_probs=34.2

Q ss_pred             chhhhhhc-CcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLI-KFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eT-gcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +++|+++| ||+|.|--.|      +-               .=.|.|.|.+.      .+++|+++|+.++.
T Consensus        39 Ir~I~eetggv~I~i~~~g------~~---------------~~~V~I~G~~~------~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           39 IRSIMEECGGVHIHFPVEG------SG---------------SDTVVIRGPSS------DVEKAKKQLLHLAE   84 (95)
T ss_dssp             HHHHHHHHTSCEEECCCTT------TT---------------CCEEEEESCHH------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCEEEeCCCC------CC---------------cceEEEEcCHH------HHHHHHHHHHHHHh
Confidence            58899999 9999886544      10               12588998763      58999999999875

>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=89.60  E-value=0.49  Score=33.57  Aligned_cols=44  Identities=9%  Similarity=0.068  Sum_probs=30.7

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      +|+|+++|||+|.|-..|      +               .+-.|.|+|. +     ..+.+|...|.+++
T Consensus        27 Ik~i~~~tg~~I~i~~~~------~---------------~~r~v~I~G~-~-----~~v~~A~~~I~~~i   70 (160)
T 2jzx_A           27 VKKMREESGARINISEGN------C---------------PERIITLAGP-T-----NAIFKAFAMIIDKL   70 (160)
T ss_dssp             HHHHHHHHCSEEEEECCT------T---------------TEEEEEEEEE-H-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEEcCCC------C---------------CceEEEEEeC-H-----HHHHHHHHHHHHHH
Confidence            589999999999997644      1               1246788886 2     23677777776554

>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=88.94  E-value=0.41  Score=34.65  Aligned_cols=50  Identities=12%  Similarity=-0.051  Sum_probs=35.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      +|+|+++|||+|.|-...      ..       +    ...+=.|.|+|..      ..+.+|..+|.++|.-
T Consensus       126 Ik~i~~~tga~I~i~~~~------~~-------~----~~~~~~v~I~G~~------~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A          126 VKAIMEQSGAWVQLSQKP------DG-------I----NLQNRVVTVSGEP------EQNRKAVELIIQKIQE  175 (178)
T ss_dssp             HHHHHHHSSCEEEECCCC---------------------CCEEEEEEESSH------HHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHCCEEEEeCCC------CC-------C----CCCceEEEEEcCH------HHHHHHHHHHHHHHHh
Confidence            589999999999997644      10       1    1122467888865      3489999999998874

>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=88.35  E-value=0.96  Score=34.43  Aligned_cols=57  Identities=7%  Similarity=0.117  Sum_probs=38.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCc----
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDE----   77 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e----   77 (127)
                      .|.||..|||+|.|-|+                          .|.|.|.-      ..++.|...|++|+.-.+-    
T Consensus       120 ik~iE~~Tg~~I~v~~~--------------------------~v~i~G~~------~~i~~Ar~~i~~li~g~~h~~vy  167 (191)
T 1tua_A          120 RRTIEEMTDTYINVGEY--------------------------EVAIIGDY------ERAMAAKQAIEMLAEGRMHSTVY  167 (191)
T ss_dssp             HHHHHHHHTCEEEECSS--------------------------EEEEEEEH------HHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHCceEEEcCC--------------------------EEEEEeCh------HHHHHHHHHHHHHHcCCCchhHH
Confidence            57899999999999652                          25555543      2378999999999875321    


Q ss_pred             -----chhHHHHHHHHHH
Q 039634           78 -----SLDHYKKQQLREL   90 (127)
Q Consensus        78 -----~~delK~~QL~eL   90 (127)
                           -..++|+..|++|
T Consensus       168 ~~~~~~~~~~k~~~~~~~  185 (191)
T 1tua_A          168 RHLERIMREIKRRERLKM  185 (191)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence                 1345566666443

>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=88.33  E-value=0.6  Score=31.77  Aligned_cols=44  Identities=9%  Similarity=0.091  Sum_probs=33.2

Q ss_pred             chhhhhhcCcE-EEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            2 TPEVDLLIKFK-VSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         2 ~K~LE~eTgcK-I~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      .|+|+++||++ |.|--                        ++=.|.|.|.+.+.     +++|.++|+.+-..
T Consensus        37 Ik~I~e~tGv~~IdI~e------------------------ddG~V~I~g~~~ea-----~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           37 IQQARKVPGVTAIELDE------------------------DTGTFRIYGESADA-----VKKARGFLEFVEDF   81 (91)
T ss_dssp             HHHHHTSTTEEEEEEET------------------------TTTEEEEEESSHHH-----HHHHHHHHSCCCCC
T ss_pred             HHHHHHHhCCeEEEEEc------------------------CCCEEEEEECCHHH-----HHHHHHHHHhhheE
Confidence            57889999998 98842                        11358899988654     79999999877554

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

Probab=88.01  E-value=0.33  Score=43.09  Aligned_cols=42  Identities=12%  Similarity=0.066  Sum_probs=32.4

Q ss_pred             CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      ++|.|+++|||+|.|-=-|                         .|.|.|.+++.     +++|+++|+.++
T Consensus       588 ~Ik~I~e~tg~~I~I~d~G-------------------------~V~I~~~~~~~-----~~~A~~~I~~i~  629 (630)
T 3u1k_A          588 NLKKLQAETGVTISQVDEE-------------------------TFSVFAPTPSA-----MHEARDFITEIC  629 (630)
T ss_dssp             HHHHHHHHHCCEEEECSSS-------------------------EEEEEESSHHH-----HHHHHHHTTC--
T ss_pred             hHHHHHHHHCCEEEEcCCc-------------------------EEEEEeCCHHH-----HHHHHHHHHHHh
Confidence            3689999999999885333                         57899988654     799999998876

>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=86.58  E-value=1.1  Score=31.75  Aligned_cols=47  Identities=13%  Similarity=0.128  Sum_probs=30.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      +|+|+++|||+|.|--.+              .++    ..+--|.|+| +++     .+.+|...|.+++
T Consensus        25 Ik~i~~~tg~~I~i~~~~--------------~~~----~~~r~v~I~G-~~e-----~v~~A~~~I~~~~   71 (163)
T 3krm_A           25 IKQLSRFASASIKIAPPE--------------TPD----SKVRMVIITG-PPE-----AQFKAQGRIYGKL   71 (163)
T ss_dssp             HHHHHHHHTCEEEECCCS--------------STT----CSEEEEEEEE-CHH-----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCeEEEcCCC--------------CCC----CCceEEEEEc-CHH-----HHHHHHHHHHHHH
Confidence            589999999999997644              111    2234588888 433     3566666665544

>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=86.11  E-value=1.1  Score=32.01  Aligned_cols=51  Identities=16%  Similarity=0.180  Sum_probs=34.7

Q ss_pred             chhhhhhcCc-EEEEecCCCCCCccccccccCCCCCCCCCCCCc-eEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKF-KVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPL-HMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgc-KI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epL-HVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|.+++.||| +|.|.+..      ..     ..+    .++.+ -|.|+|.-      ..++.|..+|+..|.
T Consensus        89 Ir~i~~~tG~~~I~i~~~~------~~-----~~~----~~~~~~~vtI~G~~------~~v~~Ak~li~~~l~  141 (144)
T 2qnd_A           89 IQEIVDKSGVVRVRIEAEN------EK-----NVP----QEEGMVPFVFVGTK------DSIANATVLLDYHLN  141 (144)
T ss_dssp             HHHHHHHHTCSEEEEEEEC------TT-----CCC----CCTTEEEEEEEEEH------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEEEcCCC------CC-----Ccc----ccCCeeEEEEEeCH------HHHHHHHHHHHHHHH
Confidence            5788999998 99998755      11     011    12332 36788865      348999999998875

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

Probab=84.18  E-value=1.5  Score=33.90  Aligned_cols=42  Identities=14%  Similarity=0.133  Sum_probs=32.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPV   75 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~   75 (127)
                      +|.||..|||+|.|-|+                          .|.|.|.-      ..++.|...|+++|.-.
T Consensus       151 ik~ie~~Tg~~I~v~~~--------------------------~v~i~G~~------~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          151 RQIIEEMSGASVSVYGK--------------------------TVAIIGNP------IQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             HHHHHHHHCCEEEEETT--------------------------EEEEEECH------HHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCceEEECCe--------------------------EEEEEeCH------HHHHHHHHHHHHHHcCC
Confidence            57899999999999541                          26677754      34789999999999753

---

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	127
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	7e-26
d1k1ga_	122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	2e-19

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

 Score = 92.2 bits (229), Expect = 7e-26
 Identities = 31/73 (42%), Positives = 42/73 (57%)

Query: 30  EIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESLDHYKKQQLRE 89
           + + KP +EHLNE LH+L+  E  +      L  AV  ++ LL P  E  D  KK +L E
Sbjct: 57  QNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLME 116

Query: 90  LAILNGTLREESP 102
           LAILNGT R+ + 
Sbjct: 117 LAILNGTYRDANL 129

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.6 bits (186), Expect = 2e-19
 Identities = 31/74 (41%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 28  KVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK---PVDESLDHYKK 84
           KV  KD       +EPLH LV A   E      +  AV  + N+LK      E  +  +K
Sbjct: 54  KVGRKDGQMLPGEDEPLHALVTANTME-----NVKKAVEQIRNILKQGIETPEDQNDLRK 108

Query: 85  QQLRELAILNGTLR 98
            QLRELA LNGTLR
Sbjct: 109 MQLRELARLNGTLR 122

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	127
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	100.0
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	99.97
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	96.64
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	96.34
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	96.31
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	96.27
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	95.86
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	95.79
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	95.79
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	95.5
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	95.45
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	95.45
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	95.13
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	94.96
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	94.81
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	94.53
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	94.39
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	94.3
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	94.29
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	94.27
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	93.99
d2cpqa1	78	Fragile X mental retardation syndrome related prot	93.14

>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=100.00  E-value=1.2e-36  Score=223.92  Aligned_cols=97  Identities=35%  Similarity=0.476  Sum_probs=91.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccc-----cCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVE-----IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVD   76 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~-----~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~   76 (127)
                      +|+||+||||||+|||||      |+|++     .++.++|+|++|||||+|+|++++..|+.+|++|+++|+++|.|++
T Consensus        30 ~K~le~eTg~kI~IrGrG------S~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~~a~~kl~~A~~~I~~lL~p~~  103 (134)
T d2bl5a1          30 AKQLEAETGCKIMVRGKG------SMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAA  103 (134)
T ss_dssp             HHHHHHHHSEEEEEESTT------SSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHHHHSSCCS
T ss_pred             HHHHHHHHCCEEEEEecC------CCcCccccccccCCCCCcCCCCCCEEEEEecCcHHHHHHHHHHHHHHHHHHcCCCc
Confidence            699999999999999999      99988     3567788999999999999999999999999999999999999999


Q ss_pred             cchhHHHHHHHHHHHHHhCcccCCCCCC
Q 039634           77 ESLDHYKKQQLRELAILNGTLREESPSM  104 (127)
Q Consensus        77 e~~delK~~QL~eLA~lNGt~r~~~~~~  104 (127)
                      +++|++|++||+|||.||||||+++...
T Consensus       104 e~~de~k~~QL~eLa~lNGt~r~~~~~~  131 (134)
T d2bl5a1         104 EGEDSLKKMKLMELAILNGTYRDANLKS  131 (134)
T ss_dssp             SSSSHHHHHHHTGGGSSSTTTSGGGGSC
T ss_pred             cchHHHHHHHHHHHHHhcCccccccCCC
Confidence            9999999999999999999999988763

>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=99.97  E-value=6e-32  Score=195.55  Aligned_cols=86  Identities=40%  Similarity=0.460  Sum_probs=77.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCcccccccc---CCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC---CC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEI---KDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK---PV   75 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~---~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~---p~   75 (127)
                      +|+||+||||||+|||||      |+||+.   .+.+.|.|++|||||+|+|++++     ++++|+++|++||.   ++
T Consensus        31 ~K~Le~eTgckI~IrGrG------S~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~-----~~~~A~~~i~~ll~~~~~~   99 (122)
T d1k1ga_          31 LKNIEKECNAKIMIRGKG------SVKEGKVGRKDGQMLPGEDEPLHALVTANTME-----NVKKAVEQIRNILKQGIET   99 (122)
T ss_dssp             HHHHHHHSCCEEEEEEST------TSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH-----HHHHHHHHHHHHHTTTTSC
T ss_pred             HHHHHHHHCCEEEEEecC------CcccccccccCCCCCCCCCCCceEEEecCChh-----hHHHHHHHHHHHHHhcCCC
Confidence            699999999999999999      999873   34667889999999999999964     58999999999995   47


Q ss_pred             CcchhHHHHHHHHHHHHHhCccc
Q 039634           76 DESLDHYKKQQLRELAILNGTLR   98 (127)
Q Consensus        76 ~e~~delK~~QL~eLA~lNGt~r   98 (127)
                      ++++|++|++||+|||+||||||
T Consensus       100 ~e~~d~~k~~Ql~eLa~lnGt~r  122 (122)
T d1k1ga_         100 PEDQNDLRKMQLRELARLNGTLR  122 (122)
T ss_dssp             CTTSSGGGGGGGHHHHHHHTCCC
T ss_pred             CCCchHHHHHHHHHHHHhcCcCC
Confidence            88899999999999999999997

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

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

Probab=96.64  E-value=0.0019  Score=43.76  Aligned_cols=43  Identities=9%  Similarity=-0.018  Sum_probs=33.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVD   76 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~   76 (127)
                      .|.||++|||+|.|-|.+                          |.|.| +++     .++.|.+.|+.|+..+.
T Consensus        35 ik~Ie~~Tg~~I~I~d~~--------------------------v~iig-~~e-----~i~~A~~~Ie~li~~~e   77 (104)
T d1tuaa2          35 RRTIEEMTDTYINVGEYE--------------------------VAIIG-DYE-----RAMAAKQAIEMLAEGRM   77 (104)
T ss_dssp             HHHHHHHHTCEEEECSSE--------------------------EEEEE-EHH-----HHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHCCeEEEeCCe--------------------------EEEEE-Cch-----hHHHHHHHHHHHHcCCC
Confidence            578999999999996643                          45666 332     48999999999998654

>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=96.34  E-value=0.0032  Score=39.06  Aligned_cols=50  Identities=14%  Similarity=0.205  Sum_probs=35.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|...+      ...      ++    ..+--|.|+|. ++     .+++|.++|.+.|.
T Consensus        25 Ik~I~~~sga~I~i~~~~------~~~------~~----~~~r~v~I~G~-~~-----~v~~A~~~I~~~is   74 (74)
T d1dtja_          25 LVEYQELTGARIQISKKG------EFL------PG----TRNRRVTITGS-PA-----ATQAAQYLISQRVT   74 (74)
T ss_dssp             HHHHHHHHCCEEEECCTT------CCS------TT----CCEEEEEEEES-HH-----HHHHHHHHHHHHCC
T ss_pred             HHHHHHHcCCEEEEccCC------CCC------CC----CCceEEEEEeC-HH-----HHHHHHHHHHHHcC
Confidence            689999999999997755      110      11    12235888885 33     48999999998873

>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=96.31  E-value=0.004  Score=38.31  Aligned_cols=49  Identities=12%  Similarity=0.232  Sum_probs=33.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      +|+|+++|||+|.|-...      .        +. . .+.+=.|.|+|. ++     .+++|.++|.++|
T Consensus        23 Ik~I~~~sga~I~i~~~~------~--------~~-~-~~~~r~v~I~G~-~~-----~v~~A~~~I~e~i   71 (71)
T d1j4wa2          23 IKSISQQSGARIELQRNP------P--------PN-A-DPNMKLFTIRGT-PQ-----QIDYARQLIEEKI   71 (71)
T ss_dssp             HHHHHHHHCCEEEEECCC------T--------TT-S-CTTEEEEEEECC-HH-----HHHHHHHHHHHHC
T ss_pred             hHHHHhhcCcEEEEeecC------C--------CC-C-CCCeEEEEEEeC-HH-----HHHHHHHHHHhhC
Confidence            689999999999996543      1        10 1 112235778884 33     4899999998875

>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=96.27  E-value=0.0027  Score=39.25  Aligned_cols=47  Identities=13%  Similarity=0.190  Sum_probs=33.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|....               ++    ..+--|.|+|. ++     .+.+|.++|+++|.
T Consensus        25 I~~I~~~tga~I~i~~~~---------------~~----~~~r~v~I~G~-~~-----~v~~A~~~I~~~i~   71 (74)
T d1j4wa1          25 IKKIQNDAGVRIQFKPDD---------------GT----TPERIAQITGP-PD-----RAQHAAEIITDLLR   71 (74)
T ss_dssp             HHHHHHHHCCEEEEECCT---------------TS----CSEEEEEEEEC-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCEEEeccCC---------------CC----CCeeEEEEEeC-HH-----HHHHHHHHHHHHHH
Confidence            689999999999997644               10    11134778885 33     38999999998875

>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=95.86  E-value=0.0088  Score=37.54  Aligned_cols=49  Identities=8%  Similarity=0.060  Sum_probs=35.3

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|.-..               +..  .+.+=+|.|+|.- +     .|++|.++|+++|.
T Consensus        30 Ik~I~~~tga~I~i~~~~---------------~~~--~~~~r~v~I~G~~-~-----~v~~A~~~I~~~i~   78 (81)
T d1x4ma1          30 IKQLQERAGVKMVMIQDG---------------PQN--TGADKPLRITGDP-Y-----KVQQAKEMVLELIR   78 (81)
T ss_dssp             HHHHHHHHTSEEEECCSC---------------CCS--SCSCEEEEEEECT-T-----THHHHHHHHHHHHC
T ss_pred             HHHHHHHhCCeEEEccCC---------------CCC--CCCceEEEEEeCH-H-----HHHHHHHHHHHHHH
Confidence            689999999999996433               111  1123478899865 3     38999999999885

>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=95.79  E-value=0.0095  Score=39.05  Aligned_cols=49  Identities=8%  Similarity=-0.006  Sum_probs=34.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|.-.+      .         ..  ...+=-|.|+| +++     .+.+|+.+|+++|.
T Consensus        37 Ik~I~~~tga~I~i~~~~------~---------~~--~~~~r~v~I~G-~~~-----~v~~A~~~I~~~i~   85 (104)
T d1we8a_          37 IRSICKASGAKITCDKES------E---------GT--LLLSRLIKISG-TQK-----EVAAAKHLILEKVS   85 (104)
T ss_dssp             HHHHHHHHCCEEEECCSS------C---------CS--SSSEEEEEEEE-EHH-----HHHHHHHHHHHHHH
T ss_pred             hHHHHHHcCCEEEECCCC------C---------CC--CCCccEEEEEe-CHH-----HHHHHHHHHHHHHh
Confidence            689999999999996544      1         00  01112477888 433     48999999999996

>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=95.79  E-value=0.008  Score=37.45  Aligned_cols=47  Identities=15%  Similarity=0.246  Sum_probs=33.6

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +++|+++|||+|.|.-..               ++    +.+=-|.|+|. ++     .+++|.++|.++|.
T Consensus        30 i~~I~~~tg~~I~i~~~~---------------~~----~~~r~v~I~G~-~~-----~v~~A~~~I~~~i~   76 (79)
T d1x4na1          30 ISRIQQESGCKIQIAPDS---------------GG----LPERSCMLTGT-PE-----SVQSAKRLLDQIVE   76 (79)
T ss_dssp             HHHHHHHSCCEEEECSCC---------------TT----CSEEEEEEEEC-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEEcCCC---------------CC----CCceEEEEEeC-HH-----HHHHHHHHHHHHHH
Confidence            689999999999995422               11    11134888884 43     48999999998875

>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=95.50  E-value=0.0074  Score=37.99  Aligned_cols=46  Identities=15%  Similarity=0.169  Sum_probs=31.2

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +++|+++|||+|.|--.+      +        +      .+=-|.|+|+.      +.+++|.++|.+++.
T Consensus        32 i~~I~~~tg~~I~~p~~~------~--------~------~~~~v~I~G~~------~~V~~A~~~I~~i~~   77 (81)
T d2ctma1          32 IRKIMDEFKVDIRFPQSG------A--------P------DPNCVTVTGLP------ENVEEAIDHILNLEE   77 (81)
T ss_dssp             HHHHHHHHTCEEECCCTT------C--------S------CTTEEEEESCH------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEeCCcc------C--------C------CCCEEEEeCCH------HHHHHHHHHHHHHHH
Confidence            689999999999985444      1        1      11247888753      237788888877653

>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=95.45  E-value=0.0084  Score=36.81  Aligned_cols=45  Identities=11%  Similarity=0.091  Sum_probs=31.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|--.+                    ..| =-|.|+|. ++     .+.+|..+|.++|.
T Consensus        26 I~~I~~~tga~I~i~~~~--------------------~~e-r~v~I~G~-~~-----~v~~A~~~I~~~l~   70 (71)
T d2axya1          26 VKKMREESGARINISEGN--------------------CPE-RIITLAGP-TN-----AIFKAFAMIIDKLE   70 (71)
T ss_dssp             HHHHHHHHCCEEEECSSC--------------------CSE-EEEEEEEC-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEEcCCC--------------------CCc-ceEEEEEC-HH-----HHHHHHHHHHHHhc
Confidence            589999999999985433                    111 13668884 33     48899999988764

>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=95.45  E-value=0.012  Score=36.15  Aligned_cols=47  Identities=13%  Similarity=0.144  Sum_probs=32.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|.-..               ++   .+ +--|.|+|. ++     .+++|..+|+++|.
T Consensus        26 I~~I~~~sga~I~i~~~~---------------~~---~~-~r~i~I~G~-~~-----~v~~A~~~I~~~i~   72 (75)
T d1zzka1          26 IKQIRHESGASIKIDEPL---------------EG---SE-DRIITITGT-QD-----QIQNAQYLLQNSVK   72 (75)
T ss_dssp             HHHHHHHHCCEEEECCTT---------------SC---SS-EEEEEEEEC-HH-----HHHHHHHHHHHHHH
T ss_pred             HHHHHhhcCCeEEEccCC---------------CC---CC-ceEEEEEeC-HH-----HHHHHHHHHHHHHH
Confidence            589999999999995422               11   11 124778884 33     48899999988764

>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=95.13  E-value=0.012  Score=38.38  Aligned_cols=43  Identities=12%  Similarity=0.090  Sum_probs=34.1

Q ss_pred             CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      |+|+|+.+|||+|.|-=.|                         .|.|.|+++..     +..|.+.|+.+..
T Consensus        22 ~ik~i~~~t~~~I~I~d~G-------------------------~V~I~g~~~~~-----~~~A~~~I~~I~~   64 (87)
T d2z0sa2          22 MLKTLEEKTECKIFVARNG-------------------------RIHLECPNEDL-----EAIAVMAIKIIDE   64 (87)
T ss_dssp             HHHHHHHHHCCEEEEETTT-------------------------EEEEECSCHHH-----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCEEEECCCc-------------------------EEEEEeCCHHH-----HHHHHHHHHHHHH
Confidence            5789999999999992212                         48899999654     7888999988865

>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=94.96  E-value=0.0075  Score=37.95  Aligned_cols=45  Identities=9%  Similarity=0.056  Sum_probs=32.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +++|+++|||+|.|-..+      +              .++ -|.|+|..      ..+++|++.|.+++.
T Consensus        32 i~~I~~~tg~~I~~p~~~------~--------------~~~-~v~I~G~~------~~v~~A~~~I~~iv~   76 (81)
T d2ctea1          32 LQDLELKTATKIQIPRPD------D--------------PSN-QIKITGTK------EGIEKARHEVLLISA   76 (81)
T ss_dssp             HHHHHHHTTCCCBCCCTT------S--------------SCC-EEEEEECH------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEECCCC------C--------------CCC-EEEEEeCH------HHHHHHHHHHHHHHH
Confidence            578999999999985444      1              111 26788865      348999999988765

>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=94.81  E-value=0.018  Score=36.76  Aligned_cols=45  Identities=13%  Similarity=0.010  Sum_probs=33.9

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +++|+++|||+|.|-..|      +              ++ --|.|+|+-      +.+++|.+.|..++.
T Consensus        32 i~~I~~~tg~~I~~p~~~------~--------------~~-~~v~I~G~~------~~V~~A~~~I~~~v~   76 (91)
T d2ctka1          32 IRKMMDEFEVNIHVPAPE------L--------------QS-DIIAITGLA------ANLDRAKAGLLERVK   76 (91)
T ss_dssp             HHHHHHHTCCEEECCCTT------T--------------TC-CEEEEEECH------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEECCCC------C--------------Cc-ceEEEECCH------HHHHHHHHHHHHHHH
Confidence            689999999999995444      1              11 258888853      348999999999886

>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=94.53  E-value=0.028  Score=34.24  Aligned_cols=46  Identities=11%  Similarity=0.158  Sum_probs=32.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      +|+|+++|||+|.|....               ++   .++ ==|.|+|. +     ..+++|..+|+..|
T Consensus        24 I~~I~~~tga~I~i~~~~---------------~~---~~~-r~v~I~G~-~-----~~v~~A~~~I~~~i   69 (70)
T d1wvna1          24 INEIRQMSGAQIKIANPV---------------EG---SSG-RQVTITGS-A-----ASISLAQYLINARL   69 (70)
T ss_dssp             HHHHHHHHCCEEEECCCC---------------TT---CSE-EEEEEEEC-H-----HHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCcEEEEcCCC---------------CC---CCc-EEEEEEeC-H-----HHHHHHHHHHHHHc
Confidence            589999999999995422               11   111 23778885 3     34899999998876

>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=94.39  E-value=0.0023  Score=39.94  Aligned_cols=43  Identities=2%  Similarity=-0.066  Sum_probs=25.6

Q ss_pred             CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      ++|+||++|||+|.|   +        .+              =-|.|+|.++..     ++.|.++|+.+..
T Consensus        22 ~Ik~i~~~tg~~I~i---~--------~~--------------g~v~I~g~~~~~-----v~~A~~~I~~i~~   64 (69)
T d2je6i3          22 MYETLTSKSGCSIFV---A--------NN--------------GRIWATCPSRFS-----EEILIEAIRKIEN   64 (69)
T ss_dssp             HHHHHHTTC---CEE---C--------TT--------------SEEEC-----CT-----TCCTHHHHTTTTT
T ss_pred             HHHHHHHHHCCEEEE---c--------CC--------------CEEEEEeCCHHH-----HHHHHHHHHHHHH
Confidence            368999999999998   2        00              138888887654     7889999988765

>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=94.30  E-value=0.021  Score=35.87  Aligned_cols=48  Identities=4%  Similarity=0.007  Sum_probs=32.5

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+|+++|||+|.|-..+      +.        +   .++. =|.|+|.-      +.+++|..+|.+++.
T Consensus        32 i~~I~~~t~~~I~~~~~~------~~--------~---~~~~-~i~I~G~~------e~v~~A~~~I~~~i~   79 (84)
T d2ctla1          32 ITQIRLEHDVNIQFPDKD------DG--------N---QPQD-QITITGYE------KNTEAARDAILRIVG   79 (84)
T ss_dssp             HHHHHHHHTCEEECCCTT------TC--------S---SCSS-EEEEESCH------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCEEEECCCC------CC--------C---CCcc-eEEEECCH------HHHHHHHHHHHHHHH
Confidence            689999999999996555      11        0   1111 26788763      347888888888764

>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=94.29  E-value=0.022  Score=36.52  Aligned_cols=43  Identities=7%  Similarity=0.047  Sum_probs=32.7

Q ss_pred             CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634            1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP   74 (127)
Q Consensus         1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p   74 (127)
                      ++|+|+++|||+|.|-=.|                         -|.|+|+ ++     .+++|.++|+.++.-
T Consensus        22 ~I~~I~~~tg~~I~i~~~g-------------------------~v~I~G~-~e-----~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3          22 MIKLLKSELDVQIVVGQNG-------------------------LIWVNGD-RR-----KVSIAEEAIYLIEQE   64 (84)
T ss_dssp             HHHHHHHHHTCEEEECTTS-------------------------EEEEESC-HH-----HHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCEEEECCCC-------------------------EEEEEeC-HH-----HHHHHHHHHHHHHHh
Confidence            3689999999999992111                         3788884 33     389999999998874

>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=94.27  E-value=0.046  Score=33.30  Aligned_cols=44  Identities=16%  Similarity=0.072  Sum_probs=32.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL   72 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL   72 (127)
                      +++|+++|||+|.|-..+      +               ++=-|.|+|.-      +.+++|.++|.+|.
T Consensus        27 i~~I~~~tg~~I~i~~~~------~---------------~~~~v~I~G~~------~~v~~A~~~I~~i~   70 (71)
T d1viga_          27 INRIKDQYKVSVRIPPDS------E---------------KSNLIRIEGDP------QGVQQAKRELLELA   70 (71)
T ss_dssp             HHHHHHHTCCEEECCCCC------S---------------SSEEEEEEESS------HHHHHHHHHHHHTC
T ss_pred             HHHHHHHhCCEEEeCCCC------C---------------CCCEEEEECCH------HHHHHHHHHHHHHh
Confidence            588999999999995444      1               11148899864      34899999999874

>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=93.99  E-value=0.04  Score=35.41  Aligned_cols=47  Identities=13%  Similarity=0.092  Sum_probs=32.1

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +|+||++|||+|.|-..+                        -.|.|.+.+... ....+++|.++|..+..
T Consensus        25 Ik~i~~~tg~~I~Id~d~------------------------g~v~i~~~~~~~-~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1          25 KAEIMRRTGTVITVDTEN------------------------SMVIVEPEAEGI-PPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             HHHHHHHHTEEEEEETTT------------------------TEEEEEESSTTS-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCEEEEEcCC------------------------CeEEEecCCccc-cHHHHHHHHHHHHHHhC
Confidence            689999999999996532                        234455544322 13567889999988754

>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=93.14  E-value=0.062  Score=33.78  Aligned_cols=44  Identities=9%  Similarity=-0.040  Sum_probs=33.4

Q ss_pred             chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634            2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK   73 (127)
Q Consensus         2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~   73 (127)
                      +++|+++|||+|.|--..                       .=.|.|.|.+++.     +++|.++|+.+..
T Consensus        30 I~~I~~~tGa~i~i~~~~-----------------------~g~v~I~g~~~ea-----v~~A~~~Ie~~~~   73 (78)
T d2cpqa1          30 IQQARKVPGVTAIELDED-----------------------TGTFRIYGESADA-----VKKARGFLEFVED   73 (78)
T ss_dssp             HHHHHTSTTEEEEEEETT-----------------------TTEEEEEESSHHH-----HHHHHHHHSCCCC
T ss_pred             HHHHHHhcCcEEEEecCC-----------------------CceEEEEECCHHH-----HHHHHHHHHHhhe
Confidence            588999999999874311                       1248899988654     8999999987654